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[prodigy] scoring module #1069

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2c9c317
prodigy module
VGPReys Oct 1, 2024
837d4f4
add examples
VGPReys Oct 1, 2024
f72c208
using prodigy as library (v3)
VGPReys Oct 2, 2024
52024ea
update examples with ligands
VGPReys Oct 2, 2024
66691fd
lint and types fixes
VGPReys Oct 2, 2024
40dfb50
remove intermediate versions
VGPReys Oct 2, 2024
dfdd289
Merge branch 'main' into prodigy-module
VGPReys Oct 3, 2024
1935b51
prodigy as core scoring module
VGPReys Oct 3, 2024
5779c30
removed runs
VGPReys Oct 3, 2024
b2eb9a8
double modules
VGPReys Oct 4, 2024
cd3616a
refinings
VGPReys Oct 4, 2024
1bd9d9b
fix distcutoff in lib
VGPReys Oct 4, 2024
de3eb0f
Merge branch 'main' into prodigy-module
VGPReys Oct 8, 2024
37c1fe6
class name fix
VGPReys Oct 8, 2024
de59a8b
add tests
VGPReys Oct 8, 2024
ad28309
fixes in impots
VGPReys Oct 8, 2024
bce908b
gaz constant
VGPReys Oct 8, 2024
3a1e6cc
Merge branch 'main' into prodigy-module
VGPReys Oct 11, 2024
f2f6533
Update pyproject.toml
VGPReys Oct 11, 2024
7f1b781
Merge branch 'main' into prodigy-module
VGPReys Oct 14, 2024
7107d14
Merge branch 'main' into prodigy-module
rvhonorato Oct 14, 2024
b434cb0
Merge branch 'main' into prodigy-module
VGPReys Nov 6, 2024
917fda8
Merge branch 'main' into prodigy-module
VGPReys Dec 10, 2024
50fe5d3
Merge branch 'main' into prodigy-module
VGPReys Jan 13, 2025
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2,844 changes: 2,844 additions & 0 deletions examples/scoring/data/homotrimer.pdb
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137 changes: 137 additions & 0 deletions examples/scoring/data/ligand-prodrg.param
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Original file line number Diff line number Diff line change
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! Put in this file your ligand parameters if needed
!
!
! This file was generated by PRODRG version 070118.0614
! PRODRG written/copyrighted by Daan van Aalten
! and Alexander Schuettelkopf
!
! Questions/comments to dava@davapc1.bioch.dundee.ac.uk
!
! When using this software in a publication, cite:
! A. W. Schuettelkopf and D. M. F. van Aalten (2004).
! PRODRG - a tool for high-throughput crystallography
! of protein-ligand complexes.
! Acta Crystallogr. D60, 1355--1363.
!
!
! *** NOTE *** IF YOU USE MORE THAN ONE PRODRG-GENERATED TOPOLOGY IN CNS,
! PLEASE CAREFULLY READ THE FAQ AS THIS MAY CAUSE PROBLEMS
!
!
set echo=off message=on end

evaluate ($pd_x = 1.0)

eval ($pd_v=$pd_x* 16000.0) BOND CA82 CA81 $pd_v 1.530
eval ($pd_v=$pd_x* 12000.0) BOND CA81 CA8 $pd_v 1.530
eval ($pd_v=$pd_x* 12000.0) BOND CA8 CA9 $pd_v 1.530
eval ($pd_v=$pd_x* 12000.0) BOND CA8 OA7 $pd_v 1.435
eval ($pd_v=$pd_x* 16000.0) BOND CA9 CA91 $pd_v 1.530
eval ($pd_v=$pd_x* 12000.0) BOND OA7 CA6 $pd_v 1.435
eval ($pd_v=$pd_x* 20000.0) BOND CA6 CA7 $pd_v 1.390
eval ($pd_v=$pd_x* 16000.0) BOND CA6 CA5 $pd_v 1.530
eval ($pd_v=$pd_x* 20000.0) BOND CA7 CA2 $pd_v 1.390
eval ($pd_v=$pd_x* 16000.0) BOND CA2 CA1 $pd_v 1.530
eval ($pd_v=$pd_x* 16000.0) BOND CA2 CA3 $pd_v 1.530
eval ($pd_v=$pd_x* 20000.0) BOND CA1 OA1B $pd_v 1.250
eval ($pd_v=$pd_x* 20000.0) BOND CA1 OA1A $pd_v 1.250
eval ($pd_v=$pd_x* 16000.0) BOND CA3 CA4 $pd_v 1.530
eval ($pd_v=$pd_x* 18000.0) BOND CA4 NA4 $pd_v 1.470
eval ($pd_v=$pd_x* 16000.0) BOND CA4 CA5 $pd_v 1.530
eval ($pd_v=$pd_x* 17900.0) BOND NA4 HAAB $pd_v 1.000
eval ($pd_v=$pd_x* 17900.0) BOND NA4 HAAC $pd_v 1.000
eval ($pd_v=$pd_x* 17900.0) BOND NA4 HAAA $pd_v 1.000
eval ($pd_v=$pd_x* 18000.0) BOND CA5 NA5 $pd_v 1.470
eval ($pd_v=$pd_x* 17900.0) BOND NA5 HAAD $pd_v 1.000
eval ($pd_v=$pd_x* 20000.0) BOND NA5 CA10 $pd_v 1.330
eval ($pd_v=$pd_x* 16000.0) BOND CA10 CA11 $pd_v 1.530
eval ($pd_v=$pd_x* 24000.0) BOND CA10 OA10 $pd_v 1.230

eval ($pd_v=$pd_x* 880.0) ANGLE CA82 CA81 CA8 $pd_v 111.000
eval ($pd_v=$pd_x* 480.0) ANGLE CA81 CA8 CA9 $pd_v 109.500
eval ($pd_v=$pd_x* 544.0) ANGLE CA81 CA8 OA7 $pd_v 109.500
eval ($pd_v=$pd_x* 544.0) ANGLE CA9 CA8 OA7 $pd_v 109.500
eval ($pd_v=$pd_x* 880.0) ANGLE CA8 CA9 CA91 $pd_v 111.000
eval ($pd_v=$pd_x* 640.0) ANGLE CA8 OA7 CA6 $pd_v 109.500
eval ($pd_v=$pd_x* 544.0) ANGLE OA7 CA6 CA7 $pd_v 109.500
eval ($pd_v=$pd_x* 544.0) ANGLE OA7 CA6 CA5 $pd_v 109.500
eval ($pd_v=$pd_x* 544.0) ANGLE CA7 CA6 CA5 $pd_v 109.500
eval ($pd_v=$pd_x* 800.0) ANGLE CA6 CA7 CA2 $pd_v 120.000
eval ($pd_v=$pd_x* 800.0) ANGLE CA7 CA2 CA1 $pd_v 120.000
eval ($pd_v=$pd_x* 800.0) ANGLE CA7 CA2 CA3 $pd_v 120.000
eval ($pd_v=$pd_x* 800.0) ANGLE CA1 CA2 CA3 $pd_v 120.000
eval ($pd_v=$pd_x* 800.0) ANGLE CA2 CA1 OA1B $pd_v 120.000
eval ($pd_v=$pd_x* 800.0) ANGLE CA2 CA1 OA1A $pd_v 120.000
eval ($pd_v=$pd_x* 960.0) ANGLE OA1B CA1 OA1A $pd_v 126.000
eval ($pd_v=$pd_x* 880.0) ANGLE CA2 CA3 CA4 $pd_v 111.000
eval ($pd_v=$pd_x* 880.0) ANGLE CA3 CA4 NA4 $pd_v 109.500
eval ($pd_v=$pd_x* 880.0) ANGLE CA3 CA4 CA5 $pd_v 111.000
eval ($pd_v=$pd_x* 880.0) ANGLE NA4 CA4 CA5 $pd_v 109.500
eval ($pd_v=$pd_x* 720.0) ANGLE CA4 NA4 HAAB $pd_v 109.500
eval ($pd_v=$pd_x* 720.0) ANGLE CA4 NA4 HAAC $pd_v 109.500
eval ($pd_v=$pd_x* 720.0) ANGLE CA4 NA4 HAAA $pd_v 109.500
eval ($pd_v=$pd_x* 640.0) ANGLE HAAB NA4 HAAC $pd_v 109.500
eval ($pd_v=$pd_x* 640.0) ANGLE HAAB NA4 HAAA $pd_v 109.500
eval ($pd_v=$pd_x* 640.0) ANGLE HAAC NA4 HAAA $pd_v 109.500
eval ($pd_v=$pd_x* 880.0) ANGLE CA6 CA5 CA4 $pd_v 111.000
eval ($pd_v=$pd_x* 880.0) ANGLE CA6 CA5 NA5 $pd_v 109.500
eval ($pd_v=$pd_x* 880.0) ANGLE CA4 CA5 NA5 $pd_v 109.500
eval ($pd_v=$pd_x* 720.0) ANGLE CA5 NA5 HAAD $pd_v 115.000
eval ($pd_v=$pd_x* 960.0) ANGLE CA5 NA5 CA10 $pd_v 122.000
eval ($pd_v=$pd_x* 560.0) ANGLE HAAD NA5 CA10 $pd_v 123.000
eval ($pd_v=$pd_x* 960.0) ANGLE NA5 CA10 CA11 $pd_v 115.000
eval ($pd_v=$pd_x* 960.0) ANGLE NA5 CA10 OA10 $pd_v 124.000
eval ($pd_v=$pd_x* 960.0) ANGLE CA11 CA10 OA10 $pd_v 121.000

eval ($pd_v=$pd_x* 800.0) IMPR CA2 CA7 CA3 CA1 $pd_v 0 0.000
eval ($pd_v=$pd_x* 800.0) IMPR CA1 CA2 OA1A OA1B $pd_v 0 0.000
eval ($pd_v=$pd_x* 800.0) IMPR NA5 CA5 HAAD CA10 $pd_v 0 0.000
eval ($pd_v=$pd_x* 800.0) IMPR CA10 NA5 CA11 OA10 $pd_v 0 0.000
eval ($pd_v=$pd_x* 400.0) IMPR CA8 CA81 CA9 OA7 $pd_v 0 35.264
eval ($pd_v=$pd_x* 400.0) IMPR CA6 OA7 CA7 CA5 $pd_v 0 35.264
eval ($pd_v=$pd_x* 400.0) IMPR CA4 CA3 NA4 CA5 $pd_v 0 35.264
eval ($pd_v=$pd_x* 400.0) IMPR NA4 CA4 HAAC HAAB $pd_v 0 35.264
eval ($pd_v=$pd_x* 400.0) IMPR CA5 CA6 NA5 CA4 $pd_v 0 35.264

eval ($pd_v=$pd_x* 19.6) DIHE OA7 CA8 CA81 CA82 $pd_v 3 0.000
eval ($pd_v=$pd_x* 19.6) DIHE CA81 CA8 CA9 CA91 $pd_v 3 0.000
eval ($pd_v=$pd_x* 8.1) DIHE CA81 CA8 OA7 CA6 $pd_v 3 0.000
eval ($pd_v=$pd_x* 8.1) DIHE CA5 CA6 OA7 CA8 $pd_v 3 0.000
eval ($pd_v=$pd_x* 1000.0) DIHE OA7 CA6 CA7 CA2 $pd_v 2 180.000
eval ($pd_v=$pd_x* 19.6) DIHE OA7 CA6 CA5 NA5 $pd_v 3 0.000
eval ($pd_v=$pd_x* 1000.0) DIHE CA3 CA2 CA7 CA6 $pd_v 2 180.000
eval ($pd_v=$pd_x* 19.6) DIHE CA7 CA2 CA1 OA1A $pd_v 2 180.000
eval ($pd_v=$pd_x* 0.1) DIHE CA7 CA2 CA3 CA4 $pd_v 6 0.000
eval ($pd_v=$pd_x* 19.6) DIHE CA2 CA3 CA4 CA5 $pd_v 3 0.000
eval ($pd_v=$pd_x* 8.1) DIHE CA3 CA4 NA4 HAAA $pd_v 3 0.000
eval ($pd_v=$pd_x* 19.6) DIHE NA5 CA5 CA4 CA3 $pd_v 3 0.000
eval ($pd_v=$pd_x* 0.1) DIHE CA6 CA5 NA5 CA10 $pd_v 6 180.000
eval ($pd_v=$pd_x* 640.0) DIHE OA10 CA10 NA5 CA5 $pd_v 2 180.000


NONBONDED CA82 0.10000 3.29633 0.10000 3.02906
NONBONDED CA81 0.10000 3.29633 0.10000 3.02906
NONBONDED CA8 0.10000 3.29633 0.10000 3.02906
NONBONDED CA9 0.10000 3.29633 0.10000 3.02906
NONBONDED CA91 0.10000 3.29633 0.10000 3.02906
NONBONDED OA7 0.10000 2.58361 0.10000 2.31634
NONBONDED CA6 0.10000 3.29633 0.10000 3.02906
NONBONDED CA7 0.10000 3.29633 0.10000 3.02906
NONBONDED CA2 0.10000 3.29633 0.10000 3.02906
NONBONDED CA1 0.10000 3.29633 0.10000 3.02906
NONBONDED OA1B 0.10000 2.58361 0.10000 2.31634
NONBONDED OA1A 0.10000 2.58361 0.10000 2.31634
NONBONDED CA3 0.10000 3.29633 0.10000 3.02906
NONBONDED CA4 0.10000 3.29633 0.10000 3.02906
NONBONDED NA4 0.10000 2.67270 0.10000 2.40543
NONBONDED HAAB 0.10000 1.42544 0.10000 1.15817
NONBONDED HAAC 0.10000 1.42544 0.10000 1.15817
NONBONDED HAAA 0.10000 1.42544 0.10000 1.15817
NONBONDED CA5 0.10000 3.29633 0.10000 3.02906
NONBONDED NA5 0.10000 2.67270 0.10000 2.40543
NONBONDED HAAD 0.10000 1.42544 0.10000 1.15817
NONBONDED CA10 0.10000 3.29633 0.10000 3.02906
NONBONDED CA11 0.10000 3.29633 0.10000 3.02906
NONBONDED OA10 0.10000 2.58361 0.10000 2.31634

set echo=on message=on end
161 changes: 161 additions & 0 deletions examples/scoring/data/ligand-prodrg.top
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Original file line number Diff line number Diff line change
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! Put in this file your ligand topology if needed
!
!
! This file was generated by PRODRG version 070118.0614
! PRODRG written/copyrighted by Daan van Aalten
! and Alexander Schuettelkopf
!
! Questions/comments to dava@davapc1.bioch.dundee.ac.uk
!
! When using this software in a publication, cite:
! A. W. Schuettelkopf and D. M. F. van Aalten (2004).
! PRODRG - a tool for high-throughput crystallography
! of protein-ligand complexes.
! Acta Crystallogr. D60, 1355--1363.
!
!
! *** NOTE *** IF YOU USE MORE THAN ONE PRODRG-GENERATED TOPOLOGY IN CNS,
! PLEASE CAREFULLY READ THE FAQ AS THIS MAY CAUSE PROBLEMS
!
!
set echo=false end
AUTOGENERATE ANGLES=FALSE END
MASS CA82 15.0350 ! equivalent to CH3
MASS CA81 14.0270 ! equivalent to CH2
MASS CA8 13.0190 ! equivalent to CS1
MASS CA9 14.0270 ! equivalent to CH2
MASS CA91 15.0350 ! equivalent to CH3
MASS OA7 15.9994 ! equivalent to OS
MASS CA6 13.0190 ! equivalent to CS1
MASS CA7 13.0190 ! equivalent to CR61
MASS CA2 12.0110 ! equivalent to CB
MASS CA1 12.0110 ! equivalent to C
MASS OA1B 15.9994 ! equivalent to OM
MASS OA1A 15.9994 ! equivalent to OM
MASS CA3 14.0270 ! equivalent to CH2
MASS CA4 13.0190 ! equivalent to CH1
MASS NA4 14.0067 ! equivalent to NL
MASS HAAB 1.0080 ! equivalent to H
MASS HAAC 1.0080 ! equivalent to H
MASS HAAA 1.0080 ! equivalent to H
MASS CA5 13.0190 ! equivalent to CH1
MASS NA5 14.0067 ! equivalent to N
MASS HAAD 1.0080 ! equivalent to H
MASS CA10 12.0110 ! equivalent to C
MASS CA11 15.0350 ! equivalent to CH3
MASS OA10 15.9994 ! equivalent to O

Residue G39
GROUP
ATOM C82 TYPE= CA82 CHARGE= 0.024 END
ATOM C81 TYPE= CA81 CHARGE= 0.062 END
ATOM C8 TYPE= CA8 CHARGE= 0.211 END
ATOM C9 TYPE= CA9 CHARGE= 0.061 END
ATOM C91 TYPE= CA91 CHARGE= 0.024 END
ATOM O7 TYPE= OA7 CHARGE=-0.182 END
ATOM C6 TYPE= CA6 CHARGE= 0.211 END
ATOM C7 TYPE= CA7 CHARGE=-0.008 END
ATOM C2 TYPE= CA2 CHARGE=-0.022 END
ATOM C1 TYPE= CA1 CHARGE= 0.361 END
ATOM O1B TYPE= OA1B CHARGE=-0.756 END
ATOM O1A TYPE= OA1A CHARGE=-0.756 END
ATOM C3 TYPE= CA3 CHARGE= 0.062 END
ATOM C4 TYPE= CA4 CHARGE= 0.124 END
ATOM N4 TYPE= NA4 CHARGE= 0.646 END
ATOM HAB TYPE= HAAB CHARGE= 0.000 END
ATOM HAC TYPE= HAAC CHARGE= 0.001 END
ATOM HAA TYPE= HAAA CHARGE= 0.000 END
ATOM C5 TYPE= CA5 CHARGE= 0.124 END
ATOM N5 TYPE= NA5 CHARGE= 0.132 END
ATOM H07 TYPE= HAAD CHARGE= 0.000 END
ATOM C10 TYPE= CA10 CHARGE= 0.361 END
ATOM C11 TYPE= CA11 CHARGE= 0.024 END
ATOM O10 TYPE= OA10 CHARGE=-0.704 END

BOND C82 C81
BOND C81 C8
BOND C8 C9
BOND C8 O7
BOND C9 C91
BOND O7 C6
BOND C6 C7
BOND C6 C5
BOND C7 C2
BOND C2 C1
BOND C2 C3
BOND C1 O1B
BOND C1 O1A
BOND C3 C4
BOND C4 N4
BOND C4 C5
BOND N4 HAB
BOND N4 HAC
BOND N4 HAA
BOND C5 N5
BOND N5 H07
BOND N5 C10
BOND C10 C11
BOND C10 O10

ANGLE C82 C81 C8
ANGLE C81 C8 C9
ANGLE C81 C8 O7
ANGLE C9 C8 O7
ANGLE C8 C9 C91
ANGLE C8 O7 C6
ANGLE O7 C6 C7
ANGLE O7 C6 C5
ANGLE C7 C6 C5
ANGLE C6 C7 C2
ANGLE C7 C2 C1
ANGLE C7 C2 C3
ANGLE C1 C2 C3
ANGLE C2 C1 O1B
ANGLE C2 C1 O1A
ANGLE O1B C1 O1A
ANGLE C2 C3 C4
ANGLE C3 C4 N4
ANGLE C3 C4 C5
ANGLE N4 C4 C5
ANGLE C4 N4 HAB
ANGLE C4 N4 HAC
ANGLE C4 N4 HAA
ANGLE HAB N4 HAC
ANGLE HAB N4 HAA
ANGLE HAC N4 HAA
ANGLE C6 C5 C4
ANGLE C6 C5 N5
ANGLE C4 C5 N5
ANGLE C5 N5 H07
ANGLE C5 N5 C10
ANGLE H07 N5 C10
ANGLE N5 C10 C11
ANGLE N5 C10 O10
ANGLE C11 C10 O10

IMPROPER C2 C7 C3 C1
IMPROPER C1 C2 O1A O1B
IMPROPER N5 C5 H07 C10
IMPROPER C10 N5 C11 O10
IMPROPER C8 C81 C9 O7
IMPROPER C6 O7 C7 C5
IMPROPER C4 C3 N4 C5
IMPROPER N4 C4 HAC HAB
IMPROPER C5 C6 N5 C4

DIHEDRAL O7 C8 C81 C82
DIHEDRAL C81 C8 C9 C91
DIHEDRAL C81 C8 O7 C6
DIHEDRAL C5 C6 O7 C8
DIHEDRAL O7 C6 C7 C2
DIHEDRAL O7 C6 C5 N5
DIHEDRAL C3 C2 C7 C6
DIHEDRAL C7 C2 C1 O1A
DIHEDRAL C7 C2 C3 C4
DIHEDRAL C2 C3 C4 C5
DIHEDRAL C3 C4 N4 HAA
DIHEDRAL N5 C5 C4 C3
DIHEDRAL C6 C5 N5 C10
DIHEDRAL O10 C10 N5 C5
END
set echo=true end
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