I have added this to bug #3431239 to which it seem be related.
With its stereochemistry mol1 fails when making an FP4 fingerprint (lots
of SMARTS matching). But without the stereochemistry it is ok.
Chris
On 31/10/2011 16:37, Mingyue Zheng wrote:
> Hi all,
> I found my python script unexpectedly quit when calculating the
> similarity between the following two molecules":
> ~~~~~~ test_fp4.py ~~~~~~~~~~~
> import pybel
>
> mol1=pybel.readstring('smi','CCCCCCCN1C[C@H](O)[C@H]([C@@H]([C@H]1CO)O)O
> mol1')
> mol2=pybel.readstring('smi','COc1ccc(cc1)Nc1c(C#N)cncc1c1ccc(c(c1)OC)OC
> mol2')
> print mol1.calcfp('FP2')|mol2.calcfp('FP2')
> print 'ok'
> print mol1.calcfp('FP4')|mol2.calcfp('FP4')
> print 'ok'
>
>>> test_fp4.py
> 0.0699300699301
> ok
> ~~~~~~~~ the end of the script and it's output~~~~~~~
> I'm using openbabel 2.3.1 and pybel1.7 for python 2.7, on a win7 system.
>
> Best,
> Mingyue
>
>
>
>
>
> 2011-11-01
> ------------------------------------------------
> Mingyue Zheng, Ph.D.
> Drug Discovery and Design Center (DDDC)
> Box 1201, Shanghai Institute of Materia Medica.
> No. 555 Rd. Zuchongzhi, Shanghai, China
> Tel: 86-021-50806600-1308
> Email: myzh...@mail.shcnc.ac.cn
>
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