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valleyridge_python3.py
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'''
Filename: ValleyRidge.py (version X)
Description:
- Predicts Major and Minor products from two transition states in reaction involving valley ridge inflections
- In order for this code to work the Gaussian frequency calculation must be run with freq=hpmodes keyword. This will ask Gaussian to print (the eigenvectors to 5 significant figures.
Usage:
Algorithm Summary:
1. Import TS1 and TS2 structures
2. Align TS1 and TS2 to minimise RMSD
3. Extract TS1 and TS2 imaginary eigenvectors
4. Translate TS2 eigenvector according to the aligned TS2 geometry
5. Find u
6. Perform QRC from g+ub (i.e. TS2 structure displaced by u in the direction of imag freq vector)
@Sanha Lee
Dec 2018
'''
############################################################
# Import Modules
############################################################
import numpy as np
import argparse
import os
import math
import sys
from rdkit import Chem
import bisect
import logging
from datetime import datetime
import itertools
############################################################
# Main Code
############################################################
def main(filename1, filename2, filename3, filename4, filename5, filename6, weight_option):
logging.basicConfig(filename='ValleyRidge_'+filename1[:-4]+'.log', level=logging.DEBUG, format='%(message)s', filemode='w')
datetime_now = datetime.now()
formatted_datetime = datetime_now.strftime("%Y %b %d %H:%M:%S")
print ('')
print ('***********************************')
print ('')
print ('ValleyRidge.py')
print ('')
print ('Python code to predict selectivity from two transition states')
print ('@author: Sanha Lee')
print ('Run date: '+formatted_datetime)
print ('')
print ('Created: ValleyRidge_'+filename1[:-4]+'.log')
print ('')
print ('***********************************')
print ('')
logging.info('\n')
logging.info('***********************************\n')
logging.info('ValleyRidge.py\n')
logging.info('Python code to predict selectivity from two transition states')
logging.info('@author: Sanha Lee')
logging.info('University of Cambridge')
logging.info('Run date: '+formatted_datetime+'\n')
logging.info('***********************************\n')
logging.info('Reading TS1: '+filename1)
logging.info('Reading TS2: '+filename2)
logging.info('Reading P1: '+filename3)
logging.info('Reading P2: '+filename4)
logging.info('Reading TS1 freq: '+filename5)
logging.info('Reading TS2 freq: '+filename6+'\n')
atoms1, geometries1 = ReadGeometries(filename1)
atoms2, geometries2 = ReadGeometries(filename2)
atoms3, geometries3 = ReadGeometries(filename3)
atoms4, geometries4 = ReadGeometries(filename4)
logging.info('No. of Atoms: '+str(len(atoms1))+'\n')
equalweightslist = SetEqualWeights(atoms1)
trueweightslist = []
WeightsToUse = equalweightslist[:]
TempToUse = 298.0
# -- Change weights for alignment if necessary
if weight_option == True:
logging.info('Alignment weight option is set to atomic weights')
for atom in atoms1:
trueweightslist += [GetAtomNum(atom)]
WeightsToUse = trueweightslist[:]
else:
logging.info('Alignment weight option is set equal for all atoms')
rdkitmolTS1 = Chem.MolFromMolFile(filename1, removeHs=False, strictParsing=False)
if not rdkitmolTS1:
logging.error("Could not create RDKIT mol for: ",filename1)
logging.error('Terminating Program')
sys.exit()
else:
logging.info('RDKIT Mol object successfully created for: '+filename1)
logging.info(rdkitmolTS1)
rdkitmolTS2 = Chem.MolFromMolFile(filename2, removeHs=False, strictParsing=False)
if not rdkitmolTS2:
logging.error("Could not create mol for: ",filename2)
logging.error('Terminating Program')
sys.exit()
else:
logging.info('Mol object successfully created for: '+filename2)
logging.info(rdkitmolTS2)
rdkitmolP1 = Chem.MolFromMolFile(filename3, removeHs=False, strictParsing=False)
if not rdkitmolP1:
logging.error("Could not create mol for: "+filename3)
logging.error('Terminating Program')
sys.exit()
else:
logging.info('Mol object successfully created for: '+filename3)
logging.info(rdkitmolP1)
rdkitmolP2 = Chem.MolFromMolFile(filename4, removeHs=False, strictParsing=False)
if not rdkitmolP2:
logging.error("Could not create mol for: "+filename4)
logging.error('Terminating Program')
sys.exit()
else:
logging.info('Mol object successfully created for: '+filename4)
logging.info(rdkitmolP2)
# -- Identify Orthogonal Bonds
P1bonds = ExtractBonds(rdkitmolP1, atoms1)
P2bonds = ExtractBonds(rdkitmolP2, atoms1)
TS1bonds = ExtractBonds(rdkitmolTS1, atoms1)
logging.info('')
logging.info('P1bonds:')
for item in P1bonds:
logging.info(str(item[0])+'-'+str(item[1]))
logging.info('')
logging.info('P2bonds:')
for item in P2bonds:
logging.info(str(item[0])+'-'+str(item[1]))
unidenticalP1P2, unidenticalP2P1 = IdentifyChangedBonds(P1bonds, P2bonds)
unidenticalTS1P1, unidenticalP1TS1 = IdentifyChangedBonds(TS1bonds, P1bonds)
unidenticalTS1P2, unidenticalP2TS1 = IdentifyChangedBonds(TS1bonds, P2bonds)
# changed_bonds1 = bonds in bondlist1 which does not exist in bondlist2
# changed_bonds2 = bonds in bondlist2 which does not exist in bondlist1
logging.info('')
logging.info('unidenticalP1P2: '+str(unidenticalP1P2))
logging.info('unidenticalP2P1: '+str(unidenticalP2P1))
logging.info('unidenticalTS1P1: '+str(unidenticalTS1P1))
logging.info('unidenticalTS1P2: '+str(unidenticalTS1P2))
logging.info('unidenticalP1TS1: '+str(unidenticalP1TS1))
logging.info('unidenticalP2TS1: '+str(unidenticalP2TS1))
orthbond1list = []
orthbond2list = []
newunidenticalP1TS1 = []
newunidenticalTS1P1 = []
newunidenticalP2TS1 = []
newunidenticalTS1P2 = []
# -- Remove Duplicated bonds in all lists
for item in unidenticalP1TS1:
if item in unidenticalP1P2:
pass
else:
newunidenticalP1TS1 += [item]
for item in unidenticalTS1P1:
if item in unidenticalP1P2 or item in unidenticalP1TS1:
pass
else:
newunidenticalTS1P1 += [item]
for item in unidenticalP2TS1:
if item in unidenticalP2P1:
pass
else:
newunidenticalP2TS1 += [item]
for item in unidenticalTS1P2:
if item in unidenticalP2P1 or item in unidenticalP2TS1:
pass
else:
newunidenticalTS1P2 += [item]
# -- Rank the bond differences found
BondrankP1 = []
BondrankP2 = []
# CaseA: When the length of B(P1|P2) >= 1 or B(P2|P1) >= 1
logging.info('')
logging.info('Case when B(P1|P2) >= 1 or B(P2|P1) >= 1')
permutationsP1P2rank, permutationsP2P1rank = RankBonds(unidenticalP1P2, unidenticalP2P1, geometries1, geometries2, geometries3, geometries4)
BondrankP1 = BondrankP1 + permutationsP1P2rank
BondrankP2 = BondrankP2 + permutationsP2P1rank
# CaseB: When the length of B(P1|P2) = 0 or B(P2|P1) = 0
# CaseC: both B(P1|P2) >= 1 or B(P2|P1) >= 1 but needs more B(|) tests
logging.info('')
logging.info('Replace B(P1|P2) with B(TS1|P1)')
permutationsTS1P1P2P1, permutationsP2P1TS1P1 = RankBonds(unidenticalTS1P1, unidenticalP2P1, geometries1, geometries2, geometries3, geometries4)
BondrankP1 = BondrankP1 + permutationsTS1P1P2P1
BondrankP2 = BondrankP2 + permutationsP2P1TS1P1
logging.info('')
logging.info('Replace B(P2|P1) with B(TS1|P2)')
permutationsP1P2TS1P2, permutationsTS1P2P1P2 = RankBonds(unidenticalP1P2, unidenticalTS1P2, geometries1, geometries2, geometries3, geometries4)
BondrankP1 = BondrankP1 + permutationsP1P2TS1P2
BondrankP2 = BondrankP2 + permutationsTS1P2P1P2
logging.info('')
logging.info('Replace B(P1|P2) with B(P1|TS1)')
permutationsP1TS1P2P1, permutationsP2P1P1TS1 = RankBonds(unidenticalP1TS1, unidenticalP2P1, geometries1, geometries2, geometries3, geometries4)
BondrankP1 = BondrankP1 + permutationsP1TS1P2P1
BondrankP2 = BondrankP2 + permutationsP2P1P1TS1
logging.info('')
logging.info('Replace B(P2|P1) with B(P2|TS1)')
permutationsP1P2P2TS1, permutationsP2TS1P1P2 = RankBonds(unidenticalP1P2, unidenticalP2TS1, geometries1, geometries2, geometries3, geometries4)
BondrankP1 = BondrankP1 + permutationsP1P2P2TS1
BondrankP2 = BondrankP2 + permutationsP2TS1P1P2
# test whether the algorithm is using bond1 to loop or bond2 to loop
logging.info('')
logging.info('BondrankP1: '+str(BondrankP1))
logging.info('BondrankP2: '+str(BondrankP2))
testlength = 0
if len(BondrankP1) >= len(BondrankP2):
testlength = len(BondrankP2)
if len(BondrankP2) >= len(BondrankP1):
testlength = len(BondrankP1)
testidx = 0
##############################
############################## Edit here
##############################
while testidx < testlength:
orthbond1list = BondrankP1[testidx]
orthbond2list = BondrankP2[testidx]
logging.info('')
logging.info('The algorithm is current using the following bonds for the major product analysis:')
logging.info('orthbond1list: '+str(orthbond1list))
logging.info('orthbond1list: '+str(orthbond2list))
orthbond1list = [(int(i)-1) for i in orthbond1list]
orthbond2list = [(int(i)-1) for i in orthbond2list]
# -- Major Product Analysis
eigenvectors1, imag_eigenvector1, real_eigenvectors1 = ReadEigenVec(filename5) # RealEigenVec format: [[vector1],[vector2],...]
eigenvectors2, imag_eigenvector2, real_eigenvectors2 = ReadEigenVec(filename6)
forceconstants1, frequencies1 = ExtractForceConsts(filename5) # Note: This function does not return the force constant corresponding to the imaginary frequency
imag_eigenvector1 = [float(i) for i in imag_eigenvector1]
real_xyzeigenvectors = []
real_floateigenvectors = []
for eigenvector in real_eigenvectors1:
real_floateigenvectors.append([])
floateigenlist = [float(item) for item in eigenvector]
real_floateigenvectors[-1] = floateigenlist
for eigenvector in real_eigenvectors1:
real_lineigenvectorcomp = [float(item) for item in eigenvector]
real_xyzeigenvectorcomp = ConvertLineartoXYZ(real_lineigenvectorcomp)
real_xyzeigenvectors.append([])
real_xyzeigenvectors[-1] = real_xyzeigenvectorcomp
logging.info('')
logging.info('-- Starting Vector Analysis --')
logging.info('')
logging.info('coord1-1: '+str(geometries1[orthbond1list[0]]))
logging.info('coord1-2: '+str(geometries1[orthbond1list[1]]))
logging.info('coord2-1: '+str(geometries1[orthbond2list[0]]))
logging.info('coord2-2: '+str(geometries1[orthbond2list[1]]))
logging.info('TS1_bond1: '+str(GetBondLength(geometries1, orthbond1list[0], orthbond1list[1])))
logging.info('TS1_bond2: '+str(GetBondLength(geometries1, orthbond2list[0], orthbond2list[1])))
# Stretch the molecule along the imaginary eigenvector and find the difference with the original atom position to find the imaginary eigenvector
lingeometries1 = ConvertXYZtoLinear(geometries1)
lindispTS1 = list(np.array(lingeometries1) + np.array(imag_eigenvector1))
dispTS1 = ConvertLineartoXYZ(lindispTS1)
dispcomp1 = GetBondLength(dispTS1, orthbond1list[0], orthbond1list[1]) - GetBondLength(geometries1, orthbond1list[0], orthbond1list[1])
dispcomp2 = GetBondLength(dispTS1, orthbond2list[0], orthbond2list[1]) - GetBondLength(geometries1, orthbond2list[0], orthbond2list[1])
Redimag_eigenvector1 = [dispcomp1,dispcomp2]
logging.info('')
logging.info('Bond Imaginary Eigenvector: '+str(Redimag_eigenvector1))
Redgeometry1 = [GetBondLength(geometries1, orthbond1list[0], orthbond1list[1]),GetBondLength(geometries1, orthbond2list[0], orthbond2list[1])]
Redgeometry2 = [GetBondLength(geometries2, orthbond1list[0], orthbond1list[1]),GetBondLength(geometries2, orthbond2list[0], orthbond2list[1])]
Redgeometry3 = [GetBondLength(geometries3, orthbond1list[0], orthbond1list[1]),GetBondLength(geometries3, orthbond2list[0], orthbond2list[1])]
Redgeometry4 = [GetBondLength(geometries4, orthbond1list[0], orthbond1list[1]),GetBondLength(geometries4, orthbond2list[0], orthbond2list[1])]
p1_ = list(np.array(Redgeometry3)-np.array(Redgeometry2))
p2_ = list(np.array(Redgeometry4)-np.array(Redgeometry2))
g_ = list(np.array(Redgeometry2)-np.array(Redgeometry1))
logging.info('')
logging.info('p1_: ')
for item in ConvertLineartoXYZ(p1_):
logging.info(str(item).strip('[]'))
logging.info('')
logging.info('p2_: ')
for item in ConvertLineartoXYZ(p2_):
logging.info(str(item).strip('[]'))
logging.info('')
logging.info('imag_eigenvector:')
for item in ConvertLineartoXYZ(imag_eigenvector1):
logging.info(str(item).strip('[]'))
logging.info('')
logging.info('g_:')
for item in ConvertLineartoXYZ(g_):
logging.info(str(item).strip('[]'))
logging.info('')
# -- Test whether the TS1 eigenvector needs to be inverted
angle_phi = abs(angle(Redimag_eigenvector1,g_))
if angle_phi > (math.pi/2):
logging.info('phi is '+str((180/math.pi)*angle_phi)+' vector a_ will be inverted.\n')
Redimag_eigenvector1 = InvertVec(Redimag_eigenvector1)
angle_phi = abs(angle(Redimag_eigenvector1,g_))
logging.info('new phi is '+str((180/math.pi)*abs(angle(Redimag_eigenvector1,g_))))
else:
logging.info('phi is '+str((180/math.pi)*angle_phi)+' vector a_ will not be inverted.\n')
angle_p1p2 = abs(angle(p1_,p2_))
mu1_ = Findmu_(Redimag_eigenvector1, p1_, g_)
mu2_ = Findmu_(Redimag_eigenvector1, p2_, g_)
lambda1_ = Findlambda_(Redimag_eigenvector1, p1_, g_)
lambda2_ = Findlambda_(Redimag_eigenvector1, p2_, g_)
if np.sign(mu1_) != np.sign(mu2_) and lambda1_ > 0 and lambda2_ > 0:
logging.info('+mu_, -mu_, +lambda_, +lambda_ combination found. The algorithm wil continue.')
break
else:
logging.info('')
logging.info('The sign test did not find +mu_, -mu_, +lambda_, +lambda_ combination. The algorithm will try different set of bonds')
testidx += 1
logging.info('')
logging.info('angle(p1,p1): '+str((180/math.pi)*angle_p1p2))
logging.info('|p1|: '+str(length(p1_)))
logging.info('|p2|: '+str(length(p2_)))
logging.info('|a|: '+str(length(imag_eigenvector1)))
logging.info('|b|: '+str(length(imag_eigenvector2)))
logging.info('|g|: '+str(length(g_)))
logging.info('')
logging.info('phi:')
logging.info(angle(imag_eigenvector1,g_)*(180/math.pi))
# -- Result Analysis --
if np.sign(mu1_) != np.sign(mu2_) and lambda1_ > 0 and lambda2_ > 0:
# -- Real Eigenvector Proudct Ratio Analysis
BondRealEigenvectors = ProjectEigenToBond(real_floateigenvectors, orthbond1list, orthbond2list, geometries1)
logging.info('')
logging.info('BondRealEigenVectors')
for item in BondRealEigenvectors:
logging.info(item)
BondRealEigenvectorLengths = [] # Find the length of the real eigenvectors projected to the two key bonds
for vector in BondRealEigenvectors:
BondRealEigenvectorLengths += [length(vector)]
TempToUse = 298.0
HalfWellWidths = CalcXs(forceconstants1, TempToUse, frequencies1)
logging.info('')
logging.info('HalfWellWidths: ')
for item in HalfWellWidths:
logging.info(item)
logging.info('')
logging.info('BondRealEigenvectorLengths:')
for item in BondRealEigenvectorLengths:
logging.info(item)
constantAs = []
for index in range(len(BondRealEigenvectors)):
const_A = HalfWellWidths[index]/BondRealEigenvectorLengths[index]
constantAs += [const_A]
logging.info('')
logging.info('const_As: ')
for item in constantAs:
logging.info(item)
m_list = ImagOrthogonalProj(BondRealEigenvectors,constantAs,Redimag_eigenvector1,g_)
ConstBs = FindConstantB(m_list,Redimag_eigenvector1,g_)
logging.info('')
logging.info('ConstBs')
for item in ConstBs:
logging.info(item)
major_length, minor_length = FindProdRatio(m_list, ConstBs, Redimag_eigenvector1)
major_ratio = major_length/(major_length + minor_length)
minor_ratio = minor_length/(major_length + minor_length)
if length(g_) < 0.5 and (180/math.pi)*angle_phi > 20 and (180/math.pi)*angle_phi < 50:
logging.info('')
logging.info('current major ratio:'+str(major_ratio))
logging.info('current minor ratio:'+str(minor_ratio))
logging.info('|g| < 0.5 and 20 < phi < 50 degs, the algorithm will change the major:minor product ratio')
major_ratio = (major_ratio - 0.58369)/0.4029
if major_ratio > 1:
major_ratio = 1
minor_ratio = 1 - major_ratio
'''
if length(g_) < 0.5 and ((180/math.pi)*angle_phi) < 20:
logging.info('')
logging.info('current major ratio:'+str(major_ratio))
logging.info('current minor ratio:'+str(minor_ratio))
logging.info('|g| < 0.5 and phi < 20 degs, the algorithm will change the major:minor product ratio')
major_ratio = (major_ratio - 0.1543659)/0.7437851
minor_ratio = 1 - major_ratio
elif length(g_) < 0.5 and 20 < ((180/math.pi)*angle_phi) and ((180/math.pi)*angle_phi) < 40:
logging.info('')
logging.info('|g| < 0.5 and 20 < phi < 40 degs, the algorithm will change the major:minor product ratio')
major_ratio = (major_ratio - 0.5417960)/0.4733665
minor_ratio = 1 - major_ratio
'''
if mu1_ > 0 and mu2_ < 0:
logging.info('')
logging.info('**** Analysis Completed ****')
logging.info('Major product is '+str(filename3))
logging.info('Minor product is '+str(filename4))
print ('')
print ('**** Analysis Completed ****')
print ('Major product is '+str(filename3))
print ('Minor product is '+str(filename4))
elif mu2_ > 0 and mu1_ < 0:
logging.info('')
logging.info('**** Analysis Completed ****')
logging.info('Major product is '+str(filename4))
logging.info('Minor product is '+str(filename3))
print ('')
print ('**** Analysis Completed ****')
print ('Major product is '+str(filename4))
print ('Minor product is '+str(filename3))
logging.info('')
logging.info('mu1_ = '+str(mu1_))
logging.info('mu2_ = '+str(mu2_))
logging.info('lambda1_ = '+str(lambda1_))
logging.info('lambda2_ = '+str(lambda2_))
logging.info('|g_| = '+str(length(g_)))
if length(g_) > 1.0:
logging.info('WARNING: |g_| is large (|g_| > 1)')
logging.info('phi = '+str((180/math.pi)*angle_phi))
logging.info('')
logging.info('The algorith will now proceed to estimate the major and minor product ratios')
logging.info('')
logging.info('Product Ratio Calculation Completed:')
logging.info('Major Product : Minor Product ratio')
logging.info(str(round(major_ratio*100, 1))+' : '+str(round(minor_ratio*100, 1))+'\n')
if round(major_ratio*100, 1) < 60.0:
logging.info('WARNING: the predicted ratio is close to 50:50')
logging.info('****************************')
logging.info('')
print ('')
print ('mu1_ = '+str(mu1_))
print ('mu2_ = '+str(mu2_))
print ('lambda1_ = '+str(lambda1_))
print ('lambda2_ = '+str(lambda2_))
print ('|g_| = '+str(length(g_)))
if length(g_) > 1.0:
print ('WARNING: |g_| is large (|g_| > 1)')
print ('phi = '+str((180/math.pi)*angle_phi))
print ('')
print ('Product Ratio Calculation Completed:')
print ('Major Product : Minor Product ratio')
print (str(round(major_ratio*100, 1))+' : '+str(round(minor_ratio*100, 1)))
if round(major_ratio*100, 1) < 60.0:
print ('WARNING: the predicted ratio is close to 50:50')
print ('')
print ('****************************')
print ('')
else:
logging.error('')
logging.error('**** Analysis Completed ****')
logging.error('+mu_, -mu_, +lambda_, +lambda_ combination not found')
logging.error('ERROR: Unable to predict the major product')
logging.error('')
logging.error('mu1_ = '+str(mu1_))
logging.error('mu2_ = '+str(mu2_))
logging.error('lambda1_ = '+str(lambda1_))
logging.error('lambda2_ = '+str(lambda2_))
logging.info('|g_| = '+str(length(g_)))
logging.info('phi = '+str((180/math.pi)*angle_phi))
logging.error('')
logging.error('The algorith will not proceed to estimate the major and minor product ratios')
logging.error('****************************')
print ('')
print ('**** Analysis Completed ****')
print ('+mu_, -mu_, +lambda_, +lambda_ combination not found')
print ('ERROR: Unable to predict the major product')
print ('')
print ('mu1_ = '+str(mu1_))
print ('mu2_ = '+str(mu2_))
print ('lambda1_ = '+str(lambda1_))
print ('lambda2_ = '+str(lambda2_))
print ('|g_| = '+str(length(g_)))
print ('phi = '+str((180/math.pi)*angle_phi))
print ('')
print ('The algorithm will not proceed to estimate the major and minor product ratios')
print ('****************************')
print ('')
############################################################
# Functions
############################################################
def SetEqualWeights(atom_list):
'''
Sets weightings used for geometry alignments
'''
weights = []
for item in atom_list:
weights += [1]
return weights
def InvertVec(vector):
InvertedVector = [(-1)*i for i in vector]
return InvertedVector
def ConvertLineartoXYZ(LinearList):
'''
Convert [x1,y1,z1,x2,y2,z2,...] format to [[x1,y1,z1],[x2,y2,z2],...]
'''
XYZlist = []
i = 0
while i < len(LinearList):
XYZlist.append(LinearList[i:i+3])
i+=3
return XYZlist
def VectorAddition(vec1,vec2):
addedvector = []
for i in range(len(vec1)):
addition = float(vec1[i]) + float(vec2[i])
addedvector += [addition]
return addedvector
def ConvertXYZtoLinear(XYZlist):
'''
Covert geometry list in [[x1,y1,z1],[x2,y2,z2],...] format to [x1,y1,z1,x2,y2,z2,...] format
'''
linearlist = []
for i in range(len(XYZlist)):
for j in range(3):
linearlist.append(XYZlist[i][j])
return linearlist
def Findmu_(vec_a, vec_b, vec_g):
'''
Finds u in point of closest approach analysis
'''
nominator = dotproduct(vec_a,vec_g)*dotproduct(vec_a,vec_b) - dotproduct(vec_b,vec_g)*dotproduct(vec_a,vec_a)
denominator = dotproduct(vec_a,vec_a)*dotproduct(vec_b,vec_b)-(dotproduct(vec_a,vec_b)**2)
return (nominator/denominator)
def Findlambda_(vec_a, vec_b, vec_g):
'''
Finds lambda in point of closest approach analysis
'''
nominator = dotproduct(vec_a,vec_g)*dotproduct(vec_b,vec_b) - dotproduct(vec_b,vec_g)*dotproduct(vec_a,vec_b)
denominator = dotproduct(vec_a,vec_a)*dotproduct(vec_b,vec_b)-(dotproduct(vec_a,vec_b)**2)
return (nominator/denominator)
def dotproduct(v1, v2):
'''
Returns dot product of vectors v1 and v2
'''
return sum((float(a)*float(b)) for a, b in zip(v1, v2))
def length(v):
'''
Returns magnitude of vector v
'''
return math.sqrt(dotproduct(v, v))
def angle(v1, v2):
'''
Returns angle between vectors v1 and v2
'''
return math.acos(round(dotproduct(v1, v2) / (length(v1) * length(v2)),5))
def FindUnitVector(vector):
'''
Returns the unit vector
'''
unit_vector = []
magnitude = length(vector)
for item in vector:
unit_vector += [item/magnitude]
return unit_vector
def ReadGeometries(GMolFile):
'''
Finds optimisation steps in the Gaussian output file and extracts the coordinates for each step.
If the output file is a frequency calculation only one geometry exists.
Returns the coordinates as a list
'''
gausfile = open(GMolFile, 'r')
GOutp = gausfile.readlines()
gausfile.close()
index = 0
atoms = []
coords = []
for index in range(len(GOutp)):
if index > 3:
if len(GOutp[index].split()) < 8:
break
else:
data = GOutp[index].split()
atoms.append(data[3])
coords.append([float(x) for x in data[0:3]])
return atoms, coords
def FindDispVec(Geom1,Geom2):
'''
The atoms must be written in same order in Geom1 and Geom2. Geom1 and Geom2 must be same molecular species otherwise this function will not work.
'''
DispVec = []
for coord in range(len(Geom1)):
coorddisp = Geom2[coord] - Geom1[coord]
DispVec.append(coorddisp)
return DispVec
def ReadEigenVec(GOutpFile):
'''
ReadEigenVec: returns eigenvectors in ascending order (as printed in Gaussian output file) of frequency.
The format is [[Eigenvector1],[Eigenvector2],...]. Edit the return at the end of the function if the
structure is not at the transition state.
'''
gausfile = open(GOutpFile, 'r')
GOutp = gausfile.readlines()
gausfile.close()
index = 0
EigenIndexes = []
EigenVectors = []
for index in range(len(GOutp)):
if "Coord Atom Element:" in GOutp[index]:
EigenIndexes.append(index + 1)
for i, gindex in enumerate(EigenIndexes):
first_line = True # not ideal location for this line
for line in GOutp[gindex:]:
if ' ' in line: # find
first_line = True
break
if 'Harmonic frequencies (cm**-1)' in line: # check for final few eigenvectors
break
else:
data = line.split()
if first_line == True:
eigenvec_element = [[] for i in range(len(data)-3)]
first_line = False
for index in range(len(data[3:])):
eigenvec_element[index].append(data[index+3])
for item in eigenvec_element:
EigenVectors += [item]
imag_eigenvector = EigenVectors[0]
real_eigenvectors = EigenVectors[1:]
return EigenVectors, imag_eigenvector, real_eigenvectors
Lookup = ['H', 'He', 'Li', 'Be', 'B', 'C', 'N', 'O', 'F', 'Ne', 'Na', 'Mg', 'Al', \
'Si', 'P', 'S', 'Cl', 'Ar', 'K', 'Ca', 'Sc', 'Ti', 'V', 'Cr', 'Mn', 'Fe', 'Co', \
'Ni', 'Cu', 'Zn', 'Ga', 'Ge', 'As', 'Se', 'Br', 'Kr', 'Rb', 'Sr', 'Y', 'Zr', \
'Nb', 'Mo', 'Tc', 'Ru', 'Rh', 'Pd', 'Ag', 'Cd', 'In', 'Sn', 'Sb', 'Te', 'I', \
'Xe', 'Cs', 'Ba', 'La', 'Ce', 'Pr', 'Nd', 'Pm', 'Sm', 'Eu', 'Gd', 'Tb', 'Dy', \
'Ho', 'Er', 'Tm', 'Yb', 'Lu', 'Hf', 'Ta', 'W', 'Re', 'Os', 'Ir', 'Pt', 'Au', \
'Hg', 'Tl', 'Pb', 'Bi', 'Po', 'At', 'Rn']
def GetAtomSymbol(AtomNum):
'''
Extracts the element symbol from Lookup list
'''
if AtomNum > 0 and AtomNum < len(Lookup):
return Lookup[AtomNum-1]
else:
logging.info( "No such element with atomic number " + str(AtomNum))
return 0
def GetAtomNum(AtomSym):
'''
Extracts the atomic number
'''
if AtomSym in Lookup:
return Lookup.index(AtomSym)+1
else:
logging.info( "No such element with atomic symbol " + AtomSym)
return 0
#calculates the RMS between the two molecules
def RMSMol(mol1, mol2, w):
e = [0.0, 0.0, 0.0]
for i in range(0, len(mol1)):
e[0] += w[i] * (mol1[i][0] - mol2[i][0])**2
e[1] += w[i] * (mol1[i][1] - mol2[i][1])**2
e[2] += w[i] * (mol1[i][2] - mol2[i][2])**2
return math.sqrt(sum(e)/sum(w))
def ExtractForceConsts(GOutpFile):
'''
Extracts the real force constants and the real frequencies from the frequency calculation
'''
gausfile = open(GOutpFile, 'r')
GOutpFile = gausfile.readlines()
gausfile.close()
index = 0
ForceConsts = []
ForceConstsIndexes = []
Frequencies = []
FrequencyIndexes = []
for index in range(len(GOutpFile)):
if "Force constants ---" in GOutpFile[index]:
ForceConstsIndexes.append(index)
FrequencyIndexes.append(index-2)
for index, line in enumerate(GOutpFile):
if index in FrequencyIndexes:
data = line.split()
FreqOnlyData = data[2:]
for freq in FreqOnlyData:
Frequencies.append(float(freq))
if index in ForceConstsIndexes:
data = line.split()
FConlydata = data[3:]
for fc in FConlydata:
ForceConsts.append(float(fc))
return ForceConsts[1:], Frequencies[1:] # do not return the first force constant which corresponds to the imaginary normal mode
def QuantisedE(ClassicalE, Frequency):
'''
Returns quantised vibrational energy
'''
EnergyList = []
PlankConst = 6.62607e-34
AvogadroConst = 6.02214e23
n_quantum = 0.0
while n_quantum < 500:
EnergyList += [PlankConst*(Frequency*100*299792458*AvogadroConst)*(0.5+n_quantum)]
n_quantum += 1
QuantumE = 0.0
if ClassicalE > EnergyList[0]:
listindex = bisect.bisect(EnergyList, ClassicalE)
QuantumE = EnergyList[listindex-1]
elif ClassicalE <= EnergyList[0]:
QuantumE = EnergyList[0]
return QuantumE
def GetBondLength(geometry, atomidx1, atomidx2):
atomcoord1 = np.array(geometry[atomidx1])
atomcoord2 = np.array(geometry[atomidx2])
bondvector = atomcoord2 - atomcoord1
bondlength = length(bondvector)
#print ('atomidx1 ', atomidx1)
#print ('atomidx2 ', atomidx2)
#print ('atomcoord1 ', atomcoord1)
#print ('atomcoord2 ', atomcoord2)
#print ('bondlength ', bondlength)
return bondlength
def ExtractBonds(rdkitmol, atomlist):
'''
Extract all bonds in the rdkit molecule and the atom indexes of atoms in the bond
'''
bondlist = []
for bond in rdkitmol.GetBonds():
bondlist.append([])
bondlist[-1] = [bond.GetBeginAtomIdx()+1, bond.GetEndAtomIdx()+1]
return bondlist
def IdentifyChangedBonds(bondlist1, bondlist2):
'''
Find the uncommon bonds in the two product bond lists
'''
changed_bonds1 = []
changed_bonds2 = []
for bond_1 in bondlist1:
bond_1.sort()
for bond_2 in bondlist2:
bond_2.sort()
for bond_1 in bondlist1:
if bond_1 in bondlist2:
pass
else:
changed_bonds1 += [bond_1]
for bond_2 in bondlist2:
if bond_2 in bondlist1:
pass
else:
changed_bonds2 += [bond_2]
return changed_bonds1, changed_bonds2
# changed_bonds1 = bonds in bondlist1 which does not exist in bondlist2
# changed_bonds2 = bonds in bondlist2 which does not exist in bondlist1
def TestBondProjSign(vector1, vector2, bondvector):
vector_sign = 1
component_to_return = 0
projdiff = list(np.array(vector2) - np.array(vector1))
logging.info('---')
logging.info('length(vector1) '+str(length(vector1)))
logging.info('length(vector2) '+str(length(vector2)))
logging.info('vector1 '+str(vector1))
logging.info('vector2 '+str(vector2))
logging.info('dotproduct(vector1,vector2): '+str(dotproduct(vector1, vector2)))
logging.info('angle(vector2,vector1) '+str(round(angle(vector2, vector1), 2)))
logging.info('angle(vector2,bondvector) '+str(round(angle(vector2, bondvector), 2)))
logging.info('angle(projdiff,bondvector) '+str(round(angle(projdiff, bondvector), 2)))
if round(angle(vector2, vector1), 2) == round(math.pi, 2) :
if round(angle(vector2, bondvector), 2) == round(math.pi, 2):
vector_sign*-1
elif round(angle(vector2, bondvector), 2) == 0:
pass
else:
logging.error('')
logging.error('****')
logging.error('ERROR: The angle between the projected vector2 and the bond vector are not 0 or 180 degrees')
logging.error('The program will terminate')
logging.error('****')
logging.error('')
sys.exit()
component_to_return = length(vector1) + length(vector2)
component_to_return = component_to_return * vector_sign
elif round(angle(vector2, vector1), 2) == 0.00 :
projdiff = list(np.array(vector2) - np.array(vector1))
if length(vector2) > length(vector1):
if round(angle(projdiff, bondvector), 2) == 0.00:
pass
elif round(angle(projdiff, bondvector), 2) == round(math.pi, 2):
vector_sign*-1
else:
logging.error('')
logging.error('****')
logging.error('ERROR: The angle between the difference in the projected vectors and the bond vector are not 0 or 180 degrees')
logging.error('The program will terminate')
logging.error('****')
logging.error('')
sys.exit()
elif length(vector1) > length(vector2):
if round(angle(projdiff, bondvector), 2) == round(math.pi, 2):