I'll try and sort out SMARTS stereo this side of Christmas. There are
several pieces to be done.
- Noel
On 31 October 2011 19:34, Chris Morley <c.mor...@gaseq.co.uk> wrote:
> 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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