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

[Thomas Heller]

Greg Landrum schrieb:
 Dear Thomas,
 
 I checked in the fix for this problem this morning.

Great.  Will you make a binary release as well, or should I
try to compile it myself?

-- 
Thanks,
Thomas

--
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

[Rdkit-discuss] Documentation

[JEAN MARC NUZILLARD]

Dear Greg,

I successfully installed RDKit_Q12010_1.
I have been pleased to see that the 2D coordinate
generation algorithm is now able to deal with
all structures in my test structure file.

I was able to generate the C++ documentation using doxygen.
How do you generate the python documentation?
I read something about HappyDoc in RDKit_Overview.pdf.
I tried to install HappyDoc but no setup.py file for its installation.

Maybe a few lines about documentation generation could be added in
the INSTALL file of the RDKit.

Best regards,

Jean-Marc Nuzillard



--
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] Documentation

[Greg Landrum]

Hi Jean-Marc,

On Mon, May 3, 2010 at 1:49 PM, JEAN MARC NUZILLARD
jm.nuzill...@univ-reims.fr wrote:
 Dear Greg,

 I successfully installed RDKit_Q12010_1.
 I have been pleased to see that the 2D coordinate
 generation algorithm is now able to deal with
 all structures in my test structure file.

glad to hear it.

 I was able to generate the C++ documentation using doxygen.
 How do you generate the python documentation?
 I read something about HappyDoc in RDKit_Overview.pdf.
 I tried to install HappyDoc but no setup.py file for its installation.

To build the python documentation you need to install epydoc:
http://epydoc.sourceforge.net/

once you have the install completed, you build the documentation as follows:

cd $RDBASE/rdkit
epydoc --config epydoc.config -o ../Docs/Code/Python

there will be some errors displayed; you can safely ignore them.

 Maybe a few lines about documentation generation could be added in
 the INSTALL file of the RDKit.

good idea, I will update the wiki and the INSTALL file.

Thanks for the suggestion,
-greg

--
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

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

[Robert DeLisle]

Greg,

I found the files of interest and ran a few tests.  The files resulting from
the tests are in the attached archive and here are the details.

The structures in question came from the non-aggregators set of Shoichet
which were available on his web page.  My original intent was to convert the
SMILES files from the Shoichet set to SDF.  This went smoothly enough until
I had to process the SDF for a different purpose.  Four structures were
found to cause problems.

In the attached archive, each offending structure has 5 associated files
named according the the NGC ID associated with the original SMILES:

.smi - The original SMILES.

.sdf - The result I had found in my SMILES to SDF conversion having nan as
the atom coordinates.

.mol - Generated manually today by:
m = Chem.MolFromSmiles('offending SMILES')
AllChem.Compute2DCoords(m)
print file ('blah.mol','w+'), Chem.MolToMolBlock(m)

_fix.smi - This is the RDKit generated SMILES for the structure.

_fix.mol - The result of the following after the code snip above:
m=Chem.MolFromSmiles(Chem.MolToSmiles(m))
AllChem.Compute2DCoords(m)
print file ('blah_fix.mol','w+'), Chem.MolToMolBlock(m)


Only 14662 did not result in a fixed mol file.  Interestingly, the first bad
conversion only has nan for coordinates of the platinum hexachloride.  After
the SMILES round-trip, all coordinates are nan.

Please let me know if you need any further details.

-Kirk








On Sat, May 1, 2010 at 10:24 PM, Greg Landrum greg.land...@gmail.comwrote:

 On Fri, Apr 30, 2010 at 12:56 PM, Greg Landrum greg.land...@gmail.com
 wrote:
 
  I don't see any problems in your script, so I have to assume that it's
  a problem with the binary you're using. I'm travelling and don't have
  a windows machine handy, so this will have to wait until I'm back home
  this weekend.

 Ok, I was able to reproduce this on my windows box. It's clearly a
 problem with the windows build:

 In [29]: m = Chem.MolFromSmiles('OC(=O)C11')

 In [30]: AllChem.Compute2DCoords(m)
 Out[30]: 0

 In [31]: print Chem.MolToMolBlock(m)
 --- print(Chem.MolToMolBlock(m))

 RDKit  2D

  8  8  0  0  0  0  0  0  0  0999 V2000
   -1.#IND1.#QNB0. O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.#IND1.#QNB0. C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.#IND1.#QNB0. O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.#IND1.#QNB0. C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.#IND1.#QNB0. C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.#IND1.#QNB0. C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.#IND1.#QNB0. C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.#IND1.#QNB0. C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  3
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  4  1  0
 M  END

 I will look into this and see where the problem lies.

 Note: whatever is going on here doesn't affect every depiction; other
 molecules do end up with correct coordinates.

 Best Regards,
 -greg


 --
 ___
 Rdkit-discuss mailing list
 Rdkit-discuss@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/rdkit-discuss



nan.tgz
Description: GNU Zip compressed data
--
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss