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Reduce2: place NH3 only at residue with resseq 1.
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@dcliebschner
dcliebschner committed Nov 10, 2021
1 parent 9f24907 commit 765881e
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Showing 3 changed files with 282 additions and 316 deletions.
19 changes: 12 additions & 7 deletions mmtbx/hydrogens/reduce_hydrogen.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@
from cctbx.maptbx.box import shift_and_box_model

ext = bp.import_ext("cctbx_geometry_restraints_ext")

get_class = iotbx.pdb.common_residue_names_get_class
# For development
print_time = False

Expand Down Expand Up @@ -110,11 +110,16 @@ def run(self):
for m in pdb_hierarchy.models():
for chain in m.chains():
rgs = chain.residue_groups()[0]
for ag in rgs.atom_groups():
if ag.get_atom("H"):
ag.remove_atom(ag.get_atom('H'))
rc = add_n_terminal_hydrogens_to_residue_group(rgs)
# rc is always empty list?
# by default, place NH3 only at residue with resseq 1
if (rgs.resseq_as_int() == 1):
for ag in rgs.atom_groups():
# what about d-amino acids
if (get_class(name=ag.resname) in
['common_amino_acid', 'modified_amino_acid']):
if ag.get_atom("H"):
ag.remove_atom(ag.get_atom('H'))
rc = add_n_terminal_hydrogens_to_residue_group(rgs)
# rc is always empty list?

pdb_hierarchy.sort_atoms_in_place()
pdb_hierarchy.atoms().reset_serial()
Expand Down Expand Up @@ -234,7 +239,7 @@ def add_missing_H_atoms_at_bogus_position(self):
pdb_hierarchy = self.model.get_hierarchy()
mon_lib_srv = self.model.get_mon_lib_srv()
#XXX This breaks for 1jxt, residue 2, TYR
get_class = iotbx.pdb.common_residue_names_get_class
#get_class = iotbx.pdb.common_residue_names_get_class
#no_H_placed_resnames = list()
for m in pdb_hierarchy.models():
for chain in m.chains():
Expand Down
196 changes: 89 additions & 107 deletions mmtbx/hydrogens/tst_add_hydrogen.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -203,15 +203,12 @@ def test_008():
ATOM 9 CE2 TYR A 139 7.064 5.676 8.095 1.00 10.00 C
ATOM 10 CZ TYR A 139 6.345 5.266 6.993 1.00 10.00 C
ATOM 11 OH TYR A 139 5.000 5.000 7.113 1.00 10.00 O
ATOM 12 H1 TYR A 139 9.830 7.211 4.654 1.00 10.00 H
ATOM 13 H2 TYR A 139 9.649 8.571 5.132 1.00 10.00 H
ATOM 14 H3 TYR A 139 10.871 8.201 4.437 1.00 10.00 H
ATOM 15 HA TYR A 139 10.487 8.115 6.973 1.00 10.00 H
ATOM 16 HB2 TYR A 139 10.961 5.881 7.464 1.00 10.00 H
ATOM 17 HB3 TYR A 139 10.893 5.529 5.916 1.00 10.00 H
ATOM 19 HD2 TYR A 139 8.896 6.220 8.714 1.00 10.00 H
ATOM 21 HE2 TYR A 139 6.643 5.772 8.919 1.00 10.00 H
ATOM 22 HH TYR A 139 4.752 5.127 7.905 1.00 10.00 H
ATOM 12 HA TYR A 139 10.487 8.115 6.973 1.00 10.00 H
ATOM 13 HB2 TYR A 139 10.961 5.881 7.464 1.00 10.00 H
ATOM 14 HB3 TYR A 139 10.893 5.529 5.916 1.00 10.00 H
ATOM 15 HD2 TYR A 139 8.896 6.220 8.714 1.00 10.00 H
ATOM 16 HE2 TYR A 139 6.643 5.772 8.919 1.00 10.00 H
ATOM 17 HH TYR A 139 4.752 5.127 7.905 1.00 10.00 H
TER
"""

Expand All @@ -224,21 +221,18 @@ def test_008():
ATOM 4 O CYS A 128 12.765 -31.329 -21.265 1.00 16.86 O
ATOM 5 CB CYS A 128 14.059 -28.357 -20.691 1.00 12.94 C
ATOM 6 SG CYS A 128 15.213 -27.350 -19.760 1.00 12.36 S
ATOM 7 H1 CYS A 128 15.324 -30.110 -19.842 1.00 11.73 H
ATOM 8 H2 CYS A 128 14.626 -30.352 -18.591 1.00 11.73 H
ATOM 9 H3 CYS A 128 14.381 -31.211 -19.738 1.00 11.73 H
ATOM 10 HA CYS A 128 13.044 -29.102 -19.148 1.00 11.51 H
ATOM 11 HB2 CYS A 128 14.526 -28.706 -21.466 1.00 12.94 H
ATOM 12 HB3 CYS A 128 13.327 -27.787 -20.974 1.00 12.94 H
ATOM 14 N CYS A 232 13.105 -25.822 -15.371 1.00 4.75 N
ATOM 15 CA CYS A 232 14.298 -26.646 -15.573 1.00 5.50 C
ATOM 16 C CYS A 232 15.596 -25.838 -15.551 1.00 5.70 C
ATOM 17 O CYS A 232 16.651 -26.346 -15.190 1.00 8.25 O
ATOM 18 CB CYS A 232 14.178 -27.497 -16.824 1.00 6.69 C
ATOM 19 SG CYS A 232 14.060 -26.477 -18.360 1.00 7.70 S
ATOM 21 HA CYS A 232 14.363 -27.258 -14.823 1.00 5.50 H
ATOM 22 HB2 CYS A 232 14.961 -28.065 -16.898 1.00 6.69 H
ATOM 23 HB3 CYS A 232 13.378 -28.042 -16.761 1.00 6.69 H
ATOM 7 HA CYS A 128 13.044 -29.102 -19.148 1.00 11.51 H
ATOM 8 HB2 CYS A 128 14.526 -28.706 -21.466 1.00 12.94 H
ATOM 9 HB3 CYS A 128 13.327 -27.787 -20.974 1.00 12.94 H
ATOM 10 N CYS A 232 13.105 -25.822 -15.371 1.00 4.75 N
ATOM 11 CA CYS A 232 14.298 -26.646 -15.573 1.00 5.50 C
ATOM 12 C CYS A 232 15.596 -25.838 -15.551 1.00 5.70 C
ATOM 14 O CYS A 232 16.651 -26.346 -15.190 1.00 8.25 O
ATOM 15 CB CYS A 232 14.178 -27.497 -16.824 1.00 6.69 C
ATOM 16 SG CYS A 232 14.060 -26.477 -18.360 1.00 7.70 S
ATOM 17 HA CYS A 232 14.363 -27.258 -14.823 1.00 5.50 H
ATOM 18 HB2 CYS A 232 14.961 -28.065 -16.898 1.00 6.69 H
ATOM 19 HB3 CYS A 232 13.378 -28.042 -16.761 1.00 6.69 H
TER
"""

Expand All @@ -251,13 +245,10 @@ def test_008():
ATOM 4 O CYS A 128 12.765 -31.329 -21.265 1.00 16.86 O
ATOM 5 CB CYS A 128 14.059 -28.357 -20.691 1.00 12.94 C
ATOM 6 SG CYS A 128 15.213 -27.350 -19.760 1.00 12.36 S
ATOM 7 H1 CYS A 128 15.324 -30.110 -19.842 1.00 11.73 H
ATOM 8 H2 CYS A 128 14.626 -30.352 -18.591 1.00 11.73 H
ATOM 9 H3 CYS A 128 14.381 -31.211 -19.738 1.00 11.73 H
ATOM 10 HA CYS A 128 13.044 -29.102 -19.148 1.00 11.51 H
ATOM 11 HB2 CYS A 128 14.526 -28.706 -21.466 1.00 12.94 H
ATOM 12 HB3 CYS A 128 13.327 -27.787 -20.974 1.00 12.94 H
ATOM 13 HG CYS A 128 16.134 -28.034 -19.410 1.00 12.36 H
ATOM 7 HA CYS A 128 13.044 -29.102 -19.148 1.00 11.51 H
ATOM 8 HB2 CYS A 128 14.526 -28.706 -21.466 1.00 12.94 H
ATOM 9 HB3 CYS A 128 13.327 -27.787 -20.974 1.00 12.94 H
ATOM 10 HG CYS A 128 16.134 -28.034 -19.410 1.00 12.36 H
TER
"""
Expand Down Expand Up @@ -295,12 +286,9 @@ def test_008():
ATOM 4 O CYS A 48 -40.407 -13.794 8.283 1.00104.56 O
ATOM 5 CB CYS A 48 -42.835 -15.275 6.303 1.00105.79 C
ATOM 6 SG CYS A 48 -43.707 -15.186 7.879 1.00101.00 S
ATOM 7 H1 CYS A 48 -41.103 -16.739 7.012 1.00 99.72 H
ATOM 8 H2 CYS A 48 -39.990 -16.294 6.189 1.00 99.72 H
ATOM 9 H3 CYS A 48 -40.108 -15.834 7.563 1.00 99.72 H
ATOM 10 HA CYS A 48 -41.063 -14.664 5.488 1.00106.82 H
ATOM 11 HB2 CYS A 48 -43.271 -14.661 5.692 1.00105.79 H
ATOM 12 HB3 CYS A 48 -42.916 -16.184 5.974 1.00105.79 H
ATOM 7 HA CYS A 48 -41.063 -14.664 5.488 1.00106.82 H
ATOM 8 HB2 CYS A 48 -43.271 -14.661 5.692 1.00105.79 H
ATOM 9 HB3 CYS A 48 -42.916 -16.184 5.974 1.00105.79 H
TER
HETATM 12 ZN ZN A 102 -44.322 -17.446 8.351 1.00 98.67 Zn
END
Expand All @@ -315,67 +303,64 @@ def test_008():
ATOM 4 O CYS A 12 -50.987 -13.597 -15.382 1.00106.09 O
ATOM 5 CB CYS A 12 -52.861 -12.775 -13.466 1.00103.91 C
ATOM 6 SG CYS A 12 -54.064 -13.357 -14.680 1.00106.39 S
ATOM 7 H1 CYS A 12 -50.975 -12.349 -12.107 1.00 95.50 H
ATOM 8 H2 CYS A 12 -50.772 -13.638 -11.469 1.00 95.50 H
ATOM 9 H3 CYS A 12 -49.974 -13.266 -12.625 1.00 95.50 H
ATOM 10 HA CYS A 12 -52.194 -14.542 -12.667 1.00103.68 H
ATOM 11 HB2 CYS A 12 -52.438 -11.981 -13.828 1.00103.91 H
ATOM 12 HB3 CYS A 12 -53.344 -12.553 -12.655 1.00103.91 H
ATOM 7 HA CYS A 12 -52.194 -14.542 -12.667 1.00103.68 H
ATOM 8 HB2 CYS A 12 -52.438 -11.981 -13.828 1.00103.91 H
ATOM 9 HB3 CYS A 12 -53.344 -12.553 -12.655 1.00103.91 H
TER
"""

pdb_str_007 = """
REMARK CYS forms a disulfide with symmetry mate --> don't place HG
REMARK from PDB 5c11
CRYST1 108.910 108.910 108.910 90.00 90.00 90.00 I 4 3 2
ATOM 1 N PRO A 11 -50.110 -12.340 -8.990 1.00 87.52 N
ATOM 2 CA PRO A 11 -49.518 -12.918 -10.200 1.00 88.41 C
ATOM 3 C PRO A 11 -50.549 -13.676 -11.025 1.00 97.43 C
ATOM 4 O PRO A 11 -51.129 -14.656 -10.556 1.00 93.89 O
ATOM 5 CB PRO A 11 -48.446 -13.865 -9.649 1.00 78.46 C
ATOM 6 CG PRO A 11 -48.110 -13.314 -8.317 1.00 80.77 C
ATOM 7 CD PRO A 11 -49.402 -12.783 -7.777 1.00 92.02 C
ATOM 8 H2 PRO A 11 -50.063 -11.383 -9.046 1.00 87.52 H
ATOM 9 H3 PRO A 11 -51.029 -12.612 -8.932 1.00 87.52 H
ATOM 10 HA PRO A 11 -49.092 -12.241 -10.748 1.00 88.41 H
ATOM 11 HB2 PRO A 11 -48.804 -14.764 -9.574 1.00 78.46 H
ATOM 12 HB3 PRO A 11 -47.671 -13.864 -10.232 1.00 78.46 H
ATOM 13 HG2 PRO A 11 -47.455 -12.604 -8.409 1.00 80.77 H
ATOM 14 HG3 PRO A 11 -47.760 -14.017 -7.748 1.00 80.77 H
ATOM 15 HD2 PRO A 11 -49.899 -13.480 -7.321 1.00 92.02 H
ATOM 16 HD3 PRO A 11 -49.246 -12.038 -7.175 1.00 92.02 H
ATOM 17 N CYS A 12 -50.777 -13.205 -12.246 1.00 95.50 N
ATOM 18 CA CYS A 12 -51.774 -13.797 -13.124 1.00103.68 C
ATOM 19 C CYS A 12 -51.135 -14.327 -14.399 1.00101.77 C
ATOM 20 O CYS A 12 -50.987 -13.597 -15.382 1.00106.09 O
ATOM 21 CB CYS A 12 -52.861 -12.775 -13.466 1.00103.91 C
ATOM 22 SG CYS A 12 -54.064 -13.357 -14.680 1.00106.39 S
ATOM 23 H CYS A 12 -50.361 -12.536 -12.590 1.00 95.50 H
ATOM 24 HA CYS A 12 -52.147 -14.558 -12.653 1.00103.68 H
ATOM 25 HB2 CYS A 12 -52.438 -11.981 -13.828 1.00103.91 H
ATOM 26 HB3 CYS A 12 -53.344 -12.553 -12.655 1.00103.91 H
ATOM 28 N LYS A 13 -50.756 -15.600 -14.375 1.00105.98 N
ATOM 29 CA LYS A 13 -50.135 -16.230 -15.528 1.00115.21 C
ATOM 30 C LYS A 13 -50.110 -17.740 -15.357 1.00105.26 C
ATOM 31 O LYS A 13 -50.331 -18.255 -14.264 1.00118.65 O
ATOM 32 CB LYS A 13 -48.714 -15.704 -15.737 1.00110.03 C
ATOM 33 CG LYS A 13 -47.784 -15.954 -14.563 1.00100.14 C
ATOM 34 CD LYS A 13 -46.379 -15.452 -14.853 1.00101.77 C
ATOM 35 CE LYS A 13 -45.456 -15.678 -13.663 1.00112.21 C
ATOM 36 NZ LYS A 13 -44.063 -15.229 -13.941 1.00110.68 N
ATOM 37 H LYS A 13 -50.849 -16.122 -13.698 1.00105.98 H
ATOM 38 HA LYS A 13 -50.648 -16.015 -16.323 1.00115.21 H
ATOM 39 HB2 LYS A 13 -48.755 -14.746 -15.882 1.00110.03 H
ATOM 40 HB3 LYS A 13 -48.332 -16.141 -16.514 1.00110.03 H
ATOM 41 HG2 LYS A 13 -48.120 -15.488 -13.782 1.00100.14 H
ATOM 42 HG3 LYS A 13 -47.738 -16.907 -14.386 1.00100.14 H
ATOM 43 HD2 LYS A 13 -46.409 -14.501 -15.041 1.00101.77 H
ATOM 44 HD3 LYS A 13 -46.017 -15.929 -15.616 1.00101.77 H
ATOM 45 HE2 LYS A 13 -45.789 -15.178 -12.902 1.00112.21 H
ATOM 46 HE3 LYS A 13 -45.432 -16.625 -13.453 1.00112.21 H
ATOM 47 HZ1 LYS A 13 -43.731 -15.679 -14.633 1.00110.68 H
ATOM 48 HZ2 LYS A 13 -43.549 -15.374 -13.229 1.00110.68 H
ATOM 49 HZ3 LYS A 13 -44.056 -14.360 -14.131 1.00110.68 H
ATOM 1 N PRO A 1 -50.110 -12.340 -8.990 1.00 87.52 N
ATOM 2 CA PRO A 1 -49.518 -12.918 -10.200 1.00 88.41 C
ATOM 3 C PRO A 1 -50.549 -13.676 -11.025 1.00 97.43 C
ATOM 4 O PRO A 1 -51.129 -14.656 -10.556 1.00 93.89 O
ATOM 5 CB PRO A 1 -48.446 -13.865 -9.649 1.00 78.46 C
ATOM 6 CG PRO A 1 -48.110 -13.314 -8.317 1.00 80.77 C
ATOM 7 CD PRO A 1 -49.402 -12.783 -7.777 1.00 92.02 C
ATOM 8 H2 PRO A 1 -50.063 -11.383 -9.046 1.00 87.52 H
ATOM 9 H3 PRO A 1 -51.029 -12.612 -8.932 1.00 87.52 H
ATOM 10 HA PRO A 1 -49.092 -12.241 -10.748 1.00 88.41 H
ATOM 11 HB2 PRO A 1 -48.804 -14.764 -9.574 1.00 78.46 H
ATOM 12 HB3 PRO A 1 -47.671 -13.864 -10.232 1.00 78.46 H
ATOM 13 HG2 PRO A 1 -47.455 -12.604 -8.409 1.00 80.77 H
ATOM 14 HG3 PRO A 1 -47.760 -14.017 -7.748 1.00 80.77 H
ATOM 15 HD2 PRO A 1 -49.899 -13.480 -7.321 1.00 92.02 H
ATOM 16 HD3 PRO A 1 -49.246 -12.038 -7.175 1.00 92.02 H
ATOM 17 N CYS A 2 -50.777 -13.205 -12.246 1.00 95.50 N
ATOM 18 CA CYS A 2 -51.774 -13.797 -13.124 1.00103.68 C
ATOM 19 C CYS A 2 -51.135 -14.327 -14.399 1.00101.77 C
ATOM 20 O CYS A 2 -50.987 -13.597 -15.382 1.00106.09 O
ATOM 21 CB CYS A 2 -52.861 -12.775 -13.466 1.00103.91 C
ATOM 22 SG CYS A 2 -54.064 -13.357 -14.680 1.00106.39 S
ATOM 23 H CYS A 2 -50.361 -12.536 -12.590 1.00 95.50 H
ATOM 24 HA CYS A 2 -52.147 -14.558 -12.653 1.00103.68 H
ATOM 25 HB2 CYS A 2 -52.438 -11.981 -13.828 1.00103.91 H
ATOM 26 HB3 CYS A 2 -53.344 -12.553 -12.655 1.00103.91 H
ATOM 28 N LYS A 3 -50.756 -15.600 -14.375 1.00105.98 N
ATOM 29 CA LYS A 3 -50.135 -16.230 -15.528 1.00115.21 C
ATOM 30 C LYS A 3 -50.110 -17.740 -15.357 1.00105.26 C
ATOM 31 O LYS A 3 -50.331 -18.255 -14.264 1.00118.65 O
ATOM 32 CB LYS A 3 -48.714 -15.704 -15.737 1.00110.03 C
ATOM 33 CG LYS A 3 -47.784 -15.954 -14.563 1.00100.14 C
ATOM 34 CD LYS A 3 -46.379 -15.452 -14.853 1.00101.77 C
ATOM 35 CE LYS A 3 -45.456 -15.678 -13.663 1.00112.21 C
ATOM 36 NZ LYS A 3 -44.063 -15.229 -13.941 1.00110.68 N
ATOM 37 H LYS A 3 -50.849 -16.122 -13.698 1.00105.98 H
ATOM 38 HA LYS A 3 -50.648 -16.015 -16.323 1.00115.21 H
ATOM 39 HB2 LYS A 3 -48.755 -14.746 -15.882 1.00110.03 H
ATOM 40 HB3 LYS A 3 -48.332 -16.141 -16.514 1.00110.03 H
ATOM 41 HG2 LYS A 3 -48.120 -15.488 -13.782 1.00100.14 H
ATOM 42 HG3 LYS A 3 -47.738 -16.907 -14.386 1.00100.14 H
ATOM 43 HD2 LYS A 3 -46.409 -14.501 -15.041 1.00101.77 H
ATOM 44 HD3 LYS A 3 -46.017 -15.929 -15.616 1.00101.77 H
ATOM 45 HE2 LYS A 3 -45.789 -15.178 -12.902 1.00112.21 H
ATOM 46 HE3 LYS A 3 -45.432 -16.625 -13.453 1.00112.21 H
ATOM 47 HZ1 LYS A 3 -43.731 -15.679 -14.633 1.00110.68 H
ATOM 48 HZ2 LYS A 3 -43.549 -15.374 -13.229 1.00110.68 H
ATOM 49 HZ3 LYS A 3 -44.056 -14.360 -14.131 1.00110.68 H
TER
"""

Expand All @@ -389,22 +374,19 @@ def test_008():
ATOM 4 O CYS A 221 -25.131 8.426 3.672 1.00 9.51 O
ATOM 5 CB CYS A 221 -24.546 8.272 7.047 1.00 9.34 C
ATOM 6 SG CYS A 221 -22.908 8.520 6.302 1.00 10.59 S
ATOM 7 H1 CYS A 221 -24.721 6.192 6.055 1.00 8.50 H
ATOM 8 H2 CYS A 221 -26.143 6.060 5.785 1.00 8.50 H
ATOM 9 H3 CYS A 221 -25.240 6.491 4.731 1.00 8.50 H
ATOM 10 HA CYS A 221 -26.500 8.030 6.365 1.00 8.62 H
ATOM 11 HB2 CYS A 221 -24.805 9.094 7.491 1.00 9.34 H
ATOM 12 HB3 CYS A 221 -24.479 7.552 7.694 1.00 9.34 H
ATOM 14 N CYS A 222 -25.649 10.119 5.071 1.00 8.82 N
ATOM 15 CA CYS A 222 -25.005 11.177 4.321 1.00 8.99 C
ATOM 16 C CYS A 222 -25.532 11.323 2.911 1.00 9.12 C
ATOM 17 O CYS A 222 -24.803 11.847 2.036 1.00 11.09 O
ATOM 18 CB CYS A 222 -23.463 10.894 4.313 1.00 11.23 C
ATOM 19 SG CYS A 222 -22.792 10.598 5.958 1.00 11.91 S
ATOM 20 H CYS A 222 -26.153 10.408 5.705 1.00 8.82 H
ATOM 21 HA CYS A 222 -25.188 12.029 4.746 1.00 8.99 H
ATOM 22 HB2 CYS A 222 -23.004 11.661 3.936 1.00 11.23 H
ATOM 23 HB3 CYS A 222 -23.291 10.107 3.773 1.00 11.23 H
ATOM 7 HA CYS A 221 -26.500 8.030 6.365 1.00 8.62 H
ATOM 8 HB2 CYS A 221 -24.805 9.094 7.491 1.00 9.34 H
ATOM 9 HB3 CYS A 221 -24.479 7.552 7.694 1.00 9.34 H
ATOM 10 N CYS A 222 -25.649 10.119 5.071 1.00 8.82 N
ATOM 11 CA CYS A 222 -25.005 11.177 4.321 1.00 8.99 C
ATOM 12 C CYS A 222 -25.532 11.323 2.911 1.00 9.12 C
ATOM 14 O CYS A 222 -24.803 11.847 2.036 1.00 11.09 O
ATOM 15 CB CYS A 222 -23.463 10.894 4.313 1.00 11.23 C
ATOM 16 SG CYS A 222 -22.792 10.598 5.958 1.00 11.91 S
ATOM 17 H CYS A 222 -26.153 10.408 5.705 1.00 8.82 H
ATOM 18 HA CYS A 222 -25.188 12.029 4.746 1.00 8.99 H
ATOM 19 HB2 CYS A 222 -23.004 11.661 3.936 1.00 11.23 H
ATOM 20 HB3 CYS A 222 -23.291 10.107 3.773 1.00 11.23 H
TER
"""

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