Re: [OpenBabel-Devel] [Open Babel] problem with conversion from smi to fs followed by similarity search

2011-10-13 Thread Noel O'Boyle
(Moving to devel mailing list) You see the lines starting with gcc-4.2 and g++-4.2. Type these in manually (copy+paste) and verify that you get the same error messages. You may have to change to a particular directory first. Then, in each line remove "-arch i386 -arch ppc" and see if they compile

[OpenBabel-Devel] [ openbabel-Bugs-3423013 ] Non-tet stereo wrongly identified as tet center

2011-10-13 Thread SourceForge . net
Bugs item #3423013, was opened at 2011-10-13 16:54 Message generated for change (Tracker Item Submitted) made by baoilleach You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3423013&group_id=40728 Please note that this message will contain a full copy of th

Re: [OpenBabel-Devel] [Open Babel] problem with conversion from smi to fs followed by similarity search

2011-10-13 Thread Noel O'Boyle
Actually, it looks like it worked. I don't see any messages about 64 bits and so forth, just warnings. With the right combination of PYTHONPATH, LD_LIBRARY_PATH (or is it DY_LDLIBRARY_PATH for mac), "import openbabel" should work. To be honest, at this point, I should really get hold of a mac and

Re: [OpenBabel-Devel] [Open Babel] problem with conversion from smi to fs followed by similarity search

2011-10-13 Thread Chris Mayne
Indeed the errors replicate without modification. Upon removing the "-arch i386 -arch ppc" flags, the same errors are generated, but only one set of them as opposed to three sets. Output is here: $ pwd /Users/cmayne/openbabel/build/openbabel/scripts $ gcc-4.2 -fno-strict-aliasing -fno-common -d

[OpenBabel-Devel] [ openbabel-Bugs-3423054 ] inconsistent fingerprint generation

2011-10-13 Thread SourceForge . net
Bugs item #3423054, was opened at 2011-10-13 13:02 Message generated for change (Tracker Item Submitted) made by cmayne You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3423054&group_id=40728 Please note that this message will contain a full copy of the co

Re: [OpenBabel-Devel] Segfault in OBForceField::MakeNewInstance()

2011-10-13 Thread David Lonie
On Wed, Oct 12, 2011 at 6:39 PM, My Th wrote: > T , 2011-10-12 17:17 -0400, David Lonie rakstīja: >> On Wed, Oct 12, 2011 at 4:53 PM, My Th wrote: >> > >> > The reason it breaks on making second instance is that you invalidate >> > plugin map pointers by deleting the instance. Those pointers are

Re: [OpenBabel-Devel] Segfault in OBForceField::MakeNewInstance()

2011-10-13 Thread My Th
C , 2011-10-13 13:53 -0400, David Lonie rakstīja: > There does seem to be a new problem that took its place. In the > attached script, I've added line 36, which will print the name of the > forcefield that was found. When I run the test script now, I get: > > Forcefield is of type: UFF > Forcefiel

Re: [OpenBabel-Devel] Segfault in OBForceField::MakeNewInstance()

2011-10-13 Thread My Th
C , 2011-10-13 23:13 +0300, My Th rakstīja: > C , 2011-10-13 13:53 -0400, David Lonie rakstīja: > > There does seem to be a new problem that took its place. In the > > attached script, I've added line 36, which will print the name of the > > forcefield that was found. When I run the test script now