Who hasn't been bitten by this? Try:
SDMolSupplier(isdf, removeHs=False) - Jean-Paul Ebejer Early Stage Researcher On 14 June 2012 10:49, <[email protected]> wrote: > > Dear RDkitters, > > when reading in a SDF gicen 3D coordinates & hydrogens set & writing it out > using SDMolSupplier. > > According to a former thread in the mailing list, I do not need to use > AddHs > http://www.mail-archive.com/[email protected]/msg02235.html > > This is my sample code: > " > from rdkit import Chem > isdf = "cyc_hex.sdf" > osdf = "cyc_hex.p.sdf" > sd_out = Chem.SDWriter(osdf) > > cpds = Chem.SDMolSupplier(isdf) > # do something here > for ent in cpds: > sd_out.write(ent) > " > > What am I doing wrong? > > > If you don't believe me, I can also provide you the input/output SDF :) > > > > Cheers & Thanks, > Paul > > This message and any attachment are confidential and may be privileged or > otherwise protected from disclosure. If you are not the intended recipient, > you must not copy this message or attachment or disclose the contents to > any other person. If you have received this transmission in error, please > notify the sender immediately and delete the message and any attachment > from your system. Merck KGaA, Darmstadt, Germany and any of its > subsidiaries do not accept liability for any omissions or errors in this > message which may arise as a result of E-Mail-transmission or for damages > resulting from any unauthorized changes of the content of this message and > any attachment thereto. Merck KGaA, Darmstadt, Germany and any of its > subsidiaries do not guarantee that this message is free of viruses and does > not accept liability for any damages caused by any virus transmitted > therewith. > > Click http://www.merckgroup.com/disclaimer to access the German, French, > Spanish and Portuguese versions of this disclaimer. > > > ------------------------------------------------------------------------------ > 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
