[Rdkit-discuss] read 2 SDF files in the loop

2010-07-01 Thread Cedric MORETTI
Hello all,
I have a little question.
I don't arrive to read 2 SDF files with RDKIT when I use the for loop.

I explain
I have a first sdf files with 1 property and a second with another properties.
I put the second SDMolSupplier instead of suppl and load a sdf file ( look 
exemple)
If I replace the SDMolSupplier by a text file the program don't have a problem.
I just search a writer to read 2 SDF 
Tks
Cedric


reader1 = Chem.SDMolSupplier(C:\Data\scaffold/Total/totalscaffold.sdf.sdf)
writer = Chem.SDWriter(C:\Data\scaffold/Eval/evalcount.sdf)
z = 0
for mol in reader1:
  h = Chem.MolToSmiles(mol)

  suppl = open('C:\Data\scaffold/Total/total.txt','r')

  for a in suppl:
r = 0
r+=1



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[Rdkit-discuss] 'SDWriter' object has no attribute 'close

2010-06-10 Thread Cedric MORETTI
Hello all,
I have I little problem with RDKIT( I hope :D)
My program don't arrive to close the SDwriter whereas I put the command 
writer.close() and Chem.SDWriter.close() in the end of programm
I just let the part of the code  that is import for understand the problem and 
the error.
I have the error when the program has finished to read the file
Tks
C


from sys import *
#from ChemScript11 import *
from cinfony import rdk
from rdkit import Chem
import time


reader1 = Chem.SDMolSupplier(sys.argv[0])
writer = Chem.SDWriter(sys.argv[1])


z = 0
for mol in reader1:

 
 [Blablablablabla ( It's to simulate a code)]
  writer.write(mol)

writer.close()
reader1.close()
Chem.SDWriter.close()


Traceback (most recent call last):
  File C:\Scripttravail\supermain.py, line 18, in module
exec(file.read())
  File string, line 51, in module
AttributeError: 'SDWriter' object has no attribute 'close

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Re: [Rdkit-discuss] 'SDWriter' object has no attribute 'close

2010-06-10 Thread Cedric MORETTI
Markus thank you, you responded to my problem.
I had read the manual RDKIT and I could not see where you need to close 
SDWRITER.
So I do not understand my error.
C
 

-Original Message-
From: markus kossner [mailto:m.koss...@tu-bs.de] 
Sent: jeudi, 10. juin 2010 15:43
To: Cedric MORETTI
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] 'SDWriter' object has no attribute 'close

Cedric MORETTI wrote:

 Hello all,

 I have I little problem with RDKIT( I hope :D)

 My program don't arrive to close the SDwriter whereas I put the 
 command writer.close() and Chem.SDWriter.close() in the end of programm

 I just let the part of the code that is import for understand the 
 problem and the error.

 I have the error when the program has finished to read the file

 Tks

 C

 from sys import *

 #from ChemScript11 import *

 from cinfony import rdk

 from rdkit import Chem

 import time

 reader1 = Chem.SDMolSupplier(sys.argv[0])

 writer = Chem.SDWriter(sys.argv[1])

 z = 0

 for mol in reader1:

 

 [Blablablablabla ( It's to simulate a code)]

 writer.write(mol)

 writer.close()

 reader1.close()

 Chem.SDWriter.close()

 Traceback (most recent call last):

 File C:\Scripttravail\supermain.py, line 18, in module

 exec(file.read())

 File string, line 51, in module

 AttributeError: 'SDWriter' object has no attribute 'close

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Hi Cedric,
the Chem.SDWriter Object does not need to be closed, does it? It is 
automatically closed at the end of your program.
It doesn't even have a method that is named 'close()' like the ones you 
might know from python text file I/O objects.
This is what the Traceback error complains when it says :
-AttributeError: 'SDWriter' object has no attribute 'close'
So you should go well with simply deleting the three lines at the end of 
your script that give the .close() commands.
Hope this helps,
Markus
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Re: [Rdkit-discuss] RDKit descriptors batch

2010-06-02 Thread Cedric MORETTI
Not tested


# script RD_descript.py
print Hello from RD_descript 

from cinfony import rdk
from rdkit import Chem
from rdkit.Chem import AvailDescriptors

for d in AvailDescriptors.descDict:
   print d


suppl = open(Nom file,r)
w = Chem.SDWriter(SDF File)
numRead = 0
numStructures = 0
for m in suppl:
   numRead += 1
   if m != None:
  numStructures += 1
  smi = Chem.MolToSmiles(m.strip())
  m.SetProp(SMILES,smi)
  print smi
  for d in AvailDescriptors.descDict:
#  print d
 pr = AvailDescriptors.descDict[d]( m.strip())
#  print str(pr)
 m.SetProp(d,str(pr))
  w.write(m)

print nombre initiale =  + str(numRead )
print nombre finale =  + str(numStructures)

From: Damjan Krstajic [mailto:dkrsta...@hotmail.com]
Sent: mercredi, 2. juin 2010 11:21
To: rdkit-discuss@lists.sourceforge.net
Subject: [Rdkit-discuss] RDKit descriptors batch

Hello,

I would like to use RDKit to calculate descriptors. I am interested in a batch 
program which would calculate the RDKit descriptors from a smiles file (.smi). 
I don't have any experience with Python. Do you have any advice on how to 
create the batch program? I am prepared to code it and give it to you so that 
others can use it.

Thanks
DK

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Re: [Rdkit-discuss] cycles in RDKIT

2010-05-28 Thread Cedric MORETTI
Tks Greg
Big big tks you very much
It was exactly my answer.


-Original Message-
From: Greg Landrum [mailto:greg.land...@gmail.com] 
Sent: mercredi, 26. mai 2010 18:33
To: Cedric MORETTI
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] cycles in RDKIT

Dear Cedric,

On Wed, May 26, 2010 at 5:12 PM, Cedric MORETTI
cedric.more...@firmenich.com wrote:
 Hello
 I'd like to know if it was possible to search in RDKIT which would isolate
 any cycles.
 I thought the search for chemical moiety C1 or C1 and save the file with
 these molecules.
 The more complicated now.
 Is it possible to find fragments containing only the cycle and the cycle?

 Basically I have a database with 70,000 molecules and I want to have the
 cyclic fragments contained in the database.
 If you have an idea to help me thank you.

I'm not sure I've understood the question, but I will try:
If you want to identify the cyclic fragements, the simplest thing to
do is to use the function Chem.DeleteSubstructs to remove all
non-cyclic atoms:
[1] from rdkit import Chem
[2] p = Chem.MolFromSmarts('[!r]')   #- this query matches any
non-ring atoms
[3] m=Chem.MolFromSmiles('Cc1c1OCC')
[4] m2=Chem.DeleteSubstructs(m,p)
[5] Chem.MolToSmiles(m2)
Out[5] 'c1c1'

In the case of molecules without cycles, this removes everything:
[6] m3 = Chem.MolFromSmiles('CCC')
[7] m4=Chem.DeleteSubstructs(m3,p)
[8] Chem.MolToSmiles(m4)
Out[8] ''

And for linked rings, it leaves you with multiple pieces:
[9] m5 = Chem.MolFromSmiles('C1CC1CCc1ccc(CC)cc1')
[10] m6=  Chem.DeleteSubstructs(m5,p)
[11] Chem.MolToSmiles(m6)
Out[11] 'c1c1.C1CC1'

Which you could split into separate molecules if you wanted to:
[14] frags = Chem.GetMolFrags(m6,asMols=True)
[15] frags
Out[15]
(rdkit.Chem.rdchem.Mol object at 0xa637e64,
 rdkit.Chem.rdchem.Mol object at 0xa64c064)
[16] [Chem.MolToSmiles(x) for x in frags]
Out[16] ['C1CC1', 'c1c1']

Is this what you were looking for?

-greg
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[Rdkit-discuss] cycles in RDKIT

2010-05-26 Thread Cedric MORETTI
Hello
I'd like to know if it was possible to search in RDKIT which would isolate any 
cycles.
I thought the search for chemical moiety C1 or C1 and save the file with 
these molecules.
The more complicated now.
Is it possible to find fragments containing only the cycle and the cycle?

Basically I have a database with 70,000 molecules and I want to have the cyclic 
fragments contained in the database.
If you have an idea to help me thank you.
Cédric


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[Rdkit-discuss] GUI Overview

2010-04-30 Thread Cedric MORETTI
Hello all,
I read the RDKit_Overview.pdf.
From this slides 19 until the slide 37 there a presentation a graphic 
interface.
Somebody know, how I could load this interface ?
Tks
Cedric


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Re: [Rdkit-discuss] Error depicting a smiles string

2010-04-30 Thread Cedric MORETTI
I use a Q42009 with the package Cinfony. 
I am in windows system ( :( )
The picture made
300x300
Size 4.75kb

-Original Message-
From: Greg Landrum [mailto:greg.land...@gmail.com] 
Sent: vendredi, 30. avril 2010 11:03
To: Cedric MORETTI
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] Error depicting a smiles string

Hi Cedric,

On Fri, Apr 30, 2010 at 4:57 AM, Cedric MORETTI
cedric.more...@firmenich.com wrote:
 I'm really interested by the possibility to draw the picture with rdkit.
 Si I test the command that Gred has written.
 The file has created but there are not image I have a white picture, it's not 
 empty...


That's not good.
I would like to find this problem. Which version of the RDKit did you
use? Did you run it on Windows or Linux?

-greg
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Re: [Rdkit-discuss] GUI Overview

2010-04-30 Thread Cedric MORETTI
Tks you Greg for your answer.

If my brain is good, I'm remember that Noel O'Boyle (the cinfony creator's) 
subscribed to RDKIT mailing-list so maybe he could answer at my question.
Cedric

-Original Message-
From: Greg Landrum [mailto:greg.land...@gmail.com] 
Sent: vendredi, 30. avril 2010 11:16
To: Cedric MORETTI
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] GUI Overview

Hi Cedric,

On Fri, Apr 30, 2010 at 5:00 AM, Cedric MORETTI
cedric.more...@firmenich.com wrote:
 Hello all,

 I read the RDKit_Overview.pdf.

 From this slides 19 until the slide 37 there a presentation a graphic
 interface.

 Somebody know, how I could load this interface ?


That user interface is no longer supported; it's very unlikely that
you will be able to get it running (you need a version of pyqt that
works with qt version 3 and that's not an easy thing to find these
days).

I really need to update that document to remove the GUI discussion.

-greg
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Re: [Rdkit-discuss] Error depicting a smiles string

2010-04-30 Thread Cedric MORETTI
Tks you Greg for your answer.

If my brain is good, I'm remember that Noel O'Boyle (the cinfony creator's) 
subscribed to RDKIT mailing-list so maybe he could answer at my question.
Cedric

-Original Message-
From: Greg Landrum [mailto:greg.land...@gmail.com] 
Sent: vendredi, 30. avril 2010 11:14
To: Cedric MORETTI
Cc: RDKit Discuss
Subject: Re: [Rdkit-discuss] Error depicting a smiles string

Hi,

On Fri, Apr 30, 2010 at 5:06 AM, Cedric MORETTI
cedric.more...@firmenich.com wrote:
 I use a Q42009 with the package Cinfony.
 I am in windows system ( :( )
 The picture made
 300x300
 Size 4.75kb

I can't answer questions about cinfony since I don't know know how it
works. Please try using the RDKit without cinfony.

Thanks,
-greg
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Re: [Rdkit-discuss] GUI Overview

2010-04-30 Thread Cedric MORETTI
My last answer is bad. I answer at the bad subject..
Tks Greg, for me, with RDKIT I has learned a Python.
So, it's a really good for my internship in chemoinfirmatics.

-Original Message-
From: Cedric MORETTI [mailto:cedric.more...@firmenich.com] 
Sent: vendredi, 30. avril 2010 11:24
To: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] GUI Overview

Tks you Greg for your answer.

If my brain is good, I'm remember that Noel O'Boyle (the cinfony creator's) 
subscribed to RDKIT mailing-list so maybe he could answer at my question.
Cedric

-Original Message-
From: Greg Landrum [mailto:greg.land...@gmail.com] 
Sent: vendredi, 30. avril 2010 11:16
To: Cedric MORETTI
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] GUI Overview

Hi Cedric,

On Fri, Apr 30, 2010 at 5:00 AM, Cedric MORETTI
cedric.more...@firmenich.com wrote:
 Hello all,

 I read the RDKit_Overview.pdf.

 From this slides 19 until the slide 37 there a presentation a graphic
 interface.

 Somebody know, how I could load this interface ?


That user interface is no longer supported; it's very unlikely that
you will be able to get it running (you need a version of pyqt that
works with qt version 3 and that's not an easy thing to find these
days).

I really need to update that document to remove the GUI discussion.

-greg
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[Rdkit-discuss] read a smi files

2010-03-25 Thread Cedric MORETTI
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

...@](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)OCCO3ZINC01616187
COc1ccc(cc1OCc23c23)C=O ZINC05294043
CC(=O)OC[C@@h]1c...@](O1)(C)Cc2c2 ZINC01641674
CC(C)C(=C1C(=O)c2c2C1=O)OZINC01592093
c1ccc2c(c1)ccc3c2ccc4c3...@h](C4=O)OZINC06118532
c1cc(ccc1C=O)OCC2C2  ZINC19806585
C1CCC(C1)[...@h]2ccc[c@H]2O   ZINC02168867
COc1(c1)C(=O)/C=C/c2ccc3c(c2)OCCO3ZINC05128906
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)CZINC01673320
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)OZINC17424830
C[C@@]1(C[C@@H]2[C@@H]2C[C@@]1(C)O)COC   ZINC05464622
CC(C)(C)C(=O)Oc1ccc2c(cc(=O)oc2c1)c3c3ZINC01940013
c1ccc(cc1)c2coc3c3c2=O ZINC00895390
Cc12c1C3c4c(4C(=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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Re: [Rdkit-discuss] read a smi files

2010-03-25 Thread Cedric MORETTI
Igor,

No it's normal 
If I put 2 slashes in the same direction (as the windows address), I have a 
problem pour read the files. 
Cedric

-Original Message-
From: Igor Filippov [Contr] [mailto:filipp...@mail.nih.gov] 
Sent: jeudi, 25. mars 2010 15:18
To: Cedric MORETTI
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] read a smi files

Cedric,

Not sure if it's relevant but I notice you have two different slashes in
the path to testsmi.smi and testsdf.sdf.


 “reader1 = Chem.SDMolSupplier(C:\Test/testsdf.sdf)”
  ^^^  ^^^

Igor


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[Rdkit-discuss] GUI Overview

2010-03-12 Thread Cedric MORETTI
Hello,
I try to install and use the GUI that can be seen in the presentation 
RDKit_Overview.pdf on slide 19.
For now only access the command line works.
Thank you
Cédric
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[Rdkit-discuss] (no subject)

2010-03-12 Thread Cedric MORETTI
Hello,
I would like to know if there is someone who uses utility Cinfony with RDKit.
I use version 0.9 of Cinfony and an old version of RDKit (May 2008).
There is no problem when using both programs. But I cannot arrive to install 
version Q2009P25, RDKit module is not found when I loaded.
Although having only replace the contents of the directory rdkit Cinfony.

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[Rdkit-discuss] rdkit and Cinfony

2010-03-12 Thread Cedric MORETTI
Hello,
I would like to know if there is someone who uses utility Cinfony with RDKit.
I use version 0.9 of Cinfony and an old version of RDKit (May 2008).
There is no problem when using both programs. But I cannot arrive to install 
version Q2009P25, RDKit module is not found when I loaded.
Although having only replace the contents of the directory rdkit Cinfony.

Tks
Cedric


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[Rdkit-discuss] rdkit installation on windows

2010-03-10 Thread Cedric MORETTI
Hi all,
I search a process to install RDKIT on Windows XP

I have installed Python 3.1 and  Cygwin.
If I read the SoftwareRequidrements (RDKIT/Docs)
I need NumPy but when I try to install NumPy I have a message error Python 2.6 
required,  which was found in the registry .
There are a problem between NumPy and Python 3.1 ?
Tks
Cedric

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