If no title is set by the format, Open Babel will use the file name as a default indicator of the origin.
Geoff > On Nov 27, 2013, at 4:20 PM, "Noel O'Boyle" <baoille...@gmail.com> wrote: > > The molecule title is appended to the SMILES string in Open Babel's > implementation of a SMILES file. When you write "smi" with Pybel you > are generating a line of a SMILES file. This is consistent with other > formats. > > More to the point of your original question, I can't see why the PDB > filename is set as the molecule title. I can't recall whether other > formats do this in general. > > - Noel > >> On 27 November 2013 21:13, Dimitri Maziuk <dmaz...@bmrb.wisc.edu> wrote: >>> On 11/27/2013 02:47 PM, Igor Filippov wrote: >>> It is documented in the Daylight specs (the main authority on SMILES): >>> http://www.daylight.com/dayhtml/doc/convert/ >>> >>> >>> - When converting to SMILES, isomeric SMILES, SMARTS or SMIRKS formats, >>> the unique ID is written after the SMILES, isomeric SMILES, SMARTS or >>> SMIRKS, e.g, c1ccccc1 BENZENE or [C,Br][C;v4] QUERY1. >> >> So opensmiles folks are mistaken when they say on >> http://www.opensmiles.org/spec/open-smiles-4-output.html "The optional >> whitespace character and data that follows it are not part of the SMILES >> specification". >> >> Whatever, as a programmer I'm really dealing with specifically smiles, >> or inchi -- I'm dealing with pybel.Molecule.write(), OBFormat, and >> formats section of the docs. There's nothing there about there being a >> part of smiles that's "unique ID" in daylight and "trailing garbage" >> from dusk till dawn. >> >> -- >> Dimitri Maziuk >> Programmer/sysadmin >> BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu >> >> >> ------------------------------------------------------------------------------ >> Rapidly troubleshoot problems before they affect your business. Most IT >> organizations don't have a clear picture of how application performance >> affects their revenue. With AppDynamics, you get 100% visibility into your >> Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics >> Pro! >> http://pubads.g.doubleclick.net/gampad/clk?id=84349351&iu=/4140/ostg.clktrk >> _______________________________________________ >> OpenBabel-discuss mailing list >> OpenBabel-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > ------------------------------------------------------------------------------ > Rapidly troubleshoot problems before they affect your business. Most IT > organizations don't have a clear picture of how application performance > affects their revenue. With AppDynamics, you get 100% visibility into your > Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! > http://pubads.g.doubleclick.net/gampad/clk?id=84349351&iu=/4140/ostg.clktrk > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss ------------------------------------------------------------------------------ Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351&iu=/4140/ostg.clktrk _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
