Re: [Rdkit-discuss] read a smi files
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Re: [Rdkit-discuss] read a smi files
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From: Greg L. <gre...@gm...> - 2010-03-25 14:23:53
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Hi Cedric,
I suggest you read section 2.2 of the Getting Started in Python file,
it explains what the "None" means and how to avoid it causing
problems.
You should also read the help documentation for SmilesMolSupplier by
doing: help(Chem.SmilesMolSupplier)
in python
Best regards,
-greg
On Thu, Mar 25, 2010 at 6:30 AM, Cedric MORETTI
<Ced...@fi...> wrote:
> 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
>
> CCCCC[C@](C)(C(C)C)O
> C1C=CC[C@@H]2[C@H]1OC(=O)O2
> C[C@@]12CCC3(C[C@@H]1CCC[C@]2(C#C)O)OCCO3
> COc1ccc(cc1OCc2cccc3c2cccc3)C=O
> CC(=O)OC[C@@H]1CO[C@](O1)(C)Cc2ccccc2
> CC(C)C(=C1C(=O)c2ccccc2C1=O)O
> c1ccc2c(c1)ccc3c2ccc4c3C[C@H](C4=O)O
> c1cc(ccc1C=O)OCC2CCCCC2
> C1CCC(C1)[C@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[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@@]12CC[C@H]3c4ccc(cc4CC[C@H]3[C@@H]1C[C@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:gre...@gm...]
> Sent: jeudi, 25. mars 2010 13:09
> To: Cedric MORETTI
> Cc: rdk...@li...
> 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
> <Ced...@fi...> 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
>>
>>
>>
>> CCCCC[C@](C)(C(C)C)O ZINC02508045
>>
>> C1C=CC[C@@H]2[C@H]1OC(=O)O2 ZINC17163557
>>
>> C[C@@]12CCC3(C[C@@H]1CCC[C@]2(C#C)O)OCCO3 ZINC01616187
>>
>> COc1ccc(cc1OCc2cccc3c2cccc3)C=O ZINC05294043
>>
>> CC(=O)OC[C@@H]1CO[C@](O1)(C)Cc2ccccc2 ZINC01641674
>>
>> CC(C)C(=C1C(=O)c2ccccc2C1=O)O ZINC01592093
>>
>> c1ccc2c(c1)ccc3c2ccc4c3C[C@H](C4=O)O ZINC06118532
>>
>> c1cc(ccc1C=O)OCC2CCCCC2 ZINC19806585
>>
>> C1CCC(C1)[C@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[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@@]12CC[C@H]3c4ccc(cc4CC[C@H]3[C@@H]1C[C@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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> transmitted from Firmenich, are confidential and solely for the use
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