P , 2012-08-27 23:22 +0200, Tim Vandermeersch rakstīja:
> Hi,
>
> I have commented out the code that caused the compile problems.
> However, I have no idea why the OBMinimizingEnergyConformerScore and
> OBMinimizingRMSDConformerScore classes Geoff added were removed. Also
> I added virtual destruc
Hi, Benoit Leblanc!
Your commit at r4990 deletes OBMinimizingEnergyConformerScore and
OBMinimizingRMSDConformerScore classes and it breaks build. Also, why
are you deleting virtual destructors introduced in r4832?
>From src/ops/conformer.cpp:159:
OBConformerSearch cs;
if (score == "en
T , 2012-06-13 12:38 -0400, Geoffrey Hutchison rakstīja:
> > Should C go directly into the 2.3.x branch or both in trunk and you'll
> > cherry-pick as necessary?
>
> I'd prefer changes go into trunk and I'll cherry-pick for the stable branch.
>
> Thanks,
> -Geoff
Done. r4873 and r4874 is for C a
O , 2012-06-12 23:56 -0400, Geoff Hutchison rakstīja:
> On Jun 12, 2012, at 11:11 AM, My Th wrote:
>
> > E is only marginally more intrusive than C, if there is no problem with
> > it I'm committing only this one, otherwise I can also commit the minimal
> > version
C , 2012-06-07 23:45 +0300, My Th rakstīja:
> C , 2012-06-07 12:02 -0400, Geoffrey Hutchison rakstīja:
> > > +size_t idx1 = mol->GetBond(bond_idx)->GetBeginAtom()->GetIdx();
> > > +size_t idx2 = mol->GetBond(bond_idx)->GetEndAtom()->GetIdx();
>
S , 2012-06-09 14:59 +0100, Noel O'Boyle rakstīja:
> Hi Reinis,
>
> Your r4832 ("conformersearch.h: Fix -Wdelete-non-virtual-dtor") is
> causing a warning when compiling the bindings with MSVC.
>
> 1>C:\Tools\openbabel\trunk\include\openbabel/conformersearch.h(65) :
> warning C4273: 'OpenBabel::O
C , 2012-06-07 11:04 -0700, Craig James rakstīja:
> On Thu, Jun 7, 2012 at 8:29 AM, My Th wrote:
> Now I got to the real culprits of this issue - previousState and
> previousBondState. They are vectors of integers holding the state of
> each atom and bond in mol
C , 2012-06-07 12:02 -0400, Geoffrey Hutchison rakstīja:
> > +size_t idx1 = mol->GetBond(bond_idx)->GetBeginAtom()->GetIdx();
> > +size_t idx2 = mol->GetBond(bond_idx)->GetEndAtom()->GetIdx();
> >
> > Still crashed for default max stack size. I'm not sure if this kind of
> > optimization i
Hi!
I was looking at bug #3508648 and it turns out that it segfaults in
expandKekulize() due to stack overflow. The routine in question uses
recursive algorithm to assign bond orders for aromatic systems. For
large molecules (1bxr has almost 50k atoms) it means that the stack can
grow quite a bit
Hi!
According to wiki [1], dev-api [2] should be updated nightly, but
looking at those pages it says "Generated on Tue Feb 28 2012 07:00:06".
Looks like automatic api doc generation is out of order. Doc build log
[3] is full of errors.
Reinis
[1] http://openbabel.org/wiki/Developer:API
[2] http
P , 2012-06-04 09:35 +0100, Chris Morley rakstīja:
> On 03/06/2012 17:58, Geoff Hutchison wrote:
> >> Right, it came in C++ from C and should be in most compilers now. I also
> >> think that this is the best option. I'll write a patch for it. Only I'm
> >> reading that inttypes.h is not available f
S , 2012-06-02 21:57 -0400, Geoff Hutchison rakstīja:
> I had some time to check SVN blame:
> http://openbabel.svn.sf.net/viewvc/openbabel/openbabel/trunk/include/openbabel/bitvec.h?annotate=4853
>
> So this is from Kevin Shepherd, which makes sense because he made some
> cleanups elsewhere in th
T , 2012-05-30 22:27 -0400, Geoff Hutchison rakstīja:
> > The one I am not quite certain about what it does is obspectrophore - it
> > seems to have no manpage, the -help output is not very helpful and a
> > wiki page on http://openbabel.org/wiki/Guides (Command-Line Programs)
> > does not exist, e
T , 2012-05-30 18:51 +0300, My Th rakstīja:
> T , 2012-05-30 16:38 +0100, Noel O'Boyle rakstīja:
> > On 30 May 2012 16:10, Craig James wrote:
> > >
> > >
> > > On Wed, May 30, 2012 at 7:59 AM, Noel O'Boyle
> > > wrote:
> > >>
&
T , 2012-05-30 16:38 +0100, Noel O'Boyle rakstīja:
> On 30 May 2012 16:10, Craig James wrote:
> >
> >
> > On Wed, May 30, 2012 at 7:59 AM, Noel O'Boyle wrote:
> >>
> >> I've just confirmed what Craig was seeing. I have CMake 2.8.5.
> >>
> >> I always install locally but once I added the installed
T , 2012-05-30 09:41 -0400, Geoff Hutchison rakstīja:
> I asked about cmake because newer versions should set env variables correctly
> to use the build dir.
>
> Geoff
I'm using cmake 2.8.8, and I have to set paths for make test, otherwise
tautomer test segfaults as I mentioned before. I'm not s
T , 2012-05-30 09:26 +0100, Noel O'Boyle rakstīja:
> On 30 May 2012 00:06, Craig James wrote:
> > On Tue, May 29, 2012 at 2:42 PM, My Th wrote:
> >>
> >> O , 2012-05-29 14:29 -0700, Craig James rakstīja:
> >> > I've confirmed absolutely on Ub
O , 2012-05-29 14:29 -0700, Craig James rakstīja:
> I've confirmed absolutely on Ubuntu: Testing in the build directory
> works. Testing with an installed OpenBabel system doesn't.
>
> I started with a completely clean computer ... it didn't even have a g
> ++ compiler, cmake, or anything else (d
O , 2012-05-29 13:48 -0700, Craig James rakstīja:
> On Tue, May 29, 2012 at 11:42 AM, My Th wrote:
> > I don't know why my results are different than the build
> platform, but
> > I'm virtually certain that the test failures are not due to
>
O , 2012-05-29 10:39 -0700, Craig James rakstīja:
> On Tue, May 29, 2012 at 9:52 AM, My Th wrote:
> O , 2012-05-29 09:24 -0700, Craig James rakstīja:
> > On Mon, May 28, 2012 at 3:08 AM, Noel O'Boyle
> wrote:
> >
> > > &g
O , 2012-05-29 09:24 -0700, Craig James rakstīja:
> On Mon, May 28, 2012 at 3:08 AM, Noel O'Boyle wrote:
>
> > > Now I've checked the tautomer tests, and it also fails with the "stock"
> > > r4758, i.e. before I changed smilesformat.cpp.
> > >
> > >$ bin/test_tautomer
> > >
> > >/home/cja
Hi!
Doing my round of cleaning compiler warnings I came across
USE_64BIT_INTEGER in bitvec.h. I couldn't find any other place it is
used and there was an issue when it is actually enabled, I submitted a
patch for it in PR#3530071.
The thing is that USE_64BIT_INTEGER has to be defined for systems
P , 2012-05-14 22:34 +0300, My Th rakstīja:
> P , 2012-05-14 15:02 -0400, Geoffrey Hutchison rakstīja:
> >
> > > I've started to clean up compiler warnings (cleaning up as fast as they
> > > are committed ;) and would like to move on from there at some point. In
C , 2012-05-24 22:53 -0400, Geoff Hutchison rakstīja:
> > Would it make sense to coordinate a switch with an OpenBabel release?
> I'm not advocating yes or no, just curious.
>
> Doesn't make much difference either way, but it's probably better not
> to impede any pending bug-fix releases. Seems
Hi!
Is the conclusion reached on this issue? And what would be the next
steps to take, if any.
SVN history import into Git is pretty straightforward if dealing just
with one branch (there are already some old and outdated imports in
Github), but for more complicated history probably more careful
O , 2012-05-15 14:20 -0400, David Lonie rakstīja:
> 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) $ g
O , 2012-05-15 14:02 -0400, Igor Filippov [Contr] rakstīja:
> >
> >
> > (master) $ git checkout -b myNewBranch
> > (myNewBranch) $ emacs someSourceCode.cpp #edit
> > (myNewBranch) $ git commit
> > (myNewBranch) $ git checkout master
> > (master) $ git merge myNewBranch
> >
>
> One important det
P , 2012-05-14 16:09 -0400, Igor Filippov [Contr] rakstīja:
> Has any of this been a problem for OpenBabel?
If it makes life harder for developers, if it offputs new contributors,
then yes it is a problem for OpenBabel. And from my perspective it has
been.
Reinis
--
P , 2012-05-14 15:48 -0400, Igor Filippov [Contr] rakstīja:
> I vote for keeping svn.
> What problem is going to be solved by moving to git?
To name few:
- Easier managing of branches and patches
- Better history record
- Pull requests (e.g. on GitHub)
- Easier distributed development
- Less space
P , 2012-05-14 15:02 -0400, Geoffrey Hutchison rakstīja:
> > My guess is that all API breaking changes are still not allowed in trunk
> > (ABI breaks would be allowed for 2.4, but API breaks only for 3.0).
>
> Right.
>
> As for the "experimental" branch, it's essentially dead. I'd probably
> keep
Hi!
I've seen that people started to break ABI in trunk so it is probably
going for the 2.4 release. In connection to that I have a question about
the v3.0 project [1] and experimental branch [2].
Experimental branch has not seen any activity in a very long time, so is
it still pursued? Or should
Hi!
Some time ago I posted patches silencing a bunch of compiler warnings
(patch #3424383), but there have been no response on them.
Now I have rebased them on top of the current trunk and attached to the
same tracker issue.
So is there an interest to fix all those warnings?
Reinis
-
Hi!
londinium.kitware has similar configuration as my computer and I'm
getting the segfault in tautomer test only if the environment variables
are not set properly and it tries to load plugins from system install of
OB 2.3.1. Could it be that on that computer there are multiple versions
of OB and
2011/12/22 Geoffrey Hutchison :
>
> On Dec 21, 2011, at 2:52 PM, My Th wrote:
>
>> My point also was not about version numbering, but rather the project v3
>> which has been documented in OB wiki with its goals. I would like to see
>> them reached.
>
> I think
T , 2011-12-21 14:04 -0500, Geoffrey Hutchison rakstīja:
> > IMHO, OBv3 goals have been set some time ago and many of them are completed
> > now, so its completion
> > should be pursued first since its easier and faster to work with the
> > existing code, especially when most of the functionality
T , 2011-12-21 01:00 -0500, Geoffrey Hutchison rakstīja:
> This e-mail has been long delayed. As 2011 draws to a close, Open Babel
> is over 10 years old! At this point, it's used by over 40 open source
> projects, downloaded over 200,000 times, and been used in over 400
> academic papers. And of c
2011/12/7 Noel O'Boyle :
> I'm afraid, it's not possible to ask disutils the location of the
> site-packages folder (believe me, I have tried, googled, everything).
> As a result, we have no choice. In any case, this simplifies
> everything and I wouldn't change it back now. The user just needs to
Hi!
Please teach CMake to install bindings in standard locations as
distutils is doing. That should help distributions also.
Reinis
--
Cloud Services Checklist: Pricing and Packaging Optimization
This white paper is int
C , 2011-11-10 17:35 -0500, Igor Filippov [Contr] rakstīja:
> > Or they could participate in the prerelease testing which now is
> > done by devs only, AFAIK.
>
> I was participating in building/testing from svn before one of the
> releases in the past, spent quite a bit of time and effort only to
C , 2011-11-10 17:04 -0500, Igor Filippov [Contr] rakstīja:
> > Solving the problems with static builds and MinGW, which I suspect
> are
> > are of interest to a minority of users, really needs input from a
> > developer who is using these features. Do you know of anyone willing
> to
> > help?
>
C , 2011-11-10 21:38 +, Chris Morley rakstīja:
> On 10/11/2011 18:20, My Th wrote:
> > Hi!
> >
> > These plugins are not wrapped for static compilation:
> > ABINITFormat
> > CacaoInternalFormat
> > CanSmilesNS
> > CASTEPFormat
> > EEMCharg
Hi!
These plugins are not wrapped for static compilation:
ABINITFormat
CacaoInternalFormat
CanSmilesNS
CASTEPFormat
EEMCharges
FPCount
GROFormat
InChICompareFormat
InChIKeyFormat
L5
MyFpType
NoCharges
OpAddFileName
OpGenAlias
OpLargest
OpNewV
OpSmallest
SecondOpAlign
Tautomers
XSFFormat
XXXFormat
C , 2011-11-10 10:35 -0500, David Lonie rakstīja:
> On Thu, Nov 10, 2011 at 10:32 AM, David Lonie wrote:
> > The reason I ask is that I'm trying to limit an OBFF calculation with
> > OBForceField::AddInt[er,ra]Group[s], which takes the atom index, but
> > it's not clear to me whether this means th
O , 2011-10-18 15:57 -0700, Craig A. James rakstīja:
> On 10/18/11 3:30 PM, My Th wrote:
> > O , 2011-10-18 22:40 +0100, Chris Morley rakstīja:
> >> On 18/10/2011 20:18, My Th wrote:
> >>> Hi!
> >>>
> >>> I have problems with your version of
O , 2011-10-18 22:40 +0100, Chris Morley rakstīja:
> On 18/10/2011 20:18, My Th wrote:
> > Hi!
> >
> > I have problems with your version of the patch. I'm using Gentoo Linux
> > with gcc 4.6.1.
> >
> > Running the test program I get this:
> > Try f
O , 2011-10-18 17:54 +0100, Chris Morley rakstīja:
> On 12/10/2011 00:15, My Th wrote:
> > Sv, 2011-10-09 23:48 +0300, My Th rakstīja:
> >> S , 2011-10-08 21:13 +0100, Chris Morley rakstīja:
> >>> On 08/10/2011 20:02, My Th wrote:
> >>>> It might be t
Pk, 2011-10-14 20:45 +0100, Chris Morley rakstīja:
> On 13/10/2011 22:04, My Th wrote:
> >
> > Other solution would be to change the constructor so that pointers in
> > plugin map are not overwritten if the instance with the same ID already
> > exists.
First task would
Pk, 2011-10-14 00:04 +0300, My Th rakstīja:
> 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,
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.
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
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 set by
> > the cons
T , 2011-10-12 15:42 -0400, David Lonie rakstīja:
> On Wed, Oct 12, 2011 at 3:25 PM, David Lonie 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.
> >
> > This works perfectly t
Sv, 2011-10-09 23:48 +0300, My Th rakstīja:
> S , 2011-10-08 21:13 +0100, Chris Morley rakstīja:
> > On 08/10/2011 20:02, My Th wrote:
> > > It might be that the changes could be implemented in other place which
> > > would shrink the patch size, but I don't know t
S , 2011-10-08 21:13 +0100, Chris Morley rakstīja:
> On 08/10/2011 20:02, My Th wrote:
> > It might be that the changes could be implemented in other place which
> > would shrink the patch size, but I don't know the OB code that well, so
> > I went for the most straightfo
S , 2011-10-08 21:13 +0100, Chris Morley rakstīja:
> On 08/10/2011 20:02, My Th wrote:
> > I have no idea how Windows dll loading works, but the code I touched
> > should be above the platform specific bits. I used the same semantics as
> > the old code had, only moved it to
S , 2011-10-08 14:26 -0400, Geoff Hutchison rakstīja:
> > As far as I know it should not break binary compatibility, but I
> might > be wrong. > > I hope this change gets in eventually in one form
> or another.
>
> The change is a good one and it will eventually go in -- I'd be OK to
> apply it to
S , 2011-10-08 17:45 +0100, Chris Morley rakstīja:
> On 08/10/2011 17:07, My Th wrote:
> > Hi!
> >
> > I have posted a patch (3411037) in tracker for plugin loading which
> > moves the plugin loading away from OBConversion constructor and loads
> > them instead on
Hi!
I have posted a patch (3411037) in tracker for plugin loading which
moves the plugin loading away from OBConversion constructor and loads
them instead on first access. I would like to get some feedback on it.
The use case for this is when the molecule is constructed in a program
without the u
Thanks for the comments!
> > 1) Patch #3311952 adding GRO format
> > http://sourceforge.net/tracker/?func=detail&aid=3311952&group_id=40728&atid=428742
>
> Great. Can we have an example file or two?
I uploaded two example files. One is a short trajectory file, the second
is a molecule in periodi
Hi!
There are still some patches in tracker I submitted which haven't been
accepted nor rejected. There are two issues I'm concerned with:
1) Patch #3311952 adding GRO format
http://sourceforge.net/tracker/?func=detail&aid=3311952&group_id=40728&atid=428742
2) Patches #3196280 and #3202124 deali
Hi!
In fact this test produces inconsistent results.. if I run it multiple
times, some of them it will pass, sometimes fail:
AssertionError: u'I[CH][C]1CN1' != 'I/C=C\\1/CN1'
or
AssertionError: u'I/C=C\\1/CN1' != 'I/C=C/1\\CN1'
Reinis
O , 2011-08-30 16:15 +0100, Noel O'Boyle rakstīja:
> Hi Geof
Hi!
I posted patch #3311952 which adds Gromacs GRO file support to
OpenBabel. That patch contains groformat.cpp and adds it to
CMakeLists.txt.
Here I attach just the groformat.cpp file for the interested. Any
comments and suggestions for improvements are welcome.
Regards,
Reinis Danne
/
; This bug is now fixed in r4494. Thanks for reporting.
>
> Your patch relies on implementation details of the iterators which may
> change in future, so instead created a temporary vector in the first
> loop, and then deleted the atoms in the vector.
>
> - Noel
>
> On 2
>
> - Noel
>
> On 27 May 2011 12:14, My Th wrote:
> > Hi!
> >
> > A while ago I posted these patches in the tracker:
> > https://sourceforge.net/tracker/?func=detail&aid=3196280&group_id=40728&atid=428742
> > https://sourceforge.net/tracker/?fu
Hi!
A while ago I posted these patches in the tracker:
https://sourceforge.net/tracker/?func=detail&aid=3196280&group_id=40728&atid=428742
https://sourceforge.net/tracker/?func=detail&aid=3196285&group_id=40728&atid=428742
The first one fixes indexing in obutil.cpp::InternalToCartesian(), the
sec
Yes, *.gro files are not supported by OB, but there is nothing specific
to CG in that format.
But OB do support *.xtc file format (read-only), which is "a compressed
version of the trajectory, containing only coordinate, time, and box
vector information". But I didn't find any other documentation
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