コード例 #1
0
ファイル: hydrogens.py プロジェクト: ryancoleman/mol2db2
 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
コード例 #2
0
ファイル: hydrogens.py プロジェクト: ryancoleman/mol2db2
 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