Sebastian Petrik wrote: > Hello there, > > I am using openbabel as part of an implementation of an automated docking > toolchain. > > I was wondering if openbabel (or pybel, or any other open source tool) can > take a 1D SMILES with no isomeric information and produce all potential > isomers (cis/trans, enantiomers, stereoisomers..) I cannot seem to find a > function for this in openbabel or the pybel API. > > Kind regards, Sebastian >
You could have a look at Frog. From: http://bioserv.rpbs.univ-paris-diderot.fr/Help/Frog2-Help.html it does: > Solve isomer ambiguities occurring in compounds expressed using the 1D > SMILES[1] or 2D SDF [2] formats, used by most academic or commercial compound > collections. Frog will process the input data, identify chiral centers and > produce a list of unambiguous smiles, each smiles corersponding to one > unambiguous isomer . Frog will also consider axial / equatorial conformations > for cycles when relevant. Note however that Frog does not consider some > stereo centers in some bridged cyclic systems since it presently only > considers one conformation per ring. > Generate from SMILES, SDF or Mol2 [3] 3D coordinates for the compounds. It is > possible to ask for multi conformations per isomer. Multi conformations are > often of great help in the process of in silico compound screening. While > relying on a ring library, Frog2 is able to generate on the fly ring > conformations thanks to DG-AMMOS[4] > Generate from 3D SDF or 3D Mol2 ensemble of conformations from a starting > conformation. > Minimize conformations generated using AMMOS[5]. Worked quite well when I tested a feq years ago, although it can miss isomers in bridged ring systems (as is mentioned). http://bioserv.rpbs.jussieu.fr/cgi-bin/Frog2 goodluck, Eiso ------------------------------------------------------------------------------ Virtualization & Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
