0.4.2

was not taking operator.name into account

README.md

@@ -62,6 +62,8 @@ This project builds on experience from previous solutions:
 ### Build with debug mode enabled:
     DEBUG=molstar npm run watch
 
+Debug/production mode in browsers can be turned on/off during runtime by calling ``setMolStarDebugMode(true/false, true/false)`` from the dev console.
+
 ### Build for production:
     NODE_ENV=production npm run build
 

data/cif-core.csv

@@ -0,0 +1,60 @@
+audit.block_doi
+
+database_code.depnum_ccdc_archive
+
+chemical.name_systematic
+chemical.name_common
+chemical.melting_point
+
+chemical_formula.moiety
+chemical_formula.sum
+chemical_formula.weight
+
+atom_type.symbol
+atom_type.description
+
+atom_type_scat.dispersion_real
+atom_type_scat.dispersion_imag
+atom_type_scat.source
+
+space_group.crystal_system
+space_group.name_H-M_full
+space_group_symop.operation_xyz
+
+cell.length_a
+cell.length_b
+cell.length_c
+cell.angle_alpha
+cell.angle_beta
+cell.angle_gamma
+cell.volume
+cell.formula_units_Z
+
+atom_site.label
+atom_site.type_symbol
+atom_site.fract_x
+atom_site.fract_y
+atom_site.fract_z
+atom_site.U_iso_or_equiv
+atom_site.adp_type
+atom_site.occupancy
+atom_site.calc_flag
+atom_site.refinement_flags
+atom_site.disorder_assembly
+atom_site.disorder_group
+
+atom_site.site_symmetry_multiplicity
+
+atom_site_aniso.label
+atom_site_aniso.U_11
+atom_site_aniso.U_22
+atom_site_aniso.U_33
+atom_site_aniso.U_23
+atom_site_aniso.U_13
+atom_site_aniso.U_12
+
+geom_bond.atom_site_label_1
+geom_bond.atom_site_label_2
+geom_bond.distance
+geom_bond.site_symmetry_2
+geom_bond.publ_flag

examples/867861-core.cif

@@ -0,0 +1,884 @@
+####################################################################### 
+# 
+# This file contains crystal structure data downloaded from the 
+# Cambridge Structural Database (CSD) hosted by the Cambridge 
+# Crystallographic Data Centre (CCDC).
+# 
+# Full information about CCDC data access policies and citation 
+# guidelines are available at http://www.ccdc.cam.ac.uk/access/V1 
+# 
+# Audit and citation data items may have been added by the CCDC. 
+# Please retain this information to preserve the provenance of 
+# this file and to allow appropriate attribution of the data. 
+# 
+#######################################################################
+
+data_n1379
+_audit_block_doi                 10.5517/ccy42jn
+_database_code_depnum_ccdc_archive 'CCDC 867861'
+loop_
+_citation_id
+_citation_doi
+_citation_year
+1 10.1002/chem.201202070 2012
+_audit_update_record             
+;
+2012-02-20 deposited with the CCDC.
+2016-10-08 downloaded from the CCDC.
+;
+
+_audit_creation_method           SHELXL-97
+_chemical_name_systematic        
+;
+?
+;
+_chemical_name_common            ?
+_chemical_melting_point          ?
+_chemical_formula_moiety         'C76 H90 N10 O14 4(C2 F3 O2) 4(C2 H3 N)'
+_chemical_formula_sum            'C92 H102 F12 N14 O22'
+_chemical_formula_weight         1983.88
+
+loop_
+_atom_type_symbol
+_atom_type_description
+_atom_type_scat_dispersion_real
+_atom_type_scat_dispersion_imag
+_atom_type_scat_source
+C C 0.0181 0.0091 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
+H H 0.0000 0.0000 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
+N N 0.0311 0.0180 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
+O O 0.0492 0.0322 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
+F F 0.0727 0.0534 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
+
+_symmetry_cell_setting           Triclinic
+_symmetry_space_group_name_H-M   P-1
+
+loop_
+_symmetry_equiv_pos_as_xyz
+'x, y, z'
+'-x, -y, -z'
+
+_cell_length_a                   11.0829(8)
+_cell_length_b                   14.6829(10)
+_cell_length_c                   16.8532(17)
+_cell_angle_alpha                105.728(6)
+_cell_angle_beta                 100.310(6)
+_cell_angle_gamma                110.620(4)
+_cell_volume                     2353.3(3)
+_cell_formula_units_Z            1
+_cell_measurement_temperature    100(2)
+_cell_measurement_reflns_used    5934
+_cell_measurement_theta_min      2.86
+_cell_measurement_theta_max      64.30
+
+_exptl_crystal_description       plate
+_exptl_crystal_colour            violet
+_exptl_crystal_size_max          0.57
+_exptl_crystal_size_mid          0.18
+_exptl_crystal_size_min          0.05
+_exptl_crystal_density_meas      ?
+_exptl_crystal_density_diffrn    1.400
+_exptl_crystal_density_method    ?
+_exptl_crystal_F_000             1036
+_exptl_absorpt_coefficient_mu    0.995
+_exptl_absorpt_correction_type   integration
+_exptl_absorpt_correction_T_min  0.6022
+_exptl_absorpt_correction_T_max  0.9482
+_exptl_absorpt_process_details   'XPREP, face-indexed'
+
+_exptl_special_details           
+;
+?
+;
+
+_diffrn_ambient_temperature      100(2)
+_diffrn_radiation_wavelength     1.54178
+_diffrn_radiation_type           CuK\a
+_diffrn_radiation_source         microsource
+_diffrn_radiation_monochromator  'Quazar optics'
+_diffrn_measurement_device_type  'Bruker APEX-II CCD'
+_diffrn_measurement_method       '\f and \w scans'
+_diffrn_detector_area_resol_mean ?
+_diffrn_reflns_number            16613
+_diffrn_reflns_av_R_equivalents  0.1477
+_diffrn_reflns_av_sigmaI/netI    0.1112
+_diffrn_reflns_limit_h_min       -12
+_diffrn_reflns_limit_h_max       8
+_diffrn_reflns_limit_k_min       -17
+_diffrn_reflns_limit_k_max       17
+_diffrn_reflns_limit_l_min       -19
+_diffrn_reflns_limit_l_max       19
+_diffrn_reflns_theta_min         2.86
+_diffrn_reflns_theta_max         64.94
+_reflns_number_total             7680
+_reflns_number_gt                5560
+_reflns_threshold_expression     >2sigma(I)
+
+_computing_data_collection       'Bruker APEX2'
+_computing_cell_refinement       'Bruker SAINT'
+_computing_data_reduction        'Bruker SAINT'
+_computing_structure_solution    'SHELXS-97 (Sheldrick, 2008)'
+_computing_structure_refinement  'SHELXL-97 (Sheldrick, 2008)'
+_computing_molecular_graphics    'Bruker SHELXTL'
+_computing_publication_material  'Bruker SHELXTL'
+
+_refine_special_details          
+;
+Refinement of F^2^ against ALL reflections. The weighted R-factor wR and
+goodness of fit S are based on F^2^, conventional R-factors R are based
+on F, with F set to zero for negative F^2^. The threshold expression of
+F^2^ > 2sigma(F^2^) is used only for calculating R-factors(gt) etc. and is
+not relevant to the choice of reflections for refinement. R-factors based
+on F^2^ are statistically about twice as large as those based on F, and R-
+factors based on ALL data will be even larger.
+Rigid bond restraints (esd 0.002) were imposed on the displacement parameters,
+as well as restraints on similar amplitudes (esd 0.002) separated by less
+than 1.7 Ang. on C27, C29, and N102.
+Distance restraints were refined on the bond between C28 and C29.
+;
+
+_refine_ls_structure_factor_coef Fsqd
+_refine_ls_matrix_type           full
+_refine_ls_weighting_scheme      calc
+_refine_ls_weighting_details     
+'calc w=1/[\s^2^(Fo^2^)+(0.1912P)^2^+4.8134P] where P=(Fo^2^+2Fc^2^)/3'
+_atom_sites_solution_primary     direct
+_atom_sites_solution_secondary   difmap
+_atom_sites_solution_hydrogens   geom
+_refine_ls_hydrogen_treatment    mixed
+_refine_ls_extinction_method     none
+_refine_ls_extinction_coef       ?
+_refine_ls_number_reflns         7680
+_refine_ls_number_parameters     633
+_refine_ls_number_restraints     1
+_refine_ls_R_factor_all          0.1349
+_refine_ls_R_factor_gt           0.1101
+_refine_ls_wR_factor_ref         0.3402
+_refine_ls_wR_factor_gt          0.3102
+_refine_ls_goodness_of_fit_ref   1.089
+_refine_ls_restrained_S_all      1.096
+_refine_ls_shift/su_max          0.000
+_refine_ls_shift/su_mean         0.000
+
+loop_
+_atom_site_label
+_atom_site_type_symbol
+_atom_site_fract_x
+_atom_site_fract_y
+_atom_site_fract_z
+_atom_site_U_iso_or_equiv
+_atom_site_adp_type
+_atom_site_occupancy
+_atom_site_symmetry_multiplicity
+_atom_site_calc_flag
+_atom_site_refinement_flags
+_atom_site_disorder_assembly
+_atom_site_disorder_group
+C1 C -0.3373(4) -0.2086(3) -0.2547(3) 0.0229(10) Uani 1 1 d . . .
+H1 H -0.3820 -0.2827 -0.2795 0.027 Uiso 1 1 calc R . .
+C2 C -0.1956(4) -0.0511(3) -0.2602(3) 0.0215(10) Uani 1 1 d . . .
+H2 H -0.1401 -0.0147 -0.2886 0.026 Uiso 1 1 calc R . .
+C3 C -0.3583(4) -0.1574(3) -0.1814(3) 0.0213(9) Uani 1 1 d . . .
+H3 H -0.4168 -0.1960 -0.1558 0.026 Uiso 1 1 calc R . .
+C4 C -0.2146(4) 0.0039(3) -0.1873(3) 0.0180(9) Uani 1 1 d . . .
+H4 H -0.1736 0.0780 -0.1660 0.022 Uiso 1 1 calc R . .
+C5 C -0.2943(4) -0.0488(3) -0.1440(3) 0.0163(9) Uani 1 1 d . . .
+C6 C -0.3053(4) 0.0091(3) -0.0600(3) 0.0170(9) Uani 1 1 d . . .
+C7 C -0.3538(4) -0.0444(3) -0.0071(3) 0.0193(9) Uani 1 1 d . . .
+H7 H -0.3850 -0.1181 -0.0264 0.023 Uiso 1 1 calc R . .
+C8 C -0.2620(4) 0.1168(3) -0.0291(3) 0.0194(9) Uani 1 1 d . . .
+H8 H -0.2304 0.1553 -0.0640 0.023 Uiso 1 1 calc R . .
+C9 C -0.3563(4) 0.0094(3) 0.0725(3) 0.0218(10) Uani 1 1 d . . .
+H9 H -0.3904 -0.0276 0.1077 0.026 Uiso 1 1 calc R . .
+C10 C -0.2648(4) 0.1679(3) 0.0515(3) 0.0190(9) Uani 1 1 d . . .
+H10 H -0.2340 0.2416 0.0724 0.023 Uiso 1 1 calc R . .
+C11 C -0.3024(4) 0.1707(4) 0.1919(3) 0.0227(10) Uani 1 1 d . . .
+H11A H -0.3772 0.1277 0.2088 0.027 Uiso 1 1 calc R . .
+H11B H -0.3094 0.2371 0.1964 0.027 Uiso 1 1 calc R . .
+C12 C -0.1670(4) 0.1920(3) 0.2509(2) 0.0184(9) Uani 1 1 d . . .
+C13 C -0.1547(5) 0.1179(4) 0.2849(3) 0.0223(10) Uani 1 1 d . . .
+H13 H -0.2328 0.0589 0.2788 0.027 Uiso 1 1 calc R . .
+C14 C -0.0541(4) 0.2821(3) 0.2667(2) 0.0204(9) Uani 1 1 d . . .
+H14 H -0.0631 0.3352 0.2475 0.024 Uiso 1 1 calc R . .
+C15 C -0.0272(5) 0.1313(4) 0.3277(3) 0.0231(10) Uani 1 1 d . . .
+H15 H -0.0192 0.0806 0.3506 0.028 Uiso 1 1 calc R . .
+C16 C 0.0731(4) 0.2946(3) 0.3110(2) 0.0195(9) Uani 1 1 d . . .
+C17 C 0.0890(4) 0.2163(3) 0.3381(2) 0.0204(10) Uani 1 1 d . . .
+C18 C 0.2252(5) 0.2149(4) 0.3687(3) 0.0273(11) Uani 1 1 d . . .
+H18A H 0.2965 0.2872 0.3968 0.033 Uiso 1 1 calc R . .
+H18B H 0.2237 0.1802 0.4116 0.033 Uiso 1 1 calc R . .
+C19 C 0.2862(4) 0.4582(4) 0.3974(3) 0.0247(10) Uani 1 1 d . . .
+H19 H 0.3032 0.4532 0.4530 0.030 Uiso 1 1 calc R . .
+C20 C 0.3577(5) 0.5371(4) 0.3739(3) 0.0279(11) Uani 1 1 d . . .
+C21 C 0.4805(5) 0.6358(4) 0.4267(3) 0.0333(12) Uani 1 1 d . . .
+H21A H 0.4882 0.6869 0.3975 0.040 Uiso 1 1 calc R . .
+H21B H 0.4699 0.6656 0.4837 0.040 Uiso 1 1 calc R . .
+C22 C 0.6303(6) 0.5857(4) 0.3599(3) 0.0374(12) Uani 1 1 d . . .
+H22A H 0.6523 0.6416 0.3355 0.045 Uiso 1 1 calc R . .
+H22B H 0.5494 0.5242 0.3176 0.045 Uiso 1 1 calc R . .
+C23 C 0.7460(6) 0.5575(5) 0.3762(4) 0.0413(13) Uani 1 1 d . . .
+H23A H 0.7730 0.5406 0.3231 0.050 Uiso 1 1 calc R . .
+H23B H 0.8246 0.6169 0.4226 0.050 Uiso 1 1 calc R . .
+C24 C 0.7952(6) 0.4206(5) 0.3967(4) 0.0496(16) Uani 1 1 d . . .
+H24A H 0.8893 0.4743 0.4264 0.060 Uiso 1 1 calc R . .
+H24B H 0.7870 0.3874 0.3353 0.060 Uiso 1 1 calc R . .
+C25 C 0.7663(11) 0.3428(7) 0.4361(4) 0.074(3) Uani 1 1 d . . .
+H25A H 0.8372 0.3165 0.4378 0.089 Uiso 1 1 calc R . .
+H25B H 0.7691 0.3754 0.4965 0.089 Uiso 1 1 calc R . .
+C26 C 0.6441(8) 0.1838(7) 0.4342(5) 0.071(2) Uani 1 1 d . . .
+H26A H 0.7153 0.1600 0.4249 0.085 Uiso 1 1 calc R . .
+H26B H 0.6577 0.2137 0.4970 0.085 Uiso 1 1 calc R . .
+C27 C 0.5204(10) 0.1080(8) 0.3921(7) 0.125(5) Uani 1 1 d . . .
+H27A H 0.5220 0.0408 0.3913 0.150 Uiso 1 1 calc R . .
+H27B H 0.4964 0.1039 0.3313 0.150 Uiso 1 1 calc R . .
+C28 C 0.3730(9) 0.0886(7) 0.4988(5) 0.097(4) Uani 1 1 d D . .
+H28A H 0.4284 0.0506 0.5097 0.116 Uiso 1 1 calc R . .
+H28B H 0.4078 0.1526 0.5510 0.116 Uiso 1 1 calc R . .
+C29 C 0.2559(11) 0.033(2) 0.4964(8) 0.281(16) Uani 1 1 d D . .
+H29A H 0.2452 0.0690 0.5518 0.337 Uiso 1 1 calc R . .
+H29B H 0.2589 -0.0322 0.5000 0.337 Uiso 1 1 calc R . .
+C30 C 0.0569(12) -0.1026(9) 0.4169(5) 0.089(3) Uani 1 1 d . . .
+H30A H 0.0442 -0.1134 0.4708 0.107 Uiso 1 1 calc R . .
+H30B H 0.1035 -0.1448 0.3928 0.107 Uiso 1 1 calc R . .
+C31 C -0.0702(10) -0.1360(6) 0.3569(6) 0.083(3) Uani 1 1 d . . .
+H31A H -0.1307 -0.2064 0.3530 0.100 Uiso 1 1 calc R . .
+H31B H -0.1113 -0.0878 0.3776 0.100 Uiso 1 1 calc R . .
+C32 C -0.1964(9) -0.1774(5) 0.2168(5) 0.067(2) Uani 1 1 d . . .
+H32A H -0.2564 -0.2441 0.2195 0.080 Uiso 1 1 calc R . .
+H32B H -0.2342 -0.1258 0.2343 0.080 Uiso 1 1 calc R . .
+C33 C -0.1881(7) -0.1926(5) 0.1297(4) 0.0593(19) Uani 1 1 d . . .
+H33A H -0.2803 -0.2327 0.0880 0.071 Uiso 1 1 calc R . .
+H33B H -0.1354 -0.2340 0.1169 0.071 Uiso 1 1 calc R . .
+C34 C -0.0909(4) -0.0989(4) 0.0440(3) 0.0231(10) Uani 1 1 d . . .
+C35 C -0.1178(5) -0.1907(4) -0.0206(3) 0.0290(11) Uani 1 1 d . . .
+H35 H -0.1660 -0.2560 -0.0162 0.035 Uiso 1 1 calc R . .
+C36 C -0.0214(4) -0.0005(3) 0.0371(3) 0.0182(9) Uani 1 1 d . . .
+C37 C 0.0055(4) 0.0950(3) 0.1019(3) 0.0212(10) Uani 1 1 d . . .
+H37 H -0.0240 0.0948 0.1515 0.025 Uiso 1 1 calc R . .
+C38 C 0.0734(4) 0.1868(4) 0.0931(3) 0.0249(10) Uani 1 1 d . . .
+H38 H 0.0914 0.2503 0.1372 0.030 Uiso 1 1 calc R . .
+N1 N -0.2553(3) -0.1567(3) -0.2921(2) 0.0202(8) Uani 1 1 d . . .
+N2 N -0.3112(3) 0.1137(3) 0.1013(2) 0.0181(8) Uani 1 1 d . . .
+N3 N 0.1854(4) 0.3880(3) 0.3242(2) 0.0221(8) Uani 1 1 d . . .
+N4 N 0.1947(4) 0.4236(3) 0.2574(2) 0.0281(9) Uani 1 1 d . . .
+N5 N 0.2991(4) 0.5136(3) 0.2881(3) 0.0315(10) Uani 1 1 d . . .
+O1 O 0.6028(3) 0.6210(3) 0.4395(2) 0.0301(8) Uani 1 1 d . . .
+O2 O 0.7045(4) 0.4689(3) 0.4018(2) 0.0429(10) Uani 1 1 d . . .
+O3 O 0.6381(7) 0.2580(4) 0.3907(4) 0.0743(17) Uani 1 1 d . . .
+O4 O 0.4041(4) 0.1218(3) 0.4321(2) 0.0412(10) Uani 1 1 d . . .
+O5 O 0.1363(5) 0.0023(6) 0.4355(3) 0.0786(19) Uani 1 1 d . . .
+O6 O -0.0597(6) -0.1394(4) 0.2749(3) 0.0757(17) Uani 1 1 d . . .
+O7 O -0.1244(3) -0.0939(3) 0.1185(2) 0.0320(8) Uani 1 1 d . . .
+C101 C 0.6294(5) 0.3676(4) 0.1211(3) 0.0286(11) Uani 1 1 d . . .
+C102 C 0.5798(8) 0.4458(5) 0.1022(5) 0.066(2) Uani 1 1 d . . .
+C103 C 0.5077(5) 0.8961(4) 0.2466(3) 0.0342(12) Uani 1 1 d . . .
+C104 C 0.3819(8) 0.8078(6) 0.2433(5) 0.077(3) Uani 1 1 d . . .
+C105 C 0.0707(7) 0.4215(5) 0.0313(4) 0.0516(16) Uani 1 1 d . . .
+C106 C 0.2104(7) 0.4969(6) 0.0645(5) 0.066(2) Uani 1 1 d . . .
+H10A H 0.2627 0.4718 0.0303 0.099 Uiso 1 1 calc R . .
+H10B H 0.2471 0.5066 0.1251 0.099 Uiso 1 1 calc R . .
+H10C H 0.2161 0.5637 0.0606 0.099 Uiso 1 1 calc R . .
+C107 C 0.0569(7) 0.6249(7) 0.2999(5) 0.071(2) Uani 1 1 d . . .
+C108 C 0.0316(8) 0.5978(7) 0.2128(5) 0.077(2) Uani 1 1 d . . .
+H10D H 0.0994 0.5753 0.1954 0.115 Uiso 1 1 calc R . .
+H10E H 0.0360 0.6581 0.1969 0.115 Uiso 1 1 calc R . .
+H10F H -0.0588 0.5404 0.1833 0.115 Uiso 1 1 calc R . .
+O101 O 0.5421(4) 0.2774(3) 0.0882(3) 0.0463(10) Uani 1 1 d . . .
+O102 O 0.7472(4) 0.4014(3) 0.1666(3) 0.0485(11) Uani 1 1 d . . .
+O103 O 0.4882(4) 0.9389(3) 0.1955(2) 0.0356(9) Uani 1 1 d . . .
+O104 O 0.6107(4) 0.9176(3) 0.3029(3) 0.0517(11) Uani 1 1 d . . .
+F101 F 0.4877(8) 0.4530(7) 0.1408(4) 0.148(3) Uani 1 1 d . . .
+F102 F 0.5188(6) 0.4177(4) 0.0191(3) 0.105(2) Uani 1 1 d . . .
+F103 F 0.6733(8) 0.5407(3) 0.1298(5) 0.160(4) Uani 1 1 d . . .
+F104 F 0.2811(5) 0.7655(4) 0.1734(3) 0.098(2) Uani 1 1 d . . .
+F105 F 0.3328(8) 0.8406(9) 0.3070(4) 0.233(7) Uani 1 1 d . . .
+F106 F 0.4002(9) 0.7351(6) 0.2617(7) 0.224(6) Uani 1 1 d . . .
+N101 N -0.0392(7) 0.3613(5) 0.0045(4) 0.0715(19) Uani 1 1 d . . .
+N102 N 0.0774(10) 0.6479(13) 0.3716(6) 0.185(7) Uani 1 1 d . . .
+
+loop_
+_atom_site_aniso_label
+_atom_site_aniso_U_11
+_atom_site_aniso_U_22
+_atom_site_aniso_U_33
+_atom_site_aniso_U_23
+_atom_site_aniso_U_13
+_atom_site_aniso_U_12
+C1 0.015(2) 0.023(2) 0.022(2) -0.0003(18) -0.0032(18) 0.0097(17)
+C2 0.021(2) 0.032(2) 0.012(2) 0.0047(17) -0.0022(17) 0.0168(19)
+C3 0.0099(19) 0.030(2) 0.021(2) 0.0059(18) -0.0007(17) 0.0104(17)
+C4 0.017(2) 0.027(2) 0.0111(19) 0.0045(16) -0.0012(16) 0.0157(18)
+C5 0.0087(18) 0.025(2) 0.0134(19) 0.0028(16) -0.0032(15) 0.0121(16)
+C6 0.0075(18) 0.031(2) 0.014(2) 0.0067(17) -0.0017(15) 0.0130(17)
+C7 0.0074(18) 0.029(2) 0.019(2) 0.0047(17) 0.0003(16) 0.0093(17)
+C8 0.0135(19) 0.028(2) 0.013(2) 0.0039(17) -0.0035(16) 0.0120(17)
+C9 0.013(2) 0.031(2) 0.020(2) 0.0072(18) 0.0012(17) 0.0105(18)
+C10 0.0112(19) 0.029(2) 0.018(2) 0.0066(17) 0.0025(16) 0.0122(17)
+C11 0.019(2) 0.038(2) 0.014(2) 0.0056(18) 0.0059(17) 0.0178(19)
+C12 0.019(2) 0.029(2) 0.0068(18) -0.0007(16) 0.0013(16) 0.0169(18)
+C13 0.024(2) 0.030(2) 0.013(2) 0.0023(17) 0.0047(18) 0.0159(19)
+C14 0.027(2) 0.027(2) 0.0079(19) -0.0015(16) 0.0012(17) 0.0200(19)
+C15 0.030(2) 0.034(2) 0.012(2) 0.0056(17) 0.0059(18) 0.023(2)
+C16 0.023(2) 0.028(2) 0.0057(18) -0.0018(16) 0.0027(16) 0.0154(19)
+C17 0.024(2) 0.032(2) 0.0063(18) -0.0012(16) 0.0008(16) 0.0209(19)
+C18 0.028(2) 0.040(3) 0.010(2) -0.0024(18) -0.0038(18) 0.025(2)
+C19 0.023(2) 0.034(2) 0.012(2) -0.0015(18) -0.0024(17) 0.017(2)
+C20 0.024(2) 0.031(2) 0.019(2) 0.0008(19) -0.0030(19) 0.011(2)
+C21 0.027(3) 0.034(3) 0.028(3) -0.001(2) 0.001(2) 0.014(2)
+C22 0.038(3) 0.046(3) 0.027(3) 0.011(2) 0.010(2) 0.018(2)
+C23 0.039(3) 0.054(3) 0.033(3) 0.012(3) 0.015(2) 0.022(3)
+C24 0.051(3) 0.061(4) 0.034(3) -0.002(3) 0.006(3) 0.038(3)
+C25 0.145(8) 0.082(5) 0.039(4) 0.023(4) 0.042(5) 0.090(6)
+C26 0.068(5) 0.096(6) 0.055(4) 0.020(4) 0.007(4) 0.053(5)
+C27 0.105(7) 0.115(7) 0.120(8) -0.033(6) -0.051(6) 0.106(7)
+C28 0.082(6) 0.105(6) 0.049(4) 0.052(4) -0.036(4) -0.012(5)
+C29 0.074(7) 0.62(4) 0.114(10) 0.252(18) 0.001(7) 0.029(14)
+C30 0.149(9) 0.141(9) 0.054(5) 0.065(5) 0.057(6) 0.113(8)
+C31 0.110(7) 0.062(5) 0.082(6) 0.050(4) 0.030(5) 0.021(5)
+C32 0.094(6) 0.046(4) 0.061(4) 0.021(3) 0.040(4) 0.021(4)
+C33 0.056(4) 0.048(4) 0.046(4) 0.013(3) 0.018(3) -0.007(3)
+C34 0.014(2) 0.035(2) 0.014(2) 0.0059(18) -0.0019(17) 0.0096(18)
+C35 0.025(2) 0.032(2) 0.021(2) 0.0050(19) -0.0033(19) 0.010(2)
+C36 0.0082(18) 0.030(2) 0.0130(19) 0.0013(17) -0.0030(15) 0.0125(17)
+C37 0.017(2) 0.032(2) 0.013(2) -0.0004(17) -0.0039(16) 0.0181(19)
+C38 0.024(2) 0.029(2) 0.016(2) -0.0031(18) -0.0035(18) 0.017(2)
+N1 0.0187(18) 0.032(2) 0.0087(16) -0.0003(14) -0.0050(14) 0.0193(16)
+N2 0.0109(16) 0.033(2) 0.0095(16) 0.0031(14) -0.0003(13) 0.0141(15)
+N3 0.0216(18) 0.030(2) 0.0120(17) -0.0001(15) -0.0016(14) 0.0163(16)
+N4 0.029(2) 0.029(2) 0.0150(18) 0.0034(16) -0.0032(16) 0.0089(17)
+N5 0.033(2) 0.032(2) 0.021(2) 0.0036(17) -0.0041(17) 0.0140(18)
+O1 0.0235(17) 0.0363(18) 0.0205(16) 0.0026(14) 0.0003(13) 0.0105(14)
+O2 0.054(2) 0.060(2) 0.031(2) 0.0152(18) 0.0199(18) 0.040(2)
+O3 0.137(5) 0.064(3) 0.083(4) 0.044(3) 0.084(4) 0.073(4)
+O4 0.0309(19) 0.049(2) 0.043(2) 0.0191(18) -0.0025(16) 0.0215(17)
+O5 0.045(3) 0.155(6) 0.048(3) 0.062(3) 0.024(2) 0.031(3)
+O6 0.093(4) 0.048(3) 0.058(3) 0.026(2) -0.016(3) 0.012(3)
+O7 0.0255(17) 0.045(2) 0.0179(16) 0.0091(14) 0.0051(14) 0.0090(15)
+C101 0.033(3) 0.030(3) 0.021(2) 0.0047(19) 0.011(2) 0.014(2)
+C102 0.082(5) 0.053(4) 0.047(4) 0.000(3) -0.010(4) 0.039(4)
+C103 0.041(3) 0.035(3) 0.021(2) 0.008(2) -0.002(2) 0.017(2)
+C104 0.073(5) 0.069(5) 0.048(4) 0.042(4) -0.023(4) -0.012(4)
+C105 0.055(4) 0.045(3) 0.055(4) 0.018(3) 0.001(3) 0.028(3)
+C106 0.057(4) 0.060(4) 0.070(5) 0.018(4) 0.001(4) 0.026(4)
+C107 0.041(4) 0.113(7) 0.059(5) 0.035(4) 0.016(3) 0.028(4)
+C108 0.057(4) 0.081(5) 0.061(5) 0.019(4) 0.011(4) 0.003(4)
+O101 0.033(2) 0.038(2) 0.060(3) 0.0192(19) 0.0048(19) 0.0098(17)
+O102 0.041(2) 0.038(2) 0.053(2) 0.0099(18) -0.0001(19) 0.0125(18)
+O103 0.038(2) 0.043(2) 0.0269(18) 0.0176(16) 0.0086(15) 0.0154(17)
+O104 0.043(2) 0.055(2) 0.045(2) 0.023(2) -0.0085(19) 0.0130(19)
+F101 0.159(6) 0.220(8) 0.099(4) 0.007(5) 0.016(4) 0.166(7)
+F102 0.148(5) 0.067(3) 0.074(3) 0.030(2) -0.031(3) 0.045(3)
+F103 0.177(7) 0.030(2) 0.180(6) 0.007(3) -0.087(5) 0.030(3)
+F104 0.073(3) 0.084(3) 0.072(3) 0.054(2) -0.037(2) -0.028(2)
+F105 0.132(6) 0.291(12) 0.076(4) 0.035(6) 0.034(4) -0.108(8)
+F106 0.161(7) 0.104(5) 0.286(11) 0.146(7) -0.127(7) -0.041(5)
+N101 0.063(4) 0.050(3) 0.082(4) 0.025(3) -0.013(3) 0.018(3)
+N102 0.077(6) 0.35(2) 0.072(6) 0.079(9) 0.015(5) 0.027(9)
+
+_geom_special_details            
+;
+All esds (except the esd in the dihedral angle between two l.s. planes)
+are estimated using the full covariance matrix. The cell esds are taken
+into account individually in the estimation of esds in distances, angles
+and torsion angles; correlations between esds in cell parameters are only
+used when they are defined by crystal symmetry. An approximate (isotropic)
+treatment of cell esds is used for estimating esds involving l.s. planes.
+;
+
+loop_
+_geom_bond_atom_site_label_1
+_geom_bond_atom_site_label_2
+_geom_bond_distance
+_geom_bond_site_symmetry_2
+_geom_bond_publ_flag
+C1 N1 1.334(6) . ?
+C1 C3 1.367(6) . ?
+C1 H1 0.9500 . ?
+C2 N1 1.353(6) . ?
+C2 C4 1.371(6) . ?
+C2 H2 0.9500 . ?
+C3 C5 1.394(6) . ?
+C3 H3 0.9500 . ?
+C4 C5 1.403(6) . ?
+C4 H4 0.9500 . ?
+C5 C6 1.490(6) . ?
+C6 C8 1.390(6) . ?
+C6 C7 1.397(6) . ?
+C7 C9 1.371(6) . ?
+C7 H7 0.9500 . ?
+C8 C10 1.375(6) . ?
+C8 H8 0.9500 . ?
+C9 N2 1.342(6) . ?
+C9 H9 0.9500 . ?
+C10 N2 1.352(6) . ?
+C10 H10 0.9500 . ?
+C11 N2 1.497(5) . ?
+C11 C12 1.517(6) . ?
+C11 H11A 0.9900 . ?
+C11 H11B 0.9900 . ?
+C12 C14 1.382(6) . ?
+C12 C13 1.396(6) . ?
+C13 C15 1.384(6) . ?
+C13 H13 0.9500 . ?
+C14 C16 1.395(6) . ?
+C14 H14 0.9500 . ?
+C15 C17 1.383(7) . ?
+C15 H15 0.9500 . ?
+C16 C17 1.400(6) . ?
+C16 N3 1.418(6) . ?
+C17 C18 1.515(6) . ?
+C18 N1 1.505(5) 2 ?
+C18 H18A 0.9900 . ?
+C18 H18B 0.9900 . ?
+C19 N3 1.356(5) . ?
+C19 C20 1.357(7) . ?
+C19 H19 0.9500 . ?
+C20 N5 1.366(6) . ?
+C20 C21 1.491(6) . ?
+C21 O1 1.435(6) . ?
+C21 H21A 0.9900 . ?
+C21 H21B 0.9900 . ?
+C22 O1 1.429(6) . ?
+C22 C23 1.484(8) . ?
+C22 H22A 0.9900 . ?
+C22 H22B 0.9900 . ?
+C23 O2 1.431(7) . ?
+C23 H23A 0.9900 . ?
+C23 H23B 0.9900 . ?
+C24 O2 1.420(7) . ?
+C24 C25 1.442(11) . ?
+C24 H24A 0.9900 . ?
+C24 H24B 0.9900 . ?
+C25 O3 1.416(11) . ?
+C25 H25A 0.9900 . ?
+C25 H25B 0.9900 . ?
+C26 C27 1.331(12) . ?
+C26 O3 1.481(9) . ?
+C26 H26A 0.9900 . ?
+C26 H26B 0.9900 . ?
+C27 O4 1.605(11) . ?
+C27 H27A 0.9900 . ?
+C27 H27B 0.9900 . ?
+C28 C29 1.252(12) . ?
+C28 O4 1.391(8) . ?
+C28 H28A 0.9900 . ?
+C28 H28B 0.9900 . ?
+C29 O5 1.361(11) . ?
+C29 H29A 0.9900 . ?
+C29 H29B 0.9900 . ?
+C30 O5 1.388(12) . ?
+C30 C31 1.407(13) . ?
+C30 H30A 0.9900 . ?
+C30 H30B 0.9900 . ?
+C31 O6 1.396(10) . ?
+C31 H31A 0.9900 . ?
+C31 H31B 0.9900 . ?
+C32 C33 1.449(9) . ?
+C32 O6 1.464(10) . ?
+C32 H32A 0.9900 . ?
+C32 H32B 0.9900 . ?
+C33 O7 1.453(7) . ?
+C33 H33A 0.9900 . ?
+C33 H33B 0.9900 . ?
+C34 O7 1.362(5) . ?
+C34 C35 1.377(7) . ?
+C34 C36 1.425(7) . ?
+C35 C38 1.404(7) 2 ?
+C35 H35 0.9500 . ?
+C36 C36 1.417(9) 2 ?
+C36 C37 1.417(6) . ?
+C37 C38 1.356(7) . ?
+C37 H37 0.9500 . ?
+C38 C35 1.404(7) 2 ?
+C38 H38 0.9500 . ?
+N1 C18 1.505(5) 2 ?
+N3 N4 1.370(5) . ?
+N4 N5 1.300(6) . ?
+C101 O101 1.227(6) . ?
+C101 O102 1.232(6) . ?
+C101 C102 1.518(9) . ?
+C102 F103 1.301(9) . ?
+C102 F102 1.318(8) . ?
+C102 F101 1.324(11) . ?
+C103 O104 1.224(6) . ?
+C103 O103 1.227(6) . ?
+C103 C104 1.512(9) . ?
+C104 F106 1.260(10) . ?
+C104 F104 1.290(7) . ?
+C104 F105 1.341(14) . ?
+C105 N101 1.139(9) . ?
+C105 C106 1.443(10) . ?
+C106 H10A 0.9800 . ?
+C106 H10B 0.9800 . ?
+C106 H10C 0.9800 . ?
+C107 N102 1.118(11) . ?
+C107 C108 1.360(11) . ?
+C108 H10D 0.9800 . ?
+C108 H10E 0.9800 . ?
+C108 H10F 0.9800 . ?
+
+loop_
+_geom_angle_atom_site_label_1
+_geom_angle_atom_site_label_2
+_geom_angle_atom_site_label_3
+_geom_angle
+_geom_angle_site_symmetry_1
+_geom_angle_site_symmetry_3
+_geom_angle_publ_flag
+N1 C1 C3 121.3(4) . . ?
+N1 C1 H1 119.3 . . ?
+C3 C1 H1 119.3 . . ?
+N1 C2 C4 120.4(4) . . ?
+N1 C2 H2 119.8 . . ?
+C4 C2 H2 119.8 . . ?
+C1 C3 C5 120.4(4) . . ?
+C1 C3 H3 119.8 . . ?
+C5 C3 H3 119.8 . . ?
+C2 C4 C5 120.4(4) . . ?
+C2 C4 H4 119.8 . . ?
+C5 C4 H4 119.8 . . ?
+C3 C5 C4 116.9(4) . . ?
+C3 C5 C6 121.8(4) . . ?
+C4 C5 C6 121.2(4) . . ?
+C8 C6 C7 117.6(4) . . ?
+C8 C6 C5 122.4(4) . . ?
+C7 C6 C5 119.9(4) . . ?
+C9 C7 C6 120.1(4) . . ?
+C9 C7 H7 120.0 . . ?
+C6 C7 H7 120.0 . . ?
+C10 C8 C6 120.4(4) . . ?
+C10 C8 H8 119.8 . . ?
+C6 C8 H8 119.8 . . ?
+N2 C9 C7 120.9(4) . . ?
+N2 C9 H9 119.5 . . ?
+C7 C9 H9 119.5 . . ?
+N2 C10 C8 120.3(4) . . ?
+N2 C10 H10 119.8 . . ?
+C8 C10 H10 119.8 . . ?
+N2 C11 C12 107.7(3) . . ?
+N2 C11 H11A 110.2 . . ?
+C12 C11 H11A 110.2 . . ?
+N2 C11 H11B 110.2 . . ?
+C12 C11 H11B 110.2 . . ?
+H11A C11 H11B 108.5 . . ?
+C14 C12 C13 119.9(4) . . ?
+C14 C12 C11 120.0(4) . . ?
+C13 C12 C11 120.0(4) . . ?
+C15 C13 C12 119.2(4) . . ?
+C15 C13 H13 120.4 . . ?
+C12 C13 H13 120.4 . . ?
+C12 C14 C16 119.7(4) . . ?
+C12 C14 H14 120.2 . . ?
+C16 C14 H14 120.2 . . ?
+C17 C15 C13 122.1(4) . . ?
+C17 C15 H15 118.9 . . ?
+C13 C15 H15 118.9 . . ?
+C14 C16 C17 121.1(4) . . ?
+C14 C16 N3 117.0(4) . . ?
+C17 C16 N3 121.8(4) . . ?
+C15 C17 C16 117.5(4) . . ?
+C15 C17 C18 119.0(4) . . ?
+C16 C17 C18 123.2(4) . . ?
+N1 C18 C17 109.0(3) 2 . ?
+N1 C18 H18A 109.9 2 . ?
+C17 C18 H18A 109.9 . . ?
+N1 C18 H18B 109.9 2 . ?
+C17 C18 H18B 109.9 . . ?
+H18A C18 H18B 108.3 . . ?
+N3 C19 C20 105.0(4) . . ?
+N3 C19 H19 127.5 . . ?
+C20 C19 H19 127.5 . . ?
+C19 C20 N5 108.7(4) . . ?
+C19 C20 C21 129.7(4) . . ?
+N5 C20 C21 121.6(5) . . ?
+O1 C21 C20 113.0(4) . . ?
+O1 C21 H21A 109.0 . . ?
+C20 C21 H21A 109.0 . . ?
+O1 C21 H21B 109.0 . . ?
+C20 C21 H21B 109.0 . . ?
+H21A C21 H21B 107.8 . . ?
+O1 C22 C23 109.1(4) . . ?
+O1 C22 H22A 109.9 . . ?
+C23 C22 H22A 109.9 . . ?
+O1 C22 H22B 109.9 . . ?
+C23 C22 H22B 109.9 . . ?
+H22A C22 H22B 108.3 . . ?
+O2 C23 C22 108.0(5) . . ?
+O2 C23 H23A 110.1 . . ?
+C22 C23 H23A 110.1 . . ?
+O2 C23 H23B 110.1 . . ?
+C22 C23 H23B 110.1 . . ?
+H23A C23 H23B 108.4 . . ?
+O2 C24 C25 110.9(6) . . ?
+O2 C24 H24A 109.5 . . ?
+C25 C24 H24A 109.5 . . ?
+O2 C24 H24B 109.5 . . ?
+C25 C24 H24B 109.5 . . ?
+H24A C24 H24B 108.0 . . ?
+O3 C25 C24 112.1(6) . . ?
+O3 C25 H25A 109.2 . . ?
+C24 C25 H25A 109.2 . . ?
+O3 C25 H25B 109.2 . . ?
+C24 C25 H25B 109.2 . . ?
+H25A C25 H25B 107.9 . . ?
+C27 C26 O3 98.8(7) . . ?
+C27 C26 H26A 112.0 . . ?
+O3 C26 H26A 112.0 . . ?
+C27 C26 H26B 112.0 . . ?
+O3 C26 H26B 112.0 . . ?
+H26A C26 H26B 109.7 . . ?
+C26 C27 O4 114.9(7) . . ?
+C26 C27 H27A 108.5 . . ?
+O4 C27 H27A 108.5 . . ?
+C26 C27 H27B 108.5 . . ?
+O4 C27 H27B 108.5 . . ?
+H27A C27 H27B 107.5 . . ?
+C29 C28 O4 124.1(6) . . ?
+C29 C28 H28A 106.3 . . ?
+O4 C28 H28A 106.3 . . ?
+C29 C28 H28B 106.3 . . ?
+O4 C28 H28B 106.3 . . ?
+H28A C28 H28B 106.4 . . ?
+C28 C29 O5 128.7(9) . . ?
+C28 C29 H29A 105.1 . . ?
+O5 C29 H29A 105.1 . . ?
+C28 C29 H29B 105.1 . . ?
+O5 C29 H29B 105.1 . . ?
+H29A C29 H29B 105.9 . . ?
+O5 C30 C31 110.9(6) . . ?
+O5 C30 H30A 109.5 . . ?
+C31 C30 H30A 109.5 . . ?
+O5 C30 H30B 109.5 . . ?
+C31 C30 H30B 109.5 . . ?
+H30A C30 H30B 108.1 . . ?
+O6 C31 C30 111.7(8) . . ?
+O6 C31 H31A 109.3 . . ?
+C30 C31 H31A 109.3 . . ?
+O6 C31 H31B 109.3 . . ?
+C30 C31 H31B 109.3 . . ?
+H31A C31 H31B 107.9 . . ?
+C33 C32 O6 108.1(6) . . ?
+C33 C32 H32A 110.1 . . ?
+O6 C32 H32A 110.1 . . ?
+C33 C32 H32B 110.1 . . ?
+O6 C32 H32B 110.1 . . ?
+H32A C32 H32B 108.4 . . ?
+C32 C33 O7 111.8(5) . . ?
+C32 C33 H33A 109.3 . . ?
+O7 C33 H33A 109.3 . . ?
+C32 C33 H33B 109.3 . . ?
+O7 C33 H33B 109.3 . . ?
+H33A C33 H33B 107.9 . . ?
+O7 C34 C35 124.0(4) . . ?
+O7 C34 C36 115.2(4) . . ?
+C35 C34 C36 120.8(4) . . ?
+C34 C35 C38 119.3(5) . 2 ?
+C34 C35 H35 120.4 . . ?
+C38 C35 H35 120.4 2 . ?
+C36 C36 C37 119.6(5) 2 . ?
+C36 C36 C34 118.4(5) 2 . ?
+C37 C36 C34 121.9(4) . . ?
+C38 C37 C36 119.9(4) . . ?
+C38 C37 H37 120.1 . . ?
+C36 C37 H37 120.1 . . ?
+C37 C38 C35 122.0(4) . 2 ?
+C37 C38 H38 119.0 . . ?
+C35 C38 H38 119.0 2 . ?
+C1 N1 C2 120.4(4) . . ?
+C1 N1 C18 120.5(4) . 2 ?
+C2 N1 C18 119.1(4) . 2 ?
+C9 N2 C10 120.6(4) . . ?
+C9 N2 C11 119.3(4) . . ?
+C10 N2 C11 119.9(4) . . ?
+C19 N3 N4 110.0(4) . . ?
+C19 N3 C16 130.4(4) . . ?
+N4 N3 C16 119.3(3) . . ?
+N5 N4 N3 107.0(3) . . ?
+N4 N5 C20 109.4(4) . . ?
+C22 O1 C21 112.0(4) . . ?
+C24 O2 C23 111.2(5) . . ?
+C25 O3 C26 101.1(6) . . ?
+C28 O4 C27 123.6(7) . . ?
+C29 O5 C30 109.4(11) . . ?
+C31 O6 C32 107.8(7) . . ?
+C34 O7 C33 116.5(4) . . ?
+O101 C101 O102 129.2(5) . . ?
+O101 C101 C102 113.1(5) . . ?
+O102 C101 C102 117.7(5) . . ?
+F103 C102 F102 108.6(7) . . ?
+F103 C102 F101 104.9(7) . . ?
+F102 C102 F101 105.0(7) . . ?
+F103 C102 C101 114.3(6) . . ?
+F102 C102 C101 112.4(5) . . ?
+F101 C102 C101 111.0(7) . . ?
+O104 C103 O103 130.2(5) . . ?
+O104 C103 C104 115.4(5) . . ?
+O103 C103 C104 114.3(5) . . ?
+F106 C104 F104 107.4(7) . . ?
+F106 C104 F105 99.1(9) . . ?
+F104 C104 F105 105.1(9) . . ?
+F106 C104 C103 115.6(8) . . ?
+F104 C104 C103 117.1(5) . . ?
+F105 C104 C103 110.5(7) . . ?
+N101 C105 C106 179.3(9) . . ?
+C105 C106 H10A 109.5 . . ?
+C105 C106 H10B 109.5 . . ?
+H10A C106 H10B 109.5 . . ?
+C105 C106 H10C 109.5 . . ?
+H10A C106 H10C 109.5 . . ?
+H10B C106 H10C 109.5 . . ?
+N102 C107 C108 179.3(14) . . ?
+C107 C108 H10D 109.5 . . ?
+C107 C108 H10E 109.5 . . ?
+H10D C108 H10E 109.5 . . ?
+C107 C108 H10F 109.5 . . ?
+H10D C108 H10F 109.5 . . ?
+H10E C108 H10F 109.5 . . ?
+
+loop_
+_geom_torsion_atom_site_label_1
+_geom_torsion_atom_site_label_2
+_geom_torsion_atom_site_label_3
+_geom_torsion_atom_site_label_4
+_geom_torsion
+_geom_torsion_site_symmetry_1
+_geom_torsion_site_symmetry_2
+_geom_torsion_site_symmetry_3
+_geom_torsion_site_symmetry_4
+_geom_torsion_publ_flag
+N1 C1 C3 C5 0.3(6) . . . . ?
+N1 C2 C4 C5 1.1(6) . . . . ?
+C1 C3 C5 C4 3.1(6) . . . . ?
+C1 C3 C5 C6 -174.6(4) . . . . ?
+C2 C4 C5 C3 -3.8(5) . . . . ?
+C2 C4 C5 C6 173.9(3) . . . . ?
+C3 C5 C6 C8 -168.8(4) . . . . ?
+C4 C5 C6 C8 13.6(5) . . . . ?
+C3 C5 C6 C7 14.7(5) . . . . ?
+C4 C5 C6 C7 -162.9(4) . . . . ?
+C8 C6 C7 C9 -0.6(5) . . . . ?
+C5 C6 C7 C9 176.0(3) . . . . ?
+C7 C6 C8 C10 1.4(5) . . . . ?
+C5 C6 C8 C10 -175.2(3) . . . . ?
+C6 C7 C9 N2 -0.7(6) . . . . ?
+C6 C8 C10 N2 -0.8(6) . . . . ?
+N2 C11 C12 C14 88.4(5) . . . . ?
+N2 C11 C12 C13 -87.7(5) . . . . ?
+C14 C12 C13 C15 -5.7(6) . . . . ?
+C11 C12 C13 C15 170.4(4) . . . . ?
+C13 C12 C14 C16 4.9(6) . . . . ?
+C11 C12 C14 C16 -171.2(4) . . . . ?
+C12 C13 C15 C17 0.2(6) . . . . ?
+C12 C14 C16 C17 1.4(6) . . . . ?
+C12 C14 C16 N3 179.1(3) . . . . ?
+C13 C15 C17 C16 5.9(6) . . . . ?
+C13 C15 C17 C18 -167.5(4) . . . . ?
+C14 C16 C17 C15 -6.7(6) . . . . ?
+N3 C16 C17 C15 175.7(4) . . . . ?
+C14 C16 C17 C18 166.4(4) . . . . ?
+N3 C16 C17 C18 -11.2(6) . . . . ?
+C15 C17 C18 N1 83.8(5) . . . 2 ?
+C16 C17 C18 N1 -89.3(5) . . . 2 ?
+N3 C19 C20 N5 0.2(5) . . . . ?
+N3 C19 C20 C21 -179.5(5) . . . . ?
+C19 C20 C21 O1 78.8(7) . . . . ?
+N5 C20 C21 O1 -100.9(6) . . . . ?
+O1 C22 C23 O2 66.1(5) . . . . ?
+O2 C24 C25 O3 65.4(6) . . . . ?
+O3 C26 C27 O4 -86.2(9) . . . . ?
+O4 C28 C29 O5 -7(4) . . . . ?
+O5 C30 C31 O6 69.5(9) . . . . ?
+O6 C32 C33 O7 -71.5(8) . . . . ?
+O7 C34 C35 C38 -177.1(4) . . . 2 ?
+C36 C34 C35 C38 1.4(6) . . . 2 ?
+O7 C34 C36 C36 177.6(4) . . . 2 ?
+C35 C34 C36 C36 -1.1(7) . . . 2 ?
+O7 C34 C36 C37 -2.5(6) . . . . ?
+C35 C34 C36 C37 178.9(4) . . . . ?
+C36 C36 C37 C38 -0.8(7) 2 . . . ?
+C34 C36 C37 C38 179.2(4) . . . . ?
+C36 C37 C38 C35 0.5(6) . . . 2 ?
+C3 C1 N1 C2 -3.1(6) . . . . ?
+C3 C1 N1 C18 175.3(4) . . . 2 ?
+C4 C2 N1 C1 2.4(6) . . . . ?
+C4 C2 N1 C18 -176.0(3) . . . 2 ?
+C7 C9 N2 C10 1.4(6) . . . . ?
+C7 C9 N2 C11 -173.8(3) . . . . ?
+C8 C10 N2 C9 -0.6(6) . . . . ?
+C8 C10 N2 C11 174.5(3) . . . . ?
+C12 C11 N2 C9 85.7(4) . . . . ?
+C12 C11 N2 C10 -89.6(4) . . . . ?
+C20 C19 N3 N4 -0.2(5) . . . . ?
+C20 C19 N3 C16 -174.0(4) . . . . ?
+C14 C16 N3 C19 129.4(5) . . . . ?
+C17 C16 N3 C19 -52.9(6) . . . . ?
+C14 C16 N3 N4 -43.9(5) . . . . ?
+C17 C16 N3 N4 133.8(4) . . . . ?
+C19 N3 N4 N5 0.2(5) . . . . ?
+C16 N3 N4 N5 174.8(4) . . . . ?
+N3 N4 N5 C20 -0.1(5) . . . . ?
+C19 C20 N5 N4 -0.1(6) . . . . ?
+C21 C20 N5 N4 179.7(4) . . . . ?
+C23 C22 O1 C21 -171.9(4) . . . . ?
+C20 C21 O1 C22 63.3(6) . . . . ?
+C25 C24 O2 C23 170.3(5) . . . . ?
+C22 C23 O2 C24 164.7(4) . . . . ?
+C24 C25 O3 C26 170.9(5) . . . . ?
+C27 C26 O3 C25 177.5(7) . . . . ?
+C29 C28 O4 C27 -129(2) . . . . ?
+C26 C27 O4 C28 -85.6(11) . . . . ?
+C28 C29 O5 C30 136(3) . . . . ?
+C31 C30 O5 C29 177.4(11) . . . . ?
+C30 C31 O6 C32 178.6(7) . . . . ?
+C33 C32 O6 C31 -173.5(6) . . . . ?
+C35 C34 O7 C33 2.2(7) . . . . ?
+C36 C34 O7 C33 -176.4(5) . . . . ?
+C32 C33 O7 C34 169.3(6) . . . . ?
+O101 C101 C102 F103 -174.2(7) . . . . ?
+O102 C101 C102 F103 6.5(10) . . . . ?
+O101 C101 C102 F102 -49.8(9) . . . . ?
+O102 C101 C102 F102 130.9(7) . . . . ?
+O101 C101 C102 F101 67.5(7) . . . . ?
+O102 C101 C102 F101 -111.9(7) . . . . ?
+O104 C103 C104 F106 -34.8(12) . . . . ?
+O103 C103 C104 F106 149.3(9) . . . . ?
+O104 C103 C104 F104 -163.1(8) . . . . ?
+O103 C103 C104 F104 21.0(11) . . . . ?
+O104 C103 C104 F105 76.7(10) . . . . ?
+O103 C103 C104 F105 -99.2(8) . . . . ?
+
+_diffrn_measured_fraction_theta_max 0.961
+_diffrn_reflns_theta_full        64.94
+_diffrn_measured_fraction_theta_full 0.961
+_refine_diff_density_max         1.693
+_refine_diff_density_min         -0.992
+_refine_diff_density_rms         0.109
+
+# start Validation Reply Form
+_vrf_PLAT213_I                   
+;
+PROBLEM: Atom C5 has ADP max/min Ratio ..... 5.1 oblat
+RESPONSE: The atoms of the glycol chain and of the CBPQT4+ ring showed elongated
+displacement parameters. Attempts to model this disorder did not significantly
+improve the refinement.
+;
+_vrf_PLAT222_I                   
+;
+PROBLEM: Large Non-Solvent H Uiso(max)/Uiso(min) .. 10.0 Ratio
+RESPONSE: Hydrogen atoms were refined as riding models with their isotropic
+displacement parameters linked to their parent atoms.
+In this case the parent atom exhibits disorder with an elongated
+displacement parameter and therefore the riding hydrogen atom is also large.
+;
+_vrf_PLAT241_I                   
+;
+PROBLEM: Check High Ueq as Compared to Neighbors for C27
+RESPONSE: C27 and C29 are part of the disordered glycol chain, however they
+are bonded to C26 and O5 which are relatively well-ordered parts of the
+structure.
+;
+
+# end Validation Reply Form
+
+
+

package.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "0.3.2",
+  "version": "0.4.2",
   "description": "A comprehensive macromolecular library.",
   "homepage": "https://github.com/molstar/molstar#readme",
   "repository": {
@@ -78,40 +78,39 @@
     "jest": "^24.9.0",
     "jest-raw-loader": "^1.0.1",
     "mini-css-extract-plugin": "^0.8.0",
-    "node-sass": "^4.12.0",
+    "node-sass": "^4.13.0",
     "raw-loader": "^3.1.0",
-    "resolve-url-loader": "^3.1.0",
+    "resolve-url-loader": "^3.1.1",
     "sass-loader": "^8.0.0",
     "simple-git": "^1.126.0",
     "style-loader": "^1.0.0",
     "ts-jest": "^24.1.0",
-    "tslint": "^5.20.0",
-    "typescript": "^3.6.4",
-    "webpack": "^4.41.0",
-    "webpack-cli": "^3.3.9"
+    "tslint": "^5.20.1",
+    "typescript": "^3.7.2",
+    "webpack": "^4.41.2",
+    "webpack-cli": "^3.3.10"
   },
   "dependencies": {
     "@types/argparse": "^1.0.36",
     "@types/benchmark": "^1.0.31",
     "@types/compression": "1.0.1",
-    "@types/express": "^4.17.1",
-    "@types/jest": "^24.0.18",
-    "@types/node": "^12.7.12",
-    "@types/node-fetch": "^2.5.2",
-    "@types/react": "^16.9.5",
-    "@types/react-dom": "^16.9.1",
+    "@types/express": "^4.17.2",
+    "@types/jest": "^24.0.23",
+    "@types/node": "^12.12.9",
+    "@types/node-fetch": "^2.5.3",
+    "@types/react": "^16.9.11",
+    "@types/react-dom": "^16.9.4",
     "@types/swagger-ui-dist": "3.0.3",
-    "@types/webgl2": "0.0.5",
     "argparse": "^1.0.10",
     "compression": "^1.7.4",
     "express": "^4.17.1",
     "graphql": "^14.5.8",
     "immutable": "^3.8.2",
     "node-fetch": "^2.6.0",
-    "react": "^16.10.2",
-    "react-dom": "^16.10.2",
+    "react": "^16.12.0",
+    "react-dom": "^16.12.0",
     "rxjs": "^6.5.3",
-    "swagger-ui-dist": "^3.23.11",
+    "swagger-ui-dist": "^3.24.3",
     "util.promisify": "^1.0.0",
     "xhr2": "^0.2.0"
   }

src/apps/basic-wrapper/index.html

@@ -105,6 +105,10 @@
 
             addControl('Apply Stripes', () => BasicMolStarWrapper.coloring.applyStripes());
 
+            addHeader('Interactivity');
+            addControl('Highlight seq_id=7', () => BasicMolStarWrapper.interactivity.highlightOn());
+            addControl('Clear Highlight', () => BasicMolStarWrapper.interactivity.clearHighlight());
+
             addHeader('Tests');
 
             addControl('Static Superposition', () => BasicMolStarWrapper.tests.staticSuperposition());

src/apps/basic-wrapper/index.ts

@@ -11,14 +11,16 @@ import { PluginCommands } from '../../mol-plugin/command';
 import { StateTransforms } from '../../mol-plugin/state/transforms';
 import { StructureRepresentation3DHelpers } from '../../mol-plugin/state/transforms/representation';
 import { Color } from '../../mol-util/color';
-import { PluginStateObject as PSO } from '../../mol-plugin/state/objects';
+import { PluginStateObject as PSO, PluginStateObject } from '../../mol-plugin/state/objects';
 import { AnimateModelIndex } from '../../mol-plugin/state/animation/built-in';
 import { StateBuilder, StateTransform } from '../../mol-state';
 import { StripedResidues } from './coloring';
-// import { BasicWrapperControls } from './controls';
 import { StaticSuperpositionTestData, buildStaticSuperposition, dynamicSuperpositionTest } from './superposition';
 import { PDBeStructureQualityReport } from '../../mol-plugin/behavior/dynamic/custom-props';
 import { CustomToastMessage } from './controls';
+import { EmptyLoci } from '../../mol-model/loci';
+import { StructureSelection } from '../../mol-model/structure';
+import { Script } from '../../mol-script/script';
 require('mol-plugin/skin/light.scss')
 
 type SupportedFormats = 'cif' | 'pdb'
@@ -63,7 +65,7 @@ class BasicWrapper {
     }
 
     private visual(visualRoot: StateBuilder.To<PSO.Molecule.Structure>) {
-        visualRoot.apply(StateTransforms.Model.StructureComplexElement, { type: 'atomic-sequence' })
+        visualRoot.apply(StateTransforms.Model.StructureComplexElement, { type: 'atomic-sequence' }, { ref: 'seq' })
             .apply(StateTransforms.Representation.StructureRepresentation3D,
                 StructureRepresentation3DHelpers.getDefaultParamsStatic(this.plugin, 'cartoon'), { ref: 'seq-visual' });
         visualRoot.apply(StateTransforms.Model.StructureComplexElement, { type: 'atomic-het' })
@@ -144,6 +146,22 @@ class BasicWrapper {
         }
     }
 
+    interactivity = {
+        highlightOn: () => {
+            const seq_id = 7;
+            const data = (this.plugin.state.dataState.select('asm')[0].obj as PluginStateObject.Molecule.Structure).data;
+            const sel = Script.getStructureSelection(Q => Q.struct.generator.atomGroups({
+                'residue-test': Q.core.rel.eq([Q.struct.atomProperty.macromolecular.label_seq_id(), seq_id]),
+                'group-by': Q.struct.atomProperty.macromolecular.residueKey()
+            }), data);
+            const loci = StructureSelection.toLociWithSourceUnits(sel);
+            this.plugin.interactivity.lociHighlights.highlightOnly({ loci });
+        },
+        clearHighlight: () => {
+            this.plugin.interactivity.lociHighlights.highlightOnly({ loci: EmptyLoci });
+        }
+    }
+
     tests = {
         staticSuperposition: async () => {
             const state = this.plugin.state.dataState;

src/apps/basic-wrapper/superposition.ts

@@ -86,7 +86,7 @@ export async function dynamicSuperpositionTest(ctx: PluginContext, src: string[]
 
     const query = compile<StructureSelection>(pivot);
     const xs = state.select(StateSelection.Generators.rootsOfType(PSO.Molecule.Structure));
-    const selections = xs.map(s => StructureSelection.toLoci(query(new QueryContext(s.obj!.data))));
+    const selections = xs.map(s => StructureSelection.toLociWithCurrentUnits(query(new QueryContext(s.obj!.data))));
 
     const transforms = superposeStructures(selections);
     const visuals = state.build();

src/apps/viewer/extensions/cellpack/model.ts

@@ -10,7 +10,7 @@ import { PluginStateObject as PSO } from '../../../../mol-plugin/state/objects';
 import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
 import { Ingredient, CellPacking, Cell } from './data';
 import { getFromPdb, getFromCellPackDB } from './util';
-import { Model, Structure, StructureSymmetry, StructureSelection, QueryContext } from '../../../../mol-model/structure';
+import { Model, Structure, StructureSymmetry, StructureSelection, QueryContext, Unit } from '../../../../mol-model/structure';
 import { trajectoryFromMmCIF } from '../../../../mol-model-formats/structure/mmcif';
 import { trajectoryFromPDB } from '../../../../mol-model-formats/structure/pdb';
 import { Mat4, Vec3, Quat } from '../../../../mol-math/linear-algebra';
@@ -268,7 +268,7 @@ export function createStructureFromCellPack(packing: CellPacking, baseUrl: strin
             for (const u of s.units) {
                 const invariantId = u.invariantId + offsetInvariantId
                 if (u.invariantId > maxInvariantId) maxInvariantId = u.invariantId
-                builder.addUnit(u.kind, u.model, u.conformation.operator, u.elements, invariantId)
+                builder.addUnit(u.kind, u.model, u.conformation.operator, u.elements, Unit.Trait.None, invariantId)
             }
             offsetInvariantId += maxInvariantId
         }
@@ -385,17 +385,17 @@ export const LoadCellPackModel = StateAction.build({
         const hue = [Math.max(0, hcl[0] - 35), Math.min(360, hcl[0] + 35)] as [number, number]
         const p = { packing: i, baseUrl: params.baseUrl }
 
-        const expression = params.preset.traceOnly
-            ? MS.struct.generator.atomGroups({
+        let cellpackTree = tree.apply(StructureFromCellpack, p)
+        if (params.preset.traceOnly) {
+            const expression = MS.struct.generator.atomGroups({
                 'atom-test': MS.core.logic.or([
                     MS.core.rel.eq([MS.ammp('label_atom_id'), 'CA']),
                     MS.core.rel.eq([MS.ammp('label_atom_id'), 'P'])
                 ])
             })
-            : MS.struct.generator.all()
-
-        tree.apply(StructureFromCellpack, p)
-            .apply(StateTransforms.Model.StructureSelectionFromExpression, { expression }, { state: { isGhost: true } })
+            cellpackTree = cellpackTree.apply(StateTransforms.Model.StructureSelectionFromExpression, { expression }, { state: { isGhost: true } })
+        }
+        cellpackTree
             .apply(StateTransforms.Representation.StructureRepresentation3D,
                 StructureRepresentation3DHelpers.createParams(ctx, Structure.Empty, {
                     repr: getReprParams(ctx, params.preset),

src/examples/proteopedia-wrapper/index.ts

@@ -28,7 +28,6 @@ import { BuiltInColorThemes } from '../../mol-theme/color';
 import { BuiltInSizeThemes } from '../../mol-theme/size';
 import { ColorNames } from '../../mol-util/color/names';
 import { InitVolumeStreaming, CreateVolumeStreamingInfo } from '../../mol-plugin/behavior/dynamic/volume-streaming/transformers';
-import { ParamDefinition } from '../../mol-util/param-definition';
 import { DefaultCanvas3DParams, Canvas3DProps } from '../../mol-canvas3d/canvas3d';
 // import { Vec3 } from 'mol-math/linear-algebra';
 // import { ParamDefinition } from 'mol-util/param-definition';
@@ -315,9 +314,11 @@ class MolStarProteopediaWrapper {
     experimentalData = {
         init: async (parent: Element) => {
             const asm = this.state.select(StateElements.Assembly)[0].obj!;
-            const params = ParamDefinition.getDefaultValues(InitVolumeStreaming.definition.params!(asm, this.plugin));
-            params.behaviorRef = StateElements.VolumeStreaming;
+            const params = InitVolumeStreaming.createDefaultParams(asm, this.plugin);
+            params.options.behaviorRef = StateElements.VolumeStreaming;
             params.defaultView = 'box';
+            params.options.channelParams['fo-fc(+ve)'] = { wireframe: true };
+            params.options.channelParams['fo-fc(-ve)'] = { wireframe: true };
             await this.plugin.runTask(this.state.applyAction(InitVolumeStreaming, params, StateElements.Assembly));
             this.experimentalDataElement = parent;
             volumeStreamingControls(this.plugin, parent);

src/examples/task.ts

@@ -28,9 +28,9 @@ function messageTree(root: Progress.Node, prefix = ''): string {
 
 function createTask<T>(delayMs: number, r: T): Task<T> {
     return Task.create('delayed value ' + r, async ctx => {
-        ctx.update('Processing delayed... ' + r, true);
+        ctx.update(`Processing delayed ${r} after ${delayMs}ms`, true);
         await Scheduler.delay(delayMs);
-        if (ctx.shouldUpdate) await ctx.update({ message: 'hello from delayed... ' });
+        if (ctx.shouldUpdate) await ctx.update({ message: `hello from delayed ${r} ${delayMs}` });
         return r;
     }, () => console.log('On abort called ' + r));
 }
@@ -63,7 +63,7 @@ export function testTree() {
         const r = await c1 + await c2 + await c3;
         if (ctx.shouldUpdate) await ctx.update({ message: 'Almost done...' });
         return r + 1;
-    });
+    }, () => console.log('On abort O'));
 }
 
 export type ChunkedState = { i: number, current: number, total: number }
@@ -115,7 +115,7 @@ async function test() {
         // const r = await Run(testTree(), abortingObserver, 250);
         // console.log(r);
 
-        const m = await ms({ i: 10 }).run(logP);
+        const m = await testTree().run(abortingObserver, 50);
         console.log(m);
     } catch (e) {
         console.error(e);

src/mol-canvas3d/camera.ts

@@ -79,12 +79,10 @@ class Camera {
     }
 
     getSnapshot() {
-        const ret = Camera.createDefaultSnapshot();
-        Camera.copySnapshot(ret, this.state);
-        return ret;
+        return Camera.copySnapshot(Camera.createDefaultSnapshot(), this.state);
     }
 
-    getFocus(target: Vec3, radius: number): Partial<Camera.Snapshot> {
+    getFocus(target: Vec3, radius: number, up?: Vec3, dir?: Vec3): Partial<Camera.Snapshot> {
         const fov = this.state.fov
         const { width, height } = this.viewport
         const aspect = width / height
@@ -92,6 +90,7 @@ class Camera {
         const targetDistance = Math.abs((radius / aspectFactor) / Math.sin(fov / 2))
 
         Vec3.sub(this.deltaDirection, this.target, this.position)
+        if (dir) Vec3.matchDirection(this.deltaDirection, dir, this.deltaDirection)
         Vec3.setMagnitude(this.deltaDirection, this.deltaDirection, targetDistance)
         Vec3.sub(this.newPosition, target, this.deltaDirection)
 
@@ -99,12 +98,13 @@ class Camera {
         state.target = Vec3.clone(target)
         state.radius = radius
         state.position = Vec3.clone(this.newPosition)
+        if (up) Vec3.matchDirection(state.up, up, state.up)
 
         return state
     }
 
-    focus(target: Vec3, radius: number, durationMs?: number) {
-        if (radius > 0) this.setState(this.getFocus(target, radius), durationMs);
+    focus(target: Vec3, radius: number, durationMs?: number, up?: Vec3, dir?: Vec3) {
+        if (radius > 0) this.setState(this.getFocus(target, radius, up, dir), durationMs);
     }
 
     project(out: Vec4, point: Vec3) {

src/mol-canvas3d/canvas3d.ts

@@ -202,7 +202,7 @@ namespace Canvas3D {
                 didRender = true
             }
 
-            return didRender && cameraChanged;
+            return didRender;
         }
 
         let forceNextDraw = false;

src/mol-canvas3d/controls/trackball.ts

@@ -21,15 +21,15 @@ const M = ModifiersKeys
 const Trigger = Binding.Trigger
 
 export const DefaultTrackballBindings = {
-    dragRotate: Binding(Trigger(B.Flag.Primary, M.create()), 'Rotate the 3D scene by dragging using ${trigger}'),
-    dragRotateZ: Binding(Trigger(B.Flag.Primary, M.create({ shift: true })), 'Rotate the 3D scene around the z-axis by dragging using ${trigger}'),
-    dragPan: Binding(Trigger(B.Flag.Secondary, M.create()), 'Pan the 3D scene by dragging using ${trigger}'),
+    dragRotate: Binding([Trigger(B.Flag.Primary, M.create())], 'Rotate the 3D scene by dragging using ${triggers}'),
+    dragRotateZ: Binding([Trigger(B.Flag.Primary, M.create({ shift: true }))], 'Rotate the 3D scene around the z-axis by dragging using ${triggers}'),
+    dragPan: Binding([Trigger(B.Flag.Secondary, M.create()), Trigger(B.Flag.Primary, M.create({ control: true }))], 'Pan the 3D scene by dragging using ${triggers}'),
     dragZoom: Binding.Empty,
-    dragFocus: Binding(Trigger(B.Flag.Forth, M.create()), 'Focus the 3D scene by dragging using ${trigger}'),
-    dragFocusZoom: Binding(Trigger(B.Flag.Auxilary, M.create()), 'Focus and zoom the 3D scene by dragging using ${trigger}'),
+    dragFocus: Binding([Trigger(B.Flag.Forth, M.create())], 'Focus the 3D scene by dragging using ${triggers}'),
+    dragFocusZoom: Binding([Trigger(B.Flag.Auxilary, M.create())], 'Focus and zoom the 3D scene by dragging using ${triggers}'),
 
-    scrollZoom: Binding(Trigger(B.Flag.Auxilary, M.create()), 'Zoom the 3D scene by scrolling using ${trigger}'),
-    scrollFocus: Binding(Trigger(B.Flag.Auxilary, M.create({ shift: true })), 'Focus the 3D scene by scrolling using ${trigger}'),
+    scrollZoom: Binding([Trigger(B.Flag.Auxilary, M.create())], 'Zoom the 3D scene by scrolling using ${triggers}'),
+    scrollFocus: Binding([Trigger(B.Flag.Auxilary, M.create({ shift: true }))], 'Focus the 3D scene by scrolling using ${triggers}'),
     scrollFocusZoom: Binding.Empty,
 }
 

src/mol-canvas3d/util.ts

@@ -6,8 +6,8 @@
 
 /** Set canvas size taking `devicePixelRatio` into account */
 export function setCanvasSize(canvas: HTMLCanvasElement, width: number, height: number) {
-    canvas.width = window.devicePixelRatio * width
-    canvas.height = window.devicePixelRatio * height
+    canvas.width = Math.round(window.devicePixelRatio * width)
+    canvas.height = Math.round(window.devicePixelRatio * height)
     Object.assign(canvas.style, { width: `${width}px`, height: `${height}px` })
 }
 
@@ -28,7 +28,7 @@ function _canvasToBlob(canvas: HTMLCanvasElement, callback: BlobCallback, type?:
     const len = bin.length
     const len32 = len >> 2
     const a8 = new Uint8Array(len)
-    const a32 = new Uint32Array( a8.buffer, 0, len32 )
+    const a32 = new Uint32Array(a8.buffer, 0, len32)
 
     let j = 0
     for (let i = 0; i < len32; ++i) {

src/mol-data/db/column.ts

@@ -343,9 +343,9 @@ function isIdentity(map: ArrayLike<number>, rowCount: number) {
 }
 
 function columnView<T>(c: Column<T>, map: ArrayLike<number>, checkIdentity: boolean): Column<T> {
-    if (!c.isDefined) return c;
+    if (!c.isDefined || c.rowCount === 0) return c;
     if (checkIdentity && isIdentity(map, c.rowCount)) return c;
-    if (!!c.__array) return arrayView(c, map);
+    if (!!c.__array && typeof c.value(0) === typeof c.__array[0]) return arrayView(c, map);
     return viewFull(c, map);
 }
 

src/mol-data/generic/unique-array.ts

@@ -20,6 +20,10 @@ namespace UniqueArray {
         array[array.length] = value;
         return true;
     }
+
+    export function has<K, T>({ keys }: UniqueArray<K, T>, key: K) {
+        return keys.has(key);
+    }
 }
 
 export { UniqueArray }

src/mol-data/int/_spec/ordered-set.spec.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  */
@@ -81,6 +81,13 @@ describe('ordered set', () => {
         expect(OrderedSet.isSubset(arr136, OrderedSet.ofSortedArray([12, 13, 16]))).toBe(false);
     });
 
+    it('isSubsetIS', () => {
+        expect(OrderedSet.isSubset(
+            Interval.ofRange(1271, 1295),
+            OrderedSet.ofSortedArray([1271, 1272, 1274, 1275, 1276, 1278, 1280, 1282, 1284, 1286, 1288, 1290, 1292, 1294])
+        )).toBe(true);
+    });
+
     it('access/membership', () => {
         expect(OrderedSet.has(empty, 10)).toBe(false);
         expect(OrderedSet.indexOf(empty, 10)).toBe(-1);

src/mol-data/int/_spec/sorted-array.spec.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  */
@@ -65,6 +65,90 @@ describe('sortedArray', () => {
 
     test('intersectionSize', SortedArray.intersectionSize(a1234, a2468), 2);
 
-    // console.log(Interval.findPredecessorIndexInInterval(Interval.ofBounds(0, 3), 2, Interval.ofBounds(0, 3)))
-    // console.log(SortedArray.findPredecessorIndexInInterval(SortedArray.ofSortedArray([0, 1, 2]), 2, Interval.ofBounds(0, 3)))
+    it('union1', () => {
+        compareArrays(
+            SortedArray.union(
+                SortedArray.ofSortedArray([830, 831, 832, 833, 834, 836, 837, 838, 839, 840, 841, 842, 843]),
+                SortedArray.ofSortedArray([835])
+            ),
+            SortedArray.ofSortedArray([830, 831, 832, 833, 834, 835, 836, 837, 838, 839, 840, 841, 842, 843])
+        )
+    })
+
+    it('union2', () => {
+        compareArrays(
+            SortedArray.union(
+                SortedArray.ofSortedArray([830, 832, 833]),
+                SortedArray.ofSortedArray([831])
+            ),
+            SortedArray.ofSortedArray([830, 831, 832, 833])
+        )
+    })
+
+    it('union3ab', () => {
+        compareArrays(
+            SortedArray.union(
+                SortedArray.ofSortedArray([830, 831, 832, 833, 834, 835]),
+                SortedArray.ofSortedArray([836, 837, 838, 839, 840, 841, 842, 843])
+            ),
+            SortedArray.ofSortedArray([830, 831, 832, 833, 834, 835, 836, 837, 838, 839, 840, 841, 842, 843])
+        )
+    })
+
+    it('union3ba', () => {
+        compareArrays(
+            SortedArray.union(
+                SortedArray.ofSortedArray([836, 837, 838, 839, 840, 841, 842, 843]),
+                SortedArray.ofSortedArray([830, 831, 832, 833, 834, 835])
+            ),
+            SortedArray.ofSortedArray([830, 831, 832, 833, 834, 835, 836, 837, 838, 839, 840, 841, 842, 843])
+        )
+    })
+
+    it('union4', () => {
+        compareArrays(
+            SortedArray.union(
+                SortedArray.ofSortedArray([1, 3, 5, 7, 9]),
+                SortedArray.ofSortedArray([2, 4, 6, 8])
+            ),
+            SortedArray.ofSortedArray([1, 2, 3, 4, 5, 6, 7, 8, 9])
+        )
+    })
+
+    it('union5', () => {
+        compareArrays(
+            SortedArray.union(
+                SortedArray.ofSortedArray([2, 3, 4, 20, 21, 22]),
+                SortedArray.ofSortedArray([10, 11, 12])
+            ),
+            SortedArray.ofSortedArray([2, 3, 4, 10, 11, 12, 20, 21, 22])
+        )
+    })
+
+    it('union6', () => {
+        compareArrays(
+            SortedArray.union(
+                SortedArray.ofSortedArray([768, 769, 770, 771, 772, 773, 774, 775, 776, 819, 820, 821, 822, 823, 824, 825, 826, 827, 828, 829, 1811, 1812, 1813, 1814, 1815, 1816, 1817, 1818, 1819]),
+                SortedArray.ofSortedArray([1751, 1752, 1753, 1754, 1755, 1756, 1757, 1758])
+            ),
+            SortedArray.ofSortedArray([768, 769, 770, 771, 772, 773, 774, 775, 776, 819, 820, 821, 822, 823, 824, 825, 826, 827, 828, 829, 1751, 1752, 1753, 1754, 1755, 1756, 1757, 1758, 1811, 1812, 1813, 1814, 1815, 1816, 1817, 1818, 1819])
+        )
+    })
+
+    it('union7', () => {
+        compareArrays(
+            SortedArray.union(
+                SortedArray.ofSortedArray([3766, 3767, 3768, 3770, 3773, 3780, 3783, 3787, 3797]),
+                SortedArray.ofSortedArray([3769, 3790, 3794])
+            ),
+            SortedArray.ofSortedArray([3766, 3767, 3768, 3769, 3770, 3773, 3780, 3783, 3787, 3790, 3794, 3797])
+        )
+    })
+
+    it('isSubset', () => {
+        expect(SortedArray.isSubset(
+            SortedArray.ofSortedArray([1271, 1272, 1273, 1274, 1275, 1276, 1277, 1278, 1279, 1280, 1281, 1282, 1283, 1284, 1285, 1286, 1287, 1288, 1289, 1290, 1291, 1292, 1293, 1294, 1295]),
+            SortedArray.ofSortedArray([1271, 1272, 1274, 1275, 1276, 1278, 1280, 1282, 1284, 1286, 1288, 1290, 1292, 1294])
+        )).toBe(true);
+    })
 });

src/mol-data/int/impl/ordered-set.ts

@@ -126,7 +126,7 @@ function isSubsetIS(a: I, b: S) {
     const minA = I.min(a), maxA = I.max(a);
     if (maxA - minA + 1 === 0) return false;
     const minB = S.min(b), maxB = S.max(b);
-    return minB >= minA && maxA <= maxB;
+    return minB >= minA && maxB <= maxA;
 }
 
 function areRangesIntersecting(a: OrderedSetImpl, b: OrderedSetImpl) {

src/mol-data/int/impl/sorted-array.ts

@@ -171,28 +171,30 @@ export function isSubset(a: Nums, b: Nums) {
     return equal === lenB;
 }
 
-export function union(a: Nums, b: Nums) {
+export function union(a: Nums, b: Nums): Nums {
     if (a === b) return a;
 
+    const lenA = a.length, lenB = b.length;
+    if (lenA === 0) return b;
+    if (lenB === 0) return a;
+    if (a[0] > b[0]) return union(b, a);
+
     const { startI, startJ, endI, endJ } = getSuitableIntersectionRange(a, b);
     const commonCount = getCommonCount(a, b, startI, startJ, endI, endJ);
 
-    const lenA = a.length, lenB = b.length;
     // A === B || B is subset of A ==> A
     if ((commonCount === lenA && commonCount === lenB) || commonCount === lenB) return a;
     // A is subset of B ===> B
     if (commonCount === lenA) return b;
 
     const indices = new Int32Array(lenA + lenB - commonCount);
-    let offset = 0;
+    let i = 0, j = 0, offset = 0;
 
     // insert the "prefixes"
-    for (let k = 0; k < startI; k++) indices[offset++] = a[k];
-    for (let k = 0; k < startJ; k++) indices[offset++] = b[k];
+    for (i = 0; i < startI; i++) indices[offset++] = a[i];
+    while (j < endJ && a[startI] > b[j]) indices[offset++] = b[j++];
 
     // insert the common part
-    let i = startI;
-    let j = startJ;
     while (i < endI && j < endJ) {
         const x = a[i], y = b[j];
         if (x < y) { indices[offset++] = x; i++; }
@@ -200,6 +202,10 @@ export function union(a: Nums, b: Nums) {
         else { indices[offset++] = x; i++; j++; }
     }
 
+    // insert the remaining common part
+    for (; i < endI; i++) indices[offset++] = a[i];
+    for (; j < endJ; j++) indices[offset++] = b[j];
+
     // insert the "tail"
     for (; i < lenA; i++) indices[offset++] = a[i];
     for (; j < lenB; j++) indices[offset++] = b[j];

src/mol-geo/geometry/mesh/builder/cylinder.ts

@@ -26,8 +26,7 @@ function setCylinderMat(m: Mat4, start: Vec3, dir: Vec3, length: number) {
     Vec3.add(tmpCylinderCenter, start, tmpCylinderMatDir)
     // ensure the direction used to create the rotation is always pointing in the same
     // direction so the triangles of adjacent cylinder will line up
-    Vec3.copy(tmpUp, up)
-    if (Vec3.dot(tmpCylinderMatDir, tmpUp) < 0) Vec3.scale(tmpUp, tmpUp, -1)
+    Vec3.matchDirection(tmpUp, up, tmpCylinderMatDir)
     Vec3.makeRotation(m, tmpUp, tmpCylinderMatDir)
     return Mat4.setTranslation(m, tmpCylinderCenter)
 }

src/mol-geo/primitive/pyramid.ts

@@ -54,6 +54,12 @@ export function Pyramid(points: ArrayLike<number>): Primitive {
     return builder.getPrimitive()
 }
 
+let triangularPyramid: Primitive
+export function TriangularPyramid() {
+    if (!triangularPyramid) triangularPyramid = Pyramid(polygon(3, true))
+    return triangularPyramid
+}
+
 let octagonalPyramid: Primitive
 export function OctagonalPyramid() {
     if (!octagonalPyramid) octagonalPyramid = Pyramid(polygon(8, true))

src/mol-gl/shader-code.ts

@@ -189,16 +189,7 @@ const glsl300VertPrefix = `#version 300 es
 #define texture2D texture
 `
 
-const glsl300FragPrefix = `#version 300 es
-layout(location = 0) out highp vec4 out_FragData0;
-layout(location = 1) out highp vec4 out_FragData1;
-layout(location = 2) out highp vec4 out_FragData2;
-layout(location = 3) out highp vec4 out_FragData3;
-layout(location = 4) out highp vec4 out_FragData4;
-layout(location = 5) out highp vec4 out_FragData5;
-layout(location = 6) out highp vec4 out_FragData6;
-layout(location = 7) out highp vec4 out_FragData7;
-
+const glsl300FragPrefixCommon = `
 #define varying in
 #define texture2D texture
 #define texture2DLodEXT textureLod
@@ -211,16 +202,29 @@ layout(location = 7) out highp vec4 out_FragData7;
 #define requiredDrawBuffers
 `
 
+function getGlsl300FragPrefix(gl: WebGL2RenderingContext, extensions: WebGLExtensions, shaderExtensions: ShaderExtensions) {
+    const prefix = [ '#version 300 es' ]
+    if (extensions.drawBuffers) {
+        const maxDrawBuffers = gl.getParameter(gl.MAX_DRAW_BUFFERS) as number
+        for (let i = 0, il = maxDrawBuffers; i < il; ++i) {
+            prefix.push(`layout(location = ${i}) out highp vec4 out_FragData${i};`)
+        }
+    }
+    prefix.push(glsl300FragPrefixCommon)
+    return prefix.join('\n') + '\n'
+}
+
 function transformGlsl300Frag(frag: string) {
-    return frag.replace(/gl_FragData\[([0-7])\]/g, 'out_FragData$1')
+    return frag.replace(/gl_FragData\[([0-9]+)\]/g, 'out_FragData$1')
 }
 
 export function addShaderDefines(gl: GLRenderingContext, extensions: WebGLExtensions, defines: ShaderDefines, shaders: ShaderCode): ShaderCode {
-    const webgl2 = isWebGL2(gl)
     const header = getDefinesCode(defines)
-    const vertPrefix = webgl2 ? glsl300VertPrefix : ''
-    const fragPrefix = webgl2 ? glsl300FragPrefix : getGlsl100FragPrefix(extensions, shaders.extensions)
-    const frag = webgl2 ? transformGlsl300Frag(shaders.frag) : shaders.frag
+    const vertPrefix = isWebGL2(gl) ? glsl300VertPrefix : ''
+    const fragPrefix = isWebGL2(gl)
+        ? getGlsl300FragPrefix(gl, extensions, shaders.extensions)
+        : getGlsl100FragPrefix(extensions, shaders.extensions)
+    const frag = isWebGL2(gl) ? transformGlsl300Frag(shaders.frag) : shaders.frag
     return {
         id: shaderCodeId(),
         vert: `${vertPrefix}${header}${shaders.vert}`,

src/mol-gl/shader/mesh.vert.ts

@@ -23,7 +23,7 @@ attribute mat4 aTransform;
 attribute float aInstance;
 attribute float aGroup;
 
-#ifndef dFlatShaded
+#if !defined(dFlatShaded) || !defined(enabledStandardDerivatives)
     #ifdef dGeoTexture
         uniform sampler2D tNormal;
     #else
@@ -38,7 +38,7 @@ void main(){
     #include assign_marker_varying
     #include assign_position
 
-    #ifndef dFlatShaded
+    #if !defined(dFlatShaded) || !defined(enabledStandardDerivatives)
         #ifdef dGeoTexture
             vec3 normal = readFromTexture(tNormal, aGroup, uGeoTexDim).xyz;
         #else

src/mol-gl/webgl/extensions.ts

@@ -5,6 +5,7 @@
  */
 
 import { GLRenderingContext, COMPAT_instanced_arrays, COMPAT_standard_derivatives, COMPAT_vertex_array_object, getInstancedArrays, getStandardDerivatives, getVertexArrayObject, COMPAT_element_index_uint, getElementIndexUint, COMPAT_texture_float, getTextureFloat, COMPAT_texture_float_linear, getTextureFloatLinear, COMPAT_blend_minmax, getBlendMinMax, getFragDepth, COMPAT_frag_depth, COMPAT_color_buffer_float, getColorBufferFloat, COMPAT_draw_buffers, getDrawBuffers, getShaderTextureLod, COMPAT_shader_texture_lod, getDepthTexture, COMPAT_depth_texture } from './compat';
+import { isDebugMode } from '../../mol-util/debug';
 
 export type WebGLExtensions = {
     instancedArrays: COMPAT_instanced_arrays
@@ -37,43 +38,45 @@ export function createExtensions(gl: GLRenderingContext): WebGLExtensions {
     }
 
     const standardDerivatives = getStandardDerivatives(gl)
-    if (standardDerivatives === null) {
-        // TODO handle non-support downstream (e.g. no flat shading)
-        // throw new Error('Could not find support for "standard_derivatives"')
+    if (isDebugMode && standardDerivatives === null) {
+        // - non-support handled downstream (flat shading option is ignored)
+        // - can't be a required extension because it is not supported by `headless-gl`
         console.log('Could not find support for "standard_derivatives"')
     }
     const textureFloatLinear = getTextureFloatLinear(gl)
-    if (textureFloatLinear === null) {
+    if (isDebugMode && textureFloatLinear === null) {
         // TODO handle non-support downstream (no gpu gaussian calc, no gpu mc???)
-        // throw new Error('Could not find support for "texture_float_linear"')
+        // - can't be a required extension because it is not supported by `headless-gl`
         console.log('Could not find support for "texture_float_linear"')
     }
     const depthTexture = getDepthTexture(gl)
-    if (depthTexture === null) {
+    if (isDebugMode && depthTexture === null) {
         console.log('Could not find support for "depth_texture"')
     }
     const blendMinMax = getBlendMinMax(gl)
-    if (blendMinMax === null) {
+    if (isDebugMode && blendMinMax === null) {
+        // TODO handle non-support downstream (e.g. no gpu gaussian calc)
+        // - can't be a required extension because it is not supported by `headless-gl`
         console.log('Could not find support for "blend_minmax"')
     }
     const vertexArrayObject = getVertexArrayObject(gl)
-    if (vertexArrayObject === null) {
+    if (isDebugMode && vertexArrayObject === null) {
         console.log('Could not find support for "vertex_array_object"')
     }
     const fragDepth = getFragDepth(gl)
-    if (fragDepth === null) {
+    if (isDebugMode && fragDepth === null) {
         console.log('Could not find support for "frag_depth"')
     }
     const colorBufferFloat = getColorBufferFloat(gl)
-    if (colorBufferFloat === null) {
+    if (isDebugMode && colorBufferFloat === null) {
         console.log('Could not find support for "color_buffer_float"')
     }
     const drawBuffers = getDrawBuffers(gl)
-    if (drawBuffers === null) {
+    if (isDebugMode && drawBuffers === null) {
         console.log('Could not find support for "draw_buffers"')
     }
     const shaderTextureLod = getShaderTextureLod(gl)
-    if (shaderTextureLod === null) {
+    if (isDebugMode && shaderTextureLod === null) {
         console.log('Could not find support for "shader_texture_lod"')
     }
 

src/mol-io/reader/_spec/common.spec.ts

@@ -0,0 +1,17 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { parseFloat as fastParseFloat, parseInt as fastParseInt } from '../../../mol-io/reader/common/text/number-parser';
+
+describe('common', () => {
+    it('number-parser fastParseFloat', () => {
+        expect(fastParseFloat('11.0829(23)', 0, 11)).toBe(11.0829)
+    });
+
+    it('number-parser fastParseInt', () => {
+        expect(fastParseInt('11(23)', 0, 11)).toBe(11)
+    });
+});

src/mol-io/reader/cif.ts

@@ -14,6 +14,7 @@ import { CCD_Schema, CCD_Database } from './cif/schema/ccd'
 import { BIRD_Schema, BIRD_Database } from './cif/schema/bird'
 import { dic_Schema, dic_Database } from './cif/schema/dic'
 import { DensityServer_Data_Schema, DensityServer_Data_Database } from './cif/schema/density-server'
+import { cifCore_Database, cifCore_Schema, cifCore_Aliases } from './cif/schema/cif-core'
 
 export const CIF = {
     parse: (data: string|Uint8Array) => typeof data === 'string' ? parseText(data) : parseBinary(data),
@@ -26,7 +27,8 @@ export const CIF = {
         CCD: (frame: CifFrame) => toDatabase<CCD_Schema, CCD_Database>(CCD_Schema, frame),
         BIRD: (frame: CifFrame) => toDatabase<BIRD_Schema, BIRD_Database>(BIRD_Schema, frame),
         dic: (frame: CifFrame) => toDatabase<dic_Schema, dic_Database>(dic_Schema, frame),
-        densityServer: (frame: CifFrame) => toDatabase<DensityServer_Data_Schema, DensityServer_Data_Database>(DensityServer_Data_Schema, frame)
+        cifCore: (frame: CifFrame) => toDatabase<cifCore_Schema, cifCore_Database>(cifCore_Schema, frame, cifCore_Aliases),
+        densityServer: (frame: CifFrame) => toDatabase<DensityServer_Data_Schema, DensityServer_Data_Database>(DensityServer_Data_Schema, frame),
     }
 }
 

src/mol-io/reader/cif/data-model.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -23,23 +23,31 @@ export function CifFile(blocks: ArrayLike<CifBlock>, name?: string): CifFile {
 
 export interface CifFrame {
     readonly header: string,
-    // Category names stored separately so that the ordering can be preserved.
+    /** Category names, stored separately so that the ordering can be preserved. */
     readonly categoryNames: ReadonlyArray<string>,
     readonly categories: CifCategories
 }
 
 export interface CifBlock extends CifFrame {
     readonly saveFrames: CifFrame[]
+    getField(name: string): CifField | undefined
 }
 
 export function CifBlock(categoryNames: string[], categories: CifCategories, header: string, saveFrames: CifFrame[] = []): CifBlock {
-    return { categoryNames, header, categories, saveFrames };
+    return {
+        categoryNames, header, categories, saveFrames,
+        getField(name: string) {
+            const [ category, field ] = name.split('.')
+            return categories[category].getField(field || '')
+        }
+    };
 }
 
-export function CifSafeFrame(categoryNames: string[], categories: CifCategories, header: string): CifFrame {
+export function CifSaveFrame(categoryNames: string[], categories: CifCategories, header: string): CifFrame {
     return { categoryNames, header, categories };
 }
 
+export type CifAliases = { readonly [name: string]: string[] }
 export type CifCategories = { readonly [name: string]: CifCategory }
 
 export interface CifCategory {

src/mol-io/reader/cif/schema.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -10,16 +10,31 @@ import { Tensor } from '../../../mol-math/linear-algebra'
 import { arrayEqual } from '../../../mol-util'
 import * as Data from './data-model'
 
-export function toDatabaseCollection<Schema extends Database.Schema>(schema: Schema, file: Data.CifFile): DatabaseCollection<Schema> {
+export namespace FieldPath {
+    export function canonical(path: string) {
+        return path.replace('.', '_').replace(/\[/, '_').replace(/(\[|\])/g, '')
+    }
+
+    export function equal(pathA: string, pathB: string) {
+        return canonical(pathA) === canonical(pathB)
+    }
+
+    export function create(category: string, field: string, asCanonical = false) {
+        const p = `${category}${field ? `.${field}` : ''}`
+        return asCanonical ? canonical(p) : p
+    }
+}
+
+export function toDatabaseCollection<Schema extends Database.Schema>(schema: Schema, file: Data.CifFile, aliases?: Data.CifAliases): DatabaseCollection<Schema> {
     const dbc: DatabaseCollection<Schema> = {}
     for (const data of file.blocks) {
-        dbc[data.header] = toDatabase(schema, data)
+        dbc[data.header] = toDatabase(schema, data, aliases)
     }
     return dbc;
 }
 
-export function toDatabase<Schema extends Database.Schema, Frame extends Database<Schema> = Database<Schema>>(schema: Schema, frame: Data.CifFrame): Frame {
-    return createDatabase(schema, frame) as Frame;
+export function toDatabase<Schema extends Database.Schema, Frame extends Database<Schema> = Database<Schema>>(schema: Schema, frame: Data.CifFrame, aliases?: Data.CifAliases): Frame {
+    return createDatabase(schema, frame, aliases) as Frame;
 }
 
 export function toTable<Schema extends Table.Schema, R extends Table<Schema> = Table<Schema>>(schema: Schema, category: Data.CifCategory): R {
@@ -51,7 +66,7 @@ function createColumn<T>(schema: Column.Schema, field: Data.CifField, value: (ro
     };
 }
 
-function createListColumn<T extends number|string>(schema: Column.Schema.List<T>, category: Data.CifCategory, key: string): Column<(number|string)[]> {
+function createListColumn<T extends number | string>(schema: Column.Schema.List<T>, category: Data.CifCategory, key: string): Column<(number | string)[]> {
     const separator = schema.separator;
     const itemParse = schema.itemParse;
 
@@ -134,15 +149,62 @@ class CategoryTable implements Table<any> { // tslint:disable-line:class-name
     }
 }
 
-function createDatabase(schema: Database.Schema, frame: Data.CifFrame): Database<any> {
+function createDatabase(schema: Database.Schema, frame: Data.CifFrame, aliases?: Data.CifAliases): Database<any> {
     const tables = Object.create(null);
     for (const k of Object.keys(schema)) {
-        tables[k] = createTable(k, (schema as any)[k], frame);
+        tables[k] = createTable(k, schema[k], frame, aliases);
     }
     return Database.ofTables(frame.header, schema, tables);
 }
 
-function createTable(key: string, schema: Table.Schema, frame: Data.CifFrame) {
-    const cat = frame.categories[key];
+type FlatFrame = { [k: string]: Data.CifField }
+
+function flattenFrame(frame: Data.CifFrame): FlatFrame {
+    const flatFrame = Object.create(null)
+    for (const c of Object.keys(frame.categories)) {
+        for (const f of frame.categories[c].fieldNames) {
+            const p =  FieldPath.create(c, f, true)
+            flatFrame[p] = frame.categories[c].getField(f)
+        }
+    }
+    return flatFrame
+}
+
+function getField(field: string, category: string, flatFrame: FlatFrame, aliases?: Data.CifAliases) {
+    const path = FieldPath.create(category, field)
+    const canonicalPath = FieldPath.canonical(path)
+    if (canonicalPath in flatFrame) return flatFrame[canonicalPath]
+    if (aliases && path in aliases) {
+        for (const aliased of aliases[path]) {
+            const canonicalAliased = FieldPath.canonical(aliased)
+            if (canonicalAliased in flatFrame) return flatFrame[canonicalAliased]
+        }
+    }
+}
+
+function createTable(key: string, schema: Table.Schema, frame: Data.CifFrame, aliases?: Data.CifAliases) {
+    let cat = frame.categories[key];
+    if (aliases) {
+        const flatFrame = flattenFrame(frame)
+        const fields: { [k: string]: Data.CifField } = Object.create(null)
+        const fieldNames: string[] = []
+        let rowCount = 0
+        for (const k of Object.keys(schema)) {
+            const field = getField(k, key, flatFrame, aliases)
+            if (field) {
+                fields[k] = field
+                fieldNames.push(k)
+                rowCount = field.rowCount
+            }
+        }
+        cat = {
+            rowCount,
+            name: key,
+            fieldNames: [...fieldNames],
+            getField(name: string) {
+                return fields[name];
+            }
+        }
+    }
     return new CategoryTable(cat || Data.CifCategory.empty(key), schema, !!cat);
 }

src/mol-io/reader/cif/schema/bird.ts

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.314, IHM 1.01, CARB draft.
+ * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.318, IHM 1.04, CARB draft.
  *
  * @author molstar/ciftools package
  */

src/mol-io/reader/cif/schema/ccd.ts

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.314, IHM 1.01, CARB draft.
+ * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.318, IHM 1.04, CARB draft.
  *
  * @author molstar/ciftools package
  */

src/mol-io/reader/cif/schema/cif-core.ts

@@ -0,0 +1,637 @@
+/**
+ * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * Code-generated 'cifCore' schema file. Dictionary versions: CifCore 3.0.11.
+ *
+ * @author molstar/ciftools package
+ */
+
+import { Database, Column } from '../../../../mol-data/db'
+
+import Schema = Column.Schema
+
+const int = Schema.int;
+const float = Schema.float;
+const str = Schema.str;
+
+export const cifCore_Schema = {
+    /**
+     * The CATEGORY of data items used to describe the parameters of
+     * the crystal unit cell and their measurement.
+     */
+    cell: {
+        /**
+         * The number of the formula units in the unit cell as specified
+         * by _chemical_formula.structural, _chemical_formula.moiety or
+         * _chemical_formula.sum.
+         */
+        formula_units_Z: int,
+        /**
+         * Volume of the crystal unit cell.
+         */
+        volume: float,
+        /**
+         * The angle between the bounding cell axes.
+         */
+        angle_alpha: float,
+        /**
+         * The angle between the bounding cell axes.
+         */
+        angle_beta: float,
+        /**
+         * The angle between the bounding cell axes.
+         */
+        angle_gamma: float,
+        /**
+         * The length of each cell axis.
+         */
+        length_a: float,
+        /**
+         * The length of each cell axis.
+         */
+        length_b: float,
+        /**
+         * The length of each cell axis.
+         */
+        length_c: float,
+    },
+    /**
+     * The CATEGORY of data items which describe the composition and
+     * chemical properties of the compound under study. The formula data
+     * items must be consistent with the density, unit-cell and Z values.
+     */
+    chemical: {
+        /**
+         * The temperature at which a crystalline solid changes to a liquid.
+         */
+        melting_point: float,
+        /**
+         * Trivial name by which the compound is commonly known.
+         */
+        name_common: str,
+        /**
+         * IUPAC or Chemical Abstracts full name of compound.
+         */
+        name_systematic: str,
+    },
+    /**
+     * The CATEGORY of data items which specify the composition and chemical
+     * properties of the compound. The formula data items must agree
+     * with those that specify the density, unit-cell and Z values.
+     *
+     * The following rules apply to the construction of the data items
+     * _chemical_formula.analytical, *.structural and *.sum. For the
+     * data item *.moiety the formula construction is broken up into
+     * residues or moieties, i.e. groups of atoms that form a molecular
+     * unit or molecular ion. The  rules given below apply within each
+     * moiety but different requirements apply to the way that moieties
+     * are connected (see _chemical_formula.moiety).
+     *
+     * 1. Only recognized element symbols may be used.
+     *
+     * 2. Each element symbol is followed by a 'count' number. A count of
+     * '1' may be omitted.
+     *
+     * 3. A space or parenthesis must separate each cluster of (element
+     * symbol + count).
+     *
+     * 4. Where a group of elements is enclosed in parentheses, the
+     * multiplier for the group must follow the closing parentheses.
+     * That is, all element and group multipliers are assumed to be
+     * printed as subscripted numbers. [An exception to this rule
+     * exists for *.moiety formulae where pre- and post-multipliers
+     * are permitted for molecular units].
+     *
+     * 5. Unless the elements are ordered in a manner that corresponds to
+     * their chemical structure, as in _chemical_formula.structural,
+     * the order of the elements within any group or moiety
+     * depends on whether or not carbon is present. If carbon is
+     * present, the order should be: C, then H, then the other
+     * elements in alphabetical order of their symbol. If carbon is
+     * not present, the elements are listed purely in alphabetic order
+     * of their symbol. This is the 'Hill' system used by Chemical
+     * Abstracts. This ordering is used in _chemical_formula.moiety
+     * and _chemical_formula.sum.
+     *
+     * _chemical_formula.iupac      '[Mo (C O)4 (C18 H33 P)2]'
+     * _chemical_formula.moiety     'C40 H66 Mo O4 P2'
+     * _chemical_formula.structural '((C O)4 (P (C6 H11)3)2)Mo'
+     * _chemical_formula.sum         'C40 H66 Mo O4 P2'
+     * _chemical_formula.weight      768.81
+     */
+    chemical_formula: {
+        /**
+         * Formula with each discrete bonded residue or ion shown as a
+         * separate moiety. See above CHEMICAL_FORMULA for rules
+         * for writing chemical formulae. In addition to the general
+         * formulae requirements, the following rules apply:
+         * 1. Moieties are separated by commas ','.
+         * 2. The order of elements within a moiety follows general rule
+         * 5 in CHEMICAL_FORMULA.
+         * 3. Parentheses are not used within moieties but may surround
+         * a moiety. Parentheses may not be nested.
+         * 4. Charges should be placed at the end of the moiety. The
+         * Singlege '+' or '-' may be preceded by a numerical multiplier
+         * and should be separated from the last (element symbol +
+         * count) by a space. Pre- or post-multipliers may be used for
+         * individual moieties.
+         */
+        moiety: str,
+        /**
+         * Chemical formulae in which all discrete bonded residues and ions are
+         * summed over the constituent elements, following the ordering given
+         * in rule 5 of the CATEGORY description. Parentheses normally not used.
+         */
+        sum: str,
+        /**
+         * Mass corresponding to the formulae _chemical_formula.structural,
+         * *_iupac, *_moiety or *_sum and, together with the Z value and cell
+         * parameters yield the density given as _exptl_crystal.density_diffrn.
+         */
+        weight: float,
+    },
+    /**
+     * The CATEGORY of data items used to specify space group
+     * information about the crystal used in the diffraction measurements.
+     *
+     * Space-group types are identified by their number as listed in
+     * International Tables for Crystallography Volume A, or by their
+     * Schoenflies symbol. Specific settings of the space groups can
+     * be identified by their Hall symbol, by specifying their
+     * symmetry operations or generators, or by giving the
+     * transformation that relates the specific setting to the
+     * reference setting based on International Tables Volume A and
+     * stored in this dictionary.
+     *
+     * The commonly used Hermann-Mauguin symbol determines the
+     * space-group type uniquely but several different Hermann-Mauguin
+     * symbols may refer to the same space-group type. A
+     * Hermann-Mauguin symbol contains information on the choice of
+     * the basis, but not on the choice of origin.
+     *
+     * Ref: International Tables for Crystallography (2002). Volume A,
+     * Space-group symmetry, edited by Th. Hahn, 5th ed.
+     * Dordrecht: Kluwer Academic Publishers.
+     */
+    space_group: {
+        /**
+         * The name of the system of geometric crystal classes of space
+         * groups (crystal system) to which the space group belongs.
+         * Note that rhombohedral space groups belong to the
+         * trigonal system.
+         */
+        crystal_system: str,
+        /**
+         * The full international Hermann-Mauguin space-group symbol as
+         * defined in Section 2.2.3 and given as the second item of the
+         * second line of each of the space-group tables of Part 7 of
+         * International Tables for Crystallography Volume A (2002).
+         *
+         * Each component of the space-group name is separated by a
+         * space or an underscore character. The use of a space is
+         * strongly recommended.  The underscore is only retained
+         * because it was used in old CIFs. It should not be used in
+         * new CIFs.
+         *
+         * Subscripts should appear without special symbols. Bars should
+         * be given as negative signs before the numbers to which they
+         * apply. The commonly used Hermann-Mauguin symbol determines the
+         * space-group type uniquely but a given space-group type may
+         * be described by more than one Hermann-Mauguin symbol. The
+         * space-group type is best described using
+         * _space_group.IT_number or _space_group.name_Schoenflies. The
+         * full international Hermann-Mauguin symbol contains information
+         * about the choice of basis for monoclinic and orthorhombic
+         * space groups but does not give information about the choice
+         * of origin. To define the setting uniquely use
+         * _space_group.name_Hall, or list the symmetry operations
+         * or generators.
+         *
+         * Ref: International Tables for Crystallography (2002). Volume A,
+         * Space-group symmetry, edited by Th. Hahn, 5th ed.
+         * Dordrecht: Kluwer Academic Publishers.
+         */
+        'name_H-M_full': str,
+    },
+    /**
+     * The CATEGORY of data items used to describe symmetry equivalent sites
+     * in the crystal unit cell.
+     */
+    space_group_symop: {
+        /**
+         * A parsable string giving one of the symmetry operations of the
+         * space group in algebraic form.  If W is a matrix representation
+         * of the rotational part of the symmetry operation defined by the
+         * positions and signs of x, y and z, and w is a column of
+         * translations defined by fractions, an equivalent position
+         * X' is generated from a given position X by the equation
+         *
+         * X' = WX + w
+         *
+         * (Note: X is used to represent bold_italics_x in International
+         * Tables for Crystallography Vol. A, Part 5)
+         *
+         * When a list of symmetry operations is given, it must contain
+         * a complete set of coordinate representatives which generates
+         * all the operations of the space group by the addition of
+         * all primitive translations of the space group. Such
+         * representatives are to be found as the coordinates of
+         * the general-equivalent position in International Tables for
+         * Crystallography Vol. A (2002), to which it is necessary to
+         * add any centring translations shown above the
+         * general-equivalent position.
+         *
+         * That is to say, it is necessary to list explicitly all the
+         * symmetry operations required to generate all the atoms in
+         * the unit cell defined by the setting used.
+         */
+        operation_xyz: str,
+    },
+    /**
+     * The CATEGORY of data items used to specify the geometry bonds in the
+     * structural model as derived from the atomic sites.
+     */
+    geom_bond: {
+        /**
+         * This label is a unique identifier for a particular site in the
+         * asymmetric unit of the crystal unit cell.
+         */
+        atom_site_label_1: str,
+        /**
+         * This label is a unique identifier for a particular site in the
+         * asymmetric unit of the crystal unit cell.
+         */
+        atom_site_label_2: str,
+        /**
+         * Intramolecular bond distance between the sites identified
+         * by _geom_bond.id
+         */
+        distance: float,
+        /**
+         * This code signals whether the angle is referred to in a
+         * publication or should be placed in a table of significant angles.
+         */
+        publ_flag: str,
+        /**
+         * The set of data items which specify the symmetry operation codes
+         * which must be applied to the atom sites involved in the geometry angle.
+         *
+         * The symmetry code of each atom site as the symmetry-equivalent position
+         * number 'n' and the cell translation number 'pqr'. These numbers are
+         * combined to form the code 'n pqr' or n_pqr.
+         *
+         * The character string n_pqr is composed as follows:
+         *
+         * n refers to the symmetry operation that is applied to the
+         * coordinates stored in _atom_site.fract_xyz. It must match a
+         * number given in _symmetry_equiv.pos_site_id.
+         *
+         * p, q and r refer to the translations that are subsequently
+         * applied to the symmetry transformed coordinates to generate
+         * the atom used in calculating the angle. These translations
+         * (x,y,z) are related to (p,q,r) by the relations
+         * p = 5 + x
+         * q = 5 + y
+         * r = 5 + z
+         */
+        site_symmetry_2: str,
+    },
+    /**
+     * The CATEGORY of data items used to record details about the
+     * creation and subsequent updating of the data block.
+     */
+    audit: {
+        /**
+         * The digital object identifier (DOI) registered to identify
+         * the data set publication represented by the current
+         * datablock. This can be used as a unique identifier for
+         * the datablock so long as the code used is a valid DOI
+         * (i.e. begins with a valid publisher prefix assigned by a
+         * Registration Agency and a suffix guaranteed to be unique
+         * by the publisher) and has had its metadata deposited
+         * with a DOI Registration Agency.
+         *
+         * A DOI is a unique character string identifying any
+         * object of intellectual property. It provides a
+         * persistent identifier for an object on a digital network
+         * and permits the association of related current data in a
+         * structured extensible way. A DOI is an implementation
+         * of the Internet concepts of Uniform Resource Name and
+         * Universal Resource Locator managed according to the
+         * specifications of the International DOI Foundation (see
+         * http://www.doi.org).
+         */
+        block_doi: str,
+    },
+    /**
+     * The CATEGORY of data items recording database deposition. These data items
+     * are assigned by database managers and should only appear in a CIF if they
+     * originate from that source.
+     */
+    database_code: {
+        /**
+         * Deposition numbers assigned by the Cambridge Crystallographic
+         * Data Centre (CCDC) to files containing structural information
+         * archived by the CCDC.
+         */
+        depnum_ccdc_archive: str,
+    },
+    /**
+     * The CATEGORY of data items used to describe atom site information
+     * used in crystallographic structure studies.
+     */
+    atom_site: {
+        /**
+         * Code for type of atomic displacement parameters used for the site.
+         */
+        adp_type: str,
+        /**
+         * A standard code to signal if the site coordinates have been
+         * determined from the intensities or calculated from the geometry
+         * of surrounding sites, or have been assigned dummy coordinates.
+         */
+        calc_flag: str,
+        /**
+         * A code which identifies a cluster of atoms that show long range
+         * positional disorder but are locally ordered. Within each such
+         * cluster of atoms, _atom_site.disorder_group is used to identify
+         * the sites that are simultaneously occupied. This field is only
+         * needed if there is more than one cluster of disordered atoms
+         * showing independent local order.
+         */
+        disorder_assembly: str,
+        /**
+         * A code that identifies a group of positionally disordered atom
+         * sites that are locally simultaneously occupied. Atoms that are
+         * positionally disordered over two or more sites (e.g. the H
+         * atoms of a methyl group that exists in two orientations) can
+         * be assigned to two or more groups. Sites belonging to the same
+         * group are simultaneously occupied, but those belonging to
+         * different groups are not. A minus prefix (e.g. "-1") is used to
+         * indicate sites disordered about a special position.
+         */
+        disorder_group: str,
+        /**
+         * Atom site coordinates as fractions of the cell length values.
+         */
+        fract_x: float,
+        /**
+         * Atom site coordinates as fractions of the cell length values.
+         */
+        fract_y: float,
+        /**
+         * Atom site coordinates as fractions of the cell length values.
+         */
+        fract_z: float,
+        /**
+         * This label is a unique identifier for a particular site in the
+         * asymmetric unit of the crystal unit cell. It is made up of
+         * components, _atom_site.label_component_0 to *_6, which may be
+         * specified as separate data items. Component 0 usually matches one
+         * of the specified _atom_type.symbol codes. This is not mandatory
+         * if an _atom_site.type_symbol item is included in the atom site
+         * list. The _atom_site.type_symbol always takes precedence over
+         * an _atom_site.label in the identification of the atom type. The
+         * label components 1 to 6 are optional, and normally only
+         * components 0 and 1 are used. Note that components 0 and 1 are
+         * concatenated, while all other components, if specified, are
+         * separated by an underline character. Underline separators are
+         * only used if higher-order components exist. If an intermediate
+         * component is not used it may be omitted provided the underline
+         * separators are inserted. For example the label 'C233__ggg' is
+         * acceptable and represents the components C, 233, '', and ggg.
+         * Each label may have a different number of components.
+         */
+        label: str,
+        /**
+         * The fraction of the atom type present at this site.
+         * The sum of the occupancies of all the atom types at this site
+         * may not significantly exceed 1.0 unless it is a dummy site. The
+         * value must lie in the 99.97% Gaussian confidence interval
+         * -3u =< x =< 1 + 3u. The _enumeration.range of 0.0:1.0 is thus
+         * correctly interpreted as meaning (0.0 - 3u) =< x =< (1.0 + 3u).
+         */
+        occupancy: float,
+        /**
+         * A concatenated series of single-letter codes which indicate the
+         * refinement restraints or constraints applied to this site. This
+         * item should not be used. It has been replaced by
+         * _atom_site.refinement_flags_posn, _adp and _occupancy. It is
+         * retained in this dictionary only to provide compatibility with
+         * legacy CIFs.
+         */
+        refinement_flags: str,
+        /**
+         * The number of different sites that are generated by the
+         * application of the space-group symmetry to the coordinates
+         * given for this site. It is equal to the multiplicity given
+         * for this Wyckoff site in International Tables for Cryst.
+         * Vol. A (2002). It is equal to the multiplicity of the general
+         * position divided by the order of the site symmetry given in
+         * _atom_site.site_symmetry_order.
+         */
+        site_symmetry_multiplicity: int,
+        /**
+         * A code to identify the atom specie(s) occupying this site.
+         * This code must match a corresponding _atom_type.symbol. The
+         * specification of this code is optional if component_0 of the
+         * _atom_site.label is used for this purpose. See _atom_type.symbol.
+         */
+        type_symbol: str,
+        /**
+         * Isotropic atomic displacement parameter, or equivalent isotropic
+         * atomic  displacement parameter, U(equiv), in angstroms squared,
+         * calculated from anisotropic atomic displacement  parameters.
+         *
+         * U(equiv) = (1/3) sum~i~[sum~j~(U^ij^ a*~i~ a*~j~ a~i~ a~j~)]
+         *
+         * a  = the real-space cell lengths
+         * a* = the reciprocal-space cell lengths
+         * Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44, 775-776.
+         */
+        U_iso_or_equiv: float,
+    },
+    /**
+     * The CATEGORY of data items used to describe the anisotropic
+     * thermal parameters of the atomic sites in a crystal structure.
+     */
+    atom_site_aniso: {
+        /**
+         * Anisotropic atomic displacement parameters are usually looped in
+         * a separate list. If this is the case, this code must match the
+         * _atom_site.label of the associated atom in the atom coordinate
+         * list and conform with the same rules described in _atom_site.label.
+         */
+        label: str,
+        /**
+         * These are the standard anisotropic atomic displacement
+         * components in angstroms squared which appear in the
+         * structure factor term:
+         *
+         * T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
+         *
+         * h = the Miller indices
+         * a* = the reciprocal-space cell lengths
+         *
+         * The unique elements of the real symmetric matrix are entered by row.
+         */
+        U_11: float,
+        /**
+         * These are the standard anisotropic atomic displacement
+         * components in angstroms squared which appear in the
+         * structure factor term:
+         *
+         * T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
+         *
+         * h = the Miller indices
+         * a* = the reciprocal-space cell lengths
+         *
+         * The unique elements of the real symmetric matrix are entered by row.
+         */
+        U_12: float,
+        /**
+         * These are the standard anisotropic atomic displacement
+         * components in angstroms squared which appear in the
+         * structure factor term:
+         *
+         * T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
+         *
+         * h = the Miller indices
+         * a* = the reciprocal-space cell lengths
+         *
+         * The unique elements of the real symmetric matrix are entered by row.
+         */
+        U_13: float,
+        /**
+         * These are the standard anisotropic atomic displacement
+         * components in angstroms squared which appear in the
+         * structure factor term:
+         *
+         * T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
+         *
+         * h = the Miller indices
+         * a* = the reciprocal-space cell lengths
+         *
+         * The unique elements of the real symmetric matrix are entered by row.
+         */
+        U_22: float,
+        /**
+         * These are the standard anisotropic atomic displacement
+         * components in angstroms squared which appear in the
+         * structure factor term:
+         *
+         * T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
+         *
+         * h = the Miller indices
+         * a* = the reciprocal-space cell lengths
+         *
+         * The unique elements of the real symmetric matrix are entered by row.
+         */
+        U_23: float,
+        /**
+         * These are the standard anisotropic atomic displacement
+         * components in angstroms squared which appear in the
+         * structure factor term:
+         *
+         * T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
+         *
+         * h = the Miller indices
+         * a* = the reciprocal-space cell lengths
+         *
+         * The unique elements of the real symmetric matrix are entered by row.
+         */
+        U_33: float,
+    },
+    /**
+     * The CATEGORY of data items used to describe atomic type information
+     * used in crystallographic structure studies.
+     */
+    atom_type: {
+        /**
+         * A description of the atom(s) designated by this atom type. In
+         * most cases this will be the element name and oxidation state of
+         * a single atom  species. For disordered or nonstoichiometric
+         * structures it will describe a combination of atom species.
+         */
+        description: str,
+        /**
+         * The identity of the atom specie(s) representing this atom type.
+         * Normally this code is the element symbol followed by the charge
+         * if there is one. The symbol may be composed of any character except
+         * an underline or a blank, with the proviso that digits designate an
+         * oxidation state and must be followed by a + or - character.
+         */
+        symbol: str,
+    },
+    /**
+     * The CATEGORY of data items used to describe atomic scattering
+     * information used in crystallographic structure studies.
+     */
+    atom_type_scat: {
+        /**
+         * The imaginary component of the anomalous dispersion scattering factors
+         * for this atom type and radiation by _diffrn_radiation_wavelength.value
+         */
+        dispersion_imag: float,
+        /**
+         * The real component of the anomalous dispersion scattering factors
+         * for this atom type and radiation by _diffrn_radiation_wavelength.value
+         */
+        dispersion_real: float,
+        /**
+         * Reference to source of scattering factors used for this atom type.
+         */
+        source: str,
+    },
+}
+
+export const cifCore_Aliases = {
+    'space_group.name_H-M_full': [
+        'symmetry_space_group_name_H-M',
+    ],
+    'space_group_symop.operation_xyz': [
+        'symmetry_equiv_pos_as_xyz',
+    ],
+    'geom_bond.atom_site_label_1': [
+        'geom_bond_atom_site_id_1',
+    ],
+    'geom_bond.atom_site_label_2': [
+        'geom_bond_atom_site_id_2',
+    ],
+    'geom_bond.distance': [
+        'geom_bond_dist',
+    ],
+    'atom_site.adp_type': [
+        'atom_site_thermal_displace_type',
+    ],
+    'atom_site.label': [
+        'atom_site_id',
+    ],
+    'atom_site.site_symmetry_multiplicity': [
+        'atom_site_symmetry_multiplicity',
+    ],
+    'atom_site_aniso.label': [
+        'atom_site_anisotrop_id',
+    ],
+    'atom_site_aniso.U_11': [
+        'atom_site_anisotrop_U_11',
+    ],
+    'atom_site_aniso.U_12': [
+        'atom_site_anisotrop_U_12',
+    ],
+    'atom_site_aniso.U_13': [
+        'atom_site_anisotrop_U_13',
+    ],
+    'atom_site_aniso.U_22': [
+        'atom_site_anisotrop_U_22',
+    ],
+    'atom_site_aniso.U_23': [
+        'atom_site_anisotrop_U_23',
+    ],
+    'atom_site_aniso.U_33': [
+        'atom_site_anisotrop_U_33',
+    ],
+}
+
+export type cifCore_Schema = typeof cifCore_Schema;
+export interface cifCore_Database extends Database<cifCore_Schema> {}

src/mol-io/reader/cif/schema/mmcif.ts

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.314, IHM 1.01, CARB draft.
+ * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.318, IHM 1.04, CARB draft.
  *
  * @author molstar/ciftools package
  */
@@ -142,12 +142,12 @@ export const mmCIF_Schema = {
          */
         id: int,
         /**
-         * A component of the identifier for this atom site.
-         * For further details, see the definition of the ATOM_SITE_ALT
-         * category.
-         *
-         * This data item is a pointer to _atom_sites_alt.id in the
-         * ATOM_SITES_ALT category.
+         * A place holder to indicate alternate conformation. The alternate conformation
+         * can be an entire polymer chain, or several residues or
+         * partial residue (several atoms within one residue). If
+         * an atom is provided in more than one position, then a
+         * non-blank alternate location indicator must be used for
+         * each of the atomic positions.
          */
         label_alt_id: str,
         /**
@@ -333,6 +333,50 @@ export const mmCIF_Schema = {
          */
         fract_transf_vector: Vector(3),
     },
+    /**
+     * Data items in the AUDIT_AUTHOR category record details about
+     * the author(s) of the data block.
+     */
+    audit_author: {
+        /**
+         * The name of an author of this data block. If there are multiple
+         * authors, _audit_author.name is looped with _audit_author.address.
+         * The family name(s), followed by a comma and including any
+         * dynastic components, precedes the first name(s) or initial(s).
+         */
+        name: str,
+        /**
+         * This data item defines the order of the author's name in the
+         * list of audit authors.
+         */
+        pdbx_ordinal: int,
+        /**
+         * The Open Researcher and Contributor ID (ORCID).
+         */
+        identifier_ORCID: str,
+    },
+    /**
+     * Data items in the AUDIT_CONFORM category describe the
+     * dictionary versions against which the data names appearing in
+     * the current data block are conformant.
+     */
+    audit_conform: {
+        /**
+         * A file name or uniform resource locator (URL) for the
+         * dictionary to which the current data block conforms.
+         */
+        dict_location: str,
+        /**
+         * The string identifying the highest-level dictionary defining
+         * data names used in this file.
+         */
+        dict_name: str,
+        /**
+         * The version number of the dictionary to which the current
+         * data block conforms.
+         */
+        dict_version: str,
+    },
     /**
      * Data items in the CELL category record details about the
      * crystallographic cell parameters.
@@ -499,6 +543,143 @@ export const mmCIF_Schema = {
          */
         pdbx_aromatic_flag: Aliased<'Y' | 'N'>(str),
     },
+    /**
+     * Data items in the CITATION category record details about the
+     * literature cited as being relevant to the contents of the data
+     * block.
+     */
+    citation: {
+        /**
+         * The name of the publisher of the citation; relevant
+         * for books or book chapters.
+         */
+        book_publisher: str,
+        /**
+         * The country/region of publication; relevant for books
+         * and book chapters.
+         */
+        country: str,
+        /**
+         * The value of _citation.id must uniquely identify a record in the
+         * CITATION list.
+         *
+         * The _citation.id 'primary' should be used to indicate the
+         * citation that the author(s) consider to be the most pertinent to
+         * the contents of the data block.
+         *
+         * Note that this item need not be a number; it can be any unique
+         * identifier.
+         */
+        id: str,
+        /**
+         * Abbreviated name of the cited journal as given in the
+         * Chemical Abstracts Service Source Index.
+         */
+        journal_abbrev: str,
+        /**
+         * The American Society for Testing and Materials (ASTM) code
+         * assigned to the journal cited (also referred to as the CODEN
+         * designator of the Chemical Abstracts Service); relevant for
+         * journal articles.
+         */
+        journal_id_ASTM: str,
+        /**
+         * The Cambridge Structural Database (CSD) code assigned to the
+         * journal cited; relevant for journal articles. This is also the
+         * system used at the Protein Data Bank (PDB).
+         */
+        journal_id_CSD: str,
+        /**
+         * The International Standard Serial Number (ISSN) code assigned to
+         * the journal cited; relevant for journal articles.
+         */
+        journal_id_ISSN: str,
+        /**
+         * Volume number of the journal cited; relevant for journal
+         * articles.
+         */
+        journal_volume: str,
+        /**
+         * The first page of the citation; relevant for journal
+         * articles, books and book chapters.
+         */
+        page_first: str,
+        /**
+         * The last page of the citation; relevant for journal
+         * articles, books and book chapters.
+         */
+        page_last: str,
+        /**
+         * The title of the citation; relevant for journal articles, books
+         * and book chapters.
+         */
+        title: str,
+        /**
+         * The year of the citation; relevant for journal articles, books
+         * and book chapters.
+         */
+        year: int,
+        /**
+         * Document Object Identifier used by doi.org to uniquely
+         * specify bibliographic entry.
+         */
+        pdbx_database_id_DOI: str,
+        /**
+         * Ascession number used by PubMed to categorize a specific
+         * bibliographic entry.
+         */
+        pdbx_database_id_PubMed: int,
+    },
+    /**
+     * Data items in the CITATION_AUTHOR category record details
+     * about the authors associated with the citations in the
+     * CITATION list.
+     */
+    citation_author: {
+        /**
+         * This data item is a pointer to _citation.id in the CITATION
+         * category.
+         */
+        citation_id: str,
+        /**
+         * Name of an author of the citation; relevant for journal
+         * articles, books and book chapters.
+         *
+         * The family name(s), followed by a comma and including any
+         * dynastic components, precedes the first name(s) or initial(s).
+         */
+        name: str,
+        /**
+         * This data item defines the order of the author's name in the
+         * list of authors of a citation.
+         */
+        ordinal: int,
+    },
+    /**
+     * Data items in the DATABASE_2 category record details about the
+     * database identifiers of the data block.
+     *
+     * These data items are assigned by database managers and should
+     * only appear in a data block if they originate from that source.
+     *
+     * The name of this category, DATABASE_2, arose because the
+     * category name DATABASE was already in use in the core CIF
+     * dictionary, but was used differently from the way it needed
+     * to be used in the mmCIF dictionary. Since CIF data names
+     * cannot be changed once they have been adopted, a new category
+     * had to be created.
+     */
+    database_2: {
+        /**
+         * An abbreviation that identifies the database.
+         */
+        database_id: Aliased<'CAS' | 'CSD' | 'EMDB' | 'ICSD' | 'MDF' | 'NDB' | 'NBS' | 'PDB' | 'PDF' | 'RCSB' | 'EBI' | 'PDBE' | 'BMRB' | 'WWPDB' | 'PDB_ACC'>(str),
+        /**
+         * The code assigned by the database identified in
+         * _database_2.database_id.
+         */
+        database_code: str,
+    },
     /**
      * Data items in the ENTITY category record details (such as
      * chemical composition, name and source) about the molecular
@@ -741,6 +922,11 @@ export const mmCIF_Schema = {
          * and to distinguish this structural result from others.
          */
         title: str,
+        /**
+         * An automatically generated descriptor for an NDB structure or
+         * the unstructured content of the PDB COMPND record.
+         */
+        pdbx_descriptor: str,
     },
     /**
      * Data items in the STRUCT_ASYM category record details about the
@@ -1680,6 +1866,20 @@ export const mmCIF_Schema = {
          */
         content_type: Aliased<'minimized average structure' | 'representative structure' | 'ensemble' | 'derivative structure' | 'native structure' | 'associated EM volume' | 'other EM volume' | 'associated NMR restraints' | 'associated structure factors' | 'associated SAS data' | 'protein target sequence and/or protocol data' | 'split' | 're-refinement' | 'complete structure' | 'unspecified' | 'other'>(str),
     },
+    pdbx_entity_nonpoly: {
+        /**
+         * This data item is a pointer to _entity.id in the ENTITY category.
+         */
+        entity_id: str,
+        /**
+         * This data item is a pointer to _chem_comp.id in the CHEM_COMP category.
+         */
+        comp_id: str,
+        /**
+         * A name for the non-polymer entity
+         */
+        name: str,
+    },
     /**
      * Data items in the CHEM_COMP_IDENTIFIER category provide
      * identifiers for chemical components.
@@ -2215,15 +2415,18 @@ export const mmCIF_Schema = {
          * This data item is a pointer to _entity.id in the ENTITY category.
          */
         entity_id: str,
+        /**
+         * Scientific name of the organism of the natural source.
+         */
+        pdbx_organism_scientific: str,
+        /**
+         * The plasmid containing the gene.
+         */
+        pdbx_plasmid_name: str,
         /**
          * This data item is an ordinal identifier for entity_src_nat data records.
          */
         pdbx_src_id: int,
-        /**
-         * This data item identifies cases in which an alternative source
-         * modeled.
-         */
-        pdbx_alt_source_flag: Aliased<'sample' | 'model'>(str),
         /**
          * The beginning polymer sequence position for the polymer section corresponding
          * to this source.
@@ -2257,19 +2460,22 @@ export const mmCIF_Schema = {
          * Identifies the gene.
          */
         pdbx_gene_src_gene: List(',', x => x),
+        /**
+         * Scientific name of the organism.
+         */
+        pdbx_gene_src_scientific_name: str,
+        /**
+         * The name of the plasmid that produced the entity in the host
+         * organism. Where full details of the protein production are available
+         * it would be expected that this item would be derived from
+         * _pdbx_construct.name of the construct pointed to from
+         * _entity_src_gen_express.plasmid_id.
+         */
+        plasmid_name: str,
         /**
          * This data item is an ordinal identifier for entity_src_gen data records.
          */
         pdbx_src_id: int,
-        /**
-         * This data item identifies cases in which an alternative source
-         * modeled.
-         */
-        pdbx_alt_source_flag: Aliased<'sample' | 'model'>(str),
-        /**
-         * This data item povides additional information about the sequence type.
-         */
-        pdbx_seq_type: Aliased<'N-terminal tag' | 'C-terminal tag' | 'Biological sequence' | 'Linker'>(str),
         /**
          * The beginning polymer sequence position for the polymer section corresponding
          * to this source.
@@ -2290,6 +2496,11 @@ export const mmCIF_Schema = {
      * about chemically synthesized molecules.
      */
     pdbx_entity_src_syn: {
+        /**
+         * The scientific name of the organism from which the sequence of
+         * the synthetic entity was derived.
+         */
+        organism_scientific: str,
         /**
          * This data item is a pointer to _entity.id in the ENTITY category.
          */
@@ -2298,11 +2509,6 @@ export const mmCIF_Schema = {
          * This data item is an ordinal identifier for pdbx_entity_src_syn data records.
          */
         pdbx_src_id: int,
-        /**
-         * This data item identifies cases in which an alternative source
-         * modeled.
-         */
-        pdbx_alt_source_flag: Aliased<'sample' | 'model'>(str),
         /**
          * The beginning polymer sequence position for the polymer section corresponding
          * to this source.
@@ -3050,7 +3256,7 @@ export const mmCIF_Schema = {
         /**
          * The type of data held in the dataset.
          */
-        data_type: Aliased<'NMR data' | '3DEM volume' | '2DEM class average' | 'EM raw micrographs' | 'SAS data' | 'CX-MS data' | 'Mass Spectrometry data' | 'EPR data' | 'H/D exchange data' | 'Single molecule FRET data' | 'Experimental model' | 'Comparative model' | 'Integrative model' | 'De Novo model' | 'Predicted contacts' | 'Mutagenesis data' | 'DNA footprinting data' | 'Hydroxyl radical footprinting data' | 'Yeast two-hybrid screening data' | 'Other'>(str),
+        data_type: Aliased<'NMR data' | '3DEM volume' | '2DEM class average' | 'EM raw micrographs' | 'SAS data' | 'CX-MS data' | 'Mass Spectrometry data' | 'EPR data' | 'H/D exchange data' | 'Single molecule FRET data' | 'Experimental model' | 'Comparative model' | 'Integrative model' | 'De Novo model' | 'Predicted contacts' | 'Mutagenesis data' | 'DNA footprinting data' | 'Hydroxyl radical footprinting data' | 'Yeast two-hybrid screening data' | 'Quantitative measurements of genetic interactions' | 'Other'>(str),
         /**
          * A flag that indicates whether the dataset is archived in
          * an IHM related database or elsewhere.
@@ -3225,7 +3431,7 @@ export const mmCIF_Schema = {
          */
         file_size_bytes: float,
         /**
-         * Textual description of what the external file is.
+         * Additional textual details regarding the external file.
          */
         details: str,
     },
@@ -3459,7 +3665,7 @@ export const mmCIF_Schema = {
         /**
          * The type of crosslinker used.
          */
-        linker_type: Aliased<'EDC' | 'DSS' | 'EGS' | 'BS3' | 'BS2G' | 'DST' | 'sulfo-SDA' | 'sulfo-SMCC' | 'DSSO' | 'Other'>(str),
+        linker_type: Aliased<'EDC' | 'DSS' | 'EGS' | 'BS3' | 'BS2G' | 'DST' | 'sulfo-SDA' | 'sulfo-SMCC' | 'DSSO' | 'DSG' | 'BSP' | 'Other'>(str),
         /**
          * Identifier to the crosslinking dataset.
          * This data item is a pointer to the _ihm_dataset_list.id in the

src/mol-io/reader/cif/text/parser.ts

@@ -1,7 +1,8 @@
 /**
- * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
 /**
@@ -23,7 +24,7 @@
  */
 
 import * as Data from '../data-model'
-import { Tokens, TokenBuilder } from '../../common/text/tokenizer'
+import { Tokens, TokenBuilder, Tokenizer } from '../../common/text/tokenizer'
 import { ReaderResult as Result } from '../../result'
 import { Task, RuntimeContext, chunkedSubtask } from '../../../../mol-task'
 
@@ -46,6 +47,8 @@ interface TokenizerState {
     position: number,
     length: number,
     isEscaped: boolean,
+    isImportGet: boolean,
+    inSaveFrame: boolean,
 
     lineNumber: number,
     tokenType: CifTokenType,
@@ -168,6 +171,23 @@ function eatMultiline(state: TokenizerState) {
     return prev;
 }
 
+function eatImportGet(state: TokenizerState) {
+    // _import.get [{'save':orient_matrix  'file':templ_attr.cif}]
+    // skipWhitespace(state)
+    while (state.position < state.length) {
+        switch (state.data.charCodeAt(state.position)) {
+            case 93:  // ]
+                ++state.position;
+                state.tokenEnd = state.position;
+                state.isImportGet = false
+                return;
+            default:
+                ++state.position;
+                break;
+        }
+    }
+}
+
 /**
  * Skips until \n or \r occurs -- therefore the newlines get handled by the "skipWhitespace" function.
  */
@@ -274,6 +294,25 @@ function isLoop(state: TokenizerState): boolean {
     return true;
 }
 
+function isImportGet(state: TokenizerState): boolean {
+    // _import.get [{'save':orient_matrix  'file':templ_attr.cif}]
+
+    if (state.tokenEnd - state.tokenStart !== 11) return false;
+
+    if (state.data.charCodeAt(state.tokenStart + 1) !== 105) return false; // i
+    if (state.data.charCodeAt(state.tokenStart + 2) !== 109) return false; // m
+    if (state.data.charCodeAt(state.tokenStart + 3) !== 112) return false; // p
+    if (state.data.charCodeAt(state.tokenStart + 4) !== 111) return false; // o
+    if (state.data.charCodeAt(state.tokenStart + 5) !== 114) return false; // r
+    if (state.data.charCodeAt(state.tokenStart + 6) !== 116) return false; // t
+    if (state.data.charCodeAt(state.tokenStart + 7) !== 46) return false; // .
+    if (state.data.charCodeAt(state.tokenStart + 8) !== 103) return false; // g
+    if (state.data.charCodeAt(state.tokenStart + 9) !== 101) return false; // e
+    if (state.data.charCodeAt(state.tokenStart + 10) !== 116) return false; // t
+
+    return true;
+}
+
 /**
  * Checks if the current token shares the namespace with string at <start,end).
  */
@@ -315,6 +354,17 @@ function getNamespace(state: TokenizerState, endIndex: number) {
     return state.data.substring(state.tokenStart, endIndex);
 }
 
+/**
+ * Returns true if the current token contain no '.', otherwise returns false.
+ */
+function isFlatNamespace(state: TokenizerState): boolean {
+    let i: number;
+    for (i = state.tokenStart; i < state.tokenEnd; ++i) {
+        if (state.data.charCodeAt(i) === 46) return false;
+    }
+    return true;
+}
+
 /**
  * String representation of the current token.
  */
@@ -336,6 +386,7 @@ function moveNextInternal(state: TokenizerState) {
     state.tokenStart = state.position;
     state.tokenEnd = state.position;
     state.isEscaped = false;
+
     let c = state.data.charCodeAt(state.position);
     switch (c) {
         case 35: // #, comment
@@ -357,20 +408,28 @@ function moveNextInternal(state: TokenizerState) {
             state.tokenType = CifTokenType.Value;
             break;
         default:
-            eatValue(state);
+            if (state.isImportGet) {
+                eatImportGet(state);
+            } else {
+                eatValue(state);
+            }
+
             // escaped is always Value
             if (state.isEscaped) {
                 state.tokenType = CifTokenType.Value;
-                // _ always means column name
+            // _ means column name, including _import.get
             } else if (state.data.charCodeAt(state.tokenStart) === 95) { // _
+                if (state.inSaveFrame && isImportGet(state)) {
+                    state.isImportGet = true
+                }
                 state.tokenType = CifTokenType.ColumnName;
-                // 5th char needs to be _ for data_ or loop_
+            // 5th char needs to be _ for data_, save_ or loop_
             } else if (state.tokenEnd - state.tokenStart >= 5 && state.data.charCodeAt(state.tokenStart + 4) === 95) {
                 if (isData(state)) state.tokenType = CifTokenType.Data;
                 else if (isSave(state)) state.tokenType = CifTokenType.Save;
                 else if (isLoop(state)) state.tokenType = CifTokenType.Loop;
                 else state.tokenType = CifTokenType.Value;
-                // all other tests failed, we are at Value token.
+            // all other tests failed, we are at Value token.
             } else {
                 state.tokenType = CifTokenType.Value;
             }
@@ -396,6 +455,8 @@ function createTokenizer(data: string, runtimeCtx: RuntimeContext): TokenizerSta
         tokenType: CifTokenType.End,
         lineNumber: 1,
         isEscaped: false,
+        isImportGet: false,
+        inSaveFrame: false,
 
         runtimeCtx
     };
@@ -410,13 +471,48 @@ interface CifCategoryResult {
     errorMessage: string;
 }
 
+interface CifCategoryData {
+    name: string,
+    rowCount: number,
+    fieldNames: string[],
+    fields: { [name: string]: Data.CifField }
+}
+
 type FrameContext = {
     categoryNames: string[],
-    categories: { [name: string]: Data.CifCategory }
+    categoryData: { [name: string]: CifCategoryData }
 }
 
 function FrameContext(): FrameContext {
-    return { categoryNames: [], categories: Object.create(null) };
+    return { categoryNames: [], categoryData: Object.create(null) };
+}
+
+function CifCategories(categoryNames: string[], categoryData: { [name: string]: CifCategoryData }): { [name: string]: Data.CifCategory } {
+    const categories = Object.create(null)
+    for (const name of categoryNames) {
+        const d = categoryData[name]
+        categories[name] = Data.CifCategory(d.name, d.rowCount, d.fieldNames, d.fields)
+    }
+    return categories
+}
+
+function CifBlock(ctx: FrameContext, header: string, saveFrames?: Data.CifFrame[]): Data.CifBlock {
+    return Data.CifBlock(ctx.categoryNames, CifCategories(ctx.categoryNames, ctx.categoryData), header, saveFrames)
+}
+
+function CifSaveFrame(ctx: FrameContext, header: string): Data.CifBlock {
+    return Data.CifBlock(ctx.categoryNames, CifCategories(ctx.categoryNames, ctx.categoryData), header)
+}
+
+function addFields(ctx: FrameContext, name: string, rowCount: number, fieldNames: string[], fields: { [k: string]: Data.CifField }) {
+    if (name in ctx.categoryData) {
+        const cat = ctx.categoryData[name]
+        cat.fieldNames.push(...fieldNames)
+        Object.assign(cat.fields, fields)
+    } else {
+        ctx.categoryData[name] = { name, rowCount, fieldNames, fields };
+        ctx.categoryNames.push(name);
+    }
 }
 
 /**
@@ -449,9 +545,7 @@ function handleSingle(tokenizer: TokenizerState, ctx: FrameContext): CifCategory
         moveNext(tokenizer);
     }
 
-    const catName = name.substr(1);
-    ctx.categories[catName] = Data.CifCategory(catName, 1, fieldNames, fields);
-    ctx.categoryNames.push(catName);
+    addFields(ctx, name.substr(1), 1, fieldNames, fields)
 
     return {
         hasError: false,
@@ -496,10 +590,13 @@ async function handleLoop(tokenizer: TokenizerState, ctx: FrameContext): Promise
 
     moveNext(tokenizer);
     const name = getNamespace(tokenizer, getNamespaceEnd(tokenizer));
+    const isFlat = isFlatNamespace(tokenizer);
     const fieldNames: string[] = [];
 
     while (tokenizer.tokenType === CifTokenType.ColumnName) {
-        fieldNames[fieldNames.length] = getTokenString(tokenizer).substring(name.length + 1);
+        fieldNames[fieldNames.length] = isFlat
+            ? getTokenString(tokenizer)
+            : getTokenString(tokenizer).substring(name.length + 1);
         moveNext(tokenizer);
     }
 
@@ -526,14 +623,19 @@ async function handleLoop(tokenizer: TokenizerState, ctx: FrameContext): Promise
     }
 
     const rowCount = (state.tokenCount / fieldCount) | 0;
-    const fields = Object.create(null);
-    for (let i = 0; i < fieldCount; i++) {
-        fields[fieldNames[i]] = Data.CifField.ofTokens(tokens[i]);
-    }
+    if (isFlat) {
+        for (let i = 0; i < fieldCount; i++) {
+            const fields = { '': Data.CifField.ofTokens(tokens[i]) };
+            addFields(ctx, fieldNames[i].substr(1), rowCount, [''], fields)
+        }
+    } else {
+        const fields = Object.create(null);
+        for (let i = 0; i < fieldCount; i++) {
+            fields[fieldNames[i]] = Data.CifField.ofTokens(tokens[i]);
+        }
 
-    const catName = name.substr(1);
-    ctx.categories[catName] = Data.CifCategory(catName, rowCount, fieldNames, fields);
-    ctx.categoryNames.push(catName);
+        addFields(ctx, name.substr(1), rowCount, fieldNames, fields)
+    }
 
     return {
         hasError: false,
@@ -568,12 +670,14 @@ async function parseInternal(data: string, runtimeCtx: RuntimeContext) {
 
     let blockCtx = FrameContext();
 
-    let inSaveFrame = false;
-
     // the next three initial values are never used in valid files
     let saveFrames: Data.CifFrame[] = [];
     let saveCtx = FrameContext();
-    let saveFrame: Data.CifFrame = Data.CifSafeFrame(saveCtx.categoryNames, saveCtx.categories, '');
+    let saveFrame: Data.CifFrame = Data.CifSaveFrame(
+        saveCtx.categoryNames, CifCategories(saveCtx.categoryNames, saveCtx.categoryData), ''
+    );
+
+    let saveHeader = ''
 
     runtimeCtx.update({ message: 'Parsing...', current: 0, max: data.length });
 
@@ -583,11 +687,11 @@ async function parseInternal(data: string, runtimeCtx: RuntimeContext) {
 
         // Data block
         if (token === CifTokenType.Data) {
-            if (inSaveFrame) {
+            if (tokenizer.inSaveFrame) {
                 return error(tokenizer.lineNumber, 'Unexpected data block inside a save frame.');
             }
             if (blockCtx.categoryNames.length > 0) {
-                dataBlocks.push(Data.CifBlock(blockCtx.categoryNames, blockCtx.categories, blockHeader, saveFrames));
+                dataBlocks.push(CifBlock(blockCtx, blockHeader, saveFrames));
             }
             blockHeader = data.substring(tokenizer.tokenStart + 5, tokenizer.tokenEnd);
             blockCtx = FrameContext();
@@ -595,47 +699,47 @@ async function parseInternal(data: string, runtimeCtx: RuntimeContext) {
             moveNext(tokenizer);
         // Save frame
         } else if (token === CifTokenType.Save) {
-            const saveHeader = data.substring(tokenizer.tokenStart + 5, tokenizer.tokenEnd);
-            if (saveHeader.length === 0) {
+            if (tokenizer.tokenEnd - tokenizer.tokenStart === 5) { // end of save frame
                 if (saveCtx.categoryNames.length > 0) {
-                    saveFrames[saveFrames.length] = saveFrame;
+                    saveFrames[saveFrames.length] = CifSaveFrame(saveCtx, saveHeader);
                 }
-                inSaveFrame = false;
-            } else {
-                if (inSaveFrame) {
+                tokenizer.inSaveFrame = false;
+            } else { // start of save frame
+                if (tokenizer.inSaveFrame) {
                     return error(tokenizer.lineNumber, 'Save frames cannot be nested.');
                 }
-                inSaveFrame = true;
-                const safeHeader = data.substring(tokenizer.tokenStart + 5, tokenizer.tokenEnd);
+                tokenizer.inSaveFrame = true;
+                saveHeader = data.substring(tokenizer.tokenStart + 5, tokenizer.tokenEnd);
                 saveCtx = FrameContext();
-                saveFrame = Data.CifSafeFrame(saveCtx.categoryNames, saveCtx.categories, safeHeader);
+                // saveFrame = CifSaveFrame(saveCtx, saveHeader);
             }
             moveNext(tokenizer);
         // Loop
         } else if (token === CifTokenType.Loop) {
-            const cat = await handleLoop(tokenizer, inSaveFrame ? saveCtx : blockCtx);
+            const cat = await handleLoop(tokenizer, tokenizer.inSaveFrame ? saveCtx : blockCtx);
             if (cat.hasError) {
                 return error(cat.errorLine, cat.errorMessage);
             }
         // Single row
         } else if (token === CifTokenType.ColumnName) {
-            const cat = handleSingle(tokenizer, inSaveFrame ? saveCtx : blockCtx);
+            const cat = handleSingle(tokenizer, tokenizer.inSaveFrame ? saveCtx : blockCtx);
             if (cat.hasError) {
                 return error(cat.errorLine, cat.errorMessage);
             }
         // Out of options
         } else {
+            console.log(tokenizer.tokenType, Tokenizer.getTokenString(tokenizer))
             return error(tokenizer.lineNumber, 'Unexpected token. Expected data_, loop_, or data name.');
         }
     }
 
     // Check if the latest save frame was closed.
-    if (inSaveFrame) {
+    if (tokenizer.inSaveFrame) {
         return error(tokenizer.lineNumber, `Unfinished save frame (${saveFrame.header}).`);
     }
 
     if (blockCtx.categoryNames.length > 0 || saveFrames.length > 0) {
-        dataBlocks.push(Data.CifBlock(blockCtx.categoryNames, blockCtx.categories, blockHeader, saveFrames));
+        dataBlocks.push(CifBlock(blockCtx, blockHeader, saveFrames));
     }
 
     return result(Data.CifFile(dataBlocks));

src/mol-math/geometry/spacegroup/construction.ts

@@ -6,11 +6,11 @@
  */
 
 import { Vec3, Mat4 } from '../../linear-algebra'
-import { SpacegroupName, TransformData, GroupData, getSpacegroupIndex, OperatorData, SpacegroupNames } from './tables'
+import { SpacegroupName, TransformData, GroupData, getSpacegroupIndex, OperatorData, SpacegroupNumber } from './tables'
 import { SymmetryOperator } from '../../geometry';
 
 interface SpacegroupCell {
-    /** Zero based spacegroup number */
+    /** Index into spacegroup data table */
     readonly index: number,
     readonly size: Vec3,
     readonly volume: number,
@@ -22,7 +22,10 @@ interface SpacegroupCell {
 }
 
 interface Spacegroup {
+    /** Hermann-Mauguin spacegroup name */
     readonly name: string,
+    /** Spacegroup number from International Tables for Crystallography */
+    readonly num: number,
     readonly cell: SpacegroupCell,
     readonly operators: ReadonlyArray<Mat4>
 }
@@ -72,14 +75,15 @@ namespace SpacegroupCell {
     }
 }
 
-
 namespace Spacegroup {
     /** P1 with [1, 1, 1] cell */
     export const ZeroP1 = create(SpacegroupCell.Zero);
 
     export function create(cell: SpacegroupCell): Spacegroup {
         const operators = GroupData[cell.index].map(i => getOperatorMatrix(OperatorData[i]));
-        return { name: SpacegroupNames[cell.index], cell, operators };
+        const name = SpacegroupName[cell.index]
+        const num = SpacegroupNumber[cell.index]
+        return { name, num, cell, operators };
     }
 
     const _ijkVec = Vec3();

src/mol-math/geometry/spacegroup/tables.ts

@@ -1,7 +1,8 @@
 /**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
 export const TransformData = [
@@ -31,26 +32,26 @@ export const TransformData = [
     [0.0, 0.0, -1.0, 0.75],
     [1.0, -1.0, 0.0, 0.0],
     [-1.0, 1.0, 0.0, 0.0],
-    [0.0, 0.0, 1.0, 0.333333333333333],
-    [0.0, 0.0, 1.0, 0.666666666666667],
-    [1.0, 0.0, 0.0, 0.666666666666667],
-    [0.0, 1.0, 0.0, 0.333333333333333],
-    [0.0, -1.0, 0.0, 0.666666666666667],
-    [1.0, -1.0, 0.0, 0.333333333333333],
-    [-1.0, 1.0, 0.0, 0.666666666666667],
-    [-1.0, 0.0, 0.0, 0.333333333333333],
-    [1.0, 0.0, 0.0, 0.333333333333333],
-    [0.0, 1.0, 0.0, 0.666666666666667],
-    [0.0, -1.0, 0.0, 0.333333333333333],
-    [1.0, -1.0, 0.0, 0.666666666666667],
-    [-1.0, 1.0, 0.0, 0.333333333333333],
-    [-1.0, 0.0, 0.0, 0.666666666666667],
-    [0.0, 0.0, -1.0, 0.333333333333333],
-    [0.0, 0.0, -1.0, 0.666666666666667],
-    [0.0, 0.0, 1.0, 0.833333333333333],
-    [0.0, 0.0, 1.0, 0.166666666666667],
-    [0.0, 0.0, -1.0, 0.833333333333333],
-    [0.0, 0.0, -1.0, 0.166666666666667],
+    [0.0, 0.0, 1.0, 1/3],
+    [0.0, 0.0, 1.0, 2/3],
+    [1.0, 0.0, 0.0, 2/3],
+    [0.0, 1.0, 0.0, 1/3],
+    [0.0, -1.0, 0.0, 2/3],
+    [1.0, -1.0, 0.0, 1/3],
+    [-1.0, 1.0, 0.0, 2/3],
+    [-1.0, 0.0, 0.0, 1/3],
+    [1.0, 0.0, 0.0, 1/3],
+    [0.0, 1.0, 0.0, 2/3],
+    [0.0, -1.0, 0.0, 1/3],
+    [1.0, -1.0, 0.0, 2/3],
+    [-1.0, 1.0, 0.0, 1/3],
+    [-1.0, 0.0, 0.0, 2/3],
+    [0.0, 0.0, -1.0, 1/3],
+    [0.0, 0.0, -1.0, 2/3],
+    [0.0, 0.0, 1.0, 5/6],
+    [0.0, 0.0, 1.0, 1/6],
+    [0.0, 0.0, -1.0, 5/6],
+    [0.0, 0.0, -1.0, 1/6],
 ];
 
 export const OperatorData = [
@@ -970,6 +971,16 @@ export const GroupData = [
     [0, 52, 16, 1, 26, 59, 20, 65],
     [0, 31, 1, 63],
     [0, 1, 24, 62],
+    [0, 15, 1, 9],  // 'P 1 21/n 1'
+    // X,Y,Z
+    // -X+1/2,Y+1/2,-Z+1/2
+    // -X,-Y,-Z
+    // X+1/2,-Y+1/2,Z+1/2
+    [0, 5, 1, 8],  // 'P 1 21/a 1'
+    // X,Y,Z
+    // -X+1/2,Y+1/2,-Z
+    // -X,-Y,-Z
+    // X+1/2,-Y+1/2,Z
     [0, 31, 1, 63, 26, 21, 65, 54],
     [0, 2, 57, 56],
     [0, 60, 3, 16],
@@ -985,7 +996,7 @@ export const GroupData = [
     [0, 22, 57, 3, 159, 279, 654, 655, 158, 274, 656, 657, 29, 18, 25, 27, 284, 658, 262, 269, 280, 659, 257, 267],
 ];
 
-export const ZeroBasedSpacegroupNumbers = {
+export const SpacegroupNameToIndexMap = {
     'P 1': 0,
     'P -1': 1,
     'P 1 2 1': 2,
@@ -1318,44 +1329,164 @@ export const ZeroBasedSpacegroupNumbers = {
     'B 1 1 2/m': 250,
     'P 1 1 2/b': 251,
     'P 1 1 21/b': 252,
-    'B 1 1 2/b': 253,
-    'P 21 2 2': 254,
-    'P 2 21 2': 255,
-    'P 21 21 2 (a)': 256,
-    'P 21 2 21': 257,
-    'P 2 21 21': 258,
-    'C 2 2 21a)': 259,
-    'C 2 2 2a': 260,
-    'F 2 2 2a': 261,
-    'I 2 2 2a': 262,
-    'P 21/m 21/m 2/n a': 263,
-    'P 42 21 2a': 264,
-    'I 2 3a': 265,
+    'P 1 21/n 1': 253,
+    'P 1 21/a 1': 254,
+    'B 1 1 2/b': 255,
+    'P 21 2 2': 256,
+    'P 2 21 2': 257,
+    'P 21 21 2 (a)': 258,
+    'P 21 2 21': 259,
+    'P 2 21 21': 260,
+    'C 2 2 21a)': 261,
+    'C 2 2 2a': 262,
+    'F 2 2 2a': 263,
+    'I 2 2 2a': 264,
+    'P 21/m 21/m 2/n a': 265,
+    'P 42 21 2a': 266,
+    'I 2 3a': 267,
 };
 
-export type SpacegroupName = keyof typeof ZeroBasedSpacegroupNumbers
+export function getSpacegroupIndexFromNumber(num: number) {
+    // 38 spacegroup variants as given CCP4s symop.lib
+    switch (num) {
+        case 1146: return 146
+        case 1148: return 149
+        case 1155: return 157
+        case 1160: return 163
+        case 1161: return 165
+        case 1166: return 171
+        case 1167: return 173
 
-export const SpacegroupNames: { [num: number]: SpacegroupName } = (function () {
+        case 1003: return 237  // 'P 1 1 2'  !(dyad along z)
+        case 1004: return 238  // 'P 1 1 21'  !(unique axis c)
+        case 1005: return 239  // 'B 1 1 2' 'B 2'
+        case 2005: return 240  // 'A 1 2 1'
+        case 3005: return 241  // 'C 1 21 1' ! (Origin on screw at 1/4X)
+        case 4005: return 242  // 'I 1 2 1' 'I 2' !!! GJK @ 2003-06-02
+        case 5005: return 243  // 'I 1 21 1'
+        case 1006: return 244  // 'P 1 1 m'
+        case 1007: return 245  // 'P 1 1 b'
+        case 1008: return 246  // 'B 1 1 m'
+        case 1009: return 247  // 'B 1 1 b'
+        case 1010: return 248  // 'P 1 1 2/m'
+        case 1011: return 249  // 'P 1 1 21/m'
+        case 1012: return 250  // 'B 1 1 2/m'
+        case 1013: return 251  // 'P 1 1 2/b'
+        case 1014: return 252  // 'P 1 1 21/b'
+        case 2014: return 253  // 'P 1 21/n 1'
+        case 3014: return 254  // 'P 1 21/a 1'
+        case 1015: return 255  // 'B 1 1 2/b'
+        case 1017: return 256  // 'P 21 2 2' !(unique axis a)
+        case 2017: return 257  // 'P 2 21 2' !(unique axis b)
+        case 1018: return 258  // 'P 21 21 2 (a)' ! origin on 21 21, shift (1/4,1/4,0)
+        case 2018: return 259  // 'P 21 2 21'  !(unique axis b)
+        case 3018: return 260  // 'P 2 21 21'  !(unique axis a)
+        case 1020: return 261  // 'C 2 2 21a)' ! P212121 with C centring, shift(1/4,0,0)
+        case 1021: return 262  // 'C 2 2 2a'  ! C21212a origin on 21 21
+        case 1022: return 263  // 'F 2 2 2a' ! same as 1018 with face centring  shift (1/4,0,0)
+        case 1023: return 264  // 'I 2 2 2a'  ! as 1018 with origin shift (1/4,1/4,1/4)
+        case 1059: return 265  // 'P 21/m 21/m 2/n a'
+        case 1094: return 266  // 'P 42 21 2a' ! (as P21212a) origin on 21 21 ie Shift 1/4,1/4,1/4
+        case 1197: return 267  // 'I 2 3a' ! Expansion of 1023 which is an expansion of 1018
+    }
+
+    let offset = 0
+    if (num > 146) ++offset
+    if (num > 148) ++offset
+    if (num > 155) ++offset
+    if (num > 160) ++offset
+    if (num > 161) ++offset
+    if (num > 166) ++offset
+    if (num > 167) ++offset
+
+    return num - 1 + offset
+}
+
+export function getSpacegroupNumberFromIndex(idx: number) {
+    if (idx < 146) return idx + 1
+    if (idx === 146) return 1146
+
+    if (idx < 149) return idx + 1 - 1
+    if (idx === 149) return 1148
+
+    if (idx < 157) return idx + 1 - 2
+    if (idx === 157) return 1155
+
+    if (idx < 163) return idx + 1 - 3
+    if (idx === 163) return 1160
+
+    if (idx < 165) return idx + 1 - 4
+    if (idx === 165) return 1161
+
+    if (idx < 171) return idx + 1 - 5
+    if (idx === 171) return 1166
+
+    if (idx < 173) return idx + 1 - 6
+    if (idx === 173) return 1167
+
+    if (idx < 237) return idx + 1 - 7
+    if (idx === 237) return 1003
+    if (idx === 238) return 1004
+    if (idx === 239) return 1005
+    if (idx === 240) return 2005
+    if (idx === 241) return 3005
+    if (idx === 242) return 4005
+    if (idx === 243) return 5005
+    if (idx === 244) return 1006
+    if (idx === 245) return 1007
+    if (idx === 246) return 1008
+    if (idx === 247) return 1009
+    if (idx === 248) return 1010
+    if (idx === 249) return 1011
+    if (idx === 250) return 1012
+    if (idx === 251) return 1013
+    if (idx === 252) return 1014
+
+    if (idx === 253) return 2014
+    if (idx === 254) return 3014
+    if (idx === 255) return 1015
+    if (idx === 256) return 1017
+    if (idx === 257) return 2017
+    if (idx === 258) return 1018
+    if (idx === 259) return 2018
+    if (idx === 260) return 3018
+    if (idx === 261) return 1020
+    if (idx === 262) return 1021
+    if (idx === 263) return 1022
+    if (idx === 264) return 1023
+    if (idx === 265) return 1059
+    if (idx === 266) return 1094
+    if (idx === 267) return 1197
+
+    throw new Error(`unknown spacegroup index '${idx}'`)
+}
+
+export type SpacegroupName = keyof typeof SpacegroupNameToIndexMap
+
+/** Maps spacegroup index to Hermann-Mauguin spacegroup name */
+export const SpacegroupName: { [idx: number]: SpacegroupName } = (function () {
     const names = Object.create(null);
-    for (const n of Object.keys(ZeroBasedSpacegroupNumbers)) {
-        names[(ZeroBasedSpacegroupNumbers as any)[n]] = n;
+    for (const n of Object.keys(SpacegroupNameToIndexMap)) {
+        names[(SpacegroupNameToIndexMap as any)[n]] = n;
     }
     return names;
 }());
 
-// return -1 if the spacegroup does not exist.
-export function getSpacegroupIndex(nameOrNumber: number | string | SpacegroupName): number {
-    let index: number
-    if (typeof nameOrNumber === 'number') {
-        // used by CCP4, see http://www.ccp4.ac.uk/html/pointless.html#setting
-        if (nameOrNumber === 1017) index = 254
-        else if (nameOrNumber === 2017) index = 255
-        else if (nameOrNumber === 2018) index = 257
-        else if (nameOrNumber === 3018) index = 258
-        else index = nameOrNumber - 1
-    } else {
-        index = ZeroBasedSpacegroupNumbers[nameOrNumber as SpacegroupName];
+/** Maps spacegroup index to spacegroup number from International Tables for Crystallography */
+export const SpacegroupNumber: { [idx: number]: number } = (function () {
+    const numbers = Object.create(null);
+    for (const n of Object.keys(SpacegroupNameToIndexMap)) {
+        const idx = (SpacegroupNameToIndexMap as any)[n]
+        numbers[idx] = getSpacegroupNumberFromIndex(idx);
     }
-    if (typeof index === 'undefined' || typeof SpacegroupNames[index] === 'undefined') return -1;
+    return numbers;
+}());
+
+/** return -1 if the spacegroup does not exist */
+export function getSpacegroupIndex(nameOrNumber: number | string | SpacegroupName): number {
+    const index = typeof nameOrNumber === 'number'
+        ? getSpacegroupIndexFromNumber(nameOrNumber)
+        : SpacegroupNameToIndexMap[nameOrNumber as SpacegroupName];
+    if (typeof index === 'undefined' || typeof SpacegroupName[index] === 'undefined') return -1;
     return index;
 }

src/mol-math/linear-algebra/3d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -25,4 +25,10 @@ import Vec4 from './3d/vec4'
 import Quat from './3d/quat'
 import { EPSILON } from './3d/common'
 
-export { Mat4, Mat3, Vec2, Vec3, Vec4, Quat, EPSILON }
+export { Mat4, Mat3, Vec2, Vec3, Vec4, Quat, EPSILON }
+
+export type Vec<T> =
+    T extends 4 ? Vec4 :
+    T extends 3 ? Vec3 :
+    T extends 2 ? Vec2 :
+    number[]

src/mol-math/linear-algebra/3d/mat4.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>

src/mol-math/linear-algebra/3d/vec3.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -23,6 +23,7 @@ import { spline as _spline, quadraticBezier as _quadraticBezier, clamp } from '.
 import { NumberArray } from '../../../mol-util/type-helpers';
 
 interface Vec3 extends Array<number> { [d: number]: number, '@type': 'vec3', length: 3 }
+interface ReadonlyVec3 extends Array<number> { readonly [d: number]: number, '@type': 'vec3', length: 3 }
 
 function Vec3() {
     return Vec3.zero();
@@ -497,13 +498,12 @@ namespace Vec3 {
     }
 
     const rotTemp = zero();
-    const flipScaling = create(-1, -1, -1);
     export function makeRotation(mat: Mat4, a: Vec3, b: Vec3): Mat4 {
         const by = angle(a, b);
         if (Math.abs(by) < 0.0001) return Mat4.setIdentity(mat);
         if (Math.abs(by - Math.PI) < EPSILON) {
             // here, axis can be [0,0,0] but the rotation is a simple flip
-            return Mat4.fromScaling(mat, flipScaling);
+            return Mat4.fromScaling(mat, negUnit);
         }
         const axis = cross(rotTemp, a, b);
         return Mat4.fromRotation(mat, by, axis);
@@ -525,6 +525,16 @@ namespace Vec3 {
         return normalize(out, cross(out, cross(out, a, b), a));
     }
 
+    /**
+     * Get a vector like `a` that point into the same general direction as `b`,
+     * i.e. where the dot product is > 0
+     */
+    export function matchDirection(out: Vec3, a: Vec3, b: Vec3) {
+        if (Vec3.dot(a, b) > 0) Vec3.copy(out, a)
+        else Vec3.negate(out, Vec3.copy(out, a))
+        return out
+    }
+
     const triangleNormalTmpAB = zero();
     const triangleNormalTmpAC = zero();
     /** Calculate normal for the triangle defined by `a`, `b` and `c` */
@@ -537,6 +547,9 @@ namespace Vec3 {
     export function toString(a: Vec3, precision?: number) {
         return `[${a[0].toPrecision(precision)} ${a[1].toPrecision(precision)} ${a[2].toPrecision(precision)}]`;
     }
+
+    export const unit: ReadonlyVec3 = Vec3.create(1, 1, 1)
+    export const negUnit: ReadonlyVec3 = Vec3.create(-1, -1, -1)
 }
 
 export default Vec3

src/mol-math/linear-algebra/matrix/matrix.ts

@@ -1,47 +1,74 @@
 /**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
 import { NumberArray } from '../../../mol-util/type-helpers';
+import { Vec } from '../3d';
 
-interface Matrix { data: NumberArray, size: number, cols: number, rows: number }
+interface Matrix<N extends number = number, M extends number = number> {
+    data: NumberArray,
+    size: number,
+    cols: N,
+    rows: M
+}
 
 namespace Matrix {
-    export function create(cols: number, rows: number, ctor: { new (size: number): NumberArray } = Float32Array): Matrix {
+    export function create<N extends number, M extends number>(cols: N, rows: M, ctor: { new (size: number): NumberArray } = Float32Array): Matrix<N, M> {
         const size = cols * rows
         return { data: new ctor(size), size, cols, rows }
     }
 
     /** Get element assuming data are stored in column-major order */
-    export function get(m: Matrix, i: number, j: number) { return m.data[m.rows * j + i]; }
-    /** Set element assuming data are stored in column-major order */
-    export function set(m: Matrix, i: number, j: number, value: number) { m.data[m.rows * j + i] = value; }
-    /** Add to element assuming data are stored in column-major order */
-    export function add(m: Matrix, i: number, j: number, value: number) { m.data[m.rows * j + i] += value; }
-    /** Zero out the matrix */
-    export function makeZero(m: Matrix) {
-        for (let i = 0, _l = m.data.length; i < _l; i++) m.data[i] = 0.0;
+    export function get(m: Matrix, i: number, j: number) {
+        return m.data[m.rows * j + i];
     }
 
-    export function fromArray(data: NumberArray, cols: number, rows: number): Matrix {
+    /** Set element assuming data are stored in column-major order */
+    export function set<N extends number, M extends number>(m: Matrix<N, M>, i: number, j: number, value: number) {
+        m.data[m.rows * j + i] = value;
+        return m
+    }
+
+    /** Add to element assuming data are stored in column-major order */
+    export function add<N extends number, M extends number>(m: Matrix<N, M>, i: number, j: number, value: number) {
+        m.data[m.rows * j + i] += value;
+        return m
+    }
+
+    /** Zero out the matrix */
+    export function makeZero<N extends number, M extends number>(m: Matrix<N, M>) {
+        m.data.fill(0.0)
+        return m
+    }
+
+    export function clone<N extends number, M extends number>(m: Matrix<N, M>): Matrix<N, M> {
+        return { data: m.data.slice(), size: m.size, cols: m.cols, rows: m.rows }
+    }
+
+    export function fromArray<N extends number, M extends number>(data: NumberArray, cols: N, rows: M): Matrix<N, M> {
         return { data, size: cols * rows, cols, rows }
     }
 
-    export function transpose(out: Matrix, mat: Matrix): Matrix {
+    export function transpose<N extends number, M extends number>(out: Matrix<M, N>, mat: Matrix<N, M>): Matrix<M, N> {
+        if (out.cols !== mat.rows || out.rows !== mat.cols) {
+            throw new Error('transpose: matrix dimensions incompatible')
+        }
+        if (out.data === mat.data) {
+            throw new Error('transpose: matrices share memory')
+        }
         const nrows = mat.rows, ncols = mat.cols
         const md = mat.data, mtd = out.data
-
         for (let i = 0, mi = 0, mti = 0; i < nrows; mti += 1, mi += ncols, ++i) {
             let ri = mti
             for (let j = 0; j < ncols; ri += nrows, j++) mtd[ri] = md[mi + j]
         }
-        return mat
+        return out
     }
 
     /** out = matA * matB' */
-    export function multiplyABt (out: Matrix, matA: Matrix, matB: Matrix) {
+    export function multiplyABt<NA extends number, NB extends number, M extends number>(out: Matrix<M, M>, matA: Matrix<NA, M>, matB: Matrix<NB, M>): Matrix<M, M> {
         const ncols = matA.cols, nrows = matA.rows, mrows = matB.rows
         const ad = matA.data, bd = matB.data, cd = out.data
 
@@ -59,10 +86,10 @@ namespace Matrix {
     }
 
     /** Get the mean of rows in `mat` */
-    export function meanRows (mat: Matrix) {
+    export function meanRows<N extends number, M extends number, V extends Vec<N>>(mat: Matrix<N, M>): V {
         const nrows = mat.rows, ncols = mat.cols
         const md = mat.data
-        const mean = new Array(ncols)
+        const mean = new Array(ncols) as V
 
         for (let j = 0; j < ncols; ++j) mean[ j ] = 0.0
         for (let i = 0, p = 0; i < nrows; ++i) {
@@ -74,7 +101,7 @@ namespace Matrix {
     }
 
     /** Subtract `row` from all rows in `mat` */
-    export function subRows (mat: Matrix, row: NumberArray) {
+    export function subRows<N extends number, M extends number>(mat: Matrix<N, M>, row: NumberArray) {
         const nrows = mat.rows, ncols = mat.cols
         const md = mat.data
 

src/mol-math/linear-algebra/matrix/principal-axes.ts

@@ -1,21 +1,17 @@
 /**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
 import Matrix from './matrix';
-import { Vec3 } from '../3d';
-// import { Vec3, Mat4 } from '../3d.js';
+import { Vec3, Mat4 } from '../3d';
 import { svd } from './svd';
+import { NumberArray } from '../../../mol-util/type-helpers';
 
-// const negateVector = Vec3.create(-1, -1, -1)
-// const tmpMatrix = Mat4.identity()
+export { PrincipalAxes }
 
-/**
- * Principal axes
- */
-class PrincipalAxes {
+interface PrincipalAxes {
     begA: Vec3
     endA: Vec3
     begB: Vec3
@@ -32,14 +28,15 @@ class PrincipalAxes {
     normVecA: Vec3
     normVecB: Vec3
     normVecC: Vec3
+}
 
+namespace PrincipalAxes {
     /**
-     * points is a 3xN matrix
+     * @param points 3xN matrix
      */
-    constructor(points: Matrix) {
+    export function ofPoints(points: Matrix<3, number>): PrincipalAxes {
         const n = points.rows
         const n3 = n / 3
-        const pointsT = Matrix.create(n, 3)
         const A = Matrix.create(3, 3)
         const W = Matrix.create(1, 3)
         const U = Matrix.create(3, 3)
@@ -47,145 +44,102 @@ class PrincipalAxes {
 
         // calculate
         const mean = Matrix.meanRows(points)
-        Matrix.subRows(points, mean)
-        Matrix.transpose(pointsT, points)
+        const pointsM = Matrix.subRows(Matrix.clone(points), mean)
+        const pointsT = Matrix.transpose(Matrix.create(n, 3), pointsM)
         Matrix.multiplyABt(A, pointsT, pointsT)
         svd(A, W, U, V)
 
         // center
-        const vm = Vec3.create(mean[0], mean[1], mean[2])
+        const center = Vec3.create(mean[0], mean[1], mean[2])
 
         // normalized
-        const van = Vec3.create(U.data[0], U.data[3], U.data[6])
-        const vbn = Vec3.create(U.data[1], U.data[4], U.data[7])
-        const vcn = Vec3.create(U.data[2], U.data[5], U.data[8])
+        const normVecA = Vec3.create(U.data[0], U.data[3], U.data[6])
+        const normVecB = Vec3.create(U.data[1], U.data[4], U.data[7])
+        const normVecC = Vec3.create(U.data[2], U.data[5], U.data[8])
 
         // scaled
-        const va = Vec3.scale(Vec3.zero(), van, Math.sqrt(W.data[0] / n3))
-        const vb = Vec3.scale(Vec3.zero(), vbn, Math.sqrt(W.data[1] / n3))
-        const vc = Vec3.scale(Vec3.zero(), vcn, Math.sqrt(W.data[2] / n3))
-        // const va = van.clone().multiplyScalar(Math.sqrt(W.data[0] / n3))
-        // const vb = vbn.clone().multiplyScalar(Math.sqrt(W.data[1] / n3))
-        // const vc = vcn.clone().multiplyScalar(Math.sqrt(W.data[2] / n3))
+        const vecA = Vec3.scale(Vec3(), normVecA, Math.sqrt(W.data[0] / n3))
+        const vecB = Vec3.scale(Vec3(), normVecB, Math.sqrt(W.data[1] / n3))
+        const vecC = Vec3.scale(Vec3(), normVecC, Math.sqrt(W.data[2] / n3))
 
         // points
-        this.begA = Vec3.sub(Vec3.clone(vm), vm, va)
-        this.endA = Vec3.add(Vec3.clone(vm), vm, va)
-        this.begB = Vec3.sub(Vec3.clone(vm), vm, vb)
-        this.endB = Vec3.add(Vec3.clone(vm), vm, vb)
-        this.begC = Vec3.sub(Vec3.clone(vm), vm, vc)
-        this.endC = Vec3.add(Vec3.clone(vm), vm, vc)
-        // this.begA = vm.clone().sub(va)
-        // this.endA = vm.clone().add(va)
-        // this.begB = vm.clone().sub(vb)
-        // this.endB = vm.clone().add(vb)
-        // this.begC = vm.clone().sub(vc)
-        // this.endC = vm.clone().add(vc)
+        const begA = Vec3.sub(Vec3.clone(center), center, vecA)
+        const endA = Vec3.add(Vec3.clone(center), center, vecA)
+        const begB = Vec3.sub(Vec3.clone(center), center, vecB)
+        const endB = Vec3.add(Vec3.clone(center), center, vecB)
+        const begC = Vec3.sub(Vec3.clone(center), center, vecC)
+        const endC = Vec3.add(Vec3.clone(center), center, vecC)
 
-        //
-
-        this.center = vm
-
-        this.vecA = va
-        this.vecB = vb
-        this.vecC = vc
-
-        this.normVecA = van
-        this.normVecB = vbn
-        this.normVecC = vcn
+        return {
+            begA, endA, begB, endB, begC, endC,
+            center,
+            vecA, vecB, vecC,
+            normVecA, normVecB, normVecC
+        }
     }
 
-    // TODO
-    // /**
-    //  * Get the basis matrix descriping the axes
-    //  * @param  {Matrix4} [optionalTarget] - target object
-    //  * @return {Matrix4} the basis
-    //  */
-    // getBasisMatrix(optionalTarget = new Matrix4()) {
-    //     const basis = optionalTarget
+    /**
+     * Set basis matrix for given axes
+     */
+    export function setBasisMatrix(out: Mat4, principalAxes: PrincipalAxes) {
+        Mat4.setAxes(out, principalAxes.normVecB, principalAxes.normVecA, principalAxes.normVecC)
+        if (Mat4.determinant(out) < 0) Mat4.scaleUniformly(out, out, -1)
+        return out
+    }
 
-    //     basis.makeBasis(this.normVecB, this.normVecA, this.normVecC)
-    //     if (basis.determinant() < 0) {
-    //         basis.scale(negateVector)
-    //     }
+    /**
+     * Get the scale/length for each dimension for a box around the axes
+     * to enclose the given positions
+     */
+    export function getProjectedScale(positions: NumberArray, principalAxes: PrincipalAxes) {
+        let d1a = -Infinity
+        let d1b = -Infinity
+        let d2a = -Infinity
+        let d2b = -Infinity
+        let d3a = -Infinity
+        let d3b = -Infinity
 
-    //     return basis
-    // }
+        const p = Vec3()
+        const t = Vec3()
 
-    // TODO
-    // /**
-    //  * Get a quaternion descriping the axes rotation
-    //  * @param  {Quaternion} [optionalTarget] - target object
-    //  * @return {Quaternion} the rotation
-    //  */
-    // getRotationQuaternion(optionalTarget = new Quaternion()) {
-    //     const q = optionalTarget
-    //     q.setFromRotationMatrix(this.getBasisMatrix(tmpMatrix))
+        const { center, normVecA, normVecB, normVecC } = principalAxes
 
-    //     return q.inverse()
-    // }
+        for (let i = 0, il = positions.length; i < il; i += 3) {
+            Vec3.projectPointOnVector(p, Vec3.fromArray(p, positions, i), normVecA, center)
+            const dp1 = Vec3.dot(normVecA, Vec3.normalize(t, Vec3.sub(t, p, center)))
+            const dt1 = Vec3.distance(p, center)
+            if (dp1 > 0) {
+                if (dt1 > d1a) d1a = dt1
+            } else {
+                if (dt1 > d1b) d1b = dt1
+            }
 
-    // TODO
-    // /**
-    //  * Get the scale/length for each dimension for a box around the axes
-    //  * to enclose the atoms of a structure
-    //  * @param  {Structure|StructureView} structure - the structure
-    //  * @return {{d1a: Number, d2a: Number, d3a: Number, d1b: Number, d2b: Number, d3b: Number}} scale
-    //  */
-    // getProjectedScaleForAtoms(structure: Structure) {
-    //     let d1a = -Infinity
-    //     let d1b = -Infinity
-    //     let d2a = -Infinity
-    //     let d2b = -Infinity
-    //     let d3a = -Infinity
-    //     let d3b = -Infinity
+            Vec3.projectPointOnVector(p, Vec3.fromArray(p, positions, i), normVecB, center)
+            const dp2 = Vec3.dot(normVecB, Vec3.normalize(t, Vec3.sub(t, p, center)))
+            const dt2 = Vec3.distance(p, center)
+            if (dp2 > 0) {
+                if (dt2 > d2a) d2a = dt2
+            } else {
+                if (dt2 > d2b) d2b = dt2
+            }
 
-    //     const p = new Vector3()
-    //     const t = new Vector3()
+            Vec3.projectPointOnVector(p, Vec3.fromArray(p, positions, i), normVecC, center)
+            const dp3 = Vec3.dot(normVecC, Vec3.normalize(t, Vec3.sub(t, p, center)))
+            const dt3 = Vec3.distance(p, center)
+            if (dp3 > 0) {
+                if (dt3 > d3a) d3a = dt3
+            } else {
+                if (dt3 > d3b) d3b = dt3
+            }
+        }
 
-    //     const center = this.center
-    //     const ax1 = this.normVecA
-    //     const ax2 = this.normVecB
-    //     const ax3 = this.normVecC
-
-    //     structure.eachAtom(function (ap: AtomProxy) {
-    //         projectPointOnVector(p.copy(ap as any), ax1, center)  // TODO
-    //         const dp1 = t.subVectors(p, center).normalize().dot(ax1)
-    //         const dt1 = p.distanceTo(center)
-    //         if (dp1 > 0) {
-    //             if (dt1 > d1a) d1a = dt1
-    //         } else {
-    //             if (dt1 > d1b) d1b = dt1
-    //         }
-
-    //         projectPointOnVector(p.copy(ap as any), ax2, center)
-    //         const dp2 = t.subVectors(p, center).normalize().dot(ax2)
-    //         const dt2 = p.distanceTo(center)
-    //         if (dp2 > 0) {
-    //             if (dt2 > d2a) d2a = dt2
-    //         } else {
-    //             if (dt2 > d2b) d2b = dt2
-    //         }
-
-    //         projectPointOnVector(p.copy(ap as any), ax3, center)
-    //         const dp3 = t.subVectors(p, center).normalize().dot(ax3)
-    //         const dt3 = p.distanceTo(center)
-    //         if (dp3 > 0) {
-    //             if (dt3 > d3a) d3a = dt3
-    //         } else {
-    //             if (dt3 > d3b) d3b = dt3
-    //         }
-    //     })
-
-    //     return {
-    //         d1a: d1a,
-    //         d2a: d2a,
-    //         d3a: d3a,
-    //         d1b: -d1b,
-    //         d2b: -d2b,
-    //         d3b: -d3b
-    //     }
-    // }
-}
-
-export default PrincipalAxes
+        return {
+            d1a: d1a,
+            d2a: d2a,
+            d3a: d3a,
+            d1b: -d1b,
+            d2b: -d2b,
+            d3b: -d3b
+        }
+    }
+}

src/mol-model-formats/structure/_spec/cif-core.spec.ts

@@ -0,0 +1,70 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { CIF } from '../../../mol-io/reader/cif';
+
+const cifCoreString = `data_n1379
+_audit_block_doi                 10.5517/ccy42jn
+_database_code_depnum_ccdc_archive 'CCDC 867861'
+loop_
+_citation_id
+_citation_doi
+_citation_year
+1 10.1002/chem.201202070 2012
+_audit_update_record
+;
+2012-02-20 deposited with the CCDC.
+2016-10-08 downloaded from the CCDC.
+;
+
+loop_
+_atom_type_symbol
+_atom_type_description
+_atom_type_scat_dispersion_real
+_atom_type_scat_dispersion_imag
+_atom_type_scat_source
+C C 0.0181 0.0091 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
+H H 0.0000 0.0000 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
+N N 0.0311 0.0180 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
+O O 0.0492 0.0322 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
+F F 0.0727 0.0534 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
+
+_cell_length_a                   11.0829(8)
+_cell_length_b                   14.6829(10)
+_cell_length_c                   16.8532(17)
+_cell_angle_alpha                105.728(6)
+_cell_angle_beta                 100.310(6)
+_cell_angle_gamma                110.620(4)
+_cell_volume                     2353.3(3)
+_cell_formula_units_Z            1
+_cell_measurement_temperature    100(2)
+_cell_measurement_reflns_used    5934
+_cell_measurement_theta_min      2.86
+_cell_measurement_theta_max      64.30
+`
+
+describe('cif-core read', () => {
+    it('frame', async () => {
+        const parsed = await CIF.parseText(cifCoreString).run()
+        if (parsed.isError) return
+        const cifFile = parsed.result
+        const block = cifFile.blocks[0]
+
+        expect(block.getField('cell_length_a')!.float(0)).toBe(11.0829)
+        expect.assertions(1)
+    });
+
+    it('schema', async () => {
+        const parsed = await CIF.parseText(cifCoreString).run()
+        if (parsed.isError) return
+        const cifFile = parsed.result
+        const block = cifFile.blocks[0]
+        const cifCore = CIF.schema.cifCore(block)
+
+        expect(cifCore.cell.length_a.value(0)).toBe(11.0829)
+        expect.assertions(1)
+    });
+});

src/mol-model-formats/structure/common/entity.ts

@@ -30,7 +30,7 @@ export class EntityBuilder {
     }
 
     getEntityId(compId: string, moleculeType: MoleculeType, chainId: string): string {
-        if (moleculeType === MoleculeType.water) {
+        if (moleculeType === MoleculeType.Water) {
             if (this.waterId === undefined) {
                 this.set('water', 'Water')
                 this.waterId = `${this.count}`

src/mol-model-formats/structure/gro.ts

@@ -36,7 +36,7 @@ function getCategories(atoms: GroAtoms) {
     let currentAsymIndex = 0
     let currentAsymId = ''
     let currentSeqId = 0
-    let prevMoleculeType = MoleculeType.unknown
+    let prevMoleculeType = MoleculeType.Unknown
     let prevResidueNumber = -1
 
     for (let i = 0, il = atoms.count; i < il; ++i) {

src/mol-model-formats/structure/mmcif/atomic.ts

@@ -15,7 +15,6 @@ import { AtomicConformation, AtomicData, AtomicHierarchy, AtomicSegments, AtomsS
 import { getAtomicIndex } from '../../../mol-model/structure/model/properties/utils/atomic-index';
 import { ElementSymbol } from '../../../mol-model/structure/model/types';
 import { Entities } from '../../../mol-model/structure/model/properties/common';
-import { getAtomicRanges } from '../../../mol-model/structure/model/properties/utils/atomic-ranges';
 import { getAtomicDerivedData } from '../../../mol-model/structure/model/properties/utils/atomic-derived';
 import { FormatData } from './parser';
 
@@ -43,6 +42,15 @@ function findHierarchyOffsets(atom_site: AtomSite) {
     return { residues, chains };
 }
 
+function substUndefinedColumn<T extends Table<any>>(table: T, a: keyof T, b: keyof T) {
+    if (!(table as any)[a].isDefined) {
+        (table as any)[a] = (table as any)[b];
+    }
+    if (!(table as any)[b].isDefined) {
+        (table as any)[b] = (table as any)[a];
+    }
+}
+
 function createHierarchyData(atom_site: AtomSite, sourceIndex: Column<number>, offsets: { residues: ArrayLike<number>, chains: ArrayLike<number> }): AtomicData {
     const atoms = Table.ofColumns(AtomsSchema, {
         type_symbol: Column.ofArray({ array: Column.mapToArray(atom_site.type_symbol, ElementSymbol), schema: Column.Schema.Aliased<ElementSymbol>(Column.Schema.str) }),
@@ -52,11 +60,20 @@ function createHierarchyData(atom_site: AtomSite, sourceIndex: Column<number>, o
         pdbx_formal_charge: atom_site.pdbx_formal_charge,
         sourceIndex
     });
+
     const residues = Table.view(atom_site, ResiduesSchema, offsets.residues);
     // Optimize the numeric columns
     Table.columnToArray(residues, 'label_seq_id', Int32Array);
     Table.columnToArray(residues, 'auth_seq_id', Int32Array);
+
     const chains = Table.view(atom_site, ChainsSchema, offsets.chains);
+
+    // Fix possibly missing auth_/label_ columns
+    substUndefinedColumn(residues, 'label_seq_id', 'auth_seq_id');
+    substUndefinedColumn(atoms, 'label_atom_id', 'auth_atom_id');
+    substUndefinedColumn(residues, 'label_comp_id', 'auth_comp_id');
+    substUndefinedColumn(chains, 'label_asym_id', 'auth_asym_id');
+
     return { atoms, residues, chains };
 }
 
@@ -100,7 +117,6 @@ export function getAtomicHierarchyAndConformation(atom_site: AtomSite, sourceInd
 
     const index = getAtomicIndex(hierarchyData, entities, hierarchySegments);
     const derived = getAtomicDerivedData(hierarchyData, index, formatData.chemicalComponentMap);
-    const hierarchyRanges = getAtomicRanges(hierarchyData, hierarchySegments, conformation, index, derived.residue.moleculeType);
-    const hierarchy: AtomicHierarchy = { ...hierarchyData, ...hierarchySegments, ...hierarchyRanges, index, derived };
+    const hierarchy: AtomicHierarchy = { ...hierarchyData, ...hierarchySegments, index, derived };
     return { sameAsPrevious: false, hierarchy, conformation };
 }

src/mol-model-formats/structure/mmcif/parser.ts

@@ -30,6 +30,7 @@ import mmCIF_Format = ModelFormat.mmCIF
 import { memoize1 } from '../../../mol-util/memoize';
 import { ElementIndex, EntityIndex } from '../../../mol-model/structure/model';
 import { AtomSiteAnisotrop } from './anisotropic';
+import { getAtomicRanges } from '../../../mol-model/structure/model/properties/utils/atomic-ranges';
 
 export async function _parse_mmCif(format: mmCIF_Format, ctx: RuntimeContext) {
     const formatData = getFormatData(format)
@@ -53,11 +54,19 @@ function checkNonStandardCrystalFrame(format: mmCIF_Format, spacegroup: Spacegro
     return false;
 }
 
+function getSpacegroupNameOrNumber(symmetry: mmCIF_Format['data']['symmetry']) {
+    const groupNumber = symmetry['Int_Tables_number'].value(0);
+    const groupName = symmetry['space_group_name_H-M'].value(0);
+    if (!symmetry['Int_Tables_number'].isDefined) return groupName
+    if (!symmetry['space_group_name_H-M'].isDefined) return groupNumber
+    return groupName
+}
+
 function getSpacegroup(format: mmCIF_Format): Spacegroup {
     const { symmetry, cell } = format.data;
     if (symmetry._rowCount === 0 || cell._rowCount === 0) return Spacegroup.ZeroP1;
-    const groupName = symmetry['space_group_name_H-M'].value(0);
-    const spaceCell = SpacegroupCell.create(groupName,
+    const nameOrNumber = getSpacegroupNameOrNumber(symmetry)
+    const spaceCell = SpacegroupCell.create(nameOrNumber,
         Vec3.create(cell.length_a.value(0), cell.length_b.value(0), cell.length_c.value(0)),
         Vec3.scale(Vec3.zero(), Vec3.create(cell.angle_alpha.value(0), cell.angle_beta.value(0), cell.angle_gamma.value(0)), Math.PI / 180));
 
@@ -171,7 +180,7 @@ function getSaccharideComponentMap(format: mmCIF_Format): SaccharideComponentMap
             const _type = type.value(i)
             if (SaccharideCompIdMap.has(_id)) {
                 map.set(_id, SaccharideCompIdMap.get(_id)!)
-            } else if (getMoleculeType(_type, _id) === MoleculeType.saccharide) {
+            } else if (getMoleculeType(_type, _id) === MoleculeType.Saccharide) {
                 map.set(_id, UnknownSaccharideComponent)
             }
         }
@@ -224,6 +233,9 @@ function createStandardModel(format: mmCIF_Format, atom_site: AtomSite, sourceIn
     }
 
     const coarse = EmptyIHMCoarse;
+    const sequence = getSequence(format.data, entities, atomic.hierarchy, coarse.hierarchy, formatData.modifiedResidues.parentId)
+    const atomicRanges = getAtomicRanges(atomic.hierarchy, entities, atomic.conformation, sequence)
+
     const entry = format.data.entry.id.valueKind(0) === Column.ValueKind.Present
         ? format.data.entry.id.value(0)
         : format.data._name;
@@ -241,9 +253,10 @@ function createStandardModel(format: mmCIF_Format, atom_site: AtomSite, sourceIn
         modelNum,
         entities,
         symmetry: getSymmetry(format),
-        sequence: getSequence(format.data, entities, atomic.hierarchy, coarse.hierarchy, formatData.modifiedResidues.parentId),
+        sequence,
         atomicHierarchy: atomic.hierarchy,
         atomicConformation: atomic.conformation,
+        atomicRanges,
         coarseHierarchy: coarse.hierarchy,
         coarseConformation: coarse.conformation,
         properties: {
@@ -259,6 +272,9 @@ function createStandardModel(format: mmCIF_Format, atom_site: AtomSite, sourceIn
 function createModelIHM(format: mmCIF_Format, data: IHMData, formatData: FormatData): Model {
     const atomic = getAtomicHierarchyAndConformation(data.atom_site, data.atom_site_sourceIndex, data.entities, formatData);
     const coarse = getIHMCoarse(data, formatData);
+    const sequence = getSequence(format.data, data.entities, atomic.hierarchy, coarse.hierarchy, formatData.modifiedResidues.parentId)
+    const atomicRanges = getAtomicRanges(atomic.hierarchy, data.entities, atomic.conformation, sequence)
+
     const entry = format.data.entry.id.valueKind(0) === Column.ValueKind.Present
         ? format.data.entry.id.value(0)
         : format.data._name;
@@ -278,9 +294,10 @@ function createModelIHM(format: mmCIF_Format, data: IHMData, formatData: FormatD
         modelNum: data.model_id,
         entities: data.entities,
         symmetry: getSymmetry(format),
-        sequence: getSequence(format.data, data.entities, atomic.hierarchy, coarse.hierarchy, formatData.modifiedResidues.parentId),
+        sequence,
         atomicHierarchy: atomic.hierarchy,
         atomicConformation: atomic.conformation,
+        atomicRanges,
         coarseHierarchy: coarse.hierarchy,
         coarseConformation: coarse.conformation,
         properties: {

src/mol-model-props/common/custom-element-property.ts

@@ -117,7 +117,7 @@ namespace CustomElementProperty {
         function LabelProvider(loci: Loci): string | undefined {
             if (loci.kind === 'element-loci') {
                 const e = loci.elements[0];
-                if (!has(e.unit.model)) return void 0;
+                if (!e || !has(e.unit.model)) return void 0;
                 return params.format!(get(StructureElement.Location.create(e.unit, e.unit.elements[OrderedSet.getAt(e.indices, 0)])));
             }
             return void 0;

src/mol-model-props/rcsb/representations/assembly-symmetry-axes.ts

@@ -55,7 +55,7 @@ export const AssemblySymmetryAxesRepresentationProvider: StructureRepresentation
     defaultValues: PD.getDefaultValues(AssemblySymmetryAxesParams),
     defaultColorTheme: 'uniform',
     defaultSizeTheme: 'uniform',
-    isApplicable: (structure: Structure) => AssemblySymmetry.get(structure.models[0]) !== undefined
+    isApplicable: (structure: Structure) => structure.models.length > 0 && AssemblySymmetry.get(structure.models[0]) !== undefined
 }
 
 //

src/mol-model/loci.ts

@@ -12,18 +12,19 @@ import { CentroidHelper } from '../mol-math/geometry/centroid-helper';
 import { Vec3 } from '../mol-math/linear-algebra';
 import { OrderedSet } from '../mol-data/int';
 import { Structure } from './structure/structure';
+import { capitalize } from '../mol-util/string';
 
 /** A Loci that includes every loci */
 export const EveryLoci = { kind: 'every-loci' as 'every-loci' }
 export type EveryLoci = typeof EveryLoci
-export function isEveryLoci(x: any): x is EveryLoci {
+export function isEveryLoci(x?: Loci): x is EveryLoci {
     return !!x && x.kind === 'every-loci';
 }
 
 /** A Loci that is empty */
 export const EmptyLoci = { kind: 'empty-loci' as 'empty-loci' }
 export type EmptyLoci = typeof EmptyLoci
-export function isEmptyLoci(x: any): x is EmptyLoci {
+export function isEmptyLoci(x?: Loci): x is EmptyLoci {
     return !!x && x.kind === 'empty-loci';
 }
 
@@ -34,7 +35,7 @@ export interface DataLoci {
     readonly tag: string
     readonly indices: OrderedSet<number>
 }
-export function isDataLoci(x: any): x is DataLoci {
+export function isDataLoci(x?: Loci): x is DataLoci {
     return !!x && x.kind === 'data-loci';
 }
 export function areDataLociEqual(a: DataLoci, b: DataLoci) {
@@ -76,7 +77,11 @@ namespace Loci {
         return false
     }
 
-    export function isEmpty(loci: Loci): boolean {
+    export function isEvery(loci?: Loci): loci is EveryLoci {
+        return !!loci && loci.kind === 'every-loci';
+    }
+
+    export function isEmpty(loci: Loci): loci is EmptyLoci {
         if (isEveryLoci(loci)) return false
         if (isEmptyLoci(loci)) return true
         if (isDataLoci(loci)) return isDataLociEmpty(loci)
@@ -92,6 +97,8 @@ namespace Loci {
         if (data instanceof Structure) {
             if (StructureElement.Loci.is(loci)) {
                 loci = StructureElement.Loci.remap(loci, data)
+            } else if (Structure.isLoci(loci)) {
+                loci = Structure.remapLoci(loci, data)
             } else if (Link.isLoci(loci)) {
                 loci = Link.remapLoci(loci, data)
             }
@@ -146,4 +153,55 @@ namespace Loci {
         const boundingSphere = getBoundingSphere(loci, tmpSphere3D)
         return boundingSphere ? Vec3.copy(center || Vec3.zero(), boundingSphere.center) : undefined
     }
+
+    //
+
+    const Granularity = {
+        'element': (loci: Loci) => loci,
+        'residue': (loci: Loci) => {
+            return StructureElement.Loci.is(loci)
+                ? StructureElement.Loci.extendToWholeResidues(loci, true)
+                : loci
+        },
+        'chain': (loci: Loci) => {
+            return StructureElement.Loci.is(loci)
+                ? StructureElement.Loci.extendToWholeChains(loci)
+                : loci
+        },
+        'structure': (loci: Loci) => {
+            return StructureElement.Loci.is(loci)
+                ? Structure.toStructureElementLoci(loci.structure)
+                : loci
+        }
+    }
+    export type Granularity = keyof typeof Granularity
+    export const GranularityOptions = Object.keys(Granularity).map(n => [n, capitalize(n)]) as [Granularity, string][]
+
+    export function applyGranularity(loci: Loci, granularity: Granularity) {
+        return Granularity[granularity](loci)
+    }
+
+    /**
+     * Converts structure related loci to StructureElement.Loci and applies
+     * granularity if given
+    */
+    export function normalize(loci: Loci, granularity?: Granularity) {
+        if (granularity !== 'element' && Link.isLoci(loci)) {
+            // convert Link.Loci to a StructureElement.Loci so granularity can be applied
+            loci = Link.toStructureElementLoci(loci)
+        }
+        if (Structure.isLoci(loci)) {
+            // convert to StructureElement.Loci
+            loci = Structure.toStructureElementLoci(loci.structure)
+        }
+        if (StructureElement.Loci.is(loci)) {
+            // ensure the root structure is used
+            loci = StructureElement.Loci.remap(loci, loci.structure.root)
+        }
+        if (granularity) {
+            // needs to be applied AFTER remapping to root
+            loci = applyGranularity(loci, granularity)
+        }
+        return loci
+    }
 }

src/mol-model/structure/model/model.ts

@@ -7,7 +7,7 @@
 
 import UUID from '../../../mol-util/uuid';
 import StructureSequence from './properties/sequence';
-import { AtomicHierarchy, AtomicConformation } from './properties/atomic';
+import { AtomicHierarchy, AtomicConformation, AtomicRanges } from './properties/atomic';
 import { ModelSymmetry } from './properties/symmetry';
 import { CoarseHierarchy, CoarseConformation } from './properties/coarse';
 import { Entities, ChemicalComponentMap, MissingResidues } from './properties/common';
@@ -42,6 +42,7 @@ export interface Model extends Readonly<{
 
     atomicHierarchy: AtomicHierarchy,
     atomicConformation: AtomicConformation,
+    atomicRanges: AtomicRanges,
 
     properties: {
         /** secondary structure provided by the input file */

src/mol-model/structure/model/properties/atomic/hierarchy.ts

@@ -8,7 +8,7 @@
 import { Column, Table } from '../../../../../mol-data/db'
 import { Segmentation } from '../../../../../mol-data/int'
 import { mmCIF_Schema as mmCIF } from '../../../../../mol-io/reader/cif/schema/mmcif'
-import { ElementSymbol, MoleculeType } from '../../types'
+import { ElementSymbol, MoleculeType, PolymerType } from '../../types'
 import { ChainIndex, EntityIndex, ResidueIndex, ElementIndex } from '../../indexing';
 import SortedRanges from '../../../../../mol-data/int/sorted-ranges';
 
@@ -116,6 +116,7 @@ export interface AtomicDerivedData {
         readonly directionFromElementIndex: ArrayLike<ElementIndex | -1>
         readonly directionToElementIndex: ArrayLike<ElementIndex | -1>
         readonly moleculeType: ArrayLike<MoleculeType>
+        readonly polymerType: ArrayLike<PolymerType>
     }
 }
 
@@ -222,7 +223,7 @@ export interface AtomicRanges {
     cyclicPolymerMap: Map<ResidueIndex, ResidueIndex>
 }
 
-type _Hierarchy = AtomicData & AtomicSegments & AtomicRanges
+type _Hierarchy = AtomicData & AtomicSegments
 export interface AtomicHierarchy extends _Hierarchy {
     index: AtomicIndex
     derived: AtomicDerivedData

src/mol-model/structure/model/properties/utils/atomic-derived.ts

@@ -7,9 +7,10 @@
 import { AtomicData } from '../atomic';
 import { AtomicIndex, AtomicDerivedData } from '../atomic/hierarchy';
 import { ElementIndex, ResidueIndex } from '../../indexing';
-import { MoleculeType, getMoleculeType, getComponentType } from '../../types';
+import { MoleculeType, getMoleculeType, getComponentType, PolymerType, getPolymerType } from '../../types';
 import { getAtomIdForAtomRole } from '../../../../../mol-model/structure/util';
 import { ChemicalComponentMap } from '../common';
+import { isProductionMode } from '../../../../../mol-util/debug';
 
 export function getAtomicDerivedData(data: AtomicData, index: AtomicIndex, chemicalComponentMap: ChemicalComponentMap): AtomicDerivedData {
     const { label_comp_id, _rowCount: n } = data.residues
@@ -18,39 +19,50 @@ export function getAtomicDerivedData(data: AtomicData, index: AtomicIndex, chemi
     const directionFromElementIndex = new Int32Array(n)
     const directionToElementIndex = new Int32Array(n)
     const moleculeType = new Uint8Array(n)
+    const polymerType = new Uint8Array(n)
 
     const moleculeTypeMap = new Map<string, MoleculeType>()
+    const polymerTypeMap = new Map<string, PolymerType>()
 
-    for (let i = 0; i < n; ++i) {
+    for (let i = 0 as ResidueIndex; i < n; ++i) {
         const compId = label_comp_id.value(i)
         const chemCompMap = chemicalComponentMap
+
         let molType: MoleculeType
+        let polyType: PolymerType
         if (moleculeTypeMap.has(compId)) {
             molType = moleculeTypeMap.get(compId)!
-        } else if (chemCompMap.has(compId)) {
-            molType = getMoleculeType(chemCompMap.get(compId)!.type, compId)
-            moleculeTypeMap.set(compId, molType)
+            polyType = polymerTypeMap.get(compId)!
         } else {
-            console.log('chemComp not found', compId)
-            molType = getMoleculeType(getComponentType(compId), compId)
+            let type: string
+            if (chemCompMap.has(compId)) {
+                type = chemCompMap.get(compId)!.type
+            } else {
+                if (!isProductionMode) console.info('chemComp not found', compId)
+                type = getComponentType(compId)
+            }
+            molType = getMoleculeType(type, compId)
             // TODO if unknown molecule type, use atom names to guess molecule type
+            polyType = getPolymerType(type, molType)
             moleculeTypeMap.set(compId, molType)
+            polymerTypeMap.set(compId, polyType)
         }
         moleculeType[i] = molType
+        polymerType[i] = polyType
 
-        const traceAtomId = getAtomIdForAtomRole(molType, 'trace')
-        let traceIndex = index.findAtomsOnResidue(i as ResidueIndex, traceAtomId)
+        const traceAtomId = getAtomIdForAtomRole(polyType, 'trace')
+        let traceIndex = index.findAtomsOnResidue(i, traceAtomId)
         if (traceIndex === -1) {
-            const coarseAtomId = getAtomIdForAtomRole(molType, 'coarseBackbone')
-            traceIndex = index.findAtomsOnResidue(i as ResidueIndex, coarseAtomId)
+            const coarseAtomId = getAtomIdForAtomRole(polyType, 'coarseBackbone')
+            traceIndex = index.findAtomsOnResidue(i, coarseAtomId)
         }
         traceElementIndex[i] = traceIndex
 
-        const directionFromAtomId = getAtomIdForAtomRole(molType, 'directionFrom')
-        directionFromElementIndex[i] = index.findAtomsOnResidue(i as ResidueIndex, directionFromAtomId)
+        const directionFromAtomId = getAtomIdForAtomRole(polyType, 'directionFrom')
+        directionFromElementIndex[i] = index.findAtomsOnResidue(i, directionFromAtomId)
 
-        const directionToAtomId = getAtomIdForAtomRole(molType, 'directionTo')
-        directionToElementIndex[i] = index.findAtomsOnResidue(i as ResidueIndex, directionToAtomId)
+        const directionToAtomId = getAtomIdForAtomRole(polyType, 'directionTo')
+        directionToElementIndex[i] = index.findAtomsOnResidue(i, directionToAtomId)
     }
 
     return {
@@ -59,6 +71,7 @@ export function getAtomicDerivedData(data: AtomicData, index: AtomicIndex, chemi
             directionFromElementIndex: directionFromElementIndex as unknown as ArrayLike<ElementIndex | -1>,
             directionToElementIndex: directionToElementIndex as unknown as ArrayLike<ElementIndex | -1>,
             moleculeType: moleculeType as unknown as ArrayLike<MoleculeType>,
+            polymerType: polymerType as unknown as ArrayLike<PolymerType>,
         }
     }
 }

src/mol-model/structure/model/properties/utils/atomic-ranges.ts

@@ -1,47 +1,52 @@
 /**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { AtomicSegments } from '../atomic';
-import { AtomicData, AtomicRanges, AtomicIndex } from '../atomic/hierarchy';
+import { AtomicRanges, AtomicIndex, AtomicHierarchy, AtomicDerivedData } from '../atomic/hierarchy';
 import { Segmentation, Interval } from '../../../../../mol-data/int';
 import SortedRanges from '../../../../../mol-data/int/sorted-ranges';
-import { MoleculeType, isPolymer } from '../../types';
+import { isPolymer, PolymerType } from '../../types';
 import { ElementIndex, ResidueIndex } from '../../indexing';
 import { getAtomIdForAtomRole } from '../../../util';
 import { AtomicConformation } from '../atomic/conformation';
 import { Vec3 } from '../../../../../mol-math/linear-algebra';
+import { Entities } from '../common';
+import StructureSequence from '../sequence';
 
-// TODO add gaps at the ends of the chains by comparing to the polymer sequence data
+function areBackboneConnected(riStart: ResidueIndex, riEnd: ResidueIndex, conformation: AtomicConformation, index: AtomicIndex, derived: AtomicDerivedData) {
+    const { polymerType, traceElementIndex, directionFromElementIndex, directionToElementIndex } = derived.residue
+    const ptStart = polymerType[riStart]
+    const ptEnd = polymerType[riEnd]
+    if (ptStart === PolymerType.NA || ptEnd === PolymerType.NA) return false
+    if (traceElementIndex[riStart] === -1 || traceElementIndex[riEnd] === -1) return false
 
-function areBackboneConnected(riStart: ResidueIndex, riEnd: ResidueIndex, data: AtomicData, segments: AtomicSegments, conformation: AtomicConformation, index: AtomicIndex, moleculeType: ArrayLike<MoleculeType>) {
-    const mtStart = moleculeType[riStart]
-    const mtEnd = moleculeType[riEnd]
-    if (!isPolymer(mtStart) || !isPolymer(mtEnd)) return false
-
-    let eiStart = index.findAtomsOnResidue(riStart, getAtomIdForAtomRole(mtStart, 'backboneStart'))
-    let eiEnd = index.findAtomsOnResidue(riEnd, getAtomIdForAtomRole(mtEnd, 'backboneEnd'))
+    let eiStart = index.findAtomsOnResidue(riStart, getAtomIdForAtomRole(ptStart, 'backboneStart'))
+    let eiEnd = index.findAtomsOnResidue(riEnd, getAtomIdForAtomRole(ptEnd, 'backboneEnd'))
 
     if (eiStart === -1 || eiEnd === -1) {
-        eiStart = index.findAtomsOnResidue(riStart, getAtomIdForAtomRole(mtStart, 'coarseBackbone'))
-        eiEnd = index.findAtomsOnResidue(riEnd, getAtomIdForAtomRole(mtEnd, 'coarseBackbone'))
+        eiStart = index.findAtomsOnResidue(riStart, getAtomIdForAtomRole(ptStart, 'coarseBackbone'))
+        eiEnd = index.findAtomsOnResidue(riEnd, getAtomIdForAtomRole(ptEnd, 'coarseBackbone'))
     }
 
     const { x, y, z } = conformation
     const pStart = Vec3.create(x[eiStart], y[eiStart], z[eiStart])
     const pEnd = Vec3.create(x[eiEnd], y[eiEnd], z[eiEnd])
-    return Vec3.distance(pStart, pEnd) < 10 // TODO better distance check, take into account if protein/nucleic and if coarse
+    const isCoarse = directionFromElementIndex[riStart] === -1 || directionToElementIndex[riStart] === -1 || directionFromElementIndex[riEnd] === -1 || directionToElementIndex[riEnd] === -1
+    return Vec3.distance(pStart, pEnd) < (isCoarse ? 10 : 3)
 }
 
-export function getAtomicRanges(data: AtomicData, segments: AtomicSegments, conformation: AtomicConformation, index: AtomicIndex, moleculeType: ArrayLike<MoleculeType>): AtomicRanges {
+export function getAtomicRanges(hierarchy: AtomicHierarchy, entities: Entities, conformation: AtomicConformation, sequence: StructureSequence): AtomicRanges {
     const polymerRanges: number[] = []
     const gapRanges: number[] = []
     const cyclicPolymerMap = new Map<ResidueIndex, ResidueIndex>()
-    const chainIt = Segmentation.transientSegments(segments.chainAtomSegments, Interval.ofBounds(0, data.atoms._rowCount))
-    const residueIt = Segmentation.transientSegments(segments.residueAtomSegments, Interval.ofBounds(0, data.atoms._rowCount))
-    const { label_seq_id } = data.residues
+    const chainIt = Segmentation.transientSegments(hierarchy.chainAtomSegments, Interval.ofBounds(0, hierarchy.atoms._rowCount))
+    const residueIt = Segmentation.transientSegments(hierarchy.residueAtomSegments, Interval.ofBounds(0, hierarchy.atoms._rowCount))
+    const { index, derived } = hierarchy
+    const { label_seq_id } = hierarchy.residues
+    const { label_entity_id } = hierarchy.chains
+    const { moleculeType, traceElementIndex } = derived.residue
 
     let prevSeqId: number
     let prevStart: number
@@ -56,9 +61,16 @@ export function getAtomicRanges(data: AtomicData, segments: AtomicSegments, conf
         prevEnd = -1
         startIndex = -1
 
-        const riStart = segments.residueAtomSegments.index[chainSegment.start]
-        const riEnd = segments.residueAtomSegments.index[chainSegment.end - 1]
-        if (areBackboneConnected(riStart, riEnd, data, segments, conformation, index, moleculeType)) {
+        const eI = entities.getEntityIndex(label_entity_id.value(chainSegment.index))
+        const seq = sequence.byEntityKey[eI]
+        const maxSeqId = seq ? seq.sequence.seqId.value(seq.sequence.seqId.rowCount - 1) : -1
+
+        // check cyclic peptides, seqIds and distance must be compatible
+        const riStart = hierarchy.residueAtomSegments.index[chainSegment.start]
+        const riEnd = hierarchy.residueAtomSegments.index[chainSegment.end - 1]
+        const seqIdStart = label_seq_id.value(riStart)
+        const seqIdEnd = label_seq_id.value(riEnd)
+        if (seqIdStart === 1 && seqIdEnd === maxSeqId && areBackboneConnected(riStart, riEnd, conformation, index, derived)) {
             cyclicPolymerMap.set(riStart, riEnd)
             cyclicPolymerMap.set(riEnd, riStart)
         }
@@ -67,7 +79,8 @@ export function getAtomicRanges(data: AtomicData, segments: AtomicSegments, conf
             const residueSegment = residueIt.move();
             const residueIndex = residueSegment.index
             const seqId = label_seq_id.value(residueIndex)
-            if (isPolymer(moleculeType[residueIndex])) {
+            // treat polymers residues that don't have a trace element resolved as gaps
+            if (isPolymer(moleculeType[residueIndex]) && traceElementIndex[residueIndex] !== -1) {
                 if (startIndex !== -1) {
                     if (seqId !== prevSeqId + 1) {
                         polymerRanges.push(startIndex, prevEnd - 1)
@@ -75,16 +88,24 @@ export function getAtomicRanges(data: AtomicData, segments: AtomicSegments, conf
                         startIndex = residueSegment.start
                     } else if (!residueIt.hasNext) {
                         polymerRanges.push(startIndex, residueSegment.end - 1)
+                        // TODO
+                        // if (seqId !== maxSeqId) {
+                        //     gapRanges.push(residueSegment.end - 1, residueSegment.end - 1)
+                        // }
                     } else {
-                        const riStart = segments.residueAtomSegments.index[residueSegment.start]
-                        const riEnd = segments.residueAtomSegments.index[prevEnd - 1]
-                        if (!areBackboneConnected(riStart, riEnd, data, segments, conformation, index, moleculeType)) {
+                        const riStart = hierarchy.residueAtomSegments.index[residueSegment.start]
+                        const riEnd = hierarchy.residueAtomSegments.index[prevEnd - 1]
+                        if (!areBackboneConnected(riStart, riEnd, conformation, hierarchy.index, derived)) {
                             polymerRanges.push(startIndex, prevEnd - 1)
                             startIndex = residueSegment.start
                         }
                     }
                 } else {
                     startIndex = residueSegment.start // start polymer
+                    // TODO
+                    // if (seqId !== 1) {
+                    //     gapRanges.push(residueSegment.start, residueSegment.start)
+                    // }
                 }
             } else {
                 if (startIndex !== -1) {

src/mol-model/structure/model/types.ts

@@ -40,30 +40,49 @@ export const enum EntityType {
 }
 
 export const enum MoleculeType {
-    /** the molecule type is not known */
-    unknown,
-    /** a known, but here not listed molecule type */
-    other,
-    /** water molecule */
-    water,
-    /** small ionic molecule */
-    ion,
-    /** protein, e.g. component type included in `ProteinComponentTypeNames` */
-    protein,
+    /** The molecule type is not known */
+    Unknown,
+    /** A known, but here not listed molecule type */
+    Other,
+    /** Water molecule */
+    Water,
+    /** Small ionic molecule */
+    Ion,
+    /** Protein, e.g. component type included in `ProteinComponentTypeNames` */
+    Protein,
     /** RNA, e.g. component type included in `RNAComponentTypeNames` */
     RNA,
     /** DNA, e.g. component type included in `DNAComponentTypeNames` */
     DNA,
     /** PNA, peptide nucleic acid, comp id included in `PeptideBaseNames` */
     PNA,
-    /** sacharide, e.g. component type included in `SaccharideComponentTypeNames` */
-    saccharide
+    /** Saccharide, e.g. component type included in `SaccharideComponentTypeNames` */
+    Saccharide
+}
+
+export const enum PolymerType {
+    /** not applicable */
+    NA,
+    Protein,
+    GammaProtein,
+    BetaProtein,
+    RNA,
+    DNA,
+    PNA,
 }
 
 export type AtomRole = 'trace' | 'directionFrom' | 'directionTo' | 'backboneStart' | 'backboneEnd' | 'coarseBackbone'
 
-export const MoleculeTypeAtomRoleId: { [k: number]: { [k in AtomRole]: Set<string> } } = {
-    [MoleculeType.protein]: {
+export const PolymerTypeAtomRoleId: { [k in PolymerType]: { [k in AtomRole]: Set<string> } } = {
+    [PolymerType.NA]: {
+        trace: new Set(),
+        directionFrom: new Set(),
+        directionTo: new Set(),
+        backboneStart: new Set(),
+        backboneEnd: new Set(),
+        coarseBackbone: new Set()
+    },
+    [PolymerType.Protein]: {
         trace: new Set(['CA']),
         directionFrom: new Set(['C']),
         directionTo: new Set(['O', 'OC1', 'O1', 'OX1', 'OXT']),
@@ -73,7 +92,23 @@ export const MoleculeTypeAtomRoleId: { [k: number]: { [k in AtomRole]: Set<strin
         // BB is often used for coarse grained models
         coarseBackbone: new Set(['CA', 'BB', 'CA1'])
     },
-    [MoleculeType.RNA]: {
+    [PolymerType.GammaProtein]: {
+        trace: new Set(['CA']),
+        directionFrom: new Set(['C']),
+        directionTo: new Set(['O']),
+        backboneStart: new Set(['N']),
+        backboneEnd: new Set(['CD']),
+        coarseBackbone: new Set(['CA'])
+    },
+    [PolymerType.BetaProtein]: {
+        trace: new Set(['CA']),
+        directionFrom: new Set(['C']),
+        directionTo: new Set(['O']),
+        backboneStart: new Set(['N']),
+        backboneEnd: new Set(['CG']),
+        coarseBackbone: new Set(['CA'])
+    },
+    [PolymerType.RNA]: {
         trace: new Set(['C4\'', 'C4*']),
         directionFrom: new Set(['C4\'', 'C4*']),
         directionTo: new Set(['C3\'', 'C3*']),
@@ -81,7 +116,7 @@ export const MoleculeTypeAtomRoleId: { [k: number]: { [k in AtomRole]: Set<strin
         backboneEnd: new Set(['O3\'', 'O3*']),
         coarseBackbone: new Set(['P'])
     },
-    [MoleculeType.DNA]: {
+    [PolymerType.DNA]: {
         trace: new Set(['C3\'', 'C3*']),
         directionFrom: new Set(['C3\'', 'C3*']),
         directionTo: new Set(['C1\'', 'C1*']),
@@ -89,7 +124,7 @@ export const MoleculeTypeAtomRoleId: { [k: number]: { [k in AtomRole]: Set<strin
         backboneEnd: new Set(['O3\'', 'O3*']),
         coarseBackbone: new Set(['P'])
     },
-    [MoleculeType.PNA]: {
+    [PolymerType.PNA]: {
         trace: new Set(['N4\'', 'N4*']),
         directionFrom: new Set(['N4\'', 'N4*']),
         directionTo: new Set(['C7\'', 'C7*']),
@@ -127,6 +162,16 @@ export const LProteinComponentTypeNames = new Set([
     'L-BETA-PEPTIDE, C-GAMMA LINKING'
 ])
 
+/** Chemical component type names for gamma protein, overlaps with D/L-linked */
+export const GammaProteinComponentTypeNames = new Set([
+    'D-GAMMA-PEPTIDE, C-DELTA LINKING', 'L-GAMMA-PEPTIDE, C-DELTA LINKING'
+])
+
+/** Chemical component type names for beta protein, overlaps with D/L-linked */
+export const BetaProteinComponentTypeNames = new Set([
+    'D-BETA-PEPTIDE, C-GAMMA LINKING', 'L-BETA-PEPTIDE, C-GAMMA LINKING'
+])
+
 /** Chemical component type names for pepdite-like protein */
 export const OtherProteinComponentTypeNames = new Set([
     'PEPTIDE LINKING', 'PEPTIDE-LIKE',
@@ -206,32 +251,53 @@ export const isPyrimidineBase = (compId: string) => PyrimidineBaseNames.has(comp
 export const PolymerNames = SetUtils.unionMany(AminoAcidNames, BaseNames)
 
 /** get the molecule type from component type and id */
-export function getMoleculeType(compType: string, compId: string) {
+export function getMoleculeType(compType: string, compId: string): MoleculeType {
     compType = compType.toUpperCase()
     compId = compId.toUpperCase()
     if (PeptideBaseNames.has(compId)) {
         return MoleculeType.PNA
     } else if (ProteinComponentTypeNames.has(compType)) {
-        return MoleculeType.protein
+        return MoleculeType.Protein
     } else if (RNAComponentTypeNames.has(compType)) {
         return MoleculeType.RNA
     } else if (DNAComponentTypeNames.has(compType)) {
         return MoleculeType.DNA
     } else if (SaccharideComponentTypeNames.has(compType)) {
-        return MoleculeType.saccharide
+        return MoleculeType.Saccharide
     } else if (WaterNames.has(compId)) {
-        return MoleculeType.water
+        return MoleculeType.Water
     } else if (IonNames.has(compId)) {
-        return MoleculeType.ion
+        return MoleculeType.Ion
     } else if (OtherComponentTypeNames.has(compType)) {
         if (SaccharideCompIdMap.has(compId)) {
             // trust our saccharide table more than given 'non-polymer' or 'other' component type
-            return MoleculeType.saccharide
+            return MoleculeType.Saccharide
         } else {
-            return MoleculeType.other
+            return MoleculeType.Other
         }
     } else {
-        return MoleculeType.unknown
+        return MoleculeType.Unknown
+    }
+}
+
+export function getPolymerType(compType: string, molType: MoleculeType): PolymerType {
+    compType = compType.toUpperCase()
+    if (molType === MoleculeType.Protein) {
+        if (GammaProteinComponentTypeNames.has(compType)) {
+            return PolymerType.GammaProtein
+        } else if (BetaProteinComponentTypeNames.has(compType)) {
+            return PolymerType.BetaProtein
+        } else {
+            return PolymerType.Protein
+        }
+    } else if (molType === MoleculeType.RNA) {
+        return PolymerType.RNA
+    } else if (molType === MoleculeType.DNA) {
+        return PolymerType.DNA
+    } else if (molType === MoleculeType.PNA) {
+        return PolymerType.PNA
+    } else {
+        return PolymerType.NA
     }
 }
 
@@ -316,7 +382,7 @@ export function isNucleic(moleculeType: MoleculeType) {
 }
 
 export function isProtein(moleculeType: MoleculeType) {
-    return moleculeType === MoleculeType.protein
+    return moleculeType === MoleculeType.Protein
 }
 
 /**

src/mol-model/structure/query/context.ts

@@ -7,8 +7,9 @@
 import { Structure, StructureElement, Unit } from '../structure';
 import { now } from '../../../mol-util/now';
 import { ElementIndex } from '../model';
-import { Link } from '../structure/unit/links';
 import { LinkType } from '../model/types';
+import { StructureSelection } from './selection';
+import { defaultLinkTest } from './queries/internal';
 
 export interface QueryContextView {
     readonly element: StructureElement.Location;
@@ -31,7 +32,10 @@ export class QueryContext implements QueryContextView {
     currentStructure: Structure = void 0 as any;
 
     /** Current link between atoms */
-    readonly atomicLink = QueryContextLinkInfo.empty<Unit.Atomic>();
+    readonly atomicLink = new QueryContextLinkInfo<Unit.Atomic>();
+
+    /** Supply this from the outside. Used by the internal.generator.current symbol */
+    currentSelection: StructureSelection | undefined = void 0;
 
     setElement(unit: Unit, e: ElementIndex) {
         this.element.unit = unit;
@@ -50,7 +54,7 @@ export class QueryContext implements QueryContextView {
 
     pushCurrentLink() {
         if (this.atomicLink) this.currentAtomicLinkStack.push(this.atomicLink);
-        (this.atomicLink as QueryContextLinkInfo<Unit.Atomic>) = QueryContextLinkInfo.empty();
+        (this.atomicLink as QueryContextLinkInfo<Unit.Atomic>) = new QueryContextLinkInfo();
         return this.atomicLink;
     }
 
@@ -88,23 +92,64 @@ export class QueryContext implements QueryContextView {
         }
     }
 
-    constructor(structure: Structure, timeoutMs = 0) {
-        this.inputStructure = structure;
-        this.timeoutMs = timeoutMs;
+    tryGetCurrentSelection() {
+        if (!this.currentSelection) throw new Error('The current selection is not assigned.');
+        return this.currentSelection;
     }
+
+    constructor(structure: Structure, options?: QueryContextOptions) {
+        this.inputStructure = structure;
+        this.timeoutMs = (options && options.timeoutMs) || 0;
+        this.currentSelection = options && options.currentSelection;
+    }
+}
+
+export interface QueryContextOptions {
+    timeoutMs?: number,
+    currentSelection?: StructureSelection
 }
 
 export interface QueryPredicate { (ctx: QueryContext): boolean }
 export interface QueryFn<T = any> { (ctx: QueryContext): T }
 
-export interface QueryContextLinkInfo<U extends Unit = Unit> {
-    link: Link.Location<U>,
-    type: LinkType,
-    order: number
-}
+export class QueryContextLinkInfo<U extends Unit = Unit> {
+    a: StructureElement.Location<U> = StructureElement.Location.create();
+    aIndex: StructureElement.UnitIndex = 0 as StructureElement.UnitIndex;
+    b: StructureElement.Location<U> = StructureElement.Location.create();
+    bIndex: StructureElement.UnitIndex = 0 as StructureElement.UnitIndex;
+    type: LinkType = LinkType.Flag.None;
+    order: number = 0;
 
-export namespace QueryContextLinkInfo {
-    export function empty<U extends Unit = Unit>(): QueryContextLinkInfo<U> {
-        return { link: Link.Location() as Link.Location<U>, type: LinkType.Flag.None, order: 0 };
+    private testFn: QueryPredicate = defaultLinkTest;
+
+    setTestFn(fn?: QueryPredicate) {
+        this.testFn = fn || defaultLinkTest;
+    }
+
+    test(ctx: QueryContext, trySwap: boolean) {
+        if (this.testFn(ctx)) return true;
+        if (trySwap) {
+            this.swap();
+            return this.testFn(ctx);
+        }
+        return false;
+    }
+
+    private swap() {
+        const idxA = this.aIndex;
+        this.aIndex = this.bIndex;
+        this.bIndex = idxA;
+
+        const unitA = this.a.unit;
+        this.a.unit = this.b.unit;
+        this.b.unit = unitA;
+
+        const eA = this.a.element;
+        this.a.element = this.b.element;
+        this.b.element = eA;
+    }
+
+    get length() {
+        return StructureElement.Location.distance(this.a, this. b);
     }
 }

src/mol-model/structure/query/queries/filters.ts

@@ -15,7 +15,6 @@ import { checkStructureMaxRadiusDistance, checkStructureMinMaxDistance } from '.
 import Structure from '../../structure/structure';
 import StructureElement from '../../structure/element';
 import { SortedArray } from '../../../../mol-data/int';
-import { defaultLinkTest } from './internal';
 
 export function pick(query: StructureQuery, pred: QueryPredicate): StructureQuery {
     return ctx => {
@@ -230,14 +229,13 @@ function withinMinMaxRadius({ queryCtx, selection, target, minRadius, maxRadius,
 
 interface IsConnectedToCtx {
     queryCtx: QueryContext,
+    disjunct: boolean,
     input: Structure,
-    target: Structure,
-    linkTest: QueryFn<boolean>,
-    tElement: StructureElement.Location
+    target: Structure
 }
 
 function checkConnected(ctx: IsConnectedToCtx, structure: Structure) {
-    const { queryCtx, input, target, linkTest, tElement } = ctx;
+    const { queryCtx, input, target, disjunct } = ctx;
     const atomicLink = queryCtx.atomicLink;
 
     const interLinks = input.links;
@@ -250,7 +248,7 @@ function checkConnected(ctx: IsConnectedToCtx, structure: Structure) {
         const linkedUnits = interLinks.getLinkedUnits(unit);
         const luCount = linkedUnits.length;
 
-        atomicLink.link.aUnit = inputUnit;
+        atomicLink.a.unit = inputUnit;
 
         const srcElements = unit.elements;
         const inputElements = inputUnit.elements;
@@ -258,33 +256,43 @@ function checkConnected(ctx: IsConnectedToCtx, structure: Structure) {
         for (let i = 0 as StructureElement.UnitIndex, _i = srcElements.length; i < _i; i++) {
             const inputIndex = SortedArray.indexOf(inputElements, srcElements[i]) as StructureElement.UnitIndex;
 
-            atomicLink.link.aIndex = inputIndex;
-            atomicLink.link.bUnit = inputUnit;
+            atomicLink.a.unit = inputUnit;
+            atomicLink.b.unit = inputUnit;
 
-            tElement.unit = unit;
+            // tElement.unit = unit;
             for (let l = offset[inputIndex], _l = offset[inputIndex + 1]; l < _l; l++) {
-                tElement.element = inputElements[b[l]];
-                if (!target.hasElement(tElement)) continue;
-                atomicLink.link.bIndex = b[l] as StructureElement.UnitIndex;
+                // tElement.element = inputElements[b[l]];
+                atomicLink.b.element = inputUnit.elements[b[l]];
+                if (disjunct && SortedArray.has(unit.elements, atomicLink.b.element)) continue;
+                if (!target.hasElement(atomicLink.b)) continue;
+
+                atomicLink.aIndex = inputIndex;
+                atomicLink.a.element = srcElements[i];
+                atomicLink.bIndex = b[l] as StructureElement.UnitIndex;
                 atomicLink.type = flags[l];
                 atomicLink.order = order[l];
-                if (linkTest(queryCtx)) return true;
+                if (atomicLink.test(queryCtx, true)) return true;
             }
 
             for (let li = 0; li < luCount; li++) {
                 const lu = linkedUnits[li];
-                tElement.unit = lu.unitB;
-                atomicLink.link.bUnit = lu.unitB;
                 const bElements = lu.unitB.elements;
                 const bonds = lu.getBonds(inputIndex);
                 for (let bi = 0, _bi = bonds.length; bi < _bi; bi++) {
                     const bond = bonds[bi];
-                    tElement.element = bElements[bond.indexB];
-                    if (!target.hasElement(tElement)) continue;
-                    atomicLink.link.bIndex = bond.indexB;
+                    atomicLink.b.unit = lu.unitB;
+                    atomicLink.b.element = bElements[bond.indexB];
+                    if (!target.hasElement(atomicLink.b)) continue;
+                    if (disjunct && structure.hasElement(atomicLink.b)) continue;
+
+                    atomicLink.a.unit = inputUnit;
+                    atomicLink.aIndex = inputIndex;
+                    atomicLink.a.element = srcElements[i];
+
+                    atomicLink.bIndex = bond.indexB;
                     atomicLink.type = bond.flag;
                     atomicLink.order = bond.order;
-                    if (linkTest(queryCtx)) return true;
+                    if (atomicLink.test(queryCtx, true)) return true;
                 }
             }
         }
@@ -311,15 +319,20 @@ export function isConnectedTo({ query, target, disjunct, invert, linkTest }: IsC
         const connCtx: IsConnectedToCtx = {
             queryCtx: ctx,
             input: ctx.inputStructure,
-            target: StructureSelection.unionStructure(targetSel),
-            linkTest: linkTest || defaultLinkTest,
-            tElement: StructureElement.Location.create()
+            disjunct,
+            target: StructureSelection.unionStructure(targetSel)
         }
 
         const ret = StructureSelection.LinearBuilder(ctx.inputStructure);
         ctx.pushCurrentLink();
+        ctx.atomicLink.setTestFn(linkTest);
+
         StructureSelection.forEach(selection, (s, sI) => {
-            if (checkConnected(connCtx, s)) ret.add(s);
+            if (checkConnected(connCtx, s)) {
+                ret.add(s);
+            } else if (invert) {
+                ret.add(s);
+            }
             if (sI % 5 === 0) ctx.throwIfTimedOut();
         })
         ctx.popCurrentLink();

src/mol-model/structure/query/queries/generators.ts

@@ -7,7 +7,7 @@
 
 import { StructureQuery } from '../query'
 import { StructureSelection } from '../selection'
-import { Unit, StructureProperties as P } from '../../structure'
+import { Unit, StructureProperties as P, StructureElement } from '../../structure'
 import { Segmentation, SortedArray } from '../../../../mol-data/int'
 import { LinearGroupingBuilder } from '../utils/builders';
 import { QueryPredicate, QueryFn, QueryContextView } from '../context';
@@ -58,7 +58,7 @@ export function atoms(params?: Partial<AtomsQueryParams>): StructureQuery {
 }
 
 function atomGroupsLinear(atomTest: QueryPredicate): StructureQuery {
-    return ctx => {
+    return function query_atomGroupsLinear(ctx) {
         const { inputStructure } = ctx;
         const { units } = inputStructure;
         const l = ctx.pushCurrentElement();
@@ -83,7 +83,7 @@ function atomGroupsLinear(atomTest: QueryPredicate): StructureQuery {
 }
 
 function atomGroupsSegmented({ unitTest, entityTest, chainTest, residueTest, atomTest }: AtomsQueryParams): StructureQuery {
-    return ctx => {
+    return function query_atomGroupsSegmented(ctx) {
         const { inputStructure } = ctx;
         const { units } = inputStructure;
         const l = ctx.pushCurrentElement();
@@ -152,7 +152,7 @@ function atomGroupsSegmented({ unitTest, entityTest, chainTest, residueTest, ato
 }
 
 function atomGroupsGrouped({ unitTest, entityTest, chainTest, residueTest, atomTest, groupBy }: AtomsQueryParams): StructureQuery {
-    return ctx => {
+    return function query_atomGroupsGrouped(ctx) {
         const { inputStructure } = ctx;
         const { units } = inputStructure;
         const l = ctx.pushCurrentElement();
@@ -224,9 +224,9 @@ function getRingStructure(unit: Unit.Atomic, ring: UnitRing, inputStructure: Str
 }
 
 export function rings(fingerprints?: ArrayLike<UnitRing.Fingerprint>): StructureQuery {
-    return ctx => {
+    return function query_rings(ctx) {
         const { units } = ctx.inputStructure;
-        let ret = StructureSelection.LinearBuilder(ctx.inputStructure);
+        const ret = StructureSelection.LinearBuilder(ctx.inputStructure);
 
         if (!fingerprints || fingerprints.length === 0) {
             for (const u of units) {
@@ -258,7 +258,7 @@ export function rings(fingerprints?: ArrayLike<UnitRing.Fingerprint>): Structure
 }
 
 export function querySelection(selection: StructureQuery, query: StructureQuery, inComplement: boolean = false): StructureQuery {
-    return ctx => {
+    return function query_querySelection(ctx) {
         const targetSel = selection(ctx);
         if (StructureSelection.structureCount(targetSel) === 0) return targetSel;
 
@@ -274,4 +274,71 @@ export function querySelection(selection: StructureQuery, query: StructureQuery,
         ctx.popInputStructure();
         return StructureSelection.withInputStructure(result, ctx.inputStructure);
     }
+}
+
+export function linkedAtomicPairs(linkTest?: QueryPredicate): StructureQuery {
+    return function query_linkedAtomicPairs(ctx) {
+        const structure = ctx.inputStructure;
+
+        const interLinks = structure.links;
+        // Note: each link is called twice, that's why we need the unique builder.
+        const ret = StructureSelection.UniqueBuilder(ctx.inputStructure);
+
+        ctx.pushCurrentLink();
+        const atomicLink = ctx.atomicLink;
+        atomicLink.setTestFn(linkTest);
+
+        // Process intra unit links
+        for (const unit of structure.units) {
+            if (unit.kind !== Unit.Kind.Atomic) continue;
+
+            const { offset: intraLinkOffset, b: intraLinkB, edgeProps: { flags, order } } = unit.links;
+            atomicLink.a.unit = unit;
+            atomicLink.b.unit = unit;
+            for (let i = 0 as StructureElement.UnitIndex, _i = unit.elements.length; i < _i; i++) {
+                atomicLink.aIndex = i as StructureElement.UnitIndex;
+                atomicLink.a.element = unit.elements[i];
+
+                // check intra unit links
+                for (let lI = intraLinkOffset[i], _lI = intraLinkOffset[i + 1]; lI < _lI; lI++) {
+                    atomicLink.bIndex = intraLinkB[lI] as StructureElement.UnitIndex;
+                    atomicLink.b.element = unit.elements[intraLinkB[lI]];
+                    atomicLink.type = flags[lI];
+                    atomicLink.order = order[lI];
+                    // No need to "swap test" because each bond direction will be visited eventually.
+                    if (atomicLink.test(ctx, false)) {
+                        const b = structure.subsetBuilder(false);
+                        b.beginUnit(unit.id);
+                        b.addElement(atomicLink.a.element);
+                        b.addElement(atomicLink.b.element);
+                        b.commitUnit();
+                        ret.add(b.getStructure());
+                    }
+                }
+            }
+        }
+
+        // Process inter unit links
+        for (const bond of interLinks.bonds) {
+            atomicLink.a.unit = bond.unitA;
+            atomicLink.a.element = bond.unitA.elements[bond.indexA];
+            atomicLink.aIndex = bond.indexA;
+            atomicLink.b.unit = bond.unitB;
+            atomicLink.b.element = bond.unitB.elements[bond.indexB];
+            atomicLink.bIndex = bond.indexB;
+            atomicLink.order = bond.order;
+            atomicLink.type = bond.flag;
+
+            // No need to "swap test" because each bond direction will be visited eventually.
+            if (atomicLink.test(ctx, false)) {
+                const b = structure.subsetBuilder(false);
+                b.addToUnit(atomicLink.a.unit.id, atomicLink.a.element);
+                b.addToUnit(atomicLink.b.unit.id, atomicLink.b.element);
+                ret.add(b.getStructure());
+            }
+        }
+
+        ctx.popCurrentLink();
+        return ret.getSelection();
+    };
 }

src/mol-model/structure/query/queries/internal.ts

@@ -4,7 +4,7 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import { Segmentation } from '../../../../mol-data/int';
+import { Segmentation, SortedArray } from '../../../../mol-data/int';
 import StructureElement from '../../../../mol-model/structure/structure/element';
 import { StructureProperties as P, Unit } from '../../structure';
 import Structure from '../../structure/structure';
@@ -12,13 +12,15 @@ import { StructureQuery } from '../query';
 import { StructureSelection } from '../selection';
 import { QueryContext } from '../context';
 import { LinkType } from '../../model/types';
+import { BundleElement, Bundle } from '../../structure/element/bundle';
+import { UnitIndex } from '../../structure/element/element';
 
 export function defaultLinkTest(ctx: QueryContext) {
     return LinkType.isCovalent(ctx.atomicLink.type);
 }
 
 export function atomicSequence(): StructureQuery {
-    return ctx => {
+    return function query_atomicSequence(ctx) {
         const { inputStructure } = ctx;
         const l = StructureElement.Location.create();
 
@@ -46,7 +48,7 @@ export function atomicSequence(): StructureQuery {
 }
 
 export function water(): StructureQuery {
-    return ctx => {
+    return function query_water(ctx) {
         const { inputStructure } = ctx;
         const l = StructureElement.Location.create();
 
@@ -65,7 +67,7 @@ export function water(): StructureQuery {
 }
 
 export function atomicHet(): StructureQuery {
-    return ctx => {
+    return function query_atomicHet(ctx) {
         const { inputStructure } = ctx;
         const l = StructureElement.Location.create();
 
@@ -95,7 +97,7 @@ export function atomicHet(): StructureQuery {
 }
 
 export function spheres(): StructureQuery {
-    return ctx => {
+    return function query_spheres(ctx) {
         const { inputStructure } = ctx;
 
         const units: Unit[] = [];
@@ -105,4 +107,23 @@ export function spheres(): StructureQuery {
         }
         return StructureSelection.Singletons(inputStructure, new Structure(units, { parent: inputStructure }));
     };
+}
+
+export function bundleElementImpl(groupedUnits: number[][], ranges: number[], set: number[]): BundleElement {
+    return {
+        groupedUnits: groupedUnits as any as SortedArray<number>[],
+        ranges: ranges as any as SortedArray<UnitIndex>,
+        set: set as any as SortedArray<UnitIndex>
+    };
+}
+
+export function bundleGenerator(elements: BundleElement[]): StructureQuery {
+    return function query_bundleGenerator(ctx) {
+        const bundle: Bundle = {
+            hash: ctx.inputStructure.hashCode,
+            elements
+        };
+
+        return StructureSelection.Sequence(ctx.inputStructure, [Bundle.toStructure(bundle, ctx.inputStructure)]);
+    };
 }

src/mol-model/structure/query/queries/modifiers.ts

@@ -15,7 +15,6 @@ import { structureIntersect, structureSubtract } from '../utils/structure-set';
 import { UniqueArray } from '../../../../mol-data/generic';
 import { StructureSubsetBuilder } from '../../structure/util/subset-builder';
 import StructureElement from '../../structure/element';
-import { defaultLinkTest } from './internal';
 
 function getWholeResidues(ctx: QueryContext, source: Structure, structure: Structure) {
     const builder = source.subsetBuilder(true);
@@ -45,7 +44,7 @@ function getWholeResidues(ctx: QueryContext, source: Structure, structure: Struc
 }
 
 export function wholeResidues(query: StructureQuery): StructureQuery {
-    return ctx => {
+    return function query_wholeResidues(ctx) {
         const inner = query(ctx);
         if (StructureSelection.isSingleton(inner)) {
             return StructureSelection.Singletons(ctx.inputStructure, getWholeResidues(ctx, ctx.inputStructure, inner.structure));
@@ -141,7 +140,7 @@ function findStructureRadius(ctx: QueryContext, eRadius: QueryFn<number>) {
 }
 
 export function includeSurroundings(query: StructureQuery, params: IncludeSurroundingsParams): StructureQuery {
-    return ctx => {
+    return function query_includeSurroundings(ctx) {
         const inner = query(ctx);
 
         if (params.elementRadius) {
@@ -180,7 +179,7 @@ export function includeSurroundings(query: StructureQuery, params: IncludeSurrou
 }
 
 export function querySelection(selection: StructureQuery, query: StructureQuery): StructureQuery {
-    return ctx => {
+    return function query_querySelection(ctx) {
         const targetSel = selection(ctx);
         if (StructureSelection.structureCount(targetSel) === 0) return targetSel;
 
@@ -198,7 +197,7 @@ export function querySelection(selection: StructureQuery, query: StructureQuery)
 }
 
 export function intersectBy(query: StructureQuery, by: StructureQuery): StructureQuery {
-    return ctx => {
+    return function query_intersectBy(ctx) {
         const selection = query(ctx);
         if (StructureSelection.structureCount(selection) === 0) return selection;
 
@@ -218,7 +217,7 @@ export function intersectBy(query: StructureQuery, by: StructureQuery): Structur
 }
 
 export function exceptBy(query: StructureQuery, by: StructureQuery): StructureQuery {
-    return ctx => {
+    return function query_exceptBy(ctx) {
         const selection = query(ctx);
         if (StructureSelection.structureCount(selection) === 0) return selection;
 
@@ -238,7 +237,7 @@ export function exceptBy(query: StructureQuery, by: StructureQuery): StructureQu
 }
 
 export function union(query: StructureQuery): StructureQuery {
-    return ctx => {
+    return function query_union(ctx) {
         const ret = StructureSelection.LinearBuilder(ctx.inputStructure);
         ret.add(StructureSelection.unionStructure(query(ctx)));
         return ret.getSelection();
@@ -246,7 +245,7 @@ export function union(query: StructureQuery): StructureQuery {
 }
 
 export function expandProperty(query: StructureQuery, property: QueryFn): StructureQuery {
-    return ctx => {
+    return function query_expandProperty(ctx) {
         const src = query(ctx);
         const propertyToStructureIndexMap = new Map<any, UniqueArray<number>>();
 
@@ -305,44 +304,44 @@ export interface IncludeConnectedParams {
 }
 
 export function includeConnected({ query, layerCount, wholeResidues, linkTest }: IncludeConnectedParams): StructureQuery {
-    const bt = linkTest || defaultLinkTest;
     const lc = Math.max(layerCount, 0);
-    return ctx => {
+    return function query_includeConnected(ctx) {
         const builder = StructureSelection.UniqueBuilder(ctx.inputStructure);
         const src = query(ctx);
         ctx.pushCurrentLink();
+        ctx.atomicLink.setTestFn(linkTest);
         StructureSelection.forEach(src, (s, sI) => {
             let incl = s;
             for (let i = 0; i < lc; i++) {
-                incl = includeConnectedStep(ctx, bt, wholeResidues, incl);
+                incl = includeConnectedStep(ctx, wholeResidues, incl);
             }
             builder.add(incl);
             if (sI % 10 === 0) ctx.throwIfTimedOut();
         });
         ctx.popCurrentLink();
+
         return builder.getSelection();
     }
 }
 
-function includeConnectedStep(ctx: QueryContext, linkTest: QueryFn<boolean>, wholeResidues: boolean, structure: Structure) {
-    const expanded = expandConnected(ctx, structure, linkTest);
+function includeConnectedStep(ctx: QueryContext, wholeResidues: boolean, structure: Structure) {
+    const expanded = expandConnected(ctx, structure);
     if (wholeResidues) return getWholeResidues(ctx, ctx.inputStructure, expanded);
     return expanded;
 }
 
-function expandConnected(ctx: QueryContext, structure: Structure, linkTest: QueryFn<boolean>) {
+function expandConnected(ctx: QueryContext, structure: Structure) {
     const inputStructure = ctx.inputStructure;
     const interLinks = inputStructure.links;
     const builder = new StructureUniqueSubsetBuilder(inputStructure);
 
-    const processedUnits = new Set<number>();
+    // Note: each link is visited twice so that link.atom-a and link.atom-b both get the "swapped values"
+    const visitedSourceUnits = new Set<number>();
 
     const atomicLink = ctx.atomicLink;
 
     // Process intra unit links
     for (const unit of structure.units) {
-        processedUnits.add(unit.id);
-
         if (unit.kind !== Unit.Kind.Atomic) {
             // add the whole unit
             builder.beginUnit(unit.id);
@@ -353,50 +352,71 @@ function expandConnected(ctx: QueryContext, structure: Structure, linkTest: Quer
             continue;
         }
 
-        const inputUnit = inputStructure.unitMap.get(unit.id) as Unit.Atomic;
-        const { offset: intraLinkOffset, b: intraLinkB, edgeProps: { flags, order } } = inputUnit.links;
+        const inputUnitA = inputStructure.unitMap.get(unit.id) as Unit.Atomic;
+        const { offset: intraLinkOffset, b: intraLinkB, edgeProps: { flags, order } } = inputUnitA.links;
 
         // Process intra unit links
-        atomicLink.link.aUnit = inputUnit;
-        atomicLink.link.bUnit = inputUnit;
+        atomicLink.a.unit = inputUnitA;
+        atomicLink.b.unit = inputUnitA;
         for (let i = 0, _i = unit.elements.length; i < _i; i++) {
             // add the current element
             builder.addToUnit(unit.id, unit.elements[i]);
 
-            const srcIndex = SortedArray.indexOf(inputUnit.elements, unit.elements[i]);
-            atomicLink.link.aIndex = srcIndex as StructureElement.UnitIndex;
+            const aIndex = SortedArray.indexOf(inputUnitA.elements, unit.elements[i]) as StructureElement.UnitIndex;
 
             // check intra unit links
-            for (let lI = intraLinkOffset[srcIndex], _lI = intraLinkOffset[srcIndex + 1]; lI < _lI; lI++) {
-                atomicLink.link.bIndex = intraLinkB[lI] as StructureElement.UnitIndex;
+            for (let lI = intraLinkOffset[aIndex], _lI = intraLinkOffset[aIndex + 1]; lI < _lI; lI++) {
+                const bIndex = intraLinkB[lI] as StructureElement.UnitIndex;
+                const bElement = inputUnitA.elements[bIndex];
+
+                // Check if the element is already present:
+                if (SortedArray.has(unit.elements, bElement) || builder.has(unit.id, bElement)) continue;
+
+                atomicLink.aIndex = aIndex;
+                atomicLink.a.element = unit.elements[i];
+                atomicLink.bIndex = bIndex;
+                atomicLink.b.element = bElement;
                 atomicLink.type = flags[lI];
                 atomicLink.order = order[lI];
-                if (linkTest(ctx)) {
-                    builder.addToUnit(unit.id, inputUnit.elements[intraLinkB[lI]]);
+
+                if (atomicLink.test(ctx, true)) {
+                    builder.addToUnit(unit.id, bElement);
                 }
             }
         }
 
         // Process inter unit links
-        for (const linkedUnit of interLinks.getLinkedUnits(inputUnit)) {
-            if (processedUnits.has(linkedUnit.unitB.id)) continue;
+        for (const linkedUnit of interLinks.getLinkedUnits(inputUnitA)) {
+            if (visitedSourceUnits.has(linkedUnit.unitB.id)) continue;
+            const currentUnitB = structure.unitMap.get(linkedUnit.unitB.id);
 
-            atomicLink.link.bUnit = linkedUnit.unitB;
             for (const aI of linkedUnit.linkedElementIndices) {
                 // check if the element is in the expanded structure
-                if (!SortedArray.has(unit.elements, inputUnit.elements[aI])) continue;
+                if (!SortedArray.has(unit.elements, inputUnitA.elements[aI])) continue;
 
-                atomicLink.link.aIndex = aI;
                 for (const bond of linkedUnit.getBonds(aI)) {
-                    atomicLink.link.bIndex = bond.indexB;
+                    const bElement = linkedUnit.unitB.elements[bond.indexB];
+
+                    // Check if the element is already present:
+                    if ((currentUnitB && SortedArray.has(currentUnitB.elements, bElement)) || builder.has(linkedUnit.unitB.id, bElement)) continue;
+
+                    atomicLink.a.unit = inputUnitA;
+                    atomicLink.aIndex = aI;
+                    atomicLink.a.element = inputUnitA.elements[aI];
+                    atomicLink.b.unit = linkedUnit.unitB;
+                    atomicLink.bIndex = bond.indexB;
+                    atomicLink.b.element = bElement;
                     atomicLink.type = bond.flag;
                     atomicLink.order = bond.order;
-                    if (linkTest(ctx)) {
-                        builder.addToUnit(linkedUnit.unitB.id, linkedUnit.unitB.elements[bond.indexB]);
+
+                    if (atomicLink.test(ctx, true)) {
+                        builder.addToUnit(linkedUnit.unitB.id, bElement);
                     }
                 }
             }
         }
+
+        visitedSourceUnits.add(inputUnitA.id);
     }
 
     return builder.getStructure();

src/mol-model/structure/query/query.ts

@@ -6,12 +6,12 @@
 
 import { Structure } from '../structure'
 import { StructureSelection } from './selection'
-import { QueryContext, QueryFn } from './context';
+import { QueryContext, QueryFn, QueryContextOptions } from './context';
 
 interface StructureQuery extends QueryFn<StructureSelection> { }
 namespace StructureQuery {
-    export function run(query: StructureQuery, structure: Structure, timeoutMs = 0) {
-        return query(new QueryContext(structure, timeoutMs));
+    export function run(query: StructureQuery, structure: Structure, options?: QueryContextOptions) {
+        return query(new QueryContext(structure, options));
     }
 }
 

src/mol-model/structure/query/selection.ts

@@ -35,7 +35,8 @@ namespace StructureSelection {
         return structureUnion(sel.source, sel.structures);
     }
 
-    export function toLoci(sel: StructureSelection): StructureElement.Loci {
+    /** Convert selection to loci and use "current structure units" in Loci elements */
+    export function toLociWithCurrentUnits(sel: StructureSelection): StructureElement.Loci {
         const elements: { unit: Unit, indices: OrderedSet<StructureElement.UnitIndex> }[] = [];
         const { unitMap } = sel.source;
 
@@ -57,7 +58,7 @@ namespace StructureSelection {
     }
 
     /** use source unit in loci.elements */
-    export function toLoci2(sel: StructureSelection): StructureElement.Loci {
+    export function toLociWithSourceUnits(sel: StructureSelection): StructureElement.Loci {
         const elements: { unit: Unit, indices: OrderedSet<StructureElement.UnitIndex> }[] = [];
         const { unitMap } = sel.source;
 

src/mol-model/structure/structure/accessible-surface-area.ts

@@ -192,7 +192,7 @@ namespace AccessibleSurfaceArea {
 
             if (isNucleic(residueType)) {
                  ctx.atomRadius[aI] = determineRadiusNucl(atomId, element, compId);
-            } else if (residueType === MoleculeType.protein) {
+            } else if (residueType === MoleculeType.Protein) {
                 ctx.atomRadius[aI] = determineRadiusAmino(atomId, element, compId);
             } else {
                 ctx.atomRadius[aI] = handleNonStandardCase(element);

src/mol-model/structure/structure/carbohydrates/compute.ts

@@ -9,7 +9,7 @@ import { Segmentation, SortedArray } from '../../../../mol-data/int';
 import { combinations } from '../../../../mol-data/util/combination';
 import { IntAdjacencyGraph } from '../../../../mol-math/graph';
 import { Vec3 } from '../../../../mol-math/linear-algebra';
-import PrincipalAxes from '../../../../mol-math/linear-algebra/matrix/principal-axes';
+import { PrincipalAxes } from '../../../../mol-math/linear-algebra/matrix/principal-axes';
 import { fillSerial } from '../../../../mol-util/array';
 import { ResidueIndex, Model } from '../../model';
 import { ElementSymbol } from '../../model/types';
@@ -195,7 +195,7 @@ export function computeCarbohydrates(structure: Structure): Carbohydrates {
                     const ringAtoms = rings.all[sugarRings[j]];
                     const anomericCarbon = getAnomericCarbon(unit, ringAtoms)
 
-                    const pa = new PrincipalAxes(getPositionMatrix(unit, ringAtoms))
+                    const pa = PrincipalAxes.ofPoints(getPositionMatrix(unit, ringAtoms))
                     const center = Vec3.copy(Vec3.zero(), pa.center)
                     const normal = Vec3.copy(Vec3.zero(), pa.normVecC)
                     const direction = getDirection(Vec3.zero(), unit, anomericCarbon, center)

src/mol-model/structure/structure/carbohydrates/constants.ts

@@ -211,26 +211,26 @@ export const MonosaccharidesColorTable: [string, Color][] = [
 const CommonSaccharideNames: { [k: string]: string[] } = {
     // Hexose
     Glc: [
-        'GLC', 'BGC',
+        'GLC', 'BGC', 'Z8T',
         'TRE', // di-saccharide but homomer
         'MLR', // tri-saccharide but homomer
     ],
     Man: ['MAN', 'BMA'],
-    Gal: ['GLA', 'GAL', 'GZL'],
-    Gul: ['4GL', 'GL0'],
-    Alt: ['Z6H', '3MK'],
-    All: ['AFD', 'ALL'],
-    Tal: [],
-    Ido: ['Z0F', '4N2'],
+    Gal: ['GLA', 'GAL', 'GZL', 'GXL', 'GIV'],
+    Gul: ['4GL', 'GL0', 'GUP', 'Z8H'],
+    Alt: ['Z6H', '3MK', 'SHD'],
+    All: ['AFD', 'ALL', 'WOO', 'Z2D'],
+    Tal: ['ZEE', 'A5C'],
+    Ido: ['ZCD', 'Z0F', '4N2'],
     // HexNAc
-    GlcNAc: ['NDG', 'NAG'],
+    GlcNAc: ['NDG', 'NAG', 'NGZ'],
     ManNAc: ['BM3', 'BM7'],
-    GalNAc: ['A2G', 'NGA'],
+    GalNAc: ['A2G', 'NGA', 'YYQ'],
     GulNAc: ['LXB'],
     AltNAc: [],
     AllNAc: ['NAA'],
     TalNAc: [],
-    IdoNAc: [],
+    IdoNAc: ['LXZ'],
     // Hexosamine
     GlcN: ['PA1', 'GCS'],
     ManN: ['95Z'],
@@ -244,24 +244,24 @@ const CommonSaccharideNames: { [k: string]: string[] } = {
     GlcA: ['GCU', 'BDP'],
     ManA: ['MAV', 'BEM'],
     GalA: ['ADA', 'GTR', 'GTK'],
-    GulA: [],
+    GulA: ['LGU'],
     AltA: [],
     AllA: [],
     TalA: ['X1X', 'X0X'],
     IdoA: ['IDR'],
     // Deoxyhexose
     Qui: ['G6D', 'YYK'],
-    Rha: ['RAM', 'RM4'],
+    Rha: ['RAM', 'RM4', 'XXR'],
     '6dGul': ['66O'],
     '6dAlt': [],
     '6dTal': [],
-    Fuc: ['FUC', 'FUL'],
+    Fuc: ['FUC', 'FUL', 'FCA', 'FCB'],
     // DeoxyhexNAc
     QuiNAc: ['Z9W'],
     RhaNAc: [],
     '6dAltNAc': [],
     '6dTalNAc': [],
-    FucNAc: [],
+    FucNAc: ['49T'],
     // Di-deoxyhexose
     Oli: ['DDA', 'RAE', 'Z5J'],
     Tyv: ['TYV'],
@@ -270,10 +270,10 @@ const CommonSaccharideNames: { [k: string]: string[] } = {
     Dig: ['Z3U'],
     Col: [],
     // Pentose
-    Ara: ['ARA', 'ARB', 'AHR', 'FUB'],
+    Ara: ['64K', 'ARA', 'ARB', 'AHR', 'FUB', 'BXY', 'BXX'],
     Lyx: ['LDY', 'Z4W'],
-    Xyl: ['XZS', 'XYP', 'XYZ'],
-    Rib: ['YYM', 'RIP', 'RIB', 'BDR'],
+    Xyl: ['XYS', 'XYP', 'XYZ', 'HSY', 'LXC'],
+    Rib: ['YYM', 'RIP', 'RIB', 'BDR', '0MK', 'Z6J', '32O'],
     // Deoxynonulosonate
     Kdn: ['KDM', 'KDN'],
     Neu5Ac: ['SIA', 'SLB'],
@@ -296,10 +296,10 @@ const CommonSaccharideNames: { [k: string]: string[] } = {
     Mur: ['1S4', 'MUR'],
     // Assigned
     Api: ['XXM'],
-    Fru: ['BDF', 'Z9N', 'FRU'],
+    Fru: ['BDF', 'Z9N', 'FRU', 'LFR'],
     Tag: ['T6T'],
     Sor: ['SOE'],
-    Psi: ['PSV'],
+    Psi: ['PSV', 'SF6', 'SF9'],
 }
 
 const UnknownSaccharideNames = [

src/mol-model/structure/structure/element/bundle.ts

@@ -12,8 +12,10 @@ import { hashFnv32a, hash2 } from '../../../../mol-data/util';
 import SortedRanges from '../../../../mol-data/int/sorted-ranges';
 import { UnitIndex } from './element';
 import { Loci } from './loci';
+import Expression from '../../../../mol-script/language/expression';
+import { MolScriptBuilder as MS } from '../../../../mol-script/language/builder';
 
-interface BundleElement {
+export interface BundleElement {
     /**
      * Array (sorted by first element in sub-array) of
      * arrays of `Unit.id`s that share the same `Unit.invariantId`
@@ -165,23 +167,39 @@ export namespace Bundle {
                 const _units = getUnitsFromIds(g, parent)
                 if (_units.length === 0) continue
 
-                const unit = _units[0] // the elements are grouped by unit.invariantId
+                const ue = _units[0].elements // the elements are grouped by unit.invariantId
                 const rangesSize = SortedRanges.size(e.ranges)
-                const _indices = new Int32Array(e.set.length + rangesSize)
+                const setSize = e.set.length
+                const _indices = new Int32Array(setSize + rangesSize)
                 let indices: SortedArray<ElementIndex>
-                if (e.ranges.length === 0) {
-                    for (let i = 0, il = e.set.length; i < il; ++i) {
-                        _indices[i] = unit.elements[e.set[i]]
+                if (rangesSize === 0) {
+                    for (let i = 0, il = setSize; i < il; ++i) {
+                        _indices[i] = ue[e.set[i]]
                     }
                     indices = SortedArray.ofSortedArray(_indices)
-                } else if (e.set.length === 0) {
-                    SortedRanges.forEach(e.ranges, (v, i) => _indices[i] = unit.elements[v])
+                } else if (setSize === 0) {
+                    SortedRanges.forEach(e.ranges, (v, i) => _indices[i] = ue[v])
                     indices = SortedArray.ofSortedArray(_indices)
                 } else {
-                    const rangesSize = SortedRanges.size(e.ranges)
-                    SortedRanges.forEach(e.ranges, (v, i) => _indices[i] = unit.elements[v])
-                    SortedRanges.forEach(e.set, (v, i) => _indices[i + rangesSize] = unit.elements[v])
-                    indices = SortedArray.ofUnsortedArray(_indices) // requires sort
+                    if (SortedArray.min(e.set) > SortedRanges.max(e.ranges)) {
+                        SortedRanges.forEach(e.ranges, (v, i) => _indices[i] = ue[v])
+                        for (let i = 0, il = setSize; i < il; ++i) {
+                            _indices[i + rangesSize] = ue[e.set[i]]
+                        }
+                        indices = SortedArray.ofSortedArray(_indices)
+                    } else if (SortedRanges.min(e.ranges) > SortedArray.max(e.set)) {
+                        for (let i = 0, il = setSize; i < il; ++i) {
+                            _indices[i] = ue[e.set[i]]
+                        }
+                        SortedRanges.forEach(e.ranges, (v, i) => _indices[i + setSize] = ue[v])
+                        indices = SortedArray.ofSortedArray(_indices)
+                    } else {
+                        SortedRanges.forEach(e.ranges, (v, i) => _indices[i] = ue[v])
+                        for (let i = 0, il = setSize; i < il; ++i) {
+                            _indices[i + rangesSize] = ue[e.set[i]]
+                        }
+                        indices = SortedArray.ofUnsortedArray(_indices) // requires sort
+                    }
                 }
 
                 for (const unit of _units) {
@@ -192,6 +210,21 @@ export namespace Bundle {
         return Structure.create(units, { parent })
     }
 
+
+    function elementToExpression(e: BundleElement): Expression {
+        return MS.internal.generator.bundleElement({
+            groupedUnits: MS.core.type.list(e.groupedUnits.map(u => MS.core.type.list(u))),
+            ranges: MS.core.type.list(e.ranges),
+            set: MS.core.type.list(e.set),
+        })
+    }
+
+    export function toExpression(bundle: Bundle): Expression {
+        return MS.internal.generator.bundle({
+            elements: MS.core.type.list(bundle.elements.map(elementToExpression))
+        });
+    }
+
     export function areEqual(a: Bundle, b: Bundle) {
         if (a.elements.length !== b.elements.length) return false
         for (let i = 0, il = a.elements.length; i < il; ++i) {

src/mol-model/structure/structure/element/location.ts

@@ -7,6 +7,7 @@
 
 import { ElementIndex } from '../../model';
 import Unit from '../unit';
+import { Vec3 } from '../../../../mol-math/linear-algebra';
 
 export { Location }
 
@@ -18,7 +19,7 @@ interface Location<U = Unit> {
 }
 
 namespace Location {
-    export function create(unit?: Unit, element?: ElementIndex): Location {
+    export function create<U extends Unit>(unit?: U, element?: ElementIndex): Location<U> {
         return { kind: 'element-location', unit: unit!, element: element || (0 as ElementIndex) };
     }
 
@@ -37,4 +38,11 @@ namespace Location {
     export function is(x: any): x is Location {
         return !!x && x.kind === 'element-location';
     }
+
+    const pA = Vec3.zero(), pB = Vec3.zero();
+    export function distance(a: Location, b: Location) {
+        a.unit.conformation.position(a.element, pA);
+        b.unit.conformation.position(b.element, pB);
+        return Vec3.distance(pA, pB);
+    }
 }

src/mol-model/structure/structure/element/loci.ts

@@ -17,8 +17,13 @@ import { sortArray, hashFnv32a, hash2 } from '../../../../mol-data/util';
 import Expression from '../../../../mol-script/language/expression';
 import { ElementIndex } from '../../model';
 import { UnitIndex } from './element';
+import { Location } from './location';
+import { ChainIndex } from '../../model/indexing';
+import { PrincipalAxes } from '../../../../mol-math/linear-algebra/matrix/principal-axes';
+import Matrix from '../../../../mol-math/linear-algebra/matrix/matrix';
+import { NumberArray } from '../../../../mol-util/type-helpers';
 
-/** Represents multiple element index locations */
+/** Represents multiple structure element index locations */
 export interface Loci {
     readonly kind: 'element-loci',
     readonly structure: Structure,
@@ -78,6 +83,29 @@ export namespace Loci {
         return Loci(structure, []);
     }
 
+    export function getFirstLocation(loci: Loci, e?: Location): Location | undefined {
+        if (isEmpty(loci)) return void 0;
+        const unit = loci.elements[0].unit;
+        const element = unit.elements[OrderedSet.getAt(loci.elements[0].indices, 0)];
+        if (e) {
+            e.unit = loci.elements[0].unit;
+            e.element = element;
+            return e;
+        }
+        return Location.create(unit, element);
+    }
+
+    export function toStructure(loci: Loci): Structure {
+        const units: Unit[] = []
+        for (const e of loci.elements) {
+            const { unit, indices } = e
+            const elements = new Int32Array(OrderedSet.size(indices))
+            OrderedSet.forEach(indices, (v, i) => elements[i] = unit.elements[v])
+            units.push(unit.getChild(SortedArray.ofSortedArray(elements)))
+        }
+        return Structure.create(units, { parent: loci.structure.parent })
+    }
+
     export function remap(loci: Loci, structure: Structure): Loci {
         if (structure === loci.structure) return loci
 
@@ -176,13 +204,38 @@ export namespace Loci {
         return false;
     }
 
-    export function extendToWholeResidues(loci: Loci): Loci {
+    /** Check if second loci is a subset of the first */
+    export function isSubset(xs: Loci, ys: Loci): boolean {
+        if (Loci.isEmpty(xs)) return Loci.isEmpty(ys);
+
+        const map = new Map<number, OrderedSet<UnitIndex>>();
+
+        for (const e of xs.elements) map.set(e.unit.id, e.indices);
+
+        let isSubset = false;
+        for (const e of ys.elements) {
+            if (!map.has(e.unit.id)) continue;
+            if (!OrderedSet.isSubset(map.get(e.unit.id)!, e.indices)) return false;
+            else isSubset = true;
+        }
+
+        return isSubset;
+    }
+
+    export function extendToWholeResidues(loci: Loci, restrictToConformation?: boolean): Loci {
         const elements: Loci['elements'][0][] = [];
+        const residueAltIds = new Set<string>()
 
         for (const lociElement of loci.elements) {
+            if (isWholeUnit(lociElement)) {
+                elements[elements.length] = lociElement;
+                continue;
+            }
+
             if (lociElement.unit.kind === Unit.Kind.Atomic) {
                 const unitElements = lociElement.unit.elements;
                 const h = lociElement.unit.model.atomicHierarchy;
+                const { label_alt_id } = lociElement.unit.model.atomicHierarchy.atoms;
 
                 const { index: residueIndex, offsets: residueOffsets } = h.residueAtomSegments;
 
@@ -190,15 +243,26 @@ export namespace Loci {
                 const indices = lociElement.indices, len = OrderedSet.size(indices);
                 let i = 0;
                 while (i < len) {
-                    const rI = residueIndex[unitElements[OrderedSet.getAt(indices, i)]];
+                    residueAltIds.clear()
+                    const eI = unitElements[OrderedSet.getAt(indices, i)]
+                    const rI = residueIndex[eI];
+                    residueAltIds.add(label_alt_id.value(eI))
                     i++;
-                    while (i < len && residueIndex[unitElements[OrderedSet.getAt(indices, i)]] === rI) {
+                    while (i < len) {
+                        const eI = unitElements[OrderedSet.getAt(indices, i)]
+                        if (residueIndex[eI] !== rI) break;
+                        residueAltIds.add(label_alt_id.value(eI))
                         i++;
                     }
-
+                    const hasSharedAltId = residueAltIds.has('')
                     for (let j = residueOffsets[rI], _j = residueOffsets[rI + 1]; j < _j; j++) {
                         const idx = OrderedSet.indexOf(unitElements, j);
-                        if (idx >= 0) newIndices[newIndices.length] = idx as UnitIndex;
+                        if (idx >= 0) {
+                            const altId = label_alt_id.value(j)
+                            if (!restrictToConformation || hasSharedAltId || !altId || residueAltIds.has(altId)) {
+                                newIndices[newIndices.length] = idx as UnitIndex;
+                            }
+                        }
                     }
                 }
 
@@ -220,44 +284,103 @@ export namespace Loci {
         }
     }
 
+    function isWholeUnit(element: Loci['elements'][0]) {
+        return element.unit.elements.length === OrderedSet.size(element.indices);
+    }
+
+    function makeIndexSet(newIndices: number[]): OrderedSet<UnitIndex> {
+        if (newIndices.length > 12 && newIndices[newIndices.length - 1] - newIndices[0] === newIndices.length - 1) {
+            return Interval.ofRange(newIndices[0], newIndices[newIndices.length - 1])
+        } else {
+            return SortedArray.ofSortedArray(newIndices)
+        }
+    }
+
+    function collectChains(unit: Unit, chainIndices: Set<ChainIndex>, elements: Loci['elements'][0][]) {
+        const { index } = getChainSegments(unit);
+        const xs = unit.elements;
+        let size = 0;
+        for (let i = 0 as UnitIndex, _i = xs.length; i < _i; i++) {
+            const eI = xs[i];
+            const cI = index[eI];
+            if (!chainIndices.has(cI)) continue;
+            size++;
+        }
+
+        if (size === unit.elements.length) {
+            elements[elements.length] = { unit, indices: Interval.ofBounds(0, size) };
+            return;
+        }
+
+        const newIndices = new Int32Array(size) as any as UnitIndex[];
+        size = 0;
+        for (let i = 0 as UnitIndex, _i = xs.length; i < _i; i++) {
+            const eI = xs[i];
+            const cI = index[eI];
+            if (!chainIndices.has(cI)) continue;
+            newIndices[size++] = i;
+        }
+
+        if (newIndices.length > 0) {
+            elements[elements.length] = { unit, indices: makeIndexSet(newIndices) };
+        }
+    }
+
+    function extendGroupToWholeChains(loci: Loci, start: number, end: number, isPartitioned: boolean, elements: Loci['elements'][0][]) {
+        const { index: chainIndex } = getChainSegments(loci.elements[0].unit);
+
+        const chainIndices = new Set<ChainIndex>();
+
+        for (let lI = start; lI < end; lI++) {
+            const lociElement = loci.elements[lI];
+            const indices = lociElement.indices;
+            const unitElements = lociElement.unit.elements;
+            for (let i = 0, _i = OrderedSet.size(indices); i < _i; i++) {
+                chainIndices.add(chainIndex[unitElements[OrderedSet.getAt(indices, i)]]);
+            }
+        }
+
+        if (isPartitioned) {
+            const baseUnit = loci.elements[0].unit;
+            // TODO: check for accidental quadratic for really large structures (but should be ok).
+            for (const unit of loci.structure.units) {
+                if (!Unit.areSameChainOperatorGroup(unit, baseUnit)) continue;
+                collectChains(unit, chainIndices, elements);
+            }
+        } else {
+            for (let lI = start; lI < end; lI++) {
+                collectChains(loci.elements[lI].unit, chainIndices, elements);
+            }
+        }
+    }
+
     export function extendToWholeChains(loci: Loci): Loci {
         const elements: Loci['elements'][0][] = [];
 
-        for (const lociElement of loci.elements) {
-            const _newIndices: UnitIndex[] = [];
-            const unitElements = lociElement.unit.elements;
-
-            const { index: chainIndex, offsets: chainOffsets } = getChainSegments(lociElement.unit)
-
-            const indices = lociElement.indices, len = OrderedSet.size(indices);
-            let i = 0;
-            while (i < len) {
-                const cI = chainIndex[unitElements[OrderedSet.getAt(indices, i)]];
-                i++;
-                while (i < len && chainIndex[unitElements[OrderedSet.getAt(indices, i)]] === cI) {
+        for (let i = 0, len = loci.elements.length; i < len; i++) {
+            const e = loci.elements[i];
+            if (Unit.Traits.is(e.unit.traits, Unit.Trait.Patitioned)) {
+                const start = i;
+                while (i < len && Unit.areSameChainOperatorGroup(loci.elements[i].unit, e.unit)) {
                     i++;
                 }
-
-                for (let j = chainOffsets[cI], _j = chainOffsets[cI + 1]; j < _j; j++) {
-                    const idx = OrderedSet.indexOf(unitElements, j);
-                    if (idx >= 0) _newIndices[_newIndices.length] = idx as UnitIndex;
+                const end = i;
+                i--;
+                extendGroupToWholeChains(loci, start, end, true, elements);
+            } else {
+                if (isWholeUnit(e)) {
+                    elements[elements.length] = e;
+                } else {
+                    extendGroupToWholeChains(loci, i, i + 1, false, elements);
                 }
             }
-
-            let newIndices: OrderedSet<UnitIndex>
-            if (_newIndices.length > 12 && _newIndices[_newIndices.length - 1] - _newIndices[0] === _newIndices.length - 1) {
-                newIndices = Interval.ofRange(_newIndices[0], _newIndices[_newIndices.length - 1])
-            } else {
-                newIndices = SortedArray.ofSortedArray(_newIndices)
-            }
-
-            elements[elements.length] = { unit: lociElement.unit, indices: newIndices };
         }
 
         return Loci(loci.structure, elements);
     }
 
-    const boundaryHelper = new BoundaryHelper(), tempPos = Vec3.zero();
+    const boundaryHelper = new BoundaryHelper();
+    const tempPosBoundary = Vec3.zero();
     export function getBoundary(loci: Loci): Boundary {
         boundaryHelper.reset(0);
 
@@ -267,8 +390,8 @@ export namespace Loci {
             const { elements } = e.unit;
             for (let i = 0, _i = OrderedSet.size(indices); i < _i; i++) {
                 const eI = elements[OrderedSet.getAt(indices, i)];
-                pos(eI, tempPos);
-                boundaryHelper.boundaryStep(tempPos, r(eI));
+                pos(eI, tempPosBoundary);
+                boundaryHelper.boundaryStep(tempPosBoundary, r(eI));
             }
         }
         boundaryHelper.finishBoundaryStep();
@@ -278,14 +401,38 @@ export namespace Loci {
             const { elements } = e.unit;
             for (let i = 0, _i = OrderedSet.size(indices); i < _i; i++) {
                 const eI = elements[OrderedSet.getAt(indices, i)];
-                pos(eI, tempPos);
-                boundaryHelper.extendStep(tempPos, r(eI));
+                pos(eI, tempPosBoundary);
+                boundaryHelper.extendStep(tempPosBoundary, r(eI));
             }
         }
 
         return { box: boundaryHelper.getBox(), sphere: boundaryHelper.getSphere() };
     }
 
+    const tempPos = Vec3.zero();
+    export function toPositionsArray(loci: Loci, positions: NumberArray, offset = 0) {
+        let m = offset
+        for (const e of loci.elements) {
+            const { indices } = e
+            const pos = e.unit.conformation.position
+            const { elements } = e.unit
+            const indexCount = OrderedSet.size(indices)
+            for (let i = 0; i < indexCount; i++) {
+                const eI = elements[OrderedSet.getAt(indices, i)]
+                pos(eI, tempPos)
+                Vec3.toArray(tempPos, positions, m + i * 3)
+            }
+            m += indexCount * 3
+        }
+        return positions
+    }
+
+    export function getPrincipalAxes(loci: Loci): PrincipalAxes {
+        const elementCount = size(loci)
+        const positions = toPositionsArray(loci, new Float32Array(3 * elementCount))
+        return PrincipalAxes.ofPoints(Matrix.fromArray(positions, 3, elementCount))
+    }
+
     function sourceIndex(unit: Unit, element: ElementIndex) {
         return Unit.isAtomic(unit)
             ? unit.model.atomicHierarchy.atoms.sourceIndex.value(element)

src/mol-model/structure/structure/element/stats.ts

@@ -2,41 +2,67 @@
  * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author David Sehnal <david.sehnal@gmail.com>
  */
 
 import { OrderedSet } from '../../../../mol-data/int';
 import Unit from '../unit';
 import { Loci } from './loci';
 import { Location } from './location';
-
+import { ChainIndex } from '../../model/indexing';
 
 export interface Stats {
     elementCount: number
+    conformationCount: number
     residueCount: number
+    chainCount: number
     unitCount: number
+    structureCount: number
 
     firstElementLoc: Location
+    firstConformationLoc: Location
     firstResidueLoc: Location
+    firstChainLoc: Location
     firstUnitLoc: Location
+    firstStructureLoc: Location
 }
 
 export namespace Stats {
     export function create(): Stats {
         return {
             elementCount: 0,
+            conformationCount: 0,
             residueCount: 0,
+            chainCount: 0,
             unitCount: 0,
+            structureCount: 0,
 
             firstElementLoc: Location.create(),
+            firstConformationLoc: Location.create(),
             firstResidueLoc: Location.create(),
+            firstChainLoc: Location.create(),
             firstUnitLoc: Location.create(),
+            firstStructureLoc: Location.create(),
         }
     }
 
+    function addCountHelper<K>(map: Map<K, number>, key: K, inc: number) {
+        const count = map.get(key) || 0
+        map.set(key, count + inc)
+    }
+
     function handleElement(stats: Stats, element: Loci['elements'][0]) {
         const { indices, unit } = element
         const { elements } = unit
         const size = OrderedSet.size(indices)
+
+        const lociResidueAltIdCounts = new Map<string, number>()
+        const residueAltIdCounts = new Map<string, number>()
+
+        if (size > 0) {
+            Location.set(stats.firstElementLoc, unit, elements[OrderedSet.start(indices)])
+        }
+
         if (size === 1) {
             stats.elementCount += 1
             if (stats.elementCount === 1) {
@@ -50,38 +76,58 @@ export namespace Stats {
         } else {
             if (Unit.isAtomic(unit)) {
                 const { index, offsets } = unit.model.atomicHierarchy.residueAtomSegments
+                const { label_alt_id } = unit.model.atomicHierarchy.atoms;
                 let i = 0
                 while (i < size) {
+                    lociResidueAltIdCounts.clear()
+                    let j = 0
                     const eI = elements[OrderedSet.getAt(indices, i)]
                     const rI = index[eI]
-                    if (offsets[rI] !== eI) {
-                        // partial residue, start missing
+                    addCountHelper(lociResidueAltIdCounts, label_alt_id.value(eI), 1)
+                    ++i
+                    ++j
+                    while (i < size) {
+                        const eI = elements[OrderedSet.getAt(indices, i)]
+                        if (index[eI] !== rI) break
+                        addCountHelper(lociResidueAltIdCounts, label_alt_id.value(eI), 1)
                         ++i
-                        stats.elementCount += 1
-                        while (i < size && index[elements[OrderedSet.getAt(indices, i)]] === rI) {
-                            ++i
-                            stats.elementCount += 1
+                        ++j
+                    }
+
+                    if (offsets[rI + 1] - offsets[rI] === j) {
+                        // full residue
+                        stats.residueCount += 1
+                        if (stats.residueCount === 1) {
+                            Location.set(stats.firstResidueLoc, unit, offsets[rI])
                         }
                     } else {
-                        ++i
-                        while (i < size && index[elements[OrderedSet.getAt(indices, i)]] === rI) {
-                            ++i
+                        // partial residue
+                        residueAltIdCounts.clear()
+                        for (let l = offsets[rI], _l = offsets[rI + 1]; l < _l; ++l) {
+                            addCountHelper(residueAltIdCounts, label_alt_id.value(l), 1)
                         }
-
-                        if (offsets[rI + 1] - 1 === elements[OrderedSet.getAt(indices, i - 1)]) {
-                            // full residue
-                            stats.residueCount += 1
-                            if (stats.residueCount === 1) {
-                                Location.set(stats.firstResidueLoc, unit, elements[OrderedSet.start(indices)])
-                            }
-                        } else {
-                            // partial residue, end missing
-                            stats.elementCount += offsets[rI + 1] - 1 - elements[OrderedSet.getAt(indices, i - 1)]
+                        // check if shared atom count match
+                        if (residueAltIdCounts.get('') === lociResidueAltIdCounts.get('')) {
+                            lociResidueAltIdCounts.forEach((v, k) => {
+                                if (residueAltIdCounts.get(k) !== v) return
+                                if (k !== '') {
+                                    stats.conformationCount += 1
+                                    if (stats.conformationCount === 1) {
+                                        for (let l = offsets[rI], _l = offsets[rI + 1]; l < _l; ++l) {
+                                            if (k === label_alt_id.value(l)) {
+                                                Location.set(stats.firstConformationLoc, unit, l)
+                                                break
+                                            }
+                                        }
+                                    }
+                                }
+                                j -= v
+                            })
                         }
+                        stats.elementCount += j
                     }
                 }
             } else {
-                // TODO
                 stats.elementCount += size
                 if (stats.elementCount === 1) {
                     Location.set(stats.firstElementLoc, unit, elements[OrderedSet.start(indices)])
@@ -90,14 +136,194 @@ export namespace Stats {
         }
     }
 
+    function handleUnitChainsSimple(stats: Stats, element: Loci['elements'][0]) {
+        const { indices, unit } = element;
+        const size = OrderedSet.size(indices);
+        if (size === 0) return;
+
+        const { elements } = unit;
+
+        if (!Unit.Traits.is(unit.traits, Unit.Trait.MultiChain)) {
+            if (size === elements.length) {
+                stats.chainCount += 1;
+                if (stats.chainCount === 1) {
+                    Location.set(stats.firstChainLoc, unit, elements[OrderedSet.start(indices)]);
+                }
+            }
+            return;
+        }
+
+        const segments = Unit.isAtomic(unit)
+            ? unit.model.atomicHierarchy.chainAtomSegments
+                : Unit.isSpheres(unit)
+            ? unit.model.coarseHierarchy.spheres.chainElementSegments
+                : Unit.isGaussians(unit)
+            ? unit.model.coarseHierarchy.gaussians.chainElementSegments
+                : void 0;
+
+        if (!segments) {
+            console.warn('StructureElement loci stats: unknown unit type');
+            return;
+        }
+
+        const { index, offsets } = segments;
+        let i = 0;
+        while (i < size) {
+            let j = 0
+            const eI = elements[OrderedSet.getAt(indices, i)];
+            const cI = index[eI];
+            ++i;
+            ++j;
+            while (i < size) {
+                const eI = elements[OrderedSet.getAt(indices, i)];
+                if (index[eI] !== cI) break;
+                ++i;
+                ++j;
+            }
+
+            if (offsets[cI + 1] - offsets[cI] === j) {
+                // full chain
+                stats.chainCount += 1;
+                if (stats.chainCount === 1) {
+                    Location.set(stats.firstChainLoc, unit, elements[offsets[cI]]);
+                }
+            }
+        }
+    }
+
+    function handleUnitChainsPartitioned(stats: Stats, lociElements: Loci['elements'], start: number, end: number) {
+        let element = lociElements[start];
+
+        // all the elements have the same model since they are part of the same group so this is ok.
+        const segments = Unit.isAtomic(element.unit)
+            ? element.unit.model.atomicHierarchy.chainAtomSegments
+                : Unit.isSpheres(element.unit)
+            ? element.unit.model.coarseHierarchy.spheres.chainElementSegments
+                : Unit.isGaussians(element.unit)
+            ? element.unit.model.coarseHierarchy.gaussians.chainElementSegments
+                : void 0;
+
+        if (!segments) {
+            console.warn('StructureElement loci stats: unknown unit type');
+            return;
+        }
+
+        const { index, offsets } = segments;
+
+        const chainCounts = new Map<ChainIndex, number>();
+
+        for (let elIndex = start; elIndex < end; elIndex++) {
+            element = lociElements[elIndex];
+
+            const { indices, unit } = element
+            const size = OrderedSet.size(indices);
+            if (size === 0) continue;
+
+            const { elements } = unit;
+
+            if (!Unit.Traits.is(unit.traits, Unit.Trait.MultiChain)) {
+                const eI = elements[OrderedSet.start(indices)];
+                addCountHelper(chainCounts, index[eI], elements.length);
+                continue;
+            }
+
+            let i = 0;
+            while (i < size) {
+                let j = 0
+                const eI = elements[OrderedSet.getAt(indices, i)];
+                const cI = index[eI];
+                ++i;
+                ++j;
+                while (i < size) {
+                    const eI = elements[OrderedSet.getAt(indices, i)];
+                    if (index[eI] !== cI) break;
+                    ++i;
+                    ++j;
+                }
+
+                addCountHelper(chainCounts, cI, j);
+            }
+        }
+
+        let firstCI = -1;
+        chainCounts.forEach((count, cI) => {
+            if (offsets[cI + 1] - offsets[cI] === count) {
+                // full chain
+                stats.chainCount += 1;
+                if (stats.chainCount === 1) {
+                    firstCI = cI;
+                }
+            }
+        });
+
+        if (firstCI < 0) return;
+
+        for (let elIndex = start; elIndex < end; elIndex++) {
+            element = lociElements[elIndex];
+
+            const { indices, unit } = element
+            const size = OrderedSet.size(indices);
+            if (size === 0) continue;
+
+            const { elements } = unit;
+
+            let i = 0;
+            while (i < size) {
+                const eI = elements[OrderedSet.getAt(indices, i)];
+                const cI = index[eI];
+                if (cI === firstCI) {
+                    Location.set(stats.firstChainLoc, unit, eI);
+                    return;
+                }
+            }
+        }
+    }
+
     export function ofLoci(loci: Loci) {
         const stats = create()
-        if (!Loci.isEmpty(loci)) {
-            for (const e of loci.elements) handleElement(stats, e)
+        if (Loci.isEmpty(loci)) return stats
+
+        let hasPartitions = false;
+        if (Loci.isWholeStructure(loci)) {
+            stats.structureCount += 1
+            if (stats.structureCount === 1) {
+                const { unit, indices } = loci.elements[0]
+                Location.set(stats.firstStructureLoc, unit, unit.elements[OrderedSet.min(indices)])
+            }
+        } else {
+            for (const e of loci.elements) {
+                handleElement(stats, e)
+                if (!Unit.Traits.is(e.unit.traits, Unit.Trait.Patitioned)) {
+                    handleUnitChainsSimple(stats, e);
+                } else {
+                    hasPartitions = true;
+                }
+            }
         }
+
+        if (hasPartitions) {
+            for (let i = 0, len = loci.elements.length; i < len; i++) {
+                const e = loci.elements[i];
+                if (!Unit.Traits.is(e.unit.traits, Unit.Trait.Patitioned)) continue;
+
+                const start = i;
+                while (i < len && Unit.areSameChainOperatorGroup(loci.elements[i].unit, e.unit)) {
+                    i++;
+                }
+                const end = i;
+                i--;
+                if (end - start === 1) {
+                    handleUnitChainsSimple(stats, e);
+                } else {
+                    handleUnitChainsPartitioned(stats, loci.elements, start, end);
+                }
+            }
+        }
+
         return stats
     }
 
+    /** Adds counts of two Stats objects together, assumes they describe different structures */
     export function add(out: Stats, a: Stats, b: Stats) {
         if (a.elementCount === 1 && b.elementCount === 0) {
             Location.copy(out.firstElementLoc, a.firstElementLoc)
@@ -105,21 +331,42 @@ export namespace Stats {
             Location.copy(out.firstElementLoc, b.firstElementLoc)
         }
 
+        if (a.conformationCount === 1 && b.conformationCount === 0) {
+            Location.copy(out.firstConformationLoc, a.firstConformationLoc)
+        } else if (a.conformationCount === 0 && b.conformationCount === 1) {
+            Location.copy(out.firstConformationLoc, b.firstConformationLoc)
+        }
+
         if (a.residueCount === 1 && b.residueCount === 0) {
             Location.copy(out.firstResidueLoc, a.firstResidueLoc)
         } else if (a.residueCount === 0 && b.residueCount === 1) {
             Location.copy(out.firstResidueLoc, b.firstResidueLoc)
         }
 
+        if (a.chainCount === 1 && b.chainCount === 0) {
+            Location.copy(out.firstChainLoc, a.firstChainLoc)
+        } else if (a.chainCount === 0 && b.chainCount === 1) {
+            Location.copy(out.firstChainLoc, b.firstChainLoc)
+        }
+
         if (a.unitCount === 1 && b.unitCount === 0) {
             Location.copy(out.firstUnitLoc, a.firstUnitLoc)
         } else if (a.unitCount === 0 && b.unitCount === 1) {
             Location.copy(out.firstUnitLoc, b.firstUnitLoc)
         }
 
+        if (a.structureCount === 1 && b.structureCount === 0) {
+            Location.copy(out.firstStructureLoc, a.firstStructureLoc)
+        } else if (a.structureCount === 0 && b.structureCount === 1) {
+            Location.copy(out.firstStructureLoc, b.firstStructureLoc)
+        }
+
         out.elementCount = a.elementCount + b.elementCount
+        out.conformationCount = a.conformationCount + b.conformationCount
         out.residueCount = a.residueCount + b.residueCount
+        out.chainCount = a.chainCount + b.chainCount
         out.unitCount = a.unitCount + b.unitCount
+        out.structureCount = a.structureCount + b.structureCount
         return out
     }
 }

src/mol-model/structure/structure/properties.ts

@@ -100,6 +100,7 @@ const residue = {
         const id = compId(l)
         return l.unit.model.properties.modifiedResidues.parentId.get(id) || id
     }),
+    isNonStandard: p(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.properties.chemicalComponentMap.get(compId(l))!.mon_nstd_flag[0] !== 'y'),
     hasMicroheterogeneity: p(hasMicroheterogeneity),
     microheterogeneityCompIds: p(microheterogeneityCompIds),
     secondary_structure_type: p(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.properties.secondaryStructure.type[l.unit.residueIndex[l.element]]),
@@ -163,6 +164,8 @@ const entity = {
 
 const unit = {
     id: p(l => l.unit.id),
+    chainGroupId: p(l => l.unit.chainGroupId),
+    multiChain: p(l => Unit.Traits.is(l.unit.traits, Unit.Trait.MultiChain)),
     object_primitive: p(l => l.unit.objectPrimitive),
     operator_name: p(l => l.unit.conformation.operator.name),
     model_index: p(l => l.unit.model.modelNum),

src/mol-model/structure/structure/structure.ts

@@ -277,10 +277,12 @@ class Structure {
         return this._props.model;
     }
 
+    /** The master-model, other models can have links to it  */
     get masterModel(): Model | undefined {
         return this._props.masterModel
     }
 
+    /** A representative model, e.g. the first model of a trajectory */
     get representativeModel(): Model | undefined {
         return this._props.representativeModel
     }
@@ -505,12 +507,12 @@ namespace Structure {
         return { kind: 'structure-loci', structure };
     }
 
-    export function toStructureElementLoci(loci: Loci): StructureElement.Loci {
+    export function toStructureElementLoci(structure: Structure): StructureElement.Loci {
         const elements: StructureElement.Loci['elements'][0][] = []
-        for (const unit of loci.structure.units) {
+        for (const unit of structure.units) {
             elements.push({ unit, indices: Interval.ofBounds(0, unit.elements.length) })
         }
-        return StructureElement.Loci(loci.structure, elements);
+        return StructureElement.Loci(structure, elements);
     }
 
     export function isLoci(x: any): x is Loci {
@@ -525,6 +527,11 @@ namespace Structure {
         return loci.structure.isEmpty
     }
 
+    export function remapLoci(loci: Loci, structure: Structure) {
+        if (structure === loci.structure) return loci
+        return Loci(structure)
+    }
+
     export function create(units: ReadonlyArray<Unit>, props?: Props): Structure {
         return new Structure(units, props);
     }
@@ -540,7 +547,8 @@ namespace Structure {
             for (let j = 0, jl = structure.units.length; j < jl; ++j) {
                 const u = structure.units[j]
                 const invariantId = u.invariantId + count
-                const newUnit = Unit.create(units.length, invariantId, u.kind, u.model, u.conformation.operator, u.elements)
+                const chainGroupId = u.chainGroupId + count
+                const newUnit = Unit.create(units.length, invariantId, chainGroupId, u.traits, u.kind, u.model, u.conformation.operator, u.elements)
                 units.push(newUnit)
             }
             count = units.length
@@ -553,10 +561,12 @@ namespace Structure {
      * Construct a Structure from a model.
      *
      * Generally, a single unit corresponds to a single chain, with the exception
-     * of consecutive "single atom chains" with same entity id.
+     * of consecutive "single atom chains" with same entity_id and same auth_asym_id.
      */
     export function ofModel(model: Model): Structure {
         const chains = model.atomicHierarchy.chainAtomSegments;
+        const { index } = model.atomicHierarchy
+        const { auth_asym_id } = model.atomicHierarchy.chains
         const builder = new StructureBuilder({ label: model.label });
 
         for (let c = 0 as ChainIndex; c < chains.count; c++) {
@@ -566,27 +576,34 @@ namespace Structure {
             // note that it assumes there are no "zero atom residues"
             let singleAtomResidues = AtomicHierarchy.chainResidueCount(model.atomicHierarchy, c) === chains.offsets[c + 1] - chains.offsets[c]
 
-            // merge all consecutive "single atom chains" with same entity id
+            // merge all consecutive "single atom chains" with same entity_id and same auth_asym_id
+            let multiChain = false
             while (c + 1 < chains.count
                 && chains.offsets[c + 1] - chains.offsets[c] === 1
                 && chains.offsets[c + 2] - chains.offsets[c + 1] === 1
             ) {
-                c++;
                 singleAtomResidues = true
-                const e1 = model.atomicHierarchy.index.getEntityFromChain(c);
-                const e2 = model.atomicHierarchy.index.getEntityFromChain(c + 1 as ChainIndex);
+                const e1 = index.getEntityFromChain(c);
+                const e2 = index.getEntityFromChain(c + 1 as ChainIndex);
                 if (e1 !== e2) break
+
+                const a1 = auth_asym_id.value(c);
+                const a2 = auth_asym_id.value(c + 1);
+                if (a1 !== a2) break
+
+                multiChain = true
+                c++;
             }
 
             const elements = SortedArray.ofBounds(start as ElementIndex, chains.offsets[c + 1] as ElementIndex);
 
             if (singleAtomResidues) {
-                partitionAtomicUnitByAtom(model, elements, builder);
+                partitionAtomicUnitByAtom(model, elements, builder, multiChain);
             } else if (elements.length > 200000 || isWaterChain(model, c)) {
                 // split up very large chains e.g. lipid bilayers, micelles or water with explicit H
-                partitionAtomicUnitByResidue(model, elements, builder);
+                partitionAtomicUnitByResidue(model, elements, builder, multiChain);
             } else {
-                builder.addUnit(Unit.Kind.Atomic, model, SymmetryOperator.Default, elements);
+                builder.addUnit(Unit.Kind.Atomic, model, SymmetryOperator.Default, elements, multiChain ? Unit.Trait.MultiChain : Unit.Trait.None);
             }
         }
 
@@ -608,23 +625,27 @@ namespace Structure {
         return model.entities.data.type.value(e) === 'water';
     }
 
-    function partitionAtomicUnitByAtom(model: Model, indices: SortedArray, builder: StructureBuilder) {
+    function partitionAtomicUnitByAtom(model: Model, indices: SortedArray, builder: StructureBuilder, multiChain: boolean) {
         const { x, y, z } = model.atomicConformation;
         const lookup = GridLookup3D({ x, y, z, indices }, 8192);
         const { offset, count, array } = lookup.buckets;
 
+        const traits = (multiChain ? Unit.Trait.MultiChain : Unit.Trait.None) | (offset.length > 1 ? Unit.Trait.Patitioned : Unit.Trait.None);
+
+        builder.beginChainGroup();
         for (let i = 0, _i = offset.length; i < _i; i++) {
             const start = offset[i];
             const set = new Int32Array(count[i]);
             for (let j = 0, _j = count[i]; j < _j; j++) {
                 set[j] = indices[array[start + j]];
             }
-            builder.addUnit(Unit.Kind.Atomic, model, SymmetryOperator.Default, SortedArray.ofSortedArray(set));
+            builder.addUnit(Unit.Kind.Atomic, model, SymmetryOperator.Default, SortedArray.ofSortedArray(set), traits);
         }
+        builder.endChainGroup();
     }
 
     // keeps atoms of residues together
-    function partitionAtomicUnitByResidue(model: Model, indices: SortedArray, builder: StructureBuilder) {
+    function partitionAtomicUnitByResidue(model: Model, indices: SortedArray, builder: StructureBuilder, multiChain: boolean) {
         const { residueAtomSegments } = model.atomicHierarchy
 
         const startIndices: number[] = []
@@ -644,6 +665,9 @@ namespace Structure {
         const lookup = GridLookup3D({ x, y, z, indices: SortedArray.ofSortedArray(startIndices) }, gridCellCount);
         const { offset, count, array } = lookup.buckets;
 
+        const traits = (multiChain ? Unit.Trait.MultiChain : Unit.Trait.None) | (offset.length > 1 ? Unit.Trait.Patitioned : Unit.Trait.None);
+
+        builder.beginChainGroup();
         for (let i = 0, _i = offset.length; i < _i; i++) {
             const start = offset[i];
             const set: number[] = [];
@@ -653,15 +677,16 @@ namespace Structure {
                     set[set.length] = l;
                 }
             }
-            builder.addUnit(Unit.Kind.Atomic, model, SymmetryOperator.Default, SortedArray.ofSortedArray(new Int32Array(set)));
+            builder.addUnit(Unit.Kind.Atomic, model, SymmetryOperator.Default, SortedArray.ofSortedArray(new Int32Array(set)), traits);
         }
+        builder.endChainGroup();
     }
 
     function addCoarseUnits(builder: StructureBuilder, model: Model, elements: CoarseElements, kind: Unit.Kind) {
         const { chainElementSegments } = elements;
         for (let cI = 0; cI < chainElementSegments.count; cI++) {
             const elements = SortedArray.ofBounds<ElementIndex>(chainElementSegments.offsets[cI], chainElementSegments.offsets[cI + 1]);
-            builder.addUnit(kind, model, SymmetryOperator.Default, elements);
+            builder.addUnit(kind, model, SymmetryOperator.Default, elements, Unit.Trait.None);
         }
     }
 
@@ -685,9 +710,22 @@ namespace Structure {
         private units: Unit[] = [];
         private invariantId = idFactory()
 
-        addUnit(kind: Unit.Kind, model: Model, operator: SymmetryOperator, elements: StructureElement.Set, invariantId?: number): Unit {
+        private chainGroupId = -1;
+        private inChainGroup = false;
+
+        beginChainGroup() {
+            this.chainGroupId++;
+            this.inChainGroup = true;
+        }
+
+        endChainGroup() {
+            this.inChainGroup = false;
+        }
+
+        addUnit(kind: Unit.Kind, model: Model, operator: SymmetryOperator, elements: StructureElement.Set, traits: Unit.Traits, invariantId?: number): Unit {
             if (invariantId === undefined) invariantId = this.invariantId()
-            const unit = Unit.create(this.units.length, invariantId, kind, model, operator, elements);
+            const chainGroupId = this.inChainGroup ? this.chainGroupId : ++this.chainGroupId;
+            const unit = Unit.create(this.units.length, invariantId, chainGroupId, traits, kind, model, operator, elements);
             this.units.push(unit);
             return unit;
         }

src/mol-model/structure/structure/unit.ts

@@ -10,7 +10,7 @@ import { Model } from '../model'
 import { GridLookup3D, Lookup3D } from '../../../mol-math/geometry'
 import { IntraUnitLinks, computeIntraUnitBonds } from './unit/links'
 import { CoarseElements, CoarseSphereConformation, CoarseGaussianConformation } from '../model/properties/coarse';
-import { ValueRef } from '../../../mol-util';
+import { ValueRef, BitFlags } from '../../../mol-util';
 import { UnitRings } from './unit/rings';
 import StructureElement from './element'
 import { ChainIndex, ResidueIndex, ElementIndex } from '../model/indexing';
@@ -33,11 +33,11 @@ namespace Unit {
     export function isSpheres(u: Unit): u is Spheres { return u.kind === Kind.Spheres; }
     export function isGaussians(u: Unit): u is Gaussians { return u.kind === Kind.Gaussians; }
 
-    export function create(id: number, invariantId: number, kind: Kind, model: Model, operator: SymmetryOperator, elements: StructureElement.Set): Unit {
+    export function create(id: number, invariantId: number, chainGroupId: number, traits: Traits, kind: Kind, model: Model, operator: SymmetryOperator, elements: StructureElement.Set): Unit {
         switch (kind) {
-            case Kind.Atomic: return new Atomic(id, invariantId, model, elements, SymmetryOperator.createMapping(operator, model.atomicConformation, void 0), AtomicProperties());
-            case Kind.Spheres: return createCoarse(id, invariantId, model, Kind.Spheres, elements, SymmetryOperator.createMapping(operator, model.coarseConformation.spheres, getSphereRadiusFunc(model)), CoarseProperties());
-            case Kind.Gaussians: return createCoarse(id, invariantId, model, Kind.Gaussians, elements, SymmetryOperator.createMapping(operator, model.coarseConformation.gaussians, getGaussianRadiusFunc(model)), CoarseProperties());
+            case Kind.Atomic: return new Atomic(id, invariantId, chainGroupId, traits, model, elements, SymmetryOperator.createMapping(operator, model.atomicConformation, void 0), AtomicProperties());
+            case Kind.Spheres: return createCoarse(id, invariantId, chainGroupId, traits, model, Kind.Spheres, elements, SymmetryOperator.createMapping(operator, model.coarseConformation.spheres, getSphereRadiusFunc(model)), CoarseProperties());
+            case Kind.Gaussians: return createCoarse(id, invariantId, chainGroupId, traits, model, Kind.Gaussians, elements, SymmetryOperator.createMapping(operator, model.coarseConformation.gaussians, getGaussianRadiusFunc(model)), CoarseProperties());
         }
     }
 
@@ -94,10 +94,23 @@ namespace Unit {
         return hash2(u.invariantId, SortedArray.hashCode(u.elements));
     }
 
+    export type Traits = BitFlags<Trait>
+    export const enum Trait {
+        None = 0x0,
+        MultiChain = 0x1,
+        Patitioned = 0x2
+    }
+    export namespace Traits {
+        export const is: (t: Traits, f: Trait) => boolean = BitFlags.has
+        export const create: (f: Trait) => Traits = BitFlags.create
+    }
+
     export interface Base {
         readonly id: number,
         /** invariant ID stays the same even if the Operator/conformation changes. */
         readonly invariantId: number,
+        readonly chainGroupId: number,
+        readonly traits: Traits,
         readonly elements: StructureElement.Set,
         readonly model: Model,
         readonly conformation: SymmetryOperator.ArrayMapping<ElementIndex>,
@@ -139,24 +152,28 @@ namespace Unit {
 
         readonly id: number;
         readonly invariantId: number;
+        /** Used to identify a single chain split into multiple units. */
+        readonly chainGroupId: number;
+        readonly traits: Traits;
         readonly elements: StructureElement.Set;
         readonly model: Model;
         readonly conformation: SymmetryOperator.ArrayMapping<ElementIndex>;
 
-        /** Reference some commonly accessed things for faster access. */
+        /** Reference `residueIndex` from `model` for faster access. */
         readonly residueIndex: ArrayLike<ResidueIndex>;
+        /** Reference `chainIndex` from `model` for faster access. */
         readonly chainIndex: ArrayLike<ChainIndex>;
 
         private props: AtomicProperties;
 
         getChild(elements: StructureElement.Set): Unit {
             if (elements.length === this.elements.length) return this;
-            return new Atomic(this.id, this.invariantId, this.model, elements, this.conformation, AtomicProperties());
+            return new Atomic(this.id, this.invariantId, this.chainGroupId, this.traits, this.model, elements, this.conformation, AtomicProperties());
         }
 
         applyOperator(id: number, operator: SymmetryOperator, dontCompose = false): Unit {
             const op = dontCompose ? operator : SymmetryOperator.compose(this.conformation.operator, operator);
-            return new Atomic(id, this.invariantId, this.model, this.elements, SymmetryOperator.createMapping(op, this.model.atomicConformation, this.conformation.r), this.props);
+            return new Atomic(id, this.invariantId, this.chainGroupId, this.traits, this.model, this.elements, SymmetryOperator.createMapping(op, this.model.atomicConformation, this.conformation.r), this.props);
         }
 
         get lookup3d() {
@@ -220,9 +237,11 @@ namespace Unit {
             return this.model.atomicHierarchy.residueAtomSegments.index[this.elements[elementIndex]];
         }
 
-        constructor(id: number, invariantId: number, model: Model, elements: StructureElement.Set, conformation: SymmetryOperator.ArrayMapping<ElementIndex>, props: AtomicProperties) {
+        constructor(id: number, invariantId: number, chainGroupId: number, traits: Traits, model: Model, elements: StructureElement.Set, conformation: SymmetryOperator.ArrayMapping<ElementIndex>, props: AtomicProperties) {
             this.id = id;
             this.invariantId = invariantId;
+            this.chainGroupId = chainGroupId;
+            this.traits = traits;
             this.model = model;
             this.elements = elements;
             this.conformation = conformation;
@@ -263,6 +282,8 @@ namespace Unit {
 
         readonly id: number;
         readonly invariantId: number;
+        readonly chainGroupId: number;
+        readonly traits: Traits;
         readonly elements: StructureElement.Set;
         readonly model: Model;
         readonly conformation: SymmetryOperator.ArrayMapping<ElementIndex>;
@@ -274,12 +295,12 @@ namespace Unit {
 
         getChild(elements: StructureElement.Set): Unit {
             if (elements.length === this.elements.length) return this as any as Unit /** lets call this an ugly temporary hack */;
-            return createCoarse(this.id, this.invariantId, this.model, this.kind, elements, this.conformation, CoarseProperties());
+            return createCoarse(this.id, this.invariantId, this.chainGroupId, this.traits, this.model, this.kind, elements, this.conformation, CoarseProperties());
         }
 
         applyOperator(id: number, operator: SymmetryOperator, dontCompose = false): Unit {
             const op = dontCompose ? operator : SymmetryOperator.compose(this.conformation.operator, operator);
-            const ret = createCoarse(id, this.invariantId, this.model, this.kind, this.elements, SymmetryOperator.createMapping(op, this.getCoarseConformation(), this.conformation.r), this.props);
+            const ret = createCoarse(id, this.invariantId, this.chainGroupId, this.traits, this.model, this.kind, this.elements, SymmetryOperator.createMapping(op, this.getCoarseConformation(), this.conformation.r), this.props);
             // (ret as Coarse<K, C>)._lookup3d = this._lookup3d;
             return ret;
         }
@@ -308,11 +329,13 @@ namespace Unit {
             return this.kind === Kind.Spheres ? this.model.coarseConformation.spheres : this.model.coarseConformation.gaussians;
         }
 
-        constructor(id: number, invariantId: number, model: Model, kind: K, elements: StructureElement.Set, conformation: SymmetryOperator.ArrayMapping<ElementIndex>, props: CoarseProperties) {
+        constructor(id: number, invariantId: number, chainGroupId: number, traits: Traits, model: Model, kind: K, elements: StructureElement.Set, conformation: SymmetryOperator.ArrayMapping<ElementIndex>, props: CoarseProperties) {
             this.kind = kind;
             this.objectPrimitive = kind === Kind.Spheres ? 'sphere' : 'gaussian'
             this.id = id;
             this.invariantId = invariantId;
+            this.chainGroupId = chainGroupId;
+            this.traits = traits;
             this.model = model;
             this.elements = elements;
             this.conformation = conformation;
@@ -336,12 +359,16 @@ namespace Unit {
         };
     }
 
-    function createCoarse<K extends Kind.Gaussians | Kind.Spheres>(id: number, invariantId: number, model: Model, kind: K, elements: StructureElement.Set, conformation: SymmetryOperator.ArrayMapping<ElementIndex>, props: CoarseProperties): Unit {
-        return new Coarse(id, invariantId, model, kind, elements, conformation, props) as any as Unit /** lets call this an ugly temporary hack */;
+    function createCoarse<K extends Kind.Gaussians | Kind.Spheres>(id: number, invariantId: number, chainGroupId: number, traits: Traits, model: Model, kind: K, elements: StructureElement.Set, conformation: SymmetryOperator.ArrayMapping<ElementIndex>, props: CoarseProperties): Unit {
+        return new Coarse(id, invariantId, chainGroupId, traits, model, kind, elements, conformation, props) as any as Unit /** lets call this an ugly temporary hack */;
     }
 
     export class Spheres extends Coarse<Kind.Spheres, CoarseSphereConformation> { }
     export class Gaussians extends Coarse<Kind.Gaussians, CoarseGaussianConformation> { }
+
+    export function areSameChainOperatorGroup(a: Unit, b: Unit) {
+        return a.chainGroupId === b.chainGroupId && a.conformation.operator.name === b.conformation.operator.name;
+    }
 }
 
 export default Unit;

src/mol-model/structure/structure/unit/pair-restraints/extract-cross-links.ts

@@ -89,7 +89,9 @@ function createCrossLinkRestraint(unitA: Unit, indexA: StructureElement.UnitInde
 
 function extractCrossLinkRestraints(structure: Structure): PairRestraints<CrossLinkRestraint> {
     const pairs: CrossLinkRestraint[] = []
-    if (!structure.models.some(m => IHMCrossLinkRestraint.fromModel(m))) return new PairRestraints(pairs)
+    if (!structure.models.some(m => IHMCrossLinkRestraint.fromModel(m))) {
+        return new PairRestraints(pairs)
+    }
 
     const n = structure.units.length
     for (let i = 0; i < n; ++i) {

src/mol-model/structure/structure/util/polymer.ts

@@ -14,7 +14,7 @@ export function getAtomicPolymerElements(unit: Unit.Atomic) {
     const { elements, model } = unit
     const { residueAtomSegments } = unit.model.atomicHierarchy
     const { traceElementIndex } = model.atomicHierarchy.derived.residue
-    const polymerIt = SortedRanges.transientSegments(unit.model.atomicHierarchy.polymerRanges, elements)
+    const polymerIt = SortedRanges.transientSegments(unit.model.atomicRanges.polymerRanges, elements)
     const residueIt = Segmentation.transientSegments(residueAtomSegments, elements)
     while (polymerIt.hasNext) {
         const polymerSegment = polymerIt.move()
@@ -51,7 +51,7 @@ export function getAtomicGapElements(unit: Unit.Atomic) {
     const { elements, model, residueIndex } = unit
     const { residueAtomSegments } = unit.model.atomicHierarchy
     const { traceElementIndex } = model.atomicHierarchy.derived.residue
-    const gapIt = SortedRanges.transientSegments(unit.model.atomicHierarchy.gapRanges, unit.elements);
+    const gapIt = SortedRanges.transientSegments(unit.model.atomicRanges.gapRanges, unit.elements);
     while (gapIt.hasNext) {
         const gapSegment = gapIt.move();
         const indexStart = residueIndex[elements[gapSegment.start]]

src/mol-model/structure/structure/util/unique-subset-builder.ts

@@ -34,6 +34,12 @@ export class StructureUniqueSubsetBuilder {
         }
     }
 
+    has(parentId: number, e: number) {
+        const unit = this.unitMap.get(parentId);
+        if (!unit) return false;
+        return UniqueArray.has(unit, e);
+    }
+
     beginUnit(parentId: number) {
         this.parentId = parentId;
         if (this.unitMap.has(parentId)) {

src/mol-model/structure/util.ts

@@ -5,7 +5,7 @@
  */
 
 import { Model, ResidueIndex, ElementIndex } from './model';
-import { MoleculeType, AtomRole, MoleculeTypeAtomRoleId, getMoleculeType } from './model/types';
+import { MoleculeType, AtomRole, PolymerTypeAtomRoleId, getMoleculeType, PolymerType } from './model/types';
 import { Vec3 } from '../../mol-math/linear-algebra';
 import { Unit } from './structure';
 import Matrix from '../../mol-math/linear-algebra/matrix/matrix';
@@ -28,7 +28,7 @@ export function getElementMoleculeType(unit: Unit, element: ElementIndex): Molec
             const cc = unit.model.properties.chemicalComponentMap.get(compId)
             if (cc) return getMoleculeType(cc.type, compId)
     }
-    return MoleculeType.unknown
+    return MoleculeType.Unknown
 }
 
 export function getAtomicMoleculeType(model: Model, rI: ResidueIndex): MoleculeType {
@@ -36,10 +36,10 @@ export function getAtomicMoleculeType(model: Model, rI: ResidueIndex): MoleculeT
 }
 
 const EmptyAtomIds = new Set<string>()
-export function getAtomIdForAtomRole(moleculeType: MoleculeType, atomRole: AtomRole) {
-    const m = MoleculeTypeAtomRoleId[moleculeType]
-    if (m !== undefined) {
-        const a = m[atomRole]
+export function getAtomIdForAtomRole(polymerType: PolymerType, atomRole: AtomRole) {
+    const p = PolymerTypeAtomRoleId[polymerType]
+    if (p !== undefined) {
+        const a = p[atomRole]
         if (a !== undefined) return a
     }
     return EmptyAtomIds
@@ -81,7 +81,7 @@ export function elementLabel(model: Model, index: ElementIndex) {
 // }
 
 const matrixPos = Vec3.zero()
-export function getPositionMatrix(unit: Unit, indices: ArrayLike<number>) {
+export function getPositionMatrix(unit: Unit, indices: ArrayLike<number>): Matrix<3, number> {
     const pos = unit.conformation.position
     const mat = Matrix.create(3, indices.length)
     const { elements } = unit

src/mol-plugin/behavior/dynamic/camera.ts

@@ -10,13 +10,17 @@ import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 import { PluginBehavior } from '../behavior';
 import { ButtonsType, ModifiersKeys } from '../../../mol-util/input/input-observer';
 import { Binding } from '../../../mol-util/binding';
+import { PluginCommands } from '../../command';
 
 const B = ButtonsType
 const M = ModifiersKeys
 const Trigger = Binding.Trigger
 
 const DefaultFocusLociBindings = {
-    clickCenterFocus: Binding(Trigger(B.Flag.Primary, M.create()), 'Center and focus the clicked element using ${trigger}.'),
+    clickCenterFocus: Binding([
+        Trigger(B.Flag.Auxilary, M.create()),
+        Trigger(B.Flag.Primary, M.create({ alt: true }))
+    ], 'Center and focus the clicked element using ${triggers}.'),
 }
 const FocusLociParams = {
     minRadius: PD.Numeric(8, { min: 1, max: 50, step: 1 }),
@@ -34,13 +38,17 @@ export const FocusLoci = PluginBehavior.create<FocusLociProps>({
         register(): void {
             this.subscribeObservable(this.ctx.behaviors.interaction.click, ({ current, buttons, modifiers }) => {
                 if (!this.ctx.canvas3d) return;
-
                 const p = this.params;
                 if (Binding.match(this.params.bindings.clickCenterFocus, buttons, modifiers)) {
-                    const sphere = Loci.getBoundingSphere(current.loci);
-                    if (sphere) {
-                        const radius = Math.max(sphere.radius + p.extraRadius, p.minRadius);
-                        this.ctx.canvas3d.camera.focus(sphere.center, radius, p.durationMs);
+                    const loci = Loci.normalize(current.loci, this.ctx.interactivity.props.granularity)
+                    if (Loci.isEmpty(loci)) {
+                        PluginCommands.Camera.Reset.dispatch(this.ctx, { })
+                    } else {
+                        const sphere = Loci.getBoundingSphere(loci);
+                        if (sphere) {
+                            const radius = Math.max(sphere.radius + p.extraRadius, p.minRadius);
+                            this.ctx.canvas3d.camera.focus(sphere.center, radius, p.durationMs);
+                        }
                     }
                 }
             });

src/mol-plugin/behavior/dynamic/custom-props/pdbe/structure-quality-report.ts

@@ -37,6 +37,7 @@ export const PDBeStructureQualityReport = PluginBehavior.create<{ autoAttach: bo
 
             switch (loci.kind) {
                 case 'element-loci':
+                    if (loci.elements.length === 0) return void 0;
                     const e = loci.elements[0];
                     const u = e.unit;
                     if (!u.model.customProperties.has(StructureQualityReport.Descriptor)) return void 0;

src/mol-plugin/behavior/dynamic/labels.ts

@@ -159,7 +159,7 @@ export const SceneLabels = PluginBehavior.create<SceneLabelsProps>({
 
                     if (p.levels.includes('ligand') && !u.polymerElements.length) {
                         const moleculeType = getElementMoleculeType(u, u.elements[0])
-                        if (moleculeType === MoleculeType.other || moleculeType === MoleculeType.saccharide) {
+                        if (moleculeType === MoleculeType.Other || moleculeType === MoleculeType.Saccharide) {
                             label = `${StructureProperties.entity.pdbx_description(l).join(', ')} (${getAsymId(u)(l)})`
                         }
                     }

src/mol-plugin/behavior/dynamic/representation.ts

@@ -16,7 +16,7 @@ import { StateSelection } from '../../../mol-state';
 import { ButtonsType, ModifiersKeys } from '../../../mol-util/input/input-observer';
 import { Binding } from '../../../mol-util/binding';
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
-import { EmptyLoci } from '../../../mol-model/loci';
+import { EmptyLoci, Loci } from '../../../mol-model/loci';
 
 const B = ButtonsType
 const M = ModifiersKeys
@@ -25,8 +25,8 @@ const Trigger = Binding.Trigger
 //
 
 const DefaultHighlightLociBindings = {
-    hoverHighlightOnly: Binding(Trigger(B.Flag.None), 'Highlight hovered element using ${trigger}'),
-    hoverHighlightOnlyExtend: Binding(Trigger(B.Flag.None, M.create({ shift: true })), 'Extend highlight from selected to hovered element along polymer using ${trigger}'),
+    hoverHighlightOnly: Binding([Trigger(B.Flag.None)], 'Highlight hovered element using ${triggers}'),
+    hoverHighlightOnlyExtend: Binding([Trigger(B.Flag.None, M.create({ shift: true }))], 'Extend highlight from selected to hovered element along polymer using ${triggers}'),
 }
 const HighlightLociParams = {
     bindings: PD.Value(DefaultHighlightLociBindings, { isHidden: true }),
@@ -74,10 +74,11 @@ export const HighlightLoci = PluginBehavior.create({
 
 const DefaultSelectLociBindings = {
     clickSelect: Binding.Empty,
-    clickSelectExtend: Binding(Trigger(B.Flag.Primary, M.create({ shift: true })), 'Extend selection to clicked element along polymer using ${trigger}.'),
-    clickSelectOnly: Binding(Trigger(B.Flag.Secondary, M.create({ control: true })), 'Select only the clicked element using ${trigger}.'),
-    clickSelectToggle: Binding(Trigger(B.Flag.Primary, M.create({ control: true })), 'Toggle selection of clicked element using ${trigger}.'),
+    clickSelectExtend: Binding([Trigger(B.Flag.Primary, M.create({ shift: true }))], 'Extend selection to clicked element along polymer using ${triggers}.'),
+    clickSelectOnly: Binding.Empty,
+    clickSelectToggle: Binding([Trigger(B.Flag.Primary, M.create())], 'Toggle selection of clicked element using ${triggers}.'),
     clickDeselect: Binding.Empty,
+    clickDeselectAllOnEmpty: Binding([Trigger(B.Flag.Primary)], 'Deselect all when clicking on nothing using ${triggers}.'),
 }
 const SelectLociParams = {
     bindings: PD.Value(DefaultSelectLociBindings, { isHidden: true }),
@@ -127,6 +128,10 @@ export const SelectLoci = PluginBehavior.create({
                 if (Binding.match(this.params.bindings.clickDeselect, buttons, modifiers)) {
                     this.ctx.interactivity.lociSelects.deselect(current)
                 }
+
+                if (Binding.match(this.params.bindings.clickDeselectAllOnEmpty, buttons, modifiers)) {
+                    if (Loci.isEmpty(current.loci)) this.ctx.interactivity.lociSelects.deselectAll()
+                }
             });
             this.ctx.interactivity.lociSelects.addProvider(this.lociMarkProvider)
 

src/mol-plugin/behavior/dynamic/selection/structure-representation-interaction.ts

@@ -26,7 +26,7 @@ const M = ModifiersKeys
 const Trigger = Binding.Trigger
 
 const DefaultStructureRepresentationInteractionBindings = {
-    clickInteractionAroundOnly: Binding(Trigger(B.Flag.Secondary, M.create()), 'Show the structure interaction around only the clicked element using ${trigger}.'),
+    clickInteractionAroundOnly: Binding([Trigger(B.Flag.Secondary, M.create()), Trigger(B.Flag.Primary, M.create({ control: true }))], 'Show the structure interaction around only the clicked element using ${triggers}.'),
 }
 const StructureRepresentationInteractionParams = {
     bindings: PD.Value(DefaultStructureRepresentationInteractionBindings, { isHidden: true }),
@@ -47,16 +47,16 @@ export class StructureRepresentationInteractionBehavior extends PluginBehavior.W
 
     private createResVisualParams(s: Structure) {
         return StructureRepresentation3DHelpers.createParams(this.plugin, s, {
-            repr: BuiltInStructureRepresentations['ball-and-stick'],
-            size: [BuiltInSizeThemes.uniform, () => ({ value: 0.85 } )]
+            repr: [BuiltInStructureRepresentations['ball-and-stick'], () => ({ sizeAspectRatio: 1 })],
+            size: [BuiltInSizeThemes.uniform, () => ({ value: 0.6 } )]
         });
     }
 
     private createSurVisualParams(s: Structure) {
         return StructureRepresentation3DHelpers.createParams(this.plugin, s, {
-            repr: BuiltInStructureRepresentations['ball-and-stick'],
+            repr: [BuiltInStructureRepresentations['ball-and-stick'], () => ({ sizeAspectRatio: 1 })],
             color: [BuiltInColorThemes['element-symbol'], () => ({ saturation: -3, lightness: 0.6 })],
-            size: [BuiltInSizeThemes.uniform, () => ({ value: 0.33 } )]
+            size: [BuiltInSizeThemes.uniform, () => ({ value: 0.3 } )]
         });
     }
 
@@ -72,8 +72,8 @@ export class StructureRepresentationInteractionBehavior extends PluginBehavior.W
 
         // Selections
         if (!refs[Tags.ResidueSel]) {
-            refs[Tags.ResidueSel] = builder.to(refs['structure-interaction-group']).apply(StateTransforms.Model.StructureSelectionFromExpression,
-                { expression: { } as any, label: 'Residue' }, { tags: Tags.ResidueSel }).ref;
+            refs[Tags.ResidueSel] = builder.to(refs['structure-interaction-group']).apply(StateTransforms.Model.StructureSelectionFromBundle,
+                { bundle: { } as any, label: 'Residue' }, { tags: Tags.ResidueSel }).ref;
         }
 
         if (!refs[Tags.SurrSel]) {
@@ -102,13 +102,14 @@ export class StructureRepresentationInteractionBehavior extends PluginBehavior.W
         if (groups.length === 0) return;
 
         const update = state.build();
+        const bundle = StructureElement.Bundle.Empty;
         const expression = MS.struct.generator.empty();
         for (const g of groups) {
             // TODO: update props of the group node to ghost
 
             const res = StateSelection.findTagInSubtree(state.tree, g.transform.ref, Tags.ResidueSel);
             const surr = StateSelection.findTagInSubtree(state.tree, g.transform.ref, Tags.SurrSel);
-            if (res) update.to(res).update(StateTransforms.Model.StructureSelectionFromExpression, old => ({ ...old, expression }));
+            if (res) update.to(res).update(StateTransforms.Model.StructureSelectionFromBundle, old => ({ ...old, bundle }));
             if (surr) update.to(surr).update(StateTransforms.Model.StructureSelectionFromExpression, old => ({ ...old, expression }));
         }
 
@@ -148,7 +149,7 @@ export class StructureRepresentationInteractionBehavior extends PluginBehavior.W
                 } else if (Link.isLoci(current.loci)) {
                     loci = Link.toStructureElementLoci(current.loci);
                 } else if (Structure.isLoci(current.loci)) {
-                    loci = Structure.toStructureElementLoci(current.loci);
+                    loci = Structure.toStructureElementLoci(current.loci.structure);
                 } else {
                     return;
                 }
@@ -166,19 +167,18 @@ export class StructureRepresentationInteractionBehavior extends PluginBehavior.W
 
                 lastLoci = loci;
 
-                const core = MS.struct.modifier.wholeResidues([
-                    StructureElement.Loci.toExpression(loci)
-                ]);
+                const residueLoci = StructureElement.Loci.extendToWholeResidues(StructureElement.Loci.remap(loci, parent.obj!.data))
+                const residueBundle = StructureElement.Bundle.fromLoci(residueLoci)
 
                 const surroundings = MS.struct.modifier.includeSurroundings({
-                    0: core,
+                    0: StructureElement.Bundle.toExpression(residueBundle),
                     radius: 5,
                     'as-whole-residues': true
                 });
 
                 const { state, builder, refs } = this.ensureShape(parent);
 
-                builder.to(refs[Tags.ResidueSel]!).update(StateTransforms.Model.StructureSelectionFromExpression, old => ({ ...old, expression: core }));
+                builder.to(refs[Tags.ResidueSel]!).update(StateTransforms.Model.StructureSelectionFromBundle, old => ({ ...old, bundle: residueBundle }));
                 builder.to(refs[Tags.SurrSel]!).update(StateTransforms.Model.StructureSelectionFromExpression, old => ({ ...old, expression: surroundings }));
 
                 PluginCommands.State.Update.dispatch(this.plugin, { state, tree: builder, options: { doNotLogTiming: true, doNotUpdateCurrent: true } });

src/mol-plugin/behavior/dynamic/volume-streaming/behavior.ts

@@ -34,12 +34,20 @@ const Trigger = Binding.Trigger
 export class VolumeStreaming extends PluginStateObject.CreateBehavior<VolumeStreaming.Behavior>({ name: 'Volume Streaming' }) { }
 
 export namespace VolumeStreaming {
-    function channelParam(label: string, color: Color, defaultValue: VolumeIsoValue, stats: VolumeData['dataStats']) {
-        return PD.Group({
-            isoValue: createIsoValueParam(defaultValue, stats),
-            color: PD.Color(color),
-            wireframe: PD.Boolean(false),
-            opacity: PD.Numeric(0.3, { min: 0, max: 1, step: 0.01 })
+
+    export interface ChannelParams {
+        isoValue: VolumeIsoValue,
+        color: Color,
+        wireframe: boolean,
+        opacity: number
+    }
+
+    function channelParam(label: string, color: Color, defaultValue: VolumeIsoValue, stats: VolumeData['dataStats'], defaults: Partial<ChannelParams> = {}) {
+        return PD.Group<ChannelParams>({
+            isoValue: createIsoValueParam(typeof defaults.isoValue !== 'undefined' ? defaults.isoValue : defaultValue, stats),
+            color: PD.Color(typeof defaults.color !== 'undefined' ? defaults.color : color),
+            wireframe: PD.Boolean(typeof defaults.wireframe !== 'undefined' ? defaults.wireframe : false),
+            opacity: PD.Numeric(typeof defaults.opacity !== 'undefined' ? defaults.opacity : 0.3, { min: 0, max: 1, step: 0.01 })
         }, { label, isExpanded: true });
     }
 
@@ -51,54 +59,67 @@ export namespace VolumeStreaming {
     };
 
     export const DefaultBindings = {
-        clickVolumeAroundOnly: Binding(Trigger(B.Flag.Secondary, M.create()), 'Show the volume around only the clicked element using ${trigger}.'),
+        clickVolumeAroundOnly: Binding([Trigger(B.Flag.Secondary, M.create()), Trigger(B.Flag.Primary, M.create({ control: true }))], 'Show the volume around only the clicked element using ${triggers}.'),
     }
 
-    export function createParams(data?: VolumeServerInfo.Data, defaultView?: ViewTypes, binding?: typeof DefaultBindings) {
+    export function createParams(options: { data?: VolumeServerInfo.Data, defaultView?: ViewTypes, binding?: typeof DefaultBindings, channelParams?: DefaultChannelParams } = { }) {
+        const { data, defaultView, binding, channelParams } = options;
+        const map = new Map<string, VolumeServerInfo.EntryData>()
+        if (data) data.entries.forEach(d => map.set(d.dataId, d))
+        const names = data ? data.entries.map(d => [d.dataId, d.dataId] as [string, string]) : []
+        const defaultKey = data ? data.entries[0].dataId : ''
+        return {
+            entry: PD.Mapped<EntryParams>(defaultKey, names, name => PD.Group(createEntryParams({ entryData: map.get(name)!, defaultView, structure: data && data.structure, channelParams }))),
+            bindings: PD.Value(binding || DefaultBindings, { isHidden: true }),
+        }
+    }
+
+    export type EntryParamDefinition = typeof createEntryParams extends (...args: any[]) => (infer T) ? T : never
+    export type EntryParams = EntryParamDefinition extends PD.Params ? PD.Values<EntryParamDefinition> : {}
+
+    export function createEntryParams(options: { entryData?: VolumeServerInfo.EntryData, defaultView?: ViewTypes, structure?: Structure, channelParams?: DefaultChannelParams }) {
+        const { entryData, defaultView, structure, channelParams = { } } = options;
+
         // fake the info
-        const info = data || { kind: 'em', header: { sampling: [fakeSampling], availablePrecisions: [{ precision: 0, maxVoxels: 0 }] }, emDefaultContourLevel: VolumeIsoValue.relative(0) };
-        const box = (data && data.structure.boundary.box) || Box3D.empty();
+        const info = entryData || { kind: 'em', header: { sampling: [fakeSampling], availablePrecisions: [{ precision: 0, maxVoxels: 0 }] }, emDefaultContourLevel: VolumeIsoValue.relative(0) };
+        const box = (structure && structure.boundary.box) || Box3D.empty();
 
         return {
             view: PD.MappedStatic(defaultView || (info.kind === 'em' ? 'cell' : 'selection-box'), {
-                'off': PD.Group({}),
+                'off': PD.Group<{}>({}),
                 'box': PD.Group({
                     bottomLeft: PD.Vec3(box.min),
                     topRight: PD.Vec3(box.max),
                 }, { description: 'Static box defined by cartesian coords.', isFlat: true }),
                 'selection-box': PD.Group({
-                    radius: PD.Numeric(5, { min: 0, max: 50, step: 0.5 }),
+                    radius: PD.Numeric(5, { min: 0, max: 50, step: 0.5 }, { description: 'Radius in \u212B within which the volume is shown.' }),
                     bottomLeft: PD.Vec3(Vec3.create(0, 0, 0), { isHidden: true }),
                     topRight: PD.Vec3(Vec3.create(0, 0, 0), { isHidden: true }),
                 }, { description: 'Box around last-interacted element.', isFlat: true }),
                 'cell': PD.Group({}),
                 // 'auto': PD.Group({  }), // TODO based on camera distance/active selection/whatever, show whole structure or slice.
-            }, { options: ViewTypeOptions as any }),
+            }, { options: ViewTypeOptions, description: 'Controls what of the volume is displayed. "Off" hides the volume alltogether. "Bounded box" shows the volume inside the given box. "Around Interaction" shows the volume around the element/atom last interacted with. "Whole Structure" shows the volume for the whole structure.' }),
             detailLevel: PD.Select<number>(Math.min(3, info.header.availablePrecisions.length - 1),
-                info.header.availablePrecisions.map((p, i) => [i, `${i + 1} [ ${Math.pow(p.maxVoxels, 1 / 3) | 0}^3 cells ]`] as [number, string])),
+                info.header.availablePrecisions.map((p, i) => [i, `${i + 1} [ ${Math.pow(p.maxVoxels, 1 / 3) | 0}^3 cells ]`] as [number, string]), { description: 'Determines the maximum number of voxels. Depending on the size of the volume options are in the range from 0 (0.52M voxels) to 6 (25.17M voxels).' }),
             channels: info.kind === 'em'
                 ? PD.Group({
-                    'em': channelParam('EM', Color(0x638F8F), info.emDefaultContourLevel || VolumeIsoValue.relative(1), info.header.sampling[0].valuesInfo[0])
+                    'em': channelParam('EM', Color(0x638F8F), info.emDefaultContourLevel || VolumeIsoValue.relative(1), info.header.sampling[0].valuesInfo[0], channelParams['em'])
                 }, { isFlat: true })
                 : PD.Group({
-                    '2fo-fc': channelParam('2Fo-Fc', Color(0x3362B2), VolumeIsoValue.relative(1.5), info.header.sampling[0].valuesInfo[0]),
-                    'fo-fc(+ve)': channelParam('Fo-Fc(+ve)', Color(0x33BB33), VolumeIsoValue.relative(3), info.header.sampling[0].valuesInfo[1]),
-                    'fo-fc(-ve)': channelParam('Fo-Fc(-ve)', Color(0xBB3333), VolumeIsoValue.relative(-3), info.header.sampling[0].valuesInfo[1]),
+                    '2fo-fc': channelParam('2Fo-Fc', Color(0x3362B2), VolumeIsoValue.relative(1.5), info.header.sampling[0].valuesInfo[0], channelParams['2fo-fc']),
+                    'fo-fc(+ve)': channelParam('Fo-Fc(+ve)', Color(0x33BB33), VolumeIsoValue.relative(3), info.header.sampling[0].valuesInfo[1], channelParams['fo-fc(+ve)']),
+                    'fo-fc(-ve)': channelParam('Fo-Fc(-ve)', Color(0xBB3333), VolumeIsoValue.relative(-3), info.header.sampling[0].valuesInfo[1], channelParams['fo-fc(-ve)']),
                 }, { isFlat: true }),
-            bindings: PD.Value(binding || DefaultBindings, { isHidden: true }),
         };
     }
 
-    export const ViewTypeOptions = [['off', 'Off'], ['box', 'Bounded Box'], ['selection-box', 'Surroundings'], ['cell', 'Whole Structure']];
+    export const ViewTypeOptions = [['off', 'Off'], ['box', 'Bounded Box'], ['selection-box', 'Around Interaction'], ['cell', 'Whole Structure']] as [ViewTypes, string][];
 
     export type ViewTypes = 'off' | 'box' | 'selection-box' | 'cell'
 
     export type ParamDefinition = typeof createParams extends (...args: any[]) => (infer T) ? T : never
     export type Params = ParamDefinition extends PD.Params ? PD.Values<ParamDefinition> : {}
 
-    type CT = typeof channelParam extends (...args: any[]) => (infer T) ? T : never
-    export type ChannelParams = CT extends PD.Group<infer T> ? T : {}
-
     type ChannelsInfo = { [name in ChannelType]?: { isoValue: VolumeIsoValue, color: Color, wireframe: boolean, opacity: number } }
     type ChannelsData = { [name in 'EM' | '2FO-FC' | 'FO-FC']?: VolumeData }
 
@@ -113,16 +134,23 @@ export namespace VolumeStreaming {
     }
     export type Channels = { [name in ChannelType]?: ChannelInfo }
 
+    export type DefaultChannelParams = { [name in ChannelType]?: Partial<ChannelParams> }
+
     export class Behavior extends PluginBehavior.WithSubscribers<Params> {
         private cache = LRUCache.create<ChannelsData>(25);
         public params: Params = {} as any;
         private lastLoci: StructureElement.Loci | EmptyLoci = EmptyLoci;
         private ref: string = '';
+        public infoMap: Map<string, VolumeServerInfo.EntryData>
 
         channels: Channels = {}
 
+        public get info () {
+            return this.infoMap.get(this.params.entry.name)!
+        }
+
         private async queryData(box?: Box3D) {
-            let url = urlCombine(this.info.serverUrl, `${this.info.kind}/${this.info.dataId.toLowerCase()}`);
+            let url = urlCombine(this.data.serverUrl, `${this.info.kind}/${this.info.dataId.toLowerCase()}`);
 
             if (box) {
                 const { min: a, max: b } = box;
@@ -132,7 +160,7 @@ export namespace VolumeStreaming {
             } else {
                 url += `/cell`;
             }
-            url += `?detail=${this.params.detailLevel}`;
+            url += `?detail=${this.params.entry.params.detailLevel}`;
 
             let data = LRUCache.get(this.cache, url);
             if (data) {
@@ -165,24 +193,30 @@ export namespace VolumeStreaming {
                 const block = parsed.result.blocks[i];
 
                 const densityServerCif = CIF.schema.densityServer(block);
-                const volume = await this.plugin.runTask(await volumeFromDensityServerData(densityServerCif));
+                const volume = await this.plugin.runTask(volumeFromDensityServerData(densityServerCif));
                 (ret as any)[block.header as any] = volume;
             }
             return ret;
         }
 
         private updateDynamicBox(box: Box3D) {
-            if (this.params.view.name !== 'selection-box') return;
+            if (this.params.entry.params.view.name !== 'selection-box') return;
 
             const state = this.plugin.state.dataState;
             const newParams: Params = {
                 ...this.params,
-                view: {
-                    name: 'selection-box' as 'selection-box',
+                entry: {
+                    name: this.params.entry.name,
                     params: {
-                        radius: this.params.view.params.radius,
-                        bottomLeft: box.min,
-                        topRight: box.max
+                        ...this.params.entry.params,
+                        view: {
+                            name: 'selection-box' as 'selection-box',
+                            params: {
+                                radius: this.params.entry.params.view.params.radius,
+                                bottomLeft: box.min,
+                                topRight: box.max
+                            }
+                        }
                     }
                 }
             };
@@ -214,7 +248,7 @@ export namespace VolumeStreaming {
 
             this.subscribeObservable(this.plugin.behaviors.interaction.click, ({ current, buttons, modifiers }) => {
                 if (!Binding.match((this.params.bindings && this.params.bindings.clickVolumeAroundOnly) || DefaultBindings.clickVolumeAroundOnly, buttons, modifiers)) return;
-                if (this.params.view.name !== 'selection-box') {
+                if (this.params.entry.params.view.name !== 'selection-box') {
                     this.lastLoci = this.getNormalizedLoci(current.loci);
                 } else {
                     this.updateInteraction(current);
@@ -228,14 +262,14 @@ export namespace VolumeStreaming {
             } else if (Link.isLoci(loci)) {
                 return Link.toStructureElementLoci(loci);
             } else if (Structure.isLoci(loci)) {
-                return Structure.toStructureElementLoci(loci);
+                return Structure.toStructureElementLoci(loci.structure);
             } else {
                 return EmptyLoci;
             }
         }
 
         private getBoxFromLoci(loci: StructureElement.Loci | EmptyLoci): Box3D {
-            if (isEmptyLoci(loci) || StructureElement.Loci.isEmpty(loci)) {
+            if (Loci.isEmpty(loci)) {
                 return Box3D.empty();
             }
 
@@ -272,34 +306,34 @@ export namespace VolumeStreaming {
         }
 
         async update(params: Params) {
-            const switchedToSelection = params.view.name === 'selection-box' && this.params && this.params.view && this.params.view.name !== 'selection-box';
+            const switchedToSelection = params.entry.params.view.name === 'selection-box' && this.params && this.params.entry && this.params.entry.params && this.params.entry.params.view && this.params.entry.params.view.name !== 'selection-box';
 
             this.params = params;
 
             let box: Box3D | undefined = void 0, emptyData = false;
 
-            switch (params.view.name) {
+            switch (params.entry.params.view.name) {
                 case 'off':
                     emptyData = true;
                     break;
                 case 'box':
-                    box = Box3D.create(params.view.params.bottomLeft, params.view.params.topRight);
+                    box = Box3D.create(params.entry.params.view.params.bottomLeft, params.entry.params.view.params.topRight);
                     emptyData = Box3D.volume(box) < 0.0001;
                     break;
                 case 'selection-box': {
                     if (switchedToSelection) {
                         box = this.getBoxFromLoci(this.lastLoci) || Box3D.empty();
                     } else {
-                        box = Box3D.create(Vec3.clone(params.view.params.bottomLeft), Vec3.clone(params.view.params.topRight));
+                        box = Box3D.create(Vec3.clone(params.entry.params.view.params.bottomLeft), Vec3.clone(params.entry.params.view.params.topRight));
                     }
-                    const r = params.view.params.radius;
+                    const r = params.entry.params.view.params.radius;
                     emptyData = Box3D.volume(box) < 0.0001;
                     Box3D.expand(box, box, Vec3.create(r, r, r));
                     break;
                 }
                 case 'cell':
                     box = this.info.kind === 'x-ray'
-                        ? this.info.structure.boundary.box
+                        ? this.data.structure.boundary.box
                         : void 0;
                     break;
             }
@@ -308,7 +342,7 @@ export namespace VolumeStreaming {
 
             if (!data) return false;
 
-            const info = params.channels as ChannelsInfo;
+            const info = params.entry.params.channels as ChannelsInfo;
 
             if (this.info.kind === 'x-ray') {
                 this.channels['2fo-fc'] = this.createChannel(data['2FO-FC'] || VolumeData.One, info['2fo-fc'], this.info.header.sampling[0].valuesInfo[0]);
@@ -333,14 +367,17 @@ export namespace VolumeStreaming {
         }
 
         getDescription() {
-            if (this.params.view.name === 'selection-box') return 'Selection';
-            if (this.params.view.name === 'box') return 'Static Box';
-            if (this.params.view.name === 'cell') return 'Cell';
+            if (this.params.entry.params.view.name === 'selection-box') return 'Selection';
+            if (this.params.entry.params.view.name === 'box') return 'Static Box';
+            if (this.params.entry.params.view.name === 'cell') return 'Cell';
             return '';
         }
 
-        constructor(public plugin: PluginContext, public info: VolumeServerInfo.Data) {
+        constructor(public plugin: PluginContext, public data: VolumeServerInfo.Data) {
             super(plugin, {} as any);
+
+            this.infoMap = new Map<string, VolumeServerInfo.EntryData>()
+            this.data.entries.forEach(info => this.infoMap.set(info.dataId, info))
         }
     }
 }

src/mol-plugin/behavior/dynamic/volume-streaming/model.ts

@@ -2,6 +2,7 @@
  * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
 import { PluginStateObject } from '../../../state/objects';
@@ -12,13 +13,16 @@ export class VolumeServerInfo extends PluginStateObject.Create<VolumeServerInfo.
 
 export namespace VolumeServerInfo {
     export type Kind = 'x-ray' | 'em'
-    export interface Data  {
-        serverUrl: string,
+    export interface EntryData  {
         kind: Kind,
         // for em, the EMDB access code, for x-ray, the PDB id
         dataId: string,
         header: VolumeServerHeader,
         emDefaultContourLevel?: VolumeIsoValue,
+    }
+    export interface Data {
+        serverUrl: string,
+        entries: EntryData[],
         structure: Structure
     }
 }

src/mol-plugin/behavior/dynamic/volume-streaming/transformers.ts

@@ -14,7 +14,7 @@ import { urlCombine } from '../../../../mol-util/url';
 import { createIsoValueParam } from '../../../../mol-repr/volume/isosurface';
 import { VolumeIsoValue } from '../../../../mol-model/volume';
 import { StateAction, StateObject, StateTransformer } from '../../../../mol-state';
-import { getStreamingMethod, getId, getContourLevel, getEmdbId } from './util';
+import { getStreamingMethod, getIds, getContourLevel, getEmdbIds } from './util';
 import { VolumeStreaming } from './behavior';
 import { VolumeRepresentation3DHelpers } from '../../../../mol-plugin/state/transforms/representation';
 import { BuiltInVolumeRepresentations } from '../../../../mol-repr/volume/registry';
@@ -22,48 +22,83 @@ import { createTheme } from '../../../../mol-theme/theme';
 import { Box3D } from '../../../../mol-math/geometry';
 import { Vec3 } from '../../../../mol-math/linear-algebra';
 
+function addEntry(entries: InfoEntryProps[], method: VolumeServerInfo.Kind, dataId: string, emDefaultContourLevel: number) {
+    entries.push({
+        source: method === 'em'
+            ? { name: 'em', params: { isoValue: VolumeIsoValue.absolute(emDefaultContourLevel || 0) } }
+            : { name: 'x-ray', params: { } },
+        dataId
+    })
+}
+
 export const InitVolumeStreaming = StateAction.build({
     display: { name: 'Volume Streaming' },
     from: SO.Molecule.Structure,
     params(a) {
         const method = getStreamingMethod(a && a.data);
-        const id = getId(a && a.data);
+        const ids = getIds(method, a && a.data);
         return {
             method: PD.Select<VolumeServerInfo.Kind>(method, [['em', 'EM'], ['x-ray', 'X-Ray']]),
-            id: PD.Text(id),
-            serverUrl: PD.Text('https://ds.litemol.org'),
+            entries: PD.ObjectList({ id: PD.Text(ids[0] || '') }, ({ id }) => id, { defaultValue: ids.map(id => ({ id })) }),
             defaultView: PD.Select<VolumeStreaming.ViewTypes>(method === 'em' ? 'cell' : 'selection-box', VolumeStreaming.ViewTypeOptions as any),
-            behaviorRef: PD.Text('', { isHidden: true }),
-            emContourProvider: PD.Select<'wwpdb' | 'pdbe'>('wwpdb', [['wwpdb', 'wwPDB'], ['pdbe', 'PDBe']], { isHidden: true }),
-            bindings: PD.Value(VolumeStreaming.DefaultBindings, { isHidden: true }),
+            options: PD.Group({
+                serverUrl: PD.Text('https://ds.litemol.org'),
+                behaviorRef: PD.Text('', { isHidden: true }),
+                emContourProvider: PD.Select<'wwpdb' | 'pdbe'>('wwpdb', [['wwpdb', 'wwPDB'], ['pdbe', 'PDBe']], { isHidden: true }),
+                bindings: PD.Value(VolumeStreaming.DefaultBindings, { isHidden: true }),
+                channelParams: PD.Value<VolumeStreaming.DefaultChannelParams>({}, { isHidden: true })
+            })
         };
     },
     isApplicable: (a) => a.data.models.length === 1
 })(({ ref, state, params }, plugin: PluginContext) => Task.create('Volume Streaming', async taskCtx => {
-    let dataId = params.id.toLowerCase(), emDefaultContourLevel: number | undefined;
-    if (params.method === 'em') {
-        await taskCtx.update('Getting EMDB info...');
-        if (!dataId.toUpperCase().startsWith('EMD')) {
-            dataId = await getEmdbId(plugin, taskCtx, dataId)
+    const entries: InfoEntryProps[] = []
+
+    for (let i = 0, il = params.entries.length; i < il; ++i) {
+        let dataId = params.entries[i].id.toLowerCase()
+        let emDefaultContourLevel: number | undefined;
+
+        if (params.method === 'em') {
+            // if pdb ids are given for method 'em', get corresponding emd ids
+            // and continue the loop
+            if (!dataId.toUpperCase().startsWith('EMD')) {
+                await taskCtx.update('Getting EMDB info...');
+                const emdbIds = await getEmdbIds(plugin, taskCtx, dataId)
+                for (let j = 0, jl = emdbIds.length; j < jl; ++j) {
+                    const emdbId = emdbIds[j]
+                    let contourLevel: number | undefined;
+                    try {
+                        contourLevel = await getContourLevel(params.options.emContourProvider, plugin, taskCtx, emdbId)
+                    } catch (e) {
+                        console.info(`Could not get map info for ${emdbId}: ${e}`)
+                        continue;
+                    }
+                    addEntry(entries, params.method, emdbId, contourLevel || 0)
+                }
+                continue;
+            }
+            try {
+                emDefaultContourLevel = await getContourLevel(params.options.emContourProvider, plugin, taskCtx, dataId);
+            } catch (e) {
+                console.info(`Could not get map info for ${dataId}: ${e}`)
+                continue;
+            }
         }
-        const contourLevel = await getContourLevel(params.emContourProvider, plugin, taskCtx, dataId);
-        emDefaultContourLevel = contourLevel || 0;
+
+        addEntry(entries, params.method, dataId, emDefaultContourLevel || 0)
     }
 
     const infoTree = state.build().to(ref)
         .apply(CreateVolumeStreamingInfo, {
-            serverUrl: params.serverUrl,
-            source: params.method === 'em'
-                ? { name: 'em', params: { isoValue: VolumeIsoValue.absolute(emDefaultContourLevel || 0) } }
-                : { name: 'x-ray', params: { } },
-            dataId
+            serverUrl: params.options.serverUrl,
+            entries
         });
 
     const infoObj = await state.updateTree(infoTree).runInContext(taskCtx);
 
     const behTree = state.build().to(infoTree.ref).apply(CreateVolumeStreamingBehavior,
-        PD.getDefaultValues(VolumeStreaming.createParams(infoObj.data, params.defaultView, params.bindings)),
-        { ref: params.behaviorRef ? params.behaviorRef : void 0 });
+        PD.getDefaultValues(VolumeStreaming.createParams({ data: infoObj.data, defaultView: params.defaultView, binding: params.options.bindings, channelParams: params.options.channelParams })),
+        { ref: params.options.behaviorRef ? params.options.behaviorRef : void 0 });
 
     if (params.method === 'em') {
         behTree.apply(VolumeStreamingVisual, { channel: 'em' }, { state: { isGhost: true } });
@@ -78,26 +113,43 @@ export const InitVolumeStreaming = StateAction.build({
 export const BoxifyVolumeStreaming = StateAction.build({
     display: { name: 'Boxify Volume Streaming', description: 'Make the current box permanent.' },
     from: VolumeStreaming,
-    isApplicable: (a) => a.data.params.view.name === 'selection-box'
+    isApplicable: (a) => a.data.params.entry.params.view.name === 'selection-box'
 })(({ a, ref, state }, plugin: PluginContext) => {
     const params = a.data.params;
-    if (params.view.name !== 'selection-box') return;
-    const box = Box3D.create(Vec3.clone(params.view.params.bottomLeft), Vec3.clone(params.view.params.topRight));
-    const r = params.view.params.radius;
+    if (params.entry.params.view.name !== 'selection-box') return;
+    const box = Box3D.create(Vec3.clone(params.entry.params.view.params.bottomLeft), Vec3.clone(params.entry.params.view.params.topRight));
+    const r = params.entry.params.view.params.radius;
     Box3D.expand(box, box, Vec3.create(r, r, r));
     const newParams: VolumeStreaming.Params = {
         ...params,
-        view: {
-            name: 'box' as 'box',
+        entry: {
+            name: params.entry.name,
             params: {
-                bottomLeft: box.min,
-                topRight: box.max
+                ...params.entry.params,
+                view: {
+                    name: 'box' as 'box',
+                    params: {
+                        bottomLeft: box.min,
+                        topRight: box.max
+                    }
+                }
             }
         }
     };
     return state.updateTree(state.build().to(ref).update(newParams));
 });
 
+const InfoEntryParams = {
+    dataId: PD.Text(''),
+    source: PD.MappedStatic('x-ray', {
+        'em': PD.Group({
+            isoValue: createIsoValueParam(VolumeIsoValue.relative(1))
+        }),
+        'x-ray': PD.Group({ })
+    })
+}
+type InfoEntryProps = PD.Values<typeof InfoEntryParams>
+
 export { CreateVolumeStreamingInfo }
 type CreateVolumeStreamingInfo = typeof CreateVolumeStreamingInfo
 const CreateVolumeStreamingInfo = PluginStateTransform.BuiltIn({
@@ -108,30 +160,34 @@ const CreateVolumeStreamingInfo = PluginStateTransform.BuiltIn({
     params(a) {
         return {
             serverUrl: PD.Text('https://ds.litemol.org'),
-            source: PD.MappedStatic('x-ray', {
-                'em': PD.Group({
-                    isoValue: createIsoValueParam(VolumeIsoValue.relative(1))
-                }),
-                'x-ray': PD.Group({ })
+            entries: PD.ObjectList<InfoEntryProps>(InfoEntryParams, ({ dataId }) => dataId, {
+                defaultValue: [{ dataId: '', source: { name: 'x-ray', params: {} } }]
             }),
-            dataId: PD.Text('')
         };
     }
 })({
     apply: ({ a, params }, plugin: PluginContext) => Task.create('', async taskCtx => {
-        const dataId = params.dataId;
-        const emDefaultContourLevel = params.source.name === 'em' ? params.source.params.isoValue : VolumeIsoValue.relative(1);
-        await taskCtx.update('Getting server header...');
-        const header = await plugin.fetch<VolumeServerHeader>({ url: urlCombine(params.serverUrl, `${params.source.name}/${dataId.toLocaleLowerCase()}`), type: 'json' }).runInContext(taskCtx);
+        const entries: VolumeServerInfo.EntryData[] = []
+        for (let i = 0, il = params.entries.length; i < il; ++i) {
+            const e = params.entries[i]
+            const dataId = e.dataId;
+            const emDefaultContourLevel = e.source.name === 'em' ? e.source.params.isoValue : VolumeIsoValue.relative(1);
+            await taskCtx.update('Getting server header...');
+            const header = await plugin.fetch<VolumeServerHeader>({ url: urlCombine(params.serverUrl, `${e.source.name}/${dataId.toLocaleLowerCase()}`), type: 'json' }).runInContext(taskCtx);
+            entries.push({
+                dataId,
+                kind: e.source.name,
+                header,
+                emDefaultContourLevel
+            })
+        }
+
         const data: VolumeServerInfo.Data = {
             serverUrl: params.serverUrl,
-            dataId,
-            kind: params.source.name,
-            header,
-            emDefaultContourLevel,
+            entries,
             structure: a.data
         };
-        return new VolumeServerInfo(data, { label: `Volume Server: ${dataId}` });
+        return new VolumeServerInfo(data, { label: 'Volume Server', description: `${entries.map(e => e.dataId). join(', ')}` });
     })
 });
 
@@ -143,21 +199,29 @@ const CreateVolumeStreamingBehavior = PluginStateTransform.BuiltIn({
     from: VolumeServerInfo,
     to: VolumeStreaming,
     params(a) {
-        return VolumeStreaming.createParams(a && a.data);
+        return VolumeStreaming.createParams({ data: a && a.data });
     }
 })({
     canAutoUpdate: ({ oldParams, newParams }) => {
-        return oldParams.view === newParams.view
-            || newParams.view.name === 'selection-box'
-            || newParams.view.name === 'off';
+        return oldParams.entry.params.view === newParams.entry.params.view
+            || newParams.entry.params.view.name === 'selection-box'
+            || newParams.entry.params.view.name === 'off';
     },
     apply: ({ a, params }, plugin: PluginContext) => Task.create('Volume streaming', async _ => {
         const behavior = new VolumeStreaming.Behavior(plugin, a.data);
         await behavior.update(params);
         return new VolumeStreaming(behavior, { label: 'Volume Streaming', description: behavior.getDescription() });
     }),
-    update({ b, newParams }) {
+    update({ a, b, oldParams, newParams }) {
         return Task.create('Update Volume Streaming', async _ => {
+            if (oldParams.entry.name !== newParams.entry.name) {
+                if ('em' in newParams.entry.params.channels) {
+                    const { emDefaultContourLevel } = b.data.infoMap.get(newParams.entry.name)!
+                    if (emDefaultContourLevel) {
+                        newParams.entry.params.channels['em'].isoValue = emDefaultContourLevel
+                    }
+                }
+            }
             const ret = await b.data.update(newParams) ? StateTransformer.UpdateResult.Updated : StateTransformer.UpdateResult.Unchanged;
             b.description = b.data.getDescription();
             return ret;

src/mol-plugin/behavior/dynamic/volume-streaming/util.ts

@@ -5,7 +5,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { Structure } from '../../../../mol-model/structure';
+import { Structure, Model } from '../../../../mol-model/structure';
 import { VolumeServerInfo } from './model';
 import { PluginContext } from '../../../../mol-plugin/context';
 import { RuntimeContext } from '../../../../mol-task';
@@ -17,28 +17,56 @@ export function getStreamingMethod(s?: Structure, defaultKind: VolumeServerInfo.
     const model = s.models[0];
     if (model.sourceData.kind !== 'mmCIF') return defaultKind;
 
-    const data = model.sourceData.data.exptl.method;
-    for (let i = 0; i < data.rowCount; i++) {
-        const v = data.value(i).toUpperCase();
-        if (v.indexOf('MICROSCOPY') >= 0) return 'em';
-    }
-    return 'x-ray';
-}
+    const { data } = model.sourceData;
 
-export function getId(s?: Structure): string {
-    if (!s) return ''
-
-    const model = s.models[0]
-    if (model.sourceData.kind !== 'mmCIF') return ''
-
-    const d = model.sourceData.data
-    for (let i = 0, il = d.pdbx_database_related._rowCount; i < il; ++i) {
-        if (d.pdbx_database_related.db_name.value(i).toUpperCase() === 'EMDB') {
-            return d.pdbx_database_related.db_id.value(i)
+    // prefer EMDB entries over structure-factors (SF) e.g. for 'ELECTRON CRYSTALLOGRAPHY' entries
+    // like 6axz or 6kj3 for which EMDB entries are available but map calculation from SF is hard
+    for (let i = 0, il = data.pdbx_database_related._rowCount; i < il; ++i) {
+        if (data.pdbx_database_related.db_name.value(i).toUpperCase() === 'EMDB') {
+            return 'em'
         }
     }
 
-    return s.models.length > 0 ? s.models[0].entryId : ''
+    if (data.pdbx_database_status.status_code_sf.isDefined && data.pdbx_database_status.status_code_sf.value(0) === 'REL') {
+        return 'x-ray'
+    }
+
+    // fallbacks
+    for (let i = 0; i < data.exptl.method.rowCount; i++) {
+        const v = data.exptl.method.value(i).toUpperCase();
+        if (v.indexOf('MICROSCOPY') >= 0) return 'em';
+    }
+    return defaultKind;
+}
+
+/** Returns EMD ID when available, otherwise falls back to PDB ID */
+export function getEmIds(model: Model): string[] {
+    const ids: string[] = []
+    if (model.sourceData.kind !== 'mmCIF') return [ model.entryId ]
+
+    const { db_id, db_name, content_type } = model.sourceData.data.pdbx_database_related
+    if (!db_name.isDefined) return [ model.entryId ]
+
+    for (let i = 0, il = db_name.rowCount; i < il; ++i) {
+        if (db_name.value(i).toUpperCase() === 'EMDB' && content_type.value(i) === 'associated EM volume') {
+            ids.push(db_id.value(i))
+        }
+    }
+
+    return ids
+}
+
+export function getXrayIds(model: Model): string[] {
+    return [ model.entryId ]
+}
+
+export function getIds(method: VolumeServerInfo.Kind, s?: Structure): string[] {
+    if (!s || !s.models.length) return []
+    const model = s.models[0]
+    switch (method) {
+        case 'em': return getEmIds(model)
+        case 'x-ray': return getXrayIds(model)
+    }
 }
 
 export async function getContourLevel(provider: 'wwpdb' | 'pdbe', plugin: PluginContext, taskCtx: RuntimeContext, emdbId: string) {
@@ -71,21 +99,21 @@ export async function getContourLevelPdbe(plugin: PluginContext, taskCtx: Runtim
     return contourLevel;
 }
 
-export async function getEmdbId(plugin: PluginContext, taskCtx: RuntimeContext, pdbId: string) {
+export async function getEmdbIds(plugin: PluginContext, taskCtx: RuntimeContext, pdbId: string) {
     // TODO: parametrize to a differnt URL? in plugin settings perhaps
     const summary = await plugin.fetch({ url: `https://www.ebi.ac.uk/pdbe/api/pdb/entry/summary/${pdbId}`, type: 'json' }).runInContext(taskCtx);
 
     const summaryEntry = summary && summary[pdbId];
-    let emdbId: string;
+    let emdbIds: string[] = [];
     if (summaryEntry && summaryEntry[0] && summaryEntry[0].related_structures) {
-        const emdb = summaryEntry[0].related_structures.filter((s: any) => s.resource === 'EMDB');
+        const emdb = summaryEntry[0].related_structures.filter((s: any) => s.resource === 'EMDB' && s.relationship === 'associated EM volume');
         if (!emdb.length) {
             throw new Error(`No related EMDB entry found for '${pdbId}'.`);
         }
-        emdbId = emdb[0].accession;
+        emdbIds.push(...emdb.map((e: { accession: string }) => e.accession));
     } else {
         throw new Error(`No related EMDB entry found for '${pdbId}'.`);
     }
 
-    return emdbId
+    return emdbIds
 }

src/mol-plugin/behavior/static/state.ts

@@ -106,10 +106,10 @@ export function Highlight(ctx: PluginContext) {
         const cell = state.select(ref)[0];
         if (!cell) return;
         if (SO.Molecule.Structure.is(cell.obj)) {
-            ctx.interactivity.lociHighlights.highlightOnly({ loci: Structure.Loci(cell.obj.data) });
+            ctx.interactivity.lociHighlights.highlightOnly({ loci: Structure.Loci(cell.obj.data) }, false);
         } else if (cell && SO.isRepresentation3D(cell.obj)) {
             const loci = SO.Molecule.Structure.is(cell.obj.data.source) ? Structure.Loci(cell.obj.data.source.data) : EveryLoci
-            ctx.interactivity.lociHighlights.highlightOnly({ loci, repr: cell.obj.data.repr });
+            ctx.interactivity.lociHighlights.highlightOnly({ loci, repr: cell.obj.data.repr }, false);
         }
 
         // TODO: highlight volumes and shapes?
@@ -119,7 +119,7 @@ export function Highlight(ctx: PluginContext) {
 
 export function ClearHighlight(ctx: PluginContext) {
     PluginCommands.State.ClearHighlight.subscribe(ctx, ({ state, ref }) => {
-        ctx.interactivity.lociHighlights.highlightOnly({ loci: EmptyLoci });
+        ctx.interactivity.lociHighlights.highlightOnly({ loci: EmptyLoci }, false);
     });
 }
 

src/mol-plugin/context.ts

@@ -11,7 +11,7 @@ import { CustomPropertyRegistry } from '../mol-model-props/common/custom-propert
 import { StructureRepresentationRegistry } from '../mol-repr/structure/registry';
 import { VolumeRepresentationRegistry } from '../mol-repr/volume/registry';
 import { State, StateTransform, StateTransformer } from '../mol-state';
-import { Task } from '../mol-task';
+import { Task, Progress } from '../mol-task';
 import { ColorTheme } from '../mol-theme/color';
 import { SizeTheme } from '../mol-theme/size';
 import { ThemeRegistryContext } from '../mol-theme/theme';
@@ -176,6 +176,10 @@ export class PluginContext {
         return this.tasks.run(task);
     }
 
+    requestTaskAbort(progress: Progress, reason?: string) {
+        this.tasks.requestAbort(progress, reason);
+    }
+
     dispose() {
         if (this.disposed) return;
         this.commands.dispose();

src/mol-plugin/index.ts

@@ -50,6 +50,7 @@ export const DefaultPluginSpec: PluginSpec = {
         PluginSpec.Action(StateTransforms.Model.StructureSelectionFromScript),
         PluginSpec.Action(StateTransforms.Representation.StructureRepresentation3D),
         PluginSpec.Action(StateTransforms.Representation.StructureLabels3D),
+        PluginSpec.Action(StateTransforms.Representation.StructureOrientation3D),
         PluginSpec.Action(StateTransforms.Representation.ModelUnitcell3D),
         PluginSpec.Action(StateTransforms.Representation.ExplodeStructureRepresentation3D),
         PluginSpec.Action(StateTransforms.Representation.UnwindStructureAssemblyRepresentation3D),

src/mol-plugin/layout.ts

@@ -10,13 +10,12 @@ import { PluginComponent } from './component';
 import { PluginContext } from './context';
 import { PluginCommands } from './command';
 
-// TODO: support collapsed state control orientation
+export type PluginLayoutControlsDisplay = 'outside' | 'portrait' | 'landscape' | 'reactive'
 export const PluginLayoutStateParams = {
     isExpanded: PD.Boolean(false),
     showControls: PD.Boolean(true),
-    outsideControls: PD.Boolean(true, { isHidden: true })
+    controlsDisplay: PD.Value<PluginLayoutControlsDisplay>('outside', { isHidden: true })
 }
-
 export type PluginLayoutStateProps = PD.Values<typeof PluginLayoutStateParams>
 
 interface RootState {
@@ -149,22 +148,22 @@ export class PluginLayout extends PluginComponent<PluginLayoutStateProps> {
                     }
 
                     const s = body.style
-                    s.top = t.top;
-                    s.bottom = t.bottom;
-                    s.left = t.left;
-                    s.right = t.right;
+                    s.top = t.top!;
+                    s.bottom = t.bottom!;
+                    s.left = t.left!;
+                    s.right = t.right!;
 
-                    s.width = t.width;
-                    s.height = t.height;
-                    s.maxWidth = t.maxWidth;
-                    s.maxHeight = t.maxHeight;
-                    s.margin = t.margin;
-                    s.marginLeft = t.marginLeft;
-                    s.marginRight = t.marginRight;
-                    s.marginTop = t.marginTop;
-                    s.marginBottom = t.marginBottom;
+                    s.width = t.width!;
+                    s.height = t.height!;
+                    s.maxWidth = t.maxWidth!;
+                    s.maxHeight = t.maxHeight!;
+                    s.margin = t.margin!;
+                    s.marginLeft = t.marginLeft!;
+                    s.marginRight = t.marginRight!;
+                    s.marginTop = t.marginTop!;
+                    s.marginBottom = t.marginBottom!;
 
-                    s.position = t.position;
+                    s.position = t.position!;
                     s.overflow = t.overflow || '';
 
                     const doc = this.getScrollElement();
@@ -172,7 +171,7 @@ export class PluginLayout extends PluginComponent<PluginLayoutStateProps> {
                     doc.scrollLeft = t.scrollLeft;
 
                     this.rootState = void 0;
-                    this.root.style.zIndex = t.zIndex;
+                    this.root.style.zIndex = t.zIndex!;
                 }
             }
         } catch (e) {

src/mol-plugin/skin/base/components/controls-base.scss

@@ -12,6 +12,10 @@
     }
 }
 
+.msp-btn-collapse {
+    padding: 0 $control-spacing / 2;
+}
+
 .msp-btn, .msp-btn:active, .msp-btn-link:focus, .msp-btn:hover {
     outline: none !important;
 }

src/mol-plugin/skin/base/components/sequence.scss

@@ -13,13 +13,15 @@
 }
 
 .msp-sequence-wrapper {
-    word-break: break-word;
-    padding: $info-vertical-padding $control-spacing $info-vertical-padding $control-spacing;
+    word-break: break-all;
+    // use $control-spacing for top to have space for sequence numebrs
+    padding: $control-spacing $control-spacing $info-vertical-padding $control-spacing;
     user-select: none;
     height: 100%;
     overflow-y: auto;
     overflow-x: hidden;
     font-size: 90%;
+    line-height: 180%;
 }
 
 .msp-sequence-wrapper-non-empty {
@@ -30,4 +32,36 @@
     span {
         cursor: pointer;
     }
+
+    .msp-sequence-residue-long {
+        margin: 0em 0.2em 0em 0.2em;
+    }
+
+    .msp-sequence-residue-long-begin {
+        margin: 0em 0.2em 0em 0em;
+    }
+
+    .msp-sequence-number {
+        color: $sequence-number-color;
+        word-break: keep-all;
+        cursor: default;
+        position: relative;
+        top: -1.1em;
+        left: 3.1em;
+        padding: 0px;
+        margin-left: -3em;
+        font-size: 80%;
+    }
+
+    .msp-sequence-number-long {
+        left: 3.3em;
+    }
+
+    .msp-sequence-number-long-negative {
+        left: 2.7em;
+    }
+
+    .msp-sequence-number-negative {
+        left: 2.5em;
+    }
 }

src/mol-plugin/skin/base/components/tasks.scss

@@ -1,16 +1,16 @@
 .msp-task-state {
-    
+
     line-height: $row-height;
     //height: $row-height;
     //position: relative;
     //margin-top: 1px;
-    
+
     > span {
         @include non-selectable;
         //display: inline-block;
         //padding: 0 $control-spacing;
     }
-    
+
     > button {
         //margin-top: -2px;
         //float: left;
@@ -29,7 +29,7 @@
     bottom: 0;
     right: 0;
     z-index: 1000;
-        
+
     .msp-overlay-background {
         position: absolute;
         top: 0;
@@ -40,7 +40,7 @@
         //background: black;
         //opacity: 0.5;
     }
-    
+
     .msp-overlay-content-wrap {
         position: absolute;
         top: 0;
@@ -51,37 +51,37 @@
         width: 100%;
         height: 100%;
     }
-    
+
     .msp-overlay-content {
-        text-align: center;          
-        
-        > div {  
-            
+        text-align: center;
+
+        > div {
+
             padding-top: 2 * $row-height;
-                         
-            .msp-task-state {    
+
+            .msp-task-state {
                 $size: $row-height;
                 text-align: center;
-                            
+
                 > div {
                     height: $size;
                     margin-top: $control-spacing;
                     position: relative;
                     text-align: center;
                     width: 100%;
-                    
+
                     > div {
                         height: $size;
                         line-height: $size;
-                        display: inline-block;                        
+                        display: inline-block;
                         background: $default-background;
                         padding: 0 ($control-spacing);
                         font-weight: bold;
                         @include non-selectable;
                     }
-                    
+
                     > button {
-                        display: inline-block;       
+                        display: inline-block;
                         margin-top: -3px;
                         font-size: 140%;
                     }
@@ -94,39 +94,41 @@
 /* background */
 
 .msp-background-tasks {
-    position: absolute;    
+    position: absolute;
     left: 0;
     bottom: 0;
     z-index: 1000;
-    
-    .msp-task-state {    
+
+    .msp-task-state {
         $size: $row-height;
-                    
+
         > div {
             height: $size;
             margin-top: 1px;
             position: relative;
             width: 100%;
             background: $default-background;
-            
+
             > div {
                 height: $size;
                 line-height: $size;
-                display: inline-block;                 
+                display: inline-block;
                 padding: 0 ($control-spacing);
                 @include non-selectable;
+                white-space: nowrap;
+                background: $default-background;
+                position: absolute;
             }
-            
+
             > button {
-                display: inline-block;       
+                display: inline-block;
                 margin-top: -3px;
-                font-size: 140%;
+                // font-size: 140%;
             }
-        }        
+        }
     }
 }
 
 // .msp-background-tasks .msp-task-state {
-//     color: 
+//     color:
 // }
-

src/mol-plugin/skin/base/components/temp.scss

@@ -62,7 +62,7 @@
         height: $row-height;
 
         text-align-last: center;
-        background: none !important;
+        background: none;
         padding: 0 $control-spacing;
 
         > option[value = _] {
@@ -187,7 +187,6 @@
     position: absolute;
     left: $control-spacing;
     top: $control-spacing;
-    z-index: 10000;
 
     .msp-traj-controls {
         line-height: $row-height;

src/mol-plugin/skin/base/layout.scss

@@ -3,27 +3,39 @@
 
 .msp-layout-standard-outside {
     position: absolute;
-    @import 'layout/controls-outside';    
+    @import 'layout/controls-outside';
 }
 
 .msp-layout-standard-landscape {
     position: absolute;
-    @import 'layout/controls-landscape';    
+    @import 'layout/controls-landscape';
 }
 
 .msp-layout-standard-portrait {
     position: absolute;
-    @import 'layout/controls-portrait';    
+    @import 'layout/controls-portrait';
 }
 
-.msp-layout-expanded {    
+.msp-layout-standard-reactive {
+    position: absolute;
+
+    @media (orientation:landscape), (min-width: 1000px) {
+        @import 'layout/controls-landscape';
+    };
+
+    @media (orientation:portrait) and (max-width: 1000px) {
+        @import 'layout/controls-portrait';
+    };
+}
+
+.msp-layout-expanded {
     position: fixed;
-        
+
     @media (orientation:landscape) {
         @import 'layout/controls-landscape';
-    };     
-    
+    };
+
     @media (orientation:portrait) {
         @import 'layout/controls-portrait';
-    }  ;
+    };
 }

src/mol-plugin/skin/base/variables.scss

@@ -80,4 +80,5 @@ $entity-tag-color: color-lower-contrast($font-color, 20%);
 
 // sequence
 $sequence-background: $default-background;
+$sequence-number-color: $hover-font-color;
 $sequence-select-width: 300px;

src/mol-plugin/state/actions/structure.ts

@@ -199,7 +199,7 @@ const DownloadStructure = StateAction.build({
             createStructureTree(ctx, traj, supportProps)
         }
     }
-    return state.updateTree(b);
+    return state.updateTree(b, { revertIfAborted: true });
 });
 
 function getDownloadParams(src: string, url: (id: string) => string, label: (id: string) => string, isBinary: boolean): StateTransformer.Params<Download>[] {

src/mol-plugin/state/transforms/helpers.ts

@@ -8,11 +8,14 @@ import { Structure } from '../../../mol-model/structure';
 import { ComputedSecondaryStructure } from '../../../mol-model-props/computed/secondary-structure';
 
 /**
- * Attaches ComputedSecondaryStructure property when unavailable in sourceData
+ * Attaches ComputedSecondaryStructure property when unavailable in sourceData and
+ * when not an archival file (i.e. no database_2.database_id field)
  */
 export async function ensureSecondaryStructure(s: Structure) {
     if (s.models.length === 1 && s.model && s.model.sourceData.kind === 'mmCIF') {
-        if (!s.model.sourceData.data.struct_conf.id.isDefined && !s.model.sourceData.data.struct_sheet_range.id.isDefined) {
+        if (!s.model.sourceData.data.struct_conf.id.isDefined && !s.model.sourceData.data.struct_sheet_range.id.isDefined &&
+            !s.model.sourceData.data.database_2.database_id.isDefined
+        ) {
             await ComputedSecondaryStructure.attachFromCifOrCompute(s)
         }
     }

src/mol-plugin/state/transforms/model.ts

@@ -28,7 +28,7 @@ import { ensureSecondaryStructure } from './helpers';
 import { Script } from '../../../mol-script/script';
 import { parse3DG } from '../../../mol-io/reader/3dg/parser';
 import { trajectoryFrom3DG } from '../../../mol-model-formats/structure/3dg';
-import { CompiledStructureSelectionQueries } from '../../util/structure-selection-helper';
+import { StructureSelectionQueries } from '../../util/structure-selection-helper';
 
 export { TrajectoryFromBlob };
 export { TrajectoryFromMmCif };
@@ -564,18 +564,18 @@ const StructureComplexElement = PluginStateTransform.BuiltIn({
 
         let query: StructureQuery, label: string;
         switch (params.type) {
-            case 'protein-and-nucleic': query = CompiledStructureSelectionQueries.proteinAndNucleic; label = 'Sequence'; break;
+            case 'protein-and-nucleic': query = StructureSelectionQueries.proteinAndNucleic.query; label = 'Sequence'; break;
 
-            case 'protein': query = CompiledStructureSelectionQueries.protein; label = 'Protein'; break;
-            case 'nucleic': query = CompiledStructureSelectionQueries.nucleic; label = 'Nucleic'; break;
+            case 'protein': query = StructureSelectionQueries.protein.query; label = 'Protein'; break;
+            case 'nucleic': query = StructureSelectionQueries.nucleic.query; label = 'Nucleic'; break;
             case 'water': query = Queries.internal.water(); label = 'Water'; break;
 
-            case 'branched': query = CompiledStructureSelectionQueries.branchedPlusConnected; label = 'Branched'; break;
-            case 'ligand': query = CompiledStructureSelectionQueries.ligandPlusConnected; label = 'Ligand'; break;
+            case 'branched': query = StructureSelectionQueries.branchedPlusConnected.query; label = 'Branched'; break;
+            case 'ligand': query = StructureSelectionQueries.ligandPlusConnected.query; label = 'Ligand'; break;
 
-            case 'modified': query = CompiledStructureSelectionQueries.modified; label = 'Modified'; break;
+            case 'modified': query = StructureSelectionQueries.modified.query; label = 'Modified'; break;
 
-            case 'coarse': query = CompiledStructureSelectionQueries.coarse; label = 'Coarse'; break;
+            case 'coarse': query = StructureSelectionQueries.coarse.query; label = 'Coarse'; break;
 
             case 'atomic-sequence': query = Queries.internal.atomicSequence(); label = 'Sequence'; break;
             case 'atomic-het': query = Queries.internal.atomicHet(); label = 'HET Groups/Ligands'; break;

src/mol-plugin/state/transforms/representation.ts

@@ -32,6 +32,7 @@ import { Transparency } from '../../../mol-theme/transparency';
 import { BaseGeometry } from '../../../mol-geo/geometry/base';
 import { Script } from '../../../mol-script/script';
 import { getUnitcellRepresentation, UnitcellParams } from '../../util/model-unitcell';
+import { getStructureOrientationRepresentation, OrientationParams } from '../../util/structure-orientation';
 
 export { StructureRepresentation3D }
 export { StructureRepresentation3DHelpers }
@@ -61,9 +62,9 @@ namespace StructureRepresentation3DHelpers {
 
     export function createParams<R extends RepresentationProvider<Structure, any, any>, C extends ColorTheme.Provider<any>, S extends SizeTheme.Provider<any>>(
             ctx: PluginContext, structure: Structure, params: {
-            repr?: R | [R, (r: R, ctx: ThemeRegistryContext, s: Structure) => RepresentationProvider.ParamValues<R>],
-            color?: C | [C, (c: C, ctx: ThemeRegistryContext) => ColorTheme.ParamValues<C>],
-            size?: S | [S, (c: S, ctx: ThemeRegistryContext) => SizeTheme.ParamValues<S>]
+            repr?: R | [R, (r: R, ctx: ThemeRegistryContext, s: Structure) => Partial<RepresentationProvider.ParamValues<R>>],
+            color?: C | [C, (c: C, ctx: ThemeRegistryContext) => Partial<ColorTheme.ParamValues<C>>],
+            size?: S | [S, (c: S, ctx: ThemeRegistryContext) => Partial<SizeTheme.ParamValues<S>>]
         }): StateTransformer.Params<StructureRepresentation3D> {
 
         const themeCtx = ctx.structureRepresentation.themeCtx
@@ -79,16 +80,18 @@ namespace StructureRepresentation3DHelpers {
         const color = params.color
             ? params.color instanceof Array ? params.color[0] : params.color
             : themeCtx.colorThemeRegistry.get(repr.defaultColorTheme);
+        const colorDefaultParams = PD.getDefaultValues(color.getParams(themeCtx))
         const colorParams = params.color instanceof Array
-            ? params.color[1](color as C, themeCtx)
-            : PD.getDefaultValues(color.getParams(themeCtx));
+            ? { ...colorDefaultParams, ...params.color[1](color as C, themeCtx) }
+            : colorDefaultParams;
 
         const size = params.size
             ? params.size instanceof Array ? params.size[0] : params.size
             : themeCtx.sizeThemeRegistry.get(repr.defaultSizeTheme);
+        const sizeDefaultParams = PD.getDefaultValues(size.getParams(themeCtx))
         const sizeParams = params.size instanceof Array
-            ? params.size[1](size as S, themeCtx)
-            : PD.getDefaultValues(size.getParams(themeCtx));
+            ? { ...sizeDefaultParams, ...params.size[1](size as S, themeCtx) }
+            : sizeDefaultParams;
 
         return ({
             type: { name: ctx.structureRepresentation.registry.getName(repr), params: reprParams },
@@ -696,4 +699,32 @@ const ModelUnitcell3D = PluginStateTransform.BuiltIn({
             return StateTransformer.UpdateResult.Updated;
         });
     }
+});
+
+export { StructureOrientation3D }
+type StructureOrientation3D = typeof StructureOrientation3D
+const StructureOrientation3D = PluginStateTransform.BuiltIn({
+    name: 'structure-orientation-3d',
+    display: 'Structure Orientation',
+    from: SO.Molecule.Structure,
+    to: SO.Shape.Representation3D,
+    params: {
+        ...OrientationParams,
+    }
+})({
+    canAutoUpdate({ oldParams, newParams }) {
+        return true;
+    },
+    apply({ a, params }) {
+        return Task.create('Structure Orientation', async ctx => {
+            const repr = await getStructureOrientationRepresentation(ctx, a.data, params);
+            return new SO.Shape.Representation3D({ repr, source: a }, { label: `Orientation` });
+        });
+    },
+    update({ a, b, newParams }) {
+        return Task.create('Structure Orientation', async ctx => {
+            await getStructureOrientationRepresentation(ctx, a.data, newParams, b.data.repr as ShapeRepresentation<any, any, any>);
+            return StateTransformer.UpdateResult.Updated;
+        });
+    }
 });

src/mol-plugin/ui/base.tsx

@@ -84,7 +84,7 @@ export abstract class CollapsableControls<P extends CollapsableProps = Collapsab
 
         return <div className={wrapClass}>
             <div className='msp-transform-header'>
-                <button className='msp-btn msp-btn-block' onClick={this.toggleCollapsed}>
+                <button className='msp-btn msp-btn-block msp-btn-collapse' onClick={this.toggleCollapsed}>
                     <span className={`msp-icon msp-icon-${this.state.isCollapsed ? 'expand' : 'collapse'}`} />
                     {this.state.header}
                 </button>