def accGeneric(donor, donorHyds, acceptor, r2, minAngle): if base.verbose: print "generic acceptor" 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" ap = acceptor.xformCoord() dp = donor.xformCoord() for bonded in acceptor.primaryNeighbors(): bp = bonded.xformCoord() if base.verbose: print "angle: %g" % angle(bp, ap, dp) ang = angle(bp, ap, dp) if ang < minAngle: if base.verbose: print "angle too sharp (%g < %g)" % (ang, minAngle) return 0 if base.verbose: print "angle(s) okay (all > %g)" % minAngle return 1
def testPhiPsi(dp, donorHyds, ap, bp, phiPlane, r2, phi, theta): 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 OK" if not testPhi(dp, ap, bp, phiPlane, phi): return 0 return testTheta(dp, donorHyds, ap, theta)
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 _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 donWater(donor, donorHyds, acceptor, sp2Orp2, sp2Or2, sp2Otheta, sp3Orp2, sp3Or2, sp3Otheta, sp3Ophi, sp3Nrp2, sp3Nr2, sp3Ntheta, sp3Nupsilon, genRp2, genR2, genTheta): if base.verbose: print "donWater" if len(donorHyds) > 0: # hydrogens explicitly present, # can immediately call donThetaTau return donThetaTau(donor, donorHyds, acceptor, sp2Orp2, sp2Otheta, sp3Orp2, sp3Otheta, sp3Ophi, sp3Nrp2, sp3Ntheta, sp3Nupsilon, genRp2, genTheta) 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" sq = sqdistance(dp, ap) if sq > sp2Or2: if base.verbose: print "dist criteria failed (%g > %g)" % ( sqrt(sq), sqrt(sp2Or2)) return 0 elif element == 'O' and geom == tetrahedral \ or element == 'N' and geom == planar: if base.verbose: print "planar N or tet O" sq = sqdistance(dp, ap) if sq > sp3Or2: if base.verbose: print "dist criteria failed (%g > %g)" % ( sqrt(sq), sqrt(sp3Or2)) return 0 elif element == 'N' and geom == tetrahedral: if base.verbose: print "tet N" sq = sqdistance(dp, ap) if sq > sp3Nr2: if base.verbose: print "dist criteria failed (%g > %g)" % ( sqrt(sq), sqrt(sp3Nr2)) return 0 else: if base.verbose: print "generic acceptor" sq = sqdistance(dp, ap) if sq > genR2: if base.verbose: print "dist criteria failed (%g > %g)" % ( sqrt(sq), sqrt(genR2)) return 0 if base.verbose: print "dist criteria OK" return donThetaTau(donor, donorHyds, acceptor, sp2Orp2, sp2Otheta, sp3Orp2, sp3Otheta, sp3Ophi, sp3Nrp2, sp3Ntheta, sp3Nupsilon, genRp2, genTheta, isWater=1)
def donGeneric(donor, donorHyds, acceptor, sp2Orp2, sp3Orp2, sp3Nrp2, sp2Or2, sp3Or2, sp3Nr2, genRp2, genR2, minHydAngle, minBondedAngle): if base.verbose: print "donGeneric" dc = donor.xformCoord() ac = acceptor.xformCoord() 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" r2 = sp2Or2 rp2 = sp2Orp2 elif element == 'O' and geom == tetrahedral \ or element == 'N' and geom == planar: if base.verbose: print "planar N or tet O" r2 = sp3Or2 rp2 = sp3Orp2 elif element == 'N' and geom == tetrahedral: if base.verbose: print "tet N" r2 = sp3Nr2 rp2 = sp3Nrp2 else: if base.verbose: print "generic acceptor" if acceptor.element.name == "S": r2 = sulphurCompensate(genR2) minBondedAngle = minBondedAngle - 9 r2 = genR2 rp2 = genRp2 ap = acceptor.xformCoord() dp = donor.xformCoord() if len(donorHyds) == 0: D2 = dc.sqdistance(ac) if D2 > r2: if base.verbose: print "dist criteria failed (%g > %g)" % ( sqrt(D2), sqrt(r2)) return 0 else: for hydPos in donorHyds: if sqdistance(hydPos, ap) < rp2: break else: if base.verbose: print "hyd dist criteria failed (all >= %g)" % ( sqrt(rp2)) return 0 if base.verbose: print "dist criteria OK" for bonded in donor.primaryNeighbors(): if bonded.element.number <= 1: continue bp = bonded.xformCoord() ang = angle(bp, dp, ap) if ang < minBondedAngle: if base.verbose: print "bonded angle too sharp (%g < %g)" % ( ang, minBondedAngle) return 0 if len(donorHyds) == 0: if base.verbose: print "No specific hydrogen positions; default accept" return 1 for hydPos in donorHyds: ang = angle(dp, hydPos, ap) if ang >= minHydAngle: if base.verbose: print "hydrogen angle okay (%g >= %g)" % ( ang, minHydAngle) return 1 if base.verbose: print "hydrogen angle(s) too sharp (< %g)" % minHydAngle 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)