def _canDonate(donor, acceptor, noProtonsOK, protons, lonePairs): # donor is fixed; can it donate to acceptor? if not lonePairs: return True if not protons: if noProtonsOK: if debug: print "can't still donate; no protons" return False raise ValueError, "No protons for %s to accept from" % ( acceptor.oslIdent()) accPos = acceptor.xformCoord() hDist, h = min(map(lambda xyz: ((xyz - accPos).sqlength(), xyz), protons)) lpDist = min(map(lambda xyz: (xyz - accPos).sqlength(), lonePairs)) # besides a proton being closest, it must be sufficiently pointed # towards the acceptor if hDist >= lpDist: from math import sqrt if debug: print "can't still donate; h dist (%g) >= lp dist (%g)" % ( sqrt(hDist), sqrt(lpDist)) elif chimera.angle(h, donor.xformCoord(), accPos) >= _testAngles[ typeInfo4Atom[donor].geometry]: if debug: print "can't still donate; angle (%g) >= test angle (%g)" % ( chimera.angle(h, donor.xformCoord(), accPos), _testAngles[ typeInfo4Atom[donor].geometry]) return hDist < lpDist and chimera.angle(h, donor.xformCoord(), accPos) < _testAngles[ typeInfo4Atom[donor].geometry]
def angle(self, items):
from Axes import Axis
from Planes import Plane
numAxes = len([i for i in items if isinstance(i, Axis)])
numPlanes = len([i for i in items if isinstance(i, Plane)])
if numAxes == 2:
axis1, axis2 = items
angle = chimera.angle(axis1.xformDirection(),
axis2.xformDirection())
if angle > 90.0:
angle = 180.0 - angle
elif numAxes == numPlanes == 1:
if isinstance(items[0], Axis):
axis, plane = items
else:
plane, axis = items
angle = chimera.angle(axis.xformDirection(), plane.xformNormal())
angle = abs(90.0 - angle)
elif numPlanes == 2:
plane1, plane2 = items
angle = chimera.angle(plane1.xformNormal(), plane2.xformNormal())
if angle > 90.0:
angle = 180.0 - angle
else:
raise ValueError("angle calculation not implemented")
return angle
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 _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 _angleLabel(self, atoms): pts = tuple([a.xformCoord() for a in atoms]) if len(pts) == 3: val = chimera.angle(*pts) else: val = chimera.dihedral(*pts) return "%.*f" % (prefs[ANGLE_PRECISION], val)
def order_retriever(self, dummies_xyz):
"""
Base class method to order dummies
for types.
Logic:
- For each dummy we look for the
one being at the opposite side
of the metal by looking for a
DZ-MET_DZ angle of 180.
Then we appned both together on
the list.
"""
new_order = []
for dummy in dummies_xyz:
if dummy not in new_order:
new_order.append(dummy)
for i in range(0, len(dummies_xyz)):
angle = chimera.angle(dummy, self.metal.labelCoord(),
dummies_xyz[i])
if abs(angle -
180) < 0.01 and dummies_xyz[i] not in new_order:
new_order.append(dummies_xyz[i])
break
return new_order
def _axisDistance(self, axis, infinite=False):
from chimera import angle, cross, Plane
# shortest distance between lines is perpendicular to both...
sDir = self.xformDirection()
aDir = axis.xformDirection()
if angle(sDir, aDir) in [0.0, 180.0]:
# parallel
return self._axisEndsDist(axis)
shortDir = cross(sDir, aDir)
# can use analytically shortest dist only if each axis
# penetrates the plane formed by the other axis and the
# perpendicular
if not infinite:
for a1, a2 in [(axis, self), (self, axis)]:
normal = cross(a1.xformDirection(), shortDir)
plane = Plane(a1.xformCenter(), normal)
d1 = plane.distance(a2.xformCenter() +
a2.xformDirection() * a2.extents[0])
d2 = plane.distance(a2.xformCenter() +
a2.xformDirection() * a2.extents[1])
if cmp(d1, 0.0) == cmp(d2, 0.0):
# both ends on same side of plane
return self._axisEndsDist(axis)
# D is perpendicular distance to origin
d1 = Plane(self.xformCenter(), shortDir).equation()[3]
d2 = Plane(axis.xformCenter(), shortDir).equation()[3]
return abs(d1 - d2)
def rotate(molecule, at, alpha):
if len(at) == 3:
try:
a1, a2, a3 = [a.coord() for a in at]
except AttributeError:
a1, a2, a3 = at
axis_a = a1 - a2
axis_b = a3 - a2
delta = chimera.angle(a1, a2, a3) - alpha
axis = chimera.cross(axis_a, axis_b)
if axis.data() == (0.0, 0.0, 0.0):
axis = chimera.cross(axis_a, axis_b + chimera.Vector(1, 0, 0))
logger.warning("Had to choose arbitrary normal vector")
pivot = a2
elif len(at) == 4:
try:
a1, a2, a3, a4 = [a.coord() for a in at]
except AttributeError:
a1, a2, a3, a4 = at
axis = a3 - a2
delta = chimera.dihedral(a1, a2, a3, a4) - alpha
pivot = a3
else:
raise ValueError(
"Atom list must contain 3 (angle) or 4 (dihedral) atoms only")
r = X.translation(pivot - ZERO) # move to origin
r.multiply(X.rotation(axis, -delta)) # rotate
r.multiply(X.translation(ZERO - pivot)) # return to orig pos
for a in molecule.atoms:
a.setCoord(r.apply(a.coord()))
def evaluate(self, ind):
atoms_coords = [a.xformCoord() for a in self.probes(ind)]
try:
angle = chimera.angle(*atoms_coords)
except TypeError: # four atoms, means dihedral
angle = chimera.dihedral(*atoms_coords)
if self.threshold == 'planar':
return abs(math.sin(math.radians(angle)))
return abs(self.threshold - angle.real)
def _angleCheck(d, a, hbondInfo): addAtoD = addDtoA = True # are the protons/lps already added to the # donor pointed toward the acceptor? if d in hbondInfo: geom = _typeInfo(d).geometry for isAcc, da in hbondInfo[d]: angle = chimera.angle(da.xformCoord(), d.xformCoord(), a.xformCoord()) if angle > _testAngles[geom]: continue if isAcc: # lone pair pointing toward acceptor; # won't work addAtoD = addDtoA = False if debug: print "can't donate; lone pair (to %s) pointing toward acceptor (angle %g)" % (da.oslIdent(), angle) break addAtoD = False if debug: print "donor already pointing (angle %g) towards acceptor (due to %s)" % (angle, da.oslIdent()) if not addAtoD and not addDtoA: return addAtoD, addDtoA if a in hbondInfo: geom = _typeInfo(a).geometry for isAcc, da in hbondInfo[a]: angle = chimera.angle(da.xformCoord(), a.xformCoord(), d.xformCoord()) if angle > _testAngles[geom]: continue if not isAcc: # proton pointing toward donor; won't work if debug: print "can't accept; proton (to %s) pointing too much toward donor (angle %g)" % (da.oslIdent(), angle) addAtoD = addDtoA = False break addDtoA = False if debug: print "acceptor already pointing too much (angle %g) towards donor (due to %s)" % (angle, da.oslIdent()) return addAtoD, addDtoA
def interpInternal(c0map, c1map, f, cs, a0, a1, a2, a3): """Computer coordinate of atom a0 by interpolating dihedral angle defined by atoms (a0, a1, a2, a3)""" import chimera c00 = c0map[a0] c01 = c0map[a1] c02 = c0map[a2] c03 = c0map[a3] length0 = c00.distance(c01) angle0 = chimera.angle(c00, c01, c02) dihed0 = chimera.dihedral(c00, c01, c02, c03) c10 = c1map[a0] c11 = c1map[a1] c12 = c1map[a2] c13 = c1map[a3] length1 = c10.distance(c11) angle1 = chimera.angle(c10, c11, c12) dihed1 = chimera.dihedral(c10, c11, c12, c13) length = length0 + (length1 - length0) * f angle = angle0 + (angle1 - angle0) * f ddihed = dihed1 - dihed0 if ddihed > 180: ddihed -= 360 elif ddihed < -180: ddihed += 360 dihed = dihed0 + ddihed * f c1 = a1.coord(cs) c2 = a2.coord(cs) c3 = a3.coord(cs) from chimera import molEdit try: c0 = molEdit.findPt(c1, c2, c3, length, angle, dihed) except ValueError: print `a1`, a1 print `a2`, a2 print `a3`, a3 raise a0.setCoord(c0, cs)
def _lenAngle(new, n1, n2, tmplMap, bondCache, angleCache):
from chimera import distance, angle
bondKey = (n1, new)
angleKey = (n2, n1, new)
try:
bl = bondCache[bondKey]
ang = angleCache[angleKey]
except KeyError:
n2pos = tmplMap[n2].coord()
n1pos = tmplMap[n1].coord()
newpos = tmplMap[new].coord()
bondCache[bondKey] = bl = distance(newpos, n1pos)
angleCache[angleKey] = ang = angle(newpos, n1pos, n2pos)
return bl, ang
def testTheta(dp, donorHyds, ap, theta): if len(donorHyds) == 0: if base.verbose: print "no hydrogens for theta test; default accept" return 1 for hydPos in donorHyds: ang = angle(ap, hydPos, dp) if ang >= theta: if base.verbose: print "theta okay (%g >= %g)" % (ang, theta) return 1 if base.verbose: print "theta failure (%g < %g)" % (ang, theta) return 0
def testTheta(dp, donorHyds, ap, theta):
if len(donorHyds) == 0:
if base.verbose:
print "no hydrogens for theta test; default accept"
return 1
for hydPos in donorHyds:
ang = angle(ap, hydPos, dp)
if ang >= theta:
if base.verbose:
print "theta okay (%g >= %g)" % (ang, theta)
return 1
if base.verbose:
print "theta failure (%g < %g)" % (ang, theta)
return 0
def _canAccept(donor, acceptor, protons, lonePairs):
# acceptor is fixed; can it accept from donor?
if not protons:
return True
if not lonePairs:
raise ValueError("No lone pairs on %s for %s to donate to" % (
acceptor, donor))
donPos = donor.xformCoord()
hDist = min(map(lambda xyz: (xyz - donPos).sqlength(), protons))
lpDist, lp = min(map(lambda xyz: ((xyz - donPos).sqlength(), xyz),
lonePairs))
# besides a lone pair being closest, it must be sufficiently pointed
# towards the donor
if lpDist >= hDist:
from math import sqrt
if debug:
print "can't still accept; lp dist (%g) >= h dist (%g)" % (sqrt(lpDist), sqrt(hDist))
elif chimera.angle(lp, acceptor.xformCoord(), donPos) >= _testAngles[
typeInfo4Atom[acceptor].geometry]:
if debug:
print "can't still accept; angle (%g) >= test angle (%g)" % ( chimera.angle(lp, acceptor.xformCoord(), donPos), _testAngles[ typeInfo4Atom[acceptor].geometry])
return lpDist < hDist and chimera.angle(lp,
acceptor.xformCoord(), donPos) < _testAngles[
typeInfo4Atom[acceptor].geometry]
def testThetaTau(dp, donorHyds, ap, pp, upsilonLow, upsilonHigh, theta): if pp: upsilonHigh = 0 - upsilonHigh upsilon = angle(pp, ap, dp) if upsilon < upsilonLow or upsilon > upsilonHigh: if base.verbose: print "upsilon (%g) failed (%g-%g)" % ( upsilon, upsilonLow, upsilonHigh) return 0 else: if base.verbose: print "can't determine upsilon; default okay" if base.verbose: print "upsilon okay" return testTheta(dp, donorHyds, ap, theta)
def _tetCheck(tet, partner, hbondInfo, tetAcc): """Check if tet can still work""" tetPos = tet.xformCoord() partnerPos = partner.xformCoord() bonded = tet.primaryNeighbors() tetInfo = hbondInfo.get(tet, []) towards = [] # if there is a real bond to the tet, we want to check the # dihedral to the new position (using a 120 angle) rather than # the angle (109.5) since the vector from the tet to the not- # yet-added positions is probably not directly along the future bond if bonded: if debug: print "checking dihedral" chkFunc = lambda op, pp=partnerPos, tp=tetPos, \ bp=bonded[0].xformCoord(): chimera.dihedral( pp, tp, bp, op) / 30.0 else: if debug: print "checking angle" chkFunc = lambda op, pp=partnerPos, tp=tetPos: chimera.angle( pp, tp, op) / 27.375 for isAcc, other in tetInfo: if isAcc == tetAcc: # same "polarity"; pointing towards is good result = True else: # opposite "polarity"; pointing towards is bad result = False angleGroup = int(chkFunc(other.xformCoord())) if angleGroup in [1,2,5,6]: # in the tetrahedral "dead zones" if debug: print "tetCheck for", tet.oslIdent(), print "; dead zone for", other.oslIdent() return False if angleGroup == 0: if debug: print "tetCheck for", tet.oslIdent(), print "; pointing towards", other.oslIdent(), print "returning", result return result towards.append(other.xformCoord()) # further tests only for 2 of 4 filled... if bonded or len(towards) != 2: return True return _tet2check(tetPos, towards[0], towards[1], partnerPos)
def formDihedral(resBud, real1, tmplRes, a, b):
res = resBud.residue
inres = filter(lambda a, rb=resBud, r=res: a.residue == r and a != rb,
real1.neighbors)
if real1.residue != res or len(inres) < 1:
raise AssertionError, "Can't form in-residue dihedral for" \
" %s of residue %s" % (bud, res.oslIdent())
real2 = inres[0]
xyz0, xyz1, xyz2 = map(lambda a, tr=tmplRes: tr.atomsMap[a.name].coord(),
(resBud, real1, real2))
xyz = a.coord()
blen = b.length()
ang = angle(xyz, xyz0, xyz1)
dihed = dihedral(xyz, xyz0, xyz1, xyz2)
return addDihedralAtom(a.name, a.element, resBud, real1, real2, blen, ang,
dihed)
def formDihedral(resBud, real1, tmplRes, a, b): res = resBud.residue inres = filter(lambda a, rb=resBud, r=res: a.residue == r and a != rb, real1.neighbors) if real1.residue != res or len(inres) < 1: raise AssertionError, "Can't form in-residue dihedral for" \ " %s of residue %s" % (bud, res.oslIdent()) real2 = inres[0] xyz0, xyz1, xyz2 = map(lambda a, tr=tmplRes: tr.atomsMap[a.name].coord(), (resBud, real1, real2)) xyz = a.coord() blen = b.length() ang = angle(xyz, xyz0, xyz1) dihed = dihedral(xyz, xyz0, xyz1, xyz2) return addDihedralAtom(a.name, a.element, resBud, real1, real2, blen, ang, dihed)
def test_include_dummies(element,
file,
charge,
geom,
dummies_xyz,
Model=Model):
# Right Values
ANGLE = {
'tetrahedral': [
60,
],
'square planar': [90, 45],
'square pyramid': [90, 45],
'octahedron': [90, 60, 45],
}
# Create metal instance
metal, metal_class = create_metal_class(element=element,
charge=charge,
geom=geom,
file=file)
# Initialize variables
metal_class.dummies_xyz = dummies_xyz
Model.geometry = geom
# Func to test
Model.include_dummies(metal_class)
# Selecting the included atoms
number_of_dummies = len(dummies_xyz)
atoms_to_select = ','.join(
['D' + str(i) for i in range(1, number_of_dummies + 1)])
rc("sel ::" + str(metal.residue.type) + '@' + atoms_to_select)
dummies = chimera.selection.currentAtoms()
# Eval Angles between them depending geometry
for i in range(0, number_of_dummies - 2):
angle = chimera.angle(dummies[i].labelCoord(),
dummies[i + 1].labelCoord(),
dummies[i + 2].labelCoord())
assert (int(round(angle)) in ANGLE[geom])
# Eval Bonds between Dummy&Metal center
for i in range(0, number_of_dummies):
bond = chimera.distance(dummies[i].labelCoord(), metal.labelCoord())
assert (abs(bond - 0.9) < 0.001)
def testPhi(dp, ap, bp, phiPlane, phi):
if phiPlane:
normal = cross(phiPlane[1] - phiPlane[0], phiPlane[2] - phiPlane[1])
normal.normalize()
D = normal * phiPlane[1].toVector()
bproj = project(bp, normal, D)
aproj = project(ap, normal, D)
dproj = project(dp, normal, D)
ang = angle(bproj, aproj, dproj)
if ang < phi:
if base.verbose:
print "phi criteria failed (%g < %g)" % (ang, phi)
return 0
if base.verbose:
print "phi criteria OK (%g >= %g)" % (ang, phi)
else:
if base.verbose:
print "phi criteria irrelevant"
return 1
def testPhi(dp, ap, bp, phiPlane, phi): if phiPlane: normal = cross(phiPlane[1] - phiPlane[0], phiPlane[2] - phiPlane[1]) normal.normalize() D = normal * phiPlane[1].toVector() bproj = project(bp, normal, D) aproj = project(ap, normal, D) dproj = project(dp, normal, D) ang = angle(bproj, aproj, dproj) if ang < phi: if base.verbose: print "phi criteria failed (%g < %g)" % (ang, phi) return 0 if base.verbose: print "phi criteria OK (%g >= %g)" % (ang, phi) else: if base.verbose: print "phi criteria irrelevant" return 1
def _pruneCheck(pivotAtom, goldHBond, testHBond): geom = _typeInfo(pivotAtom).geometry if geom < 2: return False if geom < 4 and _numBonds(pivotAtom) > 0: return False if goldHBond[0] == pivotAtom: ga = goldHBond[1] else: ga = goldHBond[0] if testHBond[0] == pivotAtom: ta = testHBond[1] else: ta = testHBond[0] angle = chimera.angle(ga.xformCoord(), pivotAtom.xformCoord(), ta.xformCoord()) fullAngle = _testAngles[geom] * 3 while angle > fullAngle / 2.0: angle -= fullAngle angle = abs(angle) return angle > fullAngle / 4.0
def addDihedralBond(a1, a2, length, angleInfo, dihedInfo):
"""Make bond between two models.
The models will be combined and the originals closed.
The new model will be opened in the same id/subid as the
non-moving model.
a1/a2 are atoms in different models.
a2 and atoms in its model will be moved to form the bond.
'length' is the bond length.
'angleInfo' is a two-tuple of sequence of three atoms and
an angle that the three atoms should form.
'dihedInfo' is like 'angleInfo', but 4 atoms.
angleInfo/dihedInfo can be None if insufficient atoms
"""
if a1.molecule == a2.molecule:
raise ValueError("Atoms to be bonded must be in different models")
# first, get the distance correct
from chimera import Xform, cross, angle, Point
dvector = a1.xformCoord() - a2.xformCoord()
dvector.length = dvector.length + length
openState = a2.molecule.openState
openState.globalXform(Xform.translation(dvector))
# then angle
if angleInfo:
atoms, angleVal = angleInfo
p1, p2, p3 = [a.xformCoord() for a in atoms]
axis = cross(p1-p2, p2-p3)
curAngle = angle(p1, p2, p3)
delta = angleVal - curAngle
v2 = p2 - Point(0.0, 0.0, 0.0)
trans1 = Xform.translation(v2)
v2.negate()
trans2 = Xform.translation(v2)
trans1.multiply(Xform.rotation(axis, delta))
trans1.multiply(trans2)
openState.globalXform(trans1)
def addDihedralBond(a1, a2, length, angleInfo, dihedInfo):
"""Make bond between two models.
The models will be combined and the originals closed.
The new model will be opened in the same id/subid as the
non-moving model.
a1/a2 are atoms in different models.
a2 and atoms in its model will be moved to form the bond.
'length' is the bond length.
'angleInfo' is a two-tuple of sequence of three atoms and
an angle that the three atoms should form.
'dihedInfo' is like 'angleInfo', but 4 atoms.
angleInfo/dihedInfo can be None if insufficient atoms
"""
if a1.molecule == a2.molecule:
raise ValueError("Atoms to be bonded must be in different models")
# first, get the distance correct
from chimera import Xform, cross, angle, Point
dvector = a1.xformCoord() - a2.xformCoord()
dvector.length = dvector.length + length
openState = a2.molecule.openState
openState.globalXform(Xform.translation(dvector))
# then angle
if angleInfo:
atoms, angleVal = angleInfo
p1, p2, p3 = [a.xformCoord() for a in atoms]
axis = cross(p1 - p2, p2 - p3)
curAngle = angle(p1, p2, p3)
delta = angleVal - curAngle
v2 = p2 - Point(0.0, 0.0, 0.0)
trans1 = Xform.translation(v2)
v2.negate()
trans2 = Xform.translation(v2)
trans1.multiply(Xform.rotation(axis, delta))
trans1.multiply(trans2)
openState.globalXform(trans1)
def measure_curvature(mset):
atoms = [m.atom for m in mset.markers()]
a2 = [a for a in atoms if len(a.bonds) == 2]
kmax = kmin = None
ksum = 0
for a in a2:
b1, b2 = a.bonds
s = 0.5 * (b1.length() + b2.length())
from chimera import angle
t = angle(a.coord() - b1.otherAtom(a).coord(),
b2.otherAtom(a).coord() - a.coord())
from math import pi
trad = t * pi / 180
k = trad / s
if kmin is None or k < kmin:
kmin = k
if kmax is None or k > kmax:
kmax = k
ksum += k
kave = ksum / len(a2) if len(a2) > 0 else None
return kave, kmin, kmax
def search_for_ligands(metal):
"""
Search for ligands near by the metal center
excluding candidates through the next steps:
1-How many electrons on the outter shell
2-Metal-Ligand distance
3-Geometry angles
4-Exclude Hydrogens and other atoms
Parameters:
-----------
metal: chimera metal object
Output:
-------
chimera ligands object
"""
# Extracted directly from:
# Metal Geom Chimera
data = []
coordLim = 4.0
from numpy import array
atoms = array(metal.molecule.atoms)
from _multiscale import get_atom_coordinates as gac
from _closepoints import find_close_points, BOXES_METHOD
ignore, close = find_close_points(BOXES_METHOD, gac(array([metal])),
gac(atoms), coordLim)
candidates = list(set(atoms[close]))
mcrd = metal.coord()
candidates.sort(lambda a1, a2: cmp(a1.coord().sqdistance(mcrd),
a2.coord().sqdistance(mcrd)))
exclude = []
userIncluded = []
for candidate in candidates:
if candidate == metal:
continue
if candidate in exclude:
continue
if candidate not in userIncluded:
valence = (candidate.element.number - 2) % 8
if valence < 5 or candidate.element.number == 1:
continue
if candidate.coord().distance(mcrd) > coordLim:
break
if candidate not in metal.bondsMap:
from chimera import angle
from chimera.idatm import typeInfo
angleOK = True
try:
cnGeom = typeInfo[candidate.idatmType].geometry
except KeyError:
cnGeom = 0
else:
if len(candidate.primaryNeighbors()) == cnGeom:
# no lone pairs, no possibility of deprotonation
continue
angleCutoff = [0.0, 72.98, 120.0, 80.0, 72.98][cnGeom]
for cnb in candidate.neighbors:
if cnb == metal:
continue
if angle(cnb.coord(), candidate.coord(),
metal.coord()) < angleCutoff:
angleOK = False
break
if not angleOK:
continue
data.append(candidate)
return data
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 testUpsilonTauAcceptor(donor, donorHyds, acceptor, r2, upsilonLow,
upsilonHigh, theta, tau, tauSym):
dc = donor.xformCoord()
ac = acceptor.xformCoord()
D2 = dc.sqdistance(ac)
if D2 > r2:
if base.verbose:
print "dist criteria failed (%g > %g)" % (sqrt(D2),
sqrt(r2))
return 0
upsilonHigh = 0 - upsilonHigh
heavys = filter(lambda a: a.element.number > 1,
donor.primaryNeighbors())
if len(heavys) != 1:
raise AtomTypeError("upsilon tau donor (%s) not bonded to"
" exactly one heavy atom" % donor.oslIdent())
ang = angle(heavys[0].xformCoord(), dc, ac)
if ang < upsilonLow or ang > upsilonHigh:
if base.verbose:
print "upsilon criteria failed (%g < %g or %g > %g)" % (
ang, upsilonLow, ang, upsilonHigh)
return 0
if base.verbose:
print "upsilon criteria OK (%g < %g < %g)" % (upsilonLow, ang,
upsilonHigh)
dp = dc
ap = ac
if not testTheta(dp, donorHyds, ap, theta):
return 0
if tau is None:
if base.verbose:
print "tau test irrelevant"
return 1
# sulfonamides and phosphonamides can have bonded NH2 groups that
# are planar enough to be declared Npl, so use the hydrogen
# positions to determine planarity if possible
if tauSym == 4:
bondedPos = hydPositions(donor)
else:
# since we expect tetrahedral hydrogens to be oppositely
# aligned from the attached tetrahedral center,
# we can't use their positions for tau testing
bondedPos = []
if 2 * len(bondedPos) != tauSym:
bondedPos = hydPositions(heavys[0], includeLonePairs=True)
donorEquiv = donor.allLocations()
for b in heavys[0].primaryNeighbors():
if b in donorEquiv or b.element.number < 2:
continue
bondedPos.append(b.xformCoord())
if not bondedPos:
if base.verbose:
print "tau indeterminate; default okay"
return 1
if 2 * len(bondedPos) != tauSym:
raise AtomTypeError("Unexpected tau symmetry (%d,"
" should be %d) for donor %s" % (
2 * len(bondedPos), tauSym, donor.oslIdent()))
normal = heavys[0].xformCoord() - dp
normal.normalize()
if tau < 0.0:
test = lambda ang, t=tau: ang <= 0.0 - t
else:
test = lambda ang, t=tau: ang >= t
projAccPos = project(ap, normal, 0.0)
projDonPos = project(dp, normal, 0.0)
for bpos in bondedPos:
projBpos = project(bpos, normal, 0.0)
ang = angle(projAccPos, projDonPos, projBpos)
if test(ang):
if tau < 0.0:
if base.verbose:
print "tau okay (%g < %g)" % (ang, -tau)
return 1
else:
if tau > 0.0:
if base.verbose:
print "tau too small (%g < %g)" % (ang,
tau)
return 0
if tau < 0.0:
if base.verbose:
print "all taus too big (> %g)" % -tau
return 0
if base.verbose:
print "all taus acceptable (> %g)" % tau
return 1
import chimera from chimera import Plane, Xform, cross, Vector, Point m = chimera.openModels.list()[0] b = chimera.selection.currentBonds()[0] bondVec = b.atoms[0].coord() - b.atoms[1].coord() bondVec.normalize() axis = Vector(1.0, 0.0, 0.0) crossProd = cross(axis, bondVec) if crossProd.sqlength() > 0: from math import acos, degrees xform = Xform.rotation(crossProd, degrees(acos(axis * bondVec))) xform.invert() else: xform = Xform.identity() m.openState.xform = xform # okay, that puts the bond parallel to the X axis, now swing the plane of # the rest of the molecule into the xy plane... molPlane = Plane([a.xformCoord() for a in m.atoms[:3]]) angle = chimera.angle(molPlane.normal, Vector(0, 0, -1)) xform2 = Xform.rotation(b.atoms[0].xformCoord()-b.atoms[1].xformCoord(), angle) xform2.multiply(xform) m.openState.xform = xform2
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)
import chimera
from chimera import Plane, Xform, cross, Vector, Point
m = chimera.openModels.list()[0]
b = chimera.selection.currentBonds()[0]
bondVec = b.atoms[0].coord() - b.atoms[1].coord()
bondVec.normalize()
axis = Vector(1.0, 0.0, 0.0)
crossProd = cross(axis, bondVec)
if crossProd.sqlength() > 0:
from math import acos, degrees
xform = Xform.rotation(crossProd, degrees(acos(axis * bondVec)))
xform.invert()
else:
xform = Xform.identity()
m.openState.xform = xform
# okay, that puts the bond parallel to the X axis, now swing the plane of
# the rest of the molecule into the xy plane...
molPlane = Plane([a.xformCoord() for a in m.atoms[:3]])
angle = chimera.angle(molPlane.normal, Vector(0, 0, -1))
xform2 = Xform.rotation(b.atoms[0].xformCoord() - b.atoms[1].xformCoord(),
angle)
xform2.multiply(xform)
m.openState.xform = xform2
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 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 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 metalClash(metalPos, pos, parentPos):
if metalPos.distance(parentPos) > _metalDist:
return False
if chimera.angle(parentPos, pos, metalPos) > 135.0:
return True
return False
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
