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write PDB conect records for S-S bridges and HETATM #1240

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merged 3 commits into from
May 30, 2022
Merged

write PDB conect records for S-S bridges and HETATM #1240

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06d6afc
write PDB conect records for S-S bridges and HETATM
Valdes-Tresanco-MS Mar 24, 2022
24f72e8
Merge branch 'v3.4' into pdb_conect_records
swails Mar 24, 2022
9257c4e
Added conect test
Valdes-Tresanco-MS Apr 11, 2022
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34 changes: 32 additions & 2 deletions parmed/formats/pdb.py
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Original file line number Diff line number Diff line change
Expand Up @@ -781,7 +781,7 @@ def _postprocess_metadata(self):
@staticmethod
def write(struct, dest, renumber=True, coordinates=None, altlocs='all',
write_anisou=False, charmm=False, use_hetatoms=True,
standard_resnames=False, increase_tercount=True, write_links=False):
standard_resnames=False, increase_tercount=True, write_links=False, conect=True):
""" Write a PDB file from a Structure instance

Parameters
Expand Down Expand Up @@ -825,7 +825,7 @@ def write(struct, dest, renumber=True, coordinates=None, altlocs='all',
atom that does not contain a SEGID identifier.
use_hetatoms: bool, optional, default True
If True, certain atoms will have the HETATM tag instead of ATOM
as per the PDB-standard.
as per the PDB-standard.
standard_resnames : bool, optional, default False
If True, common aliases for various amino and nucleic acid residues
will be converted into the PDB-standard values.
Expand All @@ -836,6 +836,9 @@ def write(struct, dest, renumber=True, coordinates=None, altlocs='all',
If True, any LINK records stored in the Structure will be written to
the LINK records near the top of the PDB file. If this is True, then
renumber *must* be False or a ValueError will be thrown
conect: bool, default True
Write CONECT records for S-S bridges and HETATM


Notes
-----
Expand Down Expand Up @@ -947,6 +950,10 @@ def print_atoms(atom, coords):
link.length,
)
dest.write(linkrec % rec)

conect_record = {}
atom_number_map = {} # store atoms number according if was renumbered or not

for model, coord in enumerate(coords):
if coords.shape[0] > 1:
dest.write('MODEL %5d\n' % (model+1))
Expand All @@ -968,6 +975,7 @@ def print_atoms(atom, coords):
else:
anum = _number_truncated_to_n_digits(pa.number, 5)
rnum = _number_truncated_to_n_digits(res.number, 4)
atom_number_map[atom.idx] = anum
last_number = anum
# Do any necessary name munging to respect the PDB spec
aname = _format_atom_name_for_pdb(pa)
Expand All @@ -976,6 +984,17 @@ def print_atoms(atom, coords):
rec = hetatomrec
else:
rec = atomrec

# get the connectivity only for the first model since they all must have the same records
if not model:
if atom.name == 'SG':
for bondedatm in atom.bond_partners:
if bondedatm.name == 'SG':
conect_record[atom.idx] = [bondedatm.idx]
break
if hetatom and atom.bond_partners and atom.residue.name not in ['WAT', 'SOL', 'HOH']:
conect_record[atom.idx] = [atm.idx for atm in atom.bond_partners]

dest.write(rec % (anum, aname, pa.altloc, resname,
res.chain[:1], rnum, res.insertion_code[:1],
x, y, z, pa.occupancy, pa.bfactor, segid,
Expand Down Expand Up @@ -1022,6 +1041,17 @@ def print_atoms(atom, coords):
if coords.shape[0] > 1:
dest.write('ENDMDL\n')

if conect and conect_record:
for atidx, bonded_atoms in conect_record.items():
if len(bonded_atoms) > 5:
dest.write('CONECT' + f"{atom_number_map[atidx]:>5d}" +
''.join([f"{atom_number_map[idx]:>5d}" for idx in bonded_atoms[:5]]) + '\n')
dest.write('CONECT' + f"{atom_number_map[atidx]:>5d}" +
''.join([f"{atom_number_map[idx]:>5d}" for idx in bonded_atoms[5:]]) + '\n')
else:
dest.write('CONECT' + f"{atom_number_map[atidx]:>5d}" +
''.join([f"{atom_number_map[idx]:>5d}" for idx in bonded_atoms]) + '\n')

dest.write("%-80s\n" % "END")
if own_handle:
dest.close()
Expand Down