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adhoc fix for 6uwi for mmCIF #1792

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merged 7 commits into from
Nov 15, 2023
Merged

adhoc fix for 6uwi for mmCIF #1792

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624b889
better fix
jamesmkrieger Nov 8, 2023
bc4aa5b
clean up
jamesmkrieger Nov 8, 2023
0bd7c95
fix for multi-model cif
jamesmkrieger Nov 8, 2023
5b1fd81
Merge branch 'master' of github.com:prody/ProDy into 6uwi
jamesmkrieger Nov 15, 2023
51ad2d9
fix parse pfam pdbs no getResnums for selection None
jamesmkrieger Nov 15, 2023
e6b0956
remove num results check for parsePfamPDBs
jamesmkrieger Nov 15, 2023
d2cfdfd
merge update
jamesmkrieger Nov 15, 2023
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6 changes: 4 additions & 2 deletions prody/database/pfam.py
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Original file line number Diff line number Diff line change
Expand Up @@ -406,8 +406,10 @@ def parsePfamPDBs(query, data=[], **kwargs):
continue

right_dbref = header[data_dict['chain']].dbrefs[right_part]
chainStart = ag.select('chain {0}'.format(data_dict['chain'])
).getResnums()[0]
chain = ag.select('chain {0}'.format(data_dict['chain']))
if chain is None:
continue
chainStart = chain.getResnums()[0]
missing = chainStart - right_dbref.first[0]
partStart = ag.getResindices()[np.where(ag.getResnums() ==
right_dbref.first[0] + missing)][0]
Expand Down
53 changes: 28 additions & 25 deletions prody/proteins/ciffile.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,8 +19,6 @@
from .cifheader import getCIFHeaderDict
from .header import buildBiomolecules, assignSecstr, isHelix, isSheet

from string import ascii_uppercase

__all__ = ['parseMMCIFStream', 'parseMMCIF', 'parseCIF']


Expand Down Expand Up @@ -311,7 +309,6 @@ def _parseMMCIFLines(atomgroup, lines, model, chain, subset,
doneAtomBlock = False
start = 0
stop = 0
warnedAltloc = False
while not doneAtomBlock:
line = lines[i]
if line[:11] == '_atom_site.':
Expand Down Expand Up @@ -443,8 +440,6 @@ def _parseMMCIFLines(atomgroup, lines, model, chain, subset,
continue

alt = line.split()[fields['label_alt_id']]
if alt not in which_altlocs and which_altlocs != 'all':
continue

if alt == '.':
alt = ' '
Expand Down Expand Up @@ -492,28 +487,36 @@ def _parseMMCIFLines(atomgroup, lines, model, chain, subset,
else:
modelSize = acount

mask = np.full(modelSize, True, dtype=bool)
if which_altlocs != 'all':
#mask out any unwanted alternative locations
mask = (altlocs == '') | (altlocs == which_altlocs)

if np.all(mask == False):
mask = (altlocs == '') | (altlocs == altlocs[0])

if addcoords:
atomgroup.addCoordset(coordinates[:modelSize])
atomgroup.addCoordset(coordinates[mask][:modelSize])
else:
atomgroup._setCoords(coordinates[:modelSize])

atomgroup.setNames(atomnames[:modelSize])
atomgroup.setResnames(resnames[:modelSize])
atomgroup.setResnums(resnums[:modelSize])
atomgroup.setSegnames(segnames[:modelSize])
atomgroup.setChids(chainids[:modelSize])
atomgroup.setFlags('hetatm', hetero[:modelSize])
atomgroup.setFlags('pdbter', termini[:modelSize])
atomgroup.setFlags('selpdbter', termini[:modelSize])
atomgroup.setAltlocs(altlocs[:modelSize])
atomgroup.setIcodes(icodes[:modelSize])
atomgroup.setSerials(serials[:modelSize])

atomgroup.setElements(elements[:modelSize])
atomgroup._setCoords(coordinates[mask][:modelSize])

atomgroup.setNames(atomnames[mask][:modelSize])
atomgroup.setResnames(resnames[mask][:modelSize])
atomgroup.setResnums(resnums[mask][:modelSize])
atomgroup.setSegnames(segnames[mask][:modelSize])
atomgroup.setChids(chainids[mask][:modelSize])
atomgroup.setFlags('hetatm', hetero[mask][:modelSize])
atomgroup.setFlags('pdbter', termini[mask][:modelSize])
atomgroup.setFlags('selpdbter', termini[mask][:modelSize])
atomgroup.setAltlocs(altlocs[mask][:modelSize])
atomgroup.setIcodes(icodes[mask][:modelSize])
atomgroup.setSerials(serials[mask][:modelSize])

atomgroup.setElements(elements[mask][:modelSize])
from prody.utilities.misctools import getMasses
atomgroup.setMasses(getMasses(elements[:modelSize]))
atomgroup.setBetas(bfactors[:modelSize])
atomgroup.setOccupancies(occupancies[:modelSize])
atomgroup.setMasses(getMasses(elements[mask][:modelSize]))
atomgroup.setBetas(bfactors[mask][:modelSize])
atomgroup.setOccupancies(occupancies[mask][:modelSize])

anisou = None
siguij = None
Expand Down Expand Up @@ -558,6 +561,6 @@ def _parseMMCIFLines(atomgroup, lines, model, chain, subset,

if model is None:
for n in range(1, nModels):
atomgroup.addCoordset(coordinates[n*modelSize:(n+1)*modelSize])
atomgroup.addCoordset(coordinates[mask][n*modelSize:(n+1)*modelSize])

return atomgroup
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