[Open Babel] maplist

Hi, I am using OBSmartsPattern to find a few different ring systems but am running into difficulties in getting the matching patterns out with GetMapList.  >From sp.Match(testmol) I get "true" so it's found something.  Then I think I >need GetMapList to get the results out.  I cannot understand

[Open Babel] Fw: extracting coordinates

Hi, I've identified some atoms matching a SMARTS pattern in a 3d sdf that I want to extract.  I used linecache.getline in Python to pull out the atoms by line number.  This works fine for one molecule in the sdf but with more than one molecule, all the headers for subsequent ones make it

[Open Babel] sd file preparation

Hi I have numerous multimolecule sd files of unknown origin.  Each file reads OK and a few initial tests in pybel work (e.g. number of molecules etc).  I now want to do molecular weight distributions, similarity and identity searching etc across them. This is not a problem but since each file ma

[Open Babel] fast index search on linux

Hi, I have installed openbabel 2.2.3 on an ubuntu 10.04 machine via the apt installer but I am having problems substructure searching an indexed database viz: > babel VS_Library_full.fs -ifs -s'N#Cc1c(Cl)1' results.smi == *** Open Babel Error  in ReadChemObject   D

Re: [Open Babel] fast index search on linux

Thanks Tim, this has solved the problem.  As you suggested, you need to make the .fs file on the same architecture you are running Openbabel From: Tim Vandermeersch To: macc_200 Cc: openbabel-discuss@lists.sourceforge.net Sent: Wed, 12 May, 2010 18:42:09

[Open Babel] pybel install via synaptic

Hi, I have installed openbabel on an ubuntu 8.04 LTS machine using synaptic and it is working fine but would like to install the python bindings too.  It looks to be installing it in a variety of /usr/share /usr/bin and /usr/lib directories but I cannot find anything relating to the setup.py scr

Re: [Open Babel] pybel install via synaptic

which stopped me looking further when I found it) thanks, Andy From: Noel O'Boyle To: macc_200 Cc: openbabel-discuss@lists.sourceforge.net Sent: Mon, 20 September, 2010 11:04:46 Subject: Re: [Open Babel] pybel install via synaptic You should either install

[Open Babel] reaction formats in pybel

Hi, Are any reaction formats (rxn etc) available in pybel.  I've found that smirks are not, at least in openbabel, but cannot find much about others thanks, Andy -- Download new Adobe(R) Flash(R) Builder(TM) 4 The

Re: [Open Babel] reaction formats in pybel

to work either.         From: Noel O'Boyle To: macc_200 Cc: openbabel-discuss@lists.sourceforge.net Sent: Mon, 18 October, 2010 11:43:28 Subject: Re: [Open Babel] reaction formats in pybel See http://openbabel.org/docs/dev/FileFormats/Reactions.html On 17 October 2010 22:41, m

[Open Babel] Fw: size limit on sd files?

Hi, I have tried to run a script, the first part of which reads an approx 1GB sd file using pybel.  However the script hangs and generates a pop-up window saying C++ error in the title bar but the window itself is transparent with no message in it.  Running the script again, the memory usage

[Open Babel] logp

Hi, I have generated a list of pybel molecules and am attempting to generate logP's but when I try mol.calcdesc(), I get OK values for Mwt, Hbond donors/acceptors but logP and TPSA are always zero.  It is clearly understanding the molecule but unwilling to tell me logP.  How can I get the value