Source code for moreaubroto
# -*- 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.
"""
##############################################################################
The calculation of Moreau-Broto autocorrelation descriptors. You can get 32
molecular decriptors. You can freely use and distribute it. If you hava
any problem, you could contact with us timely!
Authors: Zhijiang Yao and Dongsheng Cao.
Date: 2016.06.04
Email: gadsby@163.com and oriental-cds@163.com
##############################################################################
"""
from rdkit import Chem
from AtomProperty import GetRelativeAtomicProperty
import numpy
Version=1.0
################################################################
def _CalculateMoreauBrotoAutocorrelation(mol,lag=1,propertylabel='m'):
"""
#################################################################
**Internal used only**
Calculation of Moreau-Broto autocorrelation descriptors based on
different property weights.
Usage:
res=_CalculateMoreauBrotoAutocorrelation(mol, lag=1,propertylabel='m')
Input: mol is a molecule object.
lag is the topological distance between atom i and atom j.
propertylabel is the weighted property.
Output: res is a numeric value.
#################################################################
"""
Natom=mol.GetNumAtoms()
GetDistanceMatrix=Chem.GetDistanceMatrix(mol)
res=0.0
for i in range(Natom):
for j in range(Natom):
if GetDistanceMatrix[i,j]==lag:
atom1=mol.GetAtomWithIdx(i)
atom2=mol.GetAtomWithIdx(j)
temp1=GetRelativeAtomicProperty(element=atom1.GetSymbol(),propertyname=propertylabel)
temp2=GetRelativeAtomicProperty(element=atom2.GetSymbol(),propertyname=propertylabel)
res=res+temp1*temp2
else:
res=res+0.0
return round(numpy.log(res/2+1),3)
[docs]def CalculateMoreauBrotoAutoMass(mol):
"""
#################################################################
Calculation of Moreau-Broto autocorrelation descriptors based on
carbon-scaled atomic mass.
Usage:
res=CalculateMoreauBrotoAutoMass(mol)
Input: mol is a molecule object.
Output: res is a dict form containing eight moreau broto autocorrealtion
descriptors.
#################################################################
"""
res={}
for i in range(8):
res['ATSm'+str(i+1)]=_CalculateMoreauBrotoAutocorrelation(mol,lag=i+1,propertylabel='m')
return res
[docs]def CalculateMoreauBrotoAutoVolume(mol):
"""
#################################################################
Calculation of Moreau-Broto autocorrelation descriptors based on
carbon-scaled atomic van der Waals volume.
Usage:
res=CalculateMoreauBrotoAutoVolume(mol)
Input: mol is a molcule object.
Output: res is a dict form containing eight moreau broto autocorrealtion
descriptors.
#################################################################
"""
res={}
for i in range(8):
res['ATSv'+str(i+1)]=_CalculateMoreauBrotoAutocorrelation(mol,lag=i+1,propertylabel='V')
return res
[docs]def CalculateMoreauBrotoAutoElectronegativity(mol):
"""
#################################################################
Calculation of Moreau-Broto autocorrelation descriptors based on
carbon-scaled atomic Sanderson electronegativity.
Usage:
res=CalculateMoreauBrotoAutoElectronegativity(mol)
Input: mol is a molcule object.
Output: res is a dict form containing eight moreau broto autocorrealtion
descriptors.
#################################################################
"""
res={}
for i in range(8):
res['ATSe'+str(i+1)]=_CalculateMoreauBrotoAutocorrelation(mol,lag=i+1,propertylabel='En')
return res
[docs]def CalculateMoreauBrotoAutoPolarizability(mol):
"""
#################################################################
Calculation of Moreau-Broto autocorrelation descriptors based on
carbon-scaled atomic polarizability.
res=CalculateMoreauBrotoAutoPolarizability(mol)
Input: mol is a molcule object.
Output: res is a dict form containing eight moreau broto autocorrealtion
descriptors.
#################################################################
"""
res={}
for i in range(8):
res['ATSp'+str(i+1)]=_CalculateMoreauBrotoAutocorrelation(mol,lag=i+1,propertylabel='alapha')
return res
[docs]def GetMoreauBrotoAuto(mol):
"""
#################################################################
Calcualate all Moreau-Broto autocorrelation descriptors.
(carbon-scaled atomic mass, carbon-scaled atomic van der Waals volume,
carbon-scaled atomic Sanderson electronegativity,
carbon-scaled atomic polarizability)
Usage:
res=GetMoreauBrotoAuto(mol)
Input: mol is a molecule object.
Output: res is a dict form containing all moreau broto autocorrelation
descriptors.
#################################################################
"""
res={}
res.update(CalculateMoreauBrotoAutoMass(mol))
res.update(CalculateMoreauBrotoAutoVolume(mol))
res.update(CalculateMoreauBrotoAutoElectronegativity(mol))
res.update(CalculateMoreauBrotoAutoPolarizability(mol))
return res
###########################################################################
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',CalculateEstateFingerprint(m)
## print '\t',CalculateEstateValue(m)
## print '\t',CalculateMaxAtomTypeEState(m)
## print '\t', CalculateMinAtomTypeEState(m)
print len(GetMoreauBrotoAuto(m))
