Re: [OpenBabel-Devel] Many test exception on Mac OSX with -DCMAKE_BUILD_TYPE=Debug

No idea what's happening there, but you can run ctest with -V to see the process output for the failing tests. Dave On Mon, Feb 8, 2016 at 8:28 AM, David van der Spoel wrote: > Hi, > > if I compiled OB with -DCMAKE_BUILD_TYPE=Debug on my mac (OSX Mavericks, > gcc 4.9) many

Re: [OpenBabel-Devel] [Avogadro-devel] Tenure Thanks

Congrats, Geoff! It's great news that your tenure has been accepted! :-) Dave On Wed, Oct 30, 2013 at 4:10 PM, Geoffrey Hutchison geo...@pitt.edu wrote: Dear everyone, My department voted recently to recommend me for tenure here at Pitt. While this still needs approval from the Dean, it’s

[OpenBabel-Devel] shared_ptr error while compiling master

Dr. Tsafack, I've forward your error message to the openbabel development mailing list. Perhaps someone there may know what's going on with the shared pointer classes? OB devs, he is following the instructions at http://xtalopt.openmolecules.net/wiki/index.fcgi/wiki/Installation for building

Re: [OpenBabel-Devel] bug in abinitformat.cpp

(Moving this to the openbabel developers list) Can you provide a full sample file that demonstrates the issue? Thanks, Dave On Mon, Apr 29, 2013 at 2:39 PM, Cohen, Ron rco...@carnegiescience.edu wrote: It fails when the typeat goes over two lines, as in: typat 1 1 1 1 1 1

Re: [OpenBabel-Devel] bug in abinitformat.cpp

It seems to run OK. Ron On Mon, Apr 29, 2013 at 2:41 PM, David Lonie lonieda...@gmail.com wrote: (Moving this to the openbabel developers list) Can you provide a full sample file that demonstrates the issue? Thanks, Dave On Mon, Apr 29, 2013 at 2:39 PM, Cohen, Ron rco...@carnegiescience.edu

Re: [OpenBabel-Devel] bug in abinitformat.cpp

It seems to run OK. Ron On Mon, Apr 29, 2013 at 2:41 PM, David Lonie lonieda...@gmail.com wrote: (Moving this to the openbabel developers list) Can you provide a full sample file that demonstrates the issue? Thanks, Dave On Mon, Apr 29, 2013 at 2:39 PM, Cohen, Ron rco

Re: [OpenBabel-Devel] GitHub Migration

On Thu, Feb 28, 2013 at 6:16 PM, Geoffrey Hutchison geo...@pitt.edu wrote: If you'd like to access and/or write changes, you'll need to use GitHub. Hurray! What is the workflow for submitting a patch to github? Will the SVN committers have write access to openbabel/openbabel, or should we fork

Re: [OpenBabel-Devel] GitHub Migration

On Fri, Mar 1, 2013 at 2:17 AM, David van der Spoel sp...@xray.bmc.uu.sewrote: So how does one (re)gain access to git other than anonymous git clone g...@github.com:openbabel/openbabel.git I'm getting Permission denied (publickey). Someone (Geoff, I assume) will need to give you

[OpenBabel-Devel] Perceive bonds with obabel

Hi list, Is there a way to perceive bonds in a collection of atoms with obabel? I looked though the documentation, but don't see an explicit operation for this. We thought maybe converting cml -- cml might trigger bond perception, but this doesn't seem to work either. Are there any

Re: [OpenBabel-Devel] Perceive bonds with obabel

On Tue, Feb 12, 2013 at 12:00 PM, Noel O'Boyle baoille...@gmail.com wrote: Try the xyz format. That was our next guess, just wanted to make sure that I wasn't overlooking anything more straightforward. -- Free Next-Gen

[OpenBabel-Devel] Heuristic for selecting best forcefield?

Hi list, We're in the process of developing Avogadro 2, and I'm currently adding an interface to perform the obabel minimize operation on a molecule. My question: Is there a heuristic that can be used to select the best forcefield for a given molecule? As I understand it: * Ghemical is good for

Re: [OpenBabel-Devel] Heuristic for selecting best forcefield?

On Mon, Feb 4, 2013 at 11:22 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: On 2013-02-04 17:18, Geoffrey Hutchison wrote: * Are there cases where MMFF94s should be preferred to Ghemical? Everything. The heuristic should be something like MMFF94 if it works, UFF otherwise. Ghemical is

Re: [OpenBabel-Devel] Heuristic for selecting best forcefield?

I'll take a look at the sources and see if I can figure out when they'll fail, and use GAFF-MMFF94-UFF. Thanks for the feedback! Dave On Mon, Feb 4, 2013 at 1:22 PM, Geoffrey Hutchison geoff.hutchi...@gmail.com wrote: Speed? Should make no difference at all. Lennard Jones + Coulomb on

Re: [OpenBabel-Devel] Git migration?

On Tue, May 15, 2012 at 2:02 PM, Igor Filippov [Contr] filipp...@mail.nih.gov wrote: (master) $ git checkout -b myNewBranch (myNewBranch) $ emacs someSourceCode.cpp #edit (myNewBranch) $ git commit (myNewBranch) $ git checkout master (master) $ git merge myNewBranch One important

Re: [OpenBabel-Devel] Git migration?

On Mon, May 14, 2012 at 3:34 PM, My Th rei4...@gmail.com wrote: By the way, is a general migration to git still off the table? I'm OK with this, but I think we'd need a more comprehensive vote. That is two, how about others? :) Make that three ;-) A better question may be, who wants

Re: [OpenBabel-Devel] Unresolved external: etab on MSVC 2010

On Wed, May 9, 2012 at 8:57 AM, Noel O'Boyle baoille...@gmail.com wrote: On 9 May 2012 13:22, David Lonie david.lo...@kitware.com wrote: On Wed, May 9, 2012 at 7:42 AM, David Lonie david.lo...@kitware.comwrote: On Wed, May 9, 2012 at 4:42 AM, Noel O'Boyle baoille...@gmail.comwrote

Re: [OpenBabel-Devel] Unresolved external: etab on MSVC 2010

/openbabel-2.0, so OPENBABEL2_INCLUDE_DIR is C:/Program Files (x86)/openbabel/include/openbabel-2.0 OPENBABEL2_LIBRARIES is C:/Program Files (x86)/openbabel/bin/openbabel-2.lib Dave - Noel On 8 May 2012 23:18, David Lonie david.lo...@kitware.com wrote: On Tue, May 8, 2012 at 2:49 PM, Craig

Re: [OpenBabel-Devel] Unresolved external: etab on MSVC 2010

On Wed, May 9, 2012 at 7:42 AM, David Lonie david.lo...@kitware.com wrote: On Wed, May 9, 2012 at 4:42 AM, Noel O'Boyle baoille...@gmail.com wrote: In the OB docs, there's an example C++ program. Can you edit this so that it reproduces the problem? I'll give this a try. Surprisingly, I

[OpenBabel-Devel] Unresolved external: etab on MSVC 2010

Hi all, I'm setting up a new windows build environment using Windows 7 and MSVC 2010 C++ express, and my application is unable to find some of the symbols from openbabel, namely etab and obErrorLog: 2 Creating library C:/src/xtalopt/build/src/xtalopt/Release/xtalopt.lib and object

Re: [OpenBabel-Devel] Unresolved external: etab on MSVC 2010

On Tue, May 8, 2012 at 2:05 PM, Craig James cja...@emolecules.com wrote: On Tue, May 8, 2012 at 10:04 AM, David Lonie david.lo...@kitware.comwrote: Hi all, I'm setting up a new windows build environment using Windows 7 and MSVC 2010 C++ express, and my application is unable to find some

[OpenBabel-Devel] OBConformerSearch undefined references, missing vtable

I'm having an issue compiling the latest avogadro, and it looks like an issue with the new OBConformerSearch class. Can anyone reproduce? This is with a fresh checkout/build of both avogadro and openbabel. Linking CXX shared module ../../../lib/forcefieldextension.so

[OpenBabel-Devel] Forcefield optimizer tests

Hi Geoff, List, I'm working with a student to implement a BFGS minimizer for the OBForceFields. Do any utilities already exist to test these minimizers, or is there a test system that anyone can recommend? My current plan is to grab some structures from the MMFF94 test set, distort and

Re: [OpenBabel-Devel] [Avogadro-Discuss] Problem reading a .cif file (Unknown spacegroup)

Hi Jean, On Tue, Mar 27, 2012 at 2:58 PM, Jean Brefort jean.bref...@normalesup.org wrote: Can someone test attached patch? It fixes the space groups list (adding variants for groups #1 and #2, accepts unknown groups, and understand the symmetry operations from the CIF file (they changed the

Re: [OpenBabel-Devel] Turbomole Format Reader Questions

On Sun, Feb 5, 2012 at 4:28 PM, Chris Morley c.mor...@gaseq.co.uk wrote: On 05/02/2012 19:16, Ian Kirker wrote: So, I've been working on a fuller Turbomole format reader (I won't promise anything, I'm pretty new to proper C++ and it's probably going to take me a Good While to get to finishing

[OpenBabel-Devel] OBFF default line search

On Tue, Jan 3, 2012 at 11:09 PM, Geoff Hutchison ge...@geoffhutchison.net wrote: On Jan 3, 2012, at 2:45 PM, David Lonie wrote: beyond the trust radius. I didn't track down which is happening, but switching to the Newton2Num line-search method fixes the problem for me (see OBForceField

Re: [OpenBabel-Devel] OBFF default line search

On Wed, Jan 4, 2012 at 8:47 AM, Noel O'Boyle baoille...@gmail.com wrote: On 4 January 2012 12:53, David Lonie lonieda...@gmail.com wrote: On Tue, Jan 3, 2012 at 11:09 PM, Geoff Hutchison ge...@geoffhutchison.net wrote: On Jan 3, 2012, at 2:45 PM, David Lonie wrote: beyond the trust radius. I

Re: [OpenBabel-Devel] OBFF default line search

On Wed, Jan 4, 2012 at 11:04 AM, Geoffrey Hutchison ge...@geoffhutchison.net wrote: On Jan 4, 2012, at 9:19 AM, David Lonie wrote: If there is an easily parsed / imported / OBConv-ertable database of structures somewhere, it wouldn't be too difficult to come up with a test. I think

Re: [OpenBabel-Devel] OBFF default line search

On Wed, Jan 4, 2012 at 12:48 PM, Jiahao Chen jia...@mit.edu wrote: Long email ahead, but here is my implementation of BFGS and L-BFGS in Python from one of my research code, if anyone is interested in going down that route: https://gist.github.com/1561144 This is a good summary of various

Re: [OpenBabel-Devel] Question about memcpy call in OBForceField::ConjugateGradientsTakeNSteps

Hi Geoff, Thanks for moving this -- I should check autocompleted mailing list addresses more closely ;-) On Tue, Jan 3, 2012 at 11:51 AM, Geoffrey Hutchison ge...@geoffhutchison.net wrote: On Jan 3, 2012, at 11:44 AM, David Lonie wrote: which copies the data in _gradientPtr to _grad1. Trouble

Re: [OpenBabel-Devel] Question about memcpy call in OBForceField::ConjugateGradientsTakeNSteps

On Tue, Jan 3, 2012 at 12:12 PM, David Lonie lonieda...@gmail.com wrote: I'm trying to track down a bug somewhere in the forcefields that is causing this to happen: C O N J U G A T E   G R A D I E N T S STEPS = 250 STEP n     E(n)       E(n-1)    1

[OpenBabel-Devel] MolCore beginnings

On Wed, Dec 21, 2011 at 10:16 AM, Marcus D. Hanwell marcus.hanw...@kitware.com wrote: The SBIR gives us a couple of years to really engineer the components needed for cross-platform open chemistry. What we develop will be released under permissive licenses, such as the 3-clause BSD license,

[OpenBabel-Devel] Storing conformers

Hi list, I'm looking for a way to store a molecular structure and it's conformers as a string, so I figured I'd look through the support openbabel formats and try to find a standard one that supports conformers. Explicit specification of bonds is another requirement that is causing issues. A

Re: [OpenBabel-Devel] Relocatable openbabel installation / plugin path

On Tue, Nov 15, 2011 at 5:23 PM, Marcus D. Hanwell marcus.hanw...@kitware.com wrote: On Tue, Nov 15, 2011 at 5:12 PM, David Lonie lonieda...@gmail.com wrote: Hi all, I'm attempting to build a relocatable avogadro installation, and I'm having trouble with OpenBabel's plugin handling

[OpenBabel-Devel] GetIdx vs GetId vs GetIndex

Hi list, In atom.h, there are the following three functions: //! \return the internal atom index (e.g., inside an OBMol) unsigned int GetIdx() const { return((int)_idx); } unsigned int GetIndex() const { return _idx - 1; } unsigned long GetId() const { return

Re: [OpenBabel-Devel] GetIdx vs GetId vs GetIndex

On Thu, Nov 10, 2011 at 11:51 AM, Geoffrey Hutchison geo...@pitt.edu wrote: On Nov 10, 2011, at 11:47 AM, My Th wrote: The idea is to use everywhere zero-based indices in future [1], but the library is in the state of transition, so there is quite a mess with this. It's a task assigned to

Re: [OpenBabel-Devel] GetIdx vs GetId vs GetIndex

On Thu, Nov 10, 2011 at 12:13 PM, Chris Morley c.mor...@gaseq.co.uk wrote: On 10/11/2011 15:35, David Lonie wrote: The confusion caused by too much choice and the deficiencies in all of the above mean that MolCore API (the proposed re-writing of the central part of the toolkit) deserves better

[OpenBabel-Devel] Threading and OBForceField

Hi list, I'm using OBForceFields to perform quick preoptimizations in my code, and I've noticed that when I try to run multiple preoptimizations simultaneously using threads, I get random segfaults, usually in portions of OpenBabel that assign hybridizations to atoms (This happens during the call

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

On Fri, Oct 14, 2011 at 12:04 PM, My Th rei4...@gmail.com wrote: Here is a patch for plugin constructors. It is a bit big because I decompacted the macros to make them readable, but there is really only one change - an if statement which checks if the ID is already in the Map() and only if not

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

On Wed, Oct 12, 2011 at 6:39 PM, My Th rei4...@gmail.com wrote: T , 2011-10-12 17:17 -0400, David Lonie rakstīja: On Wed, Oct 12, 2011 at 4:53 PM, My Th rei4...@gmail.com wrote: The reason it breaks on making second instance is that you invalidate plugin map pointers by deleting

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

Hi list, I've written a routine that makes a copy of the UFF forcefield with MakeNewInstance() and caches it in a member variable of the my class. The function's definition is: bool MyClass::setupForcefield() { QMutexLocker locker (this-m_ffMutex); // already setup! if (m_ff !=

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

On Wed, Oct 12, 2011 at 3:25 PM, David Lonie lonieda...@gmail.com wrote: Hi list, I've written a routine that makes a copy of the UFF forcefield with MakeNewInstance() and caches it in a member variable of the my class. snip This works perfectly the first time it is used -- the forcefield

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

On Wed, Oct 12, 2011 at 4:53 PM, My Th rei4...@gmail.com wrote: T , 2011-10-12 15:42 -0400, David Lonie rakstīja: On Wed, Oct 12, 2011 at 3:25 PM, David Lonie lonieda...@gmail.com wrote: Hi list, I've written a routine that makes a copy of the UFF forcefield with MakeNewInstance

Re: [OpenBabel-Devel] OBUnitCell not compiling in SWIG bindings

On Wed, Oct 5, 2011 at 4:37 PM, Chris Morley c.mor...@gaseq.co.uk wrote: The recent changes in OBUnitCell constantness mean that the SWIG bindings do not compile in Visual C++ 9: 1..\..\..\scripts\java\openbabel-java.cpp(2945) : error C2668: 'OpenBabel::OBUnitCell::WrapFractionalCoordinate' :

Re: [OpenBabel-Devel] Building static library on MSVC 2008

On Tue, Aug 23, 2011 at 8:26 PM, David Lonie lonieda...@gmail.com wrote: Hi list, I'm trying to build openbabel-2.lib using trunk with MSVC 2008. Leaving BUILD_SHARED on produces openbabel-2.dll without any problem, but I need the static .lib for avogadro to link against. I found a bit more

Re: [OpenBabel-Devel] [Avogadro-Discuss] double bonds in avogadro

Hi Peter, On Wed, Jul 6, 2011 at 7:35 PM, Peter Schellenberg peter.schellenb...@fisica.uminho.pt wrote: I wonder how Avogadro recognizes double bonds. The concrete problem is as follows: I loaded  gaussian log files (results from DFT geometry opt.) of  molecules with conjugated bonds into

[OpenBabel-Devel] ForceFields

Hi OpenBabel'ers, Avogadro'ers, On Fri, Nov 5, 2010 at 12:09 PM, David Lonie lonieda...@gmail.com wrote: On Thu, Nov 4, 2010 at 1:52 PM, Louis Ricard louis.ric...@polytechnique.edu wrote: Hi all. I started testing the Windows installer shortly after David's message. I was puzzled by absence

Re: [OpenBabel-Devel] Segfault when deleting OBForceField

On Wed, Oct 13, 2010 at 11:47 AM, Geoffrey Hutchison ge...@geoffhutchison.net wrote: I'm getting a segfault on MSVC when I delete a pointer to an OBForceField (or indeed an OBOp). But this should work okay right? No. These are static unique objects. We don't delete formats or other plugins

[OpenBabel-Devel] Fwd: FAILED (u=1): Open Babel - Ubuntu 9.04, GCC 4.4.1, 64bit - Continuous

Hi Tim, I just received this message after pushing a change to trunk. I can't figure out what would be conflicting -- I made a change to a single format file, and it seems to be complaining about CMakeList.txt? Dave -- Forwarded message -- From: CDash ad...@www.cdash.org Date:

Re: [OpenBabel-Devel] Trunk doesn't compile

On Tue, Aug 24, 2010 at 1:51 PM, Noel O'Boyle baoille...@gmail.com wrote: On 24 August 2010 18:22, David Lonie lonieda...@gmail.com wrote: On Tue, Aug 24, 2010 at 1:20 PM, Geoffrey Hutchison ge...@geoffhutchison.net wrote: This has happened a few times recently -- Is Eigen now an official

Re: [OpenBabel-Devel] OBRandom

On Wed, Aug 11, 2010 at 11:34 PM, Geoffrey Hutchison ge...@geoffhutchison.net wrote: I've always wondered why OBRandom exists -- I would assume that the built in standard random number generators would be decent on each platform? No, that's not true. In fact, the BSD and Mac man pages for

Re: [OpenBabel-Devel] Definition of OBMol::_energy

On Wed, Aug 11, 2010 at 7:26 AM, Chris Morley c.mor...@gaseq.co.uk wrote: Although it has been touched on previously in the mailing lists, I think we need to clarify what OBMol::_energy contains. It is accessed in OBMol::SetEnergy(double) and by OBMol::GetEnergy(). Note that

Re: [OpenBabel-Devel] Quick Reference Documentation

On Fri, Jul 30, 2010 at 7:49 PM, Tim Vandermeersch tim.vandermeer...@gmail.com wrote: On Sat, Jul 31, 2010 at 1:40 AM, David Lonie lonieda...@gmail.com wrote: On Fri, Jul 30, 2010 at 1:06 PM, Geoffrey Hutchison geo...@pitt.edu wrote: Hans De Winter and Silicos whipped up a 2-page quick

Re: [OpenBabel-Devel] OBUnitCell rewrite

On Wed, Mar 3, 2010 at 4:33 AM, Vincent Favre-Nicolin vinc...@users.sourceforge.net wrote: See the attached POSCAR and POTCAR. When opened in Avogadro, the cell is displayed as shown in the screenshot. The atoms are given in fractional coordinates -- there should not be any outside the cell! At

Re: [OpenBabel-Devel] OBUnitCell rewrite -- changed behavior

On Wed, Mar 3, 2010 at 2:04 PM, Geoffrey Hutchison ge...@geoffhutchison.net wrote: Note that this could potentially break programs that use GetOrthoMatrix and GetFractionalMatrix to convert between cartesian and fractional coordinates, since the ortho and fractional matrices may be rotated

Re: [OpenBabel-Devel] OBUnitCell rewrite

On Tue, Mar 2, 2010 at 4:16 PM, Geoffrey Hutchison ge...@geoffhutchison.net wrote: Is there some method to this that I'm missing? Would anyone object to the change I propose? The main requirement is that you don't remove API. Otherwise, I think we'd all be happy to see improvements. Ok -- I

[OpenBabel-Devel] Writing new format readers for OpenBabel

Hi Jonas, On Mon, Mar 1, 2010 at 2:03 PM, Jonas Baltrusaitis jasiu...@yahoo.com wrote: I was going to try ORCA and CRYSTAL input/output implementation in OB. What's your approach when you take new format? How do you begin? What do you look for and how do you proceed? How do you test it

Re: [OpenBabel-Devel] Energy units

On Mon, Mar 1, 2010 at 5:00 PM, David Osguthorpe david.osgutho...@gmail.com wrote: On Mon, Mar 01, 2010 at 01:33:06PM -0800, Jonas Baltrusaitis wrote: I second Konstantin. Typical calculations yields values of, say, -1000.00 Hartrees, in kcal it would be x627.5 which would be

Re: [OpenBabel-Devel] Crash in Kekulize

I forgot to reply to all... On Thu, Jan 14, 2010 at 4:18 PM, Geoffrey Hutchison ge...@geoffhutchison.net wrote: The attached gamout file crashes when OB tries to read it. What version of OB are you using? Trunk? Yes, though I seem to remember this happening with 2.2.x also. Dave

Re: [OpenBabel-Devel] Electronic Transitions in OB trunk

Hi Geoff, On Mon, Nov 30, 2009 at 5:51 PM, Geoffrey Hutchison ge...@geoffhutchison.net wrote: I was taking some time to review new classes in the trunk and I wanted to ask about the electronic transition data (i.e., for UV/Vis spectra or computed excitation energies). Is there are reason you

[OpenBabel-Devel] Thread safety

Hi list, I've been using OB in a multithreaded environment for a while, and a common headache comes from the abundance of singleton classes in OB, namely for error handling/logging. If two concurrent threads call two OB functions and the logging functions are accessed at the same time, the