def _findTarget(fromAtom, atPos, toAtom, asDonor, hbondInfo, finished): if toAtom in coordinations.get(fromAtom, []): return toAtom.xformCoord() if toAtom in finished: toInfo = hbondInfo[toAtom] # known positioning already protons, lonePairs = toInfo if asDonor: positions = lonePairs else: positions = protons nearest = None for pos in positions: dsq = (pos - atPos).sqlength() if not nearest or dsq < nsq: nearest = pos nsq = dsq return nearest toHPos = [] toBonded = [] toCoplanar = [] toGeom = _typeInfo(toAtom).geometry for tb in toAtom.primaryNeighbors(): toBonded.append(tb.xformCoord()) if tb.element.number == 1: toHPos.append(tb.xformCoord()) if toGeom == planar: toAtomLocs = toAtom.allLocations() for btb in tb.primaryNeighbors(): if btb in toAtomLocs: continue toCoplanar.append(btb.xformCoord()) if asDonor: # point towards nearest lone pair targets = bondPositions(toAtom.xformCoord(), toGeom, vdwRadius(toAtom), toBonded, coPlanar=toCoplanar, toward=atPos) else: # point to nearest hydrogen if _typeInfo(toAtom).substituents <= _numBonds(toAtom): targets = toHPos else: targets = toHPos + bondPositions( toAtom.xformCoord(), toGeom, bondWithHLength(toAtom, toGeom), toBonded, coPlanar=toCoplanar, toward=atPos) nearest = None for target in targets: dsq = (target - atPos).sqlength() if not nearest or dsq < nsq: nearest = target nsq = dsq return nearest
def addNewOs(new_res, psi, **kw):
new_N = new_res.atomsMap['N'][0]
new_CA = new_res.atomsMap['CA'][0]
new_C = new_res.atomsMap['C'][0]
new_OXT = addDihedralAtom('OXT',
chimera.Element(8),
new_C,
new_CA,
new_N,
DIST_C_O,
114,
psi,
residue=new_res)
new_OXT.drawMode = kw['atomDrawMode']
new_OXT.bfactor = kw['bFactor']
addBond(new_OXT, new_C, drawMode=kw['bondDrawMode'])
avail_bond_pos = bondPositions(bondee=new_C.coord(),
geom=chimera.Atom.Planar,
bondLen=DIST_C_O,
bonded=[a.coord() for a in new_C.neighbors])
use_point = avail_bond_pos[0]
new_O = addAtom('O', chimera.Element(8), new_res, use_point)
new_O.drawMode = kw['atomDrawMode']
new_O.bfactor = kw['bFactor']
addBond(new_O, new_C, drawMode=kw['bondDrawMode'])
return new_O, new_OXT
def addNewCA(last_bbone_ats, new_res, **kw):
last_CA = last_bbone_ats['CA']
last_C = last_bbone_ats['C']
last_O = last_bbone_ats['O']
new_N = new_res.atomsMap['N'][0]
## add the CA atom (not dihedral!)
## first, find the location for the new CA atom
new_CA_bond_pos = bondPositions(
bondee=new_N.coord(),
geom=chimera.Atom.Planar,
bondLen=DIST_CA_N,
bonded=[a.coord() for a in new_N.neighbors],
coPlanar=[last_CA.coord(), last_O.coord()])
shortest_point = getShortestPoint(last_O.coord(), new_CA_bond_pos)
new_CA = addAtom('CA', chimera.Element(6), new_res, shortest_point)
new_CA.drawMode = kw['atomDrawMode']
new_CA.bfactor = kw['bFactor']
addBond(new_N, new_CA, drawMode=kw['bondDrawMode'])
return new_CA
def addHydrogens(atom, bondingInfo, namingSchema, totalHydrogens, idatmType,
invert, coordinations):
away = away2 = planar = None
geom = bondingInfo.geometry
substs = bondingInfo.substituents
curBonds = len(atom.primaryBonds())
needed = substs - curBonds
if needed <= 0:
return
atPos = atom.xformCoord()
exclude = coordinations + atom.primaryNeighbors()
if geom == 3 and curBonds == 1:
bonded = atom.primaryNeighbors()[0]
grandBonded = bonded.primaryNeighbors()
grandBonded.remove(atom)
if len(grandBonded) < 3:
planar = [a.xformCoord() for a in grandBonded]
if geom == 4 and not exclude:
away, d, natom = findNearest(atPos, atom, exclude, 3.5)
if away:
away2, d2, natom2 = findRotamerNearest(atPos, idatmType[atom],
atom, natom, 3.5)
elif geom == 4 and len(exclude) == 1:
away, d, natom = findRotamerNearest(atPos, idatmType[atom], atom,
exclude[0], 3.5)
else:
away, d, natom = findNearest(atPos, atom, exclude, 3.5)
bondedPos = []
for bonded in atom.primaryNeighbors():
bondedPos.append(bonded.xformCoord())
if coordinations:
toward = coordinations[0].xformCoord()
away2 = away
away = None
else:
toward = None
positions = bondPositions(atPos,
geom,
bondWithHLength(atom, geom),
bondedPos,
toward=toward,
coPlanar=planar,
away=away,
away2=away2)
if coordinations:
coordPos = None
for pos in positions:
d = pos.sqdistance(toward)
if coordPos is None or d < lowest:
coordPos = pos
lowest = d
positions.remove(coordPos)
if len(positions) > needed:
positions = roomiest(positions, atom, 3.5)[:needed]
for i, pos in enumerate(positions):
newHydrogen(atom, i + 1, totalHydrogens, namingSchema,
invert.apply(pos))
def xformCoord(self): primary = self.primaryNeighbors()[0] pos = bondPositions(primary.xformCoord(), 4, 1.0, bonds) class FakeCoord: pass crd = FakeCoord() crd = pos[0] return crd
def addHydrogens(atom, bondingInfo, namingSchema, totalHydrogens, idatmType, invert, coordinations): away = away2 = planar = None geom = bondingInfo.geometry substs = bondingInfo.substituents curBonds = len(atom.primaryBonds()) needed = substs - curBonds if needed <= 0: return atPos = atom.xformCoord() exclude = coordinations + atom.primaryNeighbors() if geom == 3 and curBonds == 1: bonded = atom.primaryNeighbors()[0] grandBonded = bonded.primaryNeighbors() grandBonded.remove(atom) if len(grandBonded) < 3: planar = [a.xformCoord() for a in grandBonded] if geom == 4 and not exclude: away, d, natom = findNearest(atPos, atom, exclude, 3.5) if away: away2, d2, natom2 = findRotamerNearest(atPos, idatmType[atom], atom, natom, 3.5) elif geom == 4 and len(exclude) == 1: away, d, natom = findRotamerNearest(atPos, idatmType[atom], atom, exclude[0], 3.5) else: away, d, natom = findNearest(atPos, atom, exclude, 3.5) bondedPos = [] for bonded in atom.primaryNeighbors(): bondedPos.append(bonded.xformCoord()) if coordinations: toward = coordinations[0].xformCoord() away2 = away away = None else: toward = None positions = bondPositions(atPos, geom, bondWithHLength(atom, geom), bondedPos, toward=toward, coPlanar=planar, away=away, away2=away2) if coordinations: coordPos = None for pos in positions: d = pos.sqdistance(toward) if coordPos is None or d < lowest: coordPos = pos lowest = d positions.remove(coordPos) if len(positions) > needed: positions = roomiest(positions, atom, 3.5)[:needed] for i, pos in enumerate(positions): newHydrogen(atom, i+1, totalHydrogens, namingSchema, invert.apply(pos))
def _methylate(na, n, atomNames):
added = []
aname = _getAName("C", atomNames)
from chimera.molEdit import addAtom
nn = addAtom(aname, chimera.Element('C'), na.residue, n.coord())
added.append(nn)
na.molecule.newBond(na, nn)
from chimera.bondGeom import bondPositions
for pos in bondPositions(nn.coord(), 4, 1.1, [na.coord()]):
hname = _getAName("H", atomNames)
nh = addAtom(hname, chimera.Element('H'), na.residue, pos)
added.append(nh)
na.molecule.newBond(nn, nh)
return added
def _methylate(na, n, atomNames):
added = []
aname = _getAName("C", atomNames)
from chimera.molEdit import addAtom
nn = addAtom(aname, chimera.Element('C'), na.residue, n.coord())
added.append(nn)
na.molecule.newBond(na, nn)
from chimera.bondGeom import bondPositions
for pos in bondPositions(nn.coord(), 4, 1.1, [na.coord()]):
hname = _getAName("H", atomNames)
nh = addAtom(hname, chimera.Element('H'), na.residue, pos)
added.append(nh)
na.molecule.newBond(nn, nh)
return added
def _tet2check(tetPos, toward, toward2, partnerPos): if debug: print "2 position tetCheck", for pos in bondPositions(tetPos, 4, 1.0, [], toward=toward, toward2=toward2): if debug: print chimera.angle(partnerPos, tetPos, pos), if chimera.angle(partnerPos, tetPos, pos) < _testAngles[4]: if debug: print "true" return True if debug: print "false" return False
def completeTerminalCarboxylate(cter):
from chimera.bondGeom import bondPositions
from chimera.molEdit import addAtom
if "OXT" in cter.atomsMap:
return
try:
cs = cter.atomsMap["C"]
except KeyError:
return
for c in cs: # alt locs are possible
if len(c.primaryBonds()) != 2:
return
loc = bondPositions(c.coord(), 3, 1.229,
[n.coord() for n in c.primaryNeighbors()])[0]
oxt = addAtom("OXT", chimera.Element("O"), cter, loc, bondedTo=c)
replyobj.info("Missing OXT added to C-terminal residue %s\n" % str(cter))
def addNewN(last_bbone_ats, new_res, **kw):
## add the N atom of new residue's backbone to the last residue
last_C = last_bbone_ats['C']
new_N_bond_pos = bondPositions(
bondee=last_C.coord(),
geom=chimera.Atom.Planar,
bondLen=DIST_N_C,
bonded=[a.coord() for a in last_C.neighbors])
use_point = new_N_bond_pos[0]
new_N = addAtom('N', chimera.Element(7), new_res, use_point)
new_N.drawMode = kw['atomDrawMode']
new_N.bfactor = kw['bFactor']
addBond(last_C, new_N, drawMode=kw['bondDrawMode'])
return new_N
def reposLastO(last_res, last_bbone_ats, atom_drawMode, bond_drawMode):
## reposition the last residue's 'O' atom
last_O = getBboneAtom(last_res, 'O')
last_res.molecule.deleteAtom(last_O)
last_C = last_bbone_ats['C']
last_CA = last_bbone_ats['CA']
old_O_bond_pos = bondPositions(
bondee=last_C.coord(),
geom=chimera.Atom.Planar,
bondLen=1.229,
bonded=[a.coord() for a in last_C.neighbors])
## should only be one spot left
old_O_bond_pos = old_O_bond_pos[0]
new_O = addAtom('O', chimera.Element(8), last_res, old_O_bond_pos)
new_O.drawMode = atom_drawMode
addBond(new_O, last_C, drawMode=bond_drawMode)
return new_O
def accThetaTau(donor, donorHyds, acceptor, upsilonPartner, r2, upsilonLow, upsilonHigh, theta): if base.verbose: print "accThetaTau" dp = donor.xformCoord() ap = acceptor.xformCoord() if donor.element.name == "S": r2 = sulphurCompensate(r2) if base.verbose: print "distance: %g, cut off: %g" % (distance(dp, ap), sqrt(r2)) if sqdistance(dp, ap) > r2: if base.verbose: print "dist criteria failed" return 0 if base.verbose: print "dist criteria okay" if upsilonPartner: upPos = upsilonPartner.xformCoord() else: # upsilon measured from "lone pair" (bisector of attached # atoms) bondedPos = [] for bonded in acceptor.primaryNeighbors(): bondedPos.append(bonded.xformCoord()) lonePairs = bondPositions(ap, tetrahedral, 1.0, bondedPos) bisectors = [] for lp in lonePairs: bisectors.append(ap - (lp - ap)) upPos = bisectors[0] for bs in bisectors[1:]: if base.verbose: print "Testing 'extra' lone pair" if testThetaTau(dp, donorHyds, ap, bs, upsilonLow, upsilonHigh, theta): return 1 return testThetaTau(dp, donorHyds, ap, upPos, upsilonLow, upsilonHigh, theta)
def swap(res, newRes, preserve=0, bfactor=True):
"""change 'res' into type 'newRes'"""
if res == "HIS":
res = "HIP"
fixed, buds, start, end = getResInfo(res)
tmplRes = chimera.restmplFindResidue(newRes, start, end)
if not tmplRes:
raise ValueError, "No connectivity template for residue '%s'"\
% newRes
# sanity check: does the template have the bud atoms?
for bud in buds:
if not tmplRes.atomsMap.has_key(bud):
raise ValueError, "New residue type (%s) " \
"not compatible with starting residue type (%s)" \
% (newRes, res.type)
# if bfactor not specified, find highest bfactor in molecule
# and use that for swapped-in atoms
if bfactor is False:
bfactor = None
if bfactor is True:
for a in res.molecule.atoms:
try:
if bfactor is True or a.bfactor > bfactor:
bfactor = a.bfactor
except AttributeError:
pass
if preserve:
raise ValueError, "'preserve' keyword not yet implemented"
# prune non-backbone atoms
for a in res.oslChildren():
if a.name not in fixed:
a.molecule.deleteAtom(a)
# add new sidechain
while len(buds) > 0:
bud = buds.pop()
tmplBud = tmplRes.atomsMap[bud]
resBud = res.atomsMap[bud][0]
try:
info = typeInfo[tmplBud.idatmType]
geom = info.geometry
subs = info.substituents
except KeyError:
print tmplBud.idatmType
raise AssertionError, "Can't determine atom type" \
" information for atom %s of residue %s" % (
bud, res.oslIdent())
# use coord() rather than xformCoord(): we want to set
# the new atom's coord(), to which the proper xform will
# then be applied
for a, b in tmplBud.bondsMap.items():
if a.element.number == 1:
# don't add hydrogens
continue
if res.atomsMap.has_key(a.name):
resBonder = res.atomsMap[a.name][0]
if not resBud.bondsMap.has_key(resBonder):
addBond(a, resBonder)
continue
newAtom = None
numBonded = len(resBud.bonds)
if numBonded >= subs:
raise AssertionError, \
"Too many atoms bonded to %s of" \
" residue %s" % (bud, res.oslIdent())
if numBonded == 0:
raise AssertionError, \
"Atom %s of residue %s has no" \
" neighbors after pruning?!?" % (
bud, res.oslIdent())
elif numBonded == 1:
# only one connected atom -- have to use
# dihedral
real1 = resBud.neighbors[0]
newAtom = formDihedral(resBud, real1,
tmplRes, a, b)
elif numBonded == 2:
crd = resBud.coord()
bonded = resBud.neighbors
bcrds = map(lambda a: a.coord(), bonded)
positions = bondPositions(crd, geom,
b.length(), bcrds)
if len(positions) > 1:
# need to disambiguate choices;
# check improper dihedral
# but first, make sure the bonded
# atoms are in this residue
inres = filter(lambda a, r=res:
a.residue == r, bonded)
if len(inres) == 0:
raise AssertionError, \
"Can't disambiguate " \
"tetrahedral position by " \
"forming in-residue dihedral " \
"for %s of residue %s" % (
bud, res.oslIdent())
if len(inres) == 1:
newAtom = formDihedral(resBud,
inres[0], tmplRes, a, b)
else:
# okay, check improper dihedral
tmplBonded = map(lambda a,
tra=tmplRes.atomsMap:
tra[a.name], bonded)
tmplPts = map(lambda a:
a.coord(), [a,
tmplBud] + tmplBonded)
tmplDihed = apply(dihedral,
tmplPts, {})
backPts = map(lambda a:
a.coord(), [resBud]
+ bonded)
dh1 = apply(dihedral, tuple(
positions[:1]
+ backPts), {})
dh2 = apply(dihedral, tuple(
positions[1:]
+ backPts), {})
diff1 = abs(dh1 - tmplDihed)
diff2 = abs(dh2 - tmplDihed)
if diff1 > 180:
diff1 = 360 - diff1
if diff2 > 180:
diff2 = 360 - diff2
if diff1 < diff2:
position = positions[0]
else:
position = positions[1]
else:
position = positions[0]
else:
crd = resBud.coord()
bonded = resBud.neighbors
bcrds = map(lambda a: a.coord(), bonded)
positions = bondPositions(crd, geom,
b.length(), bcrds)
if len(positions) > 1:
raise AssertionError, \
"Too many positions returned" \
" for atom %s of residue %s" % (
bud, res.oslIdent())
position = positions[0]
if not newAtom:
newAtom = addAtom(a.name, a.element,
res, position)
newAtom.drawMode = resBud.drawMode
if bfactor is not None and bfactor is not True:
newAtom.bfactor = bfactor
# TODO: need to iterate over coordSets
for bonded in a.bondsMap.keys():
if not res.atomsMap.has_key(bonded.name):
continue
addBond(newAtom, res.atomsMap[bonded.name][0])
buds.append(newAtom.name)
res.label = res.label.replace(res.type, newRes)
res.type = newRes
def swap(res, newRes, preserve=0, bfactor=True):
"""change 'res' into type 'newRes'"""
if res == "HIS":
res = "HIP"
fixed, buds, start, end = getResInfo(res)
tmplRes = chimera.restmplFindResidue(newRes, start, end)
if not tmplRes:
raise ValueError, "No connectivity template for residue '%s'"\
% newRes
# sanity check: does the template have the bud atoms?
for bud in buds:
if not tmplRes.atomsMap.has_key(bud):
raise ValueError, "New residue type (%s) " \
"not compatible with starting residue type (%s)" \
% (newRes, res.type)
# if bfactor not specified, find highest bfactor in molecule
# and use that for swapped-in atoms
if bfactor is False:
bfactor = None
if bfactor is True:
for a in res.molecule.atoms:
try:
if bfactor is True or a.bfactor > bfactor:
bfactor = a.bfactor
except AttributeError:
pass
if preserve:
raise ValueError, "'preserve' keyword not yet implemented"
# prune non-backbone atoms
for a in res.oslChildren():
if a.name not in fixed:
a.molecule.deleteAtom(a)
# add new sidechain
while len(buds) > 0:
bud = buds.pop()
tmplBud = tmplRes.atomsMap[bud]
resBud = res.atomsMap[bud][0]
try:
info = typeInfo[tmplBud.idatmType]
geom = info.geometry
subs = info.substituents
except KeyError:
print tmplBud.idatmType
raise AssertionError, "Can't determine atom type" \
" information for atom %s of residue %s" % (
bud, res.oslIdent())
# use coord() rather than xformCoord(): we want to set
# the new atom's coord(), to which the proper xform will
# then be applied
for a, b in tmplBud.bondsMap.items():
if a.element.number == 1:
# don't add hydrogens
continue
if res.atomsMap.has_key(a.name):
resBonder = res.atomsMap[a.name][0]
if not resBud.bondsMap.has_key(resBonder):
addBond(a, resBonder)
continue
newAtom = None
numBonded = len(resBud.bonds)
if numBonded >= subs:
raise AssertionError, \
"Too many atoms bonded to %s of" \
" residue %s" % (bud, res.oslIdent())
if numBonded == 0:
raise AssertionError, \
"Atom %s of residue %s has no" \
" neighbors after pruning?!?" % (
bud, res.oslIdent())
elif numBonded == 1:
# only one connected atom -- have to use
# dihedral
real1 = resBud.neighbors[0]
newAtom = formDihedral(resBud, real1, tmplRes, a, b)
elif numBonded == 2:
crd = resBud.coord()
bonded = resBud.neighbors
bcrds = map(lambda a: a.coord(), bonded)
positions = bondPositions(crd, geom, b.length(), bcrds)
if len(positions) > 1:
# need to disambiguate choices;
# check improper dihedral
# but first, make sure the bonded
# atoms are in this residue
inres = filter(lambda a, r=res: a.residue == r, bonded)
if len(inres) == 0:
raise AssertionError, \
"Can't disambiguate " \
"tetrahedral position by " \
"forming in-residue dihedral " \
"for %s of residue %s" % (
bud, res.oslIdent())
if len(inres) == 1:
newAtom = formDihedral(resBud, inres[0], tmplRes, a, b)
else:
# okay, check improper dihedral
tmplBonded = map(
lambda a, tra=tmplRes.atomsMap: tra[a.name],
bonded)
tmplPts = map(lambda a: a.coord(),
[a, tmplBud] + tmplBonded)
tmplDihed = apply(dihedral, tmplPts, {})
backPts = map(lambda a: a.coord(), [resBud] + bonded)
dh1 = apply(dihedral, tuple(positions[:1] + backPts),
{})
dh2 = apply(dihedral, tuple(positions[1:] + backPts),
{})
diff1 = abs(dh1 - tmplDihed)
diff2 = abs(dh2 - tmplDihed)
if diff1 > 180:
diff1 = 360 - diff1
if diff2 > 180:
diff2 = 360 - diff2
if diff1 < diff2:
position = positions[0]
else:
position = positions[1]
else:
position = positions[0]
else:
crd = resBud.coord()
bonded = resBud.neighbors
bcrds = map(lambda a: a.coord(), bonded)
positions = bondPositions(crd, geom, b.length(), bcrds)
if len(positions) > 1:
raise AssertionError, \
"Too many positions returned" \
" for atom %s of residue %s" % (
bud, res.oslIdent())
position = positions[0]
if not newAtom:
newAtom = addAtom(a.name, a.element, res, position)
newAtom.drawMode = resBud.drawMode
if bfactor is not None and bfactor is not True:
newAtom.bfactor = bfactor
# TODO: need to iterate over coordSets
for bonded in a.bondsMap.keys():
if not res.atomsMap.has_key(bonded.name):
continue
addBond(newAtom, res.atomsMap[bonded.name][0])
buds.append(newAtom.name)
res.label = res.label.replace(res.type, newRes)
res.type = newRes
def changeAtom(atom, element, geometry, numBonds, autoClose=True, name=None):
if len(atom.primaryBonds()) > numBonds:
raise ParamError("Atom already has more bonds than requested.\n"
"Either delete some bonds or choose a different number"
" of requested bonds.")
from chimera.molEdit import addAtom, genAtomName
changedAtoms = [atom]
if not name:
name = genAtomName(element, atom.residue)
changeAtomName(atom, name)
atom.element = element
if hasattr(atom, 'mol2type'):
delattr(atom, 'mol2type')
# if we only have one bond, correct its length
if len(atom.primaryBonds()) == 1:
neighbor = atom.primaryNeighbors()[0]
newLength = bondLength(atom, geometry, neighbor.element,
a2info=(neighbor, numBonds))
setBondLength(atom.primaryBonds()[0], newLength,
movingSide="smaller side")
if numBonds == len(atom.primaryBonds()):
return changedAtoms
from chimera.bondGeom import bondPositions
coPlanar = None
if geometry == 3 and len(atom.primaryBonds()) == 1:
n = atom.primaryNeighbors()[0]
if len(n.primaryBonds()) == 3:
coPlanar = [nn.coord() for nn in n.primaryNeighbors()
if nn != atom]
away = None
if geometry == 4 and len(atom.primaryBonds()) == 1:
n = atom.primaryNeighbors()[0]
if len(n.primaryBonds()) > 1:
nn = n.primaryNeighbors()[0]
if nn == atom:
nn = n.primaryNeighbors()[1]
away = nn.coord()
hydrogen = Element("H")
positions = bondPositions(atom.coord(), geometry,
bondLength(atom, geometry, hydrogen),
[n.coord() for n in atom.primaryNeighbors()], coPlanar=coPlanar,
away=away)[:numBonds-len(atom.primaryBonds())]
if autoClose:
if len(atom.molecule.atoms) < 100:
testAtoms = atom.molecule.atoms
else:
from CGLutil.AdaptiveTree import AdaptiveTree
tree = AdaptiveTree([a.coord().data()
for a in atom.molecule.atoms],
a.molecule.atoms, 2.5)
testAtoms = tree.searchTree(atom.coord().data(), 5.0)
else:
testAtoms = []
for pos in positions:
for ta in testAtoms:
if ta == atom:
continue
testLen = bondLength(ta, 1, hydrogen)
testLen2 = testLen * testLen
if (ta.coord() - pos).sqlength() < testLen2:
bonder = ta
# possibly knock off a hydrogen to
# accomodate the bond...
for bn in bonder.primaryNeighbors():
if bn.element.number > 1:
continue
if chimera.angle(atom.coord()
- ta.coord(), bn.coord()
- ta.coord()) > 45.0:
continue
if bn in testAtoms:
testAtoms.remove(bn)
atom.molecule.deleteAtom(bn)
break
break
else:
bonder = addAtom(genAtomName(hydrogen, atom.residue),
hydrogen, atom.residue, pos, bondedTo=atom)
changedAtoms.append(bonder)
return changedAtoms
def changeAtom(atom, element, geometry, numBonds, autoClose=True, name=None):
if len(atom.primaryBonds()) > numBonds:
raise ParamError(
"Atom already has more bonds than requested.\n"
"Either delete some bonds or choose a different number"
" of requested bonds.")
from chimera.molEdit import addAtom, genAtomName
changedAtoms = [atom]
if not name:
name = genAtomName(element, atom.residue)
changeAtomName(atom, name)
atom.element = element
if hasattr(atom, 'mol2type'):
delattr(atom, 'mol2type')
# if we only have one bond, correct its length
if len(atom.primaryBonds()) == 1:
neighbor = atom.primaryNeighbors()[0]
newLength = bondLength(atom,
geometry,
neighbor.element,
a2info=(neighbor, numBonds))
setBondLength(atom.primaryBonds()[0],
newLength,
movingSide="smaller side")
if numBonds == len(atom.primaryBonds()):
return changedAtoms
from chimera.bondGeom import bondPositions
coPlanar = None
if geometry == 3 and len(atom.primaryBonds()) == 1:
n = atom.primaryNeighbors()[0]
if len(n.primaryBonds()) == 3:
coPlanar = [
nn.coord() for nn in n.primaryNeighbors() if nn != atom
]
away = None
if geometry == 4 and len(atom.primaryBonds()) == 1:
n = atom.primaryNeighbors()[0]
if len(n.primaryBonds()) > 1:
nn = n.primaryNeighbors()[0]
if nn == atom:
nn = n.primaryNeighbors()[1]
away = nn.coord()
hydrogen = Element("H")
positions = bondPositions(atom.coord(),
geometry,
bondLength(atom, geometry, hydrogen),
[n.coord() for n in atom.primaryNeighbors()],
coPlanar=coPlanar,
away=away)[:numBonds - len(atom.primaryBonds())]
if autoClose:
if len(atom.molecule.atoms) < 100:
testAtoms = atom.molecule.atoms
else:
from CGLutil.AdaptiveTree import AdaptiveTree
tree = AdaptiveTree(
[a.coord().data() for a in atom.molecule.atoms],
a.molecule.atoms, 2.5)
testAtoms = tree.searchTree(atom.coord().data(), 5.0)
else:
testAtoms = []
for pos in positions:
for ta in testAtoms:
if ta == atom:
continue
testLen = bondLength(ta, 1, hydrogen)
testLen2 = testLen * testLen
if (ta.coord() - pos).sqlength() < testLen2:
bonder = ta
# possibly knock off a hydrogen to
# accomodate the bond...
for bn in bonder.primaryNeighbors():
if bn.element.number > 1:
continue
if chimera.angle(atom.coord() - ta.coord(),
bn.coord() - ta.coord()) > 45.0:
continue
if bn in testAtoms:
testAtoms.remove(bn)
atom.molecule.deleteAtom(bn)
break
break
else:
bonder = addAtom(genAtomName(hydrogen, atom.residue),
hydrogen,
atom.residue,
pos,
bondedTo=atom)
changedAtoms.append(bonder)
return changedAtoms
def hydPositions(heavy, includeLonePairs=False): """Return list of positions for hydrogens attached to this atom. If a hydrogen could be in one of several positions, don't return any of those. """ # first, find known attached atoms bondedHeavys = [] hyds = [] for atom in heavy.primaryNeighbors(): if atom.element.number > 1: bondedHeavys.append(atom) else: hyds.append(atom) # convert to Points hydLocs = [] for hyd in hyds: hydLocs.append(hyd.xformCoord()) if hydLocs and not includeLonePairs: # explicit hydrogens "win" over atom types return hydLocs if typeInfo.has_key(heavy.idatmType): info = typeInfo[heavy.idatmType] geom = info.geometry if includeLonePairs: subs = geom else: subs = info.substituents bondedLocs = hydLocs[:] for bHeavy in bondedHeavys: bondedLocs.append(bHeavy.xformCoord()) else: return hydLocs knownSubs = len(bondedLocs) if knownSubs >= subs or knownSubs == 0: return hydLocs # above eliminates 'single' geometry if knownSubs == 1 and geom == tetrahedral: # rotamer return hydLocs maxSubs = geom if maxSubs - subs > 0: # the "empty" bond could be anywhere return hydLocs heavyLoc = heavy.xformCoord() bondLen = Element.bondLength(heavy.element, Element(1)) if geom == planar: coPlanar = [] for bHeavy in bondedHeavys: try: bhGeom = typeInfo[bHeavy.idatmType].geometry except KeyError: bhGeom = None if bhGeom != planar: continue for atom in bHeavy.primaryNeighbors(): if atom != heavy: coPlanar.append(atom.xformCoord()) else: coPlanar = None hydLocs = hydLocs + bondPositions(heavyLoc, geom, bondLen, bondedLocs, coPlanar=coPlanar) return hydLocs
def _tryFinish(atom, hbondInfo, finished, aroAmines, prunedBy, processed):
# do we have enough info to establish all H/LP positions for atom?
bondingInfo = _typeInfo(atom)
geom = bondingInfo.geometry
# from number of donors/acceptors, determine
# if we can position Hs/lone pairs
numBonds = _numBonds(atom)
hydsToPosition = bondingInfo.substituents - numBonds
openings = geom - numBonds
donors = []
acceptors = []
all = []
for isAcc, other in hbondInfo[atom]:
all.append(other)
if isAcc:
donors.append(other)
else:
acceptors.append(other)
if len(all) < openings \
and len(donors) < openings - hydsToPosition \
and len(acceptors) < hydsToPosition:
if debug:
print "not enough info (all/donors/acceptors):", len(all), len(donors), len(acceptors)
return False
# if so, find their positions and
# record in hbondInfo; mark as finished
atPos = atom.xformCoord()
targets = []
for isAcc, other in hbondInfo[atom][:2]:
targets.append(_findTarget(atom, atPos, other, not isAcc,
hbondInfo, finished))
# for purposes of this intermediate measurement, use hydrogen
# distances instead of lone pair distances; determine true
# lone pair positions once hydrogens are found
bondedPos = []
testPositions = []
coplanar = []
for bonded in atom.primaryNeighbors():
bondedPos.append(bonded.xformCoord())
if bonded.element.number == 1:
testPositions.append(bonded.xformCoord())
if geom == planar:
for btb in bonded.primaryNeighbors():
if btb == atom:
continue
coplanar.append(btb.xformCoord())
toward = targets[0]
if len(targets) > 1:
toward2 = targets[1]
else:
toward2 = None
Hlen = bondWithHLength(atom, geom)
LPlen = vdwRadius(atom)
if debug:
print atom.oslIdent(), "co-planar:", coplanar
print atom.oslIdent(), "toward:", toward
print atom.oslIdent(), "toward2:", toward2
normals = bondPositions(atPos, geom, 1.0, bondedPos,
coPlanar=coplanar, toward=toward, toward2=toward2)
if debug:
print atom.oslIdent(), "bondPositions:", [str(x) for x in normals]
# use vectors so we can switch between lone-pair length and H-length
for normal in normals:
testPositions.append(normal - atPos)
# try to hook up positions with acceptors/donors
if atom in aroAmines:
if debug:
print "delay finishing aromatic amine"
return False
all = {}
protons = {}
lonePairs = {}
conflicting = []
for isAcc, other in hbondInfo[atom]:
if debug:
print "other:", other.oslIdent()
nearest = None
if other in finished:
oprotons, olps = hbondInfo[other]
if isAcc:
opositions = oprotons
mul = LPlen
else:
opositions = olps
mul = Hlen
for opos in opositions:
for check in testPositions:
if isinstance(check, chimera.Vector):
pos = atPos + check * mul
else:
pos = check
dsq = (opos - pos).sqlength()
if nearest is None or dsq < nsq:
nearest = check
nsq = dsq
else:
otherPos = other.xformCoord()
if isAcc:
mul = LPlen
else:
mul = Hlen
for check in testPositions:
if isinstance(check, chimera.Vector):
pos = atPos + check * mul
else:
pos = check
dsq = (pos - otherPos).sqlength()
if debug:
print "dist from other to",
if isinstance(check, chimera.Point):
print "pre-existing proton:",
elif check in all:
if check in protons:
print "new proton:",
else:
print "new lone pair:",
else:
print "unfilled position:",
import math
print math.sqrt(dsq)
if nearest is None or dsq < nsq:
nearest = check
nsq = dsq
if isinstance(nearest, chimera.Point):
# closest to known hydrogen; no help in positioning...
if isAcc:
# other is trying to donate and is nearest
# to one of our hydrogens
conflicting.append((isAcc, other))
continue
if nearest in all:
if isAcc:
if nearest in protons:
conflicting.append((isAcc, other))
elif nearest in lonePairs:
conflicting.append((isAcc, other))
continue
# check for steric conflict (frequent with metal coordination)
if isAcc:
pos = atPos + nearest * LPlen
atBump = 0.0
else:
pos = atPos + nearest * Hlen
atBump = Hrad
checkDist = 2.19 + atBump
# since searchTree is a module variable that changes,
# need to access via the module...
nearby = AddH.searchTree.searchTree(pos.data(), checkDist)
stericClash = False
okay = set([atom, other])
okay.update(atom.primaryNeighbors())
for nb in nearby:
if nb in okay:
continue
if nb.molecule != atom.molecule \
and nb.molecule.id == atom.molecule.id:
# ignore clashes with sibling submodels
continue
dChk = vdwRadius(nb) + atBump - 0.4
if dChk*dChk >= sqdistance(nb.xformCoord(), pos):
stericClash = True
if debug:
print "steric clash with", nb.oslIdent(), "(%.3f < %.3f)" % (pos.distance(nb.xformCoord()), dChk)
break
if stericClash:
conflicting.append((isAcc, other))
continue
all[nearest] = 1
if isAcc:
if debug:
print "determined lone pair"
lonePairs[nearest] = 1
else:
if debug:
print "determined proton"
protons[nearest] = 1
for isAcc, other in conflicting:
if debug:
print "Removing hbond to %s due to conflict" % other.oslIdent()
hbondInfo[atom].remove((isAcc, other))
if not hbondInfo[atom]:
del hbondInfo[atom]
if other in finished:
continue
try:
hbondInfo[other].remove((not isAcc, atom))
if not hbondInfo[other]:
del hbondInfo[other]
except ValueError:
pass
# since any conflicting hbonds may have been used to determine
# positions, determine the positions again with the remaining
# hbonds
if conflicting:
# restore hbonds pruned by the conflicting hbonds
for isAcc, other in conflicting:
if isAcc:
key = (other, atom)
else:
key = (atom, other)
for phb in prunedBy.get(key, []):
if debug:
print "restoring %s/%s hbond pruned by hbond to %s" % (phb[0].oslIdent(), phb[1].oslIdent(), other.oslIdent())
processed.remove(phb)
if atom not in hbondInfo:
if debug:
print "No non-conflicting hbonds left!"
return False
if debug:
print "calling _tryFinish with non-conflicting hbonds"
return _tryFinish(atom, hbondInfo, finished, aroAmines,
prunedBy, processed)
# did we determine enough positions?
if len(all) < openings \
and len(protons) < hydsToPosition \
and len(lonePairs) < openings - hydsToPosition:
if debug:
print "not enough hookups (all/protons/lps):", len(all), len(protons), len(lonePairs)
return False
if len(protons) < hydsToPosition:
for pos in testPositions:
if isinstance(pos, chimera.Point):
continue
if pos not in all:
protons[pos] = 1
Hlocs = []
for Hvec in protons.keys():
Hlocs.append(atPos + Hvec * Hlen)
LPlocs = []
for vec in testPositions:
if isinstance(vec, chimera.Point):
continue
if vec not in protons:
LPlocs.append(atPos + vec * LPlen)
hbondInfo[atom] = (Hlocs, LPlocs)
finished[atom] = True
return True
def addHydrogens(atomList, *args):
"""Add hydrogens to maximize h-bonding and minimize steric clashes.
First, add hydrogens that are fixed and always present. Then,
find H-bonds only to possibly-hydrogen-needing donors. For
aromatic nitogens protonate at least one on a six-membered ring.
For remaining rotamers with H-bonds, place hydrogens
to maximize H-bond interactions. Then, for remaining rotamers,
minimize steric clashes via torsion-driving.
May not work well for atoms that are already partially
hydrogenated.
"""
if debug:
print "here (test)"
if atomList:
if len(atomList[0].molecule.coordSets) > 1:
replyobj("Adding H-bond-preserving hydrogens to "
"trajectories not supported.\n")
return
if debug:
print "here 2"
global addAtoms, typeInfo4Atom, namingSchemas, hydrogenTotals, \
idatmType, inversionCache, coordinations
typeInfo4Atom, namingSchemas, hydrogenTotals, idatmType, hisNs, \
coordinations = args
inversionCache = {}
addAtoms = {}
for atom in atomList:
addAtoms[atom] = 1
from chimera import replyobj
replyobj.status("Categorizing heavy atoms\n", blankAfter=0)
problemAtoms = []
fixed = []
flat = []
aroNrings = {}
global aroAmines
aroAmines = {}
unsaturated = []
saturated = []
finished = {}
hbondInfo = {}
for a, crds in coordinations.items():
hbondInfo[a] = [(True, crd) for crd in crds]
for atom in atomList:
bondingInfo = typeInfo4Atom[atom]
numBonds = _numBonds(atom)
substs = bondingInfo.substituents
if numBonds >= substs:
continue
geom = bondingInfo.geometry
if numBonds == 0:
unsaturated.append(atom)
elif numBonds == 1:
if geom == linear:
fixed.append(atom)
elif geom == planar:
if substs == 2:
unsaturated.append(atom)
else:
if idatmType[atom] == 'Npl' \
and idatmType[
atom.primaryNeighbors()[0]] == 'Car':
# primary aromatic amine
aroAmines[atom] = True
else:
flat.append(atom)
elif geom == tetrahedral:
if substs < 4:
unsaturated.append(atom)
else:
saturated.append(atom)
else:
raise AssertionError, "bad geometry for atom" \
" (%s) with one bond partner" \
% atom.oslIdent()
elif numBonds == 2:
if geom == tetrahedral:
if substs == 3:
unsaturated.append(atom)
else:
fixed.append(atom)
elif geom == planar:
aroNring = None
if atom.element.number == 7:
for ring in atom.minimumRings():
if ring.aromatic():
aroNring = ring
break
if aroNring:
if aroNrings.has_key(aroNring):
aroNrings[aroNring].append(atom)
else:
aroNrings[aroNring] = [atom]
else:
fixed.append(atom)
else:
raise AssertionError, "bad geometry for atom" \
" (%s) with two bond partners" \
% atom.oslIdent()
elif numBonds == 3:
if geom != tetrahedral:
raise AssertionError, "bad geometry for atom" \
" (%s) with three bond partners" \
% atom.oslIdent()
fixed.append(atom)
# protonate aromatic nitrogens if only one nitrogen in ring:
multiNrings = {}
aroNs = {}
for ring, ns in aroNrings.items():
if len(ns) == 1:
fixed.append(ns[0])
elif ns[0] in hisNs:
for n in ns:
if hisNs[n]:
fixed.append(n)
else:
multiNrings[ring] = ns
for n in ns:
aroNs[n] = True
if debug:
print len(fixed), "fixed"
print len(flat), "flat"
print len(aroAmines), "primary aromatic amines"
print len(multiNrings), "aromatic multi-nitrogen rings"
print len(unsaturated), "unsaturated"
print len(saturated), "saturated rotamers"
replyobj.status("Building search tree of atom positions\n",
blankAfter=0)
# since adaptive search tree is static, it will not include
# hydrogens added after this; they will have to be found by
# looking off their heavy atoms
for needCoplanar in [False, True]:
if needCoplanar:
atoms = flat
replyobj.status("Adding co-planar hydrogens\n",
blankAfter=0)
else:
atoms = fixed
replyobj.status("Adding simple fixed hydrogens\n",
blankAfter=0)
for atom in atoms:
bondingInfo = _typeInfo(atom)
geom = bondingInfo.geometry
bondLength = bondWithHLength(atom, geom)
neighbors = []
neighborAtoms = []
for n in atom.primaryNeighbors():
neighborAtoms.append(n)
neighbors.append(n.xformCoord())
coplanar = []
if needCoplanar:
for na in neighborAtoms:
for nna in na.primaryNeighbors():
if nna != atom:
coplanar.append(
nna.xformCoord())
if len(coplanar) > 2:
problemAtoms.append(atom)
continue
Hpositions = bondPositions(atom.xformCoord(), geom,
bondLength, neighbors, coPlanar=coplanar)
_attachHydrogens(atom, Hpositions)
finished[atom] = True
hbondInfo[atom] = (Hpositions, [])
from FindHBond import findHBonds, recDistSlop, recAngleSlop
from chimera import replyobj
replyobj.status("Finding hydrogen bonds\n", blankAfter=0)
donors = {}
acceptors = {}
for atom in unsaturated:
donors[atom] = unsaturated
acceptors[atom] = unsaturated
for atom in saturated:
donors[atom] = saturated
for ring, ns in multiNrings.items():
for n in ns:
donors[n] = ring
acceptors[n] = ring
for atom in aroAmines:
donors[atom] = aroAmines
acceptors[atom] = aroAmines
hbonds = findHBonds(chimera.openModels.list(
modelTypes=[chimera.Molecule]),
distSlop=recDistSlop, angleSlop=recAngleSlop)
replyobj.info("%d hydrogen bonds\n" % len(hbonds))
# want to assign hydrogens to strongest (shortest) hydrogen
# bonds first, so sort by distance
replyobj.status("Sorting hydrogen bonds by distance\n", blankAfter=0)
sortableHbonds = []
for d, a in hbonds:
if d in donors:
sortableHbonds.append((d.xformCoord().sqdistance(
a.xformCoord()), False, (d, a)))
if a in acceptors:
sortableHbonds.append((d.xformCoord().sqdistance(
a.xformCoord()), True, (d, a)))
sortableHbonds.sort()
replyobj.status("Organizing h-bond info\n", blankAfter=0)
hbonds = {}
ambiguous = {}
relBond = {}
for dsq, isAcc, hbond in sortableHbonds:
hbonds[hbond] = isAcc
for da in hbond:
relBond.setdefault(da, []).append(hbond)
processed = set()
breakAmbiguous = False
breakNring = False
candidates = {}
candidates.update(donors)
candidates.update(acceptors)
pruned = set()
prunedBy = {}
reexamine = {}
replyobj.status("Adding hydrogens by h-bond strength\n", blankAfter=0)
while len(processed) < len(hbonds):
replyobj.status("Adding hydrogens by h-bond strength (%d/%d)\n" % (len(processed), len(hbonds)), blankAfter=0)
processedOne = False
seenAmbiguous = {}
for dsq, isAcc, hbond in sortableHbonds:
if hbond in processed:
continue
d, a = hbond
if hbond in pruned:
if hbond in reexamine:
del reexamine[hbond]
if debug:
print "re-examining", hbond[0].oslIdent(), "->", hbond[1].oslIdent()
elif not breakAmbiguous:
seenAmbiguous[d] = True
seenAmbiguous[a] = True
continue
if (d not in candidates or d in finished) \
and (a not in candidates or a in finished):
# not relevant
processed.add(hbond)
continue
if (a, d) in hbonds \
and a not in finished \
and d not in finished \
and not _resolveAnilene(d, a, aroAmines, hbondInfo) \
and _angleCheck(d, a, hbondInfo) == (True, True):
# possibly still ambiguous
# if one or both ends are aromatic nitrogen,
# then ambiguity depends on whether other
# nitrogens in ring are finished and are
# acceptors...
nring = False
try:
ns = multiNrings[acceptors[a]]
except (KeyError, TypeError):
ns = []
if len(ns) > 1:
nring = True
for n in ns:
if n not in finished:
break
protons, lps = hbondInfo[n]
if protons:
break
else:
# unambiguous, but in the
# reverse direction!
processed.add(hbond)
if debug:
print "reverse ambiguity resolved"
continue
unambiguous = False
try:
ns = multiNrings[donors[d]]
except (KeyError, TypeError):
ns = []
if len(ns) > 1:
nring = True
for n in ns:
if n not in finished:
break
protons, lps = hbondInfo[n]
if protons:
break
else:
if debug:
print "ambiguity resolved due to ring acceptors"
unambiguous = True
if not unambiguous:
if not breakAmbiguous \
or nring and not breakNring:
if debug:
print "postponing", [a.oslIdent() for a in hbond]
seenAmbiguous[d] = True
seenAmbiguous[a] = True
if hbond not in pruned:
_doPrune(hbond, pruned, relBond, processed, prunedBy)
continue
if nring:
if debug:
print "breaking ambiguous N-ring hbond"
else:
if debug:
print "breaking ambiguous hbond"
if (a, d) in hbonds:
if a in finished:
if debug:
print "breaking ambiguity because acceptor finished"
elif d in finished:
if debug:
print "breaking ambiguity because donor finished"
elif _resolveAnilene(d, a, aroAmines, hbondInfo):
if debug:
print "breaking ambiguity by resolving anilene"
elif _angleCheck(d, a, hbondInfo) != (True, True):
if debug:
print "breaking ambiguity due to angle check"
processed.add(hbond)
from math import sqrt
if debug:
print "processed", d.oslIdent(), "->", a.oslIdent(), sqrt(dsq)
# if donor or acceptor is tet,
# see if geometry can work out
if d not in finished and _typeInfo(d).geometry == 4:
if not _tetCheck(d, a, hbondInfo, False):
continue
if a not in finished and _typeInfo(a).geometry == 4:
if d in finished:
checks = []
for b in d.primaryNeighbors():
if b.element.number == 1:
checks.append(b)
else:
checks = [d]
tetOkay = True
for c in checks:
if not _tetCheck(a, c, hbondInfo, True):
tetOkay = False
break
if not tetOkay:
continue
if a in finished:
# can d still donate to a?
if not _canAccept(d, a, *hbondInfo[a]):
# can't
continue
hbondInfo.setdefault(d, []).append((False, a))
elif d in finished:
# can d still donate to a?
noProtonsOK = d in aroNs and _numBonds(d) == 2
if not _canDonate(d, a, noProtonsOK,
*hbondInfo[d]):
# nope
continue
hbondInfo.setdefault(a, []).append((True, d))
else:
addAtoD, addDtoA = _angleCheck(d, a,
hbondInfo)
if not addAtoD and not addDtoA:
continue
if addAtoD:
hbondInfo.setdefault(d, []).append(
(False, a))
if addDtoA:
hbondInfo.setdefault(a, []).append(
(True, d))
if (a, d) in hbonds:
processed.add((a, d))
processedOne = True
breakAmbigous = False
breakNring = False
if hbond not in pruned:
_doPrune(hbond, pruned, relBond, processed, prunedBy)
for end in hbond:
if end in finished or end not in candidates:
continue
if end not in hbondInfo:
# steric clash from other end
if debug:
print "no hbonds left for", end.oslIdent()
continue
if debug:
print "try to finish", end.oslIdent(),
for isAcc, da in hbondInfo[end]:
if isAcc:
print " accepting from", da.oslIdent(),
else:
print " donating to", da.oslIdent(),
print
didFinish = _tryFinish(end, hbondInfo, finished,
aroAmines, prunedBy, processed)
if not didFinish:
continue
if debug:
print "finished", end.oslIdent()
# if this atom is in candidates
# then actually add any hydrogens
if end in candidates and hbondInfo[end][0]:
_attachHydrogens(end, hbondInfo[end][0])
if debug:
print "protonated", end.oslIdent()
# if ring nitrogen, eliminate
# any hbonds where it is an acceptor
if isinstance(donors[end],chimera.Ring):
for rb in relBond[end]:
if rb[1] != end:
continue
processed.add(rb)
if a in seenAmbiguous or d in seenAmbiguous:
# revisit previously ambiguous
if debug:
print "revisiting previous ambiguous"
for da in hbond:
for rel in relBond[da]:
if rel in processed:
continue
if rel not in pruned:
continue
reexamine[rel] = True
break
if breakAmbiguous and not processedOne:
breakNring = True
breakAmbiguous = not processedOne
numFinished = 0
for a in candidates.keys():
if a in finished:
numFinished += 1
if debug:
print "finished", numFinished, "of", len(candidates), "atoms"
replyobj.status("Adding hydrogens to primary aromatic amines\n",
blankAfter=0)
if debug:
print "primary aromatic amines"
for a in aroAmines:
if a in finished:
continue
if a not in candidates:
continue
if debug:
print "amine", a.oslIdent()
finished[a] = True
numFinished += 1
# point protons right toward acceptors;
# if also accepting, finish as tet, otherwise as planar
acceptFrom = None
targets = []
atPos = a.xformCoord()
for isAcc, other in hbondInfo.get(a, []):
if isAcc:
if not acceptFrom:
if debug:
print "accept from", other.oslIdent()
acceptFrom = other.xformCoord()
continue
if debug:
print "possible donate to", other.oslIdent()
# find nearest lone pair position on acceptor
target = _findTarget(a, atPos, other, not isAcc,
hbondInfo, finished)
# make sure this proton doesn't form
# an angle < 90 degrees with any other bonds
badAngle = False
for bonded in a.primaryNeighbors():
if chimera.angle(bonded.xformCoord(),
atPos, target) < 90.0:
badAngle = True
break
if badAngle:
if debug:
print "bad angle"
continue
if targets and chimera.angle(targets[0], atPos,
target) < 90.0:
if debug:
print "bad angle"
continue
targets.append(target)
if len(targets) > 1:
break
positions = []
for target in targets:
vec = target - atPos
vec.normalize()
positions.append(atPos +
vec * bondWithHLength(a, _typeInfo(a).geometry))
if len(positions) < 2:
if acceptFrom:
geom = 4
knowns = positions + [acceptFrom]
coPlanar = None
else:
geom = 3
knowns = positions
coPlanar = []
for bonded in a.primaryNeighbors():
for b2 in bonded.primaryNeighbors():
if a == b2:
continue
coPlanar.append(b2.xformCoord())
sumVec = chimera.Vector()
for x in a.primaryNeighbors():
vec = x.xformCoord() - atPos
vec.normalize()
sumVec += vec
for k in knowns:
vec = k - atPos
vec.normalize()
sumVec += vec
sumVec.negate()
sumVec.normalize()
newPos = bondPositions(atPos, geom, bondWithHLength(a, geom),
[nb.xformCoord() for nb in a.primaryNeighbors()] + knowns,
coPlanar=coPlanar)
positions.extend(newPos)
_attachHydrogens(a, positions)
if acceptFrom:
accVec = acceptFrom - atPos
accVec.length = vdwRadius(a)
accs = [atPos + accVec]
else:
accs = []
hbondInfo[a] = (positions, accs)
if debug:
print "finished", numFinished, "of", len(candidates), "atoms"
replyobj.status("Using steric criteria to resolve partial h-bonders\n",
blankAfter=0)
for a in candidates.keys():
if a in finished:
continue
if a not in hbondInfo:
continue
finished[a] = True
numFinished += 1
bondingInfo = _typeInfo(a)
geom = bondingInfo.geometry
numBonds = _numBonds(a)
hydsToPosition = bondingInfo.substituents - numBonds
openings = geom - numBonds
hbInfo = hbondInfo[a]
towardAtom = hbInfo[0][1]
if debug:
print a.oslIdent(), "toward", towardAtom.oslIdent(),
towardPos = towardAtom.xformCoord()
toward2 = away2 = None
atPos = a.xformCoord()
if len(hbInfo) > 1:
toward2 = hbInfo[1][1].xformCoord()
if debug:
print "and toward", hbInfo[1][1].oslIdent()
elif openings > 3:
# okay, we need an "away from" atom just to position
# the rotamer
away2, dist, nearA = findNearest(atPos, a, [towardAtom],
_nearDist)
if debug:
print "and away from nearest other",
if away2:
print nearA.oslIdent(), "[%.2f]" % dist
else:
print "(none)"
else:
if debug:
print "with no other positioning determinant"
bondedPos = []
for bonded in a.primaryNeighbors():
bondedPos.append(bonded.xformCoord())
positions = bondPositions(atPos, geom,
bondWithHLength(a, geom), bondedPos,
toward=towardPos, toward2=toward2, away2=away2)
if len(positions) == hydsToPosition:
# easy, do them all...
_attachHydrogens(a, positions)
continue
used = {}
for isAcc, other in hbInfo:
nearest = None
otherPos = other.xformCoord()
for pos in positions:
dsq = (pos - otherPos).sqlength()
if not nearest or dsq < nsq:
nearest = pos
nsq = dsq
if nearest in used:
continue
used[nearest] = isAcc
remaining = []
for pos in positions:
if pos in used:
continue
remaining.append(pos)
# definitely protonate the positions where we donate...
protonate = []
for pos, isAcc in used.items():
if not isAcc:
protonate.append(pos)
# ... and the "roomiest" remaining positions.
rooms = roomiest(remaining, a, _roomDist)
needed = hydsToPosition - len(protonate)
protonate.extend(rooms[:needed])
# then the least sterically challenged...
_attachHydrogens(a, protonate)
hbondInfo[a] = (protonate, rooms[needed:])
if debug:
print "finished", numFinished, "of", len(candidates), "atoms"
replyobj.status("Adding hydrogens to non-h-bonding atoms\n",
blankAfter=0)
for a in candidates.keys():
if a in finished:
continue
if a in aroNs:
continue
finished[a] = True
numFinished += 1
bondingInfo = _typeInfo(a)
geom = bondingInfo.geometry
primaryNeighbors = a.primaryNeighbors()
numBonds = len(primaryNeighbors)
hydsToPosition = bondingInfo.substituents - numBonds
openings = geom - numBonds
away = None
away2 = None
toward = None
atPos = a.xformCoord()
if debug:
print "position", a.oslIdent(),
if openings > 2:
# okay, we need an "away from" atom for positioning
#
# if atom is tet with one bond (i.e. possible positions
# describe a circle away from the bond), then use the
# center of the circle as the test position rather
# than the atom position itself
if geom == 4 and openings == 3:
away, dist, awayAtom = findRotamerNearest(atPos,
idatmType[a], a,
primaryNeighbors[0], 3.5)
else:
away, dist, awayAtom = findNearest(atPos, a,
[], _nearDist)
# actually, if the nearest atom is a metal and we have
# a free lone pair, we want to position (the lone
# pair) towards the metal
if awayAtom and awayAtom.element in metals \
and geom - bondingInfo.substituents > 0:
if debug:
print "towards metal", awayAtom.oslIdent(), "[%.2f]" % dist,
toward = away
away = None
else:
if debug:
print "away from",
if awayAtom:
print awayAtom.oslIdent(), "[%.2f]" % dist,
else:
print "(none)",
if openings > 3 and away is not None:
# need another away from
away2, dist, nearA = findNearest(atPos, a, [awayAtom],
_nearDist)
if debug:
print "and away from",
if nearA:
print nearA.oslIdent(), "[%.2f]" % dist,
else:
print "(none)",
if debug:
print
bondedPos = []
for bonded in primaryNeighbors:
bondedPos.append(bonded.xformCoord())
positions = bondPositions(atPos, geom,
bondWithHLength(a, geom),
bondedPos, toward=toward, away=away, away2=away2)
if len(positions) == hydsToPosition:
# easy, do them all...
_attachHydrogens(a, positions)
continue
# protonate "roomiest" positions
_attachHydrogens(a, roomiest(positions, a, _roomDist)[:hydsToPosition])
if debug:
print "finished", numFinished, "of", len(candidates), "atoms"
replyobj.status("Deciding aromatic nitrogen protonation\n",
blankAfter=0)
# protonate one N of an aromatic multiple-N ring if none are yet
# protonated
for ns in multiNrings.values():
anyBonded = True
Npls = []
for n in ns:
if _numBonds(n) > 2:
break
if n not in coordinations \
and _typeInfo(n).substituents == 3:
Npls.append(n)
else:
anyBonded = False
if anyBonded:
if debug:
print ns[0].oslIdent(), "ring already protonated"
continue
if not Npls:
Npls = ns
positions = []
for n in Npls:
bondedPos = []
for bonded in n.primaryNeighbors():
bondedPos.append(bonded.xformCoord())
positions.append(bondPositions(n.xformCoord(), planar,
bondWithHLength(n, planar), bondedPos)[0])
if len(positions) == 1:
if debug:
print "protonate precise ring", Npls[0].oslIdent()
_attachHydrogens(Npls[0], positions)
else:
if debug:
print "protonate roomiest ring", roomiest(positions, Npls, _roomDist)[0][0].oslIdent()
_attachHydrogens(*roomiest(positions, Npls, _roomDist)[0])
# now correct IDATM types of these rings...
for ns in multiNrings.values():
for n in ns:
if len(n.bonds) == 3:
n.idatmType = "Npl"
else:
n.idatmType = "N2"
replyobj.status("Hydrogens added\n")
if problemAtoms:
replyobj.error("Problems adding hydrogens to %d atom(s); see Reply Log for details\n" % len(problemAtoms))
from chimera.misc import chimeraLabel
replyobj.info("Did not protonate following atoms:\n%s\n"
% "\t".join(map(chimeraLabel, problemAtoms)))
addAtoms = None
typeInfo4Atom = namingSchemas = hydrogenTotals = idatmType \
= aroAmines = inversionCache = coordinations = None
def hydPositions(heavy, includeLonePairs=False):
"""Return list of positions for hydrogens attached to this atom.
If a hydrogen could be in one of several positions, don't
return any of those.
"""
# first, find known attached atoms
bondedHeavys = []
hyds = []
for atom in heavy.primaryNeighbors():
if atom.element.number > 1:
bondedHeavys.append(atom)
else:
hyds.append(atom)
# convert to Points
hydLocs = []
for hyd in hyds:
hydLocs.append(hyd.xformCoord())
if hydLocs and not includeLonePairs:
# explicit hydrogens "win" over atom types
return hydLocs
if typeInfo.has_key(heavy.idatmType):
info = typeInfo[heavy.idatmType]
geom = info.geometry
if includeLonePairs:
subs = geom
else:
subs = info.substituents
bondedLocs = hydLocs[:]
for bHeavy in bondedHeavys:
bondedLocs.append(bHeavy.xformCoord())
else:
return hydLocs
knownSubs = len(bondedLocs)
if knownSubs >= subs or knownSubs == 0:
return hydLocs
# above eliminates 'single' geometry
if knownSubs == 1 and geom == tetrahedral:
# rotamer
return hydLocs
maxSubs = geom
if maxSubs - subs > 0:
# the "empty" bond could be anywhere
return hydLocs
heavyLoc = heavy.xformCoord()
bondLen = Element.bondLength(heavy.element, Element(1))
if geom == planar:
coPlanar = []
for bHeavy in bondedHeavys:
try:
bhGeom = typeInfo[bHeavy.idatmType].geometry
except KeyError:
bhGeom = None
if bhGeom != planar:
continue
for atom in bHeavy.primaryNeighbors():
if atom != heavy:
coPlanar.append(atom.xformCoord())
else:
coPlanar = None
hydLocs = hydLocs + bondPositions(
heavyLoc, geom, bondLen, bondedLocs, coPlanar=coPlanar)
return hydLocs
def _resolveAnilene(donor, acceptor, aroAmines, hbondInfo): # donor/acceptor are currently ambiguous; if donor and/or acceptor are # anilenes, see if they can be determined to prefer to donate/accept # respectively (if a proton and/or lone pair has been added, see if # vector to other atom is more planar or more tetrahedral) if donor in aroAmines and donor in hbondInfo: toward = None for isAcc, da in hbondInfo[donor]: if isAcc: return True if toward: break toward = da.xformCoord() else: # one proton attached donorPos = donor.xformCoord() acceptorPos = acceptor.xformCoord() attached = [ donor.primaryNeighbors()[0].xformCoord()] planars = bondPositions(donorPos, 3, N_H, attached, toward=toward) planarDist = None for planar in planars: dist = (acceptorPos - planar).sqlength() if planarDist is None or dist < planarDist: planarDist = dist for tetPos in bondPositions(donorPos, 4, N_H, attached): if (tetPos - acceptorPos).sqlength() \ < planarDist: # closer to tet position, # prefer acceptor-like behavior return False if debug: print "resolving", donor.oslIdent(), "->", acceptor.oslIdent(), "because of donor" return True if acceptor in aroAmines and acceptor in hbondInfo: toward = None for isAcc, da in hbondInfo[acceptor]: if isAcc: return False if toward: break toward = da.xformCoord() else: # one proton attached donorPos = donor.xformCoord() acceptorPos = acceptor.xformCoord() attached = [acceptor.primaryNeighbors()[0].xformCoord()] planars = bondPositions(acceptorPos, 3, N_H, attached, toward=toward) planarDist = None for planar in planars: dist = (acceptorPos - planar).sqlength() if planarDist is None or dist < planarDist: planarDist = dist for tetPos in bondPositions(acceptorPos, 4, N_H, attached): if (tetPos - donorPos).sqlength() \ < planarDist: # closer to tet position, # prefer acceptor-like behavior if debug: print "resolving", donor.oslIdent(), "->", acceptor.oslIdent(), "because of acceptor" return True return False return False
def donUpsilonTau(donor, donorHyds, acceptor, sp2Or2, sp2OupsilonLow, sp2OupsilonHigh, sp2Otheta, sp2Otau, sp3Or2, sp3OupsilonLow, sp3OupsilonHigh, sp3Otheta, sp3Otau, sp3Ophi, sp3Nr2, sp3NupsilonLow, sp3NupsilonHigh, sp3Ntheta, sp3Ntau, sp3NupsilonN, genR2, genUpsilonLow, genUpsilonHigh, genTheta, tauSym): if base.verbose: print "donUpsilonTau" accType = acceptor.idatmType if not typeInfo.has_key(accType): return 0 geom = typeInfo[accType].geometry element = acceptor.element.name if element == 'O' and geom == planar: if base.verbose: print "planar O" return testUpsilonTauAcceptor(donor, donorHyds, acceptor, sp2Or2, sp2OupsilonLow, sp2OupsilonHigh, sp2Otheta, sp2Otau, tauSym) elif element == 'O' and geom == tetrahedral \ or element == 'N' and geom == planar: if base.verbose: print "planar N or tet O" return testUpsilonTauAcceptor(donor, donorHyds, acceptor, sp3Or2, sp3OupsilonLow, sp3OupsilonHigh, sp3Otheta, sp3Otau, tauSym) elif element == 'N' and geom == tetrahedral: if base.verbose: print "tet N" # test upsilon at the N # see if lone pairs point at the donor bondedPos = [] for bonded in acceptor.primaryNeighbors(): bondedPos.append(bonded.xformCoord()) if len(bondedPos) > 1: ap = acceptor.xformCoord() dp = donor.xformCoord() lonePairs = bondPositions(ap, tetrahedral, 1.0, bondedPos) for lp in lonePairs: upPos = ap - (lp - ap) ang = angle(upPos, ap, dp) if ang >= sp3NupsilonN: if base.verbose: print "upsilon(N) okay" \ " (%g >= %g)" % (ang, sp3NupsilonN) break else: if base.verbose: print "all upsilon(N) failed (< %g)" % ( sp3NupsilonN) return 0 elif base.verbose: print "lone pair positions indeterminate at N;" \ "upsilon(N) default okay" return testUpsilonTauAcceptor(donor, donorHyds, acceptor, sp3Nr2, sp3NupsilonLow, sp3NupsilonHigh, sp3Ntheta, sp3Ntau, tauSym) else: if base.verbose: print "generic acceptor" if acceptor.element.name == "S": genR2 = sulphurCompensate(genR2) return testUpsilonTauAcceptor(donor, donorHyds, acceptor, genR2, genUpsilonLow, genUpsilonHigh, genTheta, None, None) if base.verbose: print "failed criteria" return 0
def donThetaTau(donor, donorHyds, acceptor, sp2Orp2, sp2Otheta, sp3Orp2, sp3Otheta, sp3Ophi, sp3Nrp2, sp3Ntheta, sp3Nupsilon, genRp2, genTheta, isWater=0): # 'isWater' only for hydrogenless water if base.verbose: print "donThetaTau" if len(donorHyds) == 0 and not isWater: if base.verbose: print "No hydrogens; default failure" return 0 ap = acceptor.xformCoord() dp = donor.xformCoord() accType = acceptor.idatmType if not typeInfo.has_key(accType): if base.verbose: print "Unknown acceptor type failure" return 0 geom = typeInfo[accType].geometry element = acceptor.element.name if element == 'O' and geom == planar: if base.verbose: print "planar O" for hydPos in donorHyds: if sqdistance(hydPos, ap) <= sp2Orp2: break else: if not isWater: if base.verbose: print "dist criteria failed (all > %g)"\ % sqrt(sp2Orp2) return 0 theta = sp2Otheta elif element == 'O' and geom == tetrahedral \ or element == 'N' and geom == planar: if base.verbose: print "planar N or tet O" for hydPos in donorHyds: if sqdistance(hydPos, ap) <= sp3Orp2: break else: if not isWater: if base.verbose: print "dist criteria failed (all > %g)"\ % sqrt(sp3Orp2) return 0 theta = sp3Otheta # only test phi for acceptors with two bonded atoms if len(acceptor.primaryBonds()) == 2: if base.verbose: print "testing donor phi" bonded = acceptor.primaryNeighbors() phiPlane, basePos = getPhiPlaneParams(acceptor, bonded[0], bonded[1]) if not testPhi(donor.xformCoord(), ap, basePos, phiPlane, sp3Ophi): return 0 elif element == 'N' and geom == tetrahedral: if base.verbose: print "tet N" for hydPos in donorHyds: if sqdistance(hydPos, ap) <= sp3Nrp2: break else: if not isWater: if base.verbose: print "dist criteria failed (all > %g)"\ % sqrt(sp3Nrp2) return 0 theta = sp3Ntheta # test upsilon against lone pair directions bondedPos = [] for bonded in acceptor.primaryNeighbors(): bondedPos.append(bonded.xformCoord()) lpPos = bondPositions(ap, geom, 1.0, bondedPos) if lpPos: # fixed lone pair positions for lp in bondPositions(ap, geom, 1.0, bondedPos): # invert position so that we are # measuring angles correctly ang = angle(dp, ap, ap - (lp - ap)) if ang > sp3Nupsilon: if base.verbose: print "acceptor upsilon okay"\ " (%g > %g)" % ( ang, sp3Nupsilon) break else: if base.verbose: print "all acceptor upsilons failed"\ " (< %g)" % sp3Nupsilon return 0 # else: indefinite lone pair positions; default okay else: if base.verbose: print "generic acceptor" if acceptor.element.name == "S": genRp2 = sulphurCompensate(genRp2) for hydPos in donorHyds: if sqdistance(hydPos, ap) <= genRp2: break else: if base.verbose: print "dist criteria failed (all > %g)" % sqrt( genRp2) return 0 theta = genTheta if base.verbose: print "dist criteria OK" return testTheta(dp, donorHyds, ap, theta)