Re: [Open Babel] Compiling latest openbabel source code (MacOSX) - conformer.o

OK. Many thanks Geoff. Though it might be something like that. Ken On 27 Aug 2012, at 16:33, Geoffrey Hutchison wrote: >> Having problems compiling latest source code for Openbabel on Mac OS X >> (Lion). Don't think the error is a Mac issue, but I'll let you judge... >> Cmake and make ou

[Open Babel] Compiling latest openbabel source code (MacOSX) - conformer.o

Folks Having problems compiling latest source code for Openbabel on Mac OS X (Lion). Don't think the error is a Mac issue, but I'll let you judge... Cmake and make output below. Any ideas? Cheers, Ken cmake -DCMAKE_INSTALL_PREFIX=/usr/local -DPYTHON_BINDINGS=ON -DRUN_SWIG=ON -DEIGEN3_INC

Re: [Open Babel] Openbabel svn python bindings build failure

Many thanks Geoff Cmake (2.6 patch 4) was indeed the problem. I installed the latest version (2.8.7) and rebuilt. Everything OK now. Cheers, Ken On 18 Mar 2012, at 20:20, Geoff Hutchison wrote: >> I'm having trouble building the latest SVN release (trunk) of Openbabel >> (from scratch) on

[Open Babel] Using openbabel.py to generate InChIKey with reconnect metal option

Folks I'm trying to use Openbabel to generate a non-standard InChIKey for a few of my metal cyanides and isocyanides (because configurations produce the same Standard InChIKey). Below is my code. Execution of the code leaving the comments intact yields the Standard InChI and Standard InChIKey

[Open Babel] InChI v 1.04 and CML to InChI conversion

Hi Folks I noticed that version 1.04 of the InChI software has removed the capability to generate InChIs directly from CML. Does Openbabel defer this functionality to the v 1.03 InChI code at the moment? Cheers, Ken ---

[Open Babel] Python, openbabel, generation of InChIs and InChIKeys for proton and protonated molecular hydrogen from SMILES

Hi Folks Apologies if this is a silly question (I'm not a chemist), but could someone tell me how to consistently generate InChI/InChIKeys for a proton and protonated molecular hydrogen? Openbabel seems to assume removal of electrons rather than the addition of protons. Is there an (open

[Open Babel] List of monatomic ions for all elements...

Hi Noel I've been parsing the element.txt and isotope.txt files that is provided in the distribution of OpenBabel. This has allowed me to produce a list of InChIs and InChIKeys for all the isotopes of all the elements (at least up to element 104 - after that the InChI generation code brea

Re: [Open Babel] Openbabel python bindings on Mac OS X

On 25 Jan 2011, at 14:03, Noel O'Boyle wrote: On 25 January 2011 13:31, Ken Smith wrote: Hi Noel I didn't have this problem on 7 December on my Linux system. However, I did the necessary installations (SWIG 2 and PCRE to install SWIG) and it installed OK with the following ca

Re: [Open Babel] Openbabel python bindings on Mac OS X

wig (found version "1.3.31") > -- SWIG version is 1.3.31 > -- SWIG version 2.0.0 exactly is required > > - Noel > > On 24 January 2011 23:29, Ken Smith wrote: >> Folks >> >> I've successfully installed OpenBabel and its python bindings several

Re: [Open Babel] Python import error - openbabel 2.3.0

>> >> Make sure that your new installation is found by adding its location >> to the front of LD_LIBRARY_PATH. Typically "export >> LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH" will do the trick. >> >> - Noel >> >> On 3 December 2010 16:12, K

[Open Babel] Python import error - openbabel 2.3.0

_ZTVN9OpenBabel22OBEnergyConformerScoreE Can anyone point me to a solution that allows me to use openbabel 2.3? Cheers, Ken Ken Smith Astrophysics Research Centre Queen's University Belfast Tel: +44 28 9097 5215 Email: k.w.sm...@qub.ac.uk Skype: ken_w_smith