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Unverified Commit d03646b5 authored by peastman's avatar peastman Committed by GitHub
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Merge pull request #2068 from peastman/insertion 

Preserve PDB insertion codes
parents 9a08d9be 276e8f4d
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Showing with 35 additions and 23 deletions
wrappers/python/simtk/openmm/app/modeller.py
View file @ d03646b5
......@@ -109,7 +109,7 @@ class Modeller(object):
for chain in self.topology.chains():
newChain = newTopology.addChain(chain.id)
for residue in chain.residues():
newResidue = newTopology.addResidue(residue.name, newChain, residue.id)
newResidue = newTopology.addResidue(residue.name, newChain, residue.id, residue.insertionCode)
for atom in residue.atoms():
newAtom = newTopology.addAtom(atom.name, atom.element, newResidue, atom.id)
newAtoms[atom] = newAtom
......@@ -123,7 +123,7 @@ class Modeller(object):
for chain in addTopology.chains():
newChain = newTopology.addChain(chain.id)
for residue in chain.residues():
newResidue = newTopology.addResidue(residue.name, newChain, residue.id)
newResidue = newTopology.addResidue(residue.name, newChain, residue.id, residue.insertionCode)
for atom in residue.atoms():
newAtom = newTopology.addAtom(atom.name, atom.element, newResidue, atom.id)
newAtoms[atom] = newAtom
......@@ -168,7 +168,7 @@ class Modeller(object):
newChain = newTopology.addChain(chain.id)
needNewChain = False;
if needNewResidue:
newResidue = newTopology.addResidue(residue.name, newChain, residue.id)
newResidue = newTopology.addResidue(residue.name, newChain, residue.id, residue.insertionCode)
needNewResidue = False;
newAtom = newTopology.addAtom(atom.name, atom.element, newResidue, atom.id)
newAtoms[atom] = newAtom
......@@ -210,7 +210,7 @@ class Modeller(object):
for chain in self.topology.chains():
newChain = newTopology.addChain(chain.id)
for residue in chain.residues():
newResidue = newTopology.addResidue(residue.name, newChain, residue.id)
newResidue = newTopology.addResidue(residue.name, newChain, residue.id, residue.insertionCode)
if residue.name == "HOH":
# Copy the oxygen and hydrogens
oatom = [atom for atom in residue.atoms() if atom.element == elem.oxygen]
......@@ -395,7 +395,7 @@ class Modeller(object):
for chain in self.topology.chains():
newChain = newTopology.addChain(chain.id)
for residue in chain.residues():
newResidue = newTopology.addResidue(residue.name, newChain, residue.id)
newResidue = newTopology.addResidue(residue.name, newChain, residue.id, residue.insertionCode)
for atom in residue.atoms():
newAtom = newTopology.addAtom(atom.name, atom.element, newResidue, atom.id)
newAtoms[atom] = newAtom
......@@ -691,7 +691,7 @@ class Modeller(object):
for chain in self.topology.chains():
newChain = newTopology.addChain(chain.id)
for residue in chain.residues():
newResidue = newTopology.addResidue(residue.name, newChain, residue.id)
newResidue = newTopology.addResidue(residue.name, newChain, residue.id, residue.insertionCode)
isNTerminal = (residue == chain._residues[0])
isCTerminal = (residue == chain._residues[-1])
if residue.name in Modeller._residueHydrogens:
......@@ -977,7 +977,7 @@ class Modeller(object):
for chain in self.topology.chains():
newChain = newTopology.addChain(chain.id)
for residue in chain.residues():
newResidue = newTopology.addResidue(residue.name, newChain, residue.id)
newResidue = newTopology.addResidue(residue.name, newChain, residue.id, residue.insertionCode)
# Look for a matching template.
......@@ -999,7 +999,7 @@ class Modeller(object):
# extra points.
template = None
residueNoEP = Residue(residue.name, residue.index, residue.chain, residue.id)
residueNoEP = Residue(residue.name, residue.index, residue.chain, residue.id, residue.insertionCode)
residueNoEP._atoms = [atom for atom in residue.atoms() if atom.element is not None]
if signature in forcefield._templateSignatures:
for t in forcefield._templateSignatures[signature]:
......@@ -1310,7 +1310,7 @@ class Modeller(object):
# Remove the same number of residues from each leaf.
skipFromLeaf[lipidLeaf[residue]] -= 1
else:
newResidue = membraneTopology.addResidue(residue.name, lipidChain, residue.id)
newResidue = membraneTopology.addResidue(residue.name, lipidChain, residue.id, residue.insertionCode)
for atom in residue.atoms():
newAtom = membraneTopology.addAtom(atom.name, atom.element, newResidue, atom.id)
newAtoms[atom] = newAtom
......@@ -1322,7 +1322,7 @@ class Modeller(object):
solventChain = membraneTopology.addChain()
for (residue, pos) in addedWater:
newResidue = membraneTopology.addResidue(residue.name, solventChain, residue.id)
newResidue = membraneTopology.addResidue(residue.name, solventChain, residue.id, residue.insertionCode)
for atom in residue.atoms():
newAtom = membraneTopology.addAtom(atom.name, atom.element, newResidue, atom.id)
newAtoms[atom] = newAtom
......
wrappers/python/simtk/openmm/app/pdbfile.py
View file @ d03646b5
......@@ -6,7 +6,7 @@ Simbios, the NIH National Center for Physics-Based Simulation of
Biological Structures at Stanford, funded under the NIH Roadmap for
Medical Research, grant U54 GM072970. See https://simtk.org.
Portions copyright (c) 2012-2016 Stanford University and the Authors.
Portions copyright (c) 2012-2018 Stanford University and the Authors.
Authors: Peter Eastman
Contributors:
......@@ -106,7 +106,7 @@ class PDBFile(object):
resName = residue.get_name()
if resName in PDBFile._residueNameReplacements:
resName = PDBFile._residueNameReplacements[resName]
r = top.addResidue(resName, c, str(residue.number))
r = top.addResidue(resName, c, str(residue.number), residue.insertion_code)
if resName in PDBFile._atomNameReplacements:
atomReplacements = PDBFile._atomNameReplacements[resName]
else:
......@@ -352,8 +352,10 @@ class PDBFile(object):
resName = res.name
if keepIds and len(res.id) < 5:
resId = res.id
resIC = res.insertionCode
else:
resId = "%4d" % ((resIndex+1)%10000)
resIC = " "
if res.name in nonHeterogens:
recordName = "ATOM "
else:
......@@ -370,10 +372,11 @@ class PDBFile(object):
else:
atomName = atom.name
coords = positions[posIndex]
line = "%s%5d %-4s %3s %s%4s %s%s%s 1.00 0.00 %2s " % (
recordName, atomIndex%100000, atomName, resName, chainName, resId, _format_83(coords[0]),
line = "%s%5d %-4s %3s %s%4s%1s %s%s%s 1.00 0.00 %2s " % (
recordName, atomIndex%100000, atomName, resName, chainName, resId, resIC, _format_83(coords[0]),
_format_83(coords[1]), _format_83(coords[2]), symbol)
assert len(line) == 80, 'Fixed width overflow detected'
if len(line) != 80:
raise ValueError('Fixed width overflow detected')
print(line, file=file)
posIndex += 1
atomIndex += 1
......
wrappers/python/simtk/openmm/app/pdbxfile.py
View file @ d03646b5
......@@ -6,7 +6,7 @@ Simbios, the NIH National Center for Physics-Based Simulation of
Biological Structures at Stanford, funded under the NIH Roadmap for
Medical Research, grant U54 GM072970. See https://simtk.org.
Portions copyright (c) 2015 Stanford University and the Authors.
Portions copyright (c) 2015-2018 Stanford University and the Authors.
Authors: Peter Eastman
Contributors: Jason Swails
......@@ -84,6 +84,7 @@ class PDBxFile(object):
atomIdCol = atomData.getAttributeIndex('id')
resNameCol = atomData.getAttributeIndex('auth_comp_id')
resNumCol = atomData.getAttributeIndex('auth_seq_id')
resInsertionCol = atomData.getAttributeIndex('pdbx_PDB_ins_code')
chainIdCol = atomData.getAttributeIndex('auth_asym_id')
elementCol = atomData.getAttributeIndex('type_symbol')
altIdCol = atomData.getAttributeIndex('label_alt_id')
......@@ -117,7 +118,9 @@ class PDBxFile(object):
lastResId = None
if lastResId != row[resNumCol] or lastChainId != row[chainIdCol] or (lastResId == '.' and row[atomNameCol] in atomsInResidue):
# The start of a new residue.
res = top.addResidue(row[resNameCol], chain, None if resNumCol == -1 else row[resNumCol])
resId = (None if resNumCol == -1 else row[resNumCol])
resIC = ('' if resInsertionCol == -1 else row[resInsertionCol])
res = top.addResidue(row[resNameCol], chain, resId, resIC)
lastResId = row[resNumCol]
atomsInResidue.clear()
element = None
......@@ -382,16 +385,18 @@ class PDBxFile(object):
for (resIndex, res) in enumerate(residues):
if keepIds:
resId = res.id
resIC = (res.insertionCode if len(res.insertionCode) > 0 else '.')
else:
resId = resIndex + 1
resIC = '.'
for atom in res.atoms():
coords = positions[posIndex]
if atom.element is not None:
symbol = atom.element.symbol
else:
symbol = '?'
line = "ATOM %5d %-3s %-4s . %-4s %s ? %5s . %10.4f %10.4f %10.4f 0.0 0.0 ? ? ? ? ? . %5s %4s %s %4s %5d"
print(line % (atomIndex, symbol, atom.name, res.name, chainName, resId, coords[0], coords[1], coords[2],
line = "ATOM %5d %-3s %-4s . %-4s %s ? %5s %s %10.4f %10.4f %10.4f 0.0 0.0 ? ? ? ? ? . %5s %4s %s %4s %5d"
print(line % (atomIndex, symbol, atom.name, res.name, chainName, resId, resIC, coords[0], coords[1], coords[2],
resId, res.name, chainName, atom.name, modelIndex), file=file)
posIndex += 1
atomIndex += 1
wrappers/python/simtk/openmm/app/topology.py
View file @ d03646b5
......@@ -6,7 +6,7 @@ Simbios, the NIH National Center for Physics-Based Simulation of
Biological Structures at Stanford, funded under the NIH Roadmap for
Medical Research, grant U54 GM072970. See https://simtk.org.
Portions copyright (c) 2012-2016 Stanford University and the Authors.
Portions copyright (c) 2012-2018 Stanford University and the Authors.
Authors: Peter Eastman
Contributors:
......@@ -137,7 +137,7 @@ class Topology(object):
self._chains.append(chain)
return chain
def addResidue(self, name, chain, id=None):
def addResidue(self, name, chain, id=None, insertionCode=''):
"""Create a new Residue and add it to the Topology.
Parameters
......@@ -149,6 +149,8 @@ class Topology(object):
id : string=None
An optional identifier for the residue. If this is omitted, an id
is generated based on the residue index.
insertionCode: string=''
An optional insertion code for the residue.
Returns
-------
......@@ -159,7 +161,7 @@ class Topology(object):
raise ValueError('All residues within a chain must be contiguous')
if id is None:
id = str(self._numResidues+1)
residue = Residue(name, self._numResidues, chain, id)
residue = Residue(name, self._numResidues, chain, id, insertionCode)
self._numResidues += 1
chain._residues.append(residue)
return residue
......@@ -395,7 +397,7 @@ class Chain(object):
class Residue(object):
"""A Residue object represents a residue within a Topology."""
def __init__(self, name, index, chain, id):
def __init__(self, name, index, chain, id, insertionCode):
"""Construct a new Residue. You should call addResidue() on the Topology instead of calling this directly."""
## The name of the Residue
self.name = name
......@@ -405,6 +407,8 @@ class Residue(object):
self.chain = chain
## A user defined identifier for this Residue
self.id = id
## A user defined insertion code for this Residue
self.insertionCode = insertionCode
self._atoms = []
def atoms(self):
......
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