Hi
Tks you for your explication but I have a other problem I explain...
I has written a little program
"print "Test"
from cinfony import rdk
from rdkit import Chem
suppl = Chem.SmilesMolSupplier("C:\Test/testsmi.smi")
for mol in supple
print mol.GetNumAtoms()
Normaly I understand RDkit this program read a smi file and give me the numbers
of atoms each molecule in my file
It's right ?
When I execute the program I have this answer...
Traceback (most recent call last):
File "C:/Documents and Settings/cdmo/Desktop/testtt/testtttttttttttt.py",
line 7, in <module>
print mol.GetNumAtoms()
AttributeError: 'NoneType' object has no attribute 'GetNumAtoms'
So I decided to put a print to read mol during the test.
And I have this answer
None
None
None
None
None
None
None
None
None
None
None
None
None
None
None
None
None
None
None
None
So the error message is normal but I can't understand why he doesn't arrive to
read correctly these smile in my smi files
My files have this form
cccc...@](C)(C(C)C)O
C1C=CC[C@@h]...@h]1oc(=O)O2
C[C@@]12CCC3(C[C@@h]1cc...@]2(C#C)O)OCCO3
COc1ccc(cc1OCc2cccc3c2cccc3)C=O
CC(=O)OC[C@@h]1c...@](O1)(C)Cc2ccccc2
CC(C)C(=C1C(=O)c2ccccc2C1=O)O
c1ccc2c(c1)ccc3c2ccc4c3...@h](C4=O)O
c1cc(ccc1C=O)OCC2CCCCC2
C1CCC(C1)[...@h]2ccc[c@H]2O
COc1cccc(c1)C(=O)/C=C/c2ccc3c(c2)OCCO3
Cc1cc(c(o1)C)C(=O)OCC(=O)C23CC4CC(C2)CC(C4)C3
c...@h]1ccc[c@]2(C1=CC(=O)CC2)C
CC(=O)/C(=C/c1ccco1)/C(=O)OC(C)(C)C
C[C@@H](CC[C@@H](C(=C)C)O)C=C
CC[C@@]12c...@h]3c4ccc(cc4c...@h]3[c@@h]1...@h]([C@@H]2O)O)O
C[C@@]1(C[C@@H]2CCCC[C@@H]2C[C@@]1(C)O)COC
CC(C)(C)C(=O)Oc1ccc2c(cc(=O)oc2c1)c3ccccc3
c1ccc(cc1)c2coc3ccccc3c2=O
Cc1cccc2c1C3c4c(cccc4C(=O)CC3CC2=O)C
CC(C)[C@@H]1C[C@@H]([C@@](C=C1)(C)O)O
Tks
Cedric
-----Original Message-----
From: Greg Landrum [mailto:greg.land...@gmail.com]
Sent: jeudi, 25. mars 2010 13:09
To: Cedric MORETTI
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] read a smi files
Hi,
You can read molecules from SMILES files using a SmilesMolSupplier:
suppl =
Chem.SmilesMolSupplier('benzodiazepine.smi',delimiter='\t',titleLine=False)
For more information: the SmilesMolSupplier behaves the same way as
the SDMolSupplier that is described in the
GettingStartedWithPython.pdf file distributed with the RDKit.
Best Regards,
-greg
On Thu, Mar 25, 2010 at 4:09 AM, Cedric MORETTI
<cedric.more...@firmenich.com> wrote:
> Hello,
>
> I am writing because I am seeking your help.
> I have a program that requires this input parameter
>
>
>
> "reader1 = Chem.SDMolSupplier("C:\Test/testsdf.sdf")"
>
> "writer = Chem.SDWriter("C:\Data\test_out.sdf")"
>
>
>
> I liked to read a file directly "*. smi " using this command
>
>
>
> "reader1 = Chem.MolFromSmiles(C:\Test/testsmi.smi")"
>
> "writer = Chem.SDWriter("C:\Data\test_out.sdf")"
>
>
>
> My smi file is this latter type
>
>
>
> cccc...@](C)(C(C)C)O ZINC02508045
>
> C1C=CC[C@@h]...@h]1oc(=O)O2 ZINC17163557
>
> C[C@@]12CCC3(C[C@@h]1cc...@]2(C#C)O)OCCO3 ZINC01616187
>
> COc1ccc(cc1OCc2cccc3c2cccc3)C=O ZINC05294043
>
> CC(=O)OC[C@@h]1c...@](O1)(C)Cc2ccccc2 ZINC01641674
>
> CC(C)C(=C1C(=O)c2ccccc2C1=O)O ZINC01592093
>
> c1ccc2c(c1)ccc3c2ccc4c3...@h](C4=O)O ZINC06118532
>
> c1cc(ccc1C=O)OCC2CCCCC2 ZINC19806585
>
> C1CCC(C1)[...@h]2ccc[c@H]2O ZINC02168867
>
> COc1cccc(c1)C(=O)/C=C/c2ccc3c(c2)OCCO3 ZINC05128906
>
> Cc1cc(c(o1)C)C(=O)OCC(=O)C23CC4CC(C2)CC(C4)C3
> ZINC04930263
>
> c...@h]1ccc[c@]2(C1=CC(=O)CC2)C ZINC05081132
>
> CC(=O)/C(=C/c1ccco1)/C(=O)OC(C)(C)C ZINC01673320
>
> C[C@@H](CC[C@@H](C(=C)C)O)C=C ZINC06020645
>
> CC[C@@]12c...@h]3c4ccc(cc4c...@h]3[c@@h]1...@h]([C@@H]2O)O)O
> ZINC17424830
>
> C[C@@]1(C[C@@H]2CCCC[C@@H]2C[C@@]1(C)O)COC ZINC05464622
>
> CC(C)(C)C(=O)Oc1ccc2c(cc(=O)oc2c1)c3ccccc3 ZINC01940013
>
> c1ccc(cc1)c2coc3ccccc3c2=O ZINC00895390
>
> Cc1cccc2c1C3c4c(cccc4C(=O)CC3CC2=O)C ZINC01601995
>
> CC(C)[C@@H]1C[C@@H]([C@@](C=C1)(C)O)O ZINC14588844
>
>
>
> Do you know how I can do?
> Thank you
> Moretti Cédric
>
>
>
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Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
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