Source code for Getmol
# -*- coding: utf-8 -*-
# Copyright (c) 2016-2017, Zhijiang Yao, Jie Dong and Dongsheng Cao
# All rights reserved.
# This file is part of the PyBioMed.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the PyBioMed source tree.
"""
This module is to get different formats of molecules from file and web. If you
have any question please contact me via email.
Authors: Zhijiang Yao and Dongsheng Cao.
Date: 2016.06.04
Email: gadsby@163.com
"""
import urllib
import re
import string
import os
from rdkit import Chem
Version=1.0
[docs]def ReadMolFromSDF(filename=""):
"""
Read a set of molecules by SDF file format.
Note: the output of this function is a set of molecular objects.
You need to use for statement to call each object.
Usage:
res=ReadMolFromSDF(filename)
Input: filename is a file name with path.
Output: res is a set of molecular object.
"""
molset=Chem.SDMolSupplier(filename)
return molset
[docs]def ReadMolFromMOL(filename=""):
"""
Read a molecule by mol file format.
Usage:
res=ReadMolFromMOL(filename)
Input: filename is a file name with path.
Output: res is a molecular object.
"""
mol=Chem.MolFromMolFile(filename)
return mol
[docs]def ReadMolFromSmile(smi=""):
"""
#################################################################
Read a molecule by SMILES string.
Usage:
res=ReadMolFromSmile(smi)
Input: smi is a SMILES string.
Output: res is a molecule object.
#################################################################
"""
mol = Chem.MolFromSmiles(string.strip(smi))
return mol
[docs]def ReadMolFromInchi(inchi=""):
"""
#################################################################
Read a molecule by Inchi string.
Usage:
res=ReadMolFromInchi(inchi)
Input: inchi is a InChi string.
Output: res is a molecule object.
#################################################################
"""
import pybel
temp=pybel.readstring("inchi",inchi)
smi=temp.write("smi")
mol = Chem.MolFromSmiles(string.strip(smi))
return mol
[docs]def ReadMolFromMol(filename=""):
"""
#################################################################
Read a molecule with mol file format.
Usage:
res=ReadMolFromMol(filename)
Input: filename is a file name.
Output: res is a molecule object.
#################################################################
"""
mol=Chem.MolFromMolFile(filename)
return mol
#############################################################################
[docs]def GetMolFromCAS(casid=""):
"""
Downloading the molecules from http://www.chemnet.com/cas/ by CAS ID (casid).
if you want to use this function, you must be install pybel.
"""
import pybel
casid=string.strip(casid)
localfile=urllib.urlopen('http://www.chemnet.com/cas/supplier.cgi?terms='+casid+'&l=&exact=dict')
temp=localfile.readlines()
for i in temp:
if re.findall('InChI=',i)==['InChI=']:
k=i.split(' <td align="left">')
kk=k[1].split('</td>\r\n')
if kk[0][0:5]=="InChI":
res=kk[0]
else:
res="None"
localfile.close()
mol=pybel.readstring('inchi',string.strip(res))
smile=mol.write('smi')
return string.strip(smile)
[docs]def GetMolFromEBI():
"""
"""
pass
[docs]def GetMolFromNCBI(cid=""):
"""
Downloading the molecules from http://pubchem.ncbi.nlm.nih.gov/ by cid (cid).
"""
cid=string.strip(cid)
localfile=urllib.urlopen('http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid='+cid+'&disopt=SaveSDF')
temp=localfile.readlines()
f=file("temp.sdf",'w')
f.writelines(temp)
f.close()
localfile.close()
m=Chem.MolFromMolFile("temp.sdf")
os.remove("temp.sdf")
temp=Chem.MolToSmiles(m,isomericSmiles=True)
return temp
[docs]def GetMolFromDrugbank(dbid=""):
"""
Downloading the molecules from http://www.drugbank.ca/ by dbid (dbid).
"""
dbid=string.strip(dbid)
localfile=urllib.urlopen('http://www.drugbank.ca/drugs/'+dbid+'.sdf')
temp=localfile.readlines()
f=file("temp.sdf",'w')
f.writelines(temp)
f.close()
localfile.close()
m=Chem.MolFromMolFile("temp.sdf")
os.remove("temp.sdf")
temp=Chem.MolToSmiles(m,isomericSmiles=True)
return temp
[docs]def GetMolFromKegg(kid=""):
"""
Downloading the molecules from http://www.genome.jp/ by kegg id (kid).
"""
ID=str(kid)
localfile=urllib.urlopen('http://www.genome.jp/dbget-bin/www_bget?-f+m+drug+'+ID)
temp=localfile.readlines()
f=file("temp.mol",'w')
f.writelines(temp)
f.close()
localfile.close()
m=Chem.MolFromMolFile("temp.mol")
os.remove("temp.mol")
temp=Chem.MolToSmiles(m,isomericSmiles=True)
return temp
#############################################################################
if __name__=="__main__":
print '-'*10+'START'+'-'*10
print 'Only PyBioMed is successfully installed the code below can be run！'
from PyBioMed.PyGetMol.GetProtein import timelimited
@timelimited(10)
def run_GetMolFromCAS():
temp=GetMolFromCAS(casid="50-12-4")
print temp
@timelimited(10)
def run_GetMolFromNCBI():
temp=GetMolFromNCBI(cid="2244")
print temp
@timelimited(10)
def run_GetMolFromDrugbank():
temp=GetMolFromDrugbank(dbid="DB00133")
print temp
@timelimited(10)
def run_GetMolFromKegg():
temp=GetMolFromKegg(kid="D02176")
print temp
run_GetMolFromCAS()
print '-'*25
run_GetMolFromNCBI()
print '-'*25
run_GetMolFromDrugbank()
print '-'*25
run_GetMolFromKegg()
print '-'*10+'END'+'-'*10
