def _saveCB(okay, dialog, pathInfo=None):
mav = dialog.mav
if not okay:
return
if dialog.saveRegion.get():
try:
saveSeqs, saveFileMarkups = _verifySaveRegion(mav)
except:
dialog.enter()
raise
else:
saveSeqs = mav.seqs
saveFileMarkups = mav.fileMarkups
if dialog.omitGaps.get():
saveSeqs, saveFileMarkups = _omitGapColumns(saveSeqs,
saveFileMarkups)
if dialog.appendNumberings.get():
saveSeqs = _appendNumberings(saveSeqs,
doCopy=(saveSeqs == mav.seqs))
if pathInfo is None:
pathInfo = dialog.getPathsAndTypes()
if not pathInfo:
dialog.enter()
raise ValueError, "No filename specified"
from OpenSave import osOpen
for path, fileType in pathInfo:
f = osOpen(path, "w")
saverFunc[fileType](f, mav, saveSeqs, saveFileMarkups)
f.close()
mav.status("Saved %s\n" % path)
mav._edited = False
def _saveCB(okay, dialog, pathInfo=None):
mav = dialog.mav
if not okay:
return
if dialog.saveRegion.get():
try:
saveSeqs, saveFileMarkups = _verifySaveRegion(mav)
except:
dialog.enter()
raise
else:
saveSeqs = mav.seqs
saveFileMarkups = mav.fileMarkups
if dialog.omitGaps.get():
saveSeqs, saveFileMarkups = _omitGapColumns(saveSeqs, saveFileMarkups)
if dialog.appendNumberings.get():
saveSeqs = _appendNumberings(saveSeqs, doCopy=(saveSeqs == mav.seqs))
if pathInfo is None:
pathInfo = dialog.getPathsAndTypes()
if not pathInfo:
dialog.enter()
raise ValueError, "No filename specified"
from OpenSave import osOpen
for path, fileType in pathInfo:
f = osOpen(path, "w")
saverFunc[fileType](f, mav, saveSeqs, saveFileMarkups)
f.close()
mav.status("Saved %s\n" % path)
mav._edited = False
def parse(fileName):
from OpenSave import osOpen
f = osOpen(fileName, "r")
inSequence = 0
sequences = []
for line in f.readlines():
if inSequence:
if not line or line.isspace():
inSequence = 0
continue
if line[0] == '>':
inSequence = 0
# fall through
else:
sequences[-1].extend(line.strip())
if not inSequence:
if line[0] == '>':
if sequences and len(sequences[-1]) == 0:
raise FormatSyntaxError("No sequence"
" found for %s" % sequences[-1].name)
inSequence = 1
sequences.append(Sequence(makeReadable(
line[1:])))
f.close()
if not sequences:
raise WrongFileTypeError()
return sequences, {}, {}
def writeSel(saveFile, namingStyle=None, selected=True, itemType="Residue"): from chimera.selection import currentAtoms, currentBonds, \ currentEdges, currentResidues, currentMolecules, currentGraphs classNames = [c.__name__.lower() for c in classes] try: classIndex = classNames.index(itemType.lower()) except ValueError: # might be a trailing 's'... classIndex = classNames.index(itemType.lower()[:-1]) if selected: func = [currentAtoms, currentBonds, lambda : filter( lambda b: isinstance(b, chimera.PseudoBond), currentEdges()), currentResidues, currentMolecules, currentGraphs][classIndex] else: func = [unselAtoms, unselBonds, unselPseudobonds, unselResidues, unselMolecules, unselModels][classIndex] from chimera.misc import chimeraLabel, oslCmp items = map(lambda i: (i.oslIdent(), i), func()) if items and not isinstance(items[0][1], chimera.Bond) \ and not isinstance(items[0][1], chimera.PseudoBond): items.sort(oslCmp) if saveFile == "-": import sys f = sys.stdout else: from OpenSave import osOpen, tildeExpand saveFile = tildeExpand(saveFile) f = osOpen(saveFile, "w") for ident, item in items: print>>f, chimeraLabel(item, style=namingStyle, bondSep=" <-> ") if saveFile != "-": f.close()
def parse(fileName):
from OpenSave import osOpen
f = osOpen(fileName, "r")
# skip header crap
inHeader = True
lineNum = 0
sequences = []
for line in f:
line = line.strip()
lineNum += 1
if not line:
continue
fields = line.split()
if inHeader:
if len(fields[0]) == 2:
continue
inHeader = False
if len(fields) != 2:
# since this format lacks mandatory headers,
# cannot be sure it _is_ a Pfam file and therefore
# cannot raise FormatSyntaxError
raise WrongFileTypeError()
seq = Sequence(makeReadable(fields[0]))
seq.extend(fields[1])
sequences.append(seq)
f.close()
if not sequences:
raise WrongFileTypeError()
return sequences, {}, {}
def parse(fileName):
from OpenSave import osOpen
f = osOpen(fileName, "r")
# skip header crap
inHeader = True
lineNum = 0
sequences = []
for line in f:
line = line.strip()
lineNum += 1
if not line:
continue
fields = line.split()
if inHeader:
if len(fields[0]) == 2:
continue
inHeader = False
if len(fields) != 2:
# since this format lacks mandatory headers,
# cannot be sure it _is_ a Pfam file and therefore
# cannot raise FormatSyntaxError
raise WrongFileTypeError()
seq = Sequence(makeReadable(fields[0]))
seq.extend(fields[1])
sequences.append(seq)
f.close()
if not sequences:
raise WrongFileTypeError()
return sequences, {}, {}
def writeFile(fileName): from OpenSave import osOpen f = osOpen(fileName, 'w') if _ilabelModel: labelIDs = _ilabelModel.labelMap.keys() labelIDs.sort() for labelID in labelIDs: if labelID.startswith(AUTO_ID_PREFIX): print>>f, "Label" else: print>>f, "Label %s" % labelID label = _ilabelModel.labelMap[labelID] print>>f, "\t(x,y): %s" % repr(label.pos) print>>f, "\ttext: %s" % repr(unicode(label)) print>>f, "\tshown: %s" % label.shown print>>f, "\tfont size(s): %s" % _valuesString([str(c.size) for l in label.lines for c in l]) print>>f, "\tfont style(s): %s" % _valuesString([ FONT_STYLE_LABELS[FONT_STYLE_VALUES.index(c.style)] for l in label.lines for c in l]) print>>f, "\tfont typeface(s): %s" % _valuesString([ FONT_TYPEFACE_LABELS[FONT_TYPEFACE_VALUES.index(c.fontName)] for l in label.lines for c in l]) print>>f, "\tcolor(s): %s" % _valuesString([repr(c.rgba) for l in label.lines for c in l]) f.close()
def writeFile(fileName):
from OpenSave import osOpen
f = osOpen(fileName, 'w')
if _ilabelModel:
labelIDs = _ilabelModel.labelMap.keys()
labelIDs.sort()
for labelID in labelIDs:
if labelID.startswith(AUTO_ID_PREFIX):
print >> f, "Label"
else:
print >> f, "Label %s" % labelID
label = _ilabelModel.labelMap[labelID]
print >> f, "\t(x,y): %s" % repr(label.pos)
print >> f, "\ttext: %s" % repr(unicode(label))
print >> f, "\tshown: %s" % label.shown
print >> f, "\tfont size(s): %s" % _valuesString(
[str(c.size) for l in label.lines for c in l])
print >> f, "\tfont style(s): %s" % _valuesString([
FONT_STYLE_LABELS[FONT_STYLE_VALUES.index(c.style)]
for l in label.lines for c in l
])
print >> f, "\tfont typeface(s): %s" % _valuesString([
FONT_TYPEFACE_LABELS[FONT_TYPEFACE_VALUES.index(c.fontName)]
for l in label.lines for c in l
])
print >> f, "\tcolor(s): %s" % _valuesString(
[repr(c.rgba) for l in label.lines for c in l])
f.close()
def processCastpFiles(pdb,
mouthAtoms,
mouthInfo,
pocketAtoms,
pocketInfo,
identifyAs=None):
from OpenSave import osOpen
if not identifyAs:
identifyAs = pdb[:-4]
pdb = osOpen(pdb)
mouthAtoms = osOpen(mouthAtoms)
mouthInfo = osOpen(mouthInfo)
pocketAtoms = osOpen(pocketAtoms)
pocketInfo = osOpen(pocketInfo)
from chimera import PDBio
pdbio = PDBio()
molList = pdbio.readPDBstream(pdb, "CASTp PDB", 0)[0]
pdb.close()
if not pdbio.ok():
raise IOError(pdbio.error())
if not molList:
raise ValueError("No structures in CASTp PDB file?!?")
elif len(molList) > 1:
raise ValueError("Multiple structures in CASTp PDB file?!?")
structure = molList[0]
structure.name = identifyAs
mouthInfoDicts = processMouthInfoFile(mouthInfo)
pocketInfoDicts = processPocketInfoFile(pocketInfo)
mouthInfo.close()
pocketInfo.close()
if len(mouthInfoDicts) != len(pocketInfoDicts):
raise ValueError("Number of mouths (%d) does not match number"
" of pockets (%d)." %
(len(mouthInfoDicts), len(pocketInfoDicts)))
bySerial = {}
for a in structure.atoms:
bySerial[a.serialNumber] = a
gatherAtoms(bySerial, "mouth", mouthAtoms, mouthInfoDicts)
gatherAtoms(bySerial, "pocket", pocketAtoms, pocketInfoDicts)
mouthAtoms.close()
pocketAtoms.close()
cavities = []
for mid, pid in zip(mouthInfoDicts, pocketInfoDicts):
cavities.append(CastpCavity(mid, pid))
#chimera.openModels.add([structure])
return structure, cavities
def __init__(self, f): if isinstance(f, basestring): from OpenSave import osOpen file = osOpen(f) self._readMSF(file) file.close() else: self._readMSF(f)
def __init__(self, f):
if isinstance(f, basestring):
from OpenSave import osOpen
file = osOpen(f)
self._readMSF(file)
file.close()
else:
self._readMSF(f)
def _fileOutput(fileName, outputInfo, namingStyle):
intermodel, intramodel, relaxConstraints, \
distSlop, angleSlop, modelList, hbonds = outputInfo
from OpenSave import osOpen
outFile = osOpen(fileName, 'w')
if intermodel:
outFile.write("Finding intermodel H-bonds\n")
if intramodel:
outFile.write("Finding intramodel H-bonds\n")
if relaxConstraints:
outFile.write("Constraints relaxed by %g angstroms"
" and %d degrees\n" % (distSlop, angleSlop))
else:
outFile.write("Using precise constraint criteria\n")
outFile.write("Models used:\n")
for model in modelList:
outFile.write("\t%s %s\n" % (model.oslIdent(), model.name))
outFile.write("\nH-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):\n")
# want the bonds listed in some kind of consistent
# order...
hbonds.sort(_oslSort)
# figure out field widths to make things line up
dwidth = awidth = hwidth = 0
labels = {}
from chimera.misc import chimeraLabel
for don, acc in hbonds:
labels[don] = chimeraLabel(don, style=namingStyle)
labels[acc] = chimeraLabel(acc, style=namingStyle)
dwidth = max(dwidth, len(labels[don]))
awidth = max(awidth, len(labels[acc]))
da = don.xformCoord().distance(acc.xformCoord())
dha = None
for h in don.primaryNeighbors():
if h.element.number != 1:
continue
d = h.xformCoord().distance(acc.xformCoord())
if dha is None or d < dha:
dha = d
hyd = h
if dha is None:
dhaOut = "N/A"
hydOut = "no hydrogen"
else:
dhaOut = "%5.3f" % dha
hydOut = chimeraLabel(hyd, style=namingStyle)
hwidth = max(hwidth, len(hydOut))
labels[(don, acc)] = (hydOut, da, dhaOut)
for don, acc in hbonds:
hydOut, da, dhaOut = labels[(don, acc)]
outFile.write("%*s %*s %*s %5.3f %s\n" % (
0-dwidth, labels[don], 0-awidth, labels[acc],
0-hwidth, hydOut, da, dhaOut))
if outFile != fileName:
# we opened it, so close it...
outFile.close()
def _fileChosen(okayed, dialog): if okayed: paths = dialog.getPaths() if paths: filename = paths[0] from OpenSave import osOpen outFile = osOpen(filename, "w") outFile.write(dialog._text) outFile.close() delattr(dialog, "_text")
def __init__(self, topology):
from OpenSave import osOpen
topFile = osOpen(topology, 'rb')
import os
self.topFileSize = os.stat(topology).st_size
from xdrlib import Unpacker
self.fileString = FileString(topFile, 0, self.topFileSize)
self.xdr = Unpacker(self.fileString)
version = self._readHeader()
self._readTopology(version)
def __init__(self, topology): from OpenSave import osOpen topFile = osOpen(topology, 'rb') import os self.topFileSize = os.stat(topology).st_size from xdrlib import Unpacker self.fileString = FileString(topFile, 0, self.topFileSize) self.xdr = Unpacker(self.fileString) version = self._readHeader() self._readTopology(version)
def __init__(self, topology):
from OpenSave import osOpen
self.atomNames = []
self.resNames = []
self.resIndices = []
self.bonds = []
self.elements = []
self.molInfo = {}
topFile = osOpen(topology)
while self._readLine(topFile):
pass
topFile.close()
def __init__(self, topology):
from OpenSave import osOpen
self.atomNames = []
self.resNames = []
self.resIndices = []
self.bonds = []
self.elements = []
self.molInfo = {}
topFile = osOpen(topology)
while self._readLine(topFile):
pass
topFile.close()
def _fileChosen(okayed, dialog): if okayed: paths = dialog.getPaths() if paths: filename = paths[0] from OpenSave import osOpen outFile = osOpen(filename, "w") outFile.write(dialog._output) outFile.close() if dialog._show: import urllib from chimera import help help.display(urllib.pathname2url(filename)) delattr(dialog, "_output") delattr(dialog, "_show")
def parse(fileName):
from OpenSave import osOpen
f = osOpen(fileName, "r")
inHeader = 1
sequences = []
lineNum = 0
for line in f.readlines():
lineNum += 1
if inHeader:
if line.startswith("CLUSTAL"):
inHeader = 0
firstBlock = 1
else:
if line.strip() !="":
raise WrongFileTypeError()
continue
if not line or line[0].isspace():
if sequences:
firstBlock = 0
expect = 0
continue
try:
seqName, seqBlock, numResidues = line.split()
except ValueError:
try:
seqName, seqBlock = line.split()
except ValueError:
raise FormatSyntaxError("Line %d is not "
"sequence name followed by sequence "
" contents and optional ungapped length"
% lineNum)
if firstBlock:
sequences.append(Sequence(makeReadable(seqName)))
sequences[-1].append(seqBlock)
continue
try:
seq = sequences[expect]
except IndexError:
raise FormatSyntaxError("Sequence on line %d not in"
" initial sequence block" % lineNum)
expect += 1
seq.append(seqBlock)
f.close()
if not sequences:
raise WrongFileTypeError()
return sequences, {}, {}
def parse(fileName):
from OpenSave import osOpen
f = osOpen(fileName, "r")
inHeader = 1
sequences = []
lineNum = 0
for line in f.readlines():
lineNum += 1
if inHeader:
if line.startswith("CLUSTAL"):
inHeader = 0
firstBlock = 1
else:
if line.strip() != "":
raise WrongFileTypeError()
continue
if not line or line[0].isspace():
if sequences:
firstBlock = 0
expect = 0
continue
try:
seqName, seqBlock, numResidues = line.split()
except ValueError:
try:
seqName, seqBlock = line.split()
except ValueError:
raise FormatSyntaxError(
"Line %d is not "
"sequence name followed by sequence "
" contents and optional ungapped length" % lineNum)
if firstBlock:
sequences.append(Sequence(makeReadable(seqName)))
sequences[-1].append(seqBlock)
continue
try:
seq = sequences[expect]
except IndexError:
raise FormatSyntaxError("Sequence on line %d not in"
" initial sequence block" % lineNum)
expect += 1
seq.append(seqBlock)
f.close()
if not sequences:
raise WrongFileTypeError()
return sequences, {}, {}
def _fileOutput(fileName, info, namingStyle): overlapCutoff, hbondAllowance, bondSeparation, ignoreIntraRes, \ clashes, outputGrouping = info from OpenSave import osOpen outFile = osOpen(fileName, 'w') print>>outFile, "Allowed overlap: %g" % overlapCutoff print>>outFile, "H-bond overlap reduction: %g" % hbondAllowance print>>outFile, "Ignore contacts between atoms separated by %d bonds" \ " or less" % bondSeparation if ignoreIntraRes: print>>outFile, "Ignore intra-residue contacts" else: print>>outFile, "Detect intra-residue contacts also" seen = set() data = [] from chimera.misc import chimeraLabel for a, aclashes in clashes.items(): for c, val in aclashes.items(): if (c, a) in seen: continue seen.add((a, c)) if a in outputGrouping: out1, out2 = a, c else: out1, out2 = c, a l1, l2 = chimeraLabel(out1, style=namingStyle), \ chimeraLabel(out2, style=namingStyle) data.append((val, l1, l2, out1.xformCoord().distance( out2.xformCoord()))) data.sort() data.reverse() print>>outFile, "\n%d contacts" % len(data) print>>outFile, "atom1 atom2 overlap distance" if data: fieldWidth1 = max([len(l1) for v, l1, l2, d in data]) fieldWidth2 = max([len(l2) for v, l1, l2, d in data]) for v, l1, l2, d in data: print>>outFile, "%*s %*s %5.3f %5.3f" % ( 0-fieldWidth1, l1, 0-fieldWidth2, l2, v, d) if fileName != outFile: # only close file if we opened it... outFile.close()
def _fileOutput(fileName, info, namingStyle):
overlapCutoff, hbondAllowance, bondSeparation, ignoreIntraRes, \
clashes, outputGrouping = info
from OpenSave import osOpen
outFile = osOpen(fileName, 'w')
print >> outFile, "Allowed overlap: %g" % overlapCutoff
print >> outFile, "H-bond overlap reduction: %g" % hbondAllowance
print>>outFile, "Ignore contacts between atoms separated by %d bonds" \
" or less" % bondSeparation
if ignoreIntraRes:
print >> outFile, "Ignore intra-residue contacts"
else:
print >> outFile, "Detect intra-residue contacts also"
seen = set()
data = []
from chimera.misc import chimeraLabel
for a, aclashes in clashes.items():
for c, val in aclashes.items():
if (c, a) in seen:
continue
seen.add((a, c))
if a in outputGrouping:
out1, out2 = a, c
else:
out1, out2 = c, a
l1, l2 = chimeraLabel(out1, style=namingStyle), \
chimeraLabel(out2, style=namingStyle)
data.append(
(val, l1, l2, out1.xformCoord().distance(out2.xformCoord())))
data.sort()
data.reverse()
print >> outFile, "\n%d contacts" % len(data)
print >> outFile, "atom1 atom2 overlap distance"
if data:
fieldWidth1 = max([len(l1) for v, l1, l2, d in data])
fieldWidth2 = max([len(l2) for v, l1, l2, d in data])
for v, l1, l2, d in data:
print >> outFile, "%*s %*s %5.3f %5.3f" % (
0 - fieldWidth1, l1, 0 - fieldWidth2, l2, v, d)
if fileName != outFile:
# only close file if we opened it...
outFile.close()
def open_mmcif(path):
from OpenSave import osOpen
p = osOpen(path)
#
# No bonds are created for standard mmCIF files from the PDB unless the
# library_bonds or distance_bonds options are given.
#
# It appears that mmlib 0.9.7 can only link residues of a polymer using
# distance rules. Residue templates are used for intra-residue bonds.
#
from mmLib.FileIO import LoadStructure
from mmLib.mmCIF import mmCIFSyntaxError
try:
struct = LoadStructure(fil=p, format="CIF", library_bonds=True,
auto_sort=False)
except mmCIFSyntaxError, e:
from chimera import NotABug
raise NotABug("%s: %s" % (path, str(e)))
def writeDMS(surf, fileName, writeNormals=True, displayedOnly=True):
from OpenSave import osOpen
from chimera import UserError, replyobj
m = surf.molecule
if not m:
raise UserError("No molecule for surface")
out = osOpen(fileName, "wb")
vMap = {}
for i, a in enumerate(surf.atomMap):
vMap.setdefault(a, []).append(i)
for i, a in enumerate(m.atoms):
atomPart = atomFormat(a)
crd = a.coord()
print>>out, "%s%8.3f %8.3f %8.3f A" % (atomPart, crd.x,
crd.y, crd.z)
if displayedOnly and not a.surfaceDisplay:
continue
vertices = surf.surface_piece.geometry[0]
normals = surf.surface_piece.normals
vtypes = surf.triData[1][:,2]
# vtypes (according to MSMS man page):
# 1 == toric reentrant
# 2 == inside reentrant
# 3 == inside contact
vses = surf.triData[0][:,6]
for vi in vMap.get(a, []):
v = vertices[vi]
vtype = vtypes[vi]
try:
dmsType = ('S', 'R', 'C')[vtype-1]
except IndexError:
raise ValueError("Vertex type (%d) not in"
" range 1-3" % vtype)
ses = vses[vi]
line = "%s%8.3f %8.3f %8.3f S%s0 %6.3f" % (atomPart,
v[0], v[1], v[2], dmsType, ses)
if writeNormals:
line += " %6.3f %6.3f %6.3f" \
% tuple(normals[vi])
print>>out, line
out.close()
def writeDMS(surf, fileName, writeNormals=True, displayedOnly=True):
from OpenSave import osOpen
from chimera import UserError, replyobj
m = surf.molecule
if not m:
raise UserError("No molecule for surface")
out = osOpen(fileName, "wb")
vMap = {}
for i, a in enumerate(surf.atomMap):
vMap.setdefault(a, []).append(i)
for i, a in enumerate(m.atoms):
atomPart = atomFormat(a)
crd = a.coord()
print >> out, "%s%8.3f %8.3f %8.3f A" % (atomPart, crd.x, crd.y, crd.z)
if displayedOnly and not a.surfaceDisplay:
continue
vertices = surf.surface_piece.geometry[0]
normals = surf.surface_piece.normals
vtypes = surf.triData[1][:, 2]
# vtypes (according to MSMS man page):
# 1 == toric reentrant
# 2 == inside reentrant
# 3 == inside contact
vses = surf.triData[0][:, 6]
for vi in vMap.get(a, []):
v = vertices[vi]
vtype = vtypes[vi]
try:
dmsType = ('S', 'R', 'C')[vtype - 1]
except IndexError:
raise ValueError("Vertex type (%d) not in"
" range 1-3" % vtype)
ses = vses[vi]
line = "%s%8.3f %8.3f %8.3f S%s0 %6.3f" % (atomPart, v[0], v[1],
v[2], dmsType, ses)
if writeNormals:
line += " %6.3f %6.3f %6.3f" \
% tuple(normals[vi])
print >> out, line
out.close()
def parse(fileName):
from OpenSave import osOpen
f = osOpen(fileName, "r")
want = 'init'
sequences = []
for line in f.readlines():
line = line.strip()
if want == 'init':
if len(line) < 4:
continue
if line[0] != '>' or line[3] != ';':
continue
sequences.append(Sequence(makeReadable(line[4:])))
pirType = line[1:3]
if pirType in ("P1", "F1"):
sequences[-1].nucleic = 0
else:
sequences[-1].nucleic = 1
sequences[-1].PIRtype = pirType
want = 'descript'
elif want == 'descript':
sequences[-1].descript = line
sequences[-1].PIRdescript = line
want = 'sequence'
elif want == 'sequence':
if not line:
continue
if line[-1] == '*':
want = 'init'
line = line[:-1]
sequences[-1].extend(filter(lambda c,
whsp=string.whitespace: not c in whsp, line))
f.close()
if not sequences:
raise WrongFileTypeError()
if want != 'init':
raise FormatSyntaxError("Could not find end of sequence '%s'"
% sequences[-1].name)
return sequences, {}, {}
def parse(fileName):
from OpenSave import osOpen
f = osOpen(fileName, "r")
want = 'init'
sequences = []
for line in f.readlines():
line = line.strip()
if want == 'init':
if len(line) < 4:
continue
if line[0] != '>' or line[3] != ';':
continue
sequences.append(Sequence(makeReadable(line[4:])))
pirType = line[1:3]
if pirType in ("P1", "F1"):
sequences[-1].nucleic = 0
else:
sequences[-1].nucleic = 1
sequences[-1].PIRtype = pirType
want = 'descript'
elif want == 'descript':
sequences[-1].descript = line
sequences[-1].PIRdescript = line
want = 'sequence'
elif want == 'sequence':
if not line:
continue
if line[-1] == '*':
want = 'init'
line = line[:-1]
sequences[-1].extend(
filter(lambda c, whsp=string.whitespace: not c in whsp, line))
f.close()
if not sequences:
raise WrongFileTypeError()
if want != 'init':
raise FormatSyntaxError("Could not find end of sequence '%s'" %
sequences[-1].name)
return sequences, {}, {}
def open_mmcif(path):
from OpenSave import osOpen
p = osOpen(path)
#
# No bonds are created for standard mmCIF files from the PDB unless the
# library_bonds or distance_bonds options are given.
#
# It appears that mmlib 0.9.7 can only link residues of a polymer using
# distance rules. Residue templates are used for intra-residue bonds.
#
from mmLib.FileIO import LoadStructure
from mmLib.mmCIF import mmCIFSyntaxError
try:
struct = LoadStructure(fil=p,
format="CIF",
library_bonds=True,
auto_sort=False)
except mmCIFSyntaxError, e:
from chimera import NotABug
raise NotABug("%s: %s" % (path, str(e)))
def writeSel(saveFile, namingStyle=None, selected=True, itemType="Residue"):
from chimera.selection import currentAtoms, currentBonds, \
currentEdges, currentResidues, currentMolecules, currentGraphs
classNames = [c.__name__.lower() for c in classes]
try:
classIndex = classNames.index(itemType.lower())
except ValueError:
# might be a trailing 's'...
classIndex = classNames.index(itemType.lower()[:-1])
if selected:
func = [
currentAtoms, currentBonds, lambda: filter(
lambda b: isinstance(b, chimera.PseudoBond), currentEdges()),
currentResidues, currentMolecules, currentGraphs
][classIndex]
else:
func = [
unselAtoms, unselBonds, unselPseudobonds, unselResidues,
unselMolecules, unselModels
][classIndex]
from chimera.misc import chimeraLabel, oslCmp
items = map(lambda i: (i.oslIdent(), i), func())
if items and not isinstance(items[0][1], chimera.Bond) \
and not isinstance(items[0][1], chimera.PseudoBond):
items.sort(oslCmp)
if saveFile == "-":
import sys
f = sys.stdout
else:
from OpenSave import osOpen, tildeExpand
saveFile = tildeExpand(saveFile)
f = osOpen(saveFile, "w")
for ident, item in items:
print >> f, chimeraLabel(item, style=namingStyle, bondSep=" <-> ")
if saveFile != "-":
f.close()
def Apply(self, event=None):
paths = self.getPaths()
if not paths:
raise ValueError, "No filename given for recording"
fname = paths[0]
if self.appending.get():
mode = "a"
else:
mode = "w"
from OpenSave import osOpen
file = osOpen(fname, mode)
writePython = self.commandStyle.getvalue()[:6] == "Python"
if writePython:
file.write("from chimera import runCommand\n")
if self.amount.getvalue()[:3] == "all":
cmds = self.histDialog.listbox.get()
else:
cmds = self.histDialog.listbox.getvalue()
for cmd in cmds:
if writePython:
file.write("runCommand(" + repr(cmd) + ")\n")
else:
file.write(cmd + "\n")
file.close()
def readSDF(fileName, identifyAs=None):
from OpenSave import osOpen
from chimera import UserError, Molecule, Element, openModels, replyobj
from chimera import Coord
state = "init"
f = osOpen(fileName)
mols = []
nonblank = False
for l in f:
line = l.strip()
nonblank = nonblank or line
if state == "init":
state = "post header 1"
molName = line
elif state == "post header 1":
state = "post header 2"
elif state == "post header 2":
state = "counts"
elif state == "counts":
if not line:
break
state = "atoms"
serial = 1
anums = {}
atoms = []
try:
numAtoms = int(l[:3].strip())
numBonds = int(l[3:6].strip())
except ValueError:
raise UserError("Atom/bond counts line of"
" MOL/SDF file '%s' is botched: '%s'"
% (fileName, l))
m = Molecule()
mols.append(m)
if identifyAs:
m.name = identifyAs
else:
from chimera.misc import isInformativeName
mn = molName.strip()
if isInformativeName(mn):
m.name = mn
else:
import os.path
m.name = os.path.split(fileName)[-1]
r = m.newResidue("UNK", " ", 1, " ")
elif state == "atoms":
numAtoms -= 1
if numAtoms == 0:
if numBonds:
state = "bonds"
else:
state = "properties"
try:
x = float(l[:10].strip())
y = float(l[10:20].strip())
z = float(l[21:30].strip())
elem = l[31:34].strip()
except ValueError:
raise UserError("Atom line of MOL/SDF file"
" '%s' is not x y z element...: '%s'"
% (fileName, l))
element = Element(elem)
if element.number == 0:
# lone pair or somesuch
atoms.append(None)
continue
anum = anums.get(element.name, 0) + 1
anums[element.name] = anum
a = m.newAtom("%s%d" % (element.name, anum), element)
atoms.append(a)
r.addAtom(a)
a.setCoord(Coord(x, y, z))
a.serialNumber = serial
serial += 1
elif state == "bonds":
numBonds -= 1
if numBonds == 0:
state = "properties"
try:
a1index = int(l[:3].strip())
a2index = int(l[3:6].strip())
order = int(l[6:9].strip())
except ValueError:
raise UserError("Bond line of MOL/SDF file"
" '%s' is not a1 a2 order...: '%s'"
% (fileName, l))
a1 = atoms[a1index-1]
a2 = atoms[a2index-1]
if not a1 or not a2:
continue
m.newBond(a1, a2).order = order
elif state == "properties":
if not m.atoms:
raise UserError("No atoms found for compound"
" '%s' in MOL/SDF file '%s'"
% (m.name, fileName))
if line.split() == ["M", "END"]:
state = "data"
elif state == "data":
if line == "$$$$":
nonblank = False
state = "init"
f.close()
if nonblank and state not in ["data", "init"]:
if mols:
replyobj.warning("Extraneous text after final $$$$"
" in MOL/SDF file '%s'" % fileName)
else:
raise UserError("Unexpected end of file (parser state:"
" %s) in MOL/SDF file '%s'" % (state, fileName))
return mols
def parse(fileName):
from OpenSave import osOpen
from chimera import replyobj
f = osOpen(fileName, "r")
lineNum = 0
fileAttrs = {}
fileMarkups = {}
seqAttrs = {}
seqMarkups = {}
sequences = {}
seqSequence = []
for line in f:
line = line[:-1] # drop newline
lineNum += 1
if lineNum == 1:
if line.startswith("# STOCKHOLM"):
continue
raise WrongFileTypeError()
if not line:
continue
if line.startswith('#='):
markupType = line[2:4]
markup = line[5:].strip()
def trySplit(numSplit):
fields = markup.split(None, numSplit)
if len(fields) == numSplit:
# value is empty
fields.append("")
if len(fields) != numSplit + 1:
raise FormatSyntaxError("Not enough"
" arguments after #=%s markup"
" on line %d" %
(markupType, lineNum))
return fields
if markupType == "GF":
tag, val = trySplit(1)
tag = tag.replace("_", " ")
tag = genericFileAttrs.get(tag, "Stockholm " + tag)
if tag in fileAttrs:
fileAttrs[tag] += '\n' + val
else:
fileAttrs[tag] = val
elif markupType == "GS":
seqName, tag, val = trySplit(2)
tag = tag.replace("_", " ")
attrs = seqAttrs.setdefault(seqName, {})
tag = genericSeqAttrs.get(tag, "Stockholm " + tag)
if tag in attrs:
attrs[tag] += '\n' + val
else:
attrs[tag] = val
elif markupType == "GC":
tag, val = trySplit(1)
tag = tag.replace("_", " ")
fileMarkups[tag] = fileMarkups.get(tag, "") + val
elif markupType == "GR":
seqName, tag, val = trySplit(2)
tag = tag.replace("_", " ")
seqMarkups.setdefault(seqName, {}).setdefault(tag, "")
seqMarkups[seqName][tag] += val
# ignore other types
continue
elif line.startswith('#'):
# unstructured comment
if 'comments' in fileAttrs:
fileAttrs['comments'] += "\n" + line[1:]
else:
fileAttrs['comments'] = line[1:]
continue
elif line.strip() == "//":
# end of sequence alignment blocks, but comments
# may follow this, so keep going...
continue
# sequence info...
try:
seqName, block = line.split(None, 1)
except ValueError:
raise FormatSyntaxError("Sequence info not in name/"
"contents format on line %d" % lineNum)
if seqName not in sequences:
sequences[seqName] = Sequence(makeReadable(seqName))
seqSequence.append(seqName)
sequences[seqName].extend(block)
f.close()
if not sequences:
raise FormatSyntaxError("No sequences found")
for seqName, seq in sequences.items():
if seqName in seqAttrs:
seq.attrs = seqAttrs[seqName]
if seqName in seqMarkups:
seq.markups = seqMarkups[seqName]
for tag, markup in seq.markups.items():
if len(markup) != len(seq):
replyobj.warning("Markup %s for"
" sequence %s is wrong length;"
" ignoring\n" % (tag, seqName))
del seq.markups[tag]
for seqInfo, label in [(seqAttrs, "sequence"), (seqMarkups, "residue")]:
for seqName in seqInfo.keys():
if seqName in sequences:
continue
# might be sequence name without trailing '/start-end'
for fullName in sequences.keys():
if fullName.startswith(seqName) \
and fullName[len(seqName)] == '/' \
and '/' not in fullName[len(seqName)+1:]:
break
else:
raise FormatSyntaxError(
"%s annotations "
"provided for non-existent sequence %s" %
(label.capitalize(), seqName))
replyobj.info("Updating %s %s annotions with %s "
"annotations\n" % (fullName, label, seqName))
seqInfo[fullName].update(seqInfo[seqName])
del seqInfo[seqName]
for tag, markup in fileMarkups.items():
if len(markup) != len(sequences[seqSequence[0]]):
raise FormatSyntaxError("Column annotation %s is"
" wrong length" % tag)
return map(lambda name: sequences[name], seqSequence), \
fileAttrs, fileMarkups
def Apply(self):
savePaths = self.getPaths()
if not savePaths:
replyobj.error("No save file specified\n")
return
from OpenSave import osOpen
saveFile = osOpen(savePaths[0], "w")
mols = chimera.openModels.list(modelTypes=[chimera.Molecule])
for mol in mols:
print>>saveFile, "Model %s is %s" % (mol.oslIdent(),
mol.name)
sm = self.structMeasure
selected = self.saveTypes.getcurselection()
if DISTANCES in selected:
print>>saveFile, "\nDistance information"
output = {}
for d in sm.distances:
a1, a2 = d.atoms
distID = d.id
if d.distance[-1].isdigit():
dval = d.distance
else:
# omit angstrom character
dval = d.distance[:-1]
output[distID] = "%2d %s <-> %s: %s" % (
distID, sm.atomLabel(a1),
sm.atomLabel(a2), dval)
ids = output.keys()
ids.sort()
for distID in ids:
print>>saveFile, output[distID]
if ANGLES in selected:
print>>saveFile, "\nAngles/Torsions"
printables = []
maxLabel = 0
for atoms in sm.angleInfo:
labelArgs = tuple([sm.atomLabel(a)
for a in atoms])
if len(atoms) == 3:
label = "%s -> %s -> %s" % labelArgs
func = chimera.angle
else:
label = "%s -> %s -> %s -> %s" \
% labelArgs
func = chimera.dihedral
maxLabel = max(maxLabel, len(label))
printables.append((label, "%8.3f" %
func(*tuple([a.xformCoord()
for a in atoms]))))
format = "%%%ds: %%s" % maxLabel
for printArgs in printables:
print>>saveFile, format % printArgs
if BONDROTS in selected:
print>>saveFile, "\nBond rotations"
printables = []
maxLabel = 0
for br in sm.rotations:
na, fa = sm.dihedEndAtoms(br)
label = "%s -> %s -> %s -> %s" % (
sm.atomLabel(na),
sm.atomLabel(br.atoms[0]),
sm.atomLabel(br.atoms[1]),
sm.atomLabel(fa))
maxLabel = max(maxLabel, len(label))
printables.append((label,
"%8.3f" % sm.dihedral(br),
"%8.3f" % br.get()))
format = "%%%ds: %%s (delta: %%s)" % maxLabel
for printArgs in printables:
print>>saveFile, format % printArgs
if GEOMETRIES in selected:
print>>saveFile, "\nAxes"
print>>saveFile, "axis name, length, center, direction"
from Axes import axisManager
axes = axisManager.axes
axes.sort(lambda a1, a2: cmp(a1.name, a2.name))
nameSize = max([0] + [len(a.name) for a in axes])
from chimera import Point
for axis in axes:
ends = [axis.direction * ext + axis.center
for ext in axis.extents]
cx, cy, cz = Point(ends)
dx, dy, dz = axis.direction
print>>saveFile, "%*s: %6.3f (%7.3f, %7.3f," \
" %7.3f) (%6.3f, %6.3f, %6.3f)" % (
nameSize, axis.name,
abs(axis.extents[0] - axis.extents[1]),
cx, cy, cz, dx, dy, dz)
print>>saveFile, "\nPlanes"
print>>saveFile, "plane name, center, normal, radius"
from Planes import planeManager
planes = planeManager.planes
planes.sort(lambda p1, p2: cmp(p1.name, p2.name))
nameSize = max([0] + [len(pl.name) for pl in planes])
for plane in planes:
ox, oy, oz = plane.plane.origin
nx, ny, nz = plane.plane.normal
print>>saveFile, "%*s: (%7.3f, %7.3f, %7.3f)" \
" (%6.3f, %6.3f, %6.3f) %.3f" % (nameSize, plane.name,
ox, oy, oz, nx, ny, nz, plane.radius)
saveFile.close()
def writeMol2(models, fileName, status=None, anchor=None, relModel=None,
hydNamingStyle="sybyl", multimodelHandling="individual",
skip=None, resNum=True, gaffType=False, gaffFailError=None):
"""Write a Mol2 file.
'models' are the models to write out into a file named 'fileName'.
'status', if not None, is a function that takes a string -- used
to report the progress of the write.
'anchor' is a selection (i.e. instance of a subclass of
chimera.selection.Selection) containing atoms/bonds that should
be written out to the @SETS section of the file as the rigid
framework for flexible ligand docking.
'hydNamingStyle' controls whether hydrogen names should be
"Sybyl-like" (value: sybyl) or "PDB-like" (value: pdb)
-- e.g. HG21 vs. 1HG2.
'multimodelHandling' controls whether multiple models will be
combined into a single @MOLECULE section (value: combined) or
each given its own section (value: individual).
'skip' is a list of atoms to not output
'resNum' controls whether residue sequence numbers are included
in the substructure name. Since Sybyl Mol2 files include them,
this defaults to True.
If 'gaffType' is True, outout GAFF atom types instead of Sybyl
atom types. 'gaffFailError', if specified, is the type of error
to throw (e.g. UserError) if there is no gaffType attribute for
an atom, otherwise throw the standard AttributeError.
"""
# open the given file name for writing
from OpenSave import osOpen
f = osOpen(fileName, "w")
sortFunc = serialSort = lambda a1, a2: cmp(a1.coordIndex, a2.coordIndex)
if isinstance(models, chimera.Molecule):
models = [models]
elif isinstance(models, Selection):
# create a fictitious jumbo model
if isinstance(models, ItemizedSelection):
sel = models
else:
sel = ItemizedSelection()
sel.merge(models)
sel.addImplied()
class Jumbo:
def __init__(self, sel):
self.atoms = sel.atoms()
self.residues = sel.residues()
self.bonds = sel.bonds()
self.name = "(selection)"
models = [Jumbo(sel)]
sortFunc = lambda a1, a2: cmp(a1.molecule.id, a2.molecule.id) \
or cmp(a1.molecule.subid, a2.molecule.subid) \
or serialSort(a1, a2)
multimodelHandling = "individual"
# transform...
if relModel is None:
xform = chimera.Xform.identity()
else:
xform = relModel.openState.xform
xform.invert()
# need to find amide moieties since Sybyl has an explicit amide type
if status:
status("Finding amides\n")
from ChemGroup import findGroup
amides = findGroup("amide", models)
amideNs = dict.fromkeys([amide[2] for amide in amides])
amideCNs = dict.fromkeys([amide[0] for amide in amides])
amideCNs.update(amideNs)
amideOs = dict.fromkeys([amide[1] for amide in amides])
substructureNames = None
if multimodelHandling == "combined":
# create a fictitious jumbo model
class Jumbo:
def __init__(self, models):
self.atoms = []
self.residues = []
self.bonds = []
self.name = models[0].name + " (combined)"
for m in models:
self.atoms.extend(m.atoms)
self.residues.extend(m.residues)
self.bonds.extend(m.bonds)
# if combining single-residue models,
# can be more informative to use model name
# instead of residue type for substructure
if len(models) == len(self.residues):
rtypes = [r.type for r in self.residues]
if len(set(rtypes)) < len(rtypes):
mnames = [m.name for m in models]
if len(set(mnames)) == len(mnames):
self.substructureNames = dict(
zip(self.residues, mnames))
models = [Jumbo(models)]
if hasattr(models[-1], 'substructureNames'):
substructureNames = models[-1].substructureNames
delattr(models[-1], 'substructureNames')
sortFunc = lambda a1, a2: cmp(a1.molecule.id, a2.molecule.id) \
or cmp(a1.molecule.subid, a2.molecule.subid) \
or serialSort(a1, a2)
# write out models
for mol in models:
if hasattr(mol, 'mol2comments'):
for m2c in mol.mol2comments:
print>>f, m2c
if hasattr(mol, 'solventInfo' ):
print>>f, mol.solventInfo
# molecule section header
print>>f, "%s" % MOLECULE_HEADER
# molecule name
print>>f, "%s" % mol.name
ATOM_LIST = mol.atoms
BOND_LIST = mol.bonds
if skip:
skip = set(skip)
ATOM_LIST = [a for a in ATOM_LIST if a not in skip]
BOND_LIST = [b for b in BOND_LIST
if b.atoms[0] not in skip
and b.atoms[1] not in skip]
RES_LIST = mol.residues
# Chimera has an unusual internal order for its atoms, so
# sort them by input order
if status:
status("Putting atoms in input order")
ATOM_LIST.sort(sortFunc)
# if anchor is not None, then there will be two entries in
# the @SETS section of the file...
if anchor:
sets = 2
else:
sets = 0
# number of entries for various sections...
print>>f, "%d %d %d 0 %d" % (len(ATOM_LIST), len(BOND_LIST),
len(RES_LIST), sets)
# type of molecule
if hasattr(mol, "mol2type"):
mtype = mol.mol2type
else:
mtype = "SMALL"
from chimera.resCode import nucleic3to1, protein3to1
for r in mol.residues:
if r.type in protein3to1:
mtype = "PROTEIN"
break
if r.type in nucleic3to1:
mtype = "NUCLEIC_ACID"
break
print>>f, mtype
# indicate type of charge information
if hasattr(mol, 'chargeModel'):
print>>f, mol.chargeModel
else:
print>>f, "NO_CHARGES"
if hasattr(mol, 'mol2comment'):
print>>f, "\n%s" % mol.mol2comment
else:
print>>f, "\n"
if status:
status("writing atoms\n")
# atom section header
print>>f, "%s" % ATOM_HEADER
# make a dictionary of residue indices so that we can do
# quick look ups
resIndices = {}
for i, r in enumerate(RES_LIST):
resIndices[r] = i+1
for i, atom in enumerate(ATOM_LIST):
# atom ID, starting from 1
print>>f, "%7d" % (i+1),
# atom name, possibly rearranged if it's a hydrogen
if hydNamingStyle == "sybyl" \
and not atom.name[0].isalpha():
atomName = atom.name[1:] + atom.name[0]
else:
atomName = atom.name
print>>f, "%-8s" % atomName,
# untransformed coordinate position
coord = xform.apply(atom.xformCoord())
print>>f, "%9.4f %9.4f %9.4f" % (
coord.x, coord.y, coord.z),
# atom type
if gaffType:
try:
atomType = atom.gaffType
except AttributeError:
if not gaffFailError:
raise
raise gaffFailError("%s has no Amber/GAFF type assigned.\n"
"Use the AddCharge tool to assign Amber/GAFF types."
% atom)
elif hasattr(atom, 'mol2type'):
atomType = atom.mol2type
elif atom in amideNs:
atomType = "N.am"
elif atom.residue.id.chainId == "water":
if atom.element.name == "O":
atomType = "O.t3p"
else:
atomType = "H.t3p"
elif atom.element.name == "N" and len(
[r for r in atom.minimumRings() if r.aromatic()]) > 0:
atomType = "N.ar"
elif atom.idatmType == "C2" and len([nb for nb in atom.neighbors
if nb.idatmType == "Ng+"]) > 2:
atomType = "C.cat"
else:
try:
atomType = chimera2sybyl[atom.idatmType]
except KeyError:
chimera.replyobj.warning("Atom whose"
" IDATM type has no equivalent"
" Sybyl type: %s (type: %s)\n"
% (atom.oslIdent(),
atom.idatmType))
atomType = str(atom.element)
print>>f, "%-5s" % atomType,
# residue-related info
res = atom.residue
# residue index
print>>f, "%5d" % resIndices[res],
# substructure identifier and charge
if hasattr(atom, 'charge'):
charge = atom.charge
else:
charge = 0.0
if substructureNames:
rname = substructureNames[res]
elif resNum:
rname = "%3s%-5d" % (res.type, res.id.position)
else:
rname = "%3s" % res.type
print>>f, "%s %9.4f" % (rname, charge)
if status:
status("writing bonds\n")
# bond section header
print>>f, "%s" % BOND_HEADER
# make an atom-index dictionary to speed lookups
atomIndices = {}
for i, a in enumerate(ATOM_LIST):
atomIndices[a] = i+1
for i, bond in enumerate(BOND_LIST):
a1, a2 = bond.atoms
# ID
print>>f, "%6d" % (i+1),
# atom IDs
print>>f, "%4d %4d" % (
atomIndices[a1], atomIndices[a2]),
# bond order; give it our best shot...
amideA1 = a1 in amideCNs
amideA2 = a2 in amideCNs
if amideA1 and amideA2:
print>>f, "am"
continue
if amideA1 or amideA2:
if a1 in amideOs or a2 in amideOs:
print>>f, "2"
else:
print>>f, "1"
continue
aromatic = False
for ring in bond.minimumRings():
if ring.aromatic():
aromatic = True
break
if aromatic:
print>>f, "ar"
continue
try:
geom1 = typeInfo[a1.idatmType].geometry
except KeyError:
print>>f, "1"
continue
try:
geom2 = typeInfo[a2.idatmType].geometry
except KeyError:
print>>f, "1"
continue
if geom1 not in [2,3] or geom2 not in [2,3]:
print>>f, "1"
continue
# if either endpoint atom is in an aromatic ring and
# the bond isn't, it's a single bond...
for endp in [a1, a2]:
aromatic = False
for ring in endp.minimumRings():
if ring.aromatic():
aromatic = True
break
if aromatic:
break
else:
# neither endpoint in aromatic ring
print>>f, "2"
continue
print>>f, "1"
if status:
status("writing residues")
# residue section header
print>>f, "%s" % SUBSTR_HEADER
for i, res in enumerate(RES_LIST):
# residue id field
print>>f, "%6d" % (i+1),
# residue name field
if substructureNames:
rname = substructureNames[res]
elif resNum:
rname = "%3s%-4d" % (res.type, res.id.position)
else:
rname = "%3s" % res.type
print>>f, rname,
# ID of the root atom of the residue
from chimera.misc import principalAtom
chainAtom = principalAtom(res)
if chainAtom is None:
if hasattr(res, 'atomsMap'):
chainAtom = res.atoms[0]
else:
chainAtom = res.atoms.values()[0][0]
print>>f, "%5d" % atomIndices[chainAtom],
print>>f, "RESIDUE 4",
# Sybyl seems to use chain 'A' when chain ID is blank,
# so run with that
chainID = res.id.chainId
if len(chainID.strip()) != 1:
chainID = 'A'
print>>f, "%s %3s" % (chainID, res.type),
# number of out-of-substructure bonds
crossResBonds = 0
if hasattr(res, "atomsMap"):
atoms = res.atoms
for a in atoms:
for oa in a.bondsMap.keys():
if oa.residue != res:
crossResBonds += 1
else:
atoms = [a for aList in res.atoms.values()
for a in aList]
for a in atoms:
for oa in a.bonds.keys():
if oa.residue != res:
crossResBonds += 1
print>>f, "%5d" % crossResBonds,
# print "ROOT" if first or only residue of a chain
if a.molecule.rootForAtom(a, True).atom.residue == res:
print>>f, "ROOT"
else:
print>>f
# write flexible ligand docking info
if anchor:
if status:
status("writing anchor info")
print>>f, "%s" % SET_HEADER
atomIndices = {}
for i, a in enumerate(ATOM_LIST):
atomIndices[a] = i+1
bondIndices = {}
for i, b in enumerate(BOND_LIST):
bondIndices[b] = i+1
print>>f, "ANCHOR STATIC ATOMS <user> **** Anchor Atom Set"
atoms = anchor.atoms()
print>>f, len(atoms),
for a in atoms:
if a in atomIndices:
print>>f, atomIndices[a],
print>>f
print>>f, "RIGID STATIC BONDS <user> **** Rigid Bond Set"
bonds = anchor.bonds()
print>>f, len(bonds),
for b in bonds:
if b in bondIndices:
print>>f, bondIndices[b],
print>>f
f.close()
def saveSession(filename):
replyobj.status("Initializing session save...", blankAfter=0)
from OpenSave import osOpen, tildeExpand
fullName = tildeExpand(filename)
try:
outf = osOpen(fullName, "w")
except:
replyobj.reportException("Error opening %s for writing" % filename)
return
try:
from cStringIO import StringIO
except ImportError:
from StringIO import StringIO
class SessionIO:
def __init__(self, stringIO, fileName):
self.fileName = fileName
self.stringIO = stringIO()
def __getattr__(self, attrName):
return getattr(self.stringIO, attrName)
buf = SessionIO(StringIO, fullName)
print >> outf, "import cPickle, base64"
print >> outf, "try:"
print >> outf, "\tfrom SimpleSession.versions.v45 import beginRestore,\\"
print >> outf, "\t registerAfterModelsCB, reportRestoreError, checkVersion"
print >> outf, "except ImportError:"
print >> outf, "\tfrom chimera import UserError"
print >> outf, "\traise UserError('Cannot open session that was saved in a'"
print >> outf, "\t ' newer version of Chimera; update your version')"
print >> outf, "checkVersion(%s)" % repr(version.releaseNum)
print >> outf, "import chimera"
print >> outf, "from chimera import replyobj"
print >> outf, "replyobj.status('Beginning session restore...', \\"
print >> outf, " blankAfter=0)"
print >> outf, "beginRestore()"
print >> outf, """
def restoreCoreModels():
\tfrom SimpleSession.versions.v45 import init, restoreViewer, \\
\t restoreMolecules, restoreColors, restoreSurfaces, \\
\t restoreVRML, restorePseudoBondGroups, restoreModelAssociations"""
global _id2color, _color2id
_id2color = {}
_color2id = {}
molecules = [
m for m in chimera.openModels.list(modelTypes=[chimera.Molecule],
all=True) if autoRestorable(m)
]
allSurfaces = chimera.openModels.list(modelTypes=[chimera.MSMSModel])
allVrmls = [
m for m in chimera.openModels.list(modelTypes=[chimera.VRMLModel])
if autoRestorable(m)
]
surfaces = [s for s in allSurfaces if s.molecule]
if surfaces != allSurfaces:
replyobj.warning(
"Cannot save surfaces without associated structure.\nSurface will not be saved.\n"
)
vrmls = []
for v in allVrmls:
source = v.openedAs[0]
if not source.startswith('#VRML')\
and not os.path.exists(source):
replyobj.warning("Source file for VRML model '%s' no"
" longer exists.\nThe model will not be"
" saved.\n" % v.name)
else:
vrmls.append(v)
atoms = []
bonds = []
residues = []
for m in molecules:
atoms.extend(m.atoms)
bonds.extend(m.bonds)
residues.extend(m.residues)
mgr = chimera.PseudoBondMgr.mgr()
pbGroups = []
for g in mgr.pseudoBondGroups:
if g.category.startswith("internal-chain-"):
noAutoRestore(g)
else:
pbGroups.append(g)
pseudobonds = []
pbMap = {}
for pbg in pbGroups:
pbs = [
pb for pb in pbg.pseudoBonds
if autoRestorable(pb.atoms[0].molecule)
and autoRestorable(pb.atoms[1].molecule)
]
pseudobonds.extend(pbs)
pbMap[pbg] = pbs
setSessionIDparams(molecules, residues, atoms, bonds, surfaces, vrmls,
pseudobonds, pbGroups)
replyobj.status("Gathering molecule information...", blankAfter=0)
molInfo = {}
molInfo['ids'] = summarizeVals([(m.id, m.subid) for m in molecules])
molInfo['name'] = summarizeVals([m.name for m in molecules])
molInfo['color'] = summarizeVals([colorID(m.color) for m in molecules])
molInfo['display'] = summarizeVals([m.display for m in molecules])
molInfo['lineWidth'] = summarizeVals([m.lineWidth for m in molecules])
molInfo['pointSize'] = summarizeVals([m.pointSize for m in molecules])
molInfo['stickScale'] = summarizeVals([m.stickScale for m in molecules])
molInfo['pdbHeaders'] = [m.pdbHeaders for m in molecules]
molInfo['surfaceOpacity'] = summarizeVals(
[m.surfaceOpacity for m in molecules])
molInfo['ballScale'] = summarizeVals([m.ballScale for m in molecules])
molInfo['vdwDensity'] = summarizeVals([m.vdwDensity for m in molecules])
molInfo['autochain'] = summarizeVals([m.autochain for m in molecules])
molInfo['ribbonHidesMainchain'] = summarizeVals(
[m.ribbonHidesMainchain for m in molecules])
molInfo['ribbonInsideColor'] = summarizeVals(
[colorID(m.ribbonInsideColor) for m in molecules])
molInfo['aromaticColor'] = summarizeVals(
[colorID(m.aromaticColor) for m in molecules])
molInfo['aromaticDisplay'] = summarizeVals(
[m.aromaticDisplay for m in molecules])
molInfo['aromaticLineType'] = summarizeVals(
[m.aromaticLineType for m in molecules])
molInfo['aromaticMode'] = summarizeVals(
[m.aromaticMode for m in molecules])
molInfo['hidden'] = summarizeVals(
[m in m.openState.hidden for m in molecules])
molInfo['optional'] = saveOptionalAttrs(chimera.Molecule, molecules)
print >> outf, "\tmolInfo =", pickled(molInfo)
replyobj.status("Gathering residue information...", blankAfter=0)
resInfo = {}
resInfo['molecule'] = summarizeVals(
[sessionID(r.molecule) for r in residues], consecutiveExceptions=True)
resInfo['name'] = summarizeVals([r.type for r in residues])
resInfo['chain'] = summarizeVals([r.id.chainId for r in residues],
consecutiveExceptions=True)
resInfo['insert'] = summarizeVals([r.id.insertionCode for r in residues])
resInfo['position'] = summarizeSequentialVals(
[r.id.position for r in residues])
resInfo['ribbonColor'] = summarizeVals(
[colorID(r.ribbonColor) for r in residues], consecutiveExceptions=True)
resInfo['labelColor'] = summarizeVals(
[colorID(r.labelColor) for r in residues], consecutiveExceptions=True)
resInfo['ss'] = summarizeVals([(r.isHelix, r.isStrand, r.isTurn)
for r in residues],
consecutiveExceptions=True)
resInfo['ssId'] = summarizeVals([r.ssId for r in residues],
consecutiveExceptions=True)
resInfo['ribbonDrawMode'] = summarizeVals(
[r.ribbonDrawMode for r in residues], consecutiveExceptions=True)
resInfo['ribbonDisplay'] = summarizeVals(
[r.ribbonDisplay for r in residues], consecutiveExceptions=True)
resInfo['label'] = summarizeVals([r.label for r in residues])
resInfo['labelOffset'] = summarizeVals([r.labelOffset for r in residues])
resInfo['isHet'] = summarizeVals([r.isHet for r in residues],
consecutiveExceptions=True)
resInfo['fillDisplay'] = summarizeVals([r.fillDisplay for r in residues],
consecutiveExceptions=True)
resInfo['fillMode'] = summarizeVals([r.fillMode for r in residues],
consecutiveExceptions=True)
resInfo['optional'] = saveOptionalAttrs(chimera.Residue, residues)
print >> outf, "\tresInfo =", pickled(resInfo)
replyobj.status("Gathering atom information...", blankAfter=0)
atomInfo = {}
atomInfo['altLoc'] = summarizeVals([a.altLoc for a in atoms])
atomInfo['residue'] = summarizeVals([sessionID(a.residue) for a in atoms],
consecutiveExceptions=True)
atomInfo['element'] = summarizeVals([a.element.number for a in atoms])
atomInfo['name'] = summarizeVals([a.name for a in atoms])
atomInfo['color'] = summarizeVals([colorID(a.color) for a in atoms])
atomInfo['vdwColor'] = summarizeVals([colorID(a.vdwColor) for a in atoms])
atomInfo['labelColor'] = summarizeVals(
[colorID(a.labelColor) for a in atoms])
atomInfo['surfaceColor'] = summarizeVals(
[colorID(a.surfaceColor) for a in atoms])
atomInfo['drawMode'] = summarizeVals([a.drawMode for a in atoms],
consecutiveExceptions=True)
atomInfo['display'] = summarizeVals([a.display for a in atoms],
consecutiveExceptions=True)
atomInfo['label'] = summarizeVals([a.label for a in atoms])
atomInfo['labelOffset'] = summarizeVals([a.labelOffset for a in atoms])
atomInfo['radius'] = summarizeVals([a.radius for a in atoms])
atomInfo['surfaceDisplay'] = summarizeVals(
[a.surfaceDisplay for a in atoms], consecutiveExceptions=True)
atomInfo['surfaceCategory'] = summarizeVals(
[a.surfaceCategory for a in atoms], consecutiveExceptions=True)
atomInfo['surfaceOpacity'] = summarizeVals(
[a.surfaceOpacity for a in atoms], consecutiveExceptions=True)
atomInfo['vdw'] = summarizeVals([a.vdw for a in atoms],
consecutiveExceptions=True)
atomInfo['optional'] = saveOptionalAttrs(chimera.Atom, atoms)
# only restore explicitly-set IDATM types...
atomInfo['idatmType'] = summarizeVals([(a.idatmIsExplicit and a.idatmType)
for a in atoms])
print >> outf, "\tatomInfo =", pickled(atomInfo)
replyobj.status("Gathering bond information...", blankAfter=0)
bondInfo = {}
bondInfo['atoms'] = [[sessionID(a) for a in b.atoms] for b in bonds]
bondInfo['drawMode'] = summarizeVals([b.drawMode for b in bonds],
consecutiveExceptions=True)
bondInfo['display'] = summarizeVals([b.display for b in bonds])
bondInfo['label'] = summarizeVals([b.label for b in bonds])
bondInfo['labelOffset'] = summarizeVals([b.labelOffset for b in bonds])
bondInfo['radius'] = summarizeVals([b.radius for b in bonds])
bondInfo['optional'] = saveOptionalAttrs(chimera.Bond, bonds)
print >> outf, "\tbondInfo =", pickled(bondInfo)
replyobj.status("Gathering coordinates...", blankAfter=0)
crdInfo = {}
for m in molecules:
crdSets = {}
crdInfo[sessionID(m)] = crdSets
for key, coordSet in m.coordSets.items():
crdSets[key] = [(sessionID(a), str(a.coord(coordSet)))
for a in m.atoms]
if coordSet == m.activeCoordSet:
crdSets['active'] = key
print >> outf, "\tcrdInfo =", pickled(crdInfo)
replyobj.status("Gathering surface information...", blankAfter=0)
surfInfo = {}
surfInfo['molecule'] = [sessionID(s.molecule) for s in surfaces]
surfInfo['name'] = [s.name for s in surfaces]
surfInfo['customColors'] = surfColors = []
for attrname in ('category', 'colorMode', 'density', 'drawMode', 'display',
'probeRadius', 'allComponents', 'lineWidth', 'pointSize',
'useLighting', 'twoSidedLighting', 'smoothLines',
'transparencyBlendMode', 'oneTransparentLayer'):
values = [getattr(s, attrname) for s in surfaces]
surfInfo[attrname] = summarizeVals(values)
for s in surfaces:
if s.colorMode == chimera.MSMSModel.Custom:
surfColors.append(
summarizeVals([colorID(c) for c in s.customColors]))
else:
surfColors.append(summarizeVals([]))
print >> outf, "\tsurfInfo =", sesRepr(surfInfo)
replyobj.status("Gathering VRML information...", blankAfter=0)
vrmlInfo = {}
vrmlInfo['id'] = summarizeVals([v.id for v in vrmls])
vrmlInfo['subid'] = summarizeVals([v.subid for v in vrmls])
vrmlInfo['name'] = summarizeVals([v.name for v in vrmls])
vrmlInfo['display'] = summarizeVals([v.display for v in vrmls])
vrmlInfo['vrmlString'] = vrmlStrings = []
for v in vrmls:
source = v.openedAs[0]
if source.startswith('#VRML'):
vrmlStrings.append(source)
else:
# source is file name
vrmlFile = open(source, 'r')
vrmlStrings.append(vrmlFile.read())
vrmlFile.close()
print >> outf, "\tvrmlInfo =", sesRepr(vrmlInfo)
replyobj.status("Gathering color information...", blankAfter=0)
# remember all saved colors/materials...
knownColors = {}
knownMaterials = {}
from chimera import _savedColors, _savedMaterials
for name, material in _savedMaterials.items():
knownMaterials[name] = (material.specular, material.shininess)
for name, color in _savedColors.items():
if not isinstance(color, chimera.MaterialColor):
continue
matName = color.material.name()
if matName is None: # unnamed material
matName = "mat" + str(id(color.material))
knownColors[name] = (color.ambientDiffuse, color.opacity, matName)
if matName not in knownMaterials:
mat = color.material
knownMaterials[matName] = (mat.specular, mat.shininess)
print >> outf, "\tcolors =", sesRepr(knownColors)
print >> outf, "\tmaterials =", sesRepr(knownMaterials)
replyobj.status("Gathering pseudobond information...", blankAfter=0)
pbInfo = {}
pbInfo['category'] = [g.category for g in pbGroups]
pbInfo['id'] = [g.id for g in pbGroups]
pbInfo['color'] = summarizeVals([colorID(g.color) for g in pbGroups])
pbInfo['showStubBonds'] = summarizeVals(
[g.showStubBonds for g in pbGroups])
pbInfo['lineWidth'] = summarizeVals([g.lineWidth for g in pbGroups])
pbInfo['stickScale'] = summarizeVals([g.stickScale for g in pbGroups])
pbInfo['lineType'] = summarizeVals([g.lineType for g in pbGroups])
pbInfo['bondInfo'] = pbBondInfos = []
for g in pbGroups:
pbs = pbMap[g]
info = {}
pbBondInfos.append(info)
info['atoms'] = [[sessionID(a) for a in pb.atoms] for pb in pbs]
info['drawMode'] = summarizeVals([pb.drawMode for pb in pbs])
info['display'] = summarizeVals([pb.display for pb in pbs])
info['halfbond'] = summarizeVals([pb.halfbond for pb in pbs])
info['label'] = summarizeVals([pb.label for pb in pbs])
info['color'] = summarizeVals([colorID(pb.color) for pb in pbs])
info['labelColor'] = summarizeVals(
[colorID(pb.labelColor) for pb in pbs])
print >> outf, "\tpbInfo =", sesRepr(pbInfo)
associations = {}
for m in molecules + surfaces + vrmls + pbGroups:
ams = []
for am in m.associatedModels():
if autoRestorable(am):
ams.append(sessionID(am))
if ams:
associations[sessionID(m)] = ams
print >> outf, "\tmodelAssociations =", sesRepr(associations)
replyobj.status("Gathering font information...", blankAfter=0)
from chimera.bgprefs import BACKGROUND, LABEL_FONT
from chimera import preferences
fontInfo = {'face': preferences.getOption(BACKGROUND, LABEL_FONT).get()}
replyobj.status("Gathering clip plane information...", blankAfter=0)
clipPlaneInfo = {}
for m in molecules + surfaces:
if m.useClipPlane:
pl = m.clipPlane
clipPlaneInfo[sessionID(m)] = (pl.origin.data(), pl.normal.data(),
m.useClipThickness, m.clipThickness)
replyobj.status("Gathering selection information...", blankAfter=0)
curSelIds = []
curSel = selection.copyCurrent()
selMols = curSel.molecules()
badMols = filter(lambda m: not autoRestorable(m), selMols)
if badMols:
curSel.remove(badMols)
for a in curSel.atoms():
curSelIds.append(sessionID(a))
for b in curSel.bonds():
curSelIds.append(sessionID(b))
savedSels = []
from copy import copy
for selName, sel in selection.savedSels.items():
badMols = [m for m in sel.molecules() if not autoRestorable(m)]
filtSel = copy(sel)
if badMols:
filtSel.remove(badMols)
ids = []
for a in filtSel.atoms():
ids.append(sessionID(a))
for b in filtSel.bonds():
ids.append(sessionID(b))
savedSels.append((selName, ids))
replyobj.status("Gathering transformation information...", blankAfter=0)
xfDict = {}
for m in (molecules + vrmls):
xf = m.openState.xform
rotV, angle = xf.getRotation()
rot = tuple([float(v) for v in str(rotV).split()])
trans = tuple([float(v) for v in str(xf.getTranslation()).split()])
xfDict[sessionID(m)] = ((rot, angle), trans, m.openState.active)
replyobj.status("Gathering view information...", blankAfter=0)
viewer = chimera.viewer
camera = viewer.camera
viewerAttrs = {}
for va in ("viewSize", "scaleFactor", "clipping", "highlight", "depthCue",
"depthCueRange", "showSilhouette", "silhouetteColor",
"silhouetteWidth"):
if va.endswith("Color"):
viewerAttrs[va] = colorID(getattr(viewer, va))
else:
viewerAttrs[va] = getattr(viewer, va)
cameraAttrs = {}
for ca in ("ortho", "nearFar", "focal", "center", "fieldOfView",
"eyeSeparation"):
cameraAttrs[ca] = getattr(camera, ca)
viewerInfo = {
"detail": chimera.LODControl.get().quality,
"viewerFog": colorID(viewer.depthCueColor),
"viewerBG": colorID(viewer.background),
"viewerHL": colorID(viewer.highlightColor),
"viewerAttrs": viewerAttrs,
"cameraAttrs": cameraAttrs,
"cameraMode": camera.mode(),
}
# start printing into buffer so that color map can be inserted here
replyobj.status("Writing preliminary session info...", blankAfter=0)
print >> buf, "\tviewerInfo =", sesRepr(viewerInfo)
print >> buf, """
\treplyobj.status("Initializing session restore...", blankAfter=0)
\tinit(colorInfo)
\treplyobj.status("Restoring colors...", blankAfter=0)
\trestoreColors(colors, materials)
\treplyobj.status("Restoring molecules...", blankAfter=0)
\trestoreMolecules(molInfo, resInfo, atomInfo, bondInfo, crdInfo)
\treplyobj.status("Restoring surfaces...", blankAfter=0)
\trestoreSurfaces(surfInfo)
\treplyobj.status("Restoring VRML models...", blankAfter=0)
\trestoreVRML(vrmlInfo)
\treplyobj.status("Restoring pseudobond groups...", blankAfter=0)
\trestorePseudoBondGroups(pbInfo)
\treplyobj.status("Restoring model associations...", blankAfter=0)
\trestoreModelAssociations(modelAssociations)
\treplyobj.status("Restoring camera...", blankAfter=0)
\trestoreViewer(viewerInfo)
try:
restoreCoreModels()
except:
reportRestoreError("Error restoring core models")
\treplyobj.status("Restoring extension info...", blankAfter=0)
"""
replyobj.status("Writing extension session info...", blankAfter=0)
chimera.triggers.activateTrigger(SAVE_SESSION, buf)
replyobj.status("Writing remaining session info...", blankAfter=0)
print >> buf, """
def restoreRemainder():
\tfrom SimpleSession.versions.v45 import restoreWindowSize, \\
\t restoreOpenStates, restoreSelections, restoreFontInfo, \\
\t restoreOpenModelsAttrs, restoreModelClip
"""
# any use of colors below have to have those colors also run through
# colorID() before init() gets printed, so that the color map contains
# those colors
print >> buf, "\tcurSelIds = ", sesRepr(curSelIds)
print >> buf, "\tsavedSels =", sesRepr(savedSels)
print >> buf, "\topenModelsAttrs = { 'cofrMethod': %d }" % (
chimera.openModels.cofrMethod)
if chimera.openModels.cofrMethod == chimera.openModels.Fixed:
cofr = chimera.openModels.cofr
print >> buf, "\tfrom chimera import Point"
print>> buf, "\topenModelsAttrs['cofr'] = Point(%g, %g, %g)" \
% (cofr.x, cofr.y, cofr.z)
print >> buf, "\twindowSize =", sesRepr(chimera.viewer.windowSize)
print >> buf, "\txformMap =", sesRepr(xfDict)
print >> buf, "\tfontInfo =", sesRepr(fontInfo)
print >> buf, "\tclipPlaneInfo =", sesRepr(clipPlaneInfo)
print >> buf, """
\treplyobj.status("Restoring window...", blankAfter=0)
\trestoreWindowSize(windowSize)
\treplyobj.status("Restoring open states...", blankAfter=0)
\trestoreOpenStates(xformMap)
\treplyobj.status("Restoring font info...", blankAfter=0)
\trestoreFontInfo(fontInfo)
\treplyobj.status("Restoring selections...", blankAfter=0)
\trestoreSelections(curSelIds, savedSels)
\treplyobj.status("Restoring openModel attributes...", blankAfter=0)
\trestoreOpenModelsAttrs(openModelsAttrs)
\treplyobj.status("Restoring model clipping...", blankAfter=0)
\trestoreModelClip(clipPlaneInfo)
\treplyobj.status("Restoring remaining extension info...", blankAfter=0)
try:
restoreRemainder()
except:
reportRestoreError("Error restoring post-model state")
from SimpleSession.versions.v45 import makeAfterModelsCBs
makeAfterModelsCBs()
"""
print >> buf, "from SimpleSession.versions.v45 import endRestore"
print >> buf, "replyobj.status('Finishing restore...', blankAfter=0)"
print >> buf, "endRestore()"
print >> buf, "replyobj.status('Restore finished.')"
# insert color map
print >> outf, "\tcolorInfo =", sesRepr(_id2color)
# print buffered output
print >> outf, buf.getvalue()
buf.close()
outf.close()
from versions import globals
del globals.sessionMap
_id2color = _color2id = None
replyobj.status("Session written")
def readPBinfo(fileName, category=None, clearCategory=1, lineWidth=None,
drawMode=None, leftModel=None, rightModel=None, defColor=None):
"""read a file containing pseudobond info and display those bonds
'category' defaults to 'fileName'. 'clearCategory' controls
whether the pseudobond group should be cleared of pre-existing
pseudobonds before reading the file. 'lineWidth' is a floating-
point number and controls the width of lines used to draw the
pseudobonds. This only is relevant if 'drawMode' is Wire.
'drawMode' controls the depiction style of the pseudobonds.
Possible modes are:
Wire (aka chimera.Bond_Wire) -- wireframe
Stick (aka chimera.Bond_Stick) -- sticks
'leftModel' and 'rightModel' control what models the endpoints
of the pseudobond lie in, if none are specified in the input file.
'defColor' is the color assigned to the pseudobond group as a whole,
which can be overridden by specific pseudobonds.
"""
foundErrors = False
colorCache = {}
if not category:
category = fileName
group = chimera.misc.getPseudoBondGroup(category)
if lineWidth:
group.lineWidth = lineWidth
if drawMode:
group.drawMode = drawMode
if clearCategory:
group.deleteAll()
if defColor:
if isinstance(defColor, basestring):
c = chimera.Color.lookup(defColor)
if not c:
replyobj.message(
"Cannot find color '%s'\n" % defColor)
foundErrors = True
else:
c = defColor
group.color = c
from OpenSave import osOpen
bondFile = osOpen(fileName)
lineNum = 0
for line in bondFile.readlines():
line = line.strip()
lineNum = lineNum + 1
if not line:
# blank line
continue
try:
spec1, spec2, color = line.split(None, 2)
except:
label = color = None
try:
spec1, spec2 = line.split()
except ValueError:
replyobj.message("Line %d does not have at"
" least two atom specifiers.")
foundErrors = True
continue
if color:
# try to distinguish between color name and label
try:
color, label = color.split(None, 1)
except:
label = None
if color[0] != "#":
while (label and not colors.has_key(color)):
try:
c, label = label.split(None, 1)
except:
color = " ".join([color, label])
label = None
else:
color = " ".join([color, c])
atom1 = _processSpec(spec1, leftModel)
if not atom1:
replyobj.message(
"Left atom spec of line %d of file doesn't"
" select exactly one atom."
" Skipping.\n" % lineNum)
foundErrors = True
continue
atom2 = _processSpec(spec2, leftModel)
if not atom2:
replyobj.message(
"Right atom spec of line %d of file doesn't"
" select exactly one atom."
" Skipping.\n" % lineNum)
foundErrors = True
continue
if color:
if color[0] == '#':
fieldLen = int((len(color) - 1) / 3)
if 3 * fieldLen + 1 != len(color):
replyobj.message("Bad Tk color '%s'"
" on line %d of file.\n"
% (color, lineNum))
foundErrors = True
elif colorCache.has_key(color):
color = colorCache[color]
else:
r = color[1:1+fieldLen]
g = color[1+fieldLen:1+2*fieldLen]
b = color[1+2*fieldLen:]
r = int(r, 16)
g = int(g, 16)
b = int(b, 16)
maxVal = int('f' * fieldLen, 16)
maxVal = float(maxVal)
c = chimera.MaterialColor(r/maxVal,
g/maxVal, b/maxVal)
colorCache[color] = c
color = c
else:
try:
color = getColorByName(color)
except KeyError:
replyobj.message(
"Unknown color '%s' on line %d"
" of file.\n" % (color,lineNum))
foundErrors = True
color = None
pb = group.newPseudoBond(atom1, atom2)
if color:
pb.color = color
if label:
pb.label = label
bondFile.close()
if foundErrors:
chimera.replyobj.error(
"Errors encountered while reading file.\n"
"Check reply log for details.\n")
def readFiles(fileNames, clear=True):
if not _ilabelModel:
IlabelModel()
if clear:
for label in _ilabelModel.labels[:]:
_ilabelModel.removeLabel(label)
_ilabelModel.setMajorChange()
from chimera import UserError
for fileName in fileNames:
from OpenSave import osOpen
f = osOpen(fileName)
label = labelID = text = None
for ln, line in enumerate(f):
lineNum = ln + 1
if not line.strip() or line.strip().startswith('#'):
# skip blank lines / comments
continue
if line.lower().startswith("label"):
labelID = line[5:].strip()
continue
if line[0] != '\t':
f.close()
raise UserError("%s, line %d: line must start with 'Label'"
" or tab" % (fileName, lineNum))
try:
semi = line.index(':')
except ValueError:
f.close()
raise UserError("%s, line %d: line must have semi-colon" %
(fileName, lineNum))
name = line[1:semi].lower()
if not label and name != "(x,y)":
f.close()
raise UserError("%s, line %d: xy position must immediately"
" follow 'Label' line" % (fileName, lineNum))
if label and text is None and name != "text":
f.close()
raise UserError("%s, line %d: text must immediately"
" follow xy position" % (fileName, lineNum))
value = line[semi + 1:].strip()
if name == "(x,y)":
text = None
try:
pos = eval(value)
except:
f.close()
raise UserError("%s, line %d: could not parse xy value" %
(fileName, lineNum))
if labelID:
label = _ilabelModel.newLabel(pos)
else:
label = _ilabelModel.newLabel(pos, labelID=labelID)
elif name == "text":
try:
text = eval(value)
except:
f.close()
_ilabelModel.removeLabel(label)
raise UserError(
"%s, line %d: could not parse 'text' value" %
(fileName, lineNum))
label.set(text)
elif name == "shown":
if name == "shown":
try:
label.shown = eval(value.capitalize())
except:
f.close()
_ilabelModel.removeLabel(label)
raise UserError("%s, line %d: could not parse 'shown'"
" value" % (fileName, lineNum))
else:
chars = []
for l in label.lines:
chars.extend(l)
if '),' in value:
values = value.split('),')
for i, v in enumerate(values[:-1]):
values[i] = v + ')'
elif ',' in value and not value.strip().startswith('('):
values = value.split(',')
else:
values = [value] * len(chars)
if len(values) != len(chars):
f.close()
raise UserError(
"%s, line %d: number of values not equal"
" to numbers of characters in text (and not a single"
" value)" % (fileName, lineNum))
if name.startswith("font size"):
try:
values = [eval(v) for v in values]
except:
f.close()
_ilabelModel.removeLabel(label)
raise UserError("%s, line %d: could not parse"
" 'font size' value(s)" %
(fileName, lineNum))
for c, v in zip(chars, values):
c.size = v
elif name.startswith("font style"):
for c, v in zip(chars, values):
try:
c.style = styleLookup(v.strip().lower())
except:
f.close()
_ilabelModel.removeLabel(label)
raise UserError("%s, line %d: could not parse"
" 'font style' value(s)" %
(fileName, lineNum))
elif name.startswith("font typeface"):
for c, v in zip(chars, values):
try:
c.fontName = typefaceLookup(v.strip().lower())
except:
f.close()
_ilabelModel.removeLabel(label)
raise UserError("%s, line %d: could not parse"
" 'font typeface' value(s)" %
(fileName, lineNum))
elif name.startswith("color"):
try:
values = [eval(v) for v in values]
except:
f.close()
_ilabelModel.removeLabel(label)
raise UserError("%s, line %d: could not parse"
" 'color' value(s)" %
(fileName, lineNum))
for c, v in zip(chars, values):
c.rgba = v
else:
_ilabelModel.removeLabel(label)
raise UserError(
"%s, line %d: unknown label attribute '%s'" %
(fileName, lineNum, name))
f.close()
if chimera.nogui:
dlg = None
else:
from gui import IlabelDialog
from chimera import dialogs
dlg = dialogs.find(IlabelDialog.name)
if dlg:
dlg.updateGUI("file")
def readFiles(fileNames, clear=True):
if not _ilabelModel:
IlabelModel()
if clear:
for label in _ilabelModel.labels[:]:
_ilabelModel.removeLabel(label)
_ilabelModel.setMajorChange()
from chimera import UserError
for fileName in fileNames:
from OpenSave import osOpen
f = osOpen(fileName)
label = labelID = text = None
for ln, line in enumerate(f):
lineNum = ln + 1
if not line.strip() or line.strip().startswith('#'):
# skip blank lines / comments
continue
if line.lower().startswith("label"):
labelID = line[5:].strip()
continue
if line[0] != '\t':
f.close()
raise UserError("%s, line %d: line must start with 'Label'"
" or tab" % (fileName, lineNum))
try:
semi = line.index(':')
except ValueError:
f.close()
raise UserError("%s, line %d: line must have semi-colon"
% (fileName, lineNum))
name = line[1:semi].lower()
if not label and name != "(x,y)":
f.close()
raise UserError("%s, line %d: xy position must immediately"
" follow 'Label' line" % (fileName, lineNum))
if label and text is None and name != "text":
f.close()
raise UserError("%s, line %d: text must immediately"
" follow xy position" % (fileName, lineNum))
value = line[semi+1:].strip()
if name == "(x,y)":
text = None
try:
pos = eval(value)
except:
f.close()
raise UserError("%s, line %d: could not parse xy value"
% (fileName, lineNum))
if labelID:
label = _ilabelModel.newLabel(pos)
else:
label = _ilabelModel.newLabel(pos, labelID=labelID)
elif name == "text":
try:
text = eval(value)
except:
f.close()
_ilabelModel.removeLabel(label)
raise UserError("%s, line %d: could not parse 'text' value"
% (fileName, lineNum))
label.set(text)
elif name == "shown":
if name == "shown":
try:
label.shown = eval(value.capitalize())
except:
f.close()
_ilabelModel.removeLabel(label)
raise UserError("%s, line %d: could not parse 'shown'"
" value" % (fileName, lineNum))
else:
chars = []
for l in label.lines:
chars.extend(l)
if '),' in value:
values = value.split('),')
for i, v in enumerate(values[:-1]):
values[i] = v + ')'
elif ',' in value and not value.strip().startswith('('):
values = value.split(',')
else:
values = [value] * len(chars)
if len(values) != len(chars):
f.close()
raise UserError("%s, line %d: number of values not equal"
" to numbers of characters in text (and not a single"
" value)" % (fileName, lineNum))
if name.startswith("font size"):
try:
values = [eval(v) for v in values]
except:
f.close()
_ilabelModel.removeLabel(label)
raise UserError("%s, line %d: could not parse"
" 'font size' value(s)" % (fileName, lineNum))
for c, v in zip(chars, values):
c.size = v
elif name.startswith("font style"):
for c, v in zip(chars, values):
try:
c.style = styleLookup(v.strip().lower())
except:
f.close()
_ilabelModel.removeLabel(label)
raise UserError("%s, line %d: could not parse"
" 'font style' value(s)" % (fileName, lineNum))
elif name.startswith("font typeface"):
for c, v in zip(chars, values):
try:
c.fontName = typefaceLookup(v.strip().lower())
except:
f.close()
_ilabelModel.removeLabel(label)
raise UserError("%s, line %d: could not parse"
" 'font typeface' value(s)" %
(fileName, lineNum))
elif name.startswith("color"):
try:
values = [eval(v) for v in values]
except:
f.close()
_ilabelModel.removeLabel(label)
raise UserError("%s, line %d: could not parse"
" 'color' value(s)" % (fileName, lineNum))
for c, v in zip(chars, values):
c.rgba = v
else:
_ilabelModel.removeLabel(label)
raise UserError("%s, line %d: unknown label attribute '%s'"
% (fileName, lineNum, name))
f.close()
if chimera.nogui:
dlg = None
else:
from gui import IlabelDialog
from chimera import dialogs
dlg = dialogs.find(IlabelDialog.name)
if dlg:
dlg.updateGUI("file")
def readPBinfo(fileName,
category=None,
clearCategory=1,
lineWidth=None,
drawMode=None,
leftModel=None,
rightModel=None,
defColor=None):
"""read a file containing pseudobond info and display those bonds
'category' defaults to 'fileName'. 'clearCategory' controls
whether the pseudobond group should be cleared of pre-existing
pseudobonds before reading the file. 'lineWidth' is a floating-
point number and controls the width of lines used to draw the
pseudobonds. This only is relevant if 'drawMode' is Wire.
'drawMode' controls the depiction style of the pseudobonds.
Possible modes are:
Wire (aka chimera.Bond_Wire) -- wireframe
Stick (aka chimera.Bond_Stick) -- sticks
'leftModel' and 'rightModel' control what models the endpoints
of the pseudobond lie in, if none are specified in the input file.
'defColor' is the color assigned to the pseudobond group as a whole,
which can be overridden by specific pseudobonds.
"""
foundErrors = False
colorCache = {}
if not category:
category = fileName
group = chimera.misc.getPseudoBondGroup(category)
if lineWidth:
group.lineWidth = lineWidth
if drawMode:
group.drawMode = drawMode
if clearCategory:
group.deleteAll()
if defColor:
if isinstance(defColor, basestring):
c = chimera.Color.lookup(defColor)
if not c:
replyobj.message("Cannot find color '%s'\n" % defColor)
foundErrors = True
else:
c = defColor
group.color = c
from OpenSave import osOpen
bondFile = osOpen(fileName)
lineNum = 0
for line in bondFile.readlines():
line = line.strip()
lineNum = lineNum + 1
if not line:
# blank line
continue
try:
spec1, spec2, color = line.split(None, 2)
except:
label = color = None
try:
spec1, spec2 = line.split()
except ValueError:
replyobj.message("Line %d does not have at"
" least two atom specifiers.")
foundErrors = True
continue
if color:
# try to distinguish between color name and label
try:
color, label = color.split(None, 1)
except:
label = None
if color[0] != "#":
while (label and not colors.has_key(color)):
try:
c, label = label.split(None, 1)
except:
color = " ".join([color, label])
label = None
else:
color = " ".join([color, c])
atom1 = _processSpec(spec1, leftModel)
if not atom1:
replyobj.message("Left atom spec of line %d of file doesn't"
" select exactly one atom."
" Skipping.\n" % lineNum)
foundErrors = True
continue
atom2 = _processSpec(spec2, leftModel)
if not atom2:
replyobj.message("Right atom spec of line %d of file doesn't"
" select exactly one atom."
" Skipping.\n" % lineNum)
foundErrors = True
continue
if color:
if color[0] == '#':
fieldLen = int((len(color) - 1) / 3)
if 3 * fieldLen + 1 != len(color):
replyobj.message("Bad Tk color '%s'"
" on line %d of file.\n" %
(color, lineNum))
foundErrors = True
elif colorCache.has_key(color):
color = colorCache[color]
else:
r = color[1:1 + fieldLen]
g = color[1 + fieldLen:1 + 2 * fieldLen]
b = color[1 + 2 * fieldLen:]
r = int(r, 16)
g = int(g, 16)
b = int(b, 16)
maxVal = int('f' * fieldLen, 16)
maxVal = float(maxVal)
c = chimera.MaterialColor(r / maxVal, g / maxVal,
b / maxVal)
colorCache[color] = c
color = c
else:
try:
color = getColorByName(color)
except KeyError:
replyobj.message("Unknown color '%s' on line %d"
" of file.\n" % (color, lineNum))
foundErrors = True
color = None
pb = group.newPseudoBond(atom1, atom2)
if color:
pb.color = color
if label:
pb.label = label
bondFile.close()
if foundErrors:
chimera.replyobj.error("Errors encountered while reading file.\n"
"Check reply log for details.\n")
def loadEnsemble(inputs, startFrame, endFrame, callback, relativeTo=None):
from chimera import replyobj
style = inputs[0]
files = inputs[1:]
if relativeTo:
for i, f in enumerate(files):
if not isinstance(f, basestring) or os.path.isabs(f):
continue
files[i] = os.path.join(relativeTo, f)
if style.lower().startswith("multiple"):
startFile, endFile = files
errMsg = "Can't determine numeric sequence from starting file name (%s) to ending file name (%s)" % (startFile, endFile)
for i, c in enumerate(startFile):
if i >= len(endFile):
raise ValueError(errMsg)
if endFile[i] != c:
break
else:
raise ValueError(errMsg)
# push trailing digits on the prefix back into the number part,
# otherwise ranges like 1-100 are bug problems
while i > 0 and startFile[i-1].isdigit():
i -= 1
prefixIndex = i
prefix = startFile[:i]
while i < len(startFile) and startFile[i].isdigit():
i += 1
startSuffixIndex = i
endSuffixIndex = i + len(endFile) - len(startFile)
suffix = startFile[startSuffixIndex:]
replyobj.status("Collating PDB files\n", blankAfter=0)
first = int(startFile[prefixIndex:startSuffixIndex])
if first < 1:
offset = 1 - first
first += offset
replyobj.info("Adjusting frame numbers to start at 1\n")
else:
offset = 0
try:
last = int(endFile[prefixIndex:endSuffixIndex]) + offset
except ValueError:
raise ValueError("Last file name not similar to first"
" file name\nCan't determine numeric sequence")
if startFrame is None:
startFrame = first
elif startFrame < first:
replyobj.error("Starting frame (%d) less than first"
" file's frame (%d); using the latter\n"
% (startFrame, first))
startFrame = first
if endFrame is None:
endFrame = last
elif endFrame > last:
replyobj.error("Ending frame (%d) greater than last"
" file's frame (%d); using the latter\n"
% (endFrame, last))
endFrame = last
if startFrame > endFrame:
raise ValueError("Start frame > end frame")
addMODEL = True
sf = file(startFile, "r")
for line in sf:
if line.startswith("MODEL"):
addMODEL = False
break
if line.strip() == "END":
raise ValueError("PDB files must not contain"
" END records")
sf.close()
from tempfile import mkstemp
(handle, trajFile) = mkstemp(suffix=".pdb")
os.close(handle)
collation = open(trajFile, "w")
zeroPad = len(startFile) == len(endFile)
for f in range(startFrame, endFrame+1):
if addMODEL:
print>>collation, "MODEL %8d" % f
if zeroPad:
fname = prefix + "%0*d" % (startSuffixIndex
- prefixIndex, f-offset) + suffix
else:
fname = prefix + "%d" % (f-offset) + suffix
replyobj.status("Collating file %s\n" % fname,
blankAfter=0)
try:
frameFile = open(fname, "r")
except IOError:
collation.close()
os.unlink(trajFile)
raise
collation.write(frameFile.read())
frameFile.close()
if addMODEL:
print>>collation, "ENDMDL"
collation.close()
replyobj.status("Done collating PDB files\n")
else:
trajFile = files[0]
class PdbTraj:
def __len__(self):
return len(self.molecule.coordSets)
ensemble = PdbTraj()
ensemble.name = "PDB trajectory from %s" % os.path.basename(files[0])
ensemble.startFrame = startFrame
ensemble.endFrame = endFrame
from chimera import PDBio
pdbio = PDBio()
pdbio.explodeNMR = False
replyobj.status("Reading PDB trajectory\n", blankAfter=0)
# allow for compression...
from OpenSave import osOpen
pdbStream = osOpen(trajFile)
traj, lineNum = pdbio.readPDBstream(pdbStream, trajFile, 0)
pdbStream.close()
replyobj.status("Done reading PDB trajectory\n")
if style == "multiple files":
os.unlink(trajFile)
ensemble.name += "..."
if not pdbio.ok():
raise ValueError(pdbio.error())
elif not traj:
raise ValueError("No structures in the PDB file!")
else:
traj = traj[0]
if len(traj.coordSets) < 2:
raise ValueError("The PDB file contains only one structure")
ensemble.molecule = traj
traj.name = os.path.basename(files[0])
replyobj.status("Creating interface\n", blankAfter=0)
try:
callback(ensemble)
finally:
replyobj.status("Interface created\n")
def writeMol2(models,
fileName,
status=None,
anchor=None,
relModel=None,
hydNamingStyle="sybyl",
multimodelHandling="individual",
skip=None,
resNum=True,
gaffType=False,
gaffFailError=None):
"""Write a Mol2 file.
'models' are the models to write out into a file named 'fileName'.
'status', if not None, is a function that takes a string -- used
to report the progress of the write.
'anchor' is a selection (i.e. instance of a subclass of
chimera.selection.Selection) containing atoms/bonds that should
be written out to the @SETS section of the file as the rigid
framework for flexible ligand docking.
'hydNamingStyle' controls whether hydrogen names should be
"Sybyl-like" (value: sybyl) or "PDB-like" (value: pdb)
-- e.g. HG21 vs. 1HG2.
'multimodelHandling' controls whether multiple models will be
combined into a single @MOLECULE section (value: combined) or
each given its own section (value: individual).
'skip' is a list of atoms to not output
'resNum' controls whether residue sequence numbers are included
in the substructure name. Since Sybyl Mol2 files include them,
this defaults to True.
If 'gaffType' is True, outout GAFF atom types instead of Sybyl
atom types. 'gaffFailError', if specified, is the type of error
to throw (e.g. UserError) if there is no gaffType attribute for
an atom, otherwise throw the standard AttributeError.
"""
# open the given file name for writing
from OpenSave import osOpen
f = osOpen(fileName, "w")
sortFunc = serialSort = lambda a1, a2: cmp(a1.coordIndex, a2.coordIndex)
if isinstance(models, chimera.Molecule):
models = [models]
elif isinstance(models, Selection):
# create a fictitious jumbo model
if isinstance(models, ItemizedSelection):
sel = models
else:
sel = ItemizedSelection()
sel.merge(models)
sel.addImplied()
class Jumbo:
def __init__(self, sel):
self.atoms = sel.atoms()
self.residues = sel.residues()
self.bonds = sel.bonds()
self.name = "(selection)"
models = [Jumbo(sel)]
sortFunc = lambda a1, a2: cmp(a1.molecule.id, a2.molecule.id) \
or cmp(a1.molecule.subid, a2.molecule.subid) \
or serialSort(a1, a2)
multimodelHandling = "individual"
# transform...
if relModel is None:
xform = chimera.Xform.identity()
else:
xform = relModel.openState.xform
xform.invert()
# need to find amide moieties since Sybyl has an explicit amide type
if status:
status("Finding amides\n")
from ChemGroup import findGroup
amides = findGroup("amide", models)
amideNs = dict.fromkeys([amide[2] for amide in amides])
amideCNs = dict.fromkeys([amide[0] for amide in amides])
amideCNs.update(amideNs)
amideOs = dict.fromkeys([amide[1] for amide in amides])
substructureNames = None
if multimodelHandling == "combined":
# create a fictitious jumbo model
class Jumbo:
def __init__(self, models):
self.atoms = []
self.residues = []
self.bonds = []
self.name = models[0].name + " (combined)"
for m in models:
self.atoms.extend(m.atoms)
self.residues.extend(m.residues)
self.bonds.extend(m.bonds)
# if combining single-residue models,
# can be more informative to use model name
# instead of residue type for substructure
if len(models) == len(self.residues):
rtypes = [r.type for r in self.residues]
if len(set(rtypes)) < len(rtypes):
mnames = [m.name for m in models]
if len(set(mnames)) == len(mnames):
self.substructureNames = dict(
zip(self.residues, mnames))
models = [Jumbo(models)]
if hasattr(models[-1], 'substructureNames'):
substructureNames = models[-1].substructureNames
delattr(models[-1], 'substructureNames')
sortFunc = lambda a1, a2: cmp(a1.molecule.id, a2.molecule.id) \
or cmp(a1.molecule.subid, a2.molecule.subid) \
or serialSort(a1, a2)
# write out models
for mol in models:
if hasattr(mol, 'mol2comments'):
for m2c in mol.mol2comments:
print >> f, m2c
if hasattr(mol, 'solventInfo'):
print >> f, mol.solventInfo
# molecule section header
print >> f, "%s" % MOLECULE_HEADER
# molecule name
print >> f, "%s" % mol.name
ATOM_LIST = mol.atoms
BOND_LIST = mol.bonds
if skip:
skip = set(skip)
ATOM_LIST = [a for a in ATOM_LIST if a not in skip]
BOND_LIST = [
b for b in BOND_LIST
if b.atoms[0] not in skip and b.atoms[1] not in skip
]
RES_LIST = mol.residues
# Chimera has an unusual internal order for its atoms, so
# sort them by input order
if status:
status("Putting atoms in input order")
ATOM_LIST.sort(sortFunc)
# if anchor is not None, then there will be two entries in
# the @SETS section of the file...
if anchor:
sets = 2
else:
sets = 0
# number of entries for various sections...
print >> f, "%d %d %d 0 %d" % (len(ATOM_LIST), len(BOND_LIST),
len(RES_LIST), sets)
# type of molecule
if hasattr(mol, "mol2type"):
mtype = mol.mol2type
else:
mtype = "SMALL"
from chimera.resCode import nucleic3to1, protein3to1
for r in mol.residues:
if r.type in protein3to1:
mtype = "PROTEIN"
break
if r.type in nucleic3to1:
mtype = "NUCLEIC_ACID"
break
print >> f, mtype
# indicate type of charge information
if hasattr(mol, 'chargeModel'):
print >> f, mol.chargeModel
else:
print >> f, "NO_CHARGES"
if hasattr(mol, 'mol2comment'):
print >> f, "\n%s" % mol.mol2comment
else:
print >> f, "\n"
if status:
status("writing atoms\n")
# atom section header
print >> f, "%s" % ATOM_HEADER
# make a dictionary of residue indices so that we can do
# quick look ups
resIndices = {}
for i, r in enumerate(RES_LIST):
resIndices[r] = i + 1
for i, atom in enumerate(ATOM_LIST):
# atom ID, starting from 1
print >> f, "%7d" % (i + 1),
# atom name, possibly rearranged if it's a hydrogen
if hydNamingStyle == "sybyl" \
and not atom.name[0].isalpha():
atomName = atom.name[1:] + atom.name[0]
else:
atomName = atom.name
print >> f, "%-8s" % atomName,
# untransformed coordinate position
coord = xform.apply(atom.xformCoord())
print >> f, "%9.4f %9.4f %9.4f" % (coord.x, coord.y, coord.z),
# atom type
if gaffType:
try:
atomType = atom.gaffType
except AttributeError:
if not gaffFailError:
raise
raise gaffFailError(
"%s has no Amber/GAFF type assigned.\n"
"Use the AddCharge tool to assign Amber/GAFF types." %
atom)
elif hasattr(atom, 'mol2type'):
atomType = atom.mol2type
elif atom in amideNs:
atomType = "N.am"
elif atom.residue.id.chainId == "water":
if atom.element.name == "O":
atomType = "O.t3p"
else:
atomType = "H.t3p"
elif atom.element.name == "N" and len(
[r for r in atom.minimumRings() if r.aromatic()]) > 0:
atomType = "N.ar"
elif atom.idatmType == "C2" and len(
[nb for nb in atom.neighbors if nb.idatmType == "Ng+"]) > 2:
atomType = "C.cat"
else:
try:
atomType = chimera2sybyl[atom.idatmType]
except KeyError:
chimera.replyobj.warning("Atom whose"
" IDATM type has no equivalent"
" Sybyl type: %s (type: %s)\n" %
(atom.oslIdent(), atom.idatmType))
atomType = str(atom.element)
print >> f, "%-5s" % atomType,
# residue-related info
res = atom.residue
# residue index
print >> f, "%5d" % resIndices[res],
# substructure identifier and charge
if hasattr(atom, 'charge'):
charge = atom.charge
else:
charge = 0.0
if substructureNames:
rname = substructureNames[res]
elif resNum:
rname = "%3s%-5d" % (res.type, res.id.position)
else:
rname = "%3s" % res.type
print >> f, "%s %9.4f" % (rname, charge)
if status:
status("writing bonds\n")
# bond section header
print >> f, "%s" % BOND_HEADER
# make an atom-index dictionary to speed lookups
atomIndices = {}
for i, a in enumerate(ATOM_LIST):
atomIndices[a] = i + 1
for i, bond in enumerate(BOND_LIST):
a1, a2 = bond.atoms
# ID
print >> f, "%6d" % (i + 1),
# atom IDs
print >> f, "%4d %4d" % (atomIndices[a1], atomIndices[a2]),
# bond order; give it our best shot...
amideA1 = a1 in amideCNs
amideA2 = a2 in amideCNs
if amideA1 and amideA2:
print >> f, "am"
continue
if amideA1 or amideA2:
if a1 in amideOs or a2 in amideOs:
print >> f, "2"
else:
print >> f, "1"
continue
aromatic = False
for ring in bond.minimumRings():
if ring.aromatic():
aromatic = True
break
if aromatic:
print >> f, "ar"
continue
try:
geom1 = typeInfo[a1.idatmType].geometry
except KeyError:
print >> f, "1"
continue
try:
geom2 = typeInfo[a2.idatmType].geometry
except KeyError:
print >> f, "1"
continue
if geom1 not in [2, 3] or geom2 not in [2, 3]:
print >> f, "1"
continue
# if either endpoint atom is in an aromatic ring and
# the bond isn't, it's a single bond...
for endp in [a1, a2]:
aromatic = False
for ring in endp.minimumRings():
if ring.aromatic():
aromatic = True
break
if aromatic:
break
else:
# neither endpoint in aromatic ring
print >> f, "2"
continue
print >> f, "1"
if status:
status("writing residues")
# residue section header
print >> f, "%s" % SUBSTR_HEADER
for i, res in enumerate(RES_LIST):
# residue id field
print >> f, "%6d" % (i + 1),
# residue name field
if substructureNames:
rname = substructureNames[res]
elif resNum:
rname = "%3s%-4d" % (res.type, res.id.position)
else:
rname = "%3s" % res.type
print >> f, rname,
# ID of the root atom of the residue
from chimera.misc import principalAtom
chainAtom = principalAtom(res)
if chainAtom is None:
if hasattr(res, 'atomsMap'):
chainAtom = res.atoms[0]
else:
chainAtom = res.atoms.values()[0][0]
print >> f, "%5d" % atomIndices[chainAtom],
print >> f, "RESIDUE 4",
# Sybyl seems to use chain 'A' when chain ID is blank,
# so run with that
chainID = res.id.chainId
if len(chainID.strip()) != 1:
chainID = 'A'
print >> f, "%s %3s" % (chainID, res.type),
# number of out-of-substructure bonds
crossResBonds = 0
if hasattr(res, "atomsMap"):
atoms = res.atoms
for a in atoms:
for oa in a.bondsMap.keys():
if oa.residue != res:
crossResBonds += 1
else:
atoms = [a for aList in res.atoms.values() for a in aList]
for a in atoms:
for oa in a.bonds.keys():
if oa.residue != res:
crossResBonds += 1
print >> f, "%5d" % crossResBonds,
# print "ROOT" if first or only residue of a chain
if a.molecule.rootForAtom(a, True).atom.residue == res:
print >> f, "ROOT"
else:
print >> f
# write flexible ligand docking info
if anchor:
if status:
status("writing anchor info")
print >> f, "%s" % SET_HEADER
atomIndices = {}
for i, a in enumerate(ATOM_LIST):
atomIndices[a] = i + 1
bondIndices = {}
for i, b in enumerate(BOND_LIST):
bondIndices[b] = i + 1
print >> f, "ANCHOR STATIC ATOMS <user> **** Anchor Atom Set"
atoms = anchor.atoms()
print >> f, len(atoms),
for a in atoms:
if a in atomIndices:
print >> f, atomIndices[a],
print >> f
print >> f, "RIGID STATIC BONDS <user> **** Rigid Bond Set"
bonds = anchor.bonds()
print >> f, len(bonds),
for b in bonds:
if b in bondIndices:
print >> f, bondIndices[b],
print >> f
f.close()
def readSDF(fileName, identifyAs=None):
from OpenSave import osOpen
from chimera import UserError, Molecule, Element, openModels, replyobj
from chimera import Coord
state = "init"
f = osOpen(fileName)
mols = []
nonblank = False
for l in f:
line = l.strip()
nonblank = nonblank or line
if state == "init":
state = "post header 1"
molName = line
elif state == "post header 1":
state = "post header 2"
elif state == "post header 2":
state = "counts"
elif state == "counts":
if not line:
break
state = "atoms"
serial = 1
anums = {}
atoms = []
try:
numAtoms = int(l[:3].strip())
numBonds = int(l[3:6].strip())
except ValueError:
raise UserError("Atom/bond counts line of"
" MOL/SDF file '%s' is botched: '%s'" %
(fileName, l))
m = Molecule()
mols.append(m)
if identifyAs:
m.name = identifyAs
else:
from chimera.misc import isInformativeName
mn = molName.strip()
if isInformativeName(mn):
m.name = mn
else:
import os.path
m.name = os.path.split(fileName)[-1]
r = m.newResidue("UNK", " ", 1, " ")
elif state == "atoms":
numAtoms -= 1
if numAtoms == 0:
if numBonds:
state = "bonds"
else:
state = "properties"
try:
x = float(l[:10].strip())
y = float(l[10:20].strip())
z = float(l[21:30].strip())
elem = l[31:34].strip()
except ValueError:
raise UserError("Atom line of MOL/SDF file"
" '%s' is not x y z element...: '%s'" %
(fileName, l))
element = Element(elem)
if element.number == 0:
# lone pair or somesuch
atoms.append(None)
continue
anum = anums.get(element.name, 0) + 1
anums[element.name] = anum
a = m.newAtom("%s%d" % (element.name, anum), element)
atoms.append(a)
r.addAtom(a)
a.setCoord(Coord(x, y, z))
a.serialNumber = serial
serial += 1
elif state == "bonds":
numBonds -= 1
if numBonds == 0:
state = "properties"
try:
a1index = int(l[:3].strip())
a2index = int(l[3:6].strip())
order = int(l[6:9].strip())
except ValueError:
raise UserError("Bond line of MOL/SDF file"
" '%s' is not a1 a2 order...: '%s'" %
(fileName, l))
a1 = atoms[a1index - 1]
a2 = atoms[a2index - 1]
if not a1 or not a2:
continue
m.newBond(a1, a2).order = order
elif state == "properties":
if not m.atoms:
raise UserError("No atoms found for compound"
" '%s' in MOL/SDF file '%s'" %
(m.name, fileName))
if line.split() == ["M", "END"]:
state = "data"
elif state == "data":
if line == "$$$$":
nonblank = False
state = "init"
f.close()
if nonblank and state not in ["data", "init"]:
if mols:
replyobj.warning("Extraneous text after final $$$$"
" in MOL/SDF file '%s'" % fileName)
else:
raise UserError("Unexpected end of file (parser state:"
" %s) in MOL/SDF file '%s'" % (state, fileName))
return mols
def parse(fileName):
IN_HEADER = 0
START_ATTRS = 1
IN_ATTRS = 2
IN_FEATURES = 3
IN_SEQ = 4
state = IN_HEADER
from OpenSave import osOpen
f = osOpen(fileName, "r")
sequences = []
lineNum = 0
hasOffset = 0
longest = None
fileAttrs = {}
for line in f:
line = line.rstrip() # remove trailing whitespace/newline
lineNum += 1
if lineNum == 1:
if line.startswith("!!RICH_SEQUENCE"):
continue
raise WrongFileTypeError()
if state == IN_HEADER:
if line.strip() == "..":
state = START_ATTRS
continue
if "comments" in fileAttrs:
fileAttrs["comments"] += "\n" + line
else:
fileAttrs["comments"] = line
continue
if not line.strip():
continue
if state == START_ATTRS:
if line.strip() == "{":
state = IN_ATTRS
curAttr = None
attrs = {}
elif line:
raise FormatSyntaxError("Unexpected text before"
" start of sequence on line %d"
% lineNum)
continue
if state == IN_ATTRS or state == IN_FEATURES:
if line.strip() == "sequence" and line[0] == "s":
if "RSF name" not in attrs:
raise FormatSyntaxError("sequence on "
"line %d has no name" % lineNum)
state = IN_SEQ
seq = Sequence(makeReadable(attrs["RSF name"]))
del attrs["RSF name"]
seq.attrs = attrs
if "RSF descrip" in attrs:
attrs["description"] = attrs[
"RSF descrip"]
del attrs["RSF descrip"]
sequences.append(seq)
if "RSF offset" in attrs:
seq.extend("." * int(
attrs["RSF offset"]))
hasOffset = 1
del attrs["RSF offset"]
continue
if line.startswith("feature"):
if state == IN_ATTRS:
attrs["RSF features"] = [[line[8:]]]
else:
attrs["RSF features"].append([line[8:]])
state = IN_FEATURES
continue
if state == IN_ATTRS:
if line[0].isspace():
# continuation
if not curAttr:
raise FormatSyntaxError("Bogus "
"indentation at line %d"
% lineNum)
if attrs[curAttr]:
attrs[curAttr] += "\n" + line
else:
attrs[curAttr] = line
continue
if " " in line.strip():
curAttr, val = line.split(None, 1)
curAttr.replace("_", " ")
curAttr = "RSF " + curAttr
attrs[curAttr] = val.strip()
else:
curAttr = "RSF " + line.strip().replace("_", " ")
attrs[curAttr] = ""
continue
if state == IN_FEATURES:
attrs["RSF features"][-1].append(line)
continue
if line.strip() == "}":
state = START_ATTRS
if not longest:
longest = len(seq)
else:
if len(seq) < longest:
seq.extend("." * (longest - len(seq)))
elif len(seq) > longest:
longest = len(seq)
for s in sequences[:-1]:
s.extend("." *
(longest - len(s)))
continue
seq.extend(line.strip())
if not seq[0].isalpha():
hasOffset = 1
f.close()
if state == IN_HEADER:
raise FormatSyntaxError(
"No end to header (i.e. '..' line) found")
if state == IN_ATTRS or state == IN_FEATURES:
if "RSF name" in attrs:
raise FormatSyntaxError(
"No sequence data found for sequence %s"
% attrs["RSF name"])
raise FormatSyntaxError("Sequence without sequence data")
if state == IN_SEQ:
raise FormatSyntaxError("No terminating brace for sequence %s"
% attrs["RSF name"])
if not sequences:
raise FormatSyntaxError("No sequences found")
if not hasOffset:
from chimera import replyobj
replyobj.warning("No offset fields in RSF file;"
" assuming zero offset\n")
return sequences, fileAttrs, {}
def readAIM(fileName):
import re
from OpenSave import osOpen
from chimera import UserError, Molecule, Element, openModels, replyobj
from chimera import Coord, connectMolecule, MaterialColor
anums = {}
## Open the file
getatoms = osOpen(fileName)
## Search for the string:
## 'Number of NACPs'
## which gives us the number of atoms
## and store it in numAtoms
for data in getatoms:
data = data.strip()
if data.startswith("Number of NACPs"):
a,b,c,d,e = data.split()
numAtoms = int(e)
getatoms.close()
###################################################################
f = osOpen(fileName)
readAtoms = 0
state = "init"
## Skip the 26 header lines from the mpgviz file
#f = f.readlines()[4:]
for lines in f:
lines = lines.strip()
if lines.startswith("Atom Charge X Y Z"):
f.next()
for line in f:
if readAtoms == numAtoms:
break
line = line.strip()
if state == "init":
state = "post"
m = Molecule()
r = m.newResidue("UNK", " ", 1, " ")
state = "atoms"
serial = 1
if not line: continue
elem, charge, x, y, z = line.split()
x, y, z = [float(c) for c in [x,y,z]]
## Remove the number from the atomic symbol
elem = filter(lambda x: x.isalpha(), elem)
element = Element(elem)
anum = anums.get(element.name, 0) + 1
anums[element.name] = anum
a = m.newAtom("%s%d" % (element.name, anum), element)
r.addAtom(a)
a.setCoord(Coord((x*0.52918), (y*0.52918), (z*0.52918)))
a.serialNumber = serial
serial += 1
readAtoms += 1
connectMolecule(m)
###################################################################
## Critical points
idNACP = 1
mNACP = Molecule()
rNACP = mNACP.newResidue("Nuclear atractors critical points", " ", 1, " ")
idBCP = 1
mBCP = Molecule()
rBCP = mBCP.newResidue("Bond critical points", " ", 1, " ")
idBPP = 1
mBPP = Molecule()
rBPP = mBPP.newResidue("Bond path points", " ", 1, " ")
cpnumber = 1
cpread = 0
getcriticalpoints = osOpen(fileName)
for text in getcriticalpoints:
text = text.strip()
if cpread == 0:
if text.startswith("CP#"):
readtext = text
cpread = 1
elif cpread == 1:
if text.startswith("Type = (3,-3)"):
a,b,signature,type,atom1 = text.split()
cpnum,id,a,b,x,y,z = readtext.split()
x, y, z = [float(c) for c in [x,y,z]]
## Remove the number from the atomic symbol
elem = filter(lambda x: x.isalpha(), atom1)
element = Element(elem)
anum = anums.get(element.name, 0) + 1
anums[element.name] = anum
#atomNACP = m.newAtom("%s%d" % (element.name, anum), element)
atomNACP = mNACP.newAtom("%s%s" % ("NACP# ", atom1), element)
atomNACP.serialNumber = serial
#atomNACP = mNACP.newAtom(atom1, Element("NACP"))
atomNACP.drawMode = 1
atomNACP.radius = 0.2
rNACP.addAtom(atomNACP)
atomNACP.setCoord(Coord((x*0.52918), (y*0.52918), (z*0.52918)))
cpread = 0
serial += 1
elif text.startswith("Type = (3,+3)"):
print 'CCP'
cpread = 0
elif text.startswith("Type = (3,+1)"):
print 'RCP'
cpread = 0
elif text.startswith("Type = (3,-1)"):
a,b,signature,type,atom1,atom2 = text.split()
cpnum,id,a,b,x,y,z = readtext.split()
x, y, z = [float(c) for c in [x,y,z]]
## Remove the number from the atomic symbol
elem = filter(lambda x: x.isalpha(), atom1)
element = Element(elem)
anum = anums.get(element.name, 0) + 1
anums[element.name] = anum
atomBCP = mBCP.newAtom("%s%s" % ("BCP# ", id), element)
atomBCP.serialNumber = serial
#atomBCP = mBCP.newAtom(atom1, Element("He"))
atomBCP.color = MaterialColor(1,0,0,1)
atomBCP.drawMode = 1
atomBCP.radius = 0.07
rBCP.addAtom(atomBCP)
atomBCP.setCoord(Coord((x*0.52918), (y*0.52918), (z*0.52918)))
cpread = 0
serial += 1
###################################################################
## Bond Paths
getbondpaths = osOpen(fileName)
statusSamples = 0
countSamples = 0
totalSamples = 0
skip = 0
for samples in getbondpaths:
samples = samples.strip()
if re.match("(.*)sample points along path from BCP to atom(.*)", samples):
numSamples,a,b,c,d,e,tipo,g,h,atom = samples.split()
numSamples = int(numSamples)
statusSamples = 1
totalSamples = int(totalSamples)
if statusSamples == 1:
totalSamples = totalSamples + statusSamples
if countSamples == numSamples:
countSamples = 0
statusSamples = 0
else:
try:
x,y,z,rho = samples.split()
x, y, z = [float(c) for c in [x,y,z]]
## Remove the number from the atomic symbol
elem = filter(lambda x: x.isalpha(), atom1)
element = Element(elem)
anum = anums.get(element.name, 0) + 1
anums[element.name] = anum
atomBPP = mBPP.newAtom("%s%s" % ("BPP", serial), element)
atomBPP.serialNumber = serial
#atomBPP = mBPP.newAtom(atom1, Element("kr"))
#atomBPP = mBPP.newAtom("%s%s" % ("BPP", serial), element)
atomBPP.color = MaterialColor(0,206,209,1)
atomBPP.drawMode = 1
atomBPP.radius = 0.01
rBPP.addAtom(atomBPP)
atomBPP.setCoord(Coord((x*0.52918), (y*0.52918), (z*0.52918)))
#cpread = 0
serial += 1
#cpnumber += 1
countSamples += 1
except ValueError:
countSamples += 1
continue
mNACP.isRealMolecule = False
# mNACP.noprefs = True
mBCP.isRealMolecule = False
mBCP.noprefs = True
mBPP.isRealMolecule = False
mBPP.noprefs = True
## Return molecules
return [m, mNACP, mBCP, mBPP]
def parse(fileName):
from OpenSave import osOpen
f = osOpen(fileName, "r")
doing = None
sequences = []
headerOK = False
lineNum = 0
alignStartIndex = None
for line in f:
if doing == 'alignments':
# don't strip() alignment section since it has significant
# leading spaces
line = line.rstrip()
else:
line = line.strip()
lineNum += 1
if not headerOK:
if line.lower().startswith('hssp'):
headerOK = True
continue
raise WrongFileTypeError("No initial HSSP header line")
if line.startswith('##'):
if doing == 'proteins' and not sequences:
raise FormatSyntaxError("No entries in PROTEINS section")
try:
doing = line.split()[1].lower()
except IndexError:
doing = None
if doing == 'alignments':
try:
hashes, alignments, begin, dash, end = line.strip().split()
begin = int(begin)
end = int(end)
except ValueError:
raise FormatSyntaxError(
"ALIGNMENTS line (line #%d) not of "
"the form: ## ALIGNMENTS (number) - (number)" %
lineNum)
continue
if doing == 'proteins':
if not line[0].isdigit():
continue
try:
seqName = line.split()[2]
except IndexError:
raise WrongFormatError(
"Line %d in PROTEINS section does not "
"start with [integer] : [sequence name]" % lineNum)
sequences.append(Sequence(makeReadable(seqName)))
elif doing == 'alignments':
if line.lstrip().lower().startswith('seqno'):
try:
alignStartIndex = line.index('.')
except:
raise FormatSyntaxError(
"No indication of alignment "
" starting column ('.' character) in SeqNo line "
" in ALIGNMENTS section")
continue
if alignStartIndex == None:
raise FormatSyntaxError("No initial SeqNo line in "
"ALIGNMENTS section")
block = line[alignStartIndex:]
if not block:
raise FormatSyntaxError("No alignment block given on line %d" %
lineNum)
blockLen = end - begin + 1
if len(block) > blockLen:
raise FormatSyntaxError(
"Too many characters (%d, only %d "
" sequences) in alignment block given on line %d" %
(len(block), blockLen, lineNum))
block = block + ' ' * (blockLen - len(block))
for seq, c in zip(sequences[begin - 1:end], block):
seq.append(c)
f.close()
return sequences, {}, {}
def clustalInfo(fileName=None):
if fileName is None:
return _clustalCategories, _clustalColorings
from prefs import RC_HYDROPHOBICITY
if fileName == RC_HYDROPHOBICITY:
import os.path
fileName = os.path.join(os.path.dirname(__file__),
"kdHydrophob.par")
colorInfo = {}
for colorName in [ "RED", "BLUE", "GREEN", "CYAN",
"PINK", "MAGENTA", "YELLOW", "ORANGE"]:
colorInfo[colorName] = eval("_clustal%s"
% colorName.capitalize())
from OpenSave import osOpen
from chimera import UserError
f = osOpen(fileName)
section = None
colorSeen = False
categories = []
colorings = {}
for line in f:
line = line.strip()
if line.startswith("@"):
section = line[1:].lower()
continue
if not line:
continue
if section == "rgbindex":
try:
name, sr, sg, sb = line.split()
except ValueError:
raise UserError("Line in @rgbindex section of"
" %s is not color name followed by"
" red, green and blue values: '%s'"
% (fileName, line))
try:
r, g, b = [float(x) for x in [sr, sg, sb]]
except ValueError:
raise UserError("Line in @rgbindex section of"
" %s has non-floating-point"
" red, green or blue value: '%s'"
% (fileName, line))
if r>1 or g>1 or b>1 or r<0 or g<0 or b<0:
raise UserError("Line in @rgbindex section of"
" %s has red, green or blue value"
" not in the range 0-1: '%s'"
% (fileName, line))
colorInfo[name] = rgba2tk((r, g, b))
elif section == "consensus":
try:
symbol, eq, percent, composition = line.split()
except ValueError:
raise UserError("Line in @consensus section of"
" %s is not of the form 'symbol = "
" percentage%% res-list: '%s'"
% (fileName, line))
if eq != '=':
raise UserError("Line in @consensus section of"
" %s doesn't have '=' as second"
" component: '%s'" % (fileName, line))
if percent[-1] != '%':
raise UserError("Line in @consensus section of"
" %s doesn't have '%' as last character"
" of third component: '%s'"
% (fileName, line))
try:
percentage = float(percent[:-1])
except ValueError:
raise UserError("Line in @consensus section of"
" %s doesn't have a number before the"
" '%' of third component: '%s'"
% (fileName, line))
if percentage < 0 or percentage > 100:
raise UserError("Line in @consensus section of"
" %s has a percentage not in the range"
" 0-100: '%s'" % (fileName, line))
composition = composition.replace(":", "")
categories.append((composition, percentage/100.0,
symbol))
elif section == "color":
colorSeen = True
fields = line.split()
if len(fields) not in [3,5]:
raise UserError("Line in @color section of"
" %s not of the form AA = color"
" [if consensus-list]: '%s'"
% (fileName, line))
aa, eq, color = fields[:3]
if len(aa) > 1 or not aa.islower():
raise UserError("Line in @color section of"
" %s uses amino-acid code that is not"
" a single lowercase character: '%s'"
% (fileName, line))
if eq != '=':
raise UserError("Line in @color section of"
" %s doesn't have '=' as second"
" component: '%s'" % (fileName, line))
if color not in colorInfo:
raise UserError("Line in @color section of"
" %s uses an unknown color:"
" '%s'" % (fileName, line))
if len(fields) == 3:
colorings.setdefault(aa.upper(), []).append(
(colorInfo[color], None))
continue
if fields[3] != 'if':
raise UserError("Line in @color section of"
" %s doesn't have 'if' as fourth"
" component: '%s'" % (fileName, line))
colorings.setdefault(aa.upper(), []).append(
(colorInfo[color], fields[-1].replace(":", "")))
f.close()
if not colorSeen:
raise UserError("'%s' has missing or empty @color section"
% fileName)
return categories, colorings
def loadScfFile(self, path, colorStructures=True):
if path is None:
if not self._scfDialog:
self._scfDialog = ScfDialog(
self.seqCanvas.mav.prefs[
SCF_COLOR_STRUCTURES],
command=self.loadScfCB)
self._scfDialog.enter()
return
seqs = self.seqCanvas.seqs
from OpenSave import osOpen
scfFile = osOpen(path)
lineNum = 0
regionInfo = {}
for line in scfFile.readlines():
lineNum += 1
line.strip()
if not line or line[0] == '#' \
or line.startswith('//'):
continue
for commentIntro in ['//', '#']:
commentPos = line.find(commentIntro)
if commentPos >= 0:
break
if commentPos >= 0:
comment = line[commentPos
+ len(commentIntro):].strip()
line = line[:commentPos].strip()
else:
comment = None
try:
pos1, pos2, seq1, seq2, r, g, b = map(
int, line.split())
if seq1 == -1:
# internal to jevtrace/webmol
continue
if seq1 == 0:
seq2 = -1
else:
seq1 -= 1
seq2 -= 1
except:
try:
pos, seq, r, g, b = map(int,
line.split())
pos1 = pos2 = pos
except:
replyobj.error("Bad format for line %d of %s [not 5 or 7 integers]\n" % (lineNum, path))
scfFile.close()
return
if seq == 0:
seq1 = 0
seq2 = -1
else:
seq1 = seq2 = seq - 1
key = ((r, g, b), comment)
if key in regionInfo:
regionInfo[key].append((seqs[seq1],
seqs[seq2], pos1, pos2))
else:
regionInfo[key] = [(seqs[seq1],
seqs[seq2], pos1, pos2)]
scfFile.close()
if not regionInfo:
replyobj.error("No annotations found in %s\n"
% path)
return
for rgbComment, blocks in regionInfo.items():
rgb, comment = rgbComment
rgb = map(lambda v: v/255.0, rgb)
region = self.newRegion(namePrefix="Seqsel: ",
blocks=blocks, name=comment, fill=rgb,
coverGaps=True)
if not colorStructures:
continue
c = chimera.MaterialColor(*rgb)
for res in self.regionResidues(region):
res.ribbonColor = c
for a in res.atoms:
a.color = c
self.seqCanvas.mav.status("%d scf regions created\n"
% len(regionInfo))
def addAttributes(attrFile, models=None, log=False, raiseAttrDialog=True): """add/set attributes from a file 'attrFile' indicates a file path or an opened file object. The file contains control lines and data lines. Control and data lines may be freely interspersed. The data lines are of the form: <tab>selector<tab>attribute value The selector is an atom specification (as per the Atom Specification section of the User's Guide). The attribute value is a boolean, integer, float, or string. If it is necessary to specify a string attribute that could be interpreted as one of the other types, embed the value in double quotes (it will then be evaluated as a Python string, including backslash interpretation). The control lines are of the form: name: value The possible name/value pairs are: Name Value ---- ----- attribute name of the attribute to assign to match mode expected matches per selector: "1 to 1": exactly one match per selector "non-zero": at least one match per selector "any": no constraint selectors not conforming to the match mode will generate an error recipient where to put attribute (atoms/residues/molecules) The only mandatory control line is 'attribute', which must precede any data lines. The default match mode is 1 to 1, and the default recipient is atoms. Empty lines are ignored and lines beginning with the '#' character are considered comments and ignored. 'log' controls whether information about what each selector matched is sent to the reply log. 'models' restricts any selector matching to the given models. If 'models' is None, then no restriction occurs. This function return a list of recipient/attribute tuples that actually were set in at least one object. If an error occurred, None is returned instead. """ from OpenSave import osOpen try: if isinstance(attrFile, basestring): attrFile = osOpen(attrFile) try: return _addAttr(attrFile, models, log, raiseAttrDialog) finally: attrFile.close() else: return _addAttr(attrFile, models, log, raiseAttrDialog) except SyntaxError, v: replyobj.error(str(v) + "\n") return None
