Hi,
Thanks , the SD file I was talking about was downloaded from the PDB
(ligands).
cheers
Fabian
On Fri, Sep 7, 2012 at 12:43 PM, George Papadatos <[email protected]>wrote:
> Hi Fabian,
>
> The first one is easy: the function expects a header in the file by
> default. There is a parameter that toggles this but I don't have access to
> a computer right now. There is an example in the documentation.
>
> Best regards,
>
> George
>
> Sent from my gPad
>
> On 7 Sep 2012, at 13:34, Fabian Dey <[email protected]> wrote:
>
> > Hi
> >
> > I found two issues when reading files:
> >
> > 1) I might be getting something wrong here, but it seems as if
> SmilesMolSupplier misses the very first Smiles:
> >
> > input smiles file "test.smi":
> > C mola
> > CC molb
> > CCC molc
> > CCCC mold
> >
> >
> > # python script
> > from rdkit import Chem
> > suppl = Chem.SmilesMolSupplier('test.smi');
> >
> > print "TEST-1 : %s %s"
> %(Chem.MolToSmiles(suppl[0]),suppl[0].GetProp("_Name"))
> > print ""
> >
> > for mol in suppl:
> > print "TEST-2 : %s %s" %(Chem.MolToSmiles(mol),mol.GetProp("_Name"))
> >
> > print ""
> >
> > for i,mol in enumerate(suppl):
> > print "TEST-3 : %s %s" %(Chem.MolToSmiles(mol),mol.GetProp("_Name"))
> >
> >
> > #output
> > TEST-1 : CC molb
> >
> > TEST-2 : CC molb
> > TEST-2 : CCC molc
> > TEST-2 : CCCC mold
> >
> > TEST-3 : CC molb
> > TEST-3 : CCC molc
> > TEST-3 : CCCC mold
> >
> > The first molecule "mola" is not available through the supplier (also
> happens with other smiles files).
> >
> >
> > 2) SDMolSupplier : I have a script which calculates properties from
> SDfiles read in through the corresponding supplier
> > and RDKIT occassionally reported the following errors:
> >
> > ****
> > Pre-condition Violation
> > Atomic number not found
> > Violation occurred on line 56 in file
> /home/dey/Downloads/RDKit_2012_06_1/Code/GraphMol/PeriodicTable.h
> > Failed Expression: atomicNumber<byanum.size()
> > ****
> >
> > [12:25:23] Unexpected error hit on line 6
> > [12:25:23] ERROR: moving to the begining of the next molecule
> > ERROR for molecule at position 0
> >
> >
> > It turned out that for the corresponding SD-file the atom elements were
> written in all captial letters (e.g. CL) - if these
> > were changed to the proper format (Cl) RDKIT passed without throwing an
> error. Although I can preprocess the SD-files
> > with a script, it would be nice if RDKIT could handle these cases
> internally.
> >
> > Best
> > Fabian
> >
> >
> >
> >
> >
> ------------------------------------------------------------------------------
> > Live Security Virtual Conference
> > Exclusive live event will cover all the ways today's security and
> > threat landscape has changed and how IT managers can respond. Discussions
> > will include endpoint security, mobile security and the latest in malware
> > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> > _______________________________________________
> > Rdkit-discuss mailing list
> > [email protected]
> > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
_______________________________________________
Rdkit-discuss mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
