0.4.2

was not taking operator.name into account

.vscode/extensions.json

@@ -4,7 +4,9 @@
 
 	// List of extensions which should be recommended for users of this workspace.
 	"recommendations": [
+		"firsttris.vscode-jest-runner",
 		"ms-vscode.vscode-typescript-tslint-plugin",
+		"msjsdiag.debugger-for-chrome",
 		"slevesque.shader",
 		"stpn.vscode-graphql",
 		"wayou.vscode-todo-highlight"

.vscode/launch.json

@@ -0,0 +1,16 @@
+{
+    // Use IntelliSense to learn about possible attributes.
+    // Hover to view descriptions of existing attributes.
+    // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+    "version": "0.2.0",
+    "configurations": [
+        {
+            "type": "chrome",
+            "request": "launch",
+            "name": "Launch Mol* Viewer",
+            "url": "http://localhost:1338/build/viewer/index.html",
+            "sourceMaps": true,
+            "webRoot": "${workspaceFolder}"
+        }
+    ]
+}

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
 
@@ -143,7 +145,7 @@ To get syntax highlighting for shader and graphql files add the following to Vis
 
 ## Deploy
     npm run test
-    NODE_ENV=production npm run build
+    npm run build
     node ./scripts/deploy.js # currently updates the viewer on molstar.org/viewer
 
 ## Contributing

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": "0.2.8",
+  "version": "0.4.2",
   "description": "A comprehensive macromolecular library.",
   "homepage": "https://github.com/molstar/molstar#readme",
   "repository": {
@@ -15,11 +15,11 @@
     "test": "npm run lint && jest",
     "build": "npm run build-tsc && npm run build-extra && npm run build-webpack",
     "build-tsc": "tsc",
-    "build-extra": "cpx \"src/**/*.{scss,woff,woff2,ttf,otf,eot,svg,html}\" lib/",
+    "build-extra": "cpx \"src/**/*.{scss,woff,woff2,ttf,otf,eot,svg,html,ico}\" lib/",
     "build-webpack": "webpack --mode production",
     "watch": "concurrently --kill-others \"npm:watch-tsc\" \"npm:watch-extra\" \"npm:watch-webpack\"",
     "watch-tsc": "tsc -watch",
-    "watch-extra": "cpx \"src/**/*.{scss,woff,woff2,ttf,otf,eot,svg,html}\" lib/ --watch",
+    "watch-extra": "cpx \"src/**/*.{scss,woff,woff2,ttf,otf,eot,svg,html,ico}\" lib/ --watch",
     "watch-webpack": "webpack -w --mode development --display minimal",
     "serve": "http-server -p 1338",
     "model-server": "node lib/servers/model/server.js",
@@ -65,7 +65,7 @@
   "devDependencies": {
     "benchmark": "^2.1.4",
     "circular-dependency-plugin": "^5.2.0",
-    "concurrently": "^4.1.2",
+    "concurrently": "^5.0.0",
     "cpx": "^1.5.0",
     "css-loader": "^3.2.0",
     "extra-watch-webpack-plugin": "^1.0.3",
@@ -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",
-    "sass-loader": "^7.3.1",
-    "simple-git": "^1.124.0",
+    "resolve-url-loader": "^3.1.1",
+    "sass-loader": "^8.0.0",
+    "simple-git": "^1.126.0",
     "style-loader": "^1.0.0",
-    "ts-jest": "^24.0.2",
-    "tslint": "^5.19.0",
-    "typescript": "^3.5.3",
-    "webpack": "^4.39.2",
-    "webpack-cli": "^3.3.7"
+    "ts-jest": "^24.1.0",
+    "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": "^12.7.2",
-    "@types/node-fetch": "^2.5.0",
-    "@types/react": "^16.9.2",
-    "@types/react-dom": "^16.9.0",
+    "@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": "^14.4.2",
+    "graphql": "^14.5.8",
     "immutable": "^3.8.2",
     "node-fetch": "^2.6.0",
-    "react": "^16.9.0",
-    "react-dom": "^16.9.0",
-    "rxjs": "^6.5.2",
-    "swagger-ui-dist": "^3.23.5",
+    "react": "^16.12.0",
+    "react-dom": "^16.12.0",
+    "rxjs": "^6.5.3",
+    "swagger-ui-dist": "^3.24.3",
     "util.promisify": "^1.0.0",
     "xhr2": "^0.2.0"
   }

src/apps/basic-wrapper/controls.tsx

@@ -19,4 +19,12 @@ export class BasicWrapperControls extends PluginUIComponent {
             <TransformUpdaterControl nodeRef='ihm-visual' header={{ name: 'I/HM Visual' }} initiallyCollapsed={true} />
         </div>;
     }
+}
+
+export class CustomToastMessage extends PluginUIComponent {
+    render() {
+        return <>
+            Custom <i>Toast</i> content. No timeout.
+        </>;
+    }
 }

src/apps/basic-wrapper/index.html

@@ -105,10 +105,18 @@
 
             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());
             addControl('Dynamic Superposition', () => BasicMolStarWrapper.tests.dynamicSuperposition());
+            addControl('Validation Tooltip', () => BasicMolStarWrapper.tests.toggleValidationTooltip());
+            
+            addControl('Show Toasts', () => BasicMolStarWrapper.tests.showToasts());
+            addControl('Hide Toasts', () => BasicMolStarWrapper.tests.hideToasts());
 
             ////////////////////////////////////////////////////////
 

src/apps/basic-wrapper/index.ts

@@ -11,12 +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'
@@ -61,7 +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' })
@@ -142,6 +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;
@@ -152,6 +172,28 @@ class BasicWrapper {
         dynamicSuperposition: async () => {
             await PluginCommands.State.RemoveObject.dispatch(this.plugin, { state: this.plugin.state.dataState, ref: StateTransform.RootRef });
             await dynamicSuperpositionTest(this.plugin, ['1tqn', '2hhb', '4hhb'], 'HEM');
+        },
+        toggleValidationTooltip: async () => {
+            const state = this.plugin.state.behaviorState;
+            const tree = state.build().to(PDBeStructureQualityReport.id).update(PDBeStructureQualityReport, p => ({ ...p, showTooltip: !p.showTooltip }));
+            await PluginCommands.State.Update.dispatch(this.plugin, { state, tree });
+        },
+        showToasts: () => {
+            PluginCommands.Toast.Show.dispatch(this.plugin, {
+                title: 'Toast 1',
+                message: 'This is an example text, timeout 3s',
+                key: 'toast-1',
+                timeoutMs: 3000
+            });
+            PluginCommands.Toast.Show.dispatch(this.plugin, {
+                title: 'Toast 2',
+                message: CustomToastMessage,
+                key: 'toast-2'
+            });
+        },
+        hideToasts: () => {
+            PluginCommands.Toast.Hide.dispatch(this.plugin, { key: 'toast-1' });
+            PluginCommands.Toast.Hide.dispatch(this.plugin, { key: 'toast-2' });
         }
     }
 }

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/structure-info/model.ts

@@ -15,6 +15,7 @@ import { OrderedSet } from '../../mol-data/int';
 import { openCif, downloadCif } from './helpers';
 import { Vec3 } from '../../mol-math/linear-algebra';
 import { trajectoryFromMmCIF } from '../../mol-model-formats/structure/mmcif';
+import { Sequence } from '../../mol-model/sequence';
 
 
 async function downloadFromPdb(pdb: string) {
@@ -110,9 +111,10 @@ export function printSequence(model: Model) {
     console.log('\nSequence\n=============');
     const { byEntityKey } = model.sequence;
     for (const key of Object.keys(byEntityKey)) {
-        const seq = byEntityKey[+key];
-        console.log(`${seq.entityId} (${seq.sequence.kind} ${seq.num.value(0)} (offset ${seq.sequence.offset}), ${seq.num.value(seq.num.rowCount - 1)}) (${seq.compId.value(0)}, ${seq.compId.value(seq.compId.rowCount - 1)})`);
-        console.log(`${seq.sequence.sequence}`);
+        const { sequence, entityId } = byEntityKey[+key];
+        const { seqId, compId } = sequence
+        console.log(`${entityId} (${sequence.kind} ${seqId.value(0)} (offset ${sequence.offset}), ${seqId.value(seqId.rowCount - 1)}) (${compId.value(0)}, ${compId.value(compId.rowCount - 1)})`);
+        console.log(`${Sequence.getSequenceString(sequence)}`);
     }
     console.log();
 }
@@ -159,14 +161,14 @@ export function printUnits(structure: Structure) {
             console.log(`Coarse unit ${unit.id} ${unit.conformation.operator.name} (${Unit.isSpheres(l.unit) ? 'spheres' : 'gaussians'}): ${size} elements.`);
 
             const props = StructureProperties.coarse;
-            const seq = l.unit.model.sequence;
+            const modelSeq = l.unit.model.sequence;
 
             for (let j = 0, _j = Math.min(size, 3); j < _j; j++) {
                 l.element = OrderedSet.getAt(elements, j);
 
                 const residues: string[] = [];
                 const start = props.seq_id_begin(l), end = props.seq_id_end(l);
-                const compId = seq.byEntityKey[props.entityKey(l)].compId.value;
+                const compId = modelSeq.byEntityKey[props.entityKey(l)].sequence.compId.value;
                 for (let e = start; e <= end; e++) residues.push(compId(e));
                 console.log(`${props.asym_id(l)}:${start}-${end} (${residues.join('-')}) ${props.asym_id(l)} [${props.x(l).toFixed(2)}, ${props.y(l).toFixed(2)}, ${props.z(l).toFixed(2)}]`);
             }

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
         }
@@ -297,7 +297,7 @@ export const LoadCellPackModel = StateAction.build({
                 ['spacefill', 'Spacefill'],
                 ['gaussian-surface', 'Gaussian Surface'],
                 ['point', 'Point'],
-            ])
+            ] as ['spacefill' | 'gaussian-surface' | 'point', string][])
         }, { isExpanded: true })
     },
     from: PSO.Root
@@ -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/apps/viewer/extensions/jolecule.ts

@@ -138,23 +138,19 @@ function buildSnapshot(plugin: PluginContext, template: { tree: StateTree, struc
 }
 
 function getCameraSnapshot(e: JoleculeSnapshot['camera']): Camera.Snapshot {
-    const direction = Vec3.sub(Vec3.zero(), e.pos, e.in);
+    const direction = Vec3.sub(Vec3(), e.pos, e.in);
     Vec3.normalize(direction, direction);
-    const up = Vec3.sub(Vec3.zero(), e.pos, e.up);
+    const up = Vec3.sub(Vec3(), e.pos, e.up);
     Vec3.normalize(up, up);
 
     const s: Camera.Snapshot = {
         mode: 'perspective',
-        position: Vec3.scaleAndAdd(Vec3.zero(), e.pos, direction, e.slab.zoom),
-        target: e.pos,
-        direction,
-        up,
-        near: e.slab.zoom + e.slab.z_front,
-        far: e.slab.zoom + e.slab.z_back,
-        fogNear: e.slab.zoom + e.slab.z_front,
-        fogFar: e.slab.zoom + e.slab.z_back,
         fov: Math.PI / 4,
-        zoom: 1
+        position: Vec3.scaleAndAdd(Vec3(), e.pos, direction, e.slab.zoom),
+        target: e.pos,
+        radius: (e.slab.z_back - e.slab.z_front) / 2,
+        fog: 50,
+        up,
     };
     return s;
 }

src/apps/viewer/index.html

@@ -3,6 +3,7 @@
     <head>
         <meta charset="utf-8" />
         <meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
+        <link rel="icon" href="./favicon.ico" type="image/x-icon">
         <title>Mol* Viewer</title>
         <style>
             * {

src/apps/viewer/index.ts

@@ -7,6 +7,7 @@
 
 import { createPlugin, DefaultPluginSpec } from '../../mol-plugin';
 import './index.html'
+import './favicon.ico'
 import { PluginContext } from '../../mol-plugin/context';
 import { PluginCommands } from '../../mol-plugin/command';
 import { PluginSpec } from '../../mol-plugin/spec';

src/examples/proteopedia-wrapper/annotation.ts

@@ -27,7 +27,7 @@ export const EvolutionaryConservation = CustomElementProperty.create<number>({
     name: 'proteopedia-wrapper-evolutionary-conservation',
     display: 'Evolutionary Conservation',
     async getData(model: Model) {
-        const id = model.label.toLowerCase();
+        const id = model.entryId.toLowerCase();
         const req = await fetch(`https://proteopedia.org/cgi-bin/cnsrf?${id}`);
         const json = await req.json();
         const annotations = (json && json.residueAnnotations) || [];

src/examples/proteopedia-wrapper/changelog.md

@@ -1,3 +1,9 @@
+== v3.4 ==
+
+* Fixed HET group reset.
+* Updated core.
+* Removed Camera Cliping.
+
 == v3.3 ==
 
 * Camera Clipping.

src/examples/proteopedia-wrapper/helpers.ts

@@ -18,9 +18,9 @@ export interface ModelInfo {
 
 export namespace ModelInfo {
     async function getPreferredAssembly(ctx: PluginContext, model: Model) {
-        if (model.label.length <= 3) return void 0;
+        if (model.entryId.length <= 3) return void 0;
         try {
-            const id = model.label.toLowerCase();
+            const id = model.entryId.toLowerCase();
             const src = await ctx.runTask(ctx.fetch({ url: `https://www.ebi.ac.uk/pdbe/api/pdb/entry/summary/${id}` })) as string;
             const json = JSON.parse(src);
             const data = json && json[id];

src/examples/proteopedia-wrapper/index.html

@@ -133,8 +133,8 @@
             addControl('Reset Position', () => PluginWrapper.camera.resetPosition());
             addControl('Toggle Spin', () => PluginWrapper.camera.toggleSpin());
             // Same as "wheel icon" and Viewport options
-            addControl('Clip', () => PluginWrapper.viewport.setSettings({ clip: [33, 66] }));
-            addControl('Reset Clip', () => PluginWrapper.viewport.setSettings({ clip: [1, 100] }));
+            // addControl('Clip', () => PluginWrapper.viewport.setSettings({ clip: [33, 66] }));
+            // addControl('Reset Clip', () => PluginWrapper.viewport.setSettings({ clip: [1, 100] }));
             
             addSeparator();
 

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';
@@ -37,7 +36,7 @@ require('../../mol-plugin/skin/light.scss')
 
 class MolStarProteopediaWrapper {
     static VERSION_MAJOR = 3;
-    static VERSION_MINOR = 3;
+    static VERSION_MINOR = 4;
 
     private _ev = RxEventHelper.create();
 
@@ -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);
@@ -335,7 +336,7 @@ class MolStarProteopediaWrapper {
 
     hetGroups = {
         reset: () => {
-            const update = this.state.build().delete(StateElements.HetGroupFocus);
+            const update = this.state.build().delete(StateElements.HetGroupFocusGroup);
             PluginCommands.State.Update.dispatch(this.plugin, { state: this.state, tree: update });
             PluginCommands.Camera.Reset.dispatch(this.plugin, { });
         },

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-app/component/color-theme.tsx

@@ -1,56 +0,0 @@
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import * as React from 'react'
-import { ColorTheme } from '../../mol-theme/color';
-import { Color } from '../../mol-util/color';
-
-export interface ColorThemeComponentProps {
-    colorTheme: ColorTheme<any>
-}
-
-export interface ColorThemeComponentState {
-
-}
-
-export class ColorThemeComponent extends React.Component<ColorThemeComponentProps, ColorThemeComponentState> {
-    state = {
-
-    }
-
-    render() {
-        const ct = this.props.colorTheme
-        return <div>
-            <span>Color Theme Info </span>
-
-            {ct.description ? <div><i>{ct.description}</i></div> : ''}
-            {
-                ct.legend && ct.legend.kind === 'scale-legend'
-                    ? <div
-                        style={{
-                            width: '100%',
-                            height: '30px',
-                            background: `linear-gradient(to right, ${ct.legend.colors.map(c => Color.toStyle(c)).join(', ')})`
-                        }}
-                    >
-                        <span style={{float: 'left', padding: '6px', color: 'white', fontWeight: 'bold', backgroundColor: 'rgba(0, 0, 0, 0.2)'}}>{ct.legend.minLabel}</span>
-                        <span style={{float: 'right', padding: '6px', color: 'white', fontWeight: 'bold', backgroundColor: 'rgba(0, 0, 0, 0.2)'}}>{ct.legend.maxLabel}</span>
-                    </div>
-                : ct.legend && ct.legend.kind === 'table-legend'
-                    ? <div>
-                        {ct.legend.table.map((value, i) => {
-                            const [name, color] = value
-                            return <div key={i} style={{minWidth: '60px', marginRight: '5px', display: 'inline-block'}}>
-                                <div style={{width: '30px', height: '20px', backgroundColor: Color.toStyle(color), display: 'inline-block'}}></div>
-                                {name}
-                            </div>
-                        })}
-                    </div>
-                : ''
-            }
-        </div>;
-    }
-}

src/mol-canvas3d/camera.ts

@@ -7,17 +7,11 @@
 
 import { Mat4, Vec3, Vec4, EPSILON } from '../mol-math/linear-algebra'
 import { Viewport, cameraProject, cameraUnproject } from './camera/util';
-import { Object3D } from '../mol-gl/object3d';
-import { BehaviorSubject } from 'rxjs';
 import { CameraTransitionManager } from './camera/transition';
 
 export { Camera }
 
-// TODO: slab controls that modify near/far planes?
-
-class Camera implements Object3D {
-    readonly updatedViewProjection = new BehaviorSubject<Camera>(this);
-
+class Camera {
     readonly view: Mat4 = Mat4.identity();
     readonly projection: Mat4 = Mat4.identity();
     readonly projectionView: Mat4 = Mat4.identity();
@@ -32,14 +26,17 @@ class Camera implements Object3D {
         width: 1, height: 1
     }
 
+    near = 1
+    far = 10000
+    fogNear = 5000
+    fogFar = 10000
+    zoom = 1
+
     readonly transition: CameraTransitionManager = new CameraTransitionManager(this);
 
     get position() { return this.state.position; }
     set position(v: Vec3) { Vec3.copy(this.state.position, v); }
 
-    get direction() { return this.state.direction; }
-    set direction(v: Vec3) { Vec3.copy(this.state.direction, v); }
-
     get up() { return this.state.up; }
     set up(v: Vec3) { Vec3.copy(this.state.up, v); }
 
@@ -51,10 +48,12 @@ class Camera implements Object3D {
     private deltaDirection = Vec3.zero();
     private newPosition = Vec3.zero();
 
-    updateMatrices() {
+    update() {
         const snapshot = this.state as Camera.Snapshot;
         const height = 2 * Math.tan(snapshot.fov / 2) * Vec3.distance(snapshot.position, snapshot.target);
-        snapshot.zoom = this.viewport.height / height;
+        this.zoom = this.viewport.height / height;
+
+        updateClip(this);
 
         switch (this.state.mode) {
             case 'orthographic': updateOrtho(this); break;
@@ -62,11 +61,7 @@ class Camera implements Object3D {
             default: throw new Error('unknown camera mode');
         }
 
-        const changed = !Mat4.areEqual(this.projection, this.prevProjection, EPSILON.Value) || !Mat4.areEqual(this.view, this.prevView, EPSILON.Value);
-
-        Mat4.mul(this.projectionView, this.projection, this.view)
-        Mat4.invert(this.inverseProjectionView, this.projectionView)
-
+        const changed = !Mat4.areEqual(this.projection, this.prevProjection, EPSILON) || !Mat4.areEqual(this.view, this.prevView, EPSILON);
 
         if (changed) {
             Mat4.mul(this.projectionView, this.projection, this.view)
@@ -74,57 +69,44 @@ class Camera implements Object3D {
 
             Mat4.copy(this.prevView, this.view);
             Mat4.copy(this.prevProjection, this.projection);
-            this.updatedViewProjection.next(this);
         }
 
         return changed;
     }
 
-    setState(snapshot: Partial<Camera.Snapshot>) {
-        this.transition.apply(snapshot);
+    setState(snapshot: Partial<Camera.Snapshot>, durationMs?: number) {
+        this.transition.apply(snapshot, durationMs);
     }
 
     getSnapshot() {
-        const ret = Camera.createDefaultSnapshot();
-        Camera.copySnapshot(ret, this.state);
-        return ret;
+        return Camera.copySnapshot(Camera.createDefaultSnapshot(), this.state);
     }
 
-    getFocus(target: Vec3, radius: number, dir?: Vec3): 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
         const aspectFactor = (height < width ? 1 : aspect)
-        const currentDistance = Vec3.distance(this.state.position, target)
         const targetDistance = Math.abs((radius / aspectFactor) / Math.sin(fov / 2))
 
-        const deltaDistance = Math.abs(currentDistance - targetDistance)
+        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)
 
-        if (dir) {
-            Vec3.setMagnitude(this.deltaDirection, dir, targetDistance)
-            Vec3.add(this.newPosition, target, this.deltaDirection)
-        } else {
-            Vec3.setMagnitude(this.deltaDirection, this.state.direction, deltaDistance)
-            if (currentDistance < targetDistance) Vec3.negate(this.deltaDirection, this.deltaDirection)
-            Vec3.add(this.newPosition, this.state.position, this.deltaDirection)
-        }
+        const state = Camera.copySnapshot(Camera.createDefaultSnapshot(), this.state)
+        state.target = Vec3.clone(target)
+        state.radius = radius
+        state.position = Vec3.clone(this.newPosition)
+        if (up) Vec3.matchDirection(state.up, up, state.up)
 
-        return { target, position: Vec3.clone(this.newPosition) };
+        return state
     }
 
-    focus(target: Vec3, radius: number, dir?: Vec3) {
-        if (radius > 0) this.setState(this.getFocus(target, radius, dir));
+    focus(target: Vec3, radius: number, durationMs?: number, up?: Vec3, dir?: Vec3) {
+        if (radius > 0) this.setState(this.getFocus(target, radius, up, dir), durationMs);
     }
 
-    // lookAt(target: Vec3) {
-    //     cameraLookAt(this.position, this.up, this.direction, target);
-    // }
-
-    // translate(v: Vec3) {
-    //     Vec3.add(this.position, this.position, v);
-    //     cameraLookAt(this.position, this.up, this.direction, this.target);
-    // }
-
     project(out: Vec4, point: Vec3) {
         return cameraProject(out, point, this.viewport, this.projectionView)
     }
@@ -133,10 +115,6 @@ class Camera implements Object3D {
         return cameraUnproject(out, point, this.viewport, this.inverseProjectionView)
     }
 
-    dispose() {
-        this.updatedViewProjection.complete();
-    }
-
     constructor(state?: Partial<Camera.Snapshot>, viewport = Viewport.create(-1, -1, 1, 1)) {
         this.viewport = viewport;
         Camera.copySnapshot(this.state, state);
@@ -147,13 +125,6 @@ class Camera implements Object3D {
 namespace Camera {
     export type Mode = 'perspective' | 'orthographic'
 
-    export interface ClippingInfo {
-        near: number,
-        far: number,
-        fogNear: number,
-        fogFar: number
-    }
-
     /**
      * Sets an offseted view in a larger frustum. This is useful for
      * - multi-window or multi-monitor/multi-machine setups
@@ -181,64 +152,48 @@ namespace Camera {
     export function createDefaultSnapshot(): Snapshot {
         return {
             mode: 'perspective',
+            fov: Math.PI / 4,
 
             position: Vec3.create(0, 0, 100),
-            direction: Vec3.create(0, 0, 1),
             up: Vec3.create(0, 1, 0),
-
             target: Vec3.create(0, 0, 0),
 
-            near: 1,
-            far: 10000,
-            fogNear: 1,
-            fogFar: 10000,
-
-            fov: Math.PI / 4,
-            zoom: 1,
+            radius: 10,
+            fog: 50,
         };
     }
 
     export interface Snapshot {
-        mode: Mode,
+        mode: Mode
+        fov: number
 
-        position: Vec3,
-        // Normalized camera direction
-        direction: Vec3,
-        up: Vec3,
-        target: Vec3,
+        position: Vec3
+        up: Vec3
+        target: Vec3
 
-        near: number,
-        far: number,
-        fogNear: number,
-        fogFar: number,
-
-        fov: number,
-        zoom: number,
+        radius: number
+        fog: number
     }
 
     export function copySnapshot(out: Snapshot, source?: Partial<Snapshot>) {
-        if (!source) return;
+        if (!source) return out;
 
         if (typeof source.mode !== 'undefined') out.mode = source.mode;
+        if (typeof source.fov !== 'undefined') out.fov = source.fov;
 
         if (typeof source.position !== 'undefined') Vec3.copy(out.position, source.position);
-        if (typeof source.direction !== 'undefined') Vec3.copy(out.direction, source.direction);
         if (typeof source.up !== 'undefined') Vec3.copy(out.up, source.up);
         if (typeof source.target !== 'undefined') Vec3.copy(out.target, source.target);
 
-        if (typeof source.near !== 'undefined') out.near = source.near;
-        if (typeof source.far !== 'undefined') out.far = source.far;
-        if (typeof source.fogNear !== 'undefined') out.fogNear = source.fogNear;
-        if (typeof source.fogFar !== 'undefined') out.fogFar = source.fogFar;
+        if (typeof source.radius !== 'undefined') out.radius = source.radius;
+        if (typeof source.fog !== 'undefined') out.fog = source.fog;
 
-        if (typeof source.fov !== 'undefined') out.fov = source.fov;
-        if (typeof source.zoom !== 'undefined') out.zoom = source.zoom;
+        return out;
     }
 }
 
-const _center = Vec3.zero();
 function updateOrtho(camera: Camera) {
-    const { viewport, state: { zoom, near, far }, viewOffset } = camera
+    const { viewport, zoom, near, far, viewOffset } = camera
 
     const fullLeft = -(viewport.width - viewport.x) / 2
     const fullRight = (viewport.width - viewport.x) / 2
@@ -270,16 +225,15 @@ function updateOrtho(camera: Camera) {
     Mat4.ortho(camera.projection, left, right, top, bottom, near, far)
 
     // build view matrix
-    Vec3.add(_center, camera.position, camera.direction)
-    Mat4.lookAt(camera.view, camera.position, _center, camera.up)
+    Mat4.lookAt(camera.view, camera.position, camera.target, camera.up)
 }
 
 function updatePers(camera: Camera) {
     const aspect = camera.viewport.width / camera.viewport.height
 
-    const { state: { fov, near, far }, viewOffset } = camera
+    const { near, far, viewOffset } = camera
 
-    let top = near * Math.tan(0.5 * fov)
+    let top = near * Math.tan(0.5 * camera.state.fov)
     let height = 2 * top
     let width = aspect * height
     let left = -0.5 * width
@@ -295,6 +249,33 @@ function updatePers(camera: Camera) {
     Mat4.perspective(camera.projection, left, left + width, top, top - height, near, far)
 
     // build view matrix
-    Vec3.add(_center, camera.position, camera.direction)
-    Mat4.lookAt(camera.view, camera.position, _center, camera.up)
+    Mat4.lookAt(camera.view, camera.position, camera.target, camera.up)
+}
+
+function updateClip(camera: Camera) {
+    const { radius, mode, fog } = camera.state
+
+    const cDist = Vec3.distance(camera.position, camera.target)
+    const bRadius = Math.max(1, radius)
+
+    let near = cDist - bRadius
+    let far = cDist + bRadius
+
+    const fogNearFactor = -(50 - fog) / 50
+    let fogNear = cDist - (bRadius * fogNearFactor)
+    let fogFar = cDist + bRadius
+
+    if (mode === 'perspective') {
+        // set at least to 5 to avoid slow sphere impostor rendering
+        near = Math.max(5, near)
+        far = Math.max(5, far)
+    } else {
+        near = Math.max(0, near)
+        far = Math.max(0, far)
+    }
+
+    camera.near = near;
+    camera.far = far;
+    camera.fogNear = fogNear;
+    camera.fogFar = fogFar;
 }

src/mol-canvas3d/camera/transition.ts

@@ -1,5 +1,5 @@
 /**
- * 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>
  */
@@ -22,7 +22,7 @@ class CameraTransitionManager {
     private current = Camera.createDefaultSnapshot();
 
     apply(to: Partial<Camera.Snapshot>, durationMs: number = 0, transition?: CameraTransitionManager.TransitionFunc) {
-        if (durationMs <= 0 || to.mode !== this.camera.state.mode) {
+        if (durationMs <= 0 || (typeof to.mode !== 'undefined' && to.mode !== this.camera.state.mode)) {
             this.finish(to);
             return;
         }
@@ -68,33 +68,21 @@ class CameraTransitionManager {
 namespace CameraTransitionManager {
     export type TransitionFunc = (out: Camera.Snapshot, t: number, source: Camera.Snapshot, target: Camera.Snapshot) => void
 
+    const _rot = Quat.identity();
     export function defaultTransition(out: Camera.Snapshot, t: number, source: Camera.Snapshot, target: Camera.Snapshot): void {
         Camera.copySnapshot(out, target);
 
-        // Rotate direction
-        const rot = Quat.identity();
-        Quat.slerp(rot, rot, Quat.rotationTo(Quat.zero(), source.direction, target.direction), t);
-        Vec3.transformQuat(out.direction, source.direction, rot);
-
         // Rotate up
-        Quat.setIdentity(rot);
-        Quat.slerp(rot, rot, Quat.rotationTo(Quat.zero(), source.up, target.up), t);
-        Vec3.transformQuat(out.up, source.up, rot);
+        Quat.slerp(_rot, Quat.Identity, Quat.rotationTo(_rot, source.up, target.up), t);
+        Vec3.transformQuat(out.up, source.up, _rot);
 
-        // Lerp target
+        // Lerp target, position & radius
         Vec3.lerp(out.target, source.target, target.target, t);
+        Vec3.lerp(out.position, source.position, target.position, t);
+        out.radius = lerp(source.radius, target.radius, t);
 
-        // Update position
-        const dist = -lerp(Vec3.distance(source.position, source.target), Vec3.distance(target.position, target.target), t);
-        Vec3.scale(out.position, out.direction, dist);
-        Vec3.add(out.position, out.position, out.target);
-
-        // Lerp other props
-        out.zoom = lerp(source.zoom, target.zoom, t);
+        // Lerp fov & fog
         out.fov = lerp(source.fov, target.fov, t);
-        out.near = lerp(source.near, target.near, t);
-        out.far = lerp(source.far, target.far, t);
-        out.fogNear = lerp(source.fogNear, target.fogNear, t);
-        out.fogFar = lerp(source.fogFar, target.fogFar, t);
+        out.fog = lerp(source.fog, target.fog, t);
     }
 }

src/mol-canvas3d/camera/util.ts

@@ -4,7 +4,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { Mat4, Vec3, Vec4, EPSILON } from '../../mol-math/linear-algebra'
+import { Mat4, Vec3, Vec4 } from '../../mol-math/linear-algebra'
 
 export { Viewport }
 
@@ -55,31 +55,6 @@ namespace Viewport {
 
 //
 
-const tmpVec3 = Vec3()
-
-/** Modifies the direction & up vectors in place, both are normalized */
-export function cameraLookAt(position: Vec3, up: Vec3, direction: Vec3, target: Vec3) {
-    Vec3.sub(tmpVec3, target, position)
-    Vec3.normalize(tmpVec3, tmpVec3)
-
-    if (!Vec3.isZero(tmpVec3)) {
-        // change direction vector to look at target
-        const d = Vec3.dot(tmpVec3, up)
-        if (Math.abs(d - 1) < EPSILON.Value) { // parallel
-            Vec3.scale(up, direction, -1)
-        } else if (Math.abs(d + 1) < EPSILON.Value) { // anti parallel
-            Vec3.copy(up, direction)
-        }
-        Vec3.copy(direction, tmpVec3)
-
-        // normalize up vector
-        Vec3.cross(tmpVec3, direction, up)
-        Vec3.normalize(tmpVec3, tmpVec3)
-        Vec3.cross(up, tmpVec3, direction)
-        Vec3.normalize(up, up)
-    }
-}
-
 const NEAR_RANGE = 0
 const FAR_RANGE = 1
 

src/mol-canvas3d/canvas3d.ts

@@ -32,14 +32,12 @@ import { readTexture } from '../mol-gl/compute/util';
 import { DrawPass } from './passes/draw';
 import { PickPass } from './passes/pick';
 import { Task } from '../mol-task';
+import { ImagePass, ImageProps } from './passes/image';
 
 export const Canvas3DParams = {
-    // TODO: FPS cap?
-    // maxFps: PD.Numeric(30),
     cameraMode: PD.Select('perspective', [['perspective', 'Perspective'], ['orthographic', 'Orthographic']]),
-    cameraClipDistance: PD.Numeric(0, { min: 0.0, max: 50.0, step: 0.1 }, { description: 'The distance between camera and scene at which to clip regardless of near clipping plane.' }),
-    clip: PD.Interval([1, 100], { min: 1, max: 100, step: 1 }),
-    fog: PD.Interval([50, 100], { min: 1, max: 100, step: 1 }),
+    cameraFog: PD.Numeric(50, { min: 1, max: 100, step: 1 }),
+    cameraResetDurationMs: PD.Numeric(250, { min: 0, max: 1000, step: 1 }, { description: 'The time it takes to reset the camera.' }),
 
     multiSample: PD.Group(MultiSampleParams),
     postprocessing: PD.Group(PostprocessingParams),
@@ -77,6 +75,7 @@ interface Canvas3D {
     downloadScreenshot: () => void
     getPixelData: (variant: GraphicsRenderVariant) => PixelData
     setProps: (props: Partial<Canvas3DProps>) => void
+    getImagePass: () => ImagePass
 
     /** Returns a copy of the current Canvas3D instance props */
     readonly props: Readonly<Canvas3DProps>
@@ -91,15 +90,16 @@ const requestAnimationFrame = typeof window !== 'undefined' ? window.requestAnim
 const DefaultRunTask = (task: Task<unknown>) => task.run()
 
 namespace Canvas3D {
-    export interface HighlightEvent { current: Representation.Loci, modifiers?: ModifiersKeys }
+    export interface HoverEvent { current: Representation.Loci, buttons: ButtonsType, modifiers: ModifiersKeys }
     export interface ClickEvent { current: Representation.Loci, buttons: ButtonsType, modifiers: ModifiersKeys }
 
     export function fromCanvas(canvas: HTMLCanvasElement, props: Partial<Canvas3DProps> = {}, runTask = DefaultRunTask) {
         const gl = getGLContext(canvas, {
-            alpha: false,
+            alpha: true,
             antialias: true,
             depth: true,
-            preserveDrawingBuffer: true
+            preserveDrawingBuffer: true,
+            premultipliedAlpha: false,
         })
         if (gl === null) throw new Error('Could not create a WebGL rendering context')
         const input = InputObserver.fromElement(canvas)
@@ -116,31 +116,31 @@ namespace Canvas3D {
         const startTime = now()
         const didDraw = new BehaviorSubject<now.Timestamp>(0 as now.Timestamp)
 
-        const camera = new Camera({
-            near: 0.1,
-            far: 10000,
-            position: Vec3.create(0, 0, 100),
-            mode: p.cameraMode
-        })
-
         const webgl = createContext(gl)
 
         let width = gl.drawingBufferWidth
         let height = gl.drawingBufferHeight
 
         const scene = Scene.create(webgl)
+
+        const camera = new Camera({
+            position: Vec3.create(0, 0, 100),
+            mode: p.cameraMode,
+            fog: p.cameraFog
+        })
+
         const controls = TrackballControls.create(input, camera, p.trackball)
-        const renderer = Renderer.create(webgl, camera, p.renderer)
+        const renderer = Renderer.create(webgl, p.renderer)
         const debugHelper = new BoundingSphereHelper(webgl, scene, p.debug);
         const interactionHelper = new Canvas3dInteractionHelper(identify, getLoci, input);
 
-        const drawPass = new DrawPass(webgl, renderer, scene, debugHelper)
-        const pickPass = new PickPass(webgl, renderer, scene, 0.5)
+        const drawPass = new DrawPass(webgl, renderer, scene, camera, debugHelper)
+        const pickPass = new PickPass(webgl, renderer, scene, camera, 0.5)
         const postprocessing = new PostprocessingPass(webgl, camera, drawPass, p.postprocessing)
         const multiSample = new MultiSamplePass(webgl, camera, drawPass, postprocessing, p.multiSample)
 
         let drawPending = false
-        let cameraResetRequested: boolean | Vec3 = false
+        let cameraResetRequested = false
 
         function getLoci(pickingId: PickingId) {
             let loci: Loci = EmptyLoci
@@ -148,7 +148,9 @@ namespace Canvas3D {
             reprRenderObjects.forEach((_, _repr) => {
                 const _loci = _repr.getLoci(pickingId)
                 if (!isEmptyLoci(_loci)) {
-                    if (!isEmptyLoci(loci)) console.warn('found another loci')
+                    if (!isEmptyLoci(loci)) {
+                        console.warn('found another loci, this should not happen')
+                    }
                     loci = _loci
                     repr = _repr
                 }
@@ -172,47 +174,13 @@ namespace Canvas3D {
             }
         }
 
-        let currentNear = -1, currentFar = -1, currentFogNear = -1, currentFogFar = -1
-        function setClipping() {
-            const cDist = Vec3.distance(camera.state.position, camera.state.target)
-            const bRadius = Math.max(10, scene.boundingSphere.radius)
-
-            const nearFactor = (50 - p.clip[0]) / 50
-            const farFactor = -(50 - p.clip[1]) / 50
-            let near = cDist - (bRadius * nearFactor)
-            let far = cDist + (bRadius * farFactor)
-
-            const fogNearFactor = (50 - p.fog[0]) / 50
-            const fogFarFactor = -(50 - p.fog[1]) / 50
-            let fogNear = cDist - (bRadius * fogNearFactor)
-            let fogFar = cDist + (bRadius * fogFarFactor)
-
-            if (camera.state.mode === 'perspective') {
-                // set at least to 5 to avoid slow sphere impostor rendering
-                near = Math.max(5, p.cameraClipDistance, near)
-                far = Math.max(5, far)
-                fogNear = Math.max(5, fogNear)
-                fogFar = Math.max(5, fogFar)
-            } else if (camera.state.mode === 'orthographic') {
-                if (p.cameraClipDistance > 0) {
-                    near = Math.max(p.cameraClipDistance, near)
-                }
-            }
-
-            if (near !== currentNear || far !== currentFar || fogNear !== currentFogNear || fogFar !== currentFogFar) {
-                camera.setState({ near, far, fogNear, fogFar })
-                currentNear = near, currentFar = far, currentFogNear = fogNear, currentFogFar = fogFar
-            }
-        }
-
         function render(variant: 'pick' | 'draw', force: boolean) {
             if (scene.isCommiting) return false
 
             let didRender = false
-            controls.update(currentTime);
-            // TODO: is this a good fix? Also, setClipping does not work if the user has manually set a clipping plane.
-            if (!camera.transition.inTransition) setClipping();
-            const cameraChanged = camera.updateMatrices();
+            controls.update(currentTime)
+            Viewport.set(camera.viewport, 0, 0, width, height)
+            const cameraChanged = camera.update()
             multiSample.update(force || cameraChanged, currentTime)
 
             if (force || cameraChanged || multiSample.enabled) {
@@ -221,9 +189,9 @@ namespace Canvas3D {
                         pickPass.render()
                         break;
                     case 'draw':
-                        renderer.setViewport(0, 0, width, height);
+                        renderer.setViewport(0, 0, width, height)
                         if (multiSample.enabled) {
-                            multiSample.render()
+                            multiSample.render(true)
                         } else {
                             drawPass.render(!postprocessing.enabled)
                             if (postprocessing.enabled) postprocessing.render(true)
@@ -234,7 +202,7 @@ namespace Canvas3D {
                 didRender = true
             }
 
-            return didRender && cameraChanged;
+            return didRender;
         }
 
         let forceNextDraw = false;
@@ -271,8 +239,7 @@ namespace Canvas3D {
 
             runTask(scene.commit()).then(() => {
                 if (cameraResetRequested && !scene.isCommiting) {
-                    const dir = typeof cameraResetRequested === 'boolean' ? undefined : cameraResetRequested
-                    camera.focus(scene.boundingSphere.center, scene.boundingSphere.radius, dir)
+                    camera.focus(scene.boundingSphere.center, scene.boundingSphere.radius)
                     cameraResetRequested = false
                 }
                 if (debugHelper.isEnabled) debugHelper.update()
@@ -345,11 +312,11 @@ namespace Canvas3D {
             getLoci,
 
             handleResize,
-            resetCamera: (dir?: Vec3) => {
+            resetCamera: () => {
                 if (scene.isCommiting) {
-                    cameraResetRequested = dir || true
+                    cameraResetRequested = true
                 } else {
-                    camera.focus(scene.boundingSphere.center, scene.boundingSphere.radius, dir)
+                    camera.focus(scene.boundingSphere.center, scene.boundingSphere.radius, p.cameraResetDurationMs)
                     requestDraw(true);
                 }
             },
@@ -372,9 +339,10 @@ namespace Canvas3D {
                 if (props.cameraMode !== undefined && props.cameraMode !== camera.state.mode) {
                     camera.setState({ mode: props.cameraMode })
                 }
-                if (props.cameraClipDistance !== undefined) p.cameraClipDistance = props.cameraClipDistance
-                if (props.clip !== undefined) p.clip = [props.clip[0], props.clip[1]]
-                if (props.fog !== undefined) p.fog = [props.fog[0], props.fog[1]]
+                if (props.cameraFog !== undefined && props.cameraFog !== camera.state.fog) {
+                    camera.setState({ fog: props.cameraFog })
+                }
+                if (props.cameraResetDurationMs !== undefined) p.cameraResetDurationMs = props.cameraResetDurationMs
 
                 if (props.postprocessing) postprocessing.setProps(props.postprocessing)
                 if (props.multiSample) multiSample.setProps(props.multiSample)
@@ -383,13 +351,15 @@ namespace Canvas3D {
                 if (props.debug) debugHelper.setProps(props.debug)
                 requestDraw(true)
             },
+            getImagePass: (props: Partial<ImageProps> = {}) => {
+                return new ImagePass(webgl, renderer, scene, camera, debugHelper, props)
+            },
 
             get props() {
                 return {
                     cameraMode: camera.state.mode,
-                    cameraClipDistance: p.cameraClipDistance,
-                    clip: p.clip,
-                    fog: p.fog,
+                    cameraFog: camera.state.fog,
+                    cameraResetDurationMs: p.cameraResetDurationMs,
 
                     postprocessing: { ...postprocessing.props },
                     multiSample: { ...multiSample.props },
@@ -413,7 +383,6 @@ namespace Canvas3D {
                 input.dispose()
                 controls.dispose()
                 renderer.dispose()
-                camera.dispose()
                 interactionHelper.dispose()
             }
         }

src/mol-canvas3d/controls/trackball.ts

@@ -9,10 +9,29 @@
  */
 
 import { Quat, Vec2, Vec3, EPSILON } from '../../mol-math/linear-algebra';
-import { cameraLookAt, Viewport } from '../camera/util';
-import InputObserver, { DragInput, WheelInput, ButtonsType, PinchInput } from '../../mol-util/input/input-observer';
-import { Object3D } from '../../mol-gl/object3d';
+import { Viewport } from '../camera/util';
+import InputObserver, { DragInput, WheelInput, PinchInput, ButtonsType, ModifiersKeys } from '../../mol-util/input/input-observer';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { Camera } from '../camera';
+import { absMax } from '../../mol-math/misc';
+import { Binding } from '../../mol-util/binding';
+
+const B = ButtonsType
+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 ${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 ${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 ${triggers}'),
+    scrollFocus: Binding([Trigger(B.Flag.Auxilary, M.create({ shift: true }))], 'Focus the 3D scene by scrolling using ${triggers}'),
+    scrollFocusZoom: Binding.Empty,
+}
 
 export const TrackballControlsParams = {
     noScroll: PD.Boolean(true, { isHidden: true }),
@@ -21,14 +40,16 @@ export const TrackballControlsParams = {
     zoomSpeed: PD.Numeric(6.0, { min: 0.1, max: 10, step: 0.1 }),
     panSpeed: PD.Numeric(0.8, { min: 0.1, max: 5, step: 0.1 }),
 
-    spin: PD.Boolean(false),
+    spin: PD.Boolean(false, { description: 'Spin the 3D scene around the x-axis in view space' }),
     spinSpeed: PD.Numeric(1, { min: -100, max: 100, step: 1 }),
 
     staticMoving: PD.Boolean(true, { isHidden: true }),
     dynamicDampingFactor: PD.Numeric(0.2, {}, { isHidden: true }),
 
     minDistance: PD.Numeric(0.01, {}, { isHidden: true }),
-    maxDistance: PD.Numeric(1e150, {}, { isHidden: true })
+    maxDistance: PD.Numeric(1e150, {}, { isHidden: true }),
+
+    bindings: PD.Value(DefaultTrackballBindings, { isHidden: true })
 }
 export type TrackballControlsProps = PD.Values<typeof TrackballControlsParams>
 
@@ -44,11 +65,10 @@ interface TrackballControls {
     dispose: () => void
 }
 namespace TrackballControls {
-    export function create(input: InputObserver, object: Object3D & { target: Vec3 }, props: Partial<TrackballControlsProps> = {}): TrackballControls {
+    export function create(input: InputObserver, camera: Camera, props: Partial<TrackballControlsProps> = {}): TrackballControls {
         const p = { ...PD.getDefaultValues(TrackballControlsParams), ...props }
 
-        const viewport: Viewport = { x: 0, y: 0, width: 0, height: 0 }
-        const target: Vec3 = object.target
+        const viewport = Viewport()
 
         let disposed = false
 
@@ -60,91 +80,116 @@ namespace TrackballControls {
         let _isInteracting = false;
 
         // For internal use
-        const lastPosition = Vec3.zero()
+        const lastPosition = Vec3()
 
-        const _eye = Vec3.zero()
+        const _eye = Vec3()
 
-        const _movePrev = Vec2.zero()
-        const _moveCurr = Vec2.zero()
+        const _rotPrev = Vec2()
+        const _rotCurr = Vec2()
+        const _rotLastAxis = Vec3()
+        let _rotLastAngle = 0
 
-        const _lastAxis = Vec3.zero()
-        let _lastAngle = 0
+        const _zRotPrev = Vec2()
+        const _zRotCurr = Vec2()
+        let _zRotLastAngle = 0
 
-        const _zoomStart = Vec2.zero()
-        const _zoomEnd = Vec2.zero()
+        const _zoomStart = Vec2()
+        const _zoomEnd = Vec2()
 
-        const _panStart = Vec2.zero()
-        const _panEnd = Vec2.zero()
+        const _focusStart = Vec2()
+        const _focusEnd = Vec2()
+
+        const _panStart = Vec2()
+        const _panEnd = Vec2()
 
         // Initial values for reseting
-        const target0 = Vec3.clone(target)
-        const position0 = Vec3.clone(object.position)
-        const up0 = Vec3.clone(object.up)
+        const target0 = Vec3.clone(camera.target)
+        const position0 = Vec3.clone(camera.position)
+        const up0 = Vec3.clone(camera.up)
 
-        const mouseOnScreenVec2 = Vec2.zero()
+        const mouseOnScreenVec2 = Vec2()
         function getMouseOnScreen(pageX: number, pageY: number) {
-            Vec2.set(
+            return Vec2.set(
                 mouseOnScreenVec2,
                 (pageX - viewport.x) / viewport.width,
                 (pageY - viewport.y) / viewport.height
             );
-            return mouseOnScreenVec2;
         }
 
-        const mouseOnCircleVec2 = Vec2.zero()
+        const mouseOnCircleVec2 = Vec2()
         function getMouseOnCircle(pageX: number, pageY: number) {
-            Vec2.set(
+            return Vec2.set(
                 mouseOnCircleVec2,
-                ((pageX - viewport.width * 0.5 - viewport.x) / (viewport.width * 0.5)),
-                ((viewport.height + 2 * (viewport.y - pageY)) / viewport.width) // screen.width intentional
+                (pageX - viewport.width * 0.5 - viewport.x) / (viewport.width * 0.5),
+                (viewport.height + 2 * (viewport.y - pageY)) / viewport.width // screen.width intentional
             );
-            return mouseOnCircleVec2;
         }
 
-        const rotAxis = Vec3.zero()
-        const rotQuat = Quat.zero()
-        const rotEyeDir = Vec3.zero()
-        const rotObjUpDir = Vec3.zero()
-        const rotObjSideDir = Vec3.zero()
-        const rotMoveDir = Vec3.zero()
+        const rotAxis = Vec3()
+        const rotQuat = Quat()
+        const rotEyeDir = Vec3()
+        const rotObjUpDir = Vec3()
+        const rotObjSideDir = Vec3()
+        const rotMoveDir = Vec3()
 
         function rotateCamera() {
-            Vec3.set(rotMoveDir, _moveCurr[0] - _movePrev[0], _moveCurr[1] - _movePrev[1], 0);
-            let angle = Vec3.magnitude(rotMoveDir);
+            const dx = _rotCurr[0] - _rotPrev[0]
+            const dy = _rotCurr[1] - _rotPrev[1]
+            Vec3.set(rotMoveDir, dx, dy, 0);
+
+            const angle = Vec3.magnitude(rotMoveDir) * p.rotateSpeed;
 
             if (angle) {
-                Vec3.copy(_eye, object.position)
-                Vec3.sub(_eye, _eye, target)
+                Vec3.sub(_eye, camera.position, camera.target)
 
-                Vec3.normalize(rotEyeDir, Vec3.copy(rotEyeDir, _eye))
-                Vec3.normalize(rotObjUpDir, Vec3.copy(rotObjUpDir, object.up))
+                Vec3.normalize(rotEyeDir, _eye)
+                Vec3.normalize(rotObjUpDir, camera.up)
                 Vec3.normalize(rotObjSideDir, Vec3.cross(rotObjSideDir, rotObjUpDir, rotEyeDir))
 
-                Vec3.setMagnitude(rotObjUpDir, rotObjUpDir, _moveCurr[1] - _movePrev[1])
-                Vec3.setMagnitude(rotObjSideDir, rotObjSideDir, _moveCurr[0] - _movePrev[0])
-
-                Vec3.add(rotMoveDir, Vec3.copy(rotMoveDir, rotObjUpDir), rotObjSideDir)
+                Vec3.setMagnitude(rotObjUpDir, rotObjUpDir, dy)
+                Vec3.setMagnitude(rotObjSideDir, rotObjSideDir, dx)
 
+                Vec3.add(rotMoveDir, rotObjUpDir, rotObjSideDir)
                 Vec3.normalize(rotAxis, Vec3.cross(rotAxis, rotMoveDir, _eye))
-
-                angle *= p.rotateSpeed;
                 Quat.setAxisAngle(rotQuat, rotAxis, angle)
 
                 Vec3.transformQuat(_eye, _eye, rotQuat)
-                Vec3.transformQuat(object.up, object.up, rotQuat)
+                Vec3.transformQuat(camera.up, camera.up, rotQuat)
 
-                Vec3.copy(_lastAxis, rotAxis)
-                _lastAngle = angle;
-            } else if (!p.staticMoving && _lastAngle) {
-                _lastAngle *= Math.sqrt(1.0 - p.dynamicDampingFactor);
-                Vec3.sub(_eye, Vec3.copy(_eye, object.position), target)
-                Quat.setAxisAngle(rotQuat, _lastAxis, _lastAngle)
+                Vec3.copy(_rotLastAxis, rotAxis)
+                _rotLastAngle = angle;
+            } else if (!p.staticMoving && _rotLastAngle) {
+                _rotLastAngle *= Math.sqrt(1.0 - p.dynamicDampingFactor);
+                Vec3.sub(_eye, camera.position, camera.target)
+                Quat.setAxisAngle(rotQuat, _rotLastAxis, _rotLastAngle)
 
                 Vec3.transformQuat(_eye, _eye, rotQuat)
-                Vec3.transformQuat(object.up, object.up, rotQuat)
+                Vec3.transformQuat(camera.up, camera.up, rotQuat)
             }
 
-            Vec2.copy(_movePrev, _moveCurr)
+            Vec2.copy(_rotPrev, _rotCurr)
+        }
+
+        const zRotQuat = Quat()
+
+        function zRotateCamera() {
+            const dx = _zRotCurr[0] - _zRotPrev[0]
+            const dy = _zRotCurr[1] - _zRotPrev[1]
+            const angle = p.rotateSpeed * (-dx + dy) * -0.05
+
+            if (angle) {
+                Vec3.sub(_eye, camera.position, camera.target)
+                Quat.setAxisAngle(zRotQuat, _eye, angle)
+                Vec3.transformQuat(camera.up, camera.up, zRotQuat)
+                _zRotLastAngle = angle;
+            } else if (!p.staticMoving && _zRotLastAngle) {
+                _zRotLastAngle *= Math.sqrt(1.0 - p.dynamicDampingFactor);
+                Vec3.sub(_eye, camera.position, camera.target)
+                Quat.setAxisAngle(zRotQuat, _eye, _zRotLastAngle)
+                Vec3.transformQuat(camera.up, camera.up, zRotQuat)
+            }
+
+            Vec2.copy(_zRotPrev, _zRotCurr)
         }
 
         function zoomCamera() {
@@ -160,9 +205,23 @@ namespace TrackballControls {
             }
         }
 
-        const panMouseChange = Vec2.zero()
-        const panObjUp = Vec3.zero()
-        const panOffset = Vec3.zero()
+        function focusCamera() {
+            const factor = (_focusEnd[1] - _focusStart[1]) * p.zoomSpeed
+            if (factor !== 0.0) {
+                const radius = Math.max(1, camera.state.radius + 10 * factor)
+                camera.setState({ radius })
+            }
+
+            if (p.staticMoving) {
+                Vec2.copy(_focusStart, _focusEnd)
+            } else {
+                _focusStart[1] += (_focusEnd[1] - _focusStart[1]) * p.dynamicDampingFactor
+            }
+        }
+
+        const panMouseChange = Vec2()
+        const panObjUp = Vec3()
+        const panOffset = Vec3()
 
         function panCamera() {
             Vec2.sub(panMouseChange, Vec2.copy(panMouseChange, _panEnd), _panStart)
@@ -170,14 +229,14 @@ namespace TrackballControls {
             if (Vec2.squaredMagnitude(panMouseChange)) {
                 Vec2.scale(panMouseChange, panMouseChange, Vec3.magnitude(_eye) * p.panSpeed)
 
-                Vec3.cross(panOffset, Vec3.copy(panOffset, _eye), object.up)
+                Vec3.cross(panOffset, Vec3.copy(panOffset, _eye), camera.up)
                 Vec3.setMagnitude(panOffset, panOffset, panMouseChange[0])
 
-                Vec3.setMagnitude(panObjUp, object.up, panMouseChange[1])
+                Vec3.setMagnitude(panObjUp, camera.up, panMouseChange[1])
                 Vec3.add(panOffset, panOffset, panObjUp)
 
-                Vec3.add(object.position, object.position, panOffset)
-                Vec3.add(target, target, panOffset)
+                Vec3.add(camera.position, camera.position, panOffset)
+                Vec3.add(camera.target, camera.target, panOffset)
 
                 if (p.staticMoving) {
                     Vec2.copy(_panStart, _panEnd)
@@ -193,14 +252,16 @@ namespace TrackballControls {
         function checkDistances() {
             if (Vec3.squaredMagnitude(_eye) > p.maxDistance * p.maxDistance) {
                 Vec3.setMagnitude(_eye, _eye, p.maxDistance)
-                Vec3.add(object.position, target, _eye)
+                Vec3.add(camera.position, camera.target, _eye)
                 Vec2.copy(_zoomStart, _zoomEnd)
+                Vec2.copy(_focusStart, _focusEnd)
             }
 
             if (Vec3.squaredMagnitude(_eye) < p.minDistance * p.minDistance) {
                 Vec3.setMagnitude(_eye, _eye, p.minDistance)
-                Vec3.add(object.position, target, _eye)
+                Vec3.add(camera.position, camera.target, _eye)
                 Vec2.copy(_zoomStart, _zoomEnd)
+                Vec2.copy(_focusStart, _focusEnd)
             }
         }
 
@@ -210,18 +271,19 @@ namespace TrackballControls {
             if (lastUpdated === t) return;
             if (p.spin) spin(t - lastUpdated);
 
-            Vec3.sub(_eye, object.position, target)
+            Vec3.sub(_eye, camera.position, camera.target)
 
             rotateCamera()
+            zRotateCamera()
             zoomCamera()
+            focusCamera()
             panCamera()
 
-            Vec3.add(object.position, target, _eye)
+            Vec3.add(camera.position, camera.target, _eye)
             checkDistances()
-            cameraLookAt(object.position, object.up, object.direction, target)
 
-            if (Vec3.squaredDistance(lastPosition, object.position) > EPSILON.Value) {
-                Vec3.copy(lastPosition, object.position)
+            if (Vec3.squaredDistance(lastPosition, camera.position) > EPSILON) {
+                Vec3.copy(lastPosition, camera.position)
             }
 
             lastUpdated = t;
@@ -229,53 +291,82 @@ namespace TrackballControls {
 
         /** Reset object's vectors and the target vector to their initial values */
         function reset() {
-            Vec3.copy(target, target0)
-            Vec3.copy(object.position, position0)
-            Vec3.copy(object.up, up0)
+            Vec3.copy(camera.target, target0)
+            Vec3.copy(camera.position, position0)
+            Vec3.copy(camera.up, up0)
 
-            Vec3.sub(_eye, object.position, target)
-            cameraLookAt(object.position, object.up, object.direction, target)
-            Vec3.copy(lastPosition, object.position)
+            Vec3.sub(_eye, camera.position, camera.target)
+            Vec3.copy(lastPosition, camera.position)
         }
 
         // listeners
 
-        function onDrag({ pageX, pageY, buttons, isStart }: DragInput) {
+        function onDrag({ pageX, pageY, buttons, modifiers, isStart }: DragInput) {
             _isInteracting = true;
 
+            const dragRotate = Binding.match(p.bindings.dragRotate, buttons, modifiers)
+            const dragRotateZ = Binding.match(p.bindings.dragRotateZ, buttons, modifiers)
+            const dragPan = Binding.match(p.bindings.dragPan, buttons, modifiers)
+            const dragZoom = Binding.match(p.bindings.dragZoom, buttons, modifiers)
+            const dragFocus = Binding.match(p.bindings.dragFocus, buttons, modifiers)
+            const dragFocusZoom = Binding.match(p.bindings.dragFocusZoom, buttons, modifiers)
+
+            getMouseOnCircle(pageX, pageY)
+            getMouseOnScreen(pageX, pageY)
+
             if (isStart) {
-                if (buttons === ButtonsType.Flag.Primary) {
-                    Vec2.copy(_moveCurr, getMouseOnCircle(pageX, pageY))
-                    Vec2.copy(_movePrev, _moveCurr)
-                } else if (buttons === ButtonsType.Flag.Auxilary) {
-                    Vec2.copy(_zoomStart, getMouseOnScreen(pageX, pageY))
+                if (dragRotate) {
+                    Vec2.copy(_rotCurr, mouseOnCircleVec2)
+                    Vec2.copy(_rotPrev, _rotCurr)
+                }
+                if (dragRotateZ) {
+                    Vec2.copy(_zRotCurr, mouseOnCircleVec2)
+                    Vec2.copy(_zRotPrev, _zRotCurr)
+                }
+                if (dragZoom || dragFocusZoom) {
+                    Vec2.copy(_zoomStart, mouseOnScreenVec2)
                     Vec2.copy(_zoomEnd, _zoomStart)
-                } else if (buttons === ButtonsType.Flag.Secondary) {
-                    Vec2.copy(_panStart, getMouseOnScreen(pageX, pageY))
+                }
+                if (dragFocus) {
+                    Vec2.copy(_focusStart, mouseOnScreenVec2)
+                    Vec2.copy(_focusEnd, _focusStart)
+                }
+                if (dragPan) {
+                    Vec2.copy(_panStart, mouseOnScreenVec2)
                     Vec2.copy(_panEnd, _panStart)
                 }
             }
 
-            if (buttons === ButtonsType.Flag.Primary) {
-                Vec2.copy(_moveCurr, getMouseOnCircle(pageX, pageY))
-            } else if (buttons === ButtonsType.Flag.Auxilary) {
-                Vec2.copy(_zoomEnd, getMouseOnScreen(pageX, pageY))
-            } else if (buttons === ButtonsType.Flag.Secondary) {
-                Vec2.copy(_panEnd, getMouseOnScreen(pageX, pageY))
+            if (dragRotate) Vec2.copy(_rotCurr, mouseOnCircleVec2)
+            if (dragRotateZ) Vec2.copy(_zRotCurr, mouseOnCircleVec2)
+            if (dragZoom || dragFocusZoom) Vec2.copy(_zoomEnd, mouseOnScreenVec2)
+            if (dragFocus) Vec2.copy(_focusEnd, mouseOnScreenVec2)
+            if (dragFocusZoom) {
+                const dist = Vec3.distance(camera.state.position, camera.state.target);
+                camera.setState({ radius: dist / 5 })
             }
+            if (dragPan) Vec2.copy(_panEnd, mouseOnScreenVec2)
         }
 
         function onInteractionEnd() {
             _isInteracting = false;
         }
 
-        function onWheel({ dy }: WheelInput) {
-            _zoomEnd[1] += dy * 0.0001
+        function onWheel({ dx, dy, dz, buttons, modifiers }: WheelInput) {
+            const delta = absMax(dx, dy, dz)
+            if (Binding.match(p.bindings.scrollZoom, buttons, modifiers)) {
+                _zoomEnd[1] += delta * 0.0001
+            }
+            if (Binding.match(p.bindings.scrollFocus, buttons, modifiers)) {
+                _focusEnd[1] += delta * 0.0001
+            }
         }
 
-        function onPinch({ fraction }: PinchInput) {
-            _isInteracting = true;
-            _zoomEnd[1] += (fraction - 1) * 0.1
+        function onPinch({ fraction, buttons, modifiers }: PinchInput) {
+            if (Binding.match(p.bindings.scrollZoom, buttons, modifiers)) {
+                _isInteracting = true;
+                _zoomEnd[1] += (fraction - 1) * 0.1
+            }
         }
 
         function dispose() {
@@ -292,7 +383,7 @@ namespace TrackballControls {
         function spin(deltaT: number) {
             const frameSpeed = (p.spinSpeed || 0) / 1000;
             _spinSpeed[0] = 60 * Math.min(Math.abs(deltaT), 1000 / 8) / 1000 * frameSpeed;
-            if (!_isInteracting) Vec2.add(_moveCurr, _movePrev, _spinSpeed);
+            if (!_isInteracting) Vec2.add(_rotCurr, _rotPrev, _spinSpeed);
         }
 
         // force an update at start

src/mol-canvas3d/helper/interaction-events.ts

@@ -11,13 +11,15 @@ import InputObserver, { ModifiersKeys, ButtonsType } from '../../mol-util/input/
 import { RxEventHelper } from '../../mol-util/rx-event-helper';
 
 type Canvas3D = import('../canvas3d').Canvas3D
+type HoverEvent = import('../canvas3d').Canvas3D.HoverEvent
+type ClickEvent = import('../canvas3d').Canvas3D.ClickEvent
 
 export class Canvas3dInteractionHelper {
     private ev = RxEventHelper.create();
 
     readonly events = {
-        highlight: this.ev<import('../canvas3d').Canvas3D.HighlightEvent>(),
-        click: this.ev<import('../canvas3d').Canvas3D.ClickEvent>(),
+        hover: this.ev<HoverEvent>(),
+        click: this.ev<ClickEvent>(),
     };
 
     private cX = -1;
@@ -52,14 +54,14 @@ export class Canvas3dInteractionHelper {
             return;
         }
 
-        // only highlight the latest
         if (!this.inside || this.currentIdentifyT !== t) {
             return;
         }
 
         const loci = this.getLoci(this.id);
+        // only broadcast the latest hover
         if (!Representation.Loci.areEqual(this.prevLoci, loci)) {
-            this.events.highlight.next({ current: loci, modifiers: this.modifiers });
+            this.events.hover.next({ current: loci, buttons: this.buttons, modifiers: this.modifiers });
             this.prevLoci = loci;
         }
     }
@@ -76,12 +78,13 @@ export class Canvas3dInteractionHelper {
         this.inside = false;
         if (this.prevLoci.loci !== EmptyLoci) {
             this.prevLoci = Representation.Loci.Empty;
-            this.events.highlight.next({ current: this.prevLoci });
+            this.events.hover.next({ current: this.prevLoci, buttons: this.buttons, modifiers: this.modifiers });
         }
     }
 
-    move(x: number, y: number, modifiers: ModifiersKeys) {
+    move(x: number, y: number, buttons: ButtonsType, modifiers: ModifiersKeys) {
         this.inside = true;
+        this.buttons = buttons;
         this.modifiers = modifiers;
         this.cX = x;
         this.cY = y;
@@ -98,7 +101,7 @@ export class Canvas3dInteractionHelper {
     modify(modifiers: ModifiersKeys) {
         if (this.prevLoci.loci === EmptyLoci || ModifiersKeys.areEqual(modifiers, this.modifiers)) return;
         this.modifiers = modifiers;
-        this.events.highlight.next({ current: this.prevLoci, modifiers: this.modifiers });
+        this.events.hover.next({ current: this.prevLoci, buttons: this.buttons, modifiers: this.modifiers });
     }
 
     dispose() {
@@ -107,8 +110,8 @@ export class Canvas3dInteractionHelper {
 
     constructor(private canvasIdentify: Canvas3D['identify'], private getLoci: Canvas3D['getLoci'], input: InputObserver, private maxFps: number = 15) {
         input.move.subscribe(({x, y, inside, buttons, modifiers }) => {
-            if (!inside || buttons) { return; }
-            this.move(x, y, modifiers);
+            if (!inside) return;
+            this.move(x, y, buttons, modifiers);
         });
 
         input.leave.subscribe(() => {

src/mol-canvas3d/passes/draw.ts

@@ -10,6 +10,7 @@ import Renderer from '../../mol-gl/renderer';
 import Scene from '../../mol-gl/scene';
 import { BoundingSphereHelper } from '../helper/bounding-sphere-helper';
 import { createTexture, Texture } from '../../mol-gl/webgl/texture';
+import { Camera } from '../camera';
 
 export class DrawPass {
     colorTarget: RenderTarget
@@ -18,11 +19,11 @@ export class DrawPass {
 
     private depthTarget: RenderTarget | null
 
-    constructor(private webgl: WebGLContext, private renderer: Renderer, private scene: Scene, private debugHelper: BoundingSphereHelper) {
+    constructor(private webgl: WebGLContext, private renderer: Renderer, private scene: Scene, private camera: Camera, private debugHelper: BoundingSphereHelper) {
         const { gl, extensions } = webgl
         const width = gl.drawingBufferWidth
         const height = gl.drawingBufferHeight
-        this.colorTarget = createRenderTarget(webgl, gl.drawingBufferWidth, gl.drawingBufferHeight)
+        this.colorTarget = createRenderTarget(webgl, width, height)
         this.packedDepth = !extensions.depthTexture
         this.depthTarget = this.packedDepth ? createRenderTarget(webgl, width, height) : null
         this.depthTexture = this.depthTarget ? this.depthTarget.texture : createTexture(webgl, 'image-depth', 'depth', 'ushort', 'nearest')
@@ -42,28 +43,28 @@ export class DrawPass {
     }
 
     render(toDrawingBuffer: boolean) {
-        const { webgl, renderer, scene, debugHelper, colorTarget, depthTarget } = this
-        const { gl } = webgl
+        const { webgl, renderer, scene, camera, debugHelper, colorTarget, depthTarget } = this
         if (toDrawingBuffer) {
             webgl.unbindFramebuffer()
         } else {
             colorTarget.bind()
         }
-        renderer.setViewport(0, 0, gl.drawingBufferWidth, gl.drawingBufferHeight)
-        renderer.render(scene, 'color', true)
+
+        renderer.setViewport(0, 0, colorTarget.width, colorTarget.height)
+        renderer.render(scene, camera, 'color', true)
         if (debugHelper.isEnabled) {
             debugHelper.syncVisibility()
-            renderer.render(debugHelper.scene, 'color', false)
+            renderer.render(debugHelper.scene, camera, 'color', false)
         }
 
         // do a depth pass if not rendering to drawing buffer and
         // extensions.depthTexture is unsupported (i.e. depthTarget is set)
         if (!toDrawingBuffer && depthTarget) {
             depthTarget.bind()
-            renderer.render(scene, 'depth', true)
+            renderer.render(scene, camera, 'depth', true)
             if (debugHelper.isEnabled) {
                 debugHelper.syncVisibility()
-                renderer.render(debugHelper.scene, 'depth', false)
+                renderer.render(debugHelper.scene, camera, 'depth', false)
             }
         }
     }

src/mol-canvas3d/passes/image.ts

@@ -0,0 +1,91 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { WebGLContext } from '../../mol-gl/webgl/context';
+import { RenderTarget } from '../../mol-gl/webgl/render-target';
+import Renderer from '../../mol-gl/renderer';
+import Scene from '../../mol-gl/scene';
+import { BoundingSphereHelper } from '../helper/bounding-sphere-helper';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { DrawPass } from './draw'
+import { PostprocessingPass, PostprocessingParams } from './postprocessing'
+import { MultiSamplePass, MultiSampleParams } from './multi-sample'
+import { Camera } from '../camera';
+import { Viewport } from '../camera/util';
+
+export const ImageParams = {
+    multiSample: PD.Group(MultiSampleParams),
+    postprocessing: PD.Group(PostprocessingParams),
+}
+export type ImageProps = PD.Values<typeof ImageParams>
+
+export class ImagePass {
+    private _width = 1024
+    private _height = 768
+    private _camera = new Camera()
+
+    private _colorTarget: RenderTarget
+    get colorTarget() { return this._colorTarget }
+
+    readonly drawPass: DrawPass
+    private readonly postprocessing: PostprocessingPass
+    private readonly multiSample: MultiSamplePass
+
+    get width() { return this._width }
+    get height() { return this._height }
+
+    constructor(webgl: WebGLContext, private renderer: Renderer, scene: Scene, private camera: Camera, debugHelper: BoundingSphereHelper, props: Partial<ImageProps>) {
+        const p = { ...PD.getDefaultValues(ImageParams), ...props }
+
+        this.drawPass = new DrawPass(webgl, renderer, scene, this._camera, debugHelper)
+        this.postprocessing = new PostprocessingPass(webgl, this._camera, this.drawPass, p.postprocessing)
+        this.multiSample = new MultiSamplePass(webgl, this._camera, this.drawPass, this.postprocessing, p.multiSample)
+
+        this.setSize(this._width, this._height)
+    }
+
+    setSize(width: number, height: number) {
+        this._width = width
+        this._height = height
+
+        this.drawPass.setSize(width, height)
+        this.postprocessing.setSize(width, height)
+        this.multiSample.setSize(width, height)
+    }
+
+    setProps(props: Partial<ImageProps> = {}) {
+        if (props.postprocessing) this.postprocessing.setProps(props.postprocessing)
+        if (props.multiSample) this.multiSample.setProps(props.multiSample)
+    }
+
+    render() {
+        Camera.copySnapshot(this._camera.state, this.camera.state)
+        Viewport.set(this._camera.viewport, 0, 0, this._width, this._height)
+        this._camera.update()
+
+        this.renderer.setViewport(0, 0, this._width, this._height);
+
+        if (this.multiSample.enabled) {
+            this.multiSample.render(false)
+            this._colorTarget = this.multiSample.colorTarget
+        } else {
+            this.drawPass.render(false)
+            if (this.postprocessing.enabled) {
+                this.postprocessing.render(false)
+                this._colorTarget = this.postprocessing.target
+            } else {
+                this._colorTarget = this.drawPass.colorTarget
+            }
+        }
+    }
+
+    getImageData(width: number, height: number) {
+        this.setSize(width, height)
+        this.render()
+        const pd = this.colorTarget.getPixelData()
+        return new ImageData(new Uint8ClampedArray(pd.array), pd.width, pd.height)
+    }
+}

src/mol-canvas3d/passes/multi-sample.ts

@@ -54,6 +54,7 @@ export type MultiSampleProps = PD.Values<typeof MultiSampleParams>
 
 export class MultiSamplePass {
     props: MultiSampleProps
+    colorTarget: RenderTarget
 
     private composeTarget: RenderTarget
     private holdTarget: RenderTarget
@@ -65,6 +66,7 @@ export class MultiSamplePass {
 
     constructor(private webgl: WebGLContext, private camera: Camera, private drawPass: DrawPass, private postprocessing: PostprocessingPass, props: Partial<MultiSampleProps>) {
         const { gl } = webgl
+        this.colorTarget = createRenderTarget(webgl, gl.drawingBufferWidth, gl.drawingBufferHeight)
         this.composeTarget = createRenderTarget(webgl, gl.drawingBufferWidth, gl.drawingBufferHeight)
         this.holdTarget = createRenderTarget(webgl, gl.drawingBufferWidth, gl.drawingBufferHeight)
         this.compose = getComposeRenderable(webgl, drawPass.colorTarget.texture)
@@ -92,6 +94,7 @@ export class MultiSamplePass {
     }
 
     setSize(width: number, height: number) {
+        this.colorTarget.setSize(width, height)
         this.composeTarget.setSize(width, height)
         this.holdTarget.setSize(width, height)
         ValueCell.update(this.compose.values.uTexSize, Vec2.set(this.compose.values.uTexSize.ref.value, width, height))
@@ -102,15 +105,15 @@ export class MultiSamplePass {
         if (props.sampleLevel !== undefined) this.props.sampleLevel = props.sampleLevel
     }
 
-    render() {
+    render(toDrawingBuffer: boolean) {
         if (this.props.mode === 'temporal') {
-            this.renderTemporalMultiSample()
+            this.renderTemporalMultiSample(toDrawingBuffer)
         } else {
-            this.renderMultiSample()
+            this.renderMultiSample(toDrawingBuffer)
         }
     }
 
-    private renderMultiSample() {
+    private renderMultiSample(toDrawingBuffer: boolean) {
         const { camera, compose, composeTarget, drawPass, postprocessing, webgl } = this
         const { gl, state } = webgl
 
@@ -135,7 +138,7 @@ export class MultiSamplePass {
         for (let i = 0; i < offsetList.length; ++i) {
             const offset = offsetList[i]
             Camera.setViewOffset(camera.viewOffset, width, height, offset[0], offset[1], width, height)
-            camera.updateMatrices()
+            camera.update()
 
             // the theory is that equal weights for each sample lead to an accumulation of rounding
             // errors. The following equation varies the sampleWeight per sample so that it is uniformly
@@ -168,16 +171,20 @@ export class MultiSamplePass {
         ValueCell.update(compose.values.tColor, composeTarget.texture)
         compose.update()
 
-        webgl.unbindFramebuffer()
+        if (toDrawingBuffer) {
+            webgl.unbindFramebuffer()
+        } else {
+            this.colorTarget.bind()
+        }
         gl.viewport(0, 0, width, height)
         state.disable(gl.BLEND)
         compose.render()
 
         camera.viewOffset.enabled = false
-        camera.updateMatrices()
+        camera.update()
     }
 
-    private renderTemporalMultiSample() {
+    private renderTemporalMultiSample(toDrawingBuffer: boolean) {
         const { camera, compose, composeTarget, holdTarget, postprocessing, drawPass, webgl } = this
         const { gl, state } = webgl
 
@@ -223,7 +230,7 @@ export class MultiSamplePass {
         for (let i = 0; i < numSamplesPerFrame; ++i) {
             const offset = offsetList[this.sampleIndex]
             Camera.setViewOffset(camera.viewOffset, width, height, offset[0], offset[1], width, height)
-            camera.updateMatrices()
+            camera.update()
 
             // render scene and optionally postprocess
             drawPass.render(false)
@@ -252,7 +259,11 @@ export class MultiSamplePass {
             ValueCell.update(compose.values.uWeight, 1.0)
             ValueCell.update(compose.values.tColor, composeTarget.texture)
             compose.update()
-            webgl.unbindFramebuffer()
+            if (toDrawingBuffer) {
+                webgl.unbindFramebuffer()
+            } else {
+                this.colorTarget.bind()
+            }
             gl.viewport(0, 0, width, height)
             state.disable(gl.BLEND)
             compose.render()
@@ -261,7 +272,11 @@ export class MultiSamplePass {
             ValueCell.update(compose.values.uWeight, 1.0 - accumulationWeight)
             ValueCell.update(compose.values.tColor, holdTarget.texture)
             compose.update()
-            webgl.unbindFramebuffer()
+            if (toDrawingBuffer) {
+                webgl.unbindFramebuffer()
+            } else {
+                this.colorTarget.bind()
+            }
             gl.viewport(0, 0, width, height)
             if (accumulationWeight === 0) state.disable(gl.BLEND)
             else state.enable(gl.BLEND)
@@ -269,7 +284,7 @@ export class MultiSamplePass {
         }
 
         camera.viewOffset.enabled = false
-        camera.updateMatrices()
+        camera.update()
         if (this.sampleIndex >= offsetList.length) this.sampleIndex = -1
     }
 }

src/mol-canvas3d/passes/pick.ts

@@ -10,6 +10,7 @@ import Renderer from '../../mol-gl/renderer';
 import Scene from '../../mol-gl/scene';
 import { PickingId } from '../../mol-geo/geometry/picking';
 import { decodeFloatRGB } from '../../mol-util/float-packing';
+import { Camera } from '../camera';
 
 export class PickPass {
     pickDirty = true
@@ -26,7 +27,7 @@ export class PickPass {
     private pickWidth: number
     private pickHeight: number
 
-    constructor(private webgl: WebGLContext, private renderer: Renderer, private scene: Scene, private pickBaseScale: number) {
+    constructor(private webgl: WebGLContext, private renderer: Renderer, private scene: Scene, private camera: Camera, private pickBaseScale: number) {
         const { gl } = webgl
         const width = gl.drawingBufferWidth
         const height = gl.drawingBufferHeight
@@ -64,14 +65,14 @@ export class PickPass {
     }
 
     render() {
-        const { renderer, scene } = this
+        const { renderer, scene, camera } = this
         renderer.setViewport(0, 0, this.pickWidth, this.pickHeight);
         this.objectPickTarget.bind();
-        renderer.render(scene, 'pickObject', true);
+        renderer.render(scene, camera, 'pickObject', true);
         this.instancePickTarget.bind();
-        renderer.render(scene, 'pickInstance', true);
+        renderer.render(scene, camera, 'pickInstance', true);
         this.groupPickTarget.bind();
-        renderer.render(scene, 'pickGroup', true);
+        renderer.render(scene, camera, 'pickGroup', true);
 
         this.pickDirty = false
     }

src/mol-canvas3d/passes/postprocessing.ts

@@ -160,10 +160,10 @@ export class PostprocessingPass {
     }
 
     render(toDrawingBuffer: boolean) {
-        ValueCell.update(this.renderable.values.uFar, this.camera.state.far)
-        ValueCell.update(this.renderable.values.uNear, this.camera.state.near)
-        ValueCell.update(this.renderable.values.uFogFar, this.camera.state.fogFar)
-        ValueCell.update(this.renderable.values.uFogNear, this.camera.state.fogNear)
+        ValueCell.update(this.renderable.values.uFar, this.camera.far)
+        ValueCell.update(this.renderable.values.uNear, this.camera.near)
+        ValueCell.update(this.renderable.values.uFogFar, this.camera.fogFar)
+        ValueCell.update(this.renderable.values.uFogNear, this.camera.fogNear)
         ValueCell.update(this.renderable.values.dOrthographic, this.camera.state.mode === 'orthographic' ? 1 : 0)
 
         const { gl, state } = this.webgl

src/mol-canvas3d/util.ts

@@ -4,16 +4,57 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-/** resize canvas to container element */
+/** Set canvas size taking `devicePixelRatio` into account */
+export function setCanvasSize(canvas: HTMLCanvasElement, width: number, height: number) {
+    canvas.width = Math.round(window.devicePixelRatio * width)
+    canvas.height = Math.round(window.devicePixelRatio * height)
+    Object.assign(canvas.style, { width: `${width}px`, height: `${height}px` })
+}
+
+/** Resize canvas to container element taking `devicePixelRatio` into account */
 export function resizeCanvas (canvas: HTMLCanvasElement, container: Element) {
-    let w = window.innerWidth
-    let h = window.innerHeight
+    let width = window.innerWidth
+    let height = window.innerHeight
     if (container !== document.body) {
         let bounds = container.getBoundingClientRect()
-        w = bounds.right - bounds.left
-        h = bounds.bottom - bounds.top
+        width = bounds.right - bounds.left
+        height = bounds.bottom - bounds.top
     }
-    canvas.width = window.devicePixelRatio * w
-    canvas.height = window.devicePixelRatio * h
-    Object.assign(canvas.style, { width: `${w}px`, height: `${h}px` })
+    setCanvasSize(canvas, width, height)
+}
+
+function _canvasToBlob(canvas: HTMLCanvasElement, callback: BlobCallback, type?: string, quality?: any) {
+    const bin = atob(canvas.toDataURL(type, quality).split(',')[1])
+    const len = bin.length
+    const len32 = len >> 2
+    const a8 = new Uint8Array(len)
+    const a32 = new Uint32Array(a8.buffer, 0, len32)
+
+    let j = 0
+    for (let i = 0; i < len32; ++i) {
+        a32[i] = bin.charCodeAt(j++) |
+            bin.charCodeAt(j++) << 8 |
+            bin.charCodeAt(j++) << 16 |
+            bin.charCodeAt(j++) << 24
+    }
+
+    let tailLength = len & 3;
+    while (tailLength--) a8[j] = bin.charCodeAt(j++)
+
+    callback(new Blob([a8], { type: type || 'image/png' }));
+}
+
+export async function canvasToBlob(canvas: HTMLCanvasElement, type?: string, quality?: any): Promise<Blob> {
+    return new Promise((resolve, reject) => {
+        const callback = (blob: Blob | null) => {
+            if (blob) resolve(blob)
+            else reject('no blob returned')
+        }
+
+        if (!HTMLCanvasElement.prototype.toBlob) {
+            _canvasToBlob(canvas, callback, type, quality)
+        } else {
+            canvas.toBlob(callback, type, quality)
+        }
+    })
 }

src/mol-data/db/column.ts

@@ -302,7 +302,7 @@ function arrayColumn<T extends Column.Schema>({ array, schema, valueKind }: Colu
     }
 }
 
-function windowColumn<T>(column: Column<T>, start: number, end: number) {
+function windowColumn<T>(column: Column<T>, start: number, end: number): Column<T> {
     if (!column.isDefined) return Column.Undefined(end - start, column.schema);
     if (start === 0 && end === column.rowCount) return column;
     if (!!column.__array && ColumnHelpers.isTypedArray(column.__array)) return windowTyped(column, start, end);
@@ -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/db/table.ts

@@ -218,6 +218,16 @@ namespace Table {
         return ret;
     }
 
+    export function toArrays<S extends Schema>(table: Table<S>) {
+        const arrays: { [k: string]: ArrayLike<any> } = {}
+        const { _columns } = table;
+        for (let i = 0; i < _columns.length; i++) {
+            const c = _columns[i]
+            arrays[c] = table[c].toArray();
+        }
+        return arrays as { [k in keyof S]: ArrayLike<S[k]['T']> }
+    }
+
     export function formatToString<S extends Schema>(table: Table<S>) {
         const sb = StringBuilder.create();
 

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/interval.ts

@@ -9,6 +9,7 @@ import Tuple from '../tuple'
 export const Empty = Tuple.Zero;
 export function ofRange(min: number, max: number) { return max < min ? Tuple.create(min, min) : Tuple.create(min, max + 1); }
 export function ofBounds(start: number, end: number) { return end <= start ? Tuple.create(start, start) : Tuple.create(start, end); }
+export function ofLength(length: number) { return length < 0 ? Tuple.create(0, 0) : Tuple.create(0, length); }
 export const is = Tuple.is;
 
 export const start = Tuple.fst;

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-data/int/interval.ts

@@ -14,6 +14,8 @@ namespace Interval {
     export const ofRange: <T extends number = number>(min: T, max: T) => Interval<T> = Impl.ofRange as any;
     /** Create interval from bounds [start, end), i.e. [start, end - 1] */
     export const ofBounds: <T extends number = number>(start: T, end: T) => Interval<T> = Impl.ofBounds as any;
+    /** Create interval from length [0, length), i.e. [0, length - 1] */
+    export const ofLength: <T extends number = number>(length: T) => Interval<T> = Impl.ofLength as any;
     export const is: <T extends number = number>(v: any) => v is Interval<T> = Impl.is as any;
 
     /** Test if a value is within the bounds of the interval */

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/geometry/mesh/builder/ellipsoid.ts

@@ -0,0 +1,23 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Vec3, Mat4 } from '../../../../mol-math/linear-algebra';
+import { MeshBuilder } from '../mesh-builder';
+import { getSphere } from './sphere';
+
+const tmpEllipsoidMat = Mat4.identity()
+const tmpVec = Vec3()
+
+function setEllipsoidMat(m: Mat4, center: Vec3, dirMajor: Vec3, dirMinor: Vec3, radiusScale: Vec3) {
+    Vec3.add(tmpVec, center, dirMajor)
+    Mat4.targetTo(m, center, tmpVec, dirMinor)
+    Mat4.setTranslation(m, center)
+    return Mat4.scale(m, m, radiusScale)
+}
+
+export function addEllipsoid(state: MeshBuilder.State, center: Vec3, dirMajor: Vec3, dirMinor: Vec3, radiusScale: Vec3, detail: number) {
+    MeshBuilder.addPrimitive(state, setEllipsoidMat(tmpEllipsoidMat, center, dirMajor, dirMinor, radiusScale), getSphere(detail))
+}

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

@@ -16,7 +16,7 @@ function setSphereMat(m: Mat4, center: Vec3, radius: number) {
     return Mat4.scaleUniformly(m, Mat4.fromTranslation(m, center), radius)
 }
 
-function getSphere(detail: number) {
+export function getSphere(detail: number) {
     let sphere = sphereMap.get(detail)
     if (sphere === undefined) {
         sphere = Sphere(detail)

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

@@ -101,9 +101,9 @@ export namespace MeshBuilder {
         }
     }
 
-    export function addCage(state: State, t: Mat4, cage: Cage, radius: number, detail: number) {
+    export function addCage(state: State, t: Mat4, cage: Cage, radius: number, detail: number, radialSegments: number) {
         const { vertices: va, edges: ea } = cage
-        const cylinderProps = { radiusTop: radius, radiusBottom: radius }
+        const cylinderProps = { radiusTop: radius, radiusBottom: radius, radialSegments }
         for (let i = 0, il = ea.length; i < il; i += 2) {
             Vec3.fromArray(tmpVecA, va, ea[i] * 3)
             Vec3.fromArray(tmpVecB, va, ea[i + 1] * 3)

src/mol-geo/primitive/cage.ts

@@ -4,6 +4,9 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
+import { Mat4, Vec3 } from '../../mol-math/linear-algebra'
+import { NumberArray } from '../../mol-util/type-helpers'
+
 export interface Cage {
     readonly vertices: ArrayLike<number>
     readonly edges: ArrayLike<number>
@@ -11,4 +14,24 @@ export interface Cage {
 
 export function createCage(vertices: ArrayLike<number>, edges: ArrayLike<number>): Cage {
     return { vertices, edges }
+}
+
+export function copyCage(cage: Cage): Cage {
+    return {
+        vertices: new Float32Array(cage.vertices),
+        edges: new Uint32Array(cage.edges)
+    }
+}
+
+const tmpV = Vec3.zero()
+
+/** Transform primitive in-place */
+export function transformCage(cage: Cage, t: Mat4) {
+    const { vertices } = cage
+    for (let i = 0, il = vertices.length; i < il; i += 3) {
+        // position
+        Vec3.transformMat4(tmpV, Vec3.fromArray(tmpV, vertices, i), t)
+        Vec3.toArray(tmpV, vertices as NumberArray, i)
+    }
+    return cage
 }

src/mol-geo/primitive/primitive.ts

@@ -30,6 +30,14 @@ export function createPrimitive(vertices: ArrayLike<number>, indices: ArrayLike<
     return builder.getPrimitive()
 }
 
+export function copyPrimitive(primitive: Primitive): Primitive {
+    return {
+        vertices: new Float32Array(primitive.vertices),
+        normals: new Float32Array(primitive.normals),
+        indices: new Uint32Array(primitive.indices)
+    }
+}
+
 export interface PrimitiveBuilder {
     add(a: Vec3, b: Vec3, c: Vec3): void
     getPrimitive(): Primitive

src/mol-geo/primitive/prism.ts

@@ -78,10 +78,22 @@ export function PentagonalPrism() {
 
 let hexagonalPrism: Primitive
 export function HexagonalPrism() {
-    if (!hexagonalPrism) hexagonalPrism = Prism(polygon(6, true))
+    if (!hexagonalPrism) hexagonalPrism = Prism(polygon(6, false))
     return hexagonalPrism
 }
 
+let shiftedHexagonalPrism: Primitive
+export function ShiftedHexagonalPrism() {
+    if (!shiftedHexagonalPrism) shiftedHexagonalPrism = Prism(polygon(6, true))
+    return shiftedHexagonalPrism
+}
+
+let heptagonalPrism: Primitive
+export function HeptagonalPrism() {
+    if (!heptagonalPrism) heptagonalPrism = Prism(polygon(7, false))
+    return heptagonalPrism
+}
+
 //
 
 /**
@@ -133,6 +145,6 @@ export function PentagonalPrismCage() {
 
 let hexagonalPrismCage: Cage
 export function HexagonalPrismCage() {
-    if (!hexagonalPrismCage) hexagonalPrismCage = PrismCage(polygon(6, true))
+    if (!hexagonalPrismCage) hexagonalPrismCage = PrismCage(polygon(6, false))
     return hexagonalPrismCage
 }

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/_spec/renderer.spec.ts

@@ -28,11 +28,9 @@ import { createEmptyTransparency } from '../../mol-geo/geometry/transparency-dat
 function createRenderer(gl: WebGLRenderingContext) {
     const ctx = createContext(gl)
     const camera = new Camera({
-        near: 0.01,
-        far: 10000,
         position: Vec3.create(0, 0, 50)
     })
-    const renderer = Renderer.create(ctx, camera)
+    const renderer = Renderer.create(ctx)
     return { ctx, camera, renderer }
 }
 

src/mol-gl/renderable/schema.ts

@@ -168,6 +168,7 @@ export const GlobalUniformSchema = {
     uFogFar: UniformSpec('f'),
     uFogColor: UniformSpec('v3'),
 
+    uTransparentBackground: UniformSpec('i'),
     uPickingAlphaThreshold: UniformSpec('f'),
     uInteriorDarkening: UniformSpec('f'),
 }

src/mol-gl/renderer.ts

@@ -38,14 +38,15 @@ interface Renderer {
     readonly props: Readonly<RendererProps>
 
     clear: () => void
-    render: (scene: Scene, variant: GraphicsRenderVariant, clear: boolean) => void
+    render: (scene: Scene, camera: Camera, variant: GraphicsRenderVariant, clear: boolean) => void
     setProps: (props: Partial<RendererProps>) => void
     setViewport: (x: number, y: number, width: number, height: number) => void
     dispose: () => void
 }
 
 export const RendererParams = {
-    backgroundColor: PD.Color(Color(0x000000)),
+    backgroundColor: PD.Color(Color(0x000000), { description: 'Background color of the 3D canvas' }),
+    transparentBackground: PD.Boolean(false, { description: 'Background opacity of the 3D canvas' }),
     pickingAlphaThreshold: PD.Numeric(0.5, { min: 0.0, max: 1.0, step: 0.01 }, { description: 'The minimum opacity value needed for an object to be pickable.' }),
     interiorDarkening: PD.Numeric(0.5, { min: 0.0, max: 1.0, step: 0.01 }),
 
@@ -59,39 +60,40 @@ export const RendererParams = {
 export type RendererProps = PD.Values<typeof RendererParams>
 
 namespace Renderer {
-    export function create(ctx: WebGLContext, camera: Camera, props: Partial<RendererProps> = {}): Renderer {
+    export function create(ctx: WebGLContext, props: Partial<RendererProps> = {}): Renderer {
         const { gl, state, stats } = ctx
         const p = deepClone({ ...PD.getDefaultValues(RendererParams), ...props })
 
         const viewport = Viewport()
         const bgColor = Color.toVec3Normalized(Vec3(), p.backgroundColor)
 
-        const view = Mat4.clone(camera.view)
-        const invView = Mat4.invert(Mat4.identity(), view)
-        const modelView = Mat4.clone(camera.view)
-        const invModelView = Mat4.invert(Mat4.identity(), modelView)
-        const invProjection = Mat4.invert(Mat4.identity(), camera.projection)
-        const modelViewProjection = Mat4.mul(Mat4.identity(), modelView, camera.projection)
-        const invModelViewProjection = Mat4.invert(Mat4.identity(), modelViewProjection)
+        const view = Mat4()
+        const invView = Mat4()
+        const modelView = Mat4()
+        const invModelView = Mat4()
+        const invProjection = Mat4()
+        const modelViewProjection = Mat4()
+        const invModelViewProjection = Mat4()
 
-        const viewOffset = camera.viewOffset.enabled ? Vec2.create(camera.viewOffset.offsetX * 16, camera.viewOffset.offsetY * 16) : Vec2()
+        const viewOffset = Vec2()
 
         const globalUniforms: GlobalUniformValues = {
             uModel: ValueCell.create(Mat4.identity()),
-            uView: ValueCell.create(camera.view),
+            uView: ValueCell.create(view),
             uInvView: ValueCell.create(invView),
             uModelView: ValueCell.create(modelView),
             uInvModelView: ValueCell.create(invModelView),
             uInvProjection: ValueCell.create(invProjection),
-            uProjection: ValueCell.create(Mat4.clone(camera.projection)),
+            uProjection: ValueCell.create(Mat4()),
             uModelViewProjection: ValueCell.create(modelViewProjection),
             uInvModelViewProjection: ValueCell.create(invModelViewProjection),
 
-            uIsOrtho: ValueCell.create(camera.state.mode === 'orthographic' ? 1 : 0),
+            uIsOrtho: ValueCell.create(1),
+            uViewOffset: ValueCell.create(viewOffset),
+
             uPixelRatio: ValueCell.create(ctx.pixelRatio),
             uViewportHeight: ValueCell.create(viewport.height),
             uViewport: ValueCell.create(Viewport.toVec4(Vec4(), viewport)),
-            uViewOffset: ValueCell.create(viewOffset),
 
             uLightIntensity: ValueCell.create(p.lightIntensity),
             uAmbientIntensity: ValueCell.create(p.ambientIntensity),
@@ -100,13 +102,14 @@ namespace Renderer {
             uRoughness: ValueCell.create(p.roughness),
             uReflectivity: ValueCell.create(p.reflectivity),
 
-            uCameraPosition: ValueCell.create(Vec3.clone(camera.state.position)),
-            uNear: ValueCell.create(camera.state.near),
-            uFar: ValueCell.create(camera.state.far),
-            uFogNear: ValueCell.create(camera.state.fogNear),
-            uFogFar: ValueCell.create(camera.state.fogFar),
+            uCameraPosition: ValueCell.create(Vec3()),
+            uNear: ValueCell.create(1),
+            uFar: ValueCell.create(10000),
+            uFogNear: ValueCell.create(1),
+            uFogFar: ValueCell.create(10000),
             uFogColor: ValueCell.create(bgColor),
 
+            uTransparentBackground: ValueCell.create(p.transparentBackground ? 1 : 0),
             uPickingAlphaThreshold: ValueCell.create(p.pickingAlphaThreshold),
             uInteriorDarkening: ValueCell.create(p.interiorDarkening),
         }
@@ -158,7 +161,7 @@ namespace Renderer {
             }
         }
 
-        const render = (scene: Scene, variant: GraphicsRenderVariant, clear: boolean) => {
+        const render = (scene: Scene, camera: Camera, variant: GraphicsRenderVariant, clear: boolean) => {
             ValueCell.update(globalUniforms.uModel, scene.view)
             ValueCell.update(globalUniforms.uView, camera.view)
             ValueCell.update(globalUniforms.uInvView, Mat4.invert(invView, camera.view))
@@ -173,10 +176,10 @@ namespace Renderer {
             ValueCell.update(globalUniforms.uViewOffset, camera.viewOffset.enabled ? Vec2.set(viewOffset, camera.viewOffset.offsetX * 16, camera.viewOffset.offsetY * 16) : Vec2.set(viewOffset, 0, 0))
 
             ValueCell.update(globalUniforms.uCameraPosition, camera.state.position)
-            ValueCell.update(globalUniforms.uFar, camera.state.far)
-            ValueCell.update(globalUniforms.uNear, camera.state.near)
-            ValueCell.update(globalUniforms.uFogFar, camera.state.fogFar)
-            ValueCell.update(globalUniforms.uFogNear, camera.state.fogNear)
+            ValueCell.update(globalUniforms.uFar, camera.far)
+            ValueCell.update(globalUniforms.uNear, camera.near)
+            ValueCell.update(globalUniforms.uFogFar, camera.fogFar)
+            ValueCell.update(globalUniforms.uFogNear, camera.fogNear)
 
             globalUniformsNeedUpdate = true
             state.currentRenderItemId = -1
@@ -191,7 +194,7 @@ namespace Renderer {
 
             if (clear) {
                 if (variant === 'color') {
-                    state.clearColor(bgColor[0], bgColor[1], bgColor[2], 1.0)
+                    state.clearColor(bgColor[0], bgColor[1], bgColor[2], p.transparentBackground ? 0 : 1)
                 } else {
                     state.clearColor(1, 1, 1, 1)
                 }
@@ -204,7 +207,7 @@ namespace Renderer {
                     if (r.state.opaque) renderObject(r, variant)
                 }
 
-                state.blendFunc(gl.SRC_ALPHA, gl.ONE_MINUS_SRC_ALPHA)
+                state.blendFuncSeparate(gl.SRC_ALPHA, gl.ONE_MINUS_SRC_ALPHA, gl.ONE, gl.ONE)
                 state.enable(gl.BLEND)
                 for (let i = 0, il = renderables.length; i < il; ++i) {
                     const r = renderables[i]
@@ -224,7 +227,7 @@ namespace Renderer {
             clear: () => {
                 state.depthMask(true)
                 state.colorMask(true, true, true, true)
-                state.clearColor(bgColor[0], bgColor[1], bgColor[2], 1.0)
+                state.clearColor(bgColor[0], bgColor[1], bgColor[2], p.transparentBackground ? 0 : 1)
                 gl.clear(gl.COLOR_BUFFER_BIT | gl.DEPTH_BUFFER_BIT)
             },
             render,
@@ -243,6 +246,10 @@ namespace Renderer {
                     Color.toVec3Normalized(bgColor, p.backgroundColor)
                     ValueCell.update(globalUniforms.uFogColor, Vec3.copy(globalUniforms.uFogColor.ref.value, bgColor))
                 }
+                if (props.transparentBackground !== undefined && props.transparentBackground !== p.transparentBackground) {
+                    p.transparentBackground = props.transparentBackground
+                    ValueCell.update(globalUniforms.uTransparentBackground, p.transparentBackground ? 1 : 0)
+                }
                 if (props.lightIntensity !== undefined && props.lightIntensity !== p.lightIntensity) {
                     p.lightIntensity = props.lightIntensity
                     ValueCell.update(globalUniforms.uLightIntensity, p.lightIntensity)

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/chunks/apply-fog.glsl.ts

@@ -2,10 +2,11 @@ export default `
 #ifdef dUseFog
 	float depth = length(vViewPosition);
     float fogFactor = smoothstep(uFogNear, uFogFar, depth);
-	gl_FragColor.rgb = mix(gl_FragColor.rgb, uFogColor, fogFactor);
-    float fogAlpha = (1.0 - fogFactor) * gl_FragColor.a;
-    if (fogAlpha < 0.01)
-        discard;
-    gl_FragColor = vec4(gl_FragColor.rgb, fogAlpha);
+    if (uTransparentBackground == 0) {
+	    gl_FragColor.rgb = mix(gl_FragColor.rgb, uFogColor, fogFactor);
+    } else {
+        float fogAlpha = (1.0 - fogFactor) * gl_FragColor.a;
+        gl_FragColor.a = fogAlpha;
+    }
 #endif
 `

src/mol-gl/shader/chunks/apply-light-color.glsl.ts

@@ -36,7 +36,7 @@ geometry.normal = normal;
 geometry.viewDir = normalize(vViewPosition);
 
 IncidentLight directLight;
-directLight.direction = geometry.viewDir;
+directLight.direction = vec3(0.0, 0.0, -1.0);
 directLight.color = vec3(uLightIntensity);
 
 RE_Direct_Physical(directLight, geometry, physicalMaterial, reflectedLight);

src/mol-gl/shader/chunks/common-frag-params.glsl.ts

@@ -5,7 +5,11 @@ uniform int uGroupCount;
 
 uniform vec3 uHighlightColor;
 uniform vec3 uSelectColor;
-varying float vMarker;
+#if __VERSION__ != 300
+    varying float vMarker;
+#else
+    flat in float vMarker;
+#endif
 
 varying vec3 vViewPosition;
 
@@ -18,6 +22,7 @@ uniform vec3 uFogColor;
 uniform float uAlpha;
 uniform float uPickingAlphaThreshold;
 uniform int uPickable;
+uniform int uTransparentBackground;
 
 uniform float uInteriorDarkening;
 `

src/mol-gl/shader/chunks/common-vert-params.glsl.ts

@@ -8,7 +8,11 @@ uniform int uGroupCount;
 
 uniform vec2 uMarkerTexDim;
 uniform sampler2D tMarker;
-varying float vMarker;
+#if __VERSION__ != 300
+    varying float vMarker;
+#else
+    flat out float vMarker;
+#endif
 
 varying vec3 vViewPosition;
 `

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/shader/spheres.frag.ts

@@ -124,8 +124,8 @@ void main(void){
     #elif defined(dColorType_depth)
         gl_FragColor = material;
     #else
-        vec3 normal = cameraNormal;
-        vec3 vViewPosition = -cameraPos;
+        vec3 normal = -cameraNormal;
+        vec3 vViewPosition = cameraPos;
         #include apply_light_color
 
         if (interior) {

src/mol-gl/webgl/context.ts

@@ -190,6 +190,7 @@ export interface WebGLContext {
     readonly framebufferCache: FramebufferCache
 
     readonly maxTextureSize: number
+    readonly maxRenderbufferSize: number
     readonly maxDrawBuffers: number
 
     unbindFramebuffer: () => void
@@ -212,6 +213,7 @@ export function createContext(gl: GLRenderingContext): WebGLContext {
 
     const parameters = {
         maxTextureSize: gl.getParameter(gl.MAX_TEXTURE_SIZE) as number,
+        maxRenderbufferSize: gl.getParameter(gl.MAX_RENDERBUFFER_SIZE) as number,
         maxDrawBuffers: isWebGL2(gl) ? gl.getParameter(gl.MAX_DRAW_BUFFERS) as number : 0,
         maxVertexTextureImageUnits: gl.getParameter(gl.MAX_VERTEX_TEXTURE_IMAGE_UNITS) as number,
     }
@@ -274,6 +276,7 @@ export function createContext(gl: GLRenderingContext): WebGLContext {
         framebufferCache,
 
         get maxTextureSize () { return parameters.maxTextureSize },
+        get maxRenderbufferSize () { return parameters.maxRenderbufferSize },
         get maxDrawBuffers () { return parameters.maxDrawBuffers },
 
         unbindFramebuffer: () => unbindFramebuffer(gl),

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/3dg/parser.ts

@@ -0,0 +1,57 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { ReaderResult as Result } from '../result'
+import { Task } from '../../../mol-task'
+import { parseCsv } from '../csv/parser';
+import { Column, Table } from '../../../mol-data/db';
+import { toTable } from '../cif/schema';
+
+import Schema = Column.Schema
+import { CsvTable } from '../csv/data-model';
+
+
+export const Schema3DG = {
+    /** Chromosome name */
+    chromosome: Schema.str,
+    /** Base position */
+    position: Schema.int,
+    /** X coordinate */
+    x: Schema.float,
+    /** Y coordinate */
+    y: Schema.float,
+    /** Z coordinate */
+    z: Schema.float,
+}
+export type Schema3DG = typeof Schema3DG
+
+export interface File3DG {
+    table: Table<Schema3DG>
+}
+
+const FieldNames = [ 'chromosome', 'position', 'x', 'y', 'z' ]
+
+function categoryFromTable(name: string, table: CsvTable) {
+    return {
+        name,
+        rowCount: table.rowCount,
+        fieldNames: FieldNames,
+        getField: (name: string) => {
+            return table.getColumn(FieldNames.indexOf(name).toString())
+        }
+    }
+}
+
+export function parse3DG(data: string) {
+    return Task.create<Result<File3DG>>('Parse 3DG', async ctx => {
+        const opts = { quote: '', comment: '#', delimiter: '\t', noColumnNames: true }
+        const csvFile = await parseCsv(data, opts).runInContext(ctx)
+        if (csvFile.isError) return Result.error(csvFile.message, csvFile.line)
+        const category = categoryFromTable('3dg', csvFile.result.table)
+        const table = toTable(Schema3DG, category)
+        return Result.success({ table })
+    });
+}

src/mol-io/reader/_spec/3dg.spec.ts

@@ -0,0 +1,33 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { parse3DG } from '../3dg/parser';
+
+const basic3dgString = `1(mat)	1420000	0.791377837067	10.9947291355	-13.1882897693
+1(mat)	1440000	-0.268241283699	10.5200875887	-13.0896257278
+1(mat)	1460000	-1.3853075236	10.5513787498	-13.1440142173
+1(mat)	1480000	-1.55984101733	11.4340829129	-13.6026301209
+1(mat)	1500000	-0.770991778399	11.4758488546	-14.5881137222
+1(mat)	1520000	-0.0848245107875	12.2624690808	-14.354289628
+1(mat)	1540000	-0.458643807046	12.5985791771	-13.4701149287
+1(mat)	1560000	-0.810322906201	12.2461643989	-12.3172933413
+1(mat)	1580000	-2.08211172035	12.8886838656	-12.8742007778
+1(mat)	1600000	-3.52093948201	13.1850935438	-12.4118684428`
+
+describe('3dg reader', () => {
+    it('basic', async () => {
+        const parsed = await parse3DG(basic3dgString).run();
+        expect(parsed.isError).toBe(false)
+
+        if (parsed.isError) return;
+        const { chromosome, position, x, y, z } = parsed.result.table;
+        expect(chromosome.value(0)).toBe('1(mat)')
+        expect(position.value(1)).toBe(1440000)
+        expect(x.value(5)).toBe(-0.0848245107875)
+        expect(y.value(5)).toBe(12.2624690808)
+        expect(z.value(5)).toBe(-14.354289628)
+    });
+});

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 5.313, 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 5.313, 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 5.313, 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,
         /**
@@ -213,6 +213,89 @@ export const mmCIF_Schema = {
          */
         ihm_model_id: int,
     },
+    /**
+     * Data items in the ATOM_SITE_ANISOTROP category record details
+     * about anisotropic displacement parameters.
+     * If the ATOM_SITE_ANISOTROP category is used for storing these
+     * data, the corresponding ATOM_SITE data items are not used.
+     */
+    atom_site_anisotrop: {
+        /**
+         * This data item is a pointer to _atom_site.id in the ATOM_SITE
+         * category.
+         */
+        id: int,
+        /**
+         * This data item is a pointer to _atom_type.symbol in the
+         * ATOM_TYPE category.
+         */
+        type_symbol: str,
+        /**
+         * The elements of the standard anisotropic atomic
+         * displacement matrix U, which appears in the structure-factor
+         * term as:
+         *
+         * T = exp{-2 pi^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
+         *
+         * These matrix elements may appear with atomic coordinates
+         * in the ATOM_SITE category, or they may appear in the separate
+         * ATOM_SITE_ANISOTROP category, but they may not appear in both
+         * places. Similarly, anisotropic displacements may appear as
+         * either B's or U's, but not as both.
+         *
+         * The unique elements of the real symmetric matrix are
+         * entered by row.
+         */
+        U: Matrix(3, 3),
+        /**
+         * The standard uncertainty (estimated standard deviation)
+         * of _atom_site_anisotrop.U.
+         */
+        U_esd: Matrix(3, 3),
+        /**
+         * Pointer to _atom_site.auth_seq_id
+         */
+        pdbx_auth_seq_id: str,
+        /**
+         * Pointer to _atom_site.auth_asym_id
+         */
+        pdbx_auth_asym_id: str,
+        /**
+         * Pointer to _atom_site.auth_atom_id
+         */
+        pdbx_auth_atom_id: str,
+        /**
+         * Pointer to _atom_site.auth_comp_id
+         */
+        pdbx_auth_comp_id: str,
+        /**
+         * Pointer to _atom_site.label_seq_id
+         */
+        pdbx_label_seq_id: int,
+        /**
+         * Pointer to _atom_site.label_alt_id.
+         */
+        pdbx_label_alt_id: str,
+        /**
+         * Pointer to _atom_site.label_asym_id
+         */
+        pdbx_label_asym_id: str,
+        /**
+         * Pointer to _atom_site.label_atom_id
+         */
+        pdbx_label_atom_id: str,
+        /**
+         * Pointer to _atom_site.label_comp_id
+         */
+        pdbx_label_comp_id: str,
+        /**
+         * Pointer to _atom_site.pdbx_PDB_ins_code
+         */
+        pdbx_PDB_ins_code: str,
+    },
     /**
      * Data items in the ATOM_SITES category record details about
      * the crystallographic cell and cell transformations, which are
@@ -250,6 +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.
@@ -416,6 +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
@@ -658,6 +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
@@ -1597,6 +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.
@@ -2132,15 +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.
@@ -2174,19 +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.
@@ -2207,6 +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.
          */
@@ -2215,11 +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.
@@ -2967,7 +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.
@@ -3142,7 +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,
     },
@@ -3376,7 +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-io/reader/csv/parser.ts

@@ -174,7 +174,7 @@ function moveNextInternal(state: State) {
 
     if (tokenizer.position >= tokenizer.length) {
         state.tokenType = CsvTokenType.End;
-        return true;
+        return false;
     }
 
     tokenizer.tokenStart = tokenizer.position;
@@ -209,22 +209,26 @@ function moveNext(state: State) {
 function readRecordsChunk(chunkSize: number, state: State) {
     if (state.tokenType === CsvTokenType.End) return 0
 
-    let newRecord = moveNext(state);
-    if (newRecord) ++state.recordCount
+    let counter = 0;
+    let newRecord: boolean | undefined
 
     const { tokens, tokenizer } = state;
-    let counter = 0;
+
     while (state.tokenType === CsvTokenType.Value && counter < chunkSize) {
         TokenBuilder.add(tokens[state.fieldCount % state.columnCount], tokenizer.tokenStart, tokenizer.tokenEnd);
         ++state.fieldCount
         newRecord = moveNext(state);
-        if (newRecord) ++state.recordCount
-        ++counter;
+        if (newRecord) {
+            ++state.recordCount
+            ++counter;
+        }
     }
     return counter;
 }
 
 function readRecordsChunks(state: State) {
+    let newRecord = moveNext(state);
+    if (newRecord) ++state.recordCount
     return chunkedSubtask(state.runtimeCtx, 100000, state, readRecordsChunk,
         (ctx, state) => ctx.update({ message: 'Parsing...', current: state.tokenizer.position, max: state.data.length }));
 }

src/mol-math/geometry/primitives/sphere3d.ts

@@ -124,7 +124,7 @@ namespace Sphere3D {
     export function equals(a: Sphere3D, b: Sphere3D) {
         const ar = a.radius;
         const br = b.radius;
-        return (Math.abs(ar - br) <= EPSILON.Value * Math.max(1.0, Math.abs(ar), Math.abs(br)) &&
+        return (Math.abs(ar - br) <= EPSILON * Math.max(1.0, Math.abs(ar), Math.abs(br)) &&
                 Vec3.equals(a.center, b.center));
     }
 }

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

@@ -1,17 +1,19 @@
 /**
- * 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>
  */
 
 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,
     readonly anglesInRadians: Vec3,
     /** Transfrom cartesian -> fractional coordinates within the cell */
     readonly toFractional: Mat4,
@@ -20,7 +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>
 }
@@ -34,7 +39,7 @@ namespace SpacegroupCell {
         return cell.index === 0 && cell.size[0] === 1 && cell.size[1] === 1 && cell.size[1] === 1;
     }
 
-    // returns Zero cell if the spacegroup does not exist
+    /** Returns Zero cell if the spacegroup does not exist */
     export function create(nameOrNumber: number | string | SpacegroupName, size: Vec3, anglesInRadians: Vec3): SpacegroupCell {
         const index = getSpacegroupIndex(nameOrNumber);
         if (index < 0) {
@@ -42,6 +47,8 @@ namespace SpacegroupCell {
             return Zero;
         }
 
+        const volume = size[0] * size[1] * size[2]
+
         const alpha = anglesInRadians[0];
         const beta = anglesInRadians[1];
         const gamma = anglesInRadians[2];
@@ -64,32 +71,71 @@ namespace SpacegroupCell {
         ]);
         const toFractional = Mat4.invert(Mat4.zero(), fromFractional)!;
 
-        return { index, size, anglesInRadians, toFractional, fromFractional };
+        return { index, size, volume, anglesInRadians, toFractional, fromFractional };
     }
 }
 
-
 namespace Spacegroup {
-    // P1 with [1, 1, 1] cell.
+    /** 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 _tempVec = Vec3.zero(), _tempMat = Mat4.zero();
-    export function updateOperatorMatrix(spacegroup: Spacegroup, index: number, i: number, j: number, k: number, target: Mat4) {
-        _tempVec[0] = i;
-        _tempVec[1] = j;
-        _tempVec[2] = k;
+    const _ijkVec = Vec3();
+    const _tempMat = Mat4();
+    export function setOperatorMatrix(spacegroup: Spacegroup, index: number, i: number, j: number, k: number, target: Mat4) {
+        Vec3.set(_ijkVec, i, j, k);
 
-        Mat4.fromTranslation(_tempMat, _tempVec);
-        return Mat4.mul(target, Mat4.mul(target, Mat4.mul(target, spacegroup.cell.fromFractional, _tempMat), spacegroup.operators[index]), spacegroup.cell.toFractional);
+        Mat4.fromTranslation(_tempMat, _ijkVec);
+        return Mat4.mul(
+            target,
+            Mat4.mul(
+                target,
+                Mat4.mul(target, spacegroup.cell.fromFractional, _tempMat),
+                spacegroup.operators[index]
+            ),
+            spacegroup.cell.toFractional
+        );
     }
 
     export function getSymmetryOperator(spacegroup: Spacegroup, index: number, i: number, j: number, k: number): SymmetryOperator {
-        const operator = updateOperatorMatrix(spacegroup, index, i, j, k, Mat4.zero());
+        const operator = setOperatorMatrix(spacegroup, index, i, j, k, Mat4.zero());
+        return SymmetryOperator.create(`${index + 1}_${5 + i}${5 + j}${5 + k}`, operator, { id: '', operList: [] }, '', Vec3.create(i, j, k), index);
+    }
+
+    const _translationRef = Vec3()
+    const _translationRefSymop = Vec3()
+    const _translationSymop = Vec3()
+    export function setOperatorMatrixRef(spacegroup: Spacegroup, index: number, i: number, j: number, k: number, ref: Vec3, target: Mat4) {
+        Vec3.set(_ijkVec, i, j, k);
+        Vec3.floor(_translationRef, ref)
+
+        Mat4.copy(target, spacegroup.operators[index])
+
+        Vec3.floor(_translationRefSymop, Vec3.transformMat4(_translationRefSymop, ref, target))
+
+        Mat4.getTranslation(_translationSymop, target)
+        Vec3.sub(_translationSymop, _translationSymop, _translationRefSymop)
+        Vec3.add(_translationSymop, _translationSymop, _translationRef)
+        Vec3.add(_translationSymop, _translationSymop, _ijkVec)
+
+        Mat4.setTranslation(target, _translationSymop)
+        Mat4.mul(target, spacegroup.cell.fromFractional, target)
+        Mat4.mul(target, target, spacegroup.cell.toFractional)
+        return target
+    }
+
+    /**
+     * Get Symmetry operator for transformation around the given
+     * reference point `ref` in fractional coordinates
+     */
+    export function getSymmetryOperatorRef(spacegroup: Spacegroup, index: number, i: number, j: number, k: number, ref: Vec3) {
+        const operator = setOperatorMatrixRef(spacegroup, index, i, j, k, ref, Mat4.zero());
         return SymmetryOperator.create(`${index + 1}_${5 + i}${5 + j}${5 + k}`, operator, { id: '', operList: [] }, '', Vec3.create(i, j, k), index);
     }
 

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/common.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>
@@ -17,7 +17,7 @@
  * furnished to do so, subject to the following conditions:
  */
 
-export const enum EPSILON { Value = 0.000001 }
+export const EPSILON = 0.000001;
 
 export function equalEps(a: number, b: number, eps: number) {
     return Math.abs(a - b) <= eps;

src/mol-math/linear-algebra/3d/mat3.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>
@@ -17,10 +17,11 @@
  * furnished to do so, subject to the following conditions:
  */
 
-import { Mat4 } from '../3d'
+import { Mat4, Vec3, EPSILON } from '../3d'
 import { NumberArray } from '../../../mol-util/type-helpers';
 
 interface Mat3 extends Array<number> { [d: number]: number, '@type': 'mat3', length: 9 }
+interface ReadonlyMat3 extends Array<number> { readonly [d: number]: number, '@type': 'mat3', length: 9 }
 
 function Mat3() {
     return Mat3.zero();
@@ -71,6 +72,7 @@ namespace Mat3 {
         out[offset + 6] = a[6];
         out[offset + 7] = a[7];
         out[offset + 8] = a[8];
+        return out;
     }
 
     export function fromArray(a: Mat3, array: NumberArray, offset: number) {
@@ -102,6 +104,25 @@ namespace Mat3 {
         return out;
     }
 
+    export function create(a00: number, a01: number, a02: number, a10: number, a11: number, a12: number, a20: number, a21: number, a22: number): Mat3 {
+        const out = zero();
+        out[0] = a00
+        out[1] = a01
+        out[2] = a02
+        out[3] = a10
+        out[4] = a11
+        out[5] = a12
+        out[6] = a20
+        out[7] = a21
+        out[8] = a22
+        return out;
+    }
+
+    const _id = identity();
+    export function isIdentity(m: Mat3, eps?: number) {
+        return areEqual(m, _id, typeof eps === 'undefined' ? EPSILON : eps);
+    }
+
     export function hasNaN(m: Mat3) {
         for (let i = 0; i < 9; i++) if (isNaN(m[i])) return true
         return false
@@ -114,6 +135,13 @@ namespace Mat3 {
         return Mat3.copy(Mat3.zero(), a);
     }
 
+    export function areEqual(a: Mat3, b: Mat3, eps: number) {
+        for (let i = 0; i < 9; i++) {
+            if (Math.abs(a[i] - b[i]) > eps) return false;
+        }
+        return true;
+    }
+
     export function setValue(a: Mat3, i: number, j: number, value: number) {
         a[3 * j + i] = value;
     }
@@ -198,6 +226,44 @@ namespace Mat3 {
         return out;
     }
 
+    export function symmtricFromUpper(out: Mat3, a: Mat3) {
+        if (out === a) {
+            out[3] = a[1];
+            out[6] = a[2];
+            out[7] = a[5];
+        } else {
+            out[0] = a[0];
+            out[1] = a[1];
+            out[2] = a[2];
+            out[3] = a[1];
+            out[4] = a[4];
+            out[5] = a[5];
+            out[6] = a[2];
+            out[7] = a[5];
+            out[8] = a[8];
+        }
+        return out;
+    }
+
+    export function symmtricFromLower(out: Mat3, a: Mat3) {
+        if (out === a) {
+            out[1] = a[3];
+            out[2] = a[6];
+            out[5] = a[7];
+        } else {
+            out[0] = a[0];
+            out[1] = a[3];
+            out[2] = a[6];
+            out[3] = a[3];
+            out[4] = a[4];
+            out[5] = a[7];
+            out[6] = a[6];
+            out[7] = a[7];
+            out[8] = a[8];
+        }
+        return out;
+    }
+
     export function determinant(a: Mat3) {
         const a00 = a[0], a01 = a[1], a02 = a[2];
         const a10 = a[3], a11 = a[4], a12 = a[5];
@@ -210,6 +276,172 @@ namespace Mat3 {
         // Calculate the determinant
         return a00 * b01 + a01 * b11 + a02 * b21;
     }
+
+    export function trace(a: Mat3) {
+        return a[0] + a[4] + a[8]
+    }
+
+    export function sub(out: Mat3, a: Mat3, b: Mat3) {
+        out[0] = a[0] - b[0]
+        out[1] = a[1] - b[1]
+        out[2] = a[2] - b[2]
+        out[3] = a[3] - b[3]
+        out[4] = a[4] - b[4]
+        out[5] = a[5] - b[5]
+        out[6] = a[6] - b[6]
+        out[7] = a[7] - b[7]
+        out[8] = a[8] - b[8]
+        return out
+    }
+
+    export function add(out: Mat3, a: Mat3, b: Mat3) {
+        out[0] = a[0] + b[0]
+        out[1] = a[1] + b[1]
+        out[2] = a[2] + b[2]
+        out[3] = a[3] + b[3]
+        out[4] = a[4] + b[4]
+        out[5] = a[5] + b[5]
+        out[6] = a[6] + b[6]
+        out[7] = a[7] + b[7]
+        out[8] = a[8] + b[8]
+        return out
+    }
+
+    export function mul(out: Mat3, a: Mat3, b: Mat3) {
+        const a00 = a[0], a01 = a[1], a02 = a[2],
+            a10 = a[3], a11 = a[4], a12 = a[5],
+            a20 = a[6], a21 = a[7], a22 = a[8];
+
+        const b00 = b[0], b01 = b[1], b02 = b[2],
+            b10 = b[3], b11 = b[4], b12 = b[5],
+            b20 = b[6], b21 = b[7], b22 = b[8];
+
+        out[0] = b00 * a00 + b01 * a10 + b02 * a20;
+        out[1] = b00 * a01 + b01 * a11 + b02 * a21;
+        out[2] = b00 * a02 + b01 * a12 + b02 * a22;
+
+        out[3] = b10 * a00 + b11 * a10 + b12 * a20;
+        out[4] = b10 * a01 + b11 * a11 + b12 * a21;
+        out[5] = b10 * a02 + b11 * a12 + b12 * a22;
+
+        out[6] = b20 * a00 + b21 * a10 + b22 * a20;
+        out[7] = b20 * a01 + b21 * a11 + b22 * a21;
+        out[8] = b20 * a02 + b21 * a12 + b22 * a22;
+        return out;
+    }
+
+    export function subScalar(out: Mat3, a: Mat3, s: number) {
+        out[0] = a[0] - s
+        out[1] = a[1] - s
+        out[2] = a[2] - s
+        out[3] = a[3] - s
+        out[4] = a[4] - s
+        out[5] = a[5] - s
+        out[6] = a[6] - s
+        out[7] = a[7] - s
+        out[8] = a[8] - s
+        return out
+    }
+
+    export function addScalar(out: Mat3, a: Mat3, s: number) {
+        out[0] = a[0] + s
+        out[1] = a[1] + s
+        out[2] = a[2] + s
+        out[3] = a[3] + s
+        out[4] = a[4] + s
+        out[5] = a[5] + s
+        out[6] = a[6] + s
+        out[7] = a[7] + s
+        out[8] = a[8] + s
+        return out
+    }
+
+    export function mulScalar(out: Mat3, a: Mat3, s: number) {
+        out[0] = a[0] * s
+        out[1] = a[1] * s
+        out[2] = a[2] * s
+        out[3] = a[3] * s
+        out[4] = a[4] * s
+        out[5] = a[5] * s
+        out[6] = a[6] * s
+        out[7] = a[7] * s
+        out[8] = a[8] * s
+        return out
+    }
+
+    const piThird = Math.PI / 3
+    const tmpB = Mat3()
+    /**
+     * Given a real symmetric 3x3 matrix A, compute the eigenvalues
+     *
+     * From https://en.wikipedia.org/wiki/Eigenvalue_algorithm#3.C3.973_matrices
+     */
+    export function symmetricEigenvalues(out: Vec3, a: Mat3) {
+        const p1 = a[1] * a[1] + a[2] * a[2] + a[5] * a[5]
+        if (p1 === 0) {
+            out[0] = a[0]
+            out[1] = a[4]
+            out[2] = a[8]
+        } else {
+            const q = trace(a) / 3
+            const a1 = a[0] - q
+            const a2 = a[4] - q
+            const a3 = a[8] - q
+            const p2 = a1 * a1 + a2 * a2 + a3 * a3 + 2 * p1
+            const p = Math.sqrt(p2 / 6)
+            mulScalar(tmpB, Identity, q)
+            sub(tmpB, a, tmpB)
+            mulScalar(tmpB, tmpB, (1 / p))
+            const r = determinant(tmpB) / 2
+            // In exact arithmetic for a symmetric matrix  -1 <= r <= 1
+            // but computation error can leave it slightly outside this range.
+            const phi = r <= -1 ? piThird : r >= 1 ?
+                0 : Math.acos(r) / 3
+            // the eigenvalues satisfy eig3 <= eig2 <= eig1
+            out[0] = q + 2 * p * Math.cos(phi)
+            out[2] = q + 2 * p * Math.cos(phi + (2 * piThird))
+            out[1] = 3 * q - out[0] - out[2] // since trace(A) = eig1 + eig2 + eig3
+        }
+        return out
+    }
+
+    const tmpR0 = [0.1, 0.0, 0.0] as Vec3
+    const tmpR1 = [0.1, 0.0, 0.0] as Vec3
+    const tmpR2 = [0.1, 0.0, 0.0] as Vec3
+    const tmpR0xR1 = [0.1, 0.0, 0.0] as Vec3
+    const tmpR0xR2 = [0.1, 0.0, 0.0] as Vec3
+    const tmpR1xR2 = [0.1, 0.0, 0.0] as Vec3
+    /**
+     * Calculates the eigenvector for the given eigenvalue `e` of matrix `a`
+     */
+    export function eigenvector(out: Vec3, a: Mat3, e: number) {
+        Vec3.set(tmpR0, a[0] - e, a[1], a[2])
+        Vec3.set(tmpR1, a[1], a[4] - e, a[5])
+        Vec3.set(tmpR2, a[2], a[5], a[8] - e)
+        Vec3.cross(tmpR0xR1, tmpR0, tmpR1)
+        Vec3.cross(tmpR0xR2, tmpR0, tmpR2)
+        Vec3.cross(tmpR1xR2, tmpR1, tmpR2)
+        const d0 = Vec3.dot(tmpR0xR1, tmpR0xR1)
+        const d1 = Vec3.dot(tmpR0xR2, tmpR0xR2)
+        const d2 = Vec3.dot(tmpR1xR2, tmpR1xR2)
+        let dmax = d0
+        let imax = 0
+        if (d1 > dmax) {
+            dmax = d1
+            imax = 1
+        }
+        if (d2 > dmax) imax = 2
+        if (imax === 0) {
+            Vec3.scale(out, tmpR0xR1, 1 / Math.sqrt(d0))
+        } else if (imax === 1) {
+            Vec3.scale(out, tmpR0xR2, 1 / Math.sqrt(d1))
+        } else {
+            Vec3.scale(out, tmpR1xR2, 1 / Math.sqrt(d2))
+        }
+        return out
+    }
+
+    export const Identity: ReadonlyMat3 = identity()
 }
 
 export default Mat3

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>
@@ -101,7 +101,7 @@ namespace Mat4 {
 
     const _id = identity();
     export function isIdentity(m: Mat4, eps?: number) {
-        return areEqual(m, _id, typeof eps === 'undefined' ? EPSILON.Value : eps);
+        return areEqual(m, _id, typeof eps === 'undefined' ? EPSILON : eps);
     }
 
     export function hasNaN(m: Mat4) {
@@ -141,6 +141,7 @@ namespace Mat4 {
         out[offset + 13] = a[13];
         out[offset + 14] = a[14];
         out[offset + 15] = a[15];
+        return out;
     }
 
     export function fromArray(a: Mat4, array: NumberArray, offset: number) {
@@ -499,7 +500,7 @@ namespace Mat4 {
             b10, b11, b12,
             b20, b21, b22;
 
-        if (Math.abs(len) < EPSILON.Value) {
+        if (Math.abs(len) < EPSILON) {
             return Mat4.identity();
         }
 
@@ -549,7 +550,7 @@ namespace Mat4 {
             len = Math.sqrt(x * x + y * y + z * z),
             s, c, t;
 
-        if (Math.abs(len) < EPSILON.Value) { return setIdentity(out); }
+        if (Math.abs(len) < EPSILON) { return setIdentity(out); }
 
         len = 1 / len;
         x *= len;
@@ -719,7 +720,7 @@ namespace Mat4 {
      * [ 0           1           ]
      */
     export function isRotationAndTranslation(a: Mat4, eps?: number) {
-        return _isRotationAndTranslation(a, typeof eps !== 'undefined' ? eps : EPSILON.Value)
+        return _isRotationAndTranslation(a, typeof eps !== 'undefined' ? eps : EPSILON)
     }
 
     function _isRotationAndTranslation(a: Mat4, eps: number) {
@@ -854,9 +855,9 @@ namespace Mat4 {
         const centery = center[1];
         const centerz = center[2];
 
-        if (Math.abs(eyex - centerx) < EPSILON.Value &&
-            Math.abs(eyey - centery) < EPSILON.Value &&
-            Math.abs(eyez - centerz) < EPSILON.Value
+        if (Math.abs(eyex - centerx) < EPSILON &&
+            Math.abs(eyey - centery) < EPSILON &&
+            Math.abs(eyez - centerz) < EPSILON
         ) {
             return setIdentity(out);
         }

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

@@ -28,6 +28,7 @@ import { EPSILON } from './common';
 import { NumberArray } from '../../../mol-util/type-helpers';
 
 interface Quat extends Array<number> { [d: number]: number, '@type': 'quat', length: 4 }
+interface ReadonlyQuat extends Array<number> { readonly [d: number]: number, '@type': 'quat', length: 4 }
 
 function Quat() {
     return Quat.zero();
@@ -281,7 +282,7 @@ namespace Quat {
     export function fromUnitVec3 (out: Quat, a: Vec3, b: Vec3) {
         // assumes a and b are normalized
         let r = Vec3.dot(a, b) + 1
-        if (r < EPSILON.Value) {
+        if (r < EPSILON) {
             // If u and v are exactly opposite, rotate 180 degrees
             // around an arbitrary orthogonal axis. Axis normalisation
             // can happen later, when we normalise the quaternion.
@@ -318,6 +319,7 @@ namespace Quat {
         out[offset + 1] = a[1];
         out[offset + 2] = a[2];
         out[offset + 3] = a[3];
+        return out;
     }
 
     export function fromArray(a: Quat, array: NumberArray, offset: number) {
@@ -439,6 +441,8 @@ namespace Quat {
     export function toString(a: Quat, precision?: number) {
         return `[${a[0].toPrecision(precision)} ${a[1].toPrecision(precision)} ${a[2].toPrecision(precision)}  ${a[3].toPrecision(precision)}]`;
     }
+
+    export const Identity: ReadonlyQuat = identity()
 }
 
 export default Quat

src/mol-math/linear-algebra/3d/vec2.ts

@@ -53,6 +53,7 @@ namespace Vec2 {
     export function toArray(a: Vec2, out: NumberArray, offset: number) {
         out[offset + 0] = a[0];
         out[offset + 1] = a[1];
+        return out;
     }
 
     export function fromArray(a: Vec2, array: NumberArray, offset: number) {

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();
@@ -73,6 +74,7 @@ namespace Vec3 {
         out[offset + 0] = v[0]
         out[offset + 1] = v[1]
         out[offset + 2] = v[2]
+        return out
     }
 
     export function create(x: number, y: number, z: number): Vec3 {
@@ -490,19 +492,18 @@ namespace Vec3 {
     export function equals(a: Vec3, b: Vec3) {
         const a0 = a[0], a1 = a[1], a2 = a[2];
         const b0 = b[0], b1 = b[1], b2 = b[2];
-        return (Math.abs(a0 - b0) <= EPSILON.Value * Math.max(1.0, Math.abs(a0), Math.abs(b0)) &&
-                Math.abs(a1 - b1) <= EPSILON.Value * Math.max(1.0, Math.abs(a1), Math.abs(b1)) &&
-                Math.abs(a2 - b2) <= EPSILON.Value * Math.max(1.0, Math.abs(a2), Math.abs(b2)));
+        return (Math.abs(a0 - b0) <= EPSILON * Math.max(1.0, Math.abs(a0), Math.abs(b0)) &&
+                Math.abs(a1 - b1) <= EPSILON * Math.max(1.0, Math.abs(a1), Math.abs(b1)) &&
+                Math.abs(a2 - b2) <= EPSILON * Math.max(1.0, Math.abs(a2), Math.abs(b2)));
     }
 
     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.Value) {
+        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);
@@ -524,6 +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` */
@@ -536,6 +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/3d/vec4.ts

@@ -62,6 +62,7 @@ namespace Vec4 {
         out[offset + 1] = a[1];
         out[offset + 2] = a[2];
         out[offset + 3] = a[3];
+        return out;
     }
 
     export function fromArray(a: Vec4, array: NumberArray, offset: number) {
@@ -220,10 +221,10 @@ namespace Vec4 {
     export function equals(a: Vec4, b: Vec4) {
         const a0 = a[0], a1 = a[1], a2 = a[2], a3 = a[3];
         const b0 = b[0], b1 = b[1], b2 = b[2], b3 = b[3];
-        return (Math.abs(a0 - b0) <= EPSILON.Value * Math.max(1.0, Math.abs(a0), Math.abs(b0)) &&
-                Math.abs(a1 - b1) <= EPSILON.Value * Math.max(1.0, Math.abs(a1), Math.abs(b1)) &&
-                Math.abs(a2 - b2) <= EPSILON.Value * Math.max(1.0, Math.abs(a2), Math.abs(b2)) &&
-                Math.abs(a3 - b3) <= EPSILON.Value * Math.max(1.0, Math.abs(a3), Math.abs(b3)));
+        return (Math.abs(a0 - b0) <= EPSILON * Math.max(1.0, Math.abs(a0), Math.abs(b0)) &&
+                Math.abs(a1 - b1) <= EPSILON * Math.max(1.0, Math.abs(a1), Math.abs(b1)) &&
+                Math.abs(a2 - b2) <= EPSILON * Math.max(1.0, Math.abs(a2), Math.abs(b2)) &&
+                Math.abs(a3 - b3) <= EPSILON * Math.max(1.0, Math.abs(a3), Math.abs(b3)));
     }
 
     export function toString(a: Vec4, precision?: number) {

src/mol-math/linear-algebra/_spec/mat3.spec.ts

@@ -0,0 +1,35 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Mat3, Vec3 } from '../3d'
+
+describe('Mat3', () => {
+    it('symmetricEigenvalues', () => {
+        const m = Mat3.create(
+            0.1945, -0.0219, -0.0416,
+            -0.0219, 0.1995, -0.0119,
+            -0.0416, -0.0119, 0.3673
+        )
+        const e = Vec3.create(0.377052701425898, 0.21713981522725134, 0.1671074833468507)
+        expect(Vec3.equals(e, Mat3.symmetricEigenvalues(Vec3(), m))).toBe(true);
+    });
+
+    it('eigenvectors', () => {
+        const m = Mat3.create(
+            0.1945, -0.0219, -0.0416,
+            -0.0219, 0.1995, -0.0119,
+            -0.0416, -0.0119, 0.3673
+        )
+        const e = Vec3.create(0.377052701425898, 0.21713981522725134, 0.1671074833468507)
+        const v0 = Vec3.create(-0.2176231019882068, -0.038522620041966125, 0.9752723687391808)
+        const v1 = Vec3.create(-0.5905636938047126, 0.8007524989198634, -0.10014968314142503)
+        const v2 = Vec3.create(0.7770937582036648, 0.5977553372576602, 0.19701230352667118)
+
+        expect(Vec3.equals(v0, Mat3.eigenvector(Vec3(), m, e[0]))).toBe(true);
+        expect(Vec3.equals(v1, Mat3.eigenvector(Vec3(), m, e[1]))).toBe(true);
+        expect(Vec3.equals(v2, Mat3.eigenvector(Vec3(), m, e[2]))).toBe(true);
+    });
+});

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-math/linear-algebra/tensor.ts

@@ -56,40 +56,36 @@ export namespace Tensor {
     export function ColumnMajorMatrix(rows: number, cols: number, ctor?: ArrayCtor) { return Space([rows, cols], [1, 0], ctor); }
     export function RowMajorMatrix(rows: number, cols: number, ctor?: ArrayCtor) { return Space([rows, cols], [0, 1], ctor); }
 
-    export function toMat4(space: Space, data: Tensor.Data): Mat4 {
+    export function toMat4(out: Mat4, space: Space, data: Tensor.Data): Mat4 {
         if (space.rank !== 2) throw new Error('Invalid tensor rank');
-        const mat = Mat4.zero();
         const d0 = Math.min(4, space.dimensions[0]), d1 = Math.min(4, space.dimensions[1]);
         for (let i = 0; i < d0; i++) {
-            for (let j = 0; j < d1; j++) Mat4.setValue(mat, i, j, space.get(data, i, j));
+            for (let j = 0; j < d1; j++) Mat4.setValue(out, i, j, space.get(data, i, j));
         }
-        return mat;
+        return out;
     }
 
-    export function toMat3(space: Space, data: Tensor.Data): Mat3 {
+    export function toMat3(out: Mat3, space: Space, data: Tensor.Data): Mat3 {
         if (space.rank !== 2) throw new Error('Invalid tensor rank');
-        const mat = Mat3.zero();
         const d0 = Math.min(3, space.dimensions[0]), d1 = Math.min(3, space.dimensions[1]);
         for (let i = 0; i < d0; i++) {
-            for (let j = 0; j < d1; j++) Mat3.setValue(mat, i, j, space.get(data, i, j));
+            for (let j = 0; j < d1; j++) Mat3.setValue(out, i, j, space.get(data, i, j));
         }
-        return mat;
+        return out;
     }
 
-    export function toVec3(space: Space, data: Tensor.Data): Vec3 {
+    export function toVec3(out: Vec3, space: Space, data: Tensor.Data): Vec3 {
         if (space.rank !== 1) throw new Error('Invalid tensor rank');
-        const vec = Vec3.zero();
         const d0 = Math.min(3, space.dimensions[0]);
-        for (let i = 0; i < d0; i++) vec[i] = data[i];
-        return vec;
+        for (let i = 0; i < d0; i++) out[i] = data[i];
+        return out;
     }
 
-    export function toVec4(space: Space, data: Tensor.Data): Vec4 {
+    export function toVec4(out: Vec4, space: Space, data: Tensor.Data): Vec4 {
         if (space.rank !== 1) throw new Error('Invalid tensor rank');
-        const vec = Vec4.zero();
         const d0 = Math.min(4, space.dimensions[0]);
-        for (let i = 0; i < d0; i++) vec[i] = data[i];
-        return vec;
+        for (let i = 0; i < d0; i++) out[i] = data[i];
+        return out;
     }
 
     export function areEqualExact(a: Tensor.Data, b: Tensor.Data) {

src/mol-math/misc.ts

@@ -14,4 +14,19 @@ export function radToDeg (rad: number) {
 
 export function isPowerOfTwo (x: number) {
     return (x !== 0) && (x & (x - 1)) === 0
+}
+
+/** return the value that has the largest absolute value */
+export function absMax(...values: number[]) {
+    let max = 0
+    let absMax = 0
+    for (let i = 0, il = values.length; i < il; ++i) {
+        const value = values[i]
+        const abs = Math.abs(value)
+        if (abs > absMax) {
+            max = value
+            absMax = abs
+        }
+    }
+    return max
 }

src/mol-model-formats/structure/3dg.ts

@@ -0,0 +1,79 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Model } from '../../mol-model/structure/model';
+import { Task } from '../../mol-task';
+import { ModelFormat } from './format';
+import { _parse_mmCif } from './mmcif/parser';
+import { CifCategory, CifField } from '../../mol-io/reader/cif';
+import { Column } from '../../mol-data/db';
+import { mmCIF_Schema } from '../../mol-io/reader/cif/schema/mmcif';
+import { EntityBuilder } from './common/entity';
+import { File3DG } from '../../mol-io/reader/3dg/parser';
+import { fillSerial } from '../../mol-util/array';
+import { MoleculeType } from '../../mol-model/structure/model/types';
+
+function getCategories(table: File3DG['table']) {
+    const entityIds = new Array<string>(table._rowCount)
+    const entityBuilder = new EntityBuilder()
+
+    const seqIdStarts = table.position.toArray({ array: Uint32Array })
+    const seqIdEnds = new Uint32Array(table._rowCount)
+    const stride = seqIdStarts[1] - seqIdStarts[0]
+
+    const objectRadius = stride / 3500
+
+    for (let i = 0, il = table._rowCount; i < il; ++i) {
+        const chr = table.chromosome.value(i)
+        const entityId = entityBuilder.getEntityId(chr, MoleculeType.DNA, chr)
+        entityIds[i] = entityId
+        seqIdEnds[i] = seqIdStarts[i] + stride - 1
+    }
+
+    const ihm_sphere_obj_site: CifCategory.SomeFields<mmCIF_Schema['ihm_sphere_obj_site']> = {
+        id: CifField.ofNumbers(fillSerial(new Uint32Array(table._rowCount))),
+        entity_id: CifField.ofStrings(entityIds),
+        seq_id_begin: CifField.ofNumbers(seqIdStarts),
+        seq_id_end: CifField.ofNumbers(seqIdEnds),
+        asym_id: CifField.ofColumn(table.chromosome),
+
+        Cartn_x: CifField.ofNumbers(Column.mapToArray(table.x, x => x * 10, Float32Array)),
+        Cartn_y: CifField.ofNumbers(Column.mapToArray(table.y, y => y * 10, Float32Array)),
+        Cartn_z: CifField.ofNumbers(Column.mapToArray(table.z, z => z * 10, Float32Array)),
+
+        object_radius: CifField.ofColumn(Column.ofConst(objectRadius, table._rowCount, Column.Schema.float)),
+        rmsf: CifField.ofColumn(Column.ofConst(0, table._rowCount, Column.Schema.float)),
+        model_id: CifField.ofColumn(Column.ofConst(1, table._rowCount, Column.Schema.int)),
+    }
+
+    return {
+        entity: entityBuilder.getEntityCategory(),
+        ihm_model_list: CifCategory.ofFields('ihm_model_list', {
+            model_id: CifField.ofNumbers([1]),
+            model_name: CifField.ofStrings(['3DG Model']),
+        }),
+        ihm_sphere_obj_site: CifCategory.ofFields('ihm_sphere_obj_site', ihm_sphere_obj_site)
+    }
+}
+
+async function mmCifFrom3dg(file3dg: File3DG) {
+    const categories = getCategories(file3dg.table)
+
+    return {
+        header: '3DG',
+        categoryNames: Object.keys(categories),
+        categories
+    };
+}
+
+export function trajectoryFrom3DG(file3dg: File3DG): Task<Model.Trajectory> {
+    return Task.create('Parse 3DG', async ctx => {
+        await ctx.update('Converting to mmCIF');
+        const cif = await mmCifFrom3dg(file3dg);
+        const format = ModelFormat.mmCIF(cif);
+        return _parse_mmCif(format, ctx);
+    })
+}

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/anisotropic.ts

@@ -0,0 +1,89 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Table } from '../../../mol-data/db';
+import { Model, CustomPropertyDescriptor } from '../../../mol-model/structure';
+import { mmCIF_Schema } from '../../../mol-io/reader/cif/schema/mmcif';
+import { CifWriter } from '../../../mol-io/writer/cif';
+
+export interface AtomSiteAnisotrop {
+    data: Table<AtomSiteAnisotrop.Schema['atom_site_anisotrop']>
+    /** maps atom_site-index to atom_site_anisotrop-index */
+    elementToAnsiotrop: Int32Array
+}
+
+export namespace AtomSiteAnisotrop {
+    export function getAtomSiteAnisotrop(model: Model) {
+        if (model.sourceData.kind !== 'mmCIF') return void 0;
+        const { atom_site_anisotrop } = model.sourceData.data
+        return Table.ofColumns(Schema.atom_site_anisotrop, atom_site_anisotrop);
+    }
+
+    export const PropName = '__AtomSiteAnisotrop__';
+    export function get(model: Model): AtomSiteAnisotrop | undefined {
+        if (model._staticPropertyData[PropName]) return model._staticPropertyData[PropName]
+        if (!model.customProperties.has(Descriptor)) return void 0;
+
+        const data = getAtomSiteAnisotrop(model);
+        if (!data) return void 0;
+
+        const prop = { data, elementToAnsiotrop: getElementToAnsiotrop(model, data) }
+        set(model, prop)
+
+        return prop;
+    }
+    function set(model: Model, prop: AtomSiteAnisotrop) {
+        (model._staticPropertyData[PropName] as AtomSiteAnisotrop) = prop;
+    }
+
+    export const Schema = { atom_site_anisotrop: mmCIF_Schema['atom_site_anisotrop'] };
+    export type Schema = typeof Schema
+
+    export const Descriptor: CustomPropertyDescriptor = {
+        isStatic: true,
+        name: 'atom_site_anisotrop',
+        cifExport: {
+            prefix: '',
+            categories: [{
+                name: 'atom_site_anisotrop',
+                instance(ctx) {
+                    const atom_site_anisotrop = getAtomSiteAnisotrop(ctx.firstModel);
+                    if (!atom_site_anisotrop) return CifWriter.Category.Empty;
+                    return CifWriter.Category.ofTable(atom_site_anisotrop);
+                }
+            }]
+        }
+    };
+
+    function getElementToAnsiotrop(model: Model, data: Table<Schema['atom_site_anisotrop']>) {
+        const { atomId } = model.atomicConformation
+        const atomIdToElement = new Int32Array(atomId.rowCount)
+        atomIdToElement.fill(-1)
+        for (let i = 0, il = atomId.rowCount; i < il; i++) {
+            atomIdToElement[atomId.value(i)] = i
+        }
+
+        const { id } = data
+        const elementToAnsiotrop = new Int32Array(atomId.rowCount)
+        elementToAnsiotrop.fill(-1)
+        for (let i = 0, il = id.rowCount; i < il; ++i) {
+            const ei = atomIdToElement[id.value(i)]
+            if (ei !== -1) elementToAnsiotrop[ei] = i
+        }
+
+        return elementToAnsiotrop
+    }
+
+    export async function attachFromMmCif(model: Model) {
+        if (model.customProperties.has(Descriptor)) return true;
+        if (model.sourceData.kind !== 'mmCIF') return false;
+        const atomSiteAnisotrop = getAtomSiteAnisotrop(model);
+        if (!atomSiteAnisotrop || atomSiteAnisotrop._rowCount === 0) return false;
+
+        model.customProperties.add(Descriptor);
+        return true;
+    }
+}

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

@@ -4,7 +4,7 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import { Mat4, Tensor } from '../../../mol-math/linear-algebra'
+import { Mat4, Tensor, Vec3 } from '../../../mol-math/linear-algebra'
 import { SymmetryOperator } from '../../../mol-math/geometry/symmetry-operator'
 import { Assembly, OperatorGroup, OperatorGroups } from '../../../mol-model/structure/model/properties/symmetry'
 import { Queries as Q } from '../../../mol-model/structure'
@@ -76,8 +76,8 @@ function getMatrices({ data }: mmCIF_Format): Matrices {
     const matrices = new Map<string, Mat4>();
 
     for (let i = 0, _i = pdbx_struct_oper_list._rowCount; i < _i; i++) {
-        const m = Tensor.toMat4(_schema.matrix.space, matrix.value(i));
-        const t = Tensor.toVec3(_schema.vector.space, vector.value(i));
+        const m = Tensor.toMat4(Mat4(), _schema.matrix.space, matrix.value(i));
+        const t = Tensor.toVec3(Vec3(), _schema.vector.space, vector.value(i));
         Mat4.setTranslation(m, t);
         Mat4.setValue(m, 3, 3, 1);
         matrices.set(id.value(i), m);

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

@@ -1,7 +1,8 @@
 /**
- * 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>
  */
 
 import { Column, Table } from '../../../mol-data/db';
@@ -14,7 +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';
 
@@ -26,15 +26,15 @@ function findHierarchyOffsets(atom_site: AtomSite) {
     const start = 0, end = atom_site._rowCount;
     const residues = [start as ElementIndex], chains = [start as ElementIndex];
 
-    const { label_entity_id, label_asym_id, label_seq_id, auth_seq_id, pdbx_PDB_ins_code, label_comp_id } = atom_site;
+    const { label_entity_id, label_asym_id, label_seq_id, auth_seq_id, pdbx_PDB_ins_code } = atom_site;
 
     for (let i = start + 1 as ElementIndex; i < end; i++) {
         const newChain = !label_entity_id.areValuesEqual(i - 1, i) || !label_asym_id.areValuesEqual(i - 1, i);
         const newResidue = newChain
             || !label_seq_id.areValuesEqual(i - 1, i)
             || !auth_seq_id.areValuesEqual(i - 1, i)
-            || !pdbx_PDB_ins_code.areValuesEqual(i - 1, i)
-            || !label_comp_id.areValuesEqual(i - 1, i);
+            || !pdbx_PDB_ins_code.areValuesEqual(i - 1, i);
+        // not checking label_comp_id to allow for MICROHETEROGENEITY
 
         if (newResidue) residues[residues.length] = i as ElementIndex;
         if (newChain) chains[chains.length] = i as ElementIndex;
@@ -42,6 +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) }),
@@ -51,11 +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 };
 }
 
@@ -99,7 +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 };
 }