On Sep 27, 2009, at 12:54 PM, Noel O'Boyle wrote:
> The good news is that the GUI popped up and looked pretty much like it
> should. The bad news is that it was completely unresponsive, and the
> only buttons that worked were the Mac traffic lights.
Weird. There should be wxWidgets included on e
> and this information is correct from 3131 onwards. That is, there is
> one patch to be reviewed (r3338) - everything else has already been
> merged or blocked. r3338 deals with kekulize.cpp - I didn't want to
> interfere with Craig's work here.
This was a patch from Craig. So it's safe to say th
> don't really understand how the rotorKeys work. I would appreciate if
> someone familiar with this code could doublecheck that this makes
> sense or whether the fix should be in RotorKeys instead.
Your fix is correct.
Rotor keys are a short way to handle the rotamer search. Let's say you
want
> Anyone knows how to get the fragments (not the bit
> fingerprints) before the fingerprint hashing?
I do not know of a direct way in the code, although the fingerprints
are simply a set of SMARTS patterns. You could parse the file and then
match the SMARTS against your molecules.
>
> When a test fails (e.g. file formats not available), it still
> continues and can easily segfault. Is it possible to make OB_ASSERT
I think we'd want something like OB_FATAL for that case.
-Geoff
--
Come build with us!
On Oct 6, 2009, at 12:01 PM, Noel O'Boyle wrote:
> I'm trying to profile an optimization using MMFF94 (obminimize) using
> OB22x and gprof as follows:
My suggestion would be to either:
1) Use something like Valgrind/Callgrind
2) Use a sampling program like Apple's "Shark"
If you're willing to
On Oct 6, 2009, at 12:41 PM, Craig A. James wrote:
> I'll second Geoff's recommendation of valgrind. It works on
> unmodified code, and runs it in a virtual machine that measures
> EVERY instruction that's executed. No sampling, it's the real deal.
I tend to use both Shark and Valgrind sep
On Oct 6, 2009, at 1:06 PM, Noel O'Boyle wrote:
> I was just going to check for any low hanging fruit, but it sounds
> like you've already been through this.
I think the next "low-hanging fruit" for the force fields would be to
switch to Eigen, which will give much better matrix performance
On Oct 9, 2009, at 5:19 PM, TJ O'Donnell wrote:
> I am NOT using cmake. Is that required? I took the wiki section
> about
> building OB using cmake to be for those who do use cmake.
> I am using the ./configure & make method.
I think the "resident expert" in MinGW is Igor Filippov. Here's wha
> The FindChiralCenters() function has been disabled in mol.h and
> chiral.cpp.
I think you mean in trunk, correct?
Tim has been working on updated stereochemistry routines, so the old
code is currently disabled.
-Geoff
---
> I'm trying to take a 2D molfile and use OpenBabel to prepare a
> Cartesian mop file suitable to send to MOPAC for geometrical
> optimization.
...
> Currently things seem to go wrong at stage 2.
Here's my first suggestion. "Promote" the 2D molfile to 3D:
>if (mol.GetDimension() <
> I'm trying to take a 2D molfile and use OpenBabel to prepare a
> Cartesian mop file suitable to send to MOPAC for geometrical
> optimization.
...
> Currently things seem to go wrong at stage 2.
OK, forget my last message. I just looked at the "Gen3D" code. It's
attempting to correct the pH of
a
seminar in the morning.
Thanks,
-Geoff
---
Prof. Geoffrey Hutchison
Assistant Professor, Department of Chemistry
University of Pittsburgh
http://hutchison.chem.pitt.edu/
Office: (412) 648-0492
--
Come build with us! T
On Oct 19, 2009, at 10:20 AM, Noel O'Boyle wrote:
> This could have been found with cppcheck along with a few others:
Some of these are false positives. I've used cppcheck before and it
flagged a lot. Still, it's good to go through the output periodically.
Cheers,
-Geoff
On Oct 22, 2009, at 6:10 AM, Noel O'Boyle wrote:
> I've repeated the whole procedure with the intel compiler, and there's
> no problem. So it looks like something that's gcc specific (gcc
> 4.1.2).
First, does babel itself work?
Second, are you sure everything compiled as 64-bit? Remember that
> I'm baffled by the following, and can only assume I have some
> misunderstanding of how atom Idx's are stored.
Tim started the move towards 0-based indexing for GetAtomById(). So
right now in trunk, there are two non-identical ways to access an
atom. Beware.
>int start_idx = ring->_pa
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On Oct 23, 2009, at 11:03 AM, Craig A. James wrote:
> I've now got a new version of expand_kekulize() in kekule.cpp, it
> solves a fullerene correctly in a few milliseconds. There's still a
> lot of work to do on the details, and once I have the performance
> right, we need to correct some
> 1. The "D" or "degree" in SMARTS
>
> [#6D2] is supposed to mean a a carbon atom with two bonds. However,
> it treats explicit hydrogens as a bond,
Well, that can be changed. You're the former Daylight guy -- is "D"
supposed to ignore explicit hydrogens?
> For OpenBabel 3, we should clarify
On Oct 29, 2009, at 2:40 PM, Craig A. James wrote:
> This is a good topic for OpenBabel 3. There really is no such thing
> as an "aromatic atom". Aromaticity is only a property of bonds and
> ring systems. It might make sense to eliminate the "atom-is-
> aromatic" property altogether.
Th
> I think Raman and IR intensities should be stored in different
> vectors.
If that's true, you don't need a "hasRaman" variable -- the Raman
vector would either be empty or not.
Cheers,
-Geoff
--
Come build with us!
I know a few people have asked me privately about "when is the next release"
and "do we have to wait for OB-3.0"?
So a few suggestions open to discussion
- The current trunk should become OB version 2.3, likely releasing in early
spring 2010. It will offer 2D layout, improved stereochemistry, et
> the application crashes. Would it be possible to move the error
> handling out of a singleton class, or add a mutex to ensure that these
> are not accessed simultaneously?
I'm definitely open to lightweight mutex code. The error handling code could
probably also use a ring buffer to keep the li
Sorry, I had forgotten about the new atom IDs. Yes, they are worth preserving.
> Wouldn't source compatibility, with external programs needing to be
> re-compiled and linked but not re-written, be a more practical goal,
This is *always* a goal for 2.x releases. And yes, minor bug fix releases d
> I need certain things fixed, and I have to do it now, using OpenBabel 2. I
> need a pragmatic, short-term solution. The questions I'm asking are:
> - Whether there's any interest by others in the work I'll be doing
> - Whether the current aromaticity detection in OpenBabel is bad
>scienc
> Any idea of the 2.3 schedule yet?
Considering I haven't switched to using trunk on a daily basis, I'd estimate we
need 2-3 months of stabilization, testing, documentation, and bug-fixing before
release. That puts us in February.
I'll certainly make more regular snapshot releases before that p
> The current situation is that the builder could be sitting there with
> a SMARTS of length 7 atoms which matches the molecule. Does it accept
> it or not?
So you're saying that the builder operates on the SSSR? What you describe
certainly makes sense.
One downside is that you can't have fragm
> that an exact match for 6+3 will be found first if it exists, then a 7
> membered-ring will match (which should be ignored), and then a 6
> membered ring will match. (Or do I misunderstand?)
No, you've got it. I'm just saying that the code which checks the sizes of the
fragments will need to ke
Chris,
First off, this is great. Thanks to both you and Tim. (I hear he's been working
on a 2D editor using Open Babel.)
> In this code OBDepict draws the molecule and an abstract class
> OBPainter does the rendering. There are three derived classes, all of
> which use an external library for
> http://www.chemaxon.com/marvin/examples/applets/sketch/rightName.abbrevgroup
> There is also superatom.txt file which comes with OSRA of course :)
I think Chris already borrowed superatom.txt. :-)
Thanks for the pointer to the Marvin list. I think I can probably adapt the
ChemDraw list based o
On Nov 23, 2009, at 1:48 PM, Igor Filippov wrote:
> http://www.chemaxon.com/marvin/examples/applets/sketch/rightName.abbrevgroup
> There is also superatom.txt file which comes with OSRA of course :)
Do you know if ChemAxon is willing to make this public domain or BSD-licensed?
Chris is right --
On Nov 25, 2009, at 12:36 PM, Chris Morley wrote:
> I think OB can handle quadruple bonds, in as much as you can set a
> bond order to 4. Bond order 5 is used for aromatic bonds. (MDL mol
> files use 4 for aromatic).
I think for MolCore/OB3, we have to remove this "aromatic bond is 5" idea. It
> The trunk code is compiled on at least two compilers, on several
> operating systems, built using two or more build systems, sometimes in
> a variety of configurations.
I think there are a few easy fixes -- mainly to get some nightly build testing
running again. I'm sure most of us remember w
Hi David,
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 called the oscillator strengths
"forces", rather than "intensities"?
Also, I think th
On Dec 1, 2009, at 4:19 PM, Gerd Menche wrote:
> I'm not sure, if the vdw calculation in forcefieldghemical is correct.
Tim's the one who implemented the Ghemical force field, but I know he worked
directly from the GPL'ed Ghemical code.
I *can* vouch that our implementation exactly matches the
> I made up a little tool showing the
> difference between ghemical vdw values
> and those calculated by hand.
So, I'm assuming that you'd rather us match the correct formula than the
Ghemical implementation. That's fine with me, as long as we update our
analytical gradients too.
If you send me
> Now, it's filtered from the search list with "strict search" but not
> "moderate".
That's truly weird. We should do a careful search through the wiki to look for
spam links. That's the only thing I can imagine.
-Geoff
> So I thought about changing the fragment to be composed of C atoms and
> using that to derive the canonical representation.
The problem is that if you change the fragment to C atoms, you have lots of
un-filled valence. Consider, changing the "N" in pyrrole (or S in thiophene) to
carbon. It's n
On Dec 14, 2009, at 3:59 PM, Andrew Dalke wrote:
> On Dec 14, 2009, at 9:28 PM, Geoffrey Hutchison wrote:
>> Craig, do you have another solution? Is there a wild-card or dummy atom for
>> the canonical SMILES?
>
> I haven't been tracking this, so just a reflex actio
>> I could not test this new feature, because my version of Open Babel is
>> buggy (it doesn't recognize ChemDraw documents anymore, alas!). I hope
>> they'll fix this soon. I have used a trial version of ChemDraw for my
I wasn't aware of this. It's been ages since I talked to him, can you forward
> The attached gamout file crashes when OB tries to read it.
What version of OB are you using? Trunk?
Thanks,
-Geoff
--
Throughout its 18-year history, RSA Conference consistently attracts the
world's best and brightest
On Jan 22, 2010, at 9:23 AM, Konstantin Tokarev wrote:
> Hello! I have some patches for OB (notably, support of reading of Raman
> activities from Gamess files), but they were not applied. Please, give me SNV
> access and I'll apply it myself
I'm going to check on that -- the patch tracker sho
> Is there anything else I need to do so that it is accepted? Thanks, cheers.
Nope. The main problem is that I've been swamped. I haven't seen anyone else
with SVN access add it, so I'll set aside some time for OB coding tomorrow and
get it done.
Thanks!
-Geoff
> So here is the challenge: Can you identify an aromatic atom where the number
> of electrons it donates is ambiguous, and there is no reasonable SMARTS that
> can separate the two cases? I'm going to claim that there are *no*
> situations where we don't know exactly the number of electrons eac
> Sure, that's cool, sorry about that. I just had a bit of a lazy moment at the
> end of the night. I'll email Geoff like you suggest and take care of it. (I
> understand the basics of svn, I just wasn't sure how to integrate Chris' and
> my changes.) Cheers.
The benefit of SVN is that it do
> I don't have GCC and copied this from somewhere. Will it work now with
> GCC 4.0 4.1 and 4.2 ?
Works fine for me with 4.0 and 4.2 on Mac. I'm sure we'll hear if it fails on
Linux. :-)
Thanks,
-Geoff
--
The Planet: ded
On Feb 9, 2010, at 6:59 AM, Noel O'Boyle wrote:
> We really need to get CDash set up as soon as possible. There's no way
> to stop these sorts of regressions without automated tests.
Yes, we need many more tests. They're not hard to write. We also need to fix
the tests we have. There are a few
> Don't you mean BUILD_GUI:BOOL=ON? If there's a problem I'll fix it,
> but it works for me.
There's a bug with the Mac version of wxWidgets, so on Mac, I don't build the
GUI.
Cheers,
-Geoff
--
SOLARIS 10 is the OS for D
> What repository: SVN on SF
SVN. At the moment, there are several Git mirrors, but that's exactly what they
are -- mirrors of SVN.
Hope that helps,
-Geoff
--
SOLARIS 10 is the OS for Data Centers - provides features suc
> Should I just delete the test? It doesn't seem to be doing anything very
> useful.
Yes, this seems fine. I do remember some discussion about how to free the file
handle from ReadFile -- this is probably a good time to revisit that.
-Geoff
--
The new nightly testing "bots" are turning up some routine failures. So today,
I'm going through and doing analysis on each one. I found one test that needed
updating already.
http://my.cdash.org/index.php?project=Open%20Babel
The "formula" test checks generated formulas, molecular weights, bef
> http://my.cdash.org/index.php?project=Open%20Babel
Here's another failure. This is on the SMILES/SMARTS match test (i.e., all of
these SMILES should match themselves when turned into SMARTS).
O([P@@](N)(=O)c1c1)CC
When I read this in as a SMILES and output as a SMILES, I lose chirality:
Every year, I try to write up a "State of the Project" message in January. How
about Feb. 20th? :-)
Last year, we got out 3 releases of 2.2.x, we broke the 120,000 downloads mark,
and 30+ projects. We also made great progress on the 2.3 release at the SVN
trunk.
What's currently on the develop
On Feb 20, 2010, at 11:03 AM, Noel O'Boyle wrote:
> the compiler, etc.). Functions that return sizes of vectors should be
> returning size_t types. For example:
>
>//! \return the number of conformers in this molecule
>int NumConformers(){ return((_vconf.empty())?0:_vconf.size())
On Feb 20, 2010, at 12:18 PM, Tim Vandermeersch wrote:
> best option for nitrogen. Detecting chiral (bridge-head) nitrogen
> atoms seems complex...
Well, the starting place would be to check that the nitrogen was connected to
three ring atoms. If not, it's not chiral. Then I'd check the actual
On Feb 21, 2010, at 5:50 AM, Noel O'Boyle wrote:
> Is there something we can do about this?
No, and for good reason. A build requires all components to be built. Consider
if I wanted to test whether the Python bindings compiled correctly -- I'd want
that particular build to FAIL entirely if Py
On Feb 21, 2010, at 6:24 PM, David Osguthorpe wrote:
> Im also wondering about how such block formats are best handled
I tend to suggest the principal of least surprise. Let's use "fragment" to
imply an isolated molecular fragment, and "database" to represent a whole file.
There are definitely
> The "formula" test checks generated formulas, molecular weights, before and
> after adding hydrogens. (Obviously, the results should be the same.) The
> failures stem from this SMILES pattern:
> Oc1c(O)c23ccc41c4c23
>
> The problem is that the new Kekulize method takes these oxygens fr
I should indicate that I'm trying to "firm up" the trunk -- i.e., cut down on
failing tests, fix bugs (and add tests for new bugs). My intent is to make a
snapshot on March 1st, and then every month until we release 2.3.0.
-Geoff
--
> Mods for reading UNIX files on Windows and fastsearch files.
Chris,
I'm now getting the following compile errors:
> /Volumes/Home/ghutchis/Devel/openbabel/src/fingerprint.cpp: In member
> function ‘bool OpenBabel::FptIndex::Read(std::istream*)’:
> /Volumes/Home/ghutchis/Devel/openbabel/src/fin
> use unordered_map without c++0x
>
> Modified Paths:
> --
>openbabel/trunk/src/ops/unique.cpp
This fix seems to have created other compile problems. All the build testers
are failing:
> "OpenBabel::InChIFormat::EditInchi(std::basic_string std::char_traits, std::allocator >&,
On Feb 28, 2010, at 10:21 AM, Chris Morley wrote:
> Reasons for not having a single monolithic executable are:
Well, I think you mean a single monolithic library (libopenbabel) here, but yes.
> - allows upgrading or modification without recompilation,
>by the distribution of dll or so file
On Feb 28, 2010, at 11:06 AM, Noel O'Boyle wrote:
> To be clear, we *are* already using CMake for this. To unify the
> builds, we just need to remove the 'if' statement for non-MSVC builds
> (and sort out any resulting problems).
Before we do that, let's make sure we've agreed on the number and
On Feb 22, 2010, at 11:50 AM, David Osguthorpe wrote:
> in this format you can have multiple blocks in a file as in the SDF format
> however (which I think is unlike the SDF format) in a single block there can
> be multiple
> molecules - where molecules are not separated (which sounds like they
On Mar 1, 2010, at 1:16 PM, David Osguthorpe wrote:
> separate such PDB structures so it would be useful to be able to suppress this
> in the Separate method
...
> - or indeed 10,000 water molecules as the OBMol overhead may be too much for
> 10,000
> 3 atom proper OBMol molecules (also of cours
> The best way to get started with something like that is to look at
> some other input readers to get an idea of how they work. You can find
> them under openbabel/src/formats/. There is also an example format
> reader in there too that can be used as a template.
This is exactly how I do it. I do
On Mar 1, 2010, at 3:22 PM, Noel O'Boyle wrote:
> Are there any guidelines on the preferred units, e.g. Angstrom versus
> Bohr and so forth?
Yes, all coordinates in Open Babel are in Angstrom, and all energies should be
in kcal/mol (for now).
Hope that helps,
-Geoff
---
On Mar 1, 2010, at 4:08 PM, Konstantin Tokarev wrote:
>> Yes, all coordinates in Open Babel are in Angstrom, and all energies should
>> be in kcal/mol (for now).
>
> What about energies of geometry optimization steps? It's much more convenient
> to see Hartrees
For right now, OB does not sto
On Mar 2, 2010, at 4:21 PM, David Lonie wrote:
> Would changing protected variables be considered breaking API? I want
> to get rid of the _a etc, _alpha etc, _v1 etc and just replace them
> all with matrix3x3 _m.
That would break ABI (so Avogadro would be unhappy), but in OB, that's OK.
Simila
> 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.
Cheers,
-Geoff
As part of the process of cleaning up trunk to be released for 2.3, I've been
cleaning up the test suite.
This morning, I brought back inchiwrite, and it finds a few failures --
although I can't remember whether the txt files were hand-generated, processed
by the "authentic" InChI release, or f
On Mar 3, 2010, at 10:31 AM, Noel O'Boyle wrote:
>* test/graphsymtest.cpp: There are still some cases were this test
> fails. However, it mainly has to do with N atoms becoming aromatic
> and getting an extra H atom. I'm not sure what's the best solution
> here...
>
> C
On Mar 3, 2010, at 12:40 PM, Tim Vandermeersch wrote:
> Should we change this in the unit test (i.e. use the new smiles
> string)?
I already changed it -- the aromatic SMILES is there. Any failures are with the
2 remaining non-aromatic structures.
> Do you mean the crashes in expand_kekulize?
> How to link whole OB into one library?
I'm assuming you want to statically link everything -- including formats. It's
tricky, because you can link everything into a monolithic libopenbabel.a or
libopenbabel.so. The problem is that when you link to create a binary (e.g.,
"babel"), the linker
> all with the release. For some reason what's released is not the same as
> what was in the svn so that all the testing and effort seem to have gone
> nowhere.
With the OB-2.2 series (and before), we used the automake "make dist" to create
release tars from the SVN directory. This is different i
Hi Chris,
I'm trying to sift through the output from the inchiwrite test. Some of it is
pretty good:
* We had a regression with reading 'D' as an atom symbol in molfiles. Now fixed
* I realized that Tim's new stereo code didn't consider isotopes (i.e., CH3CDHT
is chiral).
What confuses me is th
> How to set custom path for share/ of openbabel?
Do you mean the data? You can use the environment variable BABEL_DATADIR.
Cheers,
-Geoff
--
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Try the new software tools for yourself.
Matt,
Great catch. This will probably help other people, since you're not the only
one running Open Babel in a separate thread. I suspect this is the root cause
of other XML crashes -- there are a few posted to the bug tracker.
Let's commit this to SVN trunk for some testing. If it works, I'll
> Is this acceptable? I have no problem with this myself, as GCC 3.x is
> almost (but not quite) obsolete and we can just make it a requirement
> of the build.
GCC 4.0 was released on April 20, 2005, and GCC-3.4.x (as a release series) was
created in 2004.
Personally, I think it's OK to say for
> such as "FS(F)(F)(F)(F)F": two of the fluorine atoms are superposed,
...
> (as well as a missed opportunity for a warning in avogadro): the
I think there are a few things going on here. I thought I got all of these
bugs, but you clearly found a few more. ;-) In Open Babel, the force field
imp
> I've found this change necessary; either it's an obvious bug fix (we
> might get to atoms again after setting UFF_AXIAL_ATOM, and then remove
> the tag we just added).
No, that's a good fix, thanks. I'll blame it on a "thinko". I also added a fix
for your planar SO3 molecule.
Cheers,
-Geoff
-
> energy penalties: as the gradients are equal for the two atoms, they
> never get split, if the optimisation engine doesn't randomize
Ohh. I feel silly. UFF should now do this.
> I'd think the GetHyb() values should probably match the values UFF
> uses for coordination, as you propose: 5, 6, 7
> Are there any perforamnce benchmark scripts for OB? E.g., I'd like to test if
> OB compiled by Intel is faster than by GCC or if -O3 optimization with Intel
> is more effective than -O2
My suggestion would be to take some large multi-molecule file and convert it.
Or, you could also take a mul
> I ran into problems loading the NCI data set at 260,000
> compounds. I worked with TJ to try and track down the problem.
> It's in the Python or OpenBabel levels. I have a reproducible
You don't mention what version of OB you're using, but imply it's not the
latest development code. I'd highly
Currently, the InChI test is failing on UNIX platforms for reasons I can't
understand. Here's a run-down:
http://my.cdash.org/testDetails.php?test=1930810&build=58657
So the main problem is that the molecule (ferrocene) shows an error:
Not ok 1 # Mismatch in molecule #1. generated / correct
# In
On Apr 12, 2010, at 12:26 PM, Geoffrey Hutchison wrote:
> # InChI=1S/2C5H5.2C5H.2Fe/c4*1-2-4-5-3-1;;/h2*1-5H;2*1H;;/q;+2
> # InChI=1S/4C5H5.2Fe/c4*1-2-4-5-3-1;;/h4*1-5H;;/q;;2*-1;;+2
...
> * Chris: what data files could mess up the test?
I should point out that the failures al
On Apr 12, 2010, at 1:02 PM, Noel O'Boyle wrote:
> There is nothing special about CTest. You should run the test directly
> from the command-line to prove this.
I ran the test from the command-line. The test fails. Running "babel" works.
> If you look at the test code (inchiwrite.cpp, right?),
> Does the Python interface work for you on a Mac?
Yes. I have no problems with Pybel using the latest development trunk. I have
not yet tried Andrew's Python script on my Mac, but I can confirm that the C++
"babel" command has no problem.
Cheers,
-Geoff
--
s seem to fix the failures here. I think we should try to figure
out where the line-ending problem occurs (in mdlformat.cpp or alias.cpp), but I
feel much better about the results.
-Geoff
---
Prof. Geoffrey Hutchison
Assistant Professor, Department of Chemistry
University of Pittsburgh
http://hutchi
> OpenBabel fails to build on Linux after recent charge model changes:
I think this is fixed in a newer revision.
Cheers,
-Geoff
--
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OpenBabel-D
> But what to do with (2)? According to the CMake FAQ
> (http://www.cmake.org/Wiki/CMake_FAQ#Where_is_.22make_dist.22.3F),
> CMake does not make a "make dist" target. Any ideas how to handle
> this?
The basic concept from CMake is that you should just tar up the source
directory itself. That's wh
On Apr 26, 2010, at 11:56 AM, Noel O'Boyle wrote:
> But the source directory will be missing the swig files...? Maybe the
> way to go is to ensure that -DRUN_SWIG puts the Swig files into the
> source tree, and then they will be there when you tar them up...
Yes, that's right. Some files need to
> A bit complicated for me, but it looks like it's due to the recent
> changes to tokenst.h...
Yes, it was missing the sstream header.
Fixed in SVN now.
-Geoff
--
___
OpenBab
On May 7, 2010, at 8:01 AM, Tim Vandermeersch wrote:
>>> However, I can't see any reason not to treat 2D structures like 0D
>>> ones. It works very well.
As long as the stereochemistry is preserved, I don't think it matters much.
> No, sounds good. The reason why flat structures stay flat is an
> AFAIU, OpenBabel allows search of internal rotations via the list of rotable
> bonds. In OB terms, "Rotor" is a rotable bond, but I need to get rotors in
> sense of groups of atoms which take part in internal rotations.
What you're saying is that you want the list of atoms affected by a partic
> C-Se bond (e.g., in context Se-CH3) is not recognized as rotable. Is
> there any reason for it?
I assume you mean the OBBond::IsRotor() descriptor? I would check the
hybridization of the Se atom. Heavier elements do not always have assigned
hybridizations -- one reason I'd like to minimize the
> Is it possible to use bond order 0 to store H-bonds?
I think that's more of a question for Open Babel than Avogadro. The answer is
"maybe." Yes, you can store them, but there's currently no guarantee that all
of Open Babel is ready to accept bond orders of 0. For example, some code just
check
On May 26, 2010, at 10:53 AM, Konstantin Tokarev wrote:
>> For example, some code just checks for the number of bonds to an
>> atom. This would cause problems with "extra" valence.
>
> Do you mean it can cause errors? or this extra valence will be ignored?
I suspect it will cause errors. My wor
> case. For example, neither r3751 nor r3752 were included in
> yesterday's build. My builds run after 6am GMT (1am EST).
OK, we can set whatever threshold we want. I prefer moving the build time *far*
away from midnight, since daylight savings issues or clock differentials can
cause problems. H
> Let's go with 1:30 AM EST. So we should set schedule our builds to run
> after this time, right?
Yes, that's exactly right.
-Geoff
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