# -*- 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 script is used for testing.
Authors: Zhijiang Yao and Dongsheng Cao.
Date: 2016.06.14
Email: gadsby@163.com
"""
# Core Library modules
import os
[docs]def test_pymolecule():
from rdkit import Chem
from openbabel import pybel
from PyBioMed.PyMolecule.AtomProperty import (
AtomProperty,
GetAbsoluteAtomicProperty,
GetRelativeAtomicProperty,
)
from PyBioMed.PyMolecule.estate import GetEstate
from PyBioMed.PyMolecule.constitution import GetConstitutional
from PyBioMed.PyMolecule.fingerprint import CalculateECFP4Fingerprint
from PyBioMed.PyMolecule.connectivity import GetConnectivity
from PyBioMed.PyMolecule.charge import GetCharge
from PyBioMed.PyMolecule.bcut import GetBurden
from PyBioMed.PyMolecule.basak import Getbasak
from PyBioMed.PyMolecule.geary import GetGearyAuto
from PyBioMed.PyMolecule.kappa import GetKappa
from PyBioMed.PyMolecule.moe import GetMOE
from PyBioMed.PyMolecule.molproperty import GetMolecularProperty
from PyBioMed.PyMolecule.moran import GetMoranAuto
from PyBioMed.PyMolecule.moreaubroto import GetMoreauBrotoAuto
from PyBioMed.PyMolecule.topology import GetTopology
from PyBioMed.PyMolecule.ghosecrippen import GhoseCrippenFingerprint
from PyBioMed.PyMolecule.cats2d import CATS2D
print("...............................................................")
print("testing the AtomProperty module")
for i, j in AtomProperty.items():
print(j)
print(GetAbsoluteAtomicProperty(element="S", propertyname="En"))
print(GetRelativeAtomicProperty(element="S", propertyname="En"))
# ==============================================================================
# Getbasak
# ==============================================================================
print("...............................................................")
print("testing the Getbasak module")
smi5 = ["CCCCCC", "CCC(C)CC", "CC(C)CCC", "CC(C)C(C)C", "CCCCCN", "c1ccccc1N"]
for index, smi in enumerate(smi5):
m = Chem.MolFromSmiles(smi)
print(index + 1)
print(smi)
print("\t", Getbasak(m))
print(len(Getbasak(m)))
# ==============================================================================
# GetBurden, bcut model
# ==============================================================================
print("...............................................................")
print("testing the bcut module")
smi5 = ["CCOCCC", "CCC(C)CC", "CC(C)CCC", "CC(C)C(C)C", "CCCCCN", "c1ccccc1N", "C"]
for index, smi in enumerate(smi5):
m = Chem.MolFromSmiles(smi)
print(index + 1)
print(smi, "\n")
print(GetBurden(m))
print(len(GetBurden(m)))
# ==============================================================================
# GetCharge
# ==============================================================================
print("...............................................................")
print("testing the GetCharge module")
smis = ["CCCC", "CCCCC", "CCCCCC", "CC(N)C(=O)O", "CC(N)C(=O)[O-].[Na+]"]
smi5 = ["CCCCCC", "CCC(C)CC", "CC(C)CCC", "CC(C)C(C)C", "CCCCCN", "c1ccccc1N"]
for index, smi in enumerate(smis):
m = Chem.MolFromSmiles(smi)
print(index + 1)
print(smi)
print("\t", GetCharge(m))
print(len(GetCharge(m)))
# ==============================================================================
# GetConnectivity
# ==============================================================================
print("...............................................................")
print("testing the GetConnectivity module")
smis = ["CCCC", "CCCCC", "CCCCCC", "CC(N)C(=O)O", "CC(N)C(=O)[O-].[Na+]"]
smi5 = ["CCCCCC", "CCC(C)CC", "CC(C)CCC", "CC(C)C(C)C", "CCCCCN", "c1ccccc1N"]
for index, smi in enumerate(smis):
m = Chem.MolFromSmiles(smi)
print(index + 1)
print(smi)
print("\t", GetConnectivity(m))
print("\t", len(GetConnectivity(m)))
# ==============================================================================
# GetConstitutional
# ==============================================================================
print("...............................................................")
print("testing the GetConstitutional module")
smis = ["CCCC", "CCCCC", "CCCCCC", "CC(N)C(=O)O", "CC(N)C(=O)[O-].[Na+]"]
smi5 = ["CCCCCC", "CCC(C)CC", "CC(C)CCC", "CC(C)C(C)C", "CCCCCN", "c1ccccc1N"]
for index, smi in enumerate(smis):
m = Chem.MolFromSmiles(smi)
print(index + 1)
print(smi)
print("\t", GetConstitutional(m))
print(len(GetConstitutional(m)))
# ==============================================================================
# GetEstate
# ==============================================================================
print("...............................................................")
print("testing the GetEstate module")
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(GetEstate(m))
# ==============================================================================
#
# ==============================================================================
print("...............................................................")
print("fingerprint......")
ms = [
Chem.MolFromSmiles("CCOC=N"),
Chem.MolFromSmiles("NC1=NC(=CC=N1)N1C=CC2=C1C=C(O)C=C2"),
]
m2 = [pybel.readstring("smi", "CCOC=N"), pybel.readstring("smi", "CCO")]
res1 = CalculateECFP4Fingerprint(ms[0])
print(res1)
res2 = CalculateECFP4Fingerprint(ms[1])
print(res2)
# print CalculateSimilarityRdkit(res1[2],res2[2])
# print CalculateSimilarityPybel(res1,res2)
# ==============================================================================
#
# ==============================================================================
print("...............................................................")
print("testing the GetGearyAuto module")
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(GetGearyAuto(m))
# ==============================================================================
#
# ==============================================================================
print("...............................................................")
print("testing the GetKappa module")
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", GetKappa(m))
print("\t", len(GetKappa(m)))
# ==============================================================================
#
# ==============================================================================
print("...............................................................")
print("testing the GetMOE module")
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)))
# ==============================================================================
#
# ==============================================================================
print("...............................................................")
print("testing the GetMolecularProperty module")
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", GetMolecularProperty(m))
# ==============================================================================
#
# ==============================================================================
print("...............................................................")
print("testing the GetMoranAuto module")
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(GetMoranAuto(m))
# ==============================================================================
#
# ==============================================================================
print("...............................................................")
print("testing the GetMoreauBrotoAuto module")
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)))
# ==============================================================================
#
# ==============================================================================
print("...............................................................")
print("testing the GetTopology module")
smis = ["CCCC", "CCCCC", "CCCCCC", "CC(N)C(=O)O", "CC(N)C(=O)[O-]"]
for index, smi in enumerate(smis):
m = Chem.MolFromSmiles(smi)
print(index + 1)
print(smi)
print("\t", GetTopology(m))
print("\t", len(GetTopology(m)))
# ==============================================================================
#
# ==============================================================================
print("...............................................................")
print("testing the CATS2D module")
smis = ["CCCC", "CCCCC", "CCCCCC", "CC(N)C(=O)O", "CC(N)C(=O)[O-]"]
for i in smis:
mol = Chem.MolFromSmiles(i)
cats = CATS2D(mol, PathLength=10, scale=3)
print("\t", cats)
print("\t", len(cats))
# ==============================================================================
#
# ==============================================================================
print("...............................................................")
print("testing the ghoseFP module")
smis = ["CCCC", "CCCCC", "CCCCCC", "CC(N)C(=O)O", "CC(N)C(=O)[O-]"]
for i in smis:
mol = Chem.MolFromSmiles(i)
ghoseFP = GhoseCrippenFingerprint(mol)
print("\t", ghoseFP)
print("\t", len(ghoseFP))
print("testing the ghose_count module")
for i in smis:
mol = Chem.MolFromSmiles(i)
ghose_count = GhoseCrippenFingerprint(mol, count=True)
print("\t", ghose_count)
print("\t", len(ghose_count))
# ==============================================================================
#
# ==============================================================================
if __name__ == "__main__":
test_pymolecule()
