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Bug fixes with a test
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@pafonine
pafonine committed Sep 17, 2024
1 parent 5e4a68b commit 083816b
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Showing 3 changed files with 149 additions and 2 deletions.
6 changes: 4 additions & 2 deletions iotbx/pdb/hierarchy.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2562,10 +2562,12 @@ def exchangeable_hd_selections(self):
for chain in model.chains():
for residue_group in chain.residue_groups():
for i_gr1, atom_group_1 in enumerate(residue_group.atom_groups()):
elements_group1 = atom_group_1.atoms().extract_element()
elements_group1 = [
e.strip() for e in atom_group_1.atoms().extract_element()]
non_H_atoms_group1 = list(set(elements_group1) - set(['H','D']))
for i_gr2, atom_group_2 in enumerate(residue_group.atom_groups()):
elements_group2 = atom_group_2.atoms().extract_element()
elements_group2 = [
e.strip() for e in atom_group_2.atoms().extract_element()]
non_H_atoms_group2 = list(set(elements_group2) - set(['H','D']))
if non_H_atoms_group1 and non_H_atoms_group2: continue
if(atom_group_1.altloc != atom_group_2.altloc and i_gr2 > i_gr1):
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8 changes: 8 additions & 0 deletions mmtbx/model/model.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1092,6 +1092,14 @@ def get_site_symmetry_table(self):
def altlocs_present(self):
return self.get_hierarchy().altlocs_present()

def altlocs_present_only_hd(self):
noh_selection = self.selection("not (element H or element D)")
hierarchy_no_hd = self.get_hierarchy().select(noh_selection)
altlocs = hierarchy_no_hd.altlocs_present()
hd = self.get_hierarchy().exchangeable_hd_selections()
if not altlocs and len(hd)>0: return True
return False

def aa_residues_with_bound_sidechains(self):
"""
Return array of i_seqs of residue side chain atoms that are involved into
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137 changes: 137 additions & 0 deletions mmtbx/regression/model/tst_model_2.py
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Original file line number Diff line number Diff line change
Expand Up @@ -491,8 +491,145 @@ def exercise_model_filename():
m = mmtbx.model.manager(model_input=inp)
assert m.get_source_filename() is None

def exercise_altlocs_present():
pdb_str1="""
CRYST1 13.135 16.057 12.855 90.00 90.00 90.00 P 1
ATOM 1 N HIS A 3 8.135 7.414 7.855 1.00 22.05 N
ATOM 2 CA HIS A 3 7.032 6.873 7.032 1.00 18.37 C
ATOM 3 C HIS A 3 7.233 5.393 6.739 1.00 13.79 C
ATOM 4 O HIS A 3 8.085 5.000 5.991 1.00 12.07 O
ATOM 5 CB HIS A 3 6.816 7.572 5.708 1.00 21.10 C
ATOM 6 CG HIS A 3 6.273 8.956 5.759 1.00 24.64 C
ATOM 7 ND1 HIS A 3 5.237 9.382 6.577 1.00 21.60 N
ATOM 8 CD2 HIS A 3 6.625 10.039 5.000 1.00 33.23 C
ATOM 9 CE1 HIS A 3 5.000 10.626 6.356 1.00 23.45 C
ATOM 10 NE2 HIS A 3 5.834 11.057 5.402 1.00 24.68 N
ATOM 11 OXT HIS A 3 6.509 4.555 7.276 1.00 13.79 O
ATOM 12 H HIS A 3 7.879 8.235 8.404 1.00 22.05 H
ATOM 13 H2 HIS A 3 8.446 6.714 8.498 1.00 22.05 H
ATOM 14 H3 HIS A 3 8.894 7.681 7.262 1.00 22.05 H
ATOM 15 HA HIS A 3 6.135 7.043 7.628 1.00 18.37 H
ATOM 16 HB2 HIS A 3 7.776 7.626 5.195 1.00 21.10 H
ATOM 17 HB3 HIS A 3 6.114 6.977 5.123 1.00 21.10 H
ATOM 18 HD2 HIS A 3 7.384 10.073 4.233 1.00 33.23 H
ATOM 19 HE1 HIS A 3 4.253 11.224 6.857 1.00 23.45 H
ATOM 20 HD1AHIS A 3 4.740 8.798 7.250 0.50 21.60 H
ATOM 21 HE2AHIS A 3 5.867 12.008 5.035 0.50 24.68 H
ATOM 22 DD1BHIS A 3 4.740 8.798 7.250 0.50 21.60 D
ATOM 23 DE2BHIS A 3 5.867 12.008 5.035 0.50 24.68 D
TER
END
"""
pdb_str2="""
CRYST1 13.135 16.057 12.855 90.00 90.00 90.00 P 1
ATOM 1 N HIS A 3 8.135 7.414 7.855 1.00 22.05 N
ATOM 2 CA AHIS A 3 7.032 6.873 7.032 1.00 18.37 C
ATOM 2 CA BHIS A 3 7.032 6.873 7.032 1.00 18.37 C
ATOM 3 C HIS A 3 7.233 5.393 6.739 1.00 13.79 C
ATOM 4 O HIS A 3 8.085 5.000 5.991 1.00 12.07 O
ATOM 5 CB HIS A 3 6.816 7.572 5.708 1.00 21.10 C
ATOM 6 CG HIS A 3 6.273 8.956 5.759 1.00 24.64 C
ATOM 7 ND1 HIS A 3 5.237 9.382 6.577 1.00 21.60 N
ATOM 8 CD2 HIS A 3 6.625 10.039 5.000 1.00 33.23 C
ATOM 9 CE1 HIS A 3 5.000 10.626 6.356 1.00 23.45 C
ATOM 10 NE2 HIS A 3 5.834 11.057 5.402 1.00 24.68 N
ATOM 11 OXT HIS A 3 6.509 4.555 7.276 1.00 13.79 O
ATOM 12 H HIS A 3 7.879 8.235 8.404 1.00 22.05 H
ATOM 13 H2 HIS A 3 8.446 6.714 8.498 1.00 22.05 H
ATOM 14 H3 HIS A 3 8.894 7.681 7.262 1.00 22.05 H
ATOM 15 HA HIS A 3 6.135 7.043 7.628 1.00 18.37 H
ATOM 16 HB2 HIS A 3 7.776 7.626 5.195 1.00 21.10 H
ATOM 17 HB3 HIS A 3 6.114 6.977 5.123 1.00 21.10 H
ATOM 18 HD2 HIS A 3 7.384 10.073 4.233 1.00 33.23 H
ATOM 19 HE1 HIS A 3 4.253 11.224 6.857 1.00 23.45 H
ATOM 20 HD1AHIS A 3 4.740 8.798 7.250 0.50 21.60 H
ATOM 21 HE2AHIS A 3 5.867 12.008 5.035 0.50 24.68 H
ATOM 22 DD1BHIS A 3 4.740 8.798 7.250 0.50 21.60 D
ATOM 23 DE2BHIS A 3 5.867 12.008 5.035 0.50 24.68 D
TER
END
"""
pdb_str3="""
CRYST1 13.135 16.057 12.855 90.00 90.00 90.00 P 1
ATOM 1 N HIS A 3 8.135 7.414 7.855 1.00 22.05 N
ATOM 2 CA AHIS A 3 7.032 6.873 7.032 1.00 18.37 C
ATOM 2 CA BHIS A 3 7.032 6.873 7.032 1.00 18.37 C
ATOM 3 C HIS A 3 7.233 5.393 6.739 1.00 13.79 C
ATOM 4 O HIS A 3 8.085 5.000 5.991 1.00 12.07 O
ATOM 5 CB HIS A 3 6.816 7.572 5.708 1.00 21.10 C
ATOM 6 CG HIS A 3 6.273 8.956 5.759 1.00 24.64 C
ATOM 7 ND1 HIS A 3 5.237 9.382 6.577 1.00 21.60 N
ATOM 8 CD2 HIS A 3 6.625 10.039 5.000 1.00 33.23 C
ATOM 9 CE1 HIS A 3 5.000 10.626 6.356 1.00 23.45 C
ATOM 10 NE2 HIS A 3 5.834 11.057 5.402 1.00 24.68 N
ATOM 11 OXT HIS A 3 6.509 4.555 7.276 1.00 13.79 O
ATOM 12 H HIS A 3 7.879 8.235 8.404 1.00 22.05 H
ATOM 13 H2 HIS A 3 8.446 6.714 8.498 1.00 22.05 H
ATOM 14 H3 HIS A 3 8.894 7.681 7.262 1.00 22.05 H
ATOM 15 HA HIS A 3 6.135 7.043 7.628 1.00 18.37 H
ATOM 16 HB2 HIS A 3 7.776 7.626 5.195 1.00 21.10 H
ATOM 17 HB3 HIS A 3 6.114 6.977 5.123 1.00 21.10 H
ATOM 18 HD2 HIS A 3 7.384 10.073 4.233 1.00 33.23 H
ATOM 19 HE1 HIS A 3 4.253 11.224 6.857 1.00 23.45 H
TER
END
"""
pdb_str4="""
CRYST1 13.135 16.057 12.855 90.00 90.00 90.00 P 1
ATOM 1 N HIS A 3 8.135 7.414 7.855 1.00 22.05 N
ATOM 2 CA HIS A 3 7.032 6.873 7.032 1.00 18.37 C
ATOM 3 C HIS A 3 7.233 5.393 6.739 1.00 13.79 C
ATOM 4 O HIS A 3 8.085 5.000 5.991 1.00 12.07 O
ATOM 5 CB HIS A 3 6.816 7.572 5.708 1.00 21.10 C
ATOM 6 CG HIS A 3 6.273 8.956 5.759 1.00 24.64 C
ATOM 7 ND1 HIS A 3 5.237 9.382 6.577 1.00 21.60 N
ATOM 8 CD2 HIS A 3 6.625 10.039 5.000 1.00 33.23 C
ATOM 9 CE1 HIS A 3 5.000 10.626 6.356 1.00 23.45 C
ATOM 10 NE2 HIS A 3 5.834 11.057 5.402 1.00 24.68 N
ATOM 11 OXT HIS A 3 6.509 4.555 7.276 1.00 13.79 O
ATOM 12 H HIS A 3 7.879 8.235 8.404 1.00 22.05 H
ATOM 13 H2 HIS A 3 8.446 6.714 8.498 1.00 22.05 H
ATOM 14 H3 HIS A 3 8.894 7.681 7.262 1.00 22.05 H
ATOM 15 HA HIS A 3 6.135 7.043 7.628 1.00 18.37 H
ATOM 16 HB2 HIS A 3 7.776 7.626 5.195 1.00 21.10 H
ATOM 17 HB3 HIS A 3 6.114 6.977 5.123 1.00 21.10 H
ATOM 18 HD2 HIS A 3 7.384 10.073 4.233 1.00 33.23 H
ATOM 19 HE1 HIS A 3 4.253 11.224 6.857 1.00 23.45 H
TER
END
"""
pdb_inp1 = iotbx.pdb.input(source_info=None, lines=pdb_str1)
m1 = mmtbx.model.manager(model_input = pdb_inp1)
#
pdb_inp2 = iotbx.pdb.input(source_info=None, lines=pdb_str2)
m2 = mmtbx.model.manager(model_input = pdb_inp2)
#
pdb_inp3 = iotbx.pdb.input(source_info=None, lines=pdb_str3)
m3 = mmtbx.model.manager(model_input = pdb_inp3)
#
pdb_inp4 = iotbx.pdb.input(source_info=None, lines=pdb_str4)
m4 = mmtbx.model.manager(model_input = pdb_inp4)
#
assert m1.altlocs_present()
assert m1.altlocs_present_only_hd()
#
assert m2.altlocs_present()
assert not m2.altlocs_present_only_hd()
#
assert m3.altlocs_present()
assert not m3.altlocs_present_only_hd()
#
assert not m4.altlocs_present()
assert not m4.altlocs_present_only_hd()


if (__name__ == "__main__"):
t0 = time.time()
exercise_altlocs_present()
exercise_macromolecule_plus_hetatms_by_chain_selections()
exercise_ss_creation_crash()
exercise_set_b_iso()
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