def startCommand(molecule,
name="default",
method="corkscrew",
rate="linear",
frames=20,
cartesian=False):
from chimera import UserError
if len(molecule) != 1:
raise UserError("You must specify exactly one molecule")
m = molecule[0]
try:
ms = _find(name)
except UserError:
pass
else:
raise UserError("You already defined \"%s\"" % name)
kw = {
"method": method,
"rate": rate,
"frames": frames,
"cartesian": cartesian,
}
_verifyOpts(kw)
from base import Script
ms = Script(m, closeCB=_close, **kw)
_add(name, ms)
from chimera import replyobj
msg = "Interpolation \"%s\" created\n" % name
replyobj.message(msg)
replyobj.status(msg)
return ms
def _importExtension(self, path, pkgName, module):
"""Import tool at given path
Import process should cause tool to register
itself via registerExtension"""
sys.path.insert(0, os.path.join(path, pkgName))
try:
try:
# When "module" is imported, it should register
# itself. Then we delete the module from
# sys.modules so that the same name may be
# used when importing another tool.
try:
__import__(module)
except ImportError:
pass
try:
del sys.modules[module]
except KeyError:
pass
finally:
del sys.path[0]
except:
# need to give some indication of what module the
# error is occuring in, so prepend info to error
from chimera import replyobj
import traceback
replyobj.pushMode(replyobj.ERROR)
replyobj.message("Error while importing %s from %s:\n" %
(pkgName, path))
s = apply(traceback.format_exception, sys.exc_info())
replyobj.message(''.join(s))
replyobj.popMode()
def apply(self, vFunc = None, eFunc = None):
sel = selection.ItemizedSelection()
sels = [] # used as a stack when selections get composited
funcGlobals = {
"__doc__": None,
"__name__": "CodeItemizedSelection",
"__builtins__": __builtins__
}
if self.models is None:
sm = chimera.openModels.list()
else:
sm = self.models
funcLocals = {
"models": sm,
"molecules": filter(lambda m, M=Molecule:
isinstance(m, M), sm),
"sel": sel,
"sels": sels,
"selection": selection
}
try:
exec self.codeObj in funcGlobals, funcLocals
except:
from chimera import replyobj
replyobj.error(" CodeItemizedSelection failed\n")
s = apply(traceback.format_exception,
sys.exc_info())
replyobj.message(string.join(s, ''))
sel.apply(vFunc, eFunc)
def _importExtension(self, path, pkgName, module):
"""Import tool at given path
Import process should cause tool to register
itself via registerExtension"""
sys.path.insert(0, os.path.join(path, pkgName))
try:
try:
# When "module" is imported, it should register
# itself. Then we delete the module from
# sys.modules so that the same name may be
# used when importing another tool.
try:
__import__(module)
except ImportError:
pass
try:
del sys.modules[module]
except KeyError:
pass
finally:
del sys.path[0]
except:
# need to give some indication of what module the
# error is occuring in, so prepend info to error
from chimera import replyobj
import traceback
replyobj.pushMode(replyobj.ERROR)
replyobj.message("Error while importing %s from %s:\n"
% (pkgName, path))
s = apply(traceback.format_exception,
sys.exc_info())
replyobj.message(''.join(s))
replyobj.popMode()
def apply(self, vFunc=None, eFunc=None):
sel = selection.ItemizedSelection()
sels = [] # used as a stack when selections get composited
funcGlobals = {
"__doc__": None,
"__name__": "CodeItemizedSelection",
"__builtins__": __builtins__
}
if self.models is None:
sm = chimera.openModels.list()
else:
sm = self.models
funcLocals = {
"models": sm,
"molecules": filter(lambda m, M=Molecule: isinstance(m, M), sm),
"sel": sel,
"sels": sels,
"selection": selection
}
try:
exec self.codeObj in funcGlobals, funcLocals
except:
from chimera import replyobj
replyobj.error(" CodeItemizedSelection failed\n")
s = apply(traceback.format_exception, sys.exc_info())
replyobj.message(string.join(s, ''))
sel.apply(vFunc, eFunc)
def startCommand(molecule, name="default", method="corkscrew",
rate="linear", frames=20, cartesian=False):
from chimera import UserError
if len(molecule) != 1:
raise UserError("You must specify exactly one molecule")
m = molecule[0]
try:
ms = _find(name)
except UserError:
pass
else:
raise UserError("You already defined \"%s\"" % name)
kw = {
"method": method,
"rate": rate,
"frames": frames,
"cartesian": cartesian,
}
_verifyOpts(kw)
from base import Script
ms = Script(m, closeCB=_close, **kw)
_add(name, ms)
from chimera import replyobj
msg = "Interpolation \"%s\" created\n" % name
replyobj.message(msg)
replyobj.status(msg)
return ms
def interpolateCommand(molecule,
name="default",
method=None,
rate=None,
frames=None,
cartesian=False):
if len(molecule) != 1:
from chimera import UserError
raise UserError("You must specify exactly one molecule")
m = molecule[0]
ms = _find(name)
kw = {}
if method is not None:
kw["method"] = method
if rate is not None:
kw["rate"] = rate
if frames is not None:
kw["frames"] = frames
_verifyOpts(kw)
ms.addAction(m, **kw)
from chimera import replyobj
msg = "Interpolation \"%s\" updated\n" % name
replyobj.message(msg)
replyobj.status(msg)
def showFileContent(self, filename):
try:
url = self.filemap[filename]
except KeyError:
from chimera import replyobj
replyobj.message("SAXS profile: there is no file named \"%s\"" % filename)
else:
self.showURLContent("SAXS profile %s" % filename, url)
def print_path_length(): from chimera import selection bonds = selection.currentBonds() msg = '%d bonds with total length %g\n' % (len(bonds), path_length(bonds)) from chimera import replyobj replyobj.status(msg) # Show on status line replyobj.message(msg) # Record in reply log
def print_path_length():
from chimera import selection
bonds = selection.currentBonds()
msg = '%d bonds with total length %g\n' % (len(bonds), path_length(bonds))
from chimera import replyobj
replyobj.status(msg) # Show on status line
replyobj.message(msg) # Record in reply log
def message(text, show_reply_log = False):
from chimera.replyobj import message, status
message(text + '\n')
status(text, blankAfter = 0)
if show_reply_log:
from Accelerators.standard_accelerators import show_reply_log as srl
srl()
def showFileContent(self, filename):
try:
url = self.filemap[filename]
except KeyError:
from chimera import replyobj
replyobj.message("SAXS profile: there is no file named \"%s\"" %
filename)
else:
self.showURLContent("SAXS profile %s" % filename, url)
def message(text, show_reply_log=False):
from chimera.replyobj import message, status
message(text + '\n')
status(text, blankAfter=0)
if show_reply_log:
from Accelerators.standard_accelerators import show_reply_log as srl
srl()
def _close(script):
# Callback invoked when a script is changed due to
# molecules being closed. If there are still actions,
# we don't need to do anything. But if all relevant
# models are closed, then we also remove this script.
if script.actions:
return
for n, s in _motions.iteritems():
if script is s:
_remove(n)
from chimera import replyobj
replyobj.message("Morph \"%s\" removed\n" % n)
break
def _close(script):
# Callback invoked when a script is changed due to
# molecules being closed. If there are still actions,
# we don't need to do anything. But if all relevant
# models are closed, then we also remove this script.
if script.actions:
return
for n, s in _motions.iteritems():
if script is s:
_remove(n)
from chimera import replyobj
replyobj.message("Morph \"%s\" removed\n" % n)
break
def show_volume_statistics(show_reply_log = True):
from VolumeViewer import active_volume
dr = active_volume()
if dr == None:
message('No volume data opened', show_reply_log)
return
m = dr.matrix()
mean, sd, rms = mean_sd_rms(m)
descrip = subregion_description(dr)
message('%s%s: mean = %.5g, SD = %.5g, RMS = %.5g'
% (dr.name, descrip, mean, sd, rms),
show_reply_log)
def show_volume_statistics(show_reply_log=True):
from VolumeViewer import active_volume
dr = active_volume()
if dr == None:
message('No volume data opened', show_reply_log)
return
m = dr.matrix()
mean, sd, rms = mean_sd_rms(m)
descrip = subregion_description(dr)
message(
'%s%s: mean = %.5g, SD = %.5g, RMS = %.5g' %
(dr.name, descrip, mean, sd, rms), show_reply_log)
def map(self, e=None): # First check if the server can be accessed if self.checkConnection(): return else: replyobj.pushMode(replyobj.ERROR) replyobj.message( 'There has been an error while trying to\n' 'contact the server. Your registration cannot \n' 'be processed at this time.\n\n' 'If you use a proxy server to connect to the web,\n' 'try configuring the proxy settings in the \n' 'Web Access Preferences category, restarting \n' 'Chimera, and trying again.\n') replyobj.popMode() self.Close()
def makeOslMappings(molOrder, srcMolMap):
for xfileInfo in molOrder:
oldOsls = srcMolMap[xfileInfo]
filename, fileType, defaultType = xfileInfo
prefixable = 1
if fileType:
prefixable = 0
try:
mols = chimera.openModels.open(filename, type=fileType,
defaultType=defaultType, prefixableType=prefixable)
except IOError:
remapped = findFile(filename)
if remapped is None:
replyobj.message("Skipping restore of %s\n"
% filename)
continue
mols = chimera.openModels.open(remapped, type=fileType,
defaultType=defaultType,
prefixableType=prefixable)
while len(mols) < len(oldOsls):
mols += chimera.openModels.open(filename, type=fileType,
defaultType=defaultType,
prefixableType=prefixable)
for m in mols:
for r in m.residues:
r.ribbonColor = None
for a in m.atoms:
a.color = None
curOsls = [m.oslIdent() for m in mols]
oldOsls.sort(chimera.misc.oslModelCmp)
curOsls.sort(chimera.misc.oslModelCmp)
for i in range(len(oldOsls)):
updateOSLmap(oldOsls[i], curOsls[i])
# prepopulate osl lookup map
for m in mols:
i = curOsls.index(m.oslIdent())
mapped = oldOsls[i]
for r in m.residues:
_oslItemMap[mapped + getOSL(r,
start=selection.SelSubgraph)] = r
for a in m.atoms:
_oslItemMap[mapped + getOSL(a,
start=selection.SelSubgraph)] = a
def print_model_path_lengths():
from chimera import selection
bonds = selection.currentBonds()
mbonds = {}
for b in bonds:
m = b.molecule
if m in mbonds:
mbonds[m].append(b)
else:
mbonds[m] = [b]
for m, bonds in mbonds.items():
msg = ('%s: %d bonds with total length %g\n' %
(m.name, len(bonds), path_length(bonds)))
from chimera import replyobj
replyobj.status(msg) # Show on status line
replyobj.message(msg) # Record in reply log
def print_model_path_lengths():
from chimera import selection
bonds = selection.currentBonds()
mbonds = {}
for b in bonds:
m = b.molecule
if m in mbonds:
mbonds[m].append(b)
else:
mbonds[m] = [b]
for m, bonds in mbonds.items():
msg = ('%s: %d bonds with total length %g\n'
% (m.name, len(bonds), path_length(bonds)))
from chimera import replyobj
replyobj.status(msg) # Show on status line
replyobj.message(msg) # Record in reply log
def interpolateCommand(molecule, name="default", method=None, rate=None,
frames=None, cartesian=False):
if len(molecule) != 1:
from chimera import UserError
raise UserError("You must specify exactly one molecule")
m = molecule[0]
ms = _find(name)
kw = {}
if method is not None:
kw["method"] = method
if rate is not None:
kw["rate"] = rate
if frames is not None:
kw["frames"] = frames
_verifyOpts(kw)
ms.addAction(m, **kw)
from chimera import replyobj
msg = "Interpolation \"%s\" updated\n" % name
replyobj.message(msg)
replyobj.status(msg)
def apply(self, vFunc=None, eFunc=None):
"""Apply given functions to selected objects
selection.apply(vFunc=lambda...) => None
It is incumbant on the code to follow guarantees that
the the vertex function is called before the edge
function.
Note: many types of exceptions can happen when the code
is executed.
"""
funcGlobals = {
"__doc__": None,
"__name__": "CodeSelection",
"__builtins__": __builtins__
}
funcLocals = {
"models": chimera.openModels.list(),
"vFunc": vFunc,
"eFunc": eFunc,
"funcs": {
SelVertex: vFunc,
SelEdge: eFunc
}
}
# helper function, so code can call 'selApply(obj)' without
# knowing what the selection type of the object is.
funcLocals["selApply"] = lambda obj, funcs=funcLocals["funcs"]:\
funcs[obj.oslLevel()](obj)
try:
exec self.codeObj in funcGlobals, funcLocals
except:
import string
from chimera import replyobj
replyobj.pushMode(replyobj.ERROR)
replyobj.message(str(self.name()) + " Code Selection failed\n")
s = apply(traceback.format_exception, sys.exc_info())
replyobj.message(string.join(s, ''))
replyobj.popMode()
def apply(self, vFunc = None, eFunc = None):
"""Apply given functions to selected objects
selection.apply(vFunc=lambda...) => None
It is incumbant on the code to follow guarantees that
the the vertex function is called before the edge
function.
Note: many types of exceptions can happen when the code
is executed.
"""
funcGlobals = {
"__doc__": None,
"__name__": "CodeSelection",
"__builtins__": __builtins__
}
funcLocals = {
"models": chimera.openModels.list(),
"vFunc": vFunc, "eFunc" : eFunc,
"funcs": {
SelVertex: vFunc, SelEdge: eFunc
}
}
# helper function, so code can call 'selApply(obj)' without
# knowing what the selection type of the object is.
funcLocals["selApply"] = lambda obj, funcs=funcLocals["funcs"]:\
funcs[obj.oslLevel()](obj)
try:
exec self.codeObj in funcGlobals, funcLocals
except:
import string
from chimera import replyobj
replyobj.pushMode(replyobj.ERROR)
replyobj.message(str(self.name()) +
" Code Selection failed\n")
s = apply(traceback.format_exception,
sys.exc_info())
replyobj.message(string.join(s, ''))
replyobj.popMode()
def makeTrajectory(self, minimize=False, steps=60):
from chimera import replyobj
#
# It's an all-or-nothing deal. If any step requires
# minimization, all molecules must have hydrogens
# because the interpolation routines requires a 1-1
# atom mapping between the two conformations
#
if not minimize:
molMap = {}
for mol, options in self.actions:
molMap[mol] = mol
else:
import AddH
kw = {
"delSolvent": False,
"nogui": True,
"addHFunc": AddH.simpleAddHydrogens,
}
import DockPrep
from util import mapAtoms, copyMolecule
refMol = None
for mol, options in self.actions:
if self.addhMap.has_key(mol):
refMol = mol
if refMol is None:
refMol = self.actions[0][0]
replyobj.message("Add hydrogens to %s\n"
% refMol.oslIdent())
m, aMap, rMap = copyMolecule(refMol)
DockPrep.prep([m], **kw)
self.addhMap[refMol] = m
for mol, options in self.actions:
if self.addhMap.has_key(mol):
continue
amap = mapAtoms(mol, refMol,
ignoreUnmatched=True)
for a, refa in amap.iteritems():
a.idatmType = refa.idatmType
replyobj.message("Add hydrogens to %s\n"
% mol.oslIdent())
m, aMap, rMap = copyMolecule(mol)
DockPrep.prep([m], **kw)
self.addhMap[mol] = m
molMap = self.addhMap
import copy
mol, options = self.actions[0]
initOptions = copy.copy(options)
if self.motion is None:
from Motion import MolecularMotion
self.motion = MolecularMotion(molMap[mol],
mol.openState.xform,
minimize=minimize,
steps=steps,
**initOptions)
else:
self.motion.reset(minimize=minimize, steps=steps,
**initOptions)
prevMol = mol
prevOptions = copy.copy(options)
for i in range(1, len(self.actions)):
msg = "Computing interpolation %d\n" % i
replyobj.message(msg)
replyobj.status(msg)
mol, options = self.actions[i]
prevOptions.update(options)
try:
self.motion.interpolate(molMap[mol],
mol.openState.xform,
**prevOptions)
except ValueError, msg:
from chimera import UserError
raise UserError("cannot interpolate models: %s"
% msg)
prevMol = mol
def findHBonds(models, intermodel=True, intramodel=True, donors=None,
acceptors=None, distSlop=0.0, angleSlop=0.0,
interSubmodel=False, cacheDA=False):
# to restrict to specific donor/acceptor atoms, 'donors' and/or
# acceptors should be atom lists (or dictionaries with atom keys)
#
# 'cacheDA' allows donors/acceptors in molecules to be cached if
# it is anticipated that the same structures will be examined for
# H-bonds repeatedly (e.g. a dynamics trajectory).
if donors and not isinstance(donors, (dict, set)):
limitedDonors = set(donors)
else:
limitedDonors = donors
if acceptors and not isinstance(acceptors, (dict, set)):
limitedAcceptors = set(acceptors)
else:
limitedAcceptors = acceptors
global _Dcache, _Acache, _prevLimited
if cacheDA:
if limitedDonors:
dIDs = [id(d) for d in limitedDonors]
dIDs.sort()
else:
dIDs = None
if limitedAcceptors:
aIDs = [id(a) for a in limitedAcceptors]
aIDs.sort()
else:
aIDs = None
key = (dIDs, aIDs)
if _prevLimited and _prevLimited != key:
flushCache()
_prevLimited = key
from weakref import WeakKeyDictionary
if _Dcache is None:
_Dcache = WeakKeyDictionary()
_Acache = WeakKeyDictionary()
else:
flushCache()
global donorParams, acceptorParams
global processedDonorParams, processedAcceptorParams
global _computeCache
global verbose
global _problem
_problem = None
badConnectivities = 0
# Used as necessary to cache expensive calculations (by other
# functions also)
_computeCache = {}
processKey = (distSlop, angleSlop)
if processKey not in processedAcceptorParams:
# copy.deepcopy() refuses to copy functions (even as
# references), so do this instead...
aParams = []
for p in acceptorParams:
aParams.append(copy.copy(p))
for i in range(len(aParams)):
aParams[i][3] = _processArgTuple(aParams[i][3],
distSlop, angleSlop)
processedAcceptorParams[processKey] = aParams
else:
aParams = processedAcceptorParams[processKey]
# compute some info for generic acceptors/donors
genericAccInfo = {}
# oxygens...
genericOAccArgs = _processArgTuple([3.53, 90], distSlop,
angleSlop)
genericAccInfo['miscO'] = (accGeneric, genericOAccArgs)
# dictionary based on bonded atom's geometry...
genericAccInfo['O2-'] = {
single: (accGeneric, genericOAccArgs),
linear: (accGeneric, genericOAccArgs),
planar: (accPhiPsi, _processArgTuple([3.53, 90, 130],
distSlop, angleSlop)),
tetrahedral: (accGeneric, genericOAccArgs)
}
genericAccInfo['O3-'] = genericAccInfo['O2-']
genericAccInfo['O2'] = {
single: (accGeneric, genericOAccArgs),
linear: (accGeneric, genericOAccArgs),
planar: (accPhiPsi, _processArgTuple([3.30, 110, 130],
distSlop, angleSlop)),
tetrahedral: (accThetaTau, _processArgTuple(
[3.03, 100, -180, 145], distSlop, angleSlop))
}
# list based on number of known bonded atoms...
genericAccInfo['O3'] = [
(accGeneric, genericOAccArgs),
(accThetaTau, _processArgTuple([3.17, 100, -161, 145],
distSlop, angleSlop)),
(accPhiPsi, _processArgTuple([3.42, 120, 135],
distSlop, angleSlop))
]
# nitrogens...
genericNAccArgs = _processArgTuple([3.42, 90], distSlop,
angleSlop)
genericAccInfo['miscN'] = (accGeneric, genericNAccArgs)
genericAccInfo['N2'] = (accPhiPsi, _processArgTuple([3.42, 140, 135],
distSlop, angleSlop))
# tuple based on number of bonded heavy atoms...
genericN3MultHeavyAccArgs = _processArgTuple([3.30, 153, -180, 145],
distSlop, angleSlop)
genericAccInfo['N3'] = (
(accGeneric, genericNAccArgs),
# only one example to draw from; weaken by .1A, 5 degrees
(accThetaTau, _processArgTuple([3.13, 98, -180, 150],
distSlop, angleSlop)),
(accThetaTau, genericN3MultHeavyAccArgs),
(accThetaTau, genericN3MultHeavyAccArgs)
)
# one example only; weaken by .1A, 5 degrees
genericAccInfo['N1'] = (accThetaTau, _processArgTuple(
[3.40, 136, -180, 145], distSlop, angleSlop))
# sulfurs...
# one example only; weaken by .1A, 5 degrees
genericAccInfo['S2'] = (accPhiPsi, _processArgTuple([3.83, 85, 140],
distSlop, angleSlop))
genericAccInfo['Sar'] = genericAccInfo['S3-'] = (accGeneric,
_processArgTuple([3.83, 85], distSlop, angleSlop))
# now the donors...
# planar nitrogens
genDonNpl1HParams = (donThetaTau, _processArgTuple([2.23, 136,
2.23, 141, 140, 2.46, 136, 140], distSlop, angleSlop))
genDonNpl2HParams = (donUpsilonTau, _processArgTuple([3.30, 90, -153,
135, -45, 3.30, 90, -146, 140, -37.5, 130, 3.40, 108, -166, 125,
-35, 140], distSlop, angleSlop))
genDonODists = [2.41, 2.28, 2.28, 3.27, 3.14, 3.14]
genDonOParams = (donGeneric, _processArgTuple(
genDonODists, distSlop, angleSlop))
genDonNDists = [2.36, 2.48, 2.48, 3.30, 3.42, 3.42]
genDonNParams = (donGeneric, _processArgTuple(
genDonNDists, distSlop, angleSlop))
genDonSDists = [2.42, 2.42, 2.42, 3.65, 3.65, 3.65]
genDonSParams = (donGeneric, _processArgTuple(
genDonSDists, distSlop, angleSlop))
genericDonInfo = {
'O': genDonOParams,
'N': genDonNParams,
'S': genDonSParams
}
accTrees = {}
hbonds = []
hasSulfur = {}
for model in models:
replyobj.status("Finding acceptors in model '%s'\n"
% model.name, blankAfter=0)
if cacheDA \
and _Acache.has_key(model) \
and _Acache[model].has_key((distSlop, angleSlop)):
accAtoms = []
accData = []
for accAtom, data in _Acache[model][(distSlop,
angleSlop)].items():
if not accAtom.__destroyed__:
accAtoms.append(accAtom)
accData.append(data)
else:
accAtoms, accData = _findAcceptors(model, aParams,
limitedAcceptors, genericAccInfo)
if cacheDA:
cache = WeakKeyDictionary()
for i in range(len(accAtoms)):
cache[accAtoms[i]] = accData[i]
if not _Acache.has_key(model):
_Acache[model] = {}
_Acache[model][(distSlop, angleSlop)] = cache
xyz = []
hasSulfur[model] = False
for accAtom in accAtoms:
c = accAtom.xformCoord()
xyz.append([c.x, c.y, c.z])
if accAtom.element.number == Element.S:
hasSulfur[model] = True
replyobj.status("Building search tree of acceptor atoms\n",
blankAfter=0)
accTrees[model] = AdaptiveTree(xyz, accData, 3.0)
if processKey not in processedDonorParams:
# find max donor distances before they get squared..
# copy.deepcopy() refuses to copy functions (even as
# references), so do this instead...
dParams = []
for p in donorParams:
dParams.append(copy.copy(p))
for di in range(len(dParams)):
geomType = dParams[di][2]
argList = dParams[di][4]
donRad = Element.bondRadius(Element(Element.N))
if geomType == thetaTau:
maxDist = max((argList[0], argList[2],
argList[5]))
elif geomType == upsilonTau:
maxDist = max((argList[0], argList[5],
argList[11]))
elif geomType == water:
maxDist = max((argList[1], argList[4],
argList[8]))
else:
maxDist = max(genDonODists
+ genDonNDists + genDonSDists)
donRad = Element.bondRadius(Element(Element.S))
dParams[di].append(maxDist + distSlop + donRad
+ Element.bondRadius(Element(Element.H)))
for i in range(len(dParams)):
dParams[i][4] = _processArgTuple(dParams[i][4],
distSlop, angleSlop)
processedDonorParams[processKey] = dParams
else:
dParams = processedDonorParams[processKey]
genericWaterParams = _processArgTuple([2.36, 2.36 + OHbondDist, 146],
distSlop, angleSlop)
genericThetaTauParams = _processArgTuple([2.48, 132],
distSlop, angleSlop)
genericUpsilonTauParams = _processArgTuple([3.42, 90, -161, 125],
distSlop, angleSlop)
genericGenericParams = _processArgTuple([2.48, 3.42, 130, 90],
distSlop, angleSlop)
for dmi in range(len(models)):
model = models[dmi]
replyobj.status("Finding donors in model '%s'\n" % model.name,
blankAfter=0)
if cacheDA \
and _Dcache.has_key(model) \
and _Dcache[model].has_key((distSlop, angleSlop)):
donAtoms = []
donData = []
for donAtom, data in _Dcache[model][(distSlop,
angleSlop)].items():
if not donAtom.__destroyed__:
donAtoms.append(donAtom)
donData.append(data)
else:
donAtoms, donData = _findDonors(model, dParams,
limitedDonors, genericDonInfo)
if cacheDA:
cache = WeakKeyDictionary()
for i in range(len(donAtoms)):
cache[donAtoms[i]] = donData[i]
if not _Dcache.has_key(model):
_Dcache[model] = {}
_Dcache[model][(distSlop, angleSlop)] = cache
replyobj.status("Matching donors in model '%s' to acceptors\n"
% model.name, blankAfter=0)
for i in range(len(donAtoms)):
donorAtom = donAtoms[i]
geomType, tauSym, argList, testDist = donData[i]
donorHyds = hydPositions(donorAtom)
coord = donorAtom.xformCoord()
for accModel in models:
if accModel == model and not intramodel\
or accModel != model and not intermodel:
continue
if accModel.id == model.id \
and not interSubmodel \
and accModel.subid != model.subid:
continue
if hasSulfur[accModel]:
from commonGeom import SULFUR_COMP
td = testDist + SULFUR_COMP
else:
td = testDist
accs = accTrees[accModel].searchTree(
[coord.x, coord.y, coord.z], td)
if verbose:
replyobj.message("Found %d possible acceptors for donor %s:\n" % (len(accs), donorAtom.oslIdent()))
for accData in accs:
replyobj.message("\t%s\n" % accData[0].oslIdent())
for accAtom, geomFunc, args in accs:
if accAtom == donorAtom:
# e.g. hydroxyl
if verbose:
print "skipping: donor == acceptor"
continue
# exclude hbonding between
# differing alt locations of
# same residue
if accAtom.altLoc.isalnum() and donorAtom.altLoc.isalnum() and accAtom.residue == donorAtom.residue and accAtom.altLoc != donorAtom.altLoc:
continue
try:
if not apply(geomFunc,
(donorAtom, donorHyds) + args):
continue
except ConnectivityError, v:
replyobj.message("Skipping possible acceptor with bad geometry: %s\n%s\n\n" % (accAtom.oslIdent(), v))
badConnectivities += 1
continue
if verbose:
replyobj.message("\t%s satisfies acceptor criteria\n" % accAtom.oslIdent())
if geomType == upsilonTau:
donorFunc = donUpsilonTau
addArgs = genericUpsilonTauParams + [tauSym]
elif geomType == thetaTau:
donorFunc = donThetaTau
addArgs = genericThetaTauParams
elif geomType == water:
donorFunc = donWater
addArgs = genericWaterParams
else:
if donorAtom.idatmType in ["Npl", "N2+"]:
heavys = 0
for bonded in donorAtom.primaryNeighbors():
if bonded.element.number > 1:
heavys += 1
if heavys > 1:
info = genDonNpl1HParams
else:
info = genDonNpl2HParams
else:
info = genericDonInfo[donorAtom.element.name]
donorFunc, argList = info
addArgs = genericGenericParams
if donorFunc == donUpsilonTau:
# tack on generic
# tau symmetry
addArgs = genericUpsilonTauParams + [4]
elif donorFunc == donThetaTau:
addArgs = genericThetaTauParams
try:
if not apply(donorFunc,
(donorAtom, donorHyds, accAtom)
+ tuple(argList + addArgs)):
continue
except ConnectivityError, v:
replyobj.message("Skipping possible donor with bad geometry: %s\n%s\n\n" % (donorAtom.oslIdent(), v))
badConnectivities += 1
continue
except AtomTypeError, v:
_problem = ("atom type",
donorAtom, v, None)
continue
if verbose:
replyobj.message("\t%s satisfies donor criteria\n" % donorAtom.oslIdent())
hbonds.append((donorAtom, accAtom))
def doneCommand(name="default"): from chimera import replyobj _remove(name) msg = "Interpolation \"%s\" removed\n" % name replyobj.message(msg) replyobj.status(msg)
def doneCommand(name="default"):
from chimera import replyobj
_remove(name)
msg = "Interpolation \"%s\" removed\n" % name
replyobj.message(msg)
replyobj.status(msg)
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 showURLContent(self, title, url):
from chimera import replyobj
data = self.getURLContent(url)
replyobj.message("%s\n-----\n%s-----\n" % (title, data))
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 showURLContent(self, title, url):
from chimera import replyobj
data = self.getURLContent(url)
replyobj.message("%s\n-----\n%s-----\n" % (title, data))