肖高铿 2021-12-28 http://blog.molcalx.com.cn

导入openeye软件包

import sys,os
sys.path.append('/public/gkxiao/software/OpenEye-toolkits-python3-linux-x64-2021.1.1')
from openeye import oechem
from openeye import oedepict
from openeye import oegrapheme

切换工作目录

os.chdir('/public/gkxiao/work/oechem_interaction/cdk6')

导入蛋白结构

ifile = '5l2s_prot.pdb'
ifs = oechem.oemolistream()
ifs.open(ifile)
prot = oechem.OEGraphMol()
oechem.OEReadMolecule(ifs, prot)

True

导入对接好的配体，本处从复合物结构里提取。

ifile = '5l2s_ligand.mol2'
ifs = oechem.oemolistream()
ifs.open(ifile)
Abemaciclib = oechem.OEGraphMol()
oechem.OEReadMolecule(ifs, Abemaciclib)

True

用OEChem进行相互作用分析

asite = oechem.OEInteractionHintContainer(prot, Abemaciclib)
oechem.OEPerceiveInteractionHints(asite)

True

用OEDipict进行绘图

oegrapheme.OEPrepareActiveSiteDepiction(asite)

True

设置图片的尺寸

asite.SetTitle('Abemaciclib-CDK6 Interaction (PDB 5L2S)')
width = 800 
height = 600
image = oedepict.OEImage(width, height)

cframe = oedepict.OEImageFrame(image, width * 0.80, height, oedepict.OE2DPoint(0.0, 0.0))
lframe = oedepict.OEImageFrame(image, width * 0.20, height,
                                oedepict.OE2DPoint(width * 0.80, 0.0))

opts = oegrapheme.OE2DActiveSiteDisplayOptions(cframe.GetWidth(), cframe.GetHeight())
adisp = oegrapheme.OE2DActiveSiteDisplay(asite, opts)
oegrapheme.OERenderActiveSite(cframe, adisp)

lopts = oegrapheme.OE2DActiveSiteLegendDisplayOptions(12, 1)
oegrapheme.OEDrawActiveSiteLegend(lframe, adisp, lopts)

保存为图片：一张SVG格式，一张PNG格式

oedepict.OEWriteImage('5l2s-abemaciclib.svg', image)
oedepict.OEWriteImage('5l2s-abemaciclib.png', image)

True