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HETATM record type written out #2880

Merged
merged 19 commits into from
Aug 14, 2020
Merged

HETATM record type written out #2880

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e708aa7
added HETATM fmt and conditional
mieczyslaw Jul 30, 2020
884d613
fix no attribute case
mieczyslaw Jul 30, 2020
46115ce
address reviewer's comments
mieczyslaw Aug 2, 2020
9e646ec
changes as suggested by the reviewer
mieczyslaw Aug 5, 2020
0705ae8
additional comments addressed
mieczyslaw Aug 6, 2020
09278fc
use outfile fixture
mieczyslaw Aug 6, 2020
44f63c3
links sorted out
mieczyslaw Aug 6, 2020
96fbfbc
remove duplicated _CRYST1
mieczyslaw Aug 6, 2020
9c30e0f
merge current develop, solve merge conflicts in AUTHORS
mieczyslaw Aug 12, 2020
31e58bb
address reviewer comments
mieczyslaw Aug 12, 2020
908746f
match exception message
mieczyslaw Aug 12, 2020
d806658
line lenght fix
mieczyslaw Aug 12, 2020
88802f9
change PDB version to 3.3
mieczyslaw Aug 13, 2020
de923b2
resolve conflicts
mieczyslaw Aug 13, 2020
4b44ecb
Issue 2906
IAlibay Aug 14, 2020
eff5759
Merge branch 'develop' into feature/write_hetatm_record_type_issue_1753
IAlibay Aug 14, 2020
6890a31
reviewer's request
mieczyslaw Aug 14, 2020
d344006
reviewer's request
mieczyslaw Aug 14, 2020
e82974c
reviewer's request
mieczyslaw Aug 14, 2020
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23 changes: 21 additions & 2 deletions package/MDAnalysis/coordinates/PDB.py
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Original file line number Diff line number Diff line change
Expand Up @@ -528,6 +528,11 @@ class PDBWriter(base.WriterBase):
"{chainID:1s}{resSeq:4d}{iCode:1s}"
" {pos[0]:8.3f}{pos[1]:8.3f}{pos[2]:8.3f}{occupancy:6.2f}"
"{tempFactor:6.2f} {segID:<4s}{element:>2s}\n"),
'HETATM': (
"HETATM{serial:5d} {name:<4s}{altLoc:<1s}{resName:<4s}"
"{chainID:1s}{resSeq:4d}{iCode:1s}"
" {pos[0]:8.3f}{pos[1]:8.3f}{pos[2]:8.3f}{occupancy:6.2f}"
"{tempFactor:6.2f} {segID:<4s}{element:>2s}\n"),
'REMARK': "REMARK {0}\n",
'COMPND': "COMPND {0}\n",
'HEADER': "HEADER {0}\n",
Expand Down Expand Up @@ -1029,6 +1034,7 @@ def get_attr(attrname, default):
tempfactors = get_attr('tempfactors', 0.0)
atomnames = get_attr('names', 'X')

no_record_type = False
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for i, atom in enumerate(atoms):
vals = {}
vals['serial'] = util.ltruncate_int(i + 1, 5) # check for overflow here?
Expand All @@ -1044,8 +1050,21 @@ def get_attr(attrname, default):
vals['segID'] = segids[i][:4]
vals['element'] = guess_atom_element(atomnames[i].strip())[:2]

# .. _ATOM: http://www.wwpdb.org/documentation/file-format-content/format32/sect9.html#ATOM
self.pdbfile.write(self.fmt['ATOM'].format(**vals))
if hasattr(atom, 'record_type'):
if atom.record_type == 'HETATM':
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# .. _HETATM: http://www.wwpdb.org/documentation/file-format-content/format32/sect9.html#HETATM
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self.pdbfile.write(self.fmt['HETATM'].format(**vals))
else:
# .. _ATOM: http://www.wwpdb.org/documentation/file-format-content/format32/sect9.html#ATOM
self.pdbfile.write(self.fmt['ATOM'].format(**vals))
else:
# .. _ATOM: http://www.wwpdb.org/documentation/file-format-content/format32/sect9.html#ATOM
no_record_type = True
self.pdbfile.write(self.fmt['ATOM'].format(**vals))

if no_record_type:
warnings.warn("PDBWriter: No record type found for an atom - HETATM may be written out as ATOM")

if multiframe:
self.ENDMDL()
self.frames_written += 1
Expand Down