[Rdkit-discuss] Write mol/sdf files

2014-08-26 Thread acanada
Hello, What is the best approach to write mol/sdf files for a compound which I already have chebi, inChi? I have noticed that there is a class SmilesWriter to do this from the Smiles. Thank you for your help Andrés **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros

Re: [Rdkit-discuss] Write mol/sdf files

2014-08-26 Thread Paul Emsley
On 26/08/14 10:42, acanada wrote: What is the best approach to write mol/sdf files for a compound which I already have chebi, inChi? m=Chem.MolFromInchi('InChI=1S/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3') print file('foo.mol','w+'),Chem.MolToMolBlock(m)

Re: [Rdkit-discuss] Write mol/sdf files

2014-08-26 Thread acanada
Thank you for your answer. That is what I'm trying to do. Having the inchi string inside inChi variable: from rdkit import Chem m = Chem.MolFromInchi(inChi) I get this error AttributeError: 'module' object has no attribute 'MolFromInchi' I think it is well imported, isn't it? El Aug 26,

Re: [Rdkit-discuss] Write mol/sdf files

2014-08-26 Thread Nicholas Firth
Hi, I personally don't use the inChi support, but I am aware that you have to install it as an optional package. Optional packages If you would like to install the RDKit InChI support (first available in the Q2 2011 release), follow the instructions in $RDBASE/External/INCHI-API to get a

Re: [Rdkit-discuss] Write mol/sdf files

2014-08-26 Thread acanada
Thank you very much!! I'll do it Best, Andrés El Aug 26, 2014, a las 5:22 PM, Nicholas Firth escribió: Hi, I personally don't use the inChi support, but I am aware that you have to install it as an optional package. Optional packages If you would like to install the RDKit InChI

[Rdkit-discuss] cartridge build fail

2014-08-26 Thread Andrew Pannifer
Hi, I have just installed rdkit on a RHEL machine (from source) together with postgresql 9.0 (from the repo on the website). rdkit is doing fine on the ctest results and modules import fine while postgresql is also OK. In contrast, attempts to build the cartridge are not so good (results

Re: [Rdkit-discuss] cartridge build fail

2014-08-26 Thread Andrew Pannifer
just solved that problem (I had messed up the path in .bashrc when inserting the necessary rdkit path) but not out of the woods yet. The make make install make installcheck command gives me this: gcc -I/usr/local/include -I/home/apannife/rdkit2/RDKit_2014_03_1/Code -DRDKITVER='007200'

Re: [Rdkit-discuss] cartridge build fail

2014-08-26 Thread Jan Holst Jensen
On 2014-08-26 17:34, Andrew Pannifer wrote: Hi, I have just installed rdkit on a RHEL machine (from source) together with postgresql 9.0 (from the repo on the website). rdkit is doing fine on the ctest results and modules import fine while postgresql is also OK. In contrast, attempts to