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

os.chdir('/public/gkxiao/work/oechem_interaction/5mo4')

导入蛋白结构

ifile = '5mo4_prot.pdb'
ifs = oechem.oemolistream()
ifs.open(ifile)
prot = oechem.OEGraphMol()
oechem.OEReadMolecule(ifs, prot)

True

导入配体结构

ifile = '5mo4_AY7.mol2'
ifs = oechem.oemolistream()
ifs.open(ifile)
AY7 = oechem.OEGraphMol()
oechem.OEReadMolecule(ifs, AY7)

True

开始相互作用分析

xbond_ops = oechem.OEPerceiveInteractionOptions()
xbond_ops.SetMaxHalogenBondDistance(3.77)

开水绘图

asite = oechem.OEInteractionHintContainer(prot, AY7)
oechem.OEPerceiveInteractionHints(asite,xbond_ops)

True

oegrapheme.OEPrepareActiveSiteDepiction(asite)

True

设置标题与图标规格

asite.SetTitle('PDB 5MO4-AY7(ABL001)')
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))

相互作用可视化

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

lopts = oegrapheme.OE2DActiveSiteLegendDisplayOptions(10, 1)
oegrapheme.OEDrawActiveSiteLegend(lframe, adisp, lopts)

保存图片：1张为png，一张为svg

oedepict.OEWriteImage('5mo4-AY7.svg', image)
oedepict.OEWriteImage('5mo4-AY7.png', image)

True