def rotateHydrogens(self, mol2data):
'''runs after findTerminalHydrogens, rotates the rotatable hydrogens to
the angles specified by the rules. differs in that it copies everything
and makes all combinations of hydrogen rotations'''
self._findDihedrals(mol2data) #first call in case reset was not done
rotatedMol2data = mol2data.copy() #copy this one, put all new in rotated
rotatedMol2data.atomXyz = [] #clear
rotatedMol2data.inputEnergy = [] #clear
rotatedMol2data.inputHydrogens = [] #clear
rotatedMol2data.origXyzCount = mol2data.xyzCount
for xyzCount in xrange(mol2data.xyzCount): #iterate over orig conformations
indexToCoords = [] #list of lists
originals = []
for atomIndex, atomNum in enumerate(mol2data.atomNum):
if atomNum in mol2data.dihedrals.keys():
thisCoords = []
curXyz, dihedral1 = self._getCurDihedral(atomNum, xyzCount, mol2data)
thisCoords.append(curXyz[3]) #original saved here
originals.append(curXyz[3]) #also save orig here
for newAngle in mol2data.rotAngles[atomNum]:
#want to find a new rotation angle and move to that
newTheta = math.radians(newAngle) #convert to radians!!
#print dihedral1, newAngle, newTheta,
newHxyz = geometry_basic.rotateAboutLine(curXyz[1], curXyz[2], \
curXyz[3], newTheta)
thisCoords.append(newHxyz) #save new ones here
indexToCoords.append(thisCoords)
#have to make all possible combinations
combinations = combinatorics.allCombinations(indexToCoords)
for aCombo in combinations:
if aCombo != originals: #don't need to do anything for the original set
#need to copy inputEnergy and atomXyz, then replace atomXyz
atomXyzCopy = mol2data.atomXyz[xyzCount][:]
#replace hydrogen positions here
replaceIndex = 0
for atomIndex, atomNum in enumerate(mol2data.atomNum):
if atomNum in mol2data.dihedrals.keys():
atomXyzCopy[atomIndex] = aCombo[replaceIndex] #replace coord
replaceIndex += 1 #move this counter forward
rotatedMol2data.atomXyz.append(atomXyzCopy)
rotatedMol2data.inputEnergy.append(mol2data.inputEnergy[xyzCount]) #copy
rotatedMol2data.inputHydrogens.append(2) #means rotate
else: #aCombo is the original set
atomXyzCopy = mol2data.atomXyz[xyzCount][:]
rotatedMol2data.atomXyz.append(atomXyzCopy)
rotatedMol2data.inputEnergy.append(mol2data.inputEnergy[xyzCount])
rotatedMol2data.inputHydrogens.append( \
mol2data.inputHydrogens[xyzCount])
rotatedMol2data.xyzCount = len(rotatedMol2data.atomXyz) #finally set this correctly
return rotatedMol2data
def resetHydrogens(self, mol2data):
'''runs after findTerminalHydrogens, resets the rotatable hydrogens to 0
instead of the potentially bad angle they were set at.'''
self._findDihedrals(mol2data)
for xyzCount in xrange(mol2data.xyzCount): #iterate over conformations
for atomIndex, atomNum in enumerate(mol2data.atomNum):
if atomNum in mol2data.dihedrals.keys() and \
180. in mol2data.rotAngles[atomNum]: #only planar get reset
curXyz, dihedral1 = self._getCurDihedral(atomNum, xyzCount, mol2data)
#want to find a new rotation angle, 0, and reset
newTheta = 0 - dihedral1 #radians!!
#print newTheta
newHxyz = geometry_basic.rotateAboutLine(curXyz[1], curXyz[2], \
curXyz[3], newTheta)
#print curXyz[3], newHxyz
mol2data.atomXyz[xyzCount][atomIndex] = newHxyz
mol2data.inputHydrogens[xyzCount] = 1 #means reset