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pdbfixer
Commit e41a190b by peastman
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Eliminated most dependence on PdbStructure

parent ffa808a3
Showing with 31 additions and 40 deletions
pdbfixer/pdbfixer.py
......@@ -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) 2013-2014 Stanford University and the Authors.
Portions copyright (c) 2013-2015 Stanford University and the Authors.
Authors: Peter Eastman
Contributors:
......@@ -221,7 +221,6 @@ class PDBFixer(object):
self.pdb = app.PDBFile(structure)
self.topology = self.pdb.topology
self.positions = self.pdb.positions
self.structureChains = list(self.structure.iter_chains())
# Load the templates.
......@@ -462,7 +461,6 @@ class PDBFixer(object):
modeller.delete(allChains[i] for i in chainIndices)
self.topology = modeller.topology
self.positions = modeller.positions
self.structureChains = [self.structureChains[i] for i in range(len(self.structureChains)) if i not in chainIndices]
return
......@@ -481,17 +479,17 @@ class PDBFixer(object):
>>> missing_residues = fixer.missingResidues
"""
chains = [c for c in self.structureChains if any(atom.record_name == 'ATOM' for atom in c.iter_atoms())]
chains = [c for c in self.topology.chains() if len(list(c.residues())) > 0]
chainWithGaps = {}
# Find the sequence of each chain, with gaps for missing residues.
for chain in chains:
minResidue = min(r.number for r in chain.iter_residues())
maxResidue = max(r.number for r in chain.iter_residues())
minResidue = min(int(r.id) for r in chain.residues())
maxResidue = max(int(r.id) for r in chain.residues())
residues = [None]*(maxResidue-minResidue+1)
for r in chain.iter_residues():
residues[r.number-minResidue] = r.get_name()
for r in chain.residues():
residues[int(r.id)-minResidue] = r.name
chainWithGaps[chain] = residues
# Try to find the chain that matches each sequence.
......@@ -500,7 +498,7 @@ class PDBFixer(object):
chainOffset = {}
for sequence in self.structure.sequences:
for chain in chains:
if chain.chain_id != sequence.chain_id:
if chain.id != sequence.chain_id:
continue
if chain in chainSequence:
continue
......@@ -515,15 +513,15 @@ class PDBFixer(object):
# Now build the list of residues to add.
self.missingResidues = {}
for structChain, topChain in zip(self.structureChains, self.topology.chains()):
if structChain in chainSequence:
offset = chainOffset[structChain]
sequence = chainSequence[structChain].residues
gappedSequence = chainWithGaps[structChain]
for chain in self.topology.chains():
if chain in chainSequence:
offset = chainOffset[chain]
sequence = chainSequence[chain].residues
gappedSequence = chainWithGaps[chain]
index = 0
for i in range(len(sequence)):
if i < offset or i >= len(gappedSequence)+offset or gappedSequence[i-offset] is None:
key = (topChain.index, index)
key = (chain.index, index)
if key not in self.missingResidues:
self.missingResidues[key] = []
residueName = sequence[i]
......@@ -556,16 +554,16 @@ class PDBFixer(object):
# Now add ones based on MODRES records.
modres = dict(((m.chain_id, m.number, m.residue_name), m.standard_name) for m in self.structure.modified_residues)
for structChain, topChain in zip(self.structureChains, self.topology.chains()):
for structResidue, topResidue in zip(structChain.iter_residues(), topChain.residues()):
key = (structChain.chain_id, structResidue.number, structResidue.name)
modres = dict(((m.chain_id, str(m.number), m.residue_name), m.standard_name) for m in self.structure.modified_residues)
for chain in self.topology.chains():
for residue in chain.residues():
key = (chain.id, residue.id, residue.name)
if key in modres:
replacement = modres[key]
if replacement == 'DU':
replacement = 'DT'
if replacement in self.templates:
nonstandard[topResidue] = replacement
nonstandard[residue] = replacement
self.nonstandardResidues = [(r, nonstandard[r]) for r in sorted(nonstandard, key=lambda r: r.index)]
def replaceNonstandardResidues(self):
......
pdbfixer/ui.py
import simtk.openmm.app as app
from simtk.openmm.app.internal.pdbstructure import PdbStructure
import simtk.unit as unit
from pdbfixer import PDBFixer, substitutions, proteinResidues, dnaResidues, rnaResidues
import uiserver
......@@ -74,7 +73,7 @@ def addResiduesPageCallback(parameters, handler):
for i, key in enumerate(keys):
if 'add'+str(i) not in parameters:
del fixer.missingResidues[key]
displayMissingAtomsPage()
displayConvertResiduesPage()
def convertResiduesPageCallback(parameters, handler):
for i in range(len(fixer.nonstandardResidues)):
......@@ -135,7 +134,7 @@ def displayDeleteChainsPage():
content = "DNA"
else:
content = ', '.join(set(residues))
table += ' <tr><td>%d</td><td>%d</td><td>%s</td><td><input type="checkbox" name="include%d" checked></td></tr>\n' % (chain.index+1, len(residues), content, i)
table += ' <tr><td>%s</td><td>%d</td><td>%s</td><td><input type="checkbox" name="include%d" checked></td></tr>\n' % (chain.id, len(residues), content, i)
uiserver.setContent(header+loadHtmlFile("removeChains.html") % (numChains, table))
def displayAddResiduesPage():
......@@ -145,14 +144,16 @@ def displayAddResiduesPage():
displayConvertResiduesPage()
return
table = ""
chains = list(fixer.topology.chains())
for i, key in enumerate(sorted(fixer.missingResidues)):
residues = fixer.missingResidues[key]
chain = fixer.structureChains[key[0]]
if key[1] < len(chain.residues):
offset = chain.residues[key[1]].number-len(residues)-1
chain = chains[key[0]]
chainResidues = list(chain.residues())
if key[1] < len(chainResidues):
offset = int(chainResidues[key[1]].id)-len(residues)-1
else:
offset = chain.residues[-1].number
table += ' <tr><td>%d</td><td>%d to %d</td><td>%s</td><td><input type="checkbox" name="add%d" checked></td></tr>\n' % (key[0]+1, offset+1, offset+len(residues), ', '.join(residues), i)
offset = int(chainResidues[-1].id)
table += ' <tr><td>%s</td><td>%d to %d</td><td>%s</td><td><input type="checkbox" name="add%d" checked></td></tr>\n' % (chain.id, offset+1, offset+len(residues), ', '.join(residues), i)
uiserver.setContent(header+loadHtmlFile("addResidues.html") % table)
def displayConvertResiduesPage():
......@@ -161,10 +162,6 @@ def displayConvertResiduesPage():
if len(fixer.nonstandardResidues) == 0:
displayMissingAtomsPage()
return
indexInChain = {}
for structChain, topChain in zip(fixer.structureChains, fixer.topology.chains()):
for structResidue, topResidue in zip(structChain.iter_residues(), topChain.residues()):
indexInChain[topResidue] = structResidue.number
table = ''
nucleotides = ['DA', 'DC', 'DG', 'DT', 'A', 'C', 'G', 'T']
for i in range(len(fixer.nonstandardResidues)):
......@@ -179,7 +176,7 @@ def displayConvertResiduesPage():
if res == replaceWith:
selected = ' selected'
options += '<option value="%s"%s>%s</option>' % (res, selected, res)
table += ' <tr><td>%d</td><td>%s %d</td><td><select name="residue%d">%s</select></td><td><input type="checkbox" name="convert%d" checked></td></tr>\n' % (residue.chain.index+1, residue.name, indexInChain[residue], i, options, i)
table += ' <tr><td>%s</td><td>%s %s</td><td><select name="residue%d">%s</select></td><td><input type="checkbox" name="convert%d" checked></td></tr>\n' % (residue.chain.id, residue.name, residue.id, i, options, i)
uiserver.setContent(header+loadHtmlFile("convertResidues.html") % table)
def displayMissingAtomsPage():
......@@ -191,10 +188,6 @@ def displayMissingAtomsPage():
fixer.addMissingAtoms()
displayAddHydrogensPage()
return
indexInChain = {}
for structChain, topChain in zip(fixer.structureChains, fixer.topology.chains()):
for structResidue, topResidue in zip(structChain.iter_residues(), topChain.residues()):
indexInChain[topResidue] = structResidue.number
table = ""
for residue in allResidues:
atoms = []
......@@ -202,7 +195,7 @@ def displayMissingAtomsPage():
atoms.extend(atom.name for atom in fixer.missingAtoms[residue])
if residue in fixer.missingTerminals:
atoms.extend(atom for atom in fixer.missingTerminals[residue])
table += ' <tr><td>%d</td><td>%s %d</td><td>%s</td></tr>\n' % (residue.chain.index+1, residue.name, indexInChain[residue], ', '.join(atoms))
table += ' <tr><td>%s</td><td>%s %s</td><td>%s</td></tr>\n' % (residue.chain.id, residue.name, residue.id, ', '.join(atoms))
uiserver.setContent(header+loadHtmlFile("addHeavyAtoms.html") % table)
def displayAddHydrogensPage():
......
tests/test_removechains.py
......@@ -9,7 +9,7 @@ def remove_chain_ids_and_verify(pdbid, chain_ids_to_remove, expected_chain_ids_r
# Remove specified chains.
fixer.removeChains(chainIds=chain_ids_to_remove)
# Check to make sure asserted chains remain.
chain_ids_remaining = [c.chain_id for c in fixer.structureChains]
chain_ids_remaining = [c.id for c in fixer.topology.chains()]
assert_items_equal(chain_ids_remaining, expected_chain_ids_remaining)
def test_removechain_ids():
......@@ -25,7 +25,7 @@ def remove_chain_indices_and_verify(pdbid, chain_indices_to_remove, expected_cha
# Remove specified chains.
fixer.removeChains(chainIndices=chain_indices_to_remove)
# Check to make sure asserted chains remain.
chain_ids_remaining = [c.chain_id for c in fixer.structureChains]
chain_ids_remaining = [c.id for c in fixer.topology.chains()]
assert_items_equal(chain_ids_remaining, expected_chain_ids_remaining)
def test_removechain_indices():
......
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