Paolo,
?0?2?0?2?0?2 That is what I thought. However, when I try it, the function
signature isn't recognized...
$ python -V
Python 3.6.5 :: Anaconda custom (64-bit)
$ cat test.py
import rdkit
from rdkit.Chem import MolFromSmiles
from rdkit.Chem.AllChem import ReactionFromSmarts
print(f"RDKit version = {rdkit.__version__}")
mol = MolFromSmiles('OCC(O)CCCO')
rxn = ReactionFromSmarts('[O:1]>>[S:1]')
products = rxn.RunReactants([mol])
print(f"1) no. products = {len(products)}")
products = rxn.RunReactants([mol], maxProducts=1)
print(f"2) no. products = {len(products)}")
$ python test.py
RDKit version = 2018.03.3
1) no. products = 3
Traceback (most recent call last):
?0?2 File "test.py", line 13, in <module>
?0?2?0?2?0?2 products = rxn.RunReactants([mol], maxProducts=1)
Boost.Python.ArgumentError: Python argument types in
?0?2?0?2?0?2 ChemicalReaction.RunReactants(ChemicalReaction, list)
did not match C++ signature:
?0?2?0?2?0?2 RunReactants(RDKit::ChemicalReaction*, boost::python::list)
?0?2?0?2?0?2 RunReactants(RDKit::ChemicalReaction*, boost::python::tuple)
?0?2?0?2?0?2 I presume I am missing something, but what?!
?0?2?0?2?0?2 ?0?2?0?2?0?2 Francis
On 15/11/2018 17:11, Paolo Tosco wrote:
Hi Shaozhen,
that parameter can be accessed from Python, it is called maxProducts,
and it defaults to 1000 as described in the Python API docs:
http://www.rdkit.org/docs/source/rdkit.Chem.rdChemReactions.html?highlight=runreactants#rdkit.Chem.rdChemReactions.ChemicalReaction.RunReactants
Cheers,
p.
On 11/15/18 16:52, Francis Atkinson wrote:
I don't know how you access that parameter from Pythonn, I'm afraid.
Maybe someone else here can help?
On 15/11/2018 12:47, ?????? wrote:
Dear Atkinson:
From rdkit document, I found there is a parameter named numProducts
in RunReactants function, this parameter can limit the products
number, and it defaults to 1000.
How can I change this parameter??If I change this number to a small
one , I may change the run time.
I hope to solve this problem very much.
Thanks a lot.
Kind regards
Shaozhen
------------------?0?2?????????0?2------------------
*??????:*?0?2"Francis Atkinson"<[email protected]>;
*????????:*?0?22018??11??15??(??????) ????7:02
*??????:*?0?2"??????"<[email protected]>;
*????:*?0?2Re: ?????? [Rdkit-discuss] Help: How to set timeout for the
function namedRunReactants
Shaozhen,
?0?2?0?2?0?2 OK, this doesn't work for me either on my Mac, but does work as
expected on Linux (RHEL7). I'm afraid I really don't know why!
?0?2?0?2?0?2 I also don't know if this is something is to do with the version
of MacOS; I tend to do development on a Mac, but run large jobs on
Linux, so I might simply not have noticed this failure on the Mac
before.
?0?2?0?2?0?2 ?0?2?0?2?0?2 Francis
On 15/11/2018 10:14, ?????? wrote:
Hi?0?2Atkinson:
Thanks so much, and I have taken your?0?2 advice.(I saved the code as
timeout.py ,and put it on '/Users/ding/Desktop' )
But?0?2 it cannot resolve my problems.
My operating system is Mac OS.
It works well in the function mytest (in the following code).
But It cannot work in the function reaction_predict_outside (in the
following code).
If I don??t stop this function, it always make my computer down.
Could you please help me to solve this trouble?
Kind regards.
Shaozhen
>>import sys
>>sys.path.insert(0,'/Users/ding/Desktop')
>>from timeout import timeout
>>import time
>>import rdkit.Chem as Chem
>>from rdkit.Chem import AllChem
>>from rdkit.Chem import MolFromSmiles
@timeout(1)
def mytest():
print 'start'
try:
for i in range(1,10):
time.sleep(10)
except:
print 'finish'
@timeout(1)
def reaction_predict_outside(rule,rxnrs):
print 'start'
try:
rxn = AllChem.ReactionFromSmarts(rule)
outcomes = rxn.RunReactants(rxnrs)
except:
return []
if __name__ == '__main__':
mytest()
reactants =
['CC(C=CC=C(C)C=CC1=C(C)C(=O)C(OP(=O)(O)O)CC1(C)C)=CC=CC=C(C)C=CC=C(C)C=CC1=C(C)C(=O)C(OP(=O)(O)O)CC1(C)C',
'CC(C=CC=C(C)C=CC1=C(C)C(=O)C(OP(=O)(O)O)CC1(C)C)=CC=CC=C(C)C=CC=C(C)C=CC1=C(C)C(=O)C(OP(=O)(O)O)CC1(C)C',
'CC(C=CC=C(C)C=CC1=C(C)C(=O)C(OP(=O)(O)O)CC1(C)C)=CC=CC=C(C)C=CC=C(C)C=CC1=C(C)C(=O)C(OP(=O)(O)O)CC1(C)C',
'CC(C=CC=C(C)C=CC1=C(C)C(=O)C(OP(=O)(O)O)CC1(C)C)=CC=CC=C(C)C=CC=C(C)C=CC1=C(C)C(=O)C(OP(=O)(O)O)CC1(C)C',
'CC(C=CC=C(C)C=CC1=C(C)C(=O)C(OP(=O)(O)O)CC1(C)C)=CC=CC=C(C)C=CC=C(C)C=CC1=C(C)C(=O)C(OP(=O)(O)O)CC1(C)C',
'CC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCOP(=O)(O)OP(=O)(O)O']
rule =
'[O:10][P:11](=[O:12])([O:13])[O:14].[O:40][P:41](=[O:42])([O:43])[O:44].[O:30][P:31](=[O:32])([O:33])[O:34].[O:50][P:51](=[O:52])([O:53])[O:54].[O:20][P:21](=[O:22])([O:23])[O:24].[C:1]([CH3:2])=[C:3][C:4][CH2:5][C:6]([CH3:7])=[C:8][C:9][CH2:25][C:26]([CH3:27])=[C:28][C:29][CH2:35][C:36]([CH3:37])=[C:38][C:39][CH2:45][C:46]([CH3:47])=[C:48][C:49][CH2:55][C:56]([CH3:57])=[C:58][C:59][O:0]>>[C:1]([CH3:2])=[C:3][C:4][O:0].[CH2:5]=[C:6]([CH3:7])[C:8][C:9][O:10][P:11](=[O:12])([O:13])[O:14].[CH2:25]=[C:26]([CH3:27])[C:28][C:29][O:20][P:21](=[O:22])([O:23])[O:24].[CH2:45]=[C:46]([CH3:47])[C:48][C:49][O:40][P:41](=[O:42])([O:43])[O:44].[CH2:35]=[C:36]([CH3:37])[C:38][C:39][O:30][P:31](=[O:32])([O:33])[O:34].[CH2:55]=[C:56]([CH3:57])[C:58][C:59][O:50][P:51](=[O:52])([O:53])[O:54]'
rxnrs = [Chem.MolFromSmiles(reactant) for reactant in reactants]
print reaction_predict_outside(rule,rxnrs)
------------------?0?2?????????0?2------------------
*??????:*?0?2"Francis Atkinson"<[email protected]>;
*????????:*?0?22018??11??15??(??????) ????5:03
*??????:*?0?2"rdkit-discuss"<[email protected]>;
*????:*?0?2Re: [Rdkit-discuss] Help: How to set timeout for the function
namedRunReactants
Shaozen,
?0?2?0?2?0?2 I have successfully used the solution outlined in this SO
answer ...
https://stackoverflow.com/questions/2281850/timeout-function-if-it-takes-too-long-to-finish
?0?2?0?2?0?2 It uses Posix signals so it wouldn't work on older versions of
Windows (I don't know about Windows 10, what with this new
Linux-compatibility layer). It also doesn't work when running under
mod_wsgi.
?0?2?0?2?0?2 ?0?2?0?2?0?2 Francis
On 15/11/2018 04:21, ?????? wrote:
Hi:
I want to set?0?2timeout for the function named RunReactants, because
sometimes?0?2I found there needs over 10 minutes when running this
function. For example:
>>import rdkit.Chem as Chem
>>from rdkit.Chem import AllChem
>>from rdkit.Chem import MolFromSmiles,MolFromSmarts
>>from rdkit.Chem.Fingerprints import FingerprintMols
>>reactants =
['CC(C=CC=C(C)C=CC1=C(C)C(=O)C(OP(=O)(O)O)CC1(C)C)=CC=CC=C(C)C=CC=C(C)C=CC1=C(C)C(=O)C(OP(=O)(O)O)CC1(C)C',
'CC(C=CC=C(C)C=CC1=C(C)C(=O)C(OP(=O)(O)O)CC1(C)C)=CC=CC=C(C)C=CC=C(C)C=CC1=C(C)C(=O)C(OP(=O)(O)O)CC1(C)C',
'CC(C=CC=C(C)C=CC1=C(C)C(=O)C(OP(=O)(O)O)CC1(C)C)=CC=CC=C(C)C=CC=C(C)C=CC1=C(C)C(=O)C(OP(=O)(O)O)CC1(C)C',
'CC(C=CC=C(C)C=CC1=C(C)C(=O)C(OP(=O)(O)O)CC1(C)C)=CC=CC=C(C)C=CC=C(C)C=CC1=C(C)C(=O)C(OP(=O)(O)O)CC1(C)C',
'CC(C=CC=C(C)C=CC1=C(C)C(=O)C(OP(=O)(O)O)CC1(C)C)=CC=CC=C(C)C=CC=C(C)C=CC1=C(C)C(=O)C(OP(=O)(O)O)CC1(C)C',
'CC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCOP(=O)(O)OP(=O)(O)O']
>>rule =
'[O:10][P:11](=[O:12])([O:13])[O:14].[O:40][P:41](=[O:42])([O:43])[O:44].[O:30][P:31](=[O:32])([O:33])[O:34].[O:50][P:51](=[O:52])([O:53])[O:54].[O:20][P:21](=[O:22])([O:23])[O:24].[C:1]([CH3:2])=[C:3][C:4][CH2:5][C:6]([CH3:7])=[C:8][C:9][CH2:25][C:26]([CH3:27])=[C:28][C:29][CH2:35][C:36]([CH3:37])=[C:38][C:39][CH2:45][C:46]([CH3:47])=[C:48][C:49][CH2:55][C:56]([CH3:57])=[C:58][C:59][O:0]>>[C:1]([CH3:2])=[C:3][C:4][O:0].[CH2:5]=[C:6]([CH3:7])[C:8][C:9][O:10][P:11](=[O:12])([O:13])[O:14].[CH2:25]=[C:26]([CH3:27])[C:28][C:29][O:20][P:21](=[O:22])([O:23])[O:24].[CH2:45]=[C:46]([CH3:47])[C:48][C:49][O:40][P:41](=[O:42])([O:43])[O:44].[CH2:35]=[C:36]([CH3:37])[C:38][C:39][O:30][P:31](=[O:32])([O:33])[O:34].[CH2:55]=[C:56]([CH3:57])[C:58][C:59][O:50][P:51](=[O:52])([O:53])[O:54]'
>>rxnrs = [Chem.MolFromSmiles(reactant) for reactant in reactants]
>>rxn = AllChem.ReactionFromSmarts(rule)
>>outcomes = rxn.RunReactants(rxnrs)
if this functions cannnot return result within 3s, I will make it
return a empty set.
Could you help me deal with this problems?
Thanks a lot.
Yours
Shaozhen
_______________________________________________
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--
Dr Francis L Atkinson
Chemogenomics Group
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
(01223) 494473
--
Dr Francis L Atkinson
Chemogenomics Group
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
(01223) 494473
--
Dr Francis L Atkinson
Chemogenomics Group
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
(01223) 494473
_______________________________________________
Rdkit-discuss mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
_______________________________________________
Rdkit-discuss mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
--
Dr Francis L Atkinson
Chemogenomics Group
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
(01223) 494473
_______________________________________________
Rdkit-discuss mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
