OpenBabel API教程使用

OpenBabel API教程使用

自定义分子

import openbabel

# 创建实例
mol=openbabel.OBMol()
print('Should print 0 (atoms)')
print(mol.NumAtoms())

# 创建新原子
a=mol.NewAtom()
# C原子,见元素周期表
a.SetAtomicNum(6)
# 设置坐标
a.SetVector(0.0,1.0,2.0)

b = mol.NewAtom()
# 原子键索引为1
mol.AddBond(1, 2, 1)  
# 输出原子树木
print(mol.NumAtoms())
# 输出键树木
print(mol.NumBonds())

mol.Clear()

格式转换

xyz和sdf格式之间的转化

obabel tmp.xyz -ixyz -osdf -O tmp.sdf

from openbabel.pybel import (readfile,Outputfile) 
molecules = readfile(input_format, input_file)
output_file_writer = Outputfile(output_format,output_file)
for i,molecule in enumerate(molecules):
    output_file_writer.write(molecule)
output_file_writer.close()

Smiles转换

input_format="inchi"
output_format="smi"
from openbabel import openbabel
obConversion = openbabel.OBConversion()
obConversion.SetInAndOutFormats(input_format, output_format)
mol = openbabel.OBMol()
#加氢
mol.AddHydrogens()
obConversion.ReadString(mol, input_string)
output_string = obConversion.WriteString(mol).strip()

阅读文件模式

import openbabel

obConversion = openbabel.OBConversion()
obConversion.SetInAndOutFormats("pdb", "mol2")

mol = openbabel.OBMol()
obConversion.ReadFile(mol, "1ABC.pdb.gz")   # Open Babel will uncompress automatically

mol.AddHydrogens()

print(mol.NumAtoms())
print(mol.NumBonds())
print(mol.NumResidues())

obConversion.WriteFile(mol, '1abc.mol2')

添加3D构象

import sys
import pandas as pd
from openbabel import openbabel
from openbabel import pybel

gen3d = openbabel.OBOp.FindType("gen3D")

excel_file = 'test_data/blah.xlsx'
df = pd.read_excel(excel_file)
#print(df.columns)
smiles = df['SMILES ']
#print(smiles[0])
dummy_file_cml_fp2 = pybel.Outputfile('vmol', 'test_data/test_gen3d.vmol', overwrite=True)
mymol = pybel.readstring("smi", smiles[0])
#print(type(mymol.OBMol))
gen3d.Do(mymol.OBMol, "--best")
#mymol.localopt(forcefield='mmff94', steps=1000)
dummy_file_cml_fp2.write(mymol)

参考
官方文档 ： https://openbabel.org/docs/current/UseTheLibrary/Python.html
http://openbabel.org/dev-api/classOpenBabel_1_1OBMol.shtml