def cmdCombine(mols,
name="combination",
newChainIDs=True,
log=True,
close=False,
modelId=None,
refMol=None):
from chimera.misc import oslModelCmp
mols.sort(lambda m1, m2: oslModelCmp(m1.oslIdent(), m2.oslIdent()))
from Midas import MidasError
if not mols:
raise MidasError("No molecules specified")
if refMol == None:
refMol = mols[:1]
if len(refMol) == 0:
raise MidasError("No reference molecule specified")
elif len(refMol) > 1:
raise MidasError("Multiple reference molecules specified")
refMol = refMol[0]
if modelId is not None and type(modelId) != int:
try:
modelId = int(modelId[1:])
except:
raise MidasError("modelId value must be integer")
from chimera import suppressNewMoleculeProcessing, \
restoreNewMoleculeProcessing
suppressNewMoleculeProcessing()
try:
m = combine(mols, refMol, newChainIDs=newChainIDs, log=log)
except CombineError, v:
restoreNewMoleculeProcessing()
raise MidasError(v)
def aniso(targets=None, color=None, smoothing=3, scale=1.0,
showEllipsoid=True, transparency=None,
axisFactor=None, axisColor=None, axisThickness=0.01,
ellipseFactor=None, ellipseColor=None, ellipseThickness=0.02):
from Midas import MidasError
if targets is None:
targets = openModels.list(modelTypes=[Molecule])
if smoothing < 1:
raise MidasError("'smoothing' must be at least 1")
if transparency is not None:
try:
transparency /= 100.0
if transparency < 0.0 or transparency > 1.0:
raise TypeError("out of range")
except TypeError:
raise MidasError(
"transparency must be a number between zero and one")
numShown = mgr().showAniso(targets, color=color,
smoothing=smoothing, scale=scale,
showEllipsoid=showEllipsoid, ellipsoidTransparency=transparency,
axisFactor=axisFactor, axisColor=axisColor, axisThickness=axisThickness,
ellipseColor=ellipseColor, ellipseFactor=ellipseFactor,
ellipseThickness=ellipseThickness)
if not numShown:
raise MidasError("No atoms chosen or none had anisotropic"
" information")
def typefaceLookup(label):
try:
return FONT_TYPEFACE_VALUES[FONT_TYPEFACE_LABELS.index(label)]
except ValueError:
from Midas import MidasError
raise MidasError("No known font typeface '%s'; choices are: %s" %
(label, ", ".join(FONT_TYPEFACE_LABELS)))
def revMainchainCmd(cmdName, args):
# We are going to implement ~mainchain as a synonym for "display",
# so we import runCommand which simplifies doing that.
from chimera import runCommand
from Midas import MidasError
if args:
# Raising MidasError will cause the error message
# to show up in the status line as red text
raise MidasError("~mainchain takes no arguments")
# runCommand takes any legal command-line command and executes it.
runCommand("display")
def useBestRotamers(
resType,
targets,
criteria=defaultCriteria,
lib="Dunbrack",
preserve=False,
# clash options
overlapCutoff=defaults[CLASH_THRESHOLD],
hbondAllowance=defaults[HBOND_ALLOWANCE],
scoreMethod=defaults[CLASH_METHOD],
ignoreOtherModels=False,
# H-bond options
relax=True,
distSlop=recDistSlop,
angleSlop=recAngleSlop,
# density options
density=None,
log=True):
"""implementation of "swapaa" command. 'targets' is a list of Residues."""
from Midas import midas_text, MidasError
lib = lib.capitalize()
rotamers = {}
toClose = []
for res in targets:
if resType == "same":
rType = res.type
else:
rType = resType.upper()
try:
bbdep, rots = getRotamers(res, resType=rType, lib=lib, log=log)
except NoResidueRotamersError:
from SwapRes import swap, BackboneError
if log:
replyobj.info("Swapping %s to %s\n" % (res, rType))
try:
swap(res, rType, bfactor=None)
except BackboneError, v:
raise MidasError(str(v))
continue
except ImportError:
raise MidasError("No rotamer library named '%s'" % lib)
def func(cmdFile): from Midas.midas_text import processCommandFile import os.path dirName, fileName = os.path.split(cmdFile) if dirName: if not os.path.exists(dirName): from Midas import MidasError raise MidasError( "No such folder/directory: %s" % dirName) import os cwd = os.getcwd() try: os.chdir(dirName) processCommandFile(fileName) finally: os.chdir(cwd) else: processCommandFile(cmdFile) return []
def cmdMatch(refSel, matchSel, pairing=defaults[CHAIN_PAIRING],
alg=defaults[SEQUENCE_ALGORITHM],
ssFraction=defaults[SS_MIXTURE], matrix=defaults[MATRIX],
gapOpen=defaults[GAP_OPEN], hgap=defaults[HELIX_OPEN],
sgap=defaults[STRAND_OPEN], ogap=defaults[OTHER_OPEN],
iterate=defaults[ITER_CUTOFF], gapExtend=defaults[GAP_EXTEND],
showAlignment=False, computeSS=defaults[COMPUTE_SS],
matHH=defaultSSMatrix[('H', 'H')],
matSS=defaultSSMatrix[('S', 'S')],
matOO=defaultSSMatrix[('O', 'O')],
matHS=defaultSSMatrix[('H', 'S')],
matHO=defaultSSMatrix[('H', 'O')],
matSO=defaultSSMatrix[('S', 'O')]):
"""wrapper for command-line command (friendlier args)"""
from Midas import MidasError
if matrix not in SmithWaterman.matrices:
raise MidasError("No such matrix name: %s" % str(matrix))
try:
gapOpen + 1
gapExtend + 1
hgap + 1
sgap + 1
ogap + 1
except TypeError:
raise MidasError("Gap open/extend penalties must be numeric")
if pairing == CP_SPECIFIC_SPECIFIC:
matches = matchSel.chains()
elif pairing == CP_SPECIFIC_BEST:
matches = matchSel.molecules()
if pairing == CP_SPECIFIC_SPECIFIC or pairing == CP_SPECIFIC_BEST:
refs = refSel.chains()
if not refs:
raise MidasError("No reference chains specified")
if pairing == CP_SPECIFIC_BEST and len(refs) > 1:
raise MidasError("Specify a single reference"
" chain only")
else:
refMols = refSel.molecules()
if not refMols:
raise MidasError("No reference model specified")
if len(refMols) > 1:
raise MidasError("Specify a single reference"
" model only")
refs = refMols
matches = matchSel.molecules()
if not matches:
raise MidasError("No molecules/chains to match specified")
for ref in refs:
if ref in matches:
matches.remove(ref)
if not matches:
raise MidasError("Must use different reference and match"
" structures")
if pairing == CP_SPECIFIC_SPECIFIC:
if len(refs) != len(matches):
raise MidasError("Different number of reference/match"
" chains (%d ref, %d match)" %
(len(refs), len(matches)))
matchItems = zip(refs, matches)
else:
matchItems = (refs[0], matches)
ssMatrix = {}
ssMatrix[('H', 'H')] = float(matHH)
ssMatrix[('S', 'S')] = float(matSS)
ssMatrix[('O', 'O')] = float(matOO)
ssMatrix[('H', 'S')] = ssMatrix[('S', 'H')] = float(matHS)
ssMatrix[('H', 'O')] = ssMatrix[('O', 'H')] = float(matHO)
ssMatrix[('S', 'O')] = ssMatrix[('O', 'S')] = float(matSO)
if type(iterate) == bool and not iterate:
iterate = None
try:
match(pairing, matchItems, matrix, alg, gapOpen, gapExtend,
ssFraction=ssFraction, ssMatrix=ssMatrix,
iterate=iterate, showAlignment=showAlignment,
gapOpenHelix=hgap, gapOpenStrand=sgap,
gapOpenOther=ogap, computeSS=computeSS)
except UserError, v:
raise MidasError, v
def processLabel2DCmd(action,
labelID,
text=None,
color=None,
size=None,
style=None,
typeface=None,
xpos=None,
ypos=None,
visibility=None,
frames=None):
from Midas import MidasError
if type(xpos) == list or type(ypos) == list:
raise MidasError("Multiple occurances of 'xpos' or 'ypos' keywords")
try:
if xpos: xpos + 0
if ypos: ypos + 0
except:
raise MidasError("xpos/ypos values must be numeric")
global _ilabelModel
if not _ilabelModel:
IlabelModel()
model = _ilabelModel
if text is not None:
# text might have evaluated as an integer or something
text = unicode(text)
# backslash interpretation...
if '\\' in text:
if '"' not in text:
text = eval('"' + text + '"')
elif "'" not in text:
text = eval("'" + text + "'")
if action == "create":
## get the position
if xpos == None:
xpos = .5
if ypos == None:
ypos = .5
if not color:
color = chimera.Color.lookup('white')
if not size:
size = 24
if not style:
style = "normal"
if not typeface:
typeface = "sans serif"
## make a new label
try:
label = model.newLabel((xpos, ypos), labelID)
except RuntimeError, what:
raise MidasError, what
## set it's content
label.set(text or '')
## color and size the characters
changeLabelAttrs(label, size, color, styleLookup(style),
typefaceLookup(typeface))
if visibility == "hide":
label.shown = False
except ImportError:
raise MidasError("No rotamer library named '%s'" % lib)
if preserve:
rots = pruneByChis(rots, res, log=log)
rotamers[res] = rots
toClose.extend(rots)
# this implementation allows tie-breaking criteria to be skipped if
# there are no ties
for char in criteria:
if char == "d":
# density
if density == None:
if criteria is defaultCriteria:
continue
raise MidasError("Density criteria requested"
" but no density model specified")
from VolumeViewer.volume import Volume
if isinstance(density, list):
density = [d for d in density if isinstance(d, Volume)]
else:
density = [density]
if not density:
raise MidasError("No volume models in"
" specified model numbers")
if len(density) > 1:
raise MidasError("Multiple volume models in"
" specified model numbers")
allRots = []
for res, rots in rotamers.values():
chimera.openModels.add(rots, sameAs=res.molecule, hidden=True)
allRots.extend(rots)
def cmdDetectClash(testAtoms,
overlapCutoff=defaults[CLASH_THRESHOLD],
hbondAllowance=defaults[HBOND_ALLOWANCE],
test="others",
setAttrs=defaults[ACTION_ATTR],
selectClashes=defaults[ACTION_SELECT],
colorClashes=defaults[ACTION_COLOR],
clashColor=defColors[CLASH_COLOR],
nonclashColor=defColors[NONCLASH_COLOR],
makePseudobonds=defaults[ACTION_PSEUDOBONDS],
pbColor=defColors[PB_COLOR],
lineWidth=defaults[PB_WIDTH],
bondSeparation=defaults[BOND_SEPARATION],
saveFile=None,
namingStyle=None,
ignoreIntraRes=defaults[IGNORE_INTRA_RES],
interSubmodel=False,
log=defaults[ACTION_REPLYLOG],
summary=True,
continuous=False):
global _continuousID
from Midas import MidasError
if continuous:
if setAttrs or saveFile != None or log:
raise MidasError("log/setAttrs/saveFile not allowed"
" with continuous detection")
if _continuousID == None:
from inspect import getargvalues, currentframe
argNames, fArgs, fKw, frameDict = getargvalues(currentframe())
callData = [frameDict[an] for an in argNames]
def preCB(trigName, myData, changes):
if 'transformation change' in changes.reasons:
return _motionCB(myData)
_continuousID = chimera.triggers.addHandler(
'OpenState', preCB, callData)
elif _continuousID != None:
chimera.triggers.deleteHandler('OpenState', _continuousID)
_continuousID = None
if isinstance(test, basestring):
if test.startswith("other"):
test = "others"
elif test not in ('self', 'model'):
# atom spec
from chimera.specifier import evalSpec
try:
test = evalSpec(test).atoms()
except:
raise MidasError("Could not parse atom spec '%s'" % test)
clashes = detectClash(testAtoms,
test=test,
hbondAllowance=hbondAllowance,
clashThreshold=overlapCutoff,
bondSeparation=bondSeparation,
intraRes=not ignoreIntraRes,
interSubmodel=interSubmodel)
if selectClashes:
chimera.selection.setCurrent(clashes.keys())
if test == "self":
outputGrouping = set()
else:
outputGrouping = testAtoms
info = (overlapCutoff, hbondAllowance, bondSeparation, ignoreIntraRes,
clashes, outputGrouping)
if log:
import sys
# put a separator in the Reply Log
print >> sys.stdout, ""
_fileOutput(sys.stdout, info, namingStyle=namingStyle)
if saveFile == '-':
from FindHBond.MolInfoDialog import SaveMolInfoDialog
SaveMolInfoDialog(info,
_fileOutput,
initialfile="overlaps",
title="Choose Overlap Info Save File",
historyID="Overlap info")
elif saveFile is not None:
_fileOutput(saveFile, info, namingStyle=namingStyle)
if summary == True:
def _summary(msg):
from chimera import replyobj
replyobj.status(msg + '\n')
replyobj.info(msg + '\n')
summary = _summary
if summary:
if clashes:
total = 0
for clashList in clashes.values():
total += len(clashList)
summary("%d contacts" % (total / 2))
else:
summary("No contacts")
if not (setAttrs or colorClashes or makePseudobonds):
nukeGroup()
return clashes
if test in ("others", "model"):
atoms = [
a for m in chimera.openModels.list(modelTypes=[chimera.Molecule])
for a in m.atoms
]
else:
atoms = testAtoms
if setAttrs:
# delete the attribute in _all_ atoms...
for m in chimera.openModels.list(modelTypes=[chimera.Molecule]):
for a in m.atoms:
if hasattr(a, attrName):
delattr(a, attrName)
for a in atoms:
if a in clashes:
clashVals = clashes[a].values()
clashVals.sort()
setattr(a, attrName, clashVals[-1])
if colorClashes:
for a in atoms:
a.surfaceColor = None
if a in clashes:
a.color = clashColor
else:
a.color = nonclashColor
if makePseudobonds:
from chimera.misc import getPseudoBondGroup
pbg = getPseudoBondGroup(groupName)
pbg.deleteAll()
pbg.lineWidth = lineWidth
pbg.color = pbColor
seen = set()
for a in atoms:
if a not in clashes:
continue
seen.add(a)
for clasher in clashes[a].keys():
if clasher in seen:
continue
pbg.newPseudoBond(a, clasher)
else:
nukeGroup()
return clashes