RDKit sample program

new_groups.py

import sys
import re
import numpy as np
import csv 
from rdkit import Chem
names = open('fns')
def raa(fname):
	m=Chem.MolFromMolFile('../'+fname)
	natoms=len(m.GetAtoms())
	var=[]
	aroma=[]
	report=""
	for i in range(0,natoms):
		var.append(m.GetAtomWithIdx(i).IsInRing())
		aroma.append(m.GetAtomWithIdx(i).GetIsAromatic())
	if any(e is True for e in var)==True:
		report=" Ring "
		if any(e is True for e in aroma)==True:
			report+="& Aromatic "
	else:
		report+=" noncyclic "
	return report
grpnames=[]
fnames=[]
for name in names:
	word=name.split()
	m=Chem.MolFromMolFile('../'+word[0])
	grpnames.append(Chem.MolToSmiles(m))
	fnames.append(word[0])
grpnames=np.array(grpnames)
fnames=np.array(fnames)
writer=csv.writer(open("Groups.csv","w"))
writer.writerows(zip(fnames,grpnames))
#######################################################
halpatterns=['Cl','Br','F','I']
#halpatterns=['I']
nhalide=0
for i in range(0,len(grpnames)):
	dec=False
	for pattern in halpatterns:
		if re.search(pattern,grpnames[i]):
			dec = dec | True
	if dec == True:
		nhalide+=1		
#		print '%s  %15s  '%(fnames[i],grpnames[i])
print 'Total No of Halides: %5d'%(nhalide)
########################################################
ionpatterns=['\[N\+\]\(=O\)\[O\-\]','O\=\[N\+\]\(\[O\-\]\)']
nion=0
for i in range(0,len(grpnames)):
	dec=False
	for pattern in ionpatterns:
                if re.search(pattern,grpnames[i]):
			dec = dec | True
	if dec == True:
                nion+=1
#                print '%s  %15s  '%(fnames[i],grpnames[i])
print 'Total No of Nitro compounds: %5d'%(nion)
########################################################
roh=['CO$','^OC','C\(O\)']
noh=0
for i in range(0,len(grpnames)):
	dec=False
	for pattern in roh:
	        if re.search(pattern,grpnames[i]):
			dec = dec | True
	if dec == True:
		noh+=1
#	        print '%s  %15s  '%(fnames[i],grpnames[i])
print 'Total No of Alcohols: %5d'%(noh)
########################################################
rcoh=['[^O^=]C=O','O=C[^O^=]']
ncoh=0
for i in range(0,len(grpnames)):
	dec=False
	for pattern in rcoh: 
	        if re.search(pattern,grpnames[i]):
			dec = dec | True
	if dec == True:
	        ncoh+=1
#		print '%s  %15s  '%(fnames[i],grpnames[i])
print 'Total No of Aldehydes: %5d'%(ncoh)
########################################################
#rnh=['CN$','^NC[^(]','CN','(C)N']
#rnh=['CN$','NC.[^=^C]']
#nnh=0
#for pattern in rnh:
#        for i in range(0,len(grpnames)):
#                if re.search(pattern,grpnames[i]):
#                        nnh+=1
#                        print '%s  %15s  '%(fnames[i],grpnames[i])
#print 'Total No of Amines: %5d'%(nnh)
########################################################
rcn=['C[#]N','N[#]C']
ncn=0
for i in range(0,len(grpnames)):
	dec=False
	for pattern in rcn:
        	if re.search(pattern,grpnames[i]):
			dec = dec | True
	if dec == True:
	        ncn+=1
#                print '%s  %15s  '%(fnames[i],grpnames[i])
print 'Total No of Nitriles: %5d'%(ncn)