Re: [Open Babel] Fwd: stereo config
On 11/18/2013 06:56 PM, Craig James wrote: For L-Alanine: PC: InChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m0/s1 PDB: InChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m0/s1 OB: InChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m0/s1/i4+1 Are you saying there is a problem, or is this just interesting for some reason? I'm saying I had a bug in my script: I was not resetting the nitrogen after calculating N15 isotopic mass. Now if only OB stereo could do R/S and E/Z, I wouldn't have to also use rdkit... -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu signature.asc Description: OpenPGP digital signature -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Fwd: stereo config
On Wed, Nov 20, 2013 at 11:12 AM, Dimitri Maziuk dmaz...@bmrb.wisc.eduwrote: On 11/18/2013 06:56 PM, Craig James wrote: For L-Alanine: PC: InChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m0/s1 PDB: InChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m0/s1 OB: InChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m0/s1/i4+1 Are you saying there is a problem, or is this just interesting for some reason? I'm saying I had a bug in my script: I was not resetting the nitrogen after calculating N15 isotopic mass. Now if only OB stereo could do R/S and E/Z, I wouldn't have to also use rdkit... R/S and E/Z are somewhat antiquated from a cheminformatics point of view. While chemists find them intuitive enough, computing R/S and E/Z can actually take an unexpectely large amount of CPU time. OpenBabel instead uses local connectivity around a single atom or bond. Does your application require these older designations? Or could you instead use the atom- and bond-centric definitions that are built in to OpenBabel? Craig -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Fwd: stereo config
On 11/20/2013 02:16 PM, Craig James wrote: Does your application require these older designations? Or could you instead use the atom- and bond-centric definitions that are built in to OpenBabel? My applications need to work with mmCIF data model. MmCIF defines _chem_comp_atom.pdbx_stereo_config as (R, S, N) -- see http://mmcif.rcsb.org/dictionaries/mmcif_pdbx_v40.dic/Items/_chem_comp_atom.pdbx_stereo_config.html and _chem_comp_bond.pdbx_stereo_config as (E, Z, N) -- http://mmcif.rcsb.org/dictionaries/mmcif_pdbx_v40.dic/Items/_chem_comp_bond.pdbx_stereo_config.html Both items are nullable so I don't have to fill them in if the data is not available. However, if it is obtainable, I want it. -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu signature.asc Description: OpenPGP digital signature -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
[Open Babel] Fwd: stereo config
As a rule, you should always include all input files you use. Otherwise we can't say much about the output you provided. On Mon, Nov 18, 2013 at 4:09 PM, Dimitri Maziuk dmaz...@bmrb.wisc.eduwrote: On 11/16/2013 11:40 AM, Dimitri Maziuk wrote: I guess now I'll have to come up with a different test plan. So I downloaded both 2D and 3D SFDs for L- and D-Alanine from PubChem, ran them through my scripts and compared to the original and to chem. comps in ligand expo. OB generates the same output from 2D and 3D SDF. For L-Alanine: PC: InChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m0/s1 PDB: InChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m0/s1 OB: InChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m0/s1/i4+1 Are you saying there is a problem, or is this just interesting for some reason? Craig For D-Alanine: PC: InChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m1/s1 PDB: InChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m1/s1 OB: InChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m1/s1/i4+1 -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
