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MVS: topology format support (#1691)
* MVS: topology format support * bugfix * mvs: additional coordinate formats * fix
This commit is contained in:
David Sehnal
GitHub
@@ -6,6 +6,9 @@ Note that since we don't clearly distinguish between a public and private interf
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## [Unreleased]
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- Update loading message in MVS Stories Viewer
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- Add `Canvas3D.setAttribs`
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- MolViewSpec
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- Add support for "topology" formats (TOP, PRMTOP, PSF)
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- Add support for additional "coordiates" formats (NCTRAJ, DCD, TRR)
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## [v5.2.0] - 2025-10-31
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- Handle transparency updates on ImagePass
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BIN
examples/trajectory/protein.dcd
Normal file
BIN
examples/trajectory/protein.dcd
Normal file
Binary file not shown.
BIN
examples/trajectory/protein.nc
Normal file
BIN
examples/trajectory/protein.nc
Normal file
Binary file not shown.
264
examples/trajectory/protein.parm7
Normal file
264
examples/trajectory/protein.parm7
Normal file
@@ -0,0 +1,264 @@
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%VERSION VERSION_STAMP = V0001.000 DATE = 11/04/25 11:55:47
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%FLAG TITLE
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%FORMAT(20a4)
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alanine-dipeptide.solvated.pdb
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%FLAG POINTERS
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%FORMAT(10I8)
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22 7 12 9 25 11 39 19 0 0
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99 3 9 11 19 7 11 20 0 0
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0 0 0 0 0 0 0 1 10 0
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0 1
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%FLAG ATOM_NAME
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%FORMAT(20a4)
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H1 CH3 H2 H3 C O N H CA HA CB HB1 HB2 HB3 C O N H C H1
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H2 H3
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%FLAG ATOMIC_NUMBER
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%FORMAT(10I8)
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1 6 1 1 6 8 7 1 6 1
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6 1 1 1 6 8 7 1 6 1
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1 1
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%FLAG RESIDUE_LABEL
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%FORMAT(20a4)
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ACE ALA NME
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%FLAG RESIDUE_POINTER
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%FORMAT(10I8)
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1 7 17
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%FLAG RESIDUE_NUMBER
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%FORMAT(20I4)
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1 2 3
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%FLAG RESIDUE_ICODE
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%FORMAT(20a4)
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%FLAG RESIDUE_CHAINID
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%FORMAT(20a4)
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B B B
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%FLAG SOLVENT_POINTERS
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%FORMAT(3I8)
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0 1 0
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%FLAG ATOMS_PER_MOLECULE
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%FORMAT(10I8)
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22
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%FLAG MASS
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%FORMAT(5E16.8)
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3.02400000E+00 5.96200000E+00 3.02400000E+00 3.02400000E+00 1.20100000E+01
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1.60000000E+01 1.19940000E+01 3.02400000E+00 9.99400000E+00 3.02400000E+00
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5.96200000E+00 3.02400000E+00 3.02400000E+00 3.02400000E+00 1.20100000E+01
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1.60000000E+01 1.19940000E+01 3.02400000E+00 5.96200000E+00 3.02400000E+00
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3.02400000E+00 3.02400000E+00
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%FLAG CHARGE
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%FORMAT(5E16.8)
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2.04636429E+00 -6.67300626E+00 2.04636429E+00 2.04636429E+00 1.08823576E+01
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-1.03484442E+01 -7.57501011E+00 4.95464337E+00 6.14091510E-01 1.49969529E+00
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-3.32556975E+00 1.09880469E+00 1.09880469E+00 1.09880469E+00 1.08841798E+01
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-1.03484442E+01 -7.57501011E+00 4.95464337E+00 -2.71512270E+00 1.77849648E+00
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1.77849648E+00 1.77849648E+00
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%FLAG AMBER_ATOM_TYPE
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%FORMAT(20a4)
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a0 a1 a0 a0 a2 a3 a4 a5 a1 a6 a1 a0 a0 a0 a2 a3 a4 a5 a1 a6
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a6 a6
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%FLAG ATOM_TYPE_INDEX
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%FORMAT(10I8)
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1 2 1 1 3 4 5 6 2 7
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2 1 1 1 3 4 5 6 2 7
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7 7
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%FLAG NONBONDED_PARM_INDEX
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%FORMAT(10I8)
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1 2 4 7 11 16 22 2 3 5
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8 12 17 23 4 5 6 9 13 18
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24 7 8 9 10 14 19 25 11 12
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13 14 15 20 26 16 17 18 19 20
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21 27 22 23 24 25 26 27 28
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%FLAG LENNARD_JONES_ACOEF
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%FORMAT(5E16.8)
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7.51607703E+03 9.71708117E+04 1.04308023E+06 8.61541883E+04 9.24822269E+05
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8.19971662E+05 5.44261042E+04 6.47841732E+05 5.74393458E+05 3.79876399E+05
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8.96776989E+04 9.95480466E+05 8.82619071E+05 6.06829343E+05 9.44293233E+05
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1.07193645E+02 2.56678134E+03 2.27577560E+03 1.02595236E+03 2.12601181E+03
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1.39982777E-01 4.98586847E+03 6.78771368E+04 6.01816484E+04 3.69471530E+04
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6.20665998E+04 5.94667299E+01 3.25969625E+03
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%FLAG LENNARD_JONES_BCOEF
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%FORMAT(5E16.8)
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2.17257828E+01 1.26919150E+02 6.75612247E+02 1.12529845E+02 5.99015525E+02
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5.31102864E+02 1.11805549E+02 6.26720080E+02 5.55666449E+02 5.64885984E+02
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1.36131731E+02 7.36907417E+02 6.53361429E+02 6.77220874E+02 8.01323529E+02
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2.59456373E+00 2.06278363E+01 1.82891803E+01 1.53505284E+01 2.09604198E+01
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9.37598976E-02 1.76949863E+01 1.06076943E+02 9.40505981E+01 9.21192137E+01
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1.13252062E+02 1.93248820E+00 1.43076527E+01
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%FLAG NUMBER_EXCLUDED_ATOMS
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%FORMAT(10I8)
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6 7 4 3 7 3 10 4 10 7
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6 3 2 1 7 3 5 4 3 2
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1 1
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%FLAG EXCLUDED_ATOMS_LIST
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%FORMAT(10I8)
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2 3 4 5 6 7 3 4 5 6
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7 8 9 4 5 6 7 5 6 7
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6 7 8 9 10 11 15 7 8 9
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8 9 10 11 12 13 14 15 16 17
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9 10 11 15 10 11 12 13 14 15
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16 17 18 19 11 12 13 14 15 16
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17 12 13 14 15 16 17 13 14 15
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14 15 15 16 17 18 19 20 21 22
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17 18 19 18 19 20 21 22 19 20
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21 22 20 21 22 21 22 22 0
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%FLAG BOND_FORCE_CONSTANT
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%FORMAT(5E16.8)
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3.40000000E+02 4.34000000E+02 3.17000000E+02 5.70000000E+02 4.90000000E+02
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3.37000000E+02 3.10000000E+02
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%FLAG BOND_EQUIL_VALUE
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%FORMAT(5E16.8)
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1.09000000E+00 1.01000000E+00 1.52200000E+00 1.22900000E+00 1.33500000E+00
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1.44900000E+00 1.52600000E+00
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%FLAG BONDS_INC_HYDROGEN
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%FORMAT(10I8)
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0 3 1 3 6 1 3 9 1 18
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21 2 24 27 1 30 33 1 30 36
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1 30 39 1 48 51 2 54 57 1
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54 60 1 54 63 1
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%FLAG BONDS_WITHOUT_HYDROGEN
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%FORMAT(10I8)
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3 12 3 12 15 4 12 18 5 18
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24 6 24 42 3 24 30 7 42 48
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5 42 45 4 48 54 6
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%FLAG ANGLE_FORCE_CONSTANT
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%FORMAT(5E16.8)
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||||
3.50000000E+01 5.00000000E+01 5.00000000E+01 5.00000000E+01 8.00000000E+01
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7.00000000E+01 5.00000000E+01 8.00000000E+01 8.00000000E+01 6.30000000E+01
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||||
6.30000000E+01
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%FLAG ANGLE_EQUIL_VALUE
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%FORMAT(5E16.8)
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1.91113553E+00 1.91113553E+00 2.09439510E+00 2.06018665E+00 2.10137642E+00
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2.03505391E+00 2.12755636E+00 2.14500965E+00 1.91462619E+00 1.92160751E+00
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1.93906080E+00
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%FLAG ANGLES_INC_HYDROGEN
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%FORMAT(10I8)
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0 3 6 1 0 3 9 1 0 3
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12 2 6 3 9 1 6 3 12 2
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9 3 12 2 12 18 21 3 18 24
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27 2 21 18 24 4 24 30 33 2
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||||
24 30 36 2 24 30 39 2 27 24
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30 2 27 24 42 2 33 30 36 1
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33 30 39 1 36 30 39 1 42 48
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51 3 48 54 57 2 48 54 60 2
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48 54 63 2 51 48 54 4 57 54
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60 1 57 54 63 1 60 54 63 1
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%FLAG ANGLES_WITHOUT_HYDROGEN
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%FORMAT(10I8)
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3 12 15 5 3 12 18 6 12 18
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24 7 15 12 18 8 18 24 30 9
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18 24 42 10 24 42 45 5 24 42
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48 6 30 24 42 11 42 48 54 7
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45 42 48 8
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%FLAG DIHEDRAL_FORCE_CONSTANT
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%FORMAT(5E16.8)
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8.00000000E-01 8.00000000E-02 2.50000000E+00 2.50000000E+00 2.00000000E+00
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1.55555556E-01 1.10000000E+00 0.00000000E+00 0.00000000E+00 8.00000000E-01
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||||
1.80000000E+00 4.20000000E-01 2.70000000E-01 5.50000000E-01 1.58000000E+00
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4.50000000E-01 4.00000000E-01 2.00000000E-01 2.00000000E-01 1.05000000E+01
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%FLAG DIHEDRAL_PERIODICITY
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%FORMAT(5E16.8)
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1.00000000E+00 3.00000000E+00 2.00000000E+00 2.00000000E+00 1.00000000E+00
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||||
3.00000000E+00 2.00000000E+00 1.00000000E+00 1.00000000E+00 3.00000000E+00
|
||||
2.00000000E+00 3.00000000E+00 2.00000000E+00 3.00000000E+00 2.00000000E+00
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1.00000000E+00 3.00000000E+00 2.00000000E+00 1.00000000E+00 2.00000000E+00
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%FLAG DIHEDRAL_PHASE
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%FORMAT(5E16.8)
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0.00000000E+00 3.14159265E+00 3.14159265E+00 3.14159265E+00 0.00000000E+00
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0.00000000E+00 3.14159265E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
|
||||
0.00000000E+00 0.00000000E+00 0.00000000E+00 3.14159265E+00 3.14159265E+00
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3.14159265E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 3.14159265E+00
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%FLAG SCEE_SCALE_FACTOR
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%FORMAT(5E16.8)
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1.20000000E+00 0.00000000E+00 1.20000000E+00 1.20000000E+00 0.00000000E+00
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1.20000000E+00 0.00000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00
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||||
0.00000000E+00 1.20000000E+00 0.00000000E+00 1.20000000E+00 0.00000000E+00
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0.00000000E+00 1.20000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
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%FLAG SCNB_SCALE_FACTOR
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%FORMAT(5E16.8)
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2.00000000E+00 0.00000000E+00 2.00000000E+00 2.00000000E+00 0.00000000E+00
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||||
2.00000000E+00 0.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00
|
||||
0.00000000E+00 2.00000000E+00 0.00000000E+00 2.00000000E+00 0.00000000E+00
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0.00000000E+00 2.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
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%FLAG DIHEDRALS_INC_HYDROGEN
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%FORMAT(10I8)
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0 3 12 15 1 0 3 -12 15 2
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3 12 18 21 3 6 3 12 15 1
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6 3 -12 15 2 9 3 12 15 1
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9 3 -12 15 2 15 12 18 21 4
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15 12 -18 21 5 18 24 30 33 6
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||||
18 24 30 36 6 18 24 30 39 6
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||||
24 42 48 51 3 27 24 30 33 6
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27 24 30 36 6 27 24 30 39 6
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||||
27 24 42 45 1 27 24 -42 45 2
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||||
42 24 30 33 6 42 24 30 36 6
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||||
42 24 30 39 6 45 42 48 51 4
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45 42 -48 51 5 21 18 -24 -12 7
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51 48 -54 -42 7 51 48 54 60 8
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21 18 24 30 8 42 48 54 57 8
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6 3 12 18 9 42 48 54 63 8
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51 48 54 57 8 21 18 24 42 8
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0 3 12 18 9 42 48 54 60 8
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27 24 42 48 8 21 18 24 27 8
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51 48 54 63 8 9 3 12 18 9
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12 18 24 27 8
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%FLAG DIHEDRALS_WITHOUT_HYDROGEN
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%FORMAT(10I8)
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3 12 18 24 3 12 18 24 30 10
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12 18 -24 30 11 12 18 -24 30 5
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12 18 24 42 12 12 18 -24 42 13
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||||
15 12 18 24 3 18 24 42 48 14
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||||
18 24 -42 48 15 18 24 -42 48 16
|
||||
24 42 48 54 3 30 24 42 48 17
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||||
30 24 -42 48 18 30 24 -42 48 19
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||||
45 42 48 54 3 15 12 -18 -3 20
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45 42 -48 -24 20 18 24 42 45 8
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30 24 42 45 8
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%FLAG SOLTY
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%FORMAT(5E16.8)
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|
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%FLAG HBOND_ACOEF
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%FORMAT(5E16.8)
|
||||
|
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%FLAG HBOND_BCOEF
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%FORMAT(5E16.8)
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||||
|
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%FLAG HBCUT
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%FORMAT(5E16.8)
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|
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%FLAG TREE_CHAIN_CLASSIFICATION
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%FORMAT(20a4)
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BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA
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BLA BLA
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%FLAG JOIN_ARRAY
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||||
%FORMAT(10I8)
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||||
0 0 0 0 0 0 0 0 0 0
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||||
0 0 0 0 0 0 0 0 0 0
|
||||
0 0
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%FLAG IROTAT
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||||
%FORMAT(10I8)
|
||||
0 0 0 0 0 0 0 0 0 0
|
||||
0 0 0 0 0 0 0 0 0 0
|
||||
0 0
|
||||
%FLAG BOX_DIMENSIONS
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||||
%FORMAT(5E16.8)
|
||||
9.00000000E+01 3.00000000E+01 3.00000000E+01 3.00000000E+01
|
||||
%FLAG RADIUS_SET
|
||||
%FORMAT(1a80)
|
||||
0
|
||||
%FLAG RADII
|
||||
%FORMAT(5E16.8)
|
||||
0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
|
||||
0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
|
||||
0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
|
||||
0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
|
||||
0.00000000E+00 0.00000000E+00
|
||||
%FLAG SCREEN
|
||||
%FORMAT(5E16.8)
|
||||
0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
|
||||
0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
|
||||
0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
|
||||
0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
|
||||
0.00000000E+00 0.00000000E+00
|
||||
%FLAG IPOL
|
||||
%FORMAT(1I8)
|
||||
0
|
||||
26
examples/trajectory/protein.pdb
Normal file
26
examples/trajectory/protein.pdb
Normal file
@@ -0,0 +1,26 @@
|
||||
CRYST1 30.000 30.000 30.000 90.00 90.00 90.00 P 1 1
|
||||
ATOM 1 H1 ACE A 1 2.000 1.000 -0.000 0.00 0.00 H
|
||||
ATOM 2 CH3 ACE A 1 2.000 2.090 0.000 0.00 0.00 C
|
||||
ATOM 3 H2 ACE A 1 1.486 2.454 0.890 0.00 0.00 H
|
||||
ATOM 4 H3 ACE A 1 1.486 2.454 -0.890 0.00 0.00 H
|
||||
ATOM 5 C ACE A 1 3.427 2.641 -0.000 0.00 0.00 C
|
||||
ATOM 6 O ACE A 1 4.391 1.877 -0.000 0.00 0.00 O
|
||||
ATOM 7 N ALA A 2 3.555 3.970 -0.000 0.00 0.00 N
|
||||
ATOM 8 H ALA A 2 2.733 4.556 -0.000 0.00 0.00 H
|
||||
ATOM 9 CA ALA A 2 4.853 4.614 -0.000 0.00 0.00 C
|
||||
ATOM 10 HA ALA A 2 5.408 4.316 0.890 0.00 0.00 H
|
||||
ATOM 11 CB ALA A 2 5.661 4.221 -1.232 0.00 0.00 C
|
||||
ATOM 12 HB1 ALA A 2 5.123 4.521 -2.131 0.00 0.00 H
|
||||
ATOM 13 HB2 ALA A 2 6.630 4.719 -1.206 0.00 0.00 H
|
||||
ATOM 14 HB3 ALA A 2 5.809 3.141 -1.241 0.00 0.00 H
|
||||
ATOM 15 C ALA A 2 4.713 6.129 0.000 0.00 0.00 C
|
||||
ATOM 16 O ALA A 2 3.601 6.653 0.000 0.00 0.00 O
|
||||
ATOM 17 N NME A 3 5.846 6.835 0.000 0.00 0.00 N
|
||||
ATOM 18 H NME A 3 6.737 6.359 -0.000 0.00 0.00 H
|
||||
ATOM 19 C NME A 3 5.846 8.284 0.000 0.00 0.00 C
|
||||
ATOM 20 H1 NME A 3 4.819 8.648 0.000 0.00 0.00 H
|
||||
ATOM 21 H2 NME A 3 6.360 8.648 0.890 0.00 0.00 H
|
||||
ATOM 22 H3 NME A 3 6.360 8.648 -0.890 0.00 0.00 H
|
||||
TER 23 NME A 3
|
||||
CONECT 5 7
|
||||
CONECT 15 17
|
||||
14
examples/trajectory/protein.rst7
Normal file
14
examples/trajectory/protein.rst7
Normal file
@@ -0,0 +1,14 @@
|
||||
alanine-dipeptide.solvated.pdb
|
||||
22
|
||||
0.7494821 1.2436848 0.8743532 1.0856344 2.2423820 0.5955986
|
||||
0.4304414 2.9747953 1.0671825 1.0497815 2.3544810 -0.4880289
|
||||
2.5015950 2.4471725 1.0820421 3.1003812 1.5343071 1.6479120
|
||||
3.0220696 3.6519467 0.8741013 2.4411554 4.3533213 0.4373955
|
||||
4.3920715 4.0500473 1.2160543 4.7674596 3.4172266 2.0202454
|
||||
5.2805058 3.8202998 -0.0180103 4.9565949 4.4537317 -0.8438106
|
||||
6.3180425 4.0583459 0.2164072 5.2327259 2.7740601 -0.3200050
|
||||
4.4431625 5.5106563 1.7135265 3.4307644 6.2198007 1.6891606
|
||||
5.6170320 5.9613562 2.1744082 6.3997462 5.3231585 2.1616313
|
||||
5.8784762 7.3296314 2.6320299 5.1056278 8.0184146 2.2908769
|
||||
5.9253575 7.3544224 3.7207393 6.8360338 7.6745804 2.2419090
|
||||
30.0000000 30.0000000 30.0000000 90.0000000 90.0000000 90.0000000
|
||||
@@ -14,7 +14,7 @@ import { MVSTransform } from './annotation-structure-component';
|
||||
export const MVSTrajectoryWithCoordinates = MVSTransform({
|
||||
name: 'trajectory-with-coordinates',
|
||||
display: { name: 'Trajectory with Coordinates', description: 'Create a trajectory from existing model and the provided coordinates.' },
|
||||
from: PluginStateObject.Molecule.Model,
|
||||
from: [PluginStateObject.Molecule.Model, PluginStateObject.Molecule.Topology],
|
||||
to: PluginStateObject.Molecule.Trajectory,
|
||||
params: {
|
||||
coordinatesRef: ParamDefinition.Text('', { isHidden: true }),
|
||||
|
||||
@@ -8,8 +8,8 @@
|
||||
|
||||
import { PluginStateSnapshotManager } from '../../mol-plugin-state/manager/snapshots';
|
||||
import { PluginStateObject } from '../../mol-plugin-state/objects';
|
||||
import { Download, ParseCcp4, ParseCif, ParseDx } from '../../mol-plugin-state/transforms/data';
|
||||
import { CoordinatesFromLammpstraj, CoordinatesFromXtc, CustomModelProperties, CustomStructureProperties, ModelFromTrajectory, StructureComponent, StructureFromModel, TrajectoryFromGRO, TrajectoryFromLammpsTrajData, TrajectoryFromMmCif, TrajectoryFromMOL, TrajectoryFromMOL2, TrajectoryFromPDB, TrajectoryFromSDF, TrajectoryFromXYZ } from '../../mol-plugin-state/transforms/model';
|
||||
import { Download, ParseCcp4, ParseCif, ParseDx, ParsePrmtop, ParsePsf, ParseTop } from '../../mol-plugin-state/transforms/data';
|
||||
import { CoordinatesFromDcd, CoordinatesFromLammpstraj, CoordinatesFromNctraj, CoordinatesFromTrr, CoordinatesFromXtc, CustomModelProperties, CustomStructureProperties, ModelFromTrajectory, StructureComponent, StructureFromModel, TopologyFromPrmtop, TopologyFromPsf, TopologyFromTop, TrajectoryFromGRO, TrajectoryFromLammpsTrajData, TrajectoryFromMmCif, TrajectoryFromMOL, TrajectoryFromMOL2, TrajectoryFromPDB, TrajectoryFromSDF, TrajectoryFromXYZ } from '../../mol-plugin-state/transforms/model';
|
||||
import { StructureRepresentation3D, VolumeRepresentation3D } from '../../mol-plugin-state/transforms/representation';
|
||||
import { VolumeFromCcp4, VolumeFromDensityServerCif, VolumeFromDx } from '../../mol-plugin-state/transforms/volume';
|
||||
import { PluginCommands } from '../../mol-plugin/commands';
|
||||
@@ -246,7 +246,16 @@ const MolstarLoadingActions: LoadingActions<MolstarTree, MolstarLoadingContext>
|
||||
case 'mol2':
|
||||
case 'xtc':
|
||||
case 'lammpstrj':
|
||||
case 'dcd':
|
||||
case 'nctraj':
|
||||
case 'trr':
|
||||
return updateParent;
|
||||
case 'psf':
|
||||
return UpdateTarget.apply(updateParent, ParsePsf, {});
|
||||
case 'prmtop':
|
||||
return UpdateTarget.apply(updateParent, ParsePrmtop, {});
|
||||
case 'top':
|
||||
return UpdateTarget.apply(updateParent, ParseTop, {});
|
||||
case 'map':
|
||||
return UpdateTarget.apply(updateParent, ParseCcp4, {});
|
||||
case 'dx':
|
||||
@@ -260,6 +269,12 @@ const MolstarLoadingActions: LoadingActions<MolstarTree, MolstarLoadingContext>
|
||||
coordinates(updateParent: UpdateTarget, node: MolstarNode<'coordinates'>): UpdateTarget | undefined {
|
||||
const format = node.params.format;
|
||||
switch (format) {
|
||||
case 'nctraj':
|
||||
return UpdateTarget.apply(updateParent, CoordinatesFromNctraj);
|
||||
case 'dcd':
|
||||
return UpdateTarget.apply(updateParent, CoordinatesFromDcd);
|
||||
case 'trr':
|
||||
return UpdateTarget.apply(updateParent, CoordinatesFromTrr);
|
||||
case 'xtc':
|
||||
return UpdateTarget.apply(updateParent, CoordinatesFromXtc);
|
||||
case 'lammpstrj':
|
||||
@@ -303,6 +318,28 @@ const MolstarLoadingActions: LoadingActions<MolstarTree, MolstarLoadingContext>
|
||||
});
|
||||
return UpdateTarget.setMvsDependencies(result, [node.params.coordinates_ref]);
|
||||
},
|
||||
topology_with_coordinates(updateParent: UpdateTarget, node: MolstarNode<'topology_with_coordinates'>): UpdateTarget | undefined {
|
||||
let parsed: UpdateTarget;
|
||||
const format = node.params.format;
|
||||
switch (format) {
|
||||
case 'psf':
|
||||
parsed = UpdateTarget.apply(updateParent, TopologyFromPsf, {});
|
||||
break;
|
||||
case 'prmtop':
|
||||
parsed = UpdateTarget.apply(updateParent, TopologyFromPrmtop, {});
|
||||
break;
|
||||
case 'top':
|
||||
parsed = UpdateTarget.apply(updateParent, TopologyFromTop, {});
|
||||
break;
|
||||
default:
|
||||
console.error(`Unknown format in "topology_with_coordinates" node: "${format}"`);
|
||||
return undefined;
|
||||
}
|
||||
const result = UpdateTarget.apply(parsed, MVSTrajectoryWithCoordinates, {
|
||||
coordinatesRef: node.params.coordinates_ref,
|
||||
});
|
||||
return UpdateTarget.setMvsDependencies(result, [node.params.coordinates_ref]);
|
||||
},
|
||||
model(updateParent: UpdateTarget, node: MolstarSubtree<'model'>, context: MolstarLoadingContext): UpdateTarget {
|
||||
const annotations = collectAnnotationReferences(node, context);
|
||||
const model = UpdateTarget.apply(updateParent, ModelFromTrajectory, {
|
||||
|
||||
@@ -28,12 +28,22 @@ export const ParseFormatMvsToMolstar = {
|
||||
lammpstrj: { format: 'lammpstrj', is_binary: false },
|
||||
// coordinates
|
||||
xtc: { format: 'xtc', is_binary: true },
|
||||
nctraj: { format: 'nctraj', is_binary: true },
|
||||
dcd: { format: 'dcd', is_binary: true },
|
||||
trr: { format: 'trr', is_binary: true },
|
||||
// topology
|
||||
psf: { format: 'psf', is_binary: false },
|
||||
prmtop: { format: 'prmtop', is_binary: false },
|
||||
top: { format: 'top', is_binary: false },
|
||||
// maps
|
||||
map: { format: 'map', is_binary: true },
|
||||
dx: { format: 'dx', is_binary: false },
|
||||
dxbin: { format: 'dxbin', is_binary: true },
|
||||
} satisfies { [p in ParseFormatT]: { format: MolstarParseFormatT, is_binary: boolean } };
|
||||
|
||||
|
||||
const TopologyFormats = new Set<ParseFormatT>(['psf', 'prmtop', 'top']);
|
||||
|
||||
/** Conversion rules for conversion from `MVSTree` (with all parameter values) to `MolstarTree` */
|
||||
const mvsToMolstarConversionRules: ConversionRules<FullMVSTree, MolstarTree> = {
|
||||
'download': node => ({ subtree: [] }),
|
||||
@@ -68,7 +78,18 @@ const mvsToMolstarConversionRules: ConversionRules<FullMVSTree, MolstarTree> = {
|
||||
if (parent?.kind !== 'parse') throw new Error(`Parent of "structure" must be "parse", not "${parent?.kind}".`);
|
||||
const { format } = ParseFormatMvsToMolstar[parent.params.format];
|
||||
|
||||
if (node.params.coordinates_ref) {
|
||||
if (TopologyFormats.has(parent.params.format)) {
|
||||
if (!node.params.coordinates_ref) {
|
||||
throw new Error(`"structure" node with topology format "${parent.params.format}" must have "coordinates_ref" parameter.`);
|
||||
}
|
||||
return {
|
||||
subtree: [
|
||||
{ kind: 'topology_with_coordinates', params: { format, coordinates_ref: node.params.coordinates_ref } },
|
||||
{ kind: 'model', params: pickObjectKeys(node.params, ['model_index']) },
|
||||
{ kind: 'structure', params: omitObjectKeys(node.params, ['block_header', 'block_index', 'model_index', 'coordinates_ref']), custom: node.custom, ref: node.ref },
|
||||
] satisfies MolstarNode[]
|
||||
};
|
||||
} else if (node.params.coordinates_ref) {
|
||||
return {
|
||||
subtree: [
|
||||
{ kind: 'trajectory', params: { format, ...pickObjectKeys(node.params, ['block_header', 'block_index']) } },
|
||||
@@ -124,6 +145,13 @@ const StructureFormatExtensions: Record<ParseFormatT, (FileExtension | '*')[]> =
|
||||
lammpstrj: ['.lammpstrj'],
|
||||
// coordinates
|
||||
xtc: ['.xtc'],
|
||||
nctraj: ['.nc', '.nctraj'],
|
||||
dcd: ['.dcd'],
|
||||
trr: ['.trr'],
|
||||
// topology
|
||||
psf: ['.psf'],
|
||||
prmtop: ['.prmtop', '.parm7'],
|
||||
top: ['.top'],
|
||||
// volumes
|
||||
map: ['.map', '.ccp4', '.mrc', '.mrcs'],
|
||||
dx: ['.dx'],
|
||||
|
||||
@@ -55,10 +55,18 @@ export const MolstarTreeSchema = TreeSchema({
|
||||
coordinates_ref: RequiredField(str, 'Coordinates reference'),
|
||||
}),
|
||||
},
|
||||
topology_with_coordinates: {
|
||||
description: 'Auxiliary node corresponding to assigning a separate coordinates to a topology.',
|
||||
parent: ['parse'],
|
||||
params: SimpleParamsSchema({
|
||||
format: RequiredField(MolstarParseFormatT, 'File format'),
|
||||
coordinates_ref: RequiredField(str, 'Coordinates reference'),
|
||||
}),
|
||||
},
|
||||
/** Auxiliary node corresponding to Molstar's ModelFromTrajectory. */
|
||||
model: {
|
||||
description: "Auxiliary node corresponding to Molstar's ModelFromTrajectory.",
|
||||
parent: ['trajectory', 'trajectory_with_coordinates'],
|
||||
parent: ['trajectory', 'trajectory_with_coordinates', 'topology_with_coordinates'],
|
||||
params: SimpleParamsSchema(
|
||||
pickObjectKeys(FullMVSTreeSchema.nodes.structure.params.fields, ['model_index'] as const)
|
||||
),
|
||||
|
||||
@@ -25,6 +25,13 @@ export const ParseFormatT = literal(
|
||||
'lammpstrj', // + coordinates
|
||||
// coordinates
|
||||
'xtc',
|
||||
'nctraj',
|
||||
'dcd',
|
||||
'trr',
|
||||
// topology
|
||||
'psf',
|
||||
'prmtop',
|
||||
'top',
|
||||
// volumes
|
||||
'map',
|
||||
'dx',
|
||||
@@ -46,6 +53,13 @@ export const MolstarParseFormatT = literal(
|
||||
'lammpstrj',
|
||||
// coordinates
|
||||
'xtc',
|
||||
'nctraj',
|
||||
'dcd',
|
||||
'trr',
|
||||
// topology
|
||||
'psf',
|
||||
'prmtop',
|
||||
'top',
|
||||
// volumes
|
||||
'map',
|
||||
'dx',
|
||||
|
||||
Reference in New Issue
Block a user