def set_metal_contacts(self, radius):
""" For the metals given, sets the contacts of this atom that
are within a "radius" distance from that metal
"""
contacts = []
# If a metal in "all_metals" is a direct neighbor of this residue,
# then it's definitely a contact, regardless of radius, and doesn't
# need to be considered further
metals_temp = self.all_metals
metals = []
this_residue_label = self.residue_1_letter + str(self.number)
for metal_potential in metals_temp:
if this_residue_label in metal_potential.nearby_residues:
contacts.append(metal_potential)
else:
metals.append(metal_potential)
for metal in metals:
metal_coords = [float(x) for x in metal.location.split(",")]
distance = chimera.distance(
self.atom.xformCoord(),
chimera.Point(metal_coords[0], metal_coords[1],
metal_coords[2]),
)
if distance - ionicRadiusDict.get(metal.type, None) <= radius:
contacts.append(metal)
self.metal_contacts = contacts
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 getShortestPoint(ref_point, point_list):
shortest_point = None
shortest_dist = None
for p in point_list:
dist = chimera.distance(p, ref_point)
if (not shortest_dist) or dist < shortest_dist:
shortest_point = p
shortest_dist = dist
return shortest_point
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 _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 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 linearPos(bondee, bonded, bondLen, toward=None, away=None):
newBonded = []
curBonded = bonded[:]
if len(bonded) == 0:
if away:
# need 90 angle, rather than directly away
# (since otherwise second added position will then be
# directly towards)
ninety = rightAngle(away - bondee)
away = bondee + ninety
pos = singlePos(bondee, bondLen, toward, away)
newBonded.append(pos)
curBonded.append(pos)
if len(curBonded) == 1:
bondedDist = distance(bondee, curBonded[0])
bondVec = bondee - curBonded[0]
bondVec.length = bondLen
newBonded.append(bondee + bondVec)
return newBonded
def linearPos(bondee, bonded, bondLen, toward=None, away=None): newBonded = [] curBonded = bonded[:] if len(bonded) == 0: if away: # need 90 angle, rather than directly away # (since otherwise second added position will then be # directly towards) ninety = rightAngle(away - bondee) away = bondee + ninety pos = singlePos(bondee, bondLen, toward, away) newBonded.append(pos) curBonded.append(pos) if len(curBonded) == 1: bondedDist = distance(bondee, curBonded[0]) bondVec = bondee - curBonded[0] bondVec.length = bondLen newBonded.append(bondee + bondVec) return newBonded
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 set_metal_contacts(self, radius):
""" Set contacts between this residue and metals at a given radius
"""
contacts = []
for metal in self.all_metals:
for atom in self.atoms:
# Set the coordinates of this metal in a way that Point()
# can accept
metal_coords = [float(x) for x in metal.location.split(",")]
# Get the distance between this atom and this metal
distance = chimera.distance(
atom.xformCoord(),
chimera.Point(metal_coords[0], metal_coords[1],
metal_coords[2]),
)
# If we're within the distance expected, add this metal
# to the list and move to the next
if distance - ionicRadiusDict.get(metal.type, None) <= radius:
contacts.append(metal)
break
self.metal_contacts = contacts
string = str(residue) + " " + str(
aaDict[type]) + " " + str(name) + '.' + altLoc
string = re.sub(r" ARG ", ":", string)
string = re.sub(r" LYS ", ":", string)
string = re.sub(r" PRO ", ":", string)
string = re.sub(r" THR ", ":", string)
string = re.sub(r" TRP ", ":", string)
# For rlbcoor data.
resTypeChain = str(residue) + " A"
resTypeChain = re.sub(r"#0 ", "", resTypeChain)
resTypeChainIndex[string] = str(resTypeChain)
xformCoordIndex[string] = str(a1.xformCoord())
counter2 = 0
for a2 in atoms:
distance = chimera.distance(a1.xformCoord(), a2.xformCoord())
distMatrix[counter2][counter1] = str(distance)
counter2 = counter2 + 1
counter1 = counter1 + 1
### EXAMPLES OF WRITING VARIABLES TO OUTPUT FILES.
# PRINT OUT ALL RESULTS.
f_distMatrix.write("\t")
for a1 in atomsList:
atom1 = str(a1)
f_distMatrix.write(atom1)
f_distMatrix.write("\t")
f_distMatrix.write("\n")
for a1 in atomsList:
atom1 = str(a1)
def distance_regular(self, other_atom):
""" Gets the distance between this and a regular atom
"""
return chimera.distance(self.atom.xformCoord(),
other_atom.xformCoord())
def distance(self, other_atom):
""" Gets the distance between this and another extendedAtom
"""
return chimera.distance(self.atom.xformCoord(),
other_atom.atom.xformCoord())