def pairAlign(chains, cutoff, gapChar, statusPrefix=""):
chain1, chain2 = chains
# go through chain 1 and put each residue's principal
# atom in a spatial tree
from chimera.misc import principalAtom
from CGLutil.AdaptiveTree import AdaptiveTree
xyzs = []
data = []
for i in range(len(chain1)):
res = chain1.residues[i]
pa = principalAtom(res)
if not pa:
replyobj.warning("Cannot determine principal"
" atom for residue %s\n"
% res.oslIdent())
continue
xyzs.append(pa.xformCoord().data())
data.append((i, pa.xformCoord()))
tree = AdaptiveTree(xyzs, data, cutoff)
# initialize score array
from numpy import zeros
scores = zeros((len(chain1),len(chain2)), float)
scores -= 1.0
# find matches and update score array
for i2 in range(len(chain2)):
res = chain2.residues[i2]
pa = principalAtom(res)
if not pa:
replyobj.warning("Cannot determine principal"
" atom for residue %s\n"
% res.oslIdent())
continue
coord2 = pa.xformCoord()
matches = tree.searchTree(coord2.data(), cutoff)
for i1, coord1 in matches:
dist = coord1.distance(coord2)
if dist > cutoff:
continue
scores[i1][i2] = cutoff - dist
# use NeedlemanWunsch to establish alignment
from NeedlemanWunsch import nw
score, seqs = nw(chain1, chain2, scoreMatrix=scores, gapChar=gapChar,
returnSeqs=True, scoreGap=0, scoreGapOpen=0)
smallest = min(len(chain1), len(chain2))
minDots = max(len(chain1), len(chain2)) - smallest
extraDots = len(seqs[0]) - smallest - minDots
numMatches = smallest - extraDots
replyobj.status("%s%d residue pairs aligned\n"
% (statusPrefix, numMatches), log=True)
if numMatches == 0:
from chimera import UserError
raise UserError("Cannot generate alignment because no"
" residues within cutoff distance")
return score, seqs
def columnAtoms(seq, columns): from chimera.misc import principalAtom seqColumns = [seq.gapped2ungapped(i) for i in columns] if getattr(seq, 'circular', False): numRes = len(seq.residues) return [principalAtom(r) for r in [seq.residues[i % numRes] for i in seqColumns]] return [principalAtom(r) for r in [seq.residues[i] for i in seqColumns]]
def evaluate(self, pos):
coords = []
from chimera.misc import principalAtom
for mol, seq in self.mav.associations.items():
ungapped = seq.gapped2ungapped(pos)
matchMap = seq.matchMaps[mol]
if ungapped == None or ungapped not in matchMap:
continue
pa = principalAtom(matchMap[ungapped])
if not pa:
continue
coords.append(pa.xformCoord())
if len(coords) < 2:
return None
sum = 0.0
for i, crd1 in enumerate(coords):
for crd2 in coords[i + 1:]:
sum += crd1.sqdistance(crd2)
from math import sqrt
n = (len(coords) * (len(coords) - 1)) / 2
return sqrt(sum / n)
def evaluate(self, pos): coords = [] from chimera.misc import principalAtom for mol, seq in self.mav.associations.items(): ungapped = seq.gapped2ungapped(pos) matchMap = seq.matchMaps[mol] if ungapped == None or ungapped not in matchMap: continue pa = principalAtom(matchMap[ungapped]) if not pa: continue coords.append(pa.xformCoord()) if len(coords) < 2: return None sum = 0.0 for i , crd1 in enumerate(coords): for crd2 in coords[i+1:]: sum += crd1.sqdistance(crd2) from math import sqrt n = (len(coords) * (len(coords) - 1)) / 2 return sqrt(sum / n)
def match(chainPairing, matchItems, matrix, alg, gapOpen, gapExtend,
iterate=None, showAlignment=False, align=align, **alignKw):
"""Superimpose structures based on sequence alignment
'chainPairing' is the method of pairing chains to match:
CP_SPECIFIC_SPECIFIC --
Each reference chain is paired with a specified match chain
CP_SPECIFIC_BEST --
Single reference chain is paired with best seq-aligning
chain from one or more molecules
CP_BEST --
Best seq-aligning pair of chains from reference molecule and
match molecule(s) is used
"""
ksdsspCache = set()
alg = alg.lower()
if alg == "nw" or alg.startswith("needle"):
alg = "nw"
algName = "Needleman-Wunsch"
elif alg =="sw" or alg.startswith("smith"):
alg = "sw"
algName = "Smith-Waterman"
else:
raise ValueError("Unknown sequence alignment algorithm: %s"
% alg)
pairings = {}
smallMolErrMsg = "Reference and/or match model contains no nucleic or"\
" amino acid chains.\nUse the command-line 'match' command" \
" to superimpose small molecules/ligands."
if chainPairing == CP_SPECIFIC_SPECIFIC:
# specific chain(s) in each
# various sanity checks
#
# (1) can't have same chain matched to multiple refs
# (2) reference molecule can't be a match molecule
matchChains = {}
matchMols = {}
refMols = {}
for ref, match in matchItems:
if not matrixCompatible(ref, matrix):
raise UserError("Reference chain (%s) not"
" compatible with %s similarity"
" matrix" % (ref.fullName(), matrix))
if not matrixCompatible(match, matrix):
raise UserError("Match chain (%s) not"
" compatible with %s similarity"
" matrix" % (match.fullName(), matrix))
if match in matchChains:
raise UserError("Cannot match the same chain"
" to multiple reference chains")
matchChains[match] = ref
if match.molecule in refMols \
or ref.molecule in matchMols \
or match.molecule == ref.molecule:
raise UserError("Cannot have same molecule"
" model provide both reference and"
" match chains")
matchMols[match.molecule] = ref
refMols[ref.molecule] = match
if not matchChains:
raise UserError("Must select at least one reference"
" chain.\n")
for match, ref in matchChains.items():
score, s1, s2 = align(ref, match, matrix, alg,
gapOpen, gapExtend,
ksdsspCache, **alignKw)
pairings.setdefault(s2.molecule, []).append(
(score, s1, s2))
elif chainPairing == CP_SPECIFIC_BEST:
# specific chain in reference;
# best seq-aligning chain in match model(s)
ref, matches = matchItems
if not ref or not matches:
raise UserError("Must select at least one reference"
" and match item.\n")
if not matrixCompatible(ref, matrix):
raise UserError("Reference chain (%s) not compatible"
" with %s similarity matrix"
% (ref.fullName(), matrix))
for match in matches:
bestScore = None
seqs = [s for s in match.sequences()
if matrixCompatible(s, matrix)]
if not seqs and match.sequences():
raise UserError("No chains in match structure"
" %s compatible with %s similarity"
" matrix" % (match, matrix))
for seq in seqs:
score, s1, s2 = align(ref, seq, matrix, alg,
gapOpen, gapExtend,
ksdsspCache, **alignKw)
if bestScore is None or score > bestScore:
bestScore = score
pairing = (score, s1, s2)
if bestScore is None:
raise LimitationError(smallMolErrMsg)
pairings[match]= [pairing]
elif chainPairing == CP_BEST:
# best seq-aligning pair of chains between
# reference and match structure(s)
ref, matches = matchItems
if not ref or not matches:
raise UserError("Must select at least one reference"
" and match item in different models.\n")
rseqs = [s for s in ref.sequences()
if matrixCompatible(s, matrix)]
if not rseqs and ref.sequences():
raise UserError("No chains in reference structure"
" %s compatible with %s similarity"
" matrix" % (ref, matrix))
for match in matches:
bestScore = None
mseqs = [s for s in match.sequences()
if matrixCompatible(s, matrix)]
if not mseqs and match.sequences():
raise UserError("No chains in match structure"
" %s compatible with %s similarity"
" matrix" % (match, matrix))
for mseq in mseqs:
for rseq in rseqs:
score, s1, s2 = align(rseq, mseq,
matrix, alg, gapOpen, gapExtend,
ksdsspCache, **alignKw)
if bestScore is None \
or score > bestScore:
bestScore = score
pairing = (score,s1,s2)
if bestScore is None:
raise LimitationError(smallMolErrMsg)
pairings[match]= [pairing]
else:
raise ValueError("No such chain-pairing method")
from chimera.misc import principalAtom
retVals = []
for matchMol, pairs in pairings.items():
refAtoms = []
matchAtoms = []
regionInfo = {}
for score, s1, s2 in pairs:
try:
ssMatrix = alignKw['ssMatrix']
except KeyError:
ssMatrix = defaultSSMatrix
try:
ssFraction = alignKw['ssFraction']
except KeyError:
ssFraction = defaults[SS_MIXTURE]
replyobj.status("match %s (%s) with %s (%s),"
" score = %g\n" % (
s1.name, s1.molecule.oslIdent(), s2.name,
s2.molecule.oslIdent(), score), log=1)
replyobj.info("with these parameters:\n"
"\tchain pairing: %s\n\t%s using %s\n"
% (chainPairing, algName, matrix))
if ssFraction is None or ssFraction is False:
replyobj.info("\tno secondary structure"
" guidance used\n")
replyobj.info("\tgap open %g, extend %g\n" % (
gapOpen, gapExtend))
else:
if 'gapOpenHelix' in alignKw:
gh = alignKw['gapOpenHelix']
else:
gh = defaults[HELIX_OPEN]
if 'gapOpenStrand' in alignKw:
gs = alignKw['gapOpenStrand']
else:
gs = defaults[STRAND_OPEN]
if 'gapOpenOther' in alignKw:
go = alignKw['gapOpenOther']
else:
go = defaults[OTHER_OPEN]
replyobj.info("\tss fraction: %g\n"
"\tgap open (HH/SS/other) %g/%g/%g, "
"extend %g\n"
"\tss matrix: " % (ssFraction, gh, gs,
go, gapExtend))
for ss1, ss2 in ssMatrix.keys():
if ss2 < ss1:
continue
replyobj.info(" (%s, %s): %g" % (ss1,
ss2, ssMatrix[(ss1, ss2)]))
replyobj.info("\n")
if iterate is None:
replyobj.info("\tno iteration\n")
else:
replyobj.info("\titeration cutoff: %g\n"
% iterate)
if showAlignment:
from MultAlignViewer.MAViewer import MAViewer
mav = MAViewer([s1,s2], autoAssociate=None)
mav.autoAssociate = True
mav.hideHeaders(mav.headers(shownOnly=True))
mav.showHeaders([h for h in mav.headers()
if h.name == "RMSD"])
for i in range(len(s1)):
if s1[i] == "." or s2[i] == ".":
continue
refRes = s1.residues[s1.gapped2ungapped(i)]
matchRes = s2.residues[s2.gapped2ungapped(i)]
if not refRes:
continue
refAtom = principalAtom(refRes)
if not refAtom:
continue
if not matchRes:
continue
matchAtom = principalAtom(matchRes)
if not matchAtom:
continue
if refAtom.name != matchAtom.name:
# nucleic P-only trace vs. full nucleic
if refAtom.name != "P":
try:
refAtom = refAtom.residue.atomsMap["P"][0]
except KeyError:
continue
else:
try:
matchAtom = matchAtom.residue.atomsMap["P"][0]
except KeyError:
continue
refAtoms.append(refAtom)
matchAtoms.append(matchAtom)
if showAlignment and iterate is not None:
regionInfo[refAtom] = (mav, i)
import Midas
if len(matchAtoms) < 3:
replyobj.error("Fewer than 3 residues aligned; cannot"
" match %s with %s\n" % (s1.name, s2.name))
continue
try:
retVals.append(Midas.match(matchAtoms, refAtoms,
iterate=iterate, minPoints=3))
except Midas.TooFewAtomsError:
replyobj.error("Iteration produces fewer than 3"
" residues aligned.\nCannot match %s with %s"
" satisfying iteration threshold.\n"
% (s1.name, s2.name))
continue
replyobj.info("\n") # separate matches with whitespace
if regionInfo:
byMav = {}
for ra in retVals[-1][1]:
mav, index = regionInfo[ra]
byMav.setdefault(mav, []).append(index)
for mav, indices in byMav.items():
indices.sort()
from MultAlignViewer.MAViewer import \
MATCHED_REGION_INFO
name, fill, outline = MATCHED_REGION_INFO
mav.newRegion(name=name, columns=indices,
fill=fill, outline=outline)
mav.status("Residues used in final fit"
" iteration are highlighted")
return retVals
def addStandardCharges(models=None,
status=None,
phosphorylation=None,
chargeModel=None,
nogui=False,
showCharges=False):
"""add AMBER charges to well-known residues
'models' restricts the addition to the specified models
'status' is where status messages go (e.g. replyobj.status)
'phosphorylation' controls whether chain-terminal nucleic acids
will have their phosphorylation state changed to correspond to
AMBER charge files (3' phosphorylated, 5' not). A value of None
means that the user will be queried if possible [treated as True
if not possible].
'showCharges' controls whether atoms get labeled with their charge.
The return value is a 2-tuple of dictionaries: the first of which
details the residues that did not receive charges [key: residue
type, value: list of residues], and the second lists remaining
uncharged atoms [key: (residue type, atom name), value: list of
atoms]
Hydrogens need to be present.
"""
from AddAttr import addAttributes
import os.path
attrFile = os.path.join(os.path.split(__file__)[0], "amberName.defattr")
if status:
status("Defining AMBER residue types\n")
addAttributes(attrFile, models=models, raiseAttrDialog=False)
if models is None:
mols = chimera.openModels.list(modelTypes=[chimera.Molecule])
else:
mols = models
if phosphorylation != False:
if status:
status("Checking phosphorylation of chain-terminal"
" nucleic acids\n")
likeAmber = True
deletes = []
for m in mols:
for r in m.residues:
amberName = getattr(r, 'amberName', "UNK")
if len(amberName) != 2 \
or amberName[0] not in 'DR' \
or amberName[1] not in 'ACGTU' \
or 'P' not in r.atomsMap:
continue
p = r.atomsMap['P'][0]
for nb in p.neighbors:
if nb.residue != r:
break
else:
# trailing phosphate
deletes.append(r)
if deletes:
if phosphorylation is None:
if nogui or chimera.nogui:
phosphorylation = True
else:
from gui import PhosphorylateDialog
phosphorylation = PhosphorylateDialog().run(
chimera.tkgui.app)
if phosphorylation:
_phosphorylate(mols, status, deletes)
if status:
status("Adding standard charges\n")
unchargedResTypes = {}
unchargedAtoms = {}
unchargedResidues = set()
from dict import ffChargeTypeData
from SimpleSession import registerAttribute
registerAttribute(chimera.Molecule, "chargeModel")
registerAttribute(chimera.Atom, "gaffType")
if chargeModel == None:
chargeModel = defaultChargeModel
replyobj.info("Charge model: %s\n" % chargeModel)
chargeTypeData = ffChargeTypeData[chargeModel]
track = chimera.TrackChanges.get()
for m in mols:
m.chargeModel = chargeModel
track.addModified(m, ATTR_SET)
for r in m.residues:
if getattr(r, '_solvateCharged', False):
continue
if not hasattr(r, 'amberName'):
unchargedResidues.add(r)
unchargedResTypes.setdefault(r.type, []).append(r)
for a in m.atoms:
if getattr(a.residue, '_solvateCharged', False):
continue
a.charge = 0.0
track.addModified(a, ATTR_SET)
if a.residue.type in unchargedResTypes:
if showCharges:
a.label = str(a.charge)
continue
atomKeys = [a.name.lower()]
if a.element.number == 1 and a.name.lower()[0] in "dt":
atomKeys.append('h' + a.name.lower()[1:])
atomKeys.append(a.element)
for ak in atomKeys:
key = (a.residue.amberName, ak)
try:
a.charge, a.gaffType = chargeTypeData[key]
except KeyError:
continue
if showCharges:
a.label = "%+g" % a.charge
break
else:
unchargedAtoms.setdefault((a.residue.type, a.name),
[]).append(a)
# merge connected non-standard residues into a "mega" residue.
# also any standard residues directly connected
for urt, urs in unchargedResTypes.items():
for ur in urs[:]:
if urt not in unchargedResTypes:
break
if ur not in unchargedResTypes[urt]:
# connected to residue of same type and
# previously removed
continue
connected = [ur]
queue = [ur]
while queue:
curRes = queue.pop(0)
neighbors = set()
stdConnects = {}
for a in curRes.atoms:
for na in a.neighbors:
naRes = na.residue
if naRes == curRes \
or naRes in connected:
continue
# don't add standard residue
# if connected through chain
# bond
if naRes not in unchargedResidues:
from chimera.misc \
import principalAtom
pa = principalAtom(naRes)
if pa != None:
if pa.name == 'CA':
testNames = ['N', 'C']
else:
testNames = ['P', "O3'"]
if na.name in testNames and na.name not in stdConnects.get(
naRes, set()):
stdConnects.setdefault(naRes,
set()).add(na.name)
continue
neighbors.add(naRes)
neighbors = list(neighbors)
neighbors.sort(lambda r1, r2: cmp(r1.type, r2.type))
connected.extend(neighbors)
queue.extend(
[nb for nb in neighbors if nb in unchargedResidues])
# avoid using atom names with the trailing "-number"
# distinguisher if possible...
if len(connected) > 1:
fr = FakeRes(connected)
else:
fr = connected[0]
unchargedResTypes.setdefault(fr.type, []).append(fr)
for cr in connected:
if cr in unchargedResidues:
unchargedResTypes[cr.type].remove(cr)
if not unchargedResTypes[cr.type]:
del unchargedResTypes[cr.type]
continue
# remove standard-residue atoms from
# uncharged list
for ca in cr.atoms:
uas = unchargedAtoms.get((cr.type, ca.name), [])
if ca not in uas:
continue
uas.remove(ca)
if not uas:
del unchargedAtoms[(cr.type, ca.name)]
# split isolated atoms (e.g. metals) into separate "residues"
for resType, residues in unchargedResTypes.items():
bondResidues = residues
brType = resType
while True:
if len(bondResidues[0].atoms) == 1:
break
for a in bondResidues[0].atoms:
if a.bonds:
continue
hasIso = [r for r in bondResidues if a.name in r.atomsMap]
if len(hasIso) == len(bondResidues):
rem = []
else:
rem = [r for r in bondResidues if r not in hasIso]
iso = []
nonIso = rem
isoType = "%s[%s]" % (resType, a.name)
brType = "%s[non-%s]" % (brType, a.name)
for r in hasIso:
isoRes = FakeRes(
isoType, [fa for fa in r.atoms if fa.name == a.name])
iso.append(isoRes)
nonIsoAtoms = [fa for fa in r.atoms if fa.name != a.name]
if not nonIsoAtoms:
brType = None
continue
nonIsoRes = FakeRes(brType, nonIsoAtoms)
nonIso.append(nonIsoRes)
unchargedResTypes[isoType] = iso
bondResidues = nonIso
else:
# no isolated atoms
break
if brType != resType:
del unchargedResTypes[resType]
if brType != None:
unchargedResTypes[brType] = bondResidues
# despite same residue type, residues may still differ -- particularly
# terminal vs. non-terminal...
for resType, residues in unchargedResTypes.items():
if len(residues) < 2:
continue
varieties = {}
for r in residues:
key = tuple([a.name for a in r.oslChildren()])
varieties.setdefault(key, []).append(r)
if len(varieties) == 1:
continue
# in order to give the varieties distinguishing names,
# find atoms in common
keys = varieties.keys()
common = set(keys[0])
for k in keys[1:]:
common = common.intersection(set(k))
uncommon = set()
for k in keys:
uncommon = uncommon.union(set(k) - common)
del unchargedResTypes[resType]
for k, residues in varieties.items():
names = set(k)
more = names - common
less = uncommon - names
newKey = resType
if more:
newKey += " (w/%s)" % ",".join(list(more))
if less:
newKey += " (wo/%s)" % ",".join(list(less))
unchargedResTypes[newKey] = residues
if status:
status("Standard charges added\n")
return unchargedResTypes, unchargedAtoms
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 multiAlign(chains, cutoff, matchType, gapChar, circular, statusPrefix=""):
# create list of pairings between sequences
# and prune to be monotonic
trees = {}
if matchType == "all":
valFunc = min
else:
valFunc = max
# for each pair, go through the second chain residue by residue
# and compile crosslinks to other chain. As links are compiled,
# figure out what previous links are crossed and keep a running
# "penalty" function for links based on what they cross.
# Sort links by penalty and keep pruning worst link until no links
# cross.
from chimera.misc import principalAtom
from CGLutil.AdaptiveTree import AdaptiveTree
class EndPoint:
def __init__(self, seq, pos):
self.seq = seq
self.pos = pos
def contains(self, seq, pos):
return seq == self.seq and pos == self.pos
def __getattr__(self, attr):
if attr == "positions":
return { self.seq: self.pos }
raise AttributeError, \
"No such EndPoint attribute: %s" % attr
def __str__(self):
from chimera import SelResidue
if circular and self.pos >= len(self.seq):
insert = " (circular 2nd half)"
pos = self.pos - len(self.seq)
else:
pos = self.pos
insert = ""
return "EndPoint[(%s %s, %s%s)]" % (self.seq.molecule.name, self.seq.name, self.seq.residues[pos].oslIdent(SelResidue), insert)
class Link:
def __init__(self, info1, info2, val, doPenalty=False):
self.info = [info1, info2]
self.val = val
if doPenalty:
self.penalty = 0
self.crosslinks = []
def contains(self, seq, pos):
return self.info[0].contains(seq, pos) \
or self.info[1].contains(seq. pos)
def evaluate(self):
self.val = None
for s1, p1 in self.info[0].positions.items():
if circular and s1.circular and p1 >= len(s1):
p1 -= len(s1)
pa1 = pas[s1][p1]
for s2, p2 in self.info[1].positions.items():
if circular and s2.circular \
and p2 >= len(s2):
p2 -= len(s2)
pa2 = pas[s2][p2]
val = cutoff - pa1.xformCoord(
).distance(pa2.xformCoord())
if self.val is None:
self.val = val
continue
self.val = valFunc(self.val, val)
if valFunc == min and self.val < 0:
break
if valFunc == min and self.val < 0:
break
def __str__(self):
return "Link(%s, %s)" % tuple(map(str, self.info))
allLinks = []
pas = {}
pairings = {}
replyobj.status("%sFinding residue principal atoms\n" % statusPrefix,
blankAfter=0)
for seq in chains:
seqpas = []
pairing = []
for res in seq.residues:
pa = principalAtom(res)
pairing.append([])
if circular:
pairing.append([])
if not pa:
replyobj.warning("Cannot determine principal "
"atom for residue %s\n" % res.oslIdent())
seqpas.append(None)
continue
seqpas.append(pa)
pas[seq] = seqpas
pairings[seq] = pairing
if circular:
circularPairs = {}
holdData = {}
tagTmpl = "(%%d/%d)" % ((len(chains)) * (len(chains)-1) / 2)
num = 0
for i, seq1 in enumerate(chains):
len1 = len(pairings[seq1])
for seq2 in chains[i+1:]:
num += 1
tag = tagTmpl % num
len2 = len(pairings[seq2])
links1 = []
for i in range(len1):
links1.append([])
links2 = []
for i in range(len2):
links2.append([])
linkList = []
replyobj.status("%sBuilding search tree %s\n"
% (statusPrefix, tag), blankAfter=0)
try:
tree = trees[seq2]
except KeyError:
xyzs = []
data = []
for i, pa in enumerate(pas[seq2]):
if pa is None:
continue
xyzs.append(pa.xformCoord().data())
data.append((i, pa))
tree = AdaptiveTree(xyzs, data, cutoff)
replyobj.status("%sSearching tree, building links %s\n"
% (statusPrefix, tag), blankAfter=0)
for i1, pa1 in enumerate(pas[seq1]):
if pa1 is None:
continue
crd1 = pa1.xformCoord()
matches = tree.searchTree(crd1.data(), cutoff)
for i2, pa2 in matches:
dist = crd1.distance(pa2.xformCoord())
val = cutoff - dist
if val <= 0:
continue
link = Link(EndPoint(seq1, i1),
EndPoint(seq2, i2), val,
doPenalty=True)
links1[i1].append(link)
links2[i2].append(link)
linkList.append(link)
if circular:
replyobj.status("%sDetermining circularity %s\n"
% (statusPrefix, tag), blankAfter=0)
holdData[(seq1, seq2)] = (links1, links2,
linkList)
if len(linkList) < 2:
replyobj.info("Less than 2 close"
" residues for %s and %s\n"
% (seq1.molecule.name,
seq2.molecule.name))
continue
# determine optimal permutation of 1st seq;
#
# for each pair of links, find the permutation
# where they begin to cross/uncross. Use an
# array to tabulate number of crossings for
# each permutation.
crossings = [0] * len(seq1)
c2 = [0] * len(seq2)
from random import sample
numSamples = 5 * (len(seq1)+len(seq2))
for ignore in range(numSamples):
link1, link2 = sample(linkList, 2)
l1p1 = link1.info[0].pos
l1p2 = link1.info[1].pos
l2p1 = link2.info[0].pos
l2p2 = link2.info[1].pos
if l1p1 == l2p1 \
or l1p2 == l2p2:
# can never cross
continue
first = len(seq1) - max(l1p1,
l2p1)
second = len(seq1) - min(l1p1,
l2p1)
if (l1p1 < l2p1) == (
l1p2 < l2p2):
# not crossed initially;
# will cross when first
# one permutes off end
# and uncross when 2nd
# one permutes off
ranges = [(first,
second)]
else:
# crossed initially
ranges = [(0, first)]
if second < len(seq1):
ranges.append(
(second,
len(seq1)))
for start, stop in ranges:
for i in range(start,
stop):
crossings[i] +=1
first = len(seq2) - max(l1p2,
l2p2)
second = len(seq2) - min(l1p2,
l2p2)
if (l1p1 < l2p1) == (
l1p2 < l2p2):
# not crossed initially;
# will cross when first
# one permutes off end
# and uncross when 2nd
# one permutes off
ranges = [(first,
second)]
else:
# crossed initially
ranges = [(0, first)]
if second < len(seq2):
ranges.append(
(second,
len(seq2)))
for start, stop in ranges:
for i in range(start,
stop):
c2[i] +=1
# to avoid dangling ends causing bogus
# "circularities", the zero permutation has
# to be beaten significantly for a
# circularity to be declared
least = crossings[0] - 5*numSamples / len(seq1)
permute1 = [0]
for i, crossed in enumerate(crossings):
if crossed < least:
least = crossed
permute1 = [i]
elif crossed == least:
permute1.append(i)
least = c2[0] - 5*numSamples / len(seq2)
permute2 = [0]
for i, crossed in enumerate(c2):
if crossed < least:
least = crossed
permute2 = [i]
elif crossed == least:
permute2.append(i)
if permute1[0] != 0 and permute2[0] != 0:
circularPairs[(seq1, seq2)] = (
permute1[0], permute2[0])
replyobj.info("%s %s / %s %s: permute %s by %d or %s by %d\n" % (seq1.molecule.name, seq1.name, seq2.molecule.name, seq2.name, seq1.molecule.name, permute1[0], seq2.molecule.name, permute2[0]))
else:
findPruneCrosslinks(allLinks, pairings, seq1,
seq2, linkList, links1, links2, tag=tag,
statusPrefix=statusPrefix)
if circular:
replyobj.status("%sMinimizing circularities\n" % statusPrefix,
blankAfter=0)
circulars = {}
while 1:
circularVotes = {}
for seq1, seq2 in circularPairs.keys():
if seq1 in circulars or seq2 in circulars:
continue
circularVotes[seq1] = circularVotes.get(seq1,
0) + 1
circularVotes[seq2] = circularVotes.get(seq2,
0) + 1
if not circularVotes:
break
candidates = circularVotes.keys()
candidates.sort(lambda c1, c2: cmp(circularVotes[c2],
circularVotes[c1]))
circulars[candidates[0]] = True
# has to be circular against every non-circular sequence
# (avoid spurious circularities)
ejected = True
while ejected:
ejected = False
for cseq in circulars:
for seq in chains:
if seq in circulars:
continue
if (cseq, seq) not in circularPairs \
and (seq, cseq) not in circularPairs:
del circulars[cseq]
ejected = True
break
if ejected:
break
for seq in chains:
seq.circular = seq in circulars
if seq.circular:
replyobj.info("circular: %s\n"
% seq.molecule.name)
replyobj.status("%sAdjusting links for circular sequences\n"
% statusPrefix, blankAfter=0)
for seq1, seq2 in holdData.keys():
if not seq1.circular and not seq2.circular:
continue
links1, links2, linkList = holdData[(seq1, seq2)]
use1 = seq1.circular
if seq1.circular and seq2.circular:
if (seq1, seq2) in circularPairs:
permute1, permute2 = circularPairs[
(seq1, seq2)]
elif (seq2, seq1) in circularPairs:
permute2, permute1 in circularPairs[
(seq2, seq1)]
else:
continue
use1 = len(seq1) - permute1 \
< len(seq2) - permute2
if use1:
adjust, other = seq1, seq2
links = links1
else:
adjust, other = seq2, seq1
links = links2
if (adjust, other) in circularPairs:
permute = circularPairs[(adjust, other)][0]
elif (other, adjust) in circularPairs:
permute = circularPairs[(other, adjust)][1]
else:
continue
fixup = len(adjust) - permute
for link in linkList[:]: # append happens in loop
if link.info[0].seq == adjust:
myEnd = link.info[0]
otherEnd = link.info[1]
else:
myEnd = link.info[1]
otherEnd = link.info[0]
if myEnd.pos >= fixup:
continue
links[myEnd.pos].remove(link)
myEnd.pos += len(adjust)
links[myEnd.pos].append(link)
for i, seqs in enumerate(holdData.keys()):
seq1, seq2 = seqs
links1, links2, linkList = holdData[seqs]
findPruneCrosslinks(allLinks, pairings, seq1, seq2,
linkList, links1, links2, tag=tagTmpl % (i+1),
statusPrefix=statusPrefix)
class Column:
def __init__(self, positions):
if isinstance(positions, Column):
self.positions = positions.positions.copy()
else:
self.positions = positions
def contains(self, seq, pos):
return seq in self.positions \
and self.positions[seq] == pos
def participation(self):
p = 0
members = self.positions.items()
for i, sp in enumerate(members):
seq1, pos1 = sp
if circular and seq1.circular \
and pos1 >= len(seq1):
pos1 -= len(seq1)
pa1 = pas[seq1][pos1]
for seq2, pos2 in members[i+1:]:
if circular and seq2.circular \
and pos2 >= len(seq2):
pos2 -= len(seq2)
pa2 = pas[seq2][pos2]
val = cutoff - pa1.xformCoord(
).distance(pa2.xformCoord())
p += val
return p
def value(self):
value = None
info = self.positions.items()
for i, sp in enumerate(info):
seq1, pos1 = sp
if circular and seq1.circular \
and pos1 >= len(seq1):
pos1 -= len(seq1)
pa1 = pas[seq1][pos1]
for seq2, pos2 in info[i+1:]:
if circular and seq2.circular \
and pos2 >= len(seq2):
pos2 -= len(seq2)
pa2 = pas[seq2][pos2]
val = cutoff - pa1.xformCoord(
).distance(pa2.xformCoord())
if value is None:
value = val
continue
value = valFunc(value, val)
if valFunc == min and value < 0:
break
if valFunc == min and value < 0:
break
return value
def __str__(self):
from chimera import SelResidue
def circComp(seq, pos):
if circular and seq.circular and pos>=len(seq):
return pos - len(seq)
return pos
return "Column[" + ",".join(map(lambda i: "(%s %s, %s)" % (i[0].molecule.name, i[0].name, i[0].residues[circComp(i[0],i[1])].oslIdent(SelResidue)), self.positions.items())) + "]"
columns = {}
partialOrder = {}
for seq in chains:
columns[seq] = {}
partialOrder[seq] = []
seen = {}
while allLinks:
replyobj.status("%sForming columns (%d links to check)\n"
% (statusPrefix, len(allLinks)))
if allLinks[-1].val != max(map(lambda l: l.val, allLinks)):
allLinks.sort(lambda l1, l2: cmp(l1.val, l2.val))
if valFunc == min:
while len(allLinks) > 1 \
and allLinks[0].val <= 0:
allLinks.pop(0)
link = allLinks.pop()
if link.val < 0:
break
key = tuple(link.info)
if key in seen:
continue
seen[key] = 1
for info in link.info:
for seq, pos in info.positions.items():
pairings[seq][pos].remove(link)
checkInfo = {}
checkInfo.update(link.info[0].positions)
checkInfo.update(link.info[1].positions)
okay = True
for seq in link.info[0].positions.keys():
if seq in link.info[1].positions:
okay = False
break
if not okay or not _check(checkInfo, partialOrder, chains):
continue
col = Column(checkInfo)
for seq, pos in checkInfo.items():
po = partialOrder[seq]
for i, pcol in enumerate(po):
if pcol.positions[seq] > pos:
break
else:
i = len(po)
po.insert(i, col)
cols = columns[seq]
cols[col] = i
for ncol in po[i+1:]:
cols[ncol] += 1
for info in link.info:
for seq, pos in info.positions.items():
for l in pairings[seq][pos]:
if l.info[0].contains(seq, pos):
base, connect = l.info
else:
connect, base = l.info
l.info = [col, connect]
l.evaluate()
for cseq, cpos in col.positions.items():
if base.contains(cseq, cpos):
continue
pairings[cseq][cpos].append(l)
if isinstance(info, Column):
for seq in info.positions.keys():
seqCols = columns[seq]
opos = seqCols[info]
po = partialOrder[seq]
partialOrder[seq] = po[:opos] \
+ po[opos+1:]
for pcol in partialOrder[seq][opos:]:
seqCols[pcol] -= 1
del seqCols[info]
replyobj.status("%s Collating columns\n" % statusPrefix, blankAfter=0)
orderedColumns = []
while 1:
# find an initial sequence column that can lead
for seq in partialOrder.keys():
try:
col = partialOrder[seq][0]
except IndexError:
from chimera import UserError
raise UserError("Cannot generate alignment with"
" %s %s because it is not superimposed"
" on the other structures" %
(seq.molecule.name, seq.name))
for cseq in col.positions.keys():
if partialOrder[cseq][0] != col:
break
else:
# is initial element for all sequences involved
break
else:
break
orderedColumns.append(col)
for cseq in col.positions.keys():
partialOrder[cseq].pop(0)
if not partialOrder[cseq]:
del partialOrder[cseq]
# try to continue using this sequence as long as possible
while seq in partialOrder:
col = partialOrder[seq][0]
for cseq in col.positions.keys():
if partialOrder[cseq][0] != col:
break
else:
orderedColumns.append(col)
for cseq in col.positions.keys():
partialOrder[cseq].pop(0)
if not partialOrder[cseq]:
del partialOrder[cseq]
continue
break
from NeedlemanWunsch import cloneSeq
clone = {}
current = {}
for seq in chains:
clone[seq] = cloneSeq(seq)
current[seq] = -1
if circular:
clone[seq].circular = seq.circular
if seq.circular:
clone[seq].name = "2 x " + clone[seq].name
if not orderedColumns:
replyobj.status("")
replyobj.error("No residues satisfy distance constraint"
" for column!\n")
return
# for maximum benefit from the "column squeezing" step that follows,
# we need to add in the one-residue columns whose position is
# well-determined
newOrdered = [orderedColumns[0]]
for col in orderedColumns[1:]:
gap = None
for seq, pos in newOrdered[-1].positions.items():
if seq not in col.positions:
continue
if col.positions[seq] == pos + 1:
continue
if gap is not None:
# not well-determined
gap = None
break
gap = seq
if gap is not None:
for pos in range(newOrdered[-1].positions[gap]+1,
col.positions[gap]):
newOrdered.append(Column({gap: pos}))
newOrdered.append(col)
orderedColumns = newOrdered
# Squeeze column where possible:
#
# Find pairs of columns where the left-hand one could accept
# one or more residues from the right-hand one
#
# Keep looking right (if necessary) to until each row has at
# least one gap, but no more than one
#
# Squeeze
colIndex = 0
while colIndex < len(orderedColumns) - 1:
replyobj.status("%sMerging columns (%d/%d)\n" % (statusPrefix,
colIndex, len(orderedColumns)-1), blankAfter=0)
l, r = orderedColumns[colIndex:colIndex+2]
squeezable = False
for seq in r.positions.keys():
if seq not in l.positions:
squeezable = True
break
if not squeezable:
colIndex += 1
continue
gapInfo = {}
for seq in chains:
if seq in l.positions:
gapInfo[seq] = (False, l.positions[seq], 0)
else:
gapInfo[seq] = (True, None, 1)
squeezable = False
redo = False
rcols = 0
for r in orderedColumns[colIndex+1:]:
rcols += 1
# look for indeterminate residues first, so we can
# potentially form a single-residue column to complete
# the squeeze
indeterminates = False
for seq, rightPos in r.positions.items():
inGap, leftPos, numGaps = gapInfo[seq]
if leftPos is None or rightPos == leftPos + 1:
continue
if numGaps == 0:
indeterminates = True
continue
for oseq, info in gapInfo.items():
if oseq == seq:
continue
inGap, pos, numGaps = info
if inGap:
continue
if numGaps != 0:
break
else:
# squeezable
orderedColumns.insert(colIndex+rcols,
Column({seq: leftPos+1}))
redo = True
break
indeterminates = True
if redo:
break
if indeterminates:
break
for seq, info in gapInfo.items():
inGap, leftPos, numGaps = info
if seq in r.positions:
rightPos = r.positions[seq]
if inGap:
# closing a gap
gapInfo[seq] = (False,
rightPos, 1)
else:
# non gap
gapInfo[seq] = (False,
rightPos, numGaps)
else:
if not inGap and numGaps > 0:
# two gaps: no-no
break
gapInfo[seq] = (True, leftPos, 1)
else:
# check if squeeze criteria fulfilled
for inGap, leftPos, numGaps in gapInfo.values():
if numGaps == 0:
break
else:
squeezable = True
break
l = r
continue
break
if redo:
continue
if not squeezable:
colIndex += 1
continue
# squeeze
replaceCols = [Column(c)
for c in orderedColumns[colIndex:colIndex+rcols+1]]
for i, col in enumerate(replaceCols[:-1]):
rcol = replaceCols[i+1]
for seq, pos in rcol.positions.items():
if seq in col.positions:
continue
col.positions[seq] = pos
del rcol.positions[seq]
if col.value() < 0:
break
else:
assert(not replaceCols[-1].positions)
ov = 0
for col in orderedColumns[colIndex:colIndex+rcols+1]:
ov += col.participation()
nv = 0
for col in replaceCols[:-1]:
nv += col.participation()
if ov >= nv:
colIndex += 1
continue
orderedColumns[colIndex:colIndex+rcols+1] = \
replaceCols[:-1]
if colIndex > 0:
colIndex -= 1
continue
colIndex += 1
replyobj.status("%sComposing alignment\n" % statusPrefix, blankAfter=0)
for col in orderedColumns:
for seq, offset in col.positions.items():
curPos = current[seq]
diff = offset - curPos
if diff < 2:
continue
if circular and seq.circular:
if curPos >= len(seq):
frag = seq[curPos-len(seq)+1:
offset-len(seq)]
elif offset >= len(seq):
frag = seq[curPos+1:]
frag += seq[:offset-len(seq)]
else:
frag = seq[curPos+1:offset]
else:
frag = seq[curPos+1:offset]
clone[seq].append(frag)
gap = gapChar * (diff - 1)
for cseq in clone.values():
if cseq == clone[seq]:
continue
cseq.append(gap)
for seq in chains:
try:
offset = col.positions[seq]
if circular and seq.circular \
and offset >= len(seq):
char = seq[offset-len(seq)]
else:
char = seq[offset]
except KeyError:
clone[seq].append(gapChar)
continue
clone[seq].append(char)
current[seq] = offset
for seq, offset in current.items():
if circular and seq.circular:
if offset < 2 * len(seq) - 1:
if offset < len(seq) - 1:
frag = seq[offset+1:] + seq[:]
else:
frag = seq[offset-len(seq)+1:]
else:
continue
else:
if offset == len(seq) - 1:
continue
frag = seq[offset+1:]
gap = gapChar * len(frag)
for cseq in clone.values():
if cseq == clone[seq]:
cseq.append(frag)
else:
cseq.append(gap)
clones = clone.values()
from chimera.misc import oslModelCmp
clones.sort(lambda a, b: oslModelCmp(a.molecule.oslIdent(),
b.molecule.oslIdent()))
replyobj.status("%sDone\n" % statusPrefix)
return clones
def addStandardCharges(models=None, status=None, phosphorylation=None,
chargeModel=None, nogui=False, showCharges=False):
"""add AMBER charges to well-known residues
'models' restricts the addition to the specified models
'status' is where status messages go (e.g. replyobj.status)
'phosphorylation' controls whether chain-terminal nucleic acids
will have their phosphorylation state changed to correspond to
AMBER charge files (3' phosphorylated, 5' not). A value of None
means that the user will be queried if possible [treated as True
if not possible].
'showCharges' controls whether atoms get labeled with their charge.
The return value is a 2-tuple of dictionaries: the first of which
details the residues that did not receive charges [key: residue
type, value: list of residues], and the second lists remaining
uncharged atoms [key: (residue type, atom name), value: list of
atoms]
Hydrogens need to be present.
"""
from AddAttr import addAttributes
import os.path
attrFile = os.path.join(os.path.split(__file__)[0],
"amberName.defattr")
if status:
status("Defining AMBER residue types\n")
addAttributes(attrFile, models=models, raiseAttrDialog=False)
if models is None:
mols = chimera.openModels.list(modelTypes=[chimera.Molecule])
else:
mols = models
if phosphorylation != False:
if status:
status("Checking phosphorylation of chain-terminal"
" nucleic acids\n")
likeAmber = True
deletes = []
for m in mols:
for r in m.residues:
amberName = getattr(r, 'amberName', "UNK")
if len(amberName) != 2 \
or amberName[0] not in 'DR' \
or amberName[1] not in 'ACGTU' \
or 'P' not in r.atomsMap:
continue
p = r.atomsMap['P'][0]
for nb in p.neighbors:
if nb.residue != r:
break
else:
# trailing phosphate
deletes.append(r)
if deletes:
if phosphorylation is None:
if nogui or chimera.nogui:
phosphorylation = True
else:
from gui import PhosphorylateDialog
phosphorylation = PhosphorylateDialog(
).run(chimera.tkgui.app)
if phosphorylation:
_phosphorylate(mols, status, deletes)
if status:
status("Adding standard charges\n")
unchargedResTypes = {}
unchargedAtoms = {}
unchargedResidues = set()
from dict import ffChargeTypeData
from SimpleSession import registerAttribute
registerAttribute(chimera.Molecule, "chargeModel")
registerAttribute(chimera.Atom, "gaffType")
if chargeModel == None:
chargeModel = defaultChargeModel
replyobj.info("Charge model: %s\n" % chargeModel)
chargeTypeData = ffChargeTypeData[chargeModel]
track = chimera.TrackChanges.get()
for m in mols:
m.chargeModel = chargeModel
track.addModified(m, ATTR_SET)
for r in m.residues:
if getattr(r, '_solvateCharged', False):
continue
if not hasattr(r, 'amberName'):
unchargedResidues.add(r)
unchargedResTypes.setdefault(r.type,
[]).append(r)
for a in m.atoms:
if getattr(a.residue, '_solvateCharged', False):
continue
a.charge = 0.0
track.addModified(a, ATTR_SET)
if a.residue.type in unchargedResTypes:
if showCharges:
a.label = str(a.charge)
continue
atomKeys = [a.name.lower()]
if a.element.number == 1 and a.name.lower()[0] in "dt":
atomKeys.append('h' + a.name.lower()[1:])
atomKeys.append(a.element)
for ak in atomKeys:
key = (a.residue.amberName, ak)
try:
a.charge, a.gaffType = chargeTypeData[
key]
except KeyError:
continue
if showCharges:
a.label = "%+g" % a.charge
break
else:
unchargedAtoms.setdefault((a.residue.type,
a.name), []).append(a)
# merge connected non-standard residues into a "mega" residue.
# also any standard residues directly connected
for urt, urs in unchargedResTypes.items():
for ur in urs[:]:
if urt not in unchargedResTypes:
break
if ur not in unchargedResTypes[urt]:
# connected to residue of same type and
# previously removed
continue
connected = [ur]
queue = [ur]
while queue:
curRes = queue.pop(0)
neighbors = set()
stdConnects = {}
for a in curRes.atoms:
for na in a.neighbors:
naRes = na.residue
if naRes == curRes \
or naRes in connected:
continue
# don't add standard residue
# if connected through chain
# bond
if naRes not in unchargedResidues:
from chimera.misc \
import principalAtom
pa = principalAtom(
naRes)
if pa != None:
if pa.name == 'CA':
testNames = ['N', 'C']
else:
testNames = ['P', "O3'"]
if na.name in testNames and na.name not in stdConnects.get(naRes, set()):
stdConnects.setdefault(naRes, set()).add(na.name)
continue
neighbors.add(naRes)
neighbors = list(neighbors)
neighbors.sort(lambda r1, r2:
cmp(r1.type, r2.type))
connected.extend(neighbors)
queue.extend([nb for nb in neighbors
if nb in unchargedResidues])
# avoid using atom names with the trailing "-number"
# distinguisher if possible...
if len(connected) > 1:
fr = FakeRes(connected)
else:
fr = connected[0]
unchargedResTypes.setdefault(fr.type, []).append(fr)
for cr in connected:
if cr in unchargedResidues:
unchargedResTypes[cr.type].remove(cr)
if not unchargedResTypes[cr.type]:
del unchargedResTypes[cr.type]
continue
# remove standard-residue atoms from
# uncharged list
for ca in cr.atoms:
uas = unchargedAtoms.get((cr.type,
ca.name), [])
if ca not in uas:
continue
uas.remove(ca)
if not uas:
del unchargedAtoms[(cr.type,
ca.name)]
# split isolated atoms (e.g. metals) into separate "residues"
for resType, residues in unchargedResTypes.items():
bondResidues = residues
brType = resType
while True:
if len(bondResidues[0].atoms) == 1:
break
for a in bondResidues[0].atoms:
if a.bonds:
continue
hasIso = [r for r in bondResidues
if a.name in r.atomsMap]
if len(hasIso) == len(bondResidues):
rem = []
else:
rem = [r for r in bondResidues
if r not in hasIso]
iso = []
nonIso = rem
isoType = "%s[%s]" % (resType, a.name)
brType = "%s[non-%s]" % (brType, a.name)
for r in hasIso:
isoRes = FakeRes(isoType, [fa
for fa in r.atoms
if fa.name == a.name])
iso.append(isoRes)
nonIsoAtoms = [fa for fa in r.atoms
if fa.name != a.name]
if not nonIsoAtoms:
brType = None
continue
nonIsoRes = FakeRes(brType, nonIsoAtoms)
nonIso.append(nonIsoRes)
unchargedResTypes[isoType] = iso
bondResidues = nonIso
else:
# no isolated atoms
break
if brType != resType:
del unchargedResTypes[resType]
if brType != None:
unchargedResTypes[brType] = bondResidues
# despite same residue type, residues may still differ -- particularly
# terminal vs. non-terminal...
for resType, residues in unchargedResTypes.items():
if len(residues) < 2:
continue
varieties = {}
for r in residues:
key = tuple([a.name for a in r.oslChildren()])
varieties.setdefault(key, []).append(r)
if len(varieties) == 1:
continue
# in order to give the varieties distinguishing names,
# find atoms in common
keys = varieties.keys()
common = set(keys[0])
for k in keys[1:]:
common = common.intersection(set(k))
uncommon = set()
for k in keys:
uncommon = uncommon.union(set(k) - common)
del unchargedResTypes[resType]
for k, residues in varieties.items():
names = set(k)
more = names - common
less = uncommon - names
newKey = resType
if more:
newKey += " (w/%s)" % ",".join(list(more))
if less:
newKey += " (wo/%s)" % ",".join(list(less))
unchargedResTypes[newKey] = residues
if status:
status("Standard charges added\n")
return unchargedResTypes, unchargedAtoms
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 multiAlign(chains, cutoff, matchType, gapChar, circular, statusPrefix=""):
# create list of pairings between sequences
# and prune to be monotonic
trees = {}
if matchType == "all":
valFunc = min
else:
valFunc = max
# for each pair, go through the second chain residue by residue
# and compile crosslinks to other chain. As links are compiled,
# figure out what previous links are crossed and keep a running
# "penalty" function for links based on what they cross.
# Sort links by penalty and keep pruning worst link until no links
# cross.
from chimera.misc import principalAtom
from CGLutil.AdaptiveTree import AdaptiveTree
class EndPoint:
def __init__(self, seq, pos):
self.seq = seq
self.pos = pos
def contains(self, seq, pos):
return seq == self.seq and pos == self.pos
def __getattr__(self, attr):
if attr == "positions":
return {self.seq: self.pos}
raise AttributeError, \
"No such EndPoint attribute: %s" % attr
def __str__(self):
from chimera import SelResidue
if circular and self.pos >= len(self.seq):
insert = " (circular 2nd half)"
pos = self.pos - len(self.seq)
else:
pos = self.pos
insert = ""
return "EndPoint[(%s %s, %s%s)]" % (
self.seq.molecule.name, self.seq.name,
self.seq.residues[pos].oslIdent(SelResidue), insert)
class Link:
def __init__(self, info1, info2, val, doPenalty=False):
self.info = [info1, info2]
self.val = val
if doPenalty:
self.penalty = 0
self.crosslinks = []
def contains(self, seq, pos):
return self.info[0].contains(seq, pos) \
or self.info[1].contains(seq. pos)
def evaluate(self):
self.val = None
for s1, p1 in self.info[0].positions.items():
if circular and s1.circular and p1 >= len(s1):
p1 -= len(s1)
pa1 = pas[s1][p1]
for s2, p2 in self.info[1].positions.items():
if circular and s2.circular \
and p2 >= len(s2):
p2 -= len(s2)
pa2 = pas[s2][p2]
val = cutoff - pa1.xformCoord().distance(pa2.xformCoord())
if self.val is None:
self.val = val
continue
self.val = valFunc(self.val, val)
if valFunc == min and self.val < 0:
break
if valFunc == min and self.val < 0:
break
def __str__(self):
return "Link(%s, %s)" % tuple(map(str, self.info))
allLinks = []
pas = {}
pairings = {}
replyobj.status("%sFinding residue principal atoms\n" % statusPrefix,
blankAfter=0)
for seq in chains:
seqpas = []
pairing = []
for res in seq.residues:
pa = principalAtom(res)
pairing.append([])
if circular:
pairing.append([])
if not pa:
replyobj.warning("Cannot determine principal "
"atom for residue %s\n" % res.oslIdent())
seqpas.append(None)
continue
seqpas.append(pa)
pas[seq] = seqpas
pairings[seq] = pairing
if circular:
circularPairs = {}
holdData = {}
tagTmpl = "(%%d/%d)" % ((len(chains)) * (len(chains) - 1) / 2)
num = 0
for i, seq1 in enumerate(chains):
len1 = len(pairings[seq1])
for seq2 in chains[i + 1:]:
num += 1
tag = tagTmpl % num
len2 = len(pairings[seq2])
links1 = []
for i in range(len1):
links1.append([])
links2 = []
for i in range(len2):
links2.append([])
linkList = []
replyobj.status("%sBuilding search tree %s\n" %
(statusPrefix, tag),
blankAfter=0)
try:
tree = trees[seq2]
except KeyError:
xyzs = []
data = []
for i, pa in enumerate(pas[seq2]):
if pa is None:
continue
xyzs.append(pa.xformCoord().data())
data.append((i, pa))
tree = AdaptiveTree(xyzs, data, cutoff)
replyobj.status("%sSearching tree, building links %s\n" %
(statusPrefix, tag),
blankAfter=0)
for i1, pa1 in enumerate(pas[seq1]):
if pa1 is None:
continue
crd1 = pa1.xformCoord()
matches = tree.searchTree(crd1.data(), cutoff)
for i2, pa2 in matches:
dist = crd1.distance(pa2.xformCoord())
val = cutoff - dist
if val <= 0:
continue
link = Link(EndPoint(seq1, i1),
EndPoint(seq2, i2),
val,
doPenalty=True)
links1[i1].append(link)
links2[i2].append(link)
linkList.append(link)
if circular:
replyobj.status("%sDetermining circularity %s\n" %
(statusPrefix, tag),
blankAfter=0)
holdData[(seq1, seq2)] = (links1, links2, linkList)
if len(linkList) < 2:
replyobj.info("Less than 2 close"
" residues for %s and %s\n" %
(seq1.molecule.name, seq2.molecule.name))
continue
# determine optimal permutation of 1st seq;
#
# for each pair of links, find the permutation
# where they begin to cross/uncross. Use an
# array to tabulate number of crossings for
# each permutation.
crossings = [0] * len(seq1)
c2 = [0] * len(seq2)
from random import sample
numSamples = 5 * (len(seq1) + len(seq2))
for ignore in range(numSamples):
link1, link2 = sample(linkList, 2)
l1p1 = link1.info[0].pos
l1p2 = link1.info[1].pos
l2p1 = link2.info[0].pos
l2p2 = link2.info[1].pos
if l1p1 == l2p1 \
or l1p2 == l2p2:
# can never cross
continue
first = len(seq1) - max(l1p1, l2p1)
second = len(seq1) - min(l1p1, l2p1)
if (l1p1 < l2p1) == (l1p2 < l2p2):
# not crossed initially;
# will cross when first
# one permutes off end
# and uncross when 2nd
# one permutes off
ranges = [(first, second)]
else:
# crossed initially
ranges = [(0, first)]
if second < len(seq1):
ranges.append((second, len(seq1)))
for start, stop in ranges:
for i in range(start, stop):
crossings[i] += 1
first = len(seq2) - max(l1p2, l2p2)
second = len(seq2) - min(l1p2, l2p2)
if (l1p1 < l2p1) == (l1p2 < l2p2):
# not crossed initially;
# will cross when first
# one permutes off end
# and uncross when 2nd
# one permutes off
ranges = [(first, second)]
else:
# crossed initially
ranges = [(0, first)]
if second < len(seq2):
ranges.append((second, len(seq2)))
for start, stop in ranges:
for i in range(start, stop):
c2[i] += 1
# to avoid dangling ends causing bogus
# "circularities", the zero permutation has
# to be beaten significantly for a
# circularity to be declared
least = crossings[0] - 5 * numSamples / len(seq1)
permute1 = [0]
for i, crossed in enumerate(crossings):
if crossed < least:
least = crossed
permute1 = [i]
elif crossed == least:
permute1.append(i)
least = c2[0] - 5 * numSamples / len(seq2)
permute2 = [0]
for i, crossed in enumerate(c2):
if crossed < least:
least = crossed
permute2 = [i]
elif crossed == least:
permute2.append(i)
if permute1[0] != 0 and permute2[0] != 0:
circularPairs[(seq1, seq2)] = (permute1[0], permute2[0])
replyobj.info(
"%s %s / %s %s: permute %s by %d or %s by %d\n" %
(seq1.molecule.name, seq1.name, seq2.molecule.name,
seq2.name, seq1.molecule.name, permute1[0],
seq2.molecule.name, permute2[0]))
else:
findPruneCrosslinks(allLinks,
pairings,
seq1,
seq2,
linkList,
links1,
links2,
tag=tag,
statusPrefix=statusPrefix)
if circular:
replyobj.status("%sMinimizing circularities\n" % statusPrefix,
blankAfter=0)
circulars = {}
while 1:
circularVotes = {}
for seq1, seq2 in circularPairs.keys():
if seq1 in circulars or seq2 in circulars:
continue
circularVotes[seq1] = circularVotes.get(seq1, 0) + 1
circularVotes[seq2] = circularVotes.get(seq2, 0) + 1
if not circularVotes:
break
candidates = circularVotes.keys()
candidates.sort(
lambda c1, c2: cmp(circularVotes[c2], circularVotes[c1]))
circulars[candidates[0]] = True
# has to be circular against every non-circular sequence
# (avoid spurious circularities)
ejected = True
while ejected:
ejected = False
for cseq in circulars:
for seq in chains:
if seq in circulars:
continue
if (cseq, seq) not in circularPairs \
and (seq, cseq) not in circularPairs:
del circulars[cseq]
ejected = True
break
if ejected:
break
for seq in chains:
seq.circular = seq in circulars
if seq.circular:
replyobj.info("circular: %s\n" % seq.molecule.name)
replyobj.status("%sAdjusting links for circular sequences\n" %
statusPrefix,
blankAfter=0)
for seq1, seq2 in holdData.keys():
if not seq1.circular and not seq2.circular:
continue
links1, links2, linkList = holdData[(seq1, seq2)]
use1 = seq1.circular
if seq1.circular and seq2.circular:
if (seq1, seq2) in circularPairs:
permute1, permute2 = circularPairs[(seq1, seq2)]
elif (seq2, seq1) in circularPairs:
permute2, permute1 in circularPairs[(seq2, seq1)]
else:
continue
use1 = len(seq1) - permute1 \
< len(seq2) - permute2
if use1:
adjust, other = seq1, seq2
links = links1
else:
adjust, other = seq2, seq1
links = links2
if (adjust, other) in circularPairs:
permute = circularPairs[(adjust, other)][0]
elif (other, adjust) in circularPairs:
permute = circularPairs[(other, adjust)][1]
else:
continue
fixup = len(adjust) - permute
for link in linkList[:]: # append happens in loop
if link.info[0].seq == adjust:
myEnd = link.info[0]
otherEnd = link.info[1]
else:
myEnd = link.info[1]
otherEnd = link.info[0]
if myEnd.pos >= fixup:
continue
links[myEnd.pos].remove(link)
myEnd.pos += len(adjust)
links[myEnd.pos].append(link)
for i, seqs in enumerate(holdData.keys()):
seq1, seq2 = seqs
links1, links2, linkList = holdData[seqs]
findPruneCrosslinks(allLinks,
pairings,
seq1,
seq2,
linkList,
links1,
links2,
tag=tagTmpl % (i + 1),
statusPrefix=statusPrefix)
class Column:
def __init__(self, positions):
if isinstance(positions, Column):
self.positions = positions.positions.copy()
else:
self.positions = positions
def contains(self, seq, pos):
return seq in self.positions \
and self.positions[seq] == pos
def participation(self):
p = 0
members = self.positions.items()
for i, sp in enumerate(members):
seq1, pos1 = sp
if circular and seq1.circular \
and pos1 >= len(seq1):
pos1 -= len(seq1)
pa1 = pas[seq1][pos1]
for seq2, pos2 in members[i + 1:]:
if circular and seq2.circular \
and pos2 >= len(seq2):
pos2 -= len(seq2)
pa2 = pas[seq2][pos2]
val = cutoff - pa1.xformCoord().distance(pa2.xformCoord())
p += val
return p
def value(self):
value = None
info = self.positions.items()
for i, sp in enumerate(info):
seq1, pos1 = sp
if circular and seq1.circular \
and pos1 >= len(seq1):
pos1 -= len(seq1)
pa1 = pas[seq1][pos1]
for seq2, pos2 in info[i + 1:]:
if circular and seq2.circular \
and pos2 >= len(seq2):
pos2 -= len(seq2)
pa2 = pas[seq2][pos2]
val = cutoff - pa1.xformCoord().distance(pa2.xformCoord())
if value is None:
value = val
continue
value = valFunc(value, val)
if valFunc == min and value < 0:
break
if valFunc == min and value < 0:
break
return value
def __str__(self):
from chimera import SelResidue
def circComp(seq, pos):
if circular and seq.circular and pos >= len(seq):
return pos - len(seq)
return pos
return "Column[" + ",".join(
map(
lambda i: "(%s %s, %s)" %
(i[0].molecule.name, i[0].name, i[0].residues[circComp(
i[0], i[1])].oslIdent(SelResidue)),
self.positions.items())) + "]"
columns = {}
partialOrder = {}
for seq in chains:
columns[seq] = {}
partialOrder[seq] = []
seen = {}
while allLinks:
replyobj.status("%sForming columns (%d links to check)\n" %
(statusPrefix, len(allLinks)))
if allLinks[-1].val != max(map(lambda l: l.val, allLinks)):
allLinks.sort(lambda l1, l2: cmp(l1.val, l2.val))
if valFunc == min:
while len(allLinks) > 1 \
and allLinks[0].val <= 0:
allLinks.pop(0)
link = allLinks.pop()
if link.val < 0:
break
key = tuple(link.info)
if key in seen:
continue
seen[key] = 1
for info in link.info:
for seq, pos in info.positions.items():
pairings[seq][pos].remove(link)
checkInfo = {}
checkInfo.update(link.info[0].positions)
checkInfo.update(link.info[1].positions)
okay = True
for seq in link.info[0].positions.keys():
if seq in link.info[1].positions:
okay = False
break
if not okay or not _check(checkInfo, partialOrder, chains):
continue
col = Column(checkInfo)
for seq, pos in checkInfo.items():
po = partialOrder[seq]
for i, pcol in enumerate(po):
if pcol.positions[seq] > pos:
break
else:
i = len(po)
po.insert(i, col)
cols = columns[seq]
cols[col] = i
for ncol in po[i + 1:]:
cols[ncol] += 1
for info in link.info:
for seq, pos in info.positions.items():
for l in pairings[seq][pos]:
if l.info[0].contains(seq, pos):
base, connect = l.info
else:
connect, base = l.info
l.info = [col, connect]
l.evaluate()
for cseq, cpos in col.positions.items():
if base.contains(cseq, cpos):
continue
pairings[cseq][cpos].append(l)
if isinstance(info, Column):
for seq in info.positions.keys():
seqCols = columns[seq]
opos = seqCols[info]
po = partialOrder[seq]
partialOrder[seq] = po[:opos] \
+ po[opos+1:]
for pcol in partialOrder[seq][opos:]:
seqCols[pcol] -= 1
del seqCols[info]
replyobj.status("%s Collating columns\n" % statusPrefix, blankAfter=0)
orderedColumns = []
while 1:
# find an initial sequence column that can lead
for seq in partialOrder.keys():
try:
col = partialOrder[seq][0]
except IndexError:
from chimera import UserError
raise UserError("Cannot generate alignment with"
" %s %s because it is not superimposed"
" on the other structures" %
(seq.molecule.name, seq.name))
for cseq in col.positions.keys():
if partialOrder[cseq][0] != col:
break
else:
# is initial element for all sequences involved
break
else:
break
orderedColumns.append(col)
for cseq in col.positions.keys():
partialOrder[cseq].pop(0)
if not partialOrder[cseq]:
del partialOrder[cseq]
# try to continue using this sequence as long as possible
while seq in partialOrder:
col = partialOrder[seq][0]
for cseq in col.positions.keys():
if partialOrder[cseq][0] != col:
break
else:
orderedColumns.append(col)
for cseq in col.positions.keys():
partialOrder[cseq].pop(0)
if not partialOrder[cseq]:
del partialOrder[cseq]
continue
break
from NeedlemanWunsch import cloneSeq
clone = {}
current = {}
for seq in chains:
clone[seq] = cloneSeq(seq)
current[seq] = -1
if circular:
clone[seq].circular = seq.circular
if seq.circular:
clone[seq].name = "2 x " + clone[seq].name
if not orderedColumns:
replyobj.status("")
replyobj.error("No residues satisfy distance constraint"
" for column!\n")
return
# for maximum benefit from the "column squeezing" step that follows,
# we need to add in the one-residue columns whose position is
# well-determined
newOrdered = [orderedColumns[0]]
for col in orderedColumns[1:]:
gap = None
for seq, pos in newOrdered[-1].positions.items():
if seq not in col.positions:
continue
if col.positions[seq] == pos + 1:
continue
if gap is not None:
# not well-determined
gap = None
break
gap = seq
if gap is not None:
for pos in range(newOrdered[-1].positions[gap] + 1,
col.positions[gap]):
newOrdered.append(Column({gap: pos}))
newOrdered.append(col)
orderedColumns = newOrdered
# Squeeze column where possible:
#
# Find pairs of columns where the left-hand one could accept
# one or more residues from the right-hand one
#
# Keep looking right (if necessary) to until each row has at
# least one gap, but no more than one
#
# Squeeze
colIndex = 0
while colIndex < len(orderedColumns) - 1:
replyobj.status("%sMerging columns (%d/%d)\n" %
(statusPrefix, colIndex, len(orderedColumns) - 1),
blankAfter=0)
l, r = orderedColumns[colIndex:colIndex + 2]
squeezable = False
for seq in r.positions.keys():
if seq not in l.positions:
squeezable = True
break
if not squeezable:
colIndex += 1
continue
gapInfo = {}
for seq in chains:
if seq in l.positions:
gapInfo[seq] = (False, l.positions[seq], 0)
else:
gapInfo[seq] = (True, None, 1)
squeezable = False
redo = False
rcols = 0
for r in orderedColumns[colIndex + 1:]:
rcols += 1
# look for indeterminate residues first, so we can
# potentially form a single-residue column to complete
# the squeeze
indeterminates = False
for seq, rightPos in r.positions.items():
inGap, leftPos, numGaps = gapInfo[seq]
if leftPos is None or rightPos == leftPos + 1:
continue
if numGaps == 0:
indeterminates = True
continue
for oseq, info in gapInfo.items():
if oseq == seq:
continue
inGap, pos, numGaps = info
if inGap:
continue
if numGaps != 0:
break
else:
# squeezable
orderedColumns.insert(colIndex + rcols,
Column({seq: leftPos + 1}))
redo = True
break
indeterminates = True
if redo:
break
if indeterminates:
break
for seq, info in gapInfo.items():
inGap, leftPos, numGaps = info
if seq in r.positions:
rightPos = r.positions[seq]
if inGap:
# closing a gap
gapInfo[seq] = (False, rightPos, 1)
else:
# non gap
gapInfo[seq] = (False, rightPos, numGaps)
else:
if not inGap and numGaps > 0:
# two gaps: no-no
break
gapInfo[seq] = (True, leftPos, 1)
else:
# check if squeeze criteria fulfilled
for inGap, leftPos, numGaps in gapInfo.values():
if numGaps == 0:
break
else:
squeezable = True
break
l = r
continue
break
if redo:
continue
if not squeezable:
colIndex += 1
continue
# squeeze
replaceCols = [
Column(c) for c in orderedColumns[colIndex:colIndex + rcols + 1]
]
for i, col in enumerate(replaceCols[:-1]):
rcol = replaceCols[i + 1]
for seq, pos in rcol.positions.items():
if seq in col.positions:
continue
col.positions[seq] = pos
del rcol.positions[seq]
if col.value() < 0:
break
else:
assert (not replaceCols[-1].positions)
ov = 0
for col in orderedColumns[colIndex:colIndex + rcols + 1]:
ov += col.participation()
nv = 0
for col in replaceCols[:-1]:
nv += col.participation()
if ov >= nv:
colIndex += 1
continue
orderedColumns[colIndex:colIndex+rcols+1] = \
replaceCols[:-1]
if colIndex > 0:
colIndex -= 1
continue
colIndex += 1
replyobj.status("%sComposing alignment\n" % statusPrefix, blankAfter=0)
for col in orderedColumns:
for seq, offset in col.positions.items():
curPos = current[seq]
diff = offset - curPos
if diff < 2:
continue
if circular and seq.circular:
if curPos >= len(seq):
frag = seq[curPos - len(seq) + 1:offset - len(seq)]
elif offset >= len(seq):
frag = seq[curPos + 1:]
frag += seq[:offset - len(seq)]
else:
frag = seq[curPos + 1:offset]
else:
frag = seq[curPos + 1:offset]
clone[seq].append(frag)
gap = gapChar * (diff - 1)
for cseq in clone.values():
if cseq == clone[seq]:
continue
cseq.append(gap)
for seq in chains:
try:
offset = col.positions[seq]
if circular and seq.circular \
and offset >= len(seq):
char = seq[offset - len(seq)]
else:
char = seq[offset]
except KeyError:
clone[seq].append(gapChar)
continue
clone[seq].append(char)
current[seq] = offset
for seq, offset in current.items():
if circular and seq.circular:
if offset < 2 * len(seq) - 1:
if offset < len(seq) - 1:
frag = seq[offset + 1:] + seq[:]
else:
frag = seq[offset - len(seq) + 1:]
else:
continue
else:
if offset == len(seq) - 1:
continue
frag = seq[offset + 1:]
gap = gapChar * len(frag)
for cseq in clone.values():
if cseq == clone[seq]:
cseq.append(frag)
else:
cseq.append(gap)
clones = clone.values()
from chimera.misc import oslModelCmp
clones.sort(
lambda a, b: oslModelCmp(a.molecule.oslIdent(), b.molecule.oslIdent()))
replyobj.status("%sDone\n" % statusPrefix)
return clones
def pairAlign(chains, cutoff, gapChar, statusPrefix=""):
chain1, chain2 = chains
# go through chain 1 and put each residue's principal
# atom in a spatial tree
from chimera.misc import principalAtom
from CGLutil.AdaptiveTree import AdaptiveTree
xyzs = []
data = []
for i in range(len(chain1)):
res = chain1.residues[i]
pa = principalAtom(res)
if not pa:
replyobj.warning("Cannot determine principal"
" atom for residue %s\n" % res.oslIdent())
continue
xyzs.append(pa.xformCoord().data())
data.append((i, pa.xformCoord()))
tree = AdaptiveTree(xyzs, data, cutoff)
# initialize score array
from numpy import zeros
scores = zeros((len(chain1), len(chain2)), float)
scores -= 1.0
# find matches and update score array
for i2 in range(len(chain2)):
res = chain2.residues[i2]
pa = principalAtom(res)
if not pa:
replyobj.warning("Cannot determine principal"
" atom for residue %s\n" % res.oslIdent())
continue
coord2 = pa.xformCoord()
matches = tree.searchTree(coord2.data(), cutoff)
for i1, coord1 in matches:
dist = coord1.distance(coord2)
if dist > cutoff:
continue
scores[i1][i2] = cutoff - dist
# use NeedlemanWunsch to establish alignment
from NeedlemanWunsch import nw
score, seqs = nw(chain1,
chain2,
scoreMatrix=scores,
gapChar=gapChar,
returnSeqs=True,
scoreGap=0,
scoreGapOpen=0)
smallest = min(len(chain1), len(chain2))
minDots = max(len(chain1), len(chain2)) - smallest
extraDots = len(seqs[0]) - smallest - minDots
numMatches = smallest - extraDots
replyobj.status("%s%d residue pairs aligned\n" %
(statusPrefix, numMatches),
log=True)
if numMatches == 0:
from chimera import UserError
raise UserError("Cannot generate alignment because no"
" residues within cutoff distance")
return score, seqs