Evaluate TK.

Now I’m evaluating OETK.
I think all toolkits are very useful for drug design.
OEMedChem TK is new tool for Chemoinformatics.
The tool kit implemented MMP Analysis engine.
I used the TK and draw the transform via Python notebook.
OETK can integrate IPython notebook, so I can visualise molecule on the fly.
I couldn’t understand details of option.
So, I could only draw very simple smiles….
Upload code snippet to github
https://github.com/iwatobipen/mishimasyk/blob/master/OE_MMP.ipynb
Hmm… It worked.
I’ll study more and more about the TK ASAP…(there are no more time for evaluation.)

# coding: utf-8

from __future__ import print_function

from openeye import oechem
from openeye import oemedchem

mol = oechem.OEGraphMol()

ifs = oechem.oemolistream()
ofs = oechem.oemolostream()
ifs.SetFormat(oechem.OEFormat_SDF)


ifs.open('cdk2.sdf')
ifs.rewind()

mols =[ ]

for m in ifs.GetOEGraphMols():
    newmol = oechem.OEGraphMol(m)
    mols.append(newmol)
print(len(mols))


opts = oemedchem.OEMatchedPairAnalyzerOptions()
mmp = oemedchem.OEMatchedPairAnalyzer( opts )

record = 0
for m in mols:
    record += 1
    status = mmp.AddMol(m, record)


print(mmp.NumMatchedPairs())

chemctxt = oemedchem.OEMatchedPairContext_AllBonds

extractMode = (oemedchem.OEMatchedPairTransformExtractMode_NoSMARTS+
              oemedchem.OEMatchedPairTransformExtractMode_AddAttachmentPts+
              oemedchem.OEMatchedPairTransformExtractMode_AddMCSCorrespondence)

transforms = []
for mmptransform in oemedchem.OEMatchedPairGetTransforms(mmp,
                                                        chemctxt,
                                                        extractMode):
    transforms.append(mmptransform)

tf1=transforms[0]

from openeye import oedepict
from IPython.display import Image
print(tf1.GetTransform())
w,h=400,300
image = oedepict.OEImage(w,h)
qmol = oechem.OEGraphMol()
oechem.OEParseSmiles(qmol,tf1.GetTransform())
oedepict.OEPrepareDepiction(qmol)
oedepict.OERenderMolecule(image,qmol)
Image(data=oedepict.OEWriteImageToString('png',img))

広告

• programming