# -*- 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 mainly implements the calculation of MOE-type descriptors, which
include LabuteASA, TPSA, slogPVSA, MRVSA, PEOEVSA, EstateVSA and VSAEstate,
respectively (60).
If you have any question about these indices please contact me via email.
Authors: Zhijiang Yao and Dongsheng Cao.
Date: 2016.06.04
Email: gadsby@163.com and oriental-cds@163.com
##############################################################################
"""
from rdkit import Chem
from rdkit.Chem import MolSurf as MOE
from rdkit.Chem.EState import EState_VSA as EVSA
Version=1.0
################################################################
[docs]def CalculateLabuteASA(mol):
"""
#################################################################
Calculation of Labute's Approximate Surface Area (ASA from MOE)
Usage:
result=CalculateLabuteASA(mol)
Input: mol is a molecule object
Output: result is a dict form
#################################################################
"""
res={}
temp=MOE.pyLabuteASA(mol,includeHs=1)
res['LabuteASA']=round(temp,3)
return res
[docs]def CalculateTPSA(mol):
"""
#################################################################
Calculation of topological polar surface area based on fragments.
Implementation based on the Daylight contrib program tpsa.
Usage:
result=CalculateTPSA(mol)
Input: mol is a molecule object
Output: result is a dict form
#################################################################
"""
res={}
temp=MOE.TPSA(mol)
res['MTPSA']=round(temp,3)
return res
[docs]def CalculateSLOGPVSA(mol,bins=None):
"""
#################################################################
MOE-type descriptors using LogP contributions and surface
area contributions.
logpBins=[-0.4,-0.2,0,0.1,0.15,0.2,0.25,0.3,0.4,0.5,0.6]
You can specify your own bins to compute some descriptors.
Usage:
result=CalculateSLOGPVSA(mol)
Input: mol is a molecule object
Output: result is a dict form
#################################################################
"""
temp=MOE.SlogP_VSA_(mol,bins,force=1)
res={}
for i,j in enumerate(temp):
res['slogPVSA'+str(i)]=round(j,3)
return res
[docs]def CalculateSMRVSA(mol,bins=None):
"""
#################################################################
MOE-type descriptors using MR contributions and surface
area contributions.
mrBins=[1.29, 1.82, 2.24, 2.45, 2.75, 3.05, 3.63,3.8,4.0]
You can specify your own bins to compute some descriptors.
Usage:
result=CalculateSMRVSA(mol)
Input: mol is a molecule object
Output: result is a dict form
#################################################################
"""
temp=MOE.SMR_VSA_(mol,bins,force=1)
res={}
for i,j in enumerate(temp):
res['MRVSA'+str(i)]=round(j,3)
return res
[docs]def CalculatePEOEVSA(mol,bins=None):
"""
#################################################################
MOE-type descriptors using partial charges and surface
area contributions.
chgBins=[-.3,-.25,-.20,-.15,-.10,-.05,0,.05,.10,.15,.20,.25,.30]
You can specify your own bins to compute some descriptors
Usage:
result=CalculatePEOEVSA(mol)
Input: mol is a molecule object
Output: result is a dict form
#################################################################
"""
temp=MOE.PEOE_VSA_(mol,bins,force=1)
res={}
for i,j in enumerate(temp):
res['PEOEVSA'+str(i)]=round(j,3)
return res
[docs]def CalculateEstateVSA(mol,bins=None):
"""
#################################################################
MOE-type descriptors using Estate indices and surface area
contributions.
estateBins=[-0.390,0.290,0.717,1.165,1.540,1.807,2.05,4.69,9.17,15.0]
You can specify your own bins to compute some descriptors
Usage:
result=CalculateEstateVSA(mol)
Input: mol is a molecule object
Output: result is a dict form
#################################################################
"""
temp=EVSA.EState_VSA_(mol,bins,force=1)
res={}
for i,j in enumerate(temp):
res['EstateVSA'+str(i)]=round(j,3)
return res
[docs]def CalculateVSAEstate(mol,bins=None):
"""
#################################################################
MOE-type descriptors using Estate indices and surface
area contributions.
vsaBins=[4.78,5.00,5.410,5.740,6.00,6.07,6.45,7.00,11.0]
You can specify your own bins to compute some descriptors
Usage:
result=CalculateVSAEstate(mol)
Input: mol is a molecule object
Output: result is a dict form
#################################################################
"""
temp=EVSA.VSA_EState_(mol,bins,force=1)
res={}
for i,j in enumerate(temp):
res['VSAEstate'+str(i)]=round(j,3)
return res
[docs]def GetMOE(mol):
"""
#################################################################
The calculation of MOE-type descriptors (ALL).
Usage:
result=GetMOE(mol)
Input: mol is a molecule object
Output: result is a dict form
#################################################################
"""
result={}
result.update(CalculateLabuteASA(mol))
result.update(CalculateTPSA(mol))
result.update(CalculateSLOGPVSA(mol,bins=None))
result.update(CalculateSMRVSA(mol,bins=None))
result.update(CalculatePEOEVSA(mol,bins=None))
result.update(CalculateEstateVSA(mol,bins=None))
result.update(CalculateVSAEstate(mol,bins=None))
return result
#########################################################################
if __name__=="__main__":
smi5=['COCCCC','CCC(C)CC','CC(C)CCC','CC(C)C(C)C','CCOCCN','c1ccccc1N']
smis = ['CCCC','CCCCC','CCCCCC','CC(N)C(=O)O','CC(N)C(=O)[O-].[Na+]']
for index, smi in enumerate(smis):
m = Chem.MolFromSmiles(smi)
print index+1
print smi
print '\t',GetMOE(m)
print '\t', len(GetMOE(m))
