Re: [OpenBabel-Devel] Debugging tests
Any suggestion?
On 2024-02-14 21:35, David van der Spoel wrote:
Dear devs,
I'm trying to debug the output of a test for a patch that I wrote:
230/233 Test #230: pybindtest_obconv_writers ***Failed Error
regular expression found in output. Regex=[FAIL] 0.73
Running it with
% export CTEST_OUTPUT_ON_FAILURE=1
% cmake -P
"/Users/spoel/tmp/openbabel/build/test/pybindtest_obconv_writers.cmake"
>& output.txt
Yields in the output.txt the following from what I deduce that
coordinates are generated incorrectly. Is that correct? Is there a way
to analyze this in a more comprehensible manner?
Traceback (most recent call last):
File "/Users/spoel/tmp/openbabel/test/testobconv_writers.py", line
2761, in test_default
self.assertWriters(self.fmt, """\
File "/Users/spoel/tmp/openbabel/test/testobconv_writers.py", line
258, in assertWriters
test_write_string(self, mol, conv, expected_output, normalize)
File "/Users/spoel/tmp/openbabel/test/testobconv_writers.py", line
165, in test_write_string
test_case.assertMultiLineEqual(output.replace("\r\n", "\n"),
expected_output.replace("\r\n", "\n"))
AssertionError: '{\n [1926 chars]102014\n ],\n "y": [[1072
chars]]\n}' != '{\n [1926 chars]102012\
n ],\n "y": [[1070 chars]]\n}'
{
"conformers": [
{
"x": [
1.5846,
1.5703,
2.4295,
3.3031,
3.3175,
0.0,
-1.0005,
2.313816216007316,
0.669250157347277,
2.4146659588503769,
4.189331679349326,
4.052466878708012,
- -1.4648575597102014
? ^
+ -1.4648575597102012
? ^
],
"y": [
- -0.0249,
- 0.9755,
- 1.4882,
?^^^
+ 1.5846,
? ++ ^
- 1.0004,
?^^^
+ 1.5703,
? ++ ^
- -0.0,
? ^^ ^
+ 2.4295,
? ^
+ 3.3031,
+ 3.3175,
0.0,
- 0.0051,
? ^ -
+ -1.0005,
? ^^ +
- -0.7551518129467202,
- 1.4786234252700852,
- 2.520093381713039,
- 1.5291886255562557,
- -0.7244637238690441,
- 0.8189433858796095
+ 2.313816216007316,
+ 0.669250157347277,
+ 2.4146659588503769,
+ 4.189331679349326,
+ 4.052466878708012,
+ -1.4648575597102012
],
--
David van der Spoel, Ph.D.,
Professor of Computational Molecular Biophysics
Uppsala University.
http://virtualchemistry.org
När du har kontakt med oss på Uppsala universitet med e-post så
innebär det att vi behandlar dina personuppgifter. För att läsa mer om
hur vi gör det kan du läsa här:
http://www.uu.se/om-uu/dataskydd-personuppgifter/
E-mailing Uppsala University means that we will process your personal
data. For more information on how this is performed, please read here:
http://www.uu.se/en/about-uu/data-protection-policy
___
OpenBabel-Devel mailing list
OpenBabel-Devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-devel
VARNING: Klicka inte på länkar och öppna inte bilagor om du inte
känner igen avsändaren och vet att innehållet är säkert.
CAUTION: Do not click on links or open attachments unless you
recognise the sender and know the content is safe.
--
David van der Spoel, Ph.D.,
Professor of Computational Molecular Biophysics
Uppsala University.
http://virtualchemistry.org
När du har kontakt med oss på Uppsala universitet med e-post så innebär det att
vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du
läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/
E-mailing Uppsala University means that we will process your personal data. For
more information on how this is performed, please read here:
http://www.uu.se/en/about-uu/data-protection-policy
___
OpenBabel-Devel mailing list
OpenBabel-Devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-devel
[OpenBabel-Devel] Debugging tests
Dear devs,
I'm trying to debug the output of a test for a patch that I wrote:
230/233 Test #230: pybindtest_obconv_writers ***Failed Error
regular expression found in output. Regex=[FAIL] 0.73
Running it with
% export CTEST_OUTPUT_ON_FAILURE=1
% cmake -P
"/Users/spoel/tmp/openbabel/build/test/pybindtest_obconv_writers.cmake"
>& output.txt
Yields in the output.txt the following from what I deduce that
coordinates are generated incorrectly. Is that correct? Is there a way
to analyze this in a more comprehensible manner?
Traceback (most recent call last):
File "/Users/spoel/tmp/openbabel/test/testobconv_writers.py", line
2761, in test_default
self.assertWriters(self.fmt, """\
File "/Users/spoel/tmp/openbabel/test/testobconv_writers.py", line
258, in assertWriters
test_write_string(self, mol, conv, expected_output, normalize)
File "/Users/spoel/tmp/openbabel/test/testobconv_writers.py", line
165, in test_write_string
test_case.assertMultiLineEqual(output.replace("\r\n", "\n"),
expected_output.replace("\r\n", "\n"))
AssertionError: '{\n [1926 chars]102014\n ],\n "y": [[1072
chars]]\n}' != '{\n [1926 chars]102012\
n ],\n "y": [[1070 chars]]\n}'
{
"conformers": [
{
"x": [
1.5846,
1.5703,
2.4295,
3.3031,
3.3175,
0.0,
-1.0005,
2.313816216007316,
0.669250157347277,
2.4146659588503769,
4.189331679349326,
4.052466878708012,
- -1.4648575597102014
? ^
+ -1.4648575597102012
? ^
],
"y": [
- -0.0249,
- 0.9755,
- 1.4882,
?^^^
+ 1.5846,
? ++ ^
- 1.0004,
?^^^
+ 1.5703,
? ++ ^
- -0.0,
? ^^ ^
+ 2.4295,
? ^
+ 3.3031,
+ 3.3175,
0.0,
- 0.0051,
? ^ -
+ -1.0005,
? ^^ +
- -0.7551518129467202,
- 1.4786234252700852,
- 2.520093381713039,
- 1.5291886255562557,
- -0.7244637238690441,
- 0.8189433858796095
+ 2.313816216007316,
+ 0.669250157347277,
+ 2.4146659588503769,
+ 4.189331679349326,
+ 4.052466878708012,
+ -1.4648575597102012
],
--
David van der Spoel, Ph.D.,
Professor of Computational Molecular Biophysics
Uppsala University.
http://virtualchemistry.org
När du har kontakt med oss på Uppsala universitet med e-post så innebär det att
vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du
läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/
E-mailing Uppsala University means that we will process your personal data. For
more information on how this is performed, please read here:
http://www.uu.se/en/about-uu/data-protection-policy
___
OpenBabel-Devel mailing list
OpenBabel-Devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] Non-integer bond orders for resonant groups
On 2021-07-27 12:33, David van der Spoel wrote:
On 2021-07-27 10:39, Noel O'Boyle wrote:
OBBond.IsAromatic(). See the docs.
Thanks for the suggestion. That works fine for aromatic rings, but not
for COO- or NO2 groups. Is there another flag to test, I cannot find
anything in the documentation.
An OBbond.IsResonant() would be great...
Just some feed back that I was able to implement a hack in my own code
turning both aromatic bonds and specific others like COO- into bond
orders of 1.5.
Cheers, David.
I would not use Smarts patterns to type atoms or bonds, but rather do
it in code. The former is just too error prone, slow and less readable.
On Tue, 27 Jul 2021, 07:18 David van der Spoel,
mailto:david.vandersp...@icm.uu.se>>
wrote:
On 2021-07-27 07:51, Noel O'Boyle wrote:
> Is there a particular problem you are trying to solve where
underlying
> kekule representation is causing a problem?
>
Yes, I am extracting bond orders from OB and they go into my force
field
code. Different bond orders means different bond properties which in
addition yield different charges in my force field code.
If I understand it correctly the kekulization code checks for
resonance
but in order to get the chemistry of single and double bonds
right we
had to add over 100 lines to bondtyp.txt, so I am not sure that
the code
alone is enough.
If it would be easy to extract the aromaticity of a bond that
would be
sufficient for my purpose indeed.
>
> On Mon, 26 Jul 2021, 21:28 David Koes, mailto:dk...@pitt.edu>
> <mailto:dk...@pitt.edu <mailto:dk...@pitt.edu>>> wrote:
>
> In my opinion, if the only fractional value will be 1.5 then
> non-integer
> bond orders aren't worth the pain of breaking compatibility
since
> this
> state can be (and is, for rings) represented by setting the
aromatic
> property of the bond. Perhaps we should provide additional,
more
> nuanced properties to indicate resonance vs aromaticity?
>
> If there is a reason for fractions other than 1.5, then I
think this
> should be a separate property entirely (e.g., like formal
charges vs
> partial charges).
>
> I would point out that although O=CO is represented with a
double and
> single bond, the oxygens still get an identical partial
charge as the
> carboxylic acid group is recognized as such:
> print(pybel.readstring('smi','O=CO').write('mol2'))
>
> David Koes
>
> Associate Professor
> Computational & Systems Biology
> University of Pittsburgh
>
> On 7/26/21 5:36 AM, David van der Spoel wrote:
> > Hi,
> >
> > maybe this has been discussed earlier, but I would like to
hear your
> > opinion on implementing non-integer bond orders. For e.g.
> benzene the
> > average CC bond order would be 1.5, and likewise for COO-
groups
> or NOO
> > groups. Quantum-chemically such resonant groups turn out
to be
> > symmetrical and e.g. with identical charges on the O in
those cases.
> >
> > When using integer bond orders we are enforcing an asymmetry
> that is not
> > there. So would it be worthwhile implementing non-integer
bond
> orders or
> > is there a workaround that I am overlooking?
> >
> > Cheers,
> >
> > --
> > David van der Spoel, Ph.D.,
> > Professor of Computational Molecular Biophysics
> > Uppsala University.
>
>
> ___
> OpenBabel-Devel mailing list
> OpenBabel-Devel@lists.sourceforge.net
<mailto:OpenBabel-Devel@lists.sourceforge.net>
> <mailto:OpenBabel-Devel@lists.sourceforge.net
<mailto:OpenBabel-Devel@lists.sourceforge.net>>
> https://lists.sourceforge.net/lists/listinfo/openbabel-devel
<https://lists.sourceforge.net/lists/listinfo/openbabel-devel>
>
<https://lists.sourceforge.net/lists/listinfo/openbabel-devel
<https://lists.sourceforge.net/lists/listinfo/openbabel-devel>>
>
--
David van der Spoel, Ph.D.,
Professor of Computational Molecular Biophysics
Uppsala University.
http://virtualchemistry.org <http://virtualchemistry.org>
När du har kontakt med oss på Uppsala universitet med e-post så
innebär det att vi behandlar dina personuppgifter. För att läsa
mer om hur vi gör det kan du läsa här:
Re: [OpenBabel-Devel] Non-integer bond orders for resonant groups
On 2021-07-27 10:39, Noel O'Boyle wrote:
OBBond.IsAromatic(). See the docs.
Thanks for the suggestion. That works fine for aromatic rings, but not
for COO- or NO2 groups. Is there another flag to test, I cannot find
anything in the documentation.
An OBbond.IsResonant() would be great...
I would not use Smarts patterns to type atoms or bonds, but rather do
it in code. The former is just too error prone, slow and less readable.
On Tue, 27 Jul 2021, 07:18 David van der Spoel,
mailto:david.vandersp...@icm.uu.se>> wrote:
On 2021-07-27 07:51, Noel O'Boyle wrote:
> Is there a particular problem you are trying to solve where
underlying
> kekule representation is causing a problem?
>
Yes, I am extracting bond orders from OB and they go into my force
field
code. Different bond orders means different bond properties which in
addition yield different charges in my force field code.
If I understand it correctly the kekulization code checks for
resonance
but in order to get the chemistry of single and double bonds right we
had to add over 100 lines to bondtyp.txt, so I am not sure that
the code
alone is enough.
If it would be easy to extract the aromaticity of a bond that would be
sufficient for my purpose indeed.
>
> On Mon, 26 Jul 2021, 21:28 David Koes, mailto:dk...@pitt.edu>
> <mailto:dk...@pitt.edu <mailto:dk...@pitt.edu>>> wrote:
>
> In my opinion, if the only fractional value will be 1.5 then
> non-integer
> bond orders aren't worth the pain of breaking compatibility
since
> this
> state can be (and is, for rings) represented by setting the
aromatic
> property of the bond. Perhaps we should provide additional,
more
> nuanced properties to indicate resonance vs aromaticity?
>
> If there is a reason for fractions other than 1.5, then I
think this
> should be a separate property entirely (e.g., like formal
charges vs
> partial charges).
>
> I would point out that although O=CO is represented with a
double and
> single bond, the oxygens still get an identical partial
charge as the
> carboxylic acid group is recognized as such:
> print(pybel.readstring('smi','O=CO').write('mol2'))
>
> David Koes
>
> Associate Professor
> Computational & Systems Biology
> University of Pittsburgh
>
> On 7/26/21 5:36 AM, David van der Spoel wrote:
> > Hi,
> >
> > maybe this has been discussed earlier, but I would like to
hear your
> > opinion on implementing non-integer bond orders. For e.g.
> benzene the
> > average CC bond order would be 1.5, and likewise for COO-
groups
> or NOO
> > groups. Quantum-chemically such resonant groups turn out to be
> > symmetrical and e.g. with identical charges on the O in
those cases.
> >
> > When using integer bond orders we are enforcing an asymmetry
> that is not
> > there. So would it be worthwhile implementing non-integer bond
> orders or
> > is there a workaround that I am overlooking?
> >
> > Cheers,
> >
> > --
> > David van der Spoel, Ph.D.,
> > Professor of Computational Molecular Biophysics
> > Uppsala University.
>
>
> ___
> OpenBabel-Devel mailing list
> OpenBabel-Devel@lists.sourceforge.net
<mailto:OpenBabel-Devel@lists.sourceforge.net>
> <mailto:OpenBabel-Devel@lists.sourceforge.net
<mailto:OpenBabel-Devel@lists.sourceforge.net>>
> https://lists.sourceforge.net/lists/listinfo/openbabel-devel
<https://lists.sourceforge.net/lists/listinfo/openbabel-devel>
>
<https://lists.sourceforge.net/lists/listinfo/openbabel-devel
<https://lists.sourceforge.net/lists/listinfo/openbabel-devel>>
>
--
David van der Spoel, Ph.D.,
Professor of Computational Molecular Biophysics
Uppsala University.
http://virtualchemistry.org <http://virtualchemistry.org>
När du har kontakt med oss på Uppsala universitet med e-post så
innebär det att vi behandlar dina personuppgifter. För att läsa
mer om hur vi gör det kan du läsa här:
http://www.uu.se/om-uu/dataskydd-personuppgifter/
<http://www.uu.se/om-uu/dataskydd-personuppgifter/>
E-mailing Uppsala University means that we will process your
personal data. For more in
Re: [OpenBabel-Devel] Non-integer bond orders for resonant groups
On 2021-07-27 07:51, Noel O'Boyle wrote:
Is there a particular problem you are trying to solve where underlying
kekule representation is causing a problem?
Yes, I am extracting bond orders from OB and they go into my force field
code. Different bond orders means different bond properties which in
addition yield different charges in my force field code.
If I understand it correctly the kekulization code checks for resonance
but in order to get the chemistry of single and double bonds right we
had to add over 100 lines to bondtyp.txt, so I am not sure that the code
alone is enough.
If it would be easy to extract the aromaticity of a bond that would be
sufficient for my purpose indeed.
On Mon, 26 Jul 2021, 21:28 David Koes, mailto:dk...@pitt.edu>> wrote:
In my opinion, if the only fractional value will be 1.5 then
non-integer
bond orders aren't worth the pain of breaking compatibility since
this
state can be (and is, for rings) represented by setting the aromatic
property of the bond. Perhaps we should provide additional, more
nuanced properties to indicate resonance vs aromaticity?
If there is a reason for fractions other than 1.5, then I think this
should be a separate property entirely (e.g., like formal charges vs
partial charges).
I would point out that although O=CO is represented with a double and
single bond, the oxygens still get an identical partial charge as the
carboxylic acid group is recognized as such:
print(pybel.readstring('smi','O=CO').write('mol2'))
David Koes
Associate Professor
Computational & Systems Biology
University of Pittsburgh
On 7/26/21 5:36 AM, David van der Spoel wrote:
> Hi,
>
> maybe this has been discussed earlier, but I would like to hear your
> opinion on implementing non-integer bond orders. For e.g.
benzene the
> average CC bond order would be 1.5, and likewise for COO- groups
or NOO
> groups. Quantum-chemically such resonant groups turn out to be
> symmetrical and e.g. with identical charges on the O in those cases.
>
> When using integer bond orders we are enforcing an asymmetry
that is not
> there. So would it be worthwhile implementing non-integer bond
orders or
> is there a workaround that I am overlooking?
>
> Cheers,
>
> --
> David van der Spoel, Ph.D.,
> Professor of Computational Molecular Biophysics
> Uppsala University.
___
OpenBabel-Devel mailing list
OpenBabel-Devel@lists.sourceforge.net
<mailto:OpenBabel-Devel@lists.sourceforge.net>
https://lists.sourceforge.net/lists/listinfo/openbabel-devel
<https://lists.sourceforge.net/lists/listinfo/openbabel-devel>
--
David van der Spoel, Ph.D.,
Professor of Computational Molecular Biophysics
Uppsala University.
http://virtualchemistry.org
När du har kontakt med oss på Uppsala universitet med e-post så innebär det att
vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du
läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/
E-mailing Uppsala University means that we will process your personal data. For
more information on how this is performed, please read here:
http://www.uu.se/en/about-uu/data-protection-policy
___
OpenBabel-Devel mailing list
OpenBabel-Devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-devel
[OpenBabel-Devel] Non-integer bond orders for resonant groups
Hi, maybe this has been discussed earlier, but I would like to hear your opinion on implementing non-integer bond orders. For e.g. benzene the average CC bond order would be 1.5, and likewise for COO- groups or NOO groups. Quantum-chemically such resonant groups turn out to be symmetrical and e.g. with identical charges on the O in those cases. When using integer bond orders we are enforcing an asymmetry that is not there. So would it be worthwhile implementing non-integer bond orders or is there a workaround that I am overlooking? Cheers, -- David van der Spoel, Ph.D., Professor of Computational Molecular Biophysics Uppsala University. http://virtualchemistry.org När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] charge for bond order perception
On 2021-06-08 19:03, David Koes wrote: That sounds great. I for one will never complain about inconveniences induced by adding additional testing. You should be able to gzip the files and read the gz version directly with obabel to save on space. Now I've made a pull request with a test for bond orders and atom types. https://github.com/openbabel/openbabel/pull/2385 David Koes Associate Professor Computational & Systems Biology University of Pittsburgh On 6/8/21 11:50 AM, David van der Spoel wrote: We have a script that reads a Gaussian file and a reference sdf file and compares whether the double bonds are in the same place and whether generated atom types for the GAFF force field are the same. It uses the openbabel python interface such as to keep everything in memory and not create a ton of temporary files or tedious parsing of stdout. Would that be an option? The crux is then that we need to add largish Gaussian output files to the repository. -- David van der Spoel, Ph.D., Professor of Computational Molecular Biophysics Uppsala University. http://virtualchemistry.org När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] charge for bond order perception
On 2021-06-08 17:37, David Koes wrote: If all the issues manifest themselves with calls to obabel, I would add functions to test/testbabel.py (the filename is a throwback to when obabel was babel). You can see an example in this pull request: https://github.com/openbabel/openbabel/pull/2379 Or, if you are feeling adventurous, I think it would be great if we had a plain text file of obabel commands that are run with the expected outputs following some standard naming convention. For example, maybe each line is of the form: # files/correct_output and the test function compares the standard out of running the command to the correct_output file. This would make it much easier to add tests if it is appropriate to compare file outputs exactly. We have a script that reads a Gaussian file and a reference sdf file and compares whether the double bonds are in the same place and whether generated atom types for the GAFF force field are the same. It uses the openbabel python interface such as to keep everything in memory and not create a ton of temporary files or tedious parsing of stdout. Would that be an option? The crux is then that we need to add largish Gaussian output files to the repository. Thanks, David Koes Associate Professor Computational & Systems Biology University of Pittsburgh On 6/8/21 11:22 AM, David van der Spoel wrote: On 2021-06-08 15:42, David Koes wrote: Hi Madeleine, It sounds like you have a really excellent set of test structures. It would be fantastic if you could contribute these to the testing framework. We would be happy to do that, but maybe you can give a suggestion on where in the testing framework? Or should we just add a new python script there with in and output data? FYI, we have made quite a few fixes already that likely are of interest to others: % git diff master:data/bondtyp.txt data/bondtyp.txt | wc 128 7844532 -- David van der Spoel, Ph.D., Professor of Computational Molecular Biophysics Uppsala University. http://virtualchemistry.org När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] charge for bond order perception
On 2021-06-08 15:42, David Koes wrote: Hi Madeleine, It sounds like you have a really excellent set of test structures. It would be fantastic if you could contribute these to the testing framework. We would be happy to do that, but maybe you can give a suggestion on where in the testing framework? Or should we just add a new python script there with in and output data? FYI, we have made quite a few fixes already that likely are of interest to others: % git diff master:data/bondtyp.txt data/bondtyp.txt | wc 128 7844532 David Koes Associate Professor Computational & Systems Biology University of Pittsburgh On 6/8/21 8:15 AM, Marie-Madeleine Walz wrote: Hi David, thank you for your advice regarding using AssignTotalChargeToAtoms. Adding it resulted in less errors in the bond order assignment. Unfortunately, it did not remove e.g. the error with sulfite (SO3^2-) that is still getting three double bonds. Another issue is that some of the small rings (e.g. thiirene, C2H2S) are not recognised as rings. This is really confusing as the coordinates fullfil the requirement set in mol.cpp, ConnectTheDots(), lines 3027-3028: // bonded if closer than elemental Rcov + tolerance cutoff = SQUARE(rad[j] + rad[k] + 0.45); If you have any advice I would really appreciate it. With kind regards, Madeleine ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel -- David van der Spoel, Ph.D., Professor of Computational Molecular Biophysics Uppsala University. http://virtualchemistry.org När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] bondtyper.cpp
On 2021-05-13 21:52, Ghahremanpour, Mohammad wrote: Hi David, Thanks for your reply. It is practical to manually specify the formal charge of the atoms in the input file for a few compounds, the problem arises when you work with many compounds in different file formats. In this case, it would be good to have a backup plan. It seems that if the bond order of bonds and the formal charge of atoms are specified correctly, Kekulization works fine in most cases, if I am not mistaken. So in the problematic cases we have been working on, we use Gaussian output files. The total charge of the compound is set correctly in the obmol structure when reading the file, but not which atom it is on (Gaussian does not do this kind of analysis). I uploaded an issue with input files to reproduce the problem here: https://github.com/openbabel/openbabel/issues/2366 It would definitely help to see what other people suggest before changing the source code or the format of data files. Any suggestion is highly appreciated. Cheers, Mohammad On May 13, 2021, at 3:33 PM, David Koes wrote: Hi Mohammad, bondtyper.txt does not have any ability to set formal charges. If you need to do something more sophisticated than matching with SMARTS to set bond orders you need to modify the C++ code. Whether what you are proposing is the right thing to do, I leave to others to decide. I would typically assume that the formal charge should be specified in the input file. Also, I'm not sure bondtyping is the right place for Kekulization fixes. David Koes Associate Professor Computational & Systems Biology University of Pittsburgh On 5/13/21 10:50 AM, Ghahremanpour, Mohammad wrote: Hi David, In order to make kekulization work on imidazolium rings, I hard coded SMARTS in bondtyper.cpp, where I explicitly set the formal charge of one of the nitrogens to 1 and also set the bond order to 2 for two of the bonds in the ring. Doing this, kekulization works fine. As pointed out by you, the SMARTS for bond typing should be defined in bondtyp.txt data file not hardcoded in the source file. I did it but kelulizataion fails again, as the result of which the imidazolium ring is considered as AL instead of AR. I think the problem is the formal charge which is set to 0 for all atoms by default. While, for rings like imidazolium, the formal charge of the nitrogen with four bonds is 1. In bondtyper.cpp, there are other examples were the formal charges are set explicitly, oxido-n+ (e.g., pyridine-N-oxide). I was wondering if there is some data file to tabulate formal charge for specific cases like this. I checked atomtyp.txt, not formal charge is stored there. Thanks, Mohammad -- David van der Spoel, Ph.D., Professor of Computational Molecular Biophysics Uppsala University. http://virtualchemistry.org När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] bondtyper.cpp
On 2021-05-11 21:00, David Koes wrote: Hi David, The data file _should_ be being used as long as openbabel can find it. The hardcoded values in the C++ source code are there as a fallback when the data files can't be found. I recently had a pull request merged that updates the C++ versions to match the data files (previously they were very out of date resulting in bad behavior when the data files couldn't be found due to, for example, openbabel being installed in strange place): https://github.com/openbabel/openbabel/pull/2328 If you want to improve the bond typing, change the data files, not the source code. If the problem is the source code has bad bond typing, update to a version with the pull request and rebuild. Thanks for your reply. The problem was that charged ring systems are not detected in all cases. In order to fix this, we could add this information to bondtyp.txt (including code to parse it), or make an additional data file. The advantage of adding it to bondtyp.txt is that (in this case) the smarts defining the ring are in one place only. A separate file would have the advantage that bondtyp.txt does not have to change its format. Preferences? Or are there other ways to make OB detect charge localization? Cheers, David. Thanks, David Koes Associate Professor Computational & Systems Biology University of Pittsburgh On 5/11/21 2:51 PM, David van der Spoel wrote: Hi, is anyone working on bondtyper.cpp? Apparently, the data file bondtyp.txt is not used at all and the information about bonding is hardcoded in the C++ source code. I would be happy to help, but before spending considerable effort it would be good to know if there is a plan for this part of the code. Cheers, -- David van der Spoel, Ph.D., Professor of Computational Molecular Biophysics Uppsala University. https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fvirtualchemistry.org%2F&data=04%7C01%7Cdkoes%40pitt.edu%7C7c0df21efdda4474888708d914addb90%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C1%7C637563559213381322%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=lffer4K7HY%2BExwngNb%2F3r0JFz1yQYRiWrYXz7Pd7ZGY%3D&reserved=0 -- David van der Spoel, Ph.D., Professor of Computational Molecular Biophysics Uppsala University. http://virtualchemistry.org När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
[OpenBabel-Devel] bondtyper.cpp
Hi, is anyone working on bondtyper.cpp? Apparently, the data file bondtyp.txt is not used at all and the information about bonding is hardcoded in the C++ source code. I would be happy to help, but before spending considerable effort it would be good to know if there is a plan for this part of the code. Cheers, -- David van der Spoel, Ph.D., Professor of Computational Molecular Biophysics Uppsala University. http://virtualchemistry.org När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
[OpenBabel-Devel] Installing on MacOS
Hi, I am having a bad time installing OB on my Mac. Once I finish building, and am still in the build directory, I can run e.g. % bin/obthermo water-g4.log.gz obthermo - extract thermochemistry data from quantum chemistry logfiles Number of rotatable bonds: 0 Please supply --dbdt option to get reliable heat capacity at constant pressure. Found symmetry number 2 in input file. DeltaHform(0K)-54.9145 kcal/mol Temperature 298.15 K However, once in its install directory the following happens when I invoke the program from my home dir: % obthermo water-g4.log.gz == *** Open Babel Error in openLib /Users/spoel/GG/openbabel-dev/install/lib/openbabel/3.1.1/acesformat.so did not load properly. Error: dlopen(/Users/spoel/GG/openbabel-dev/install/lib/openbabel/3.1.1/acesformat.so, 9): Library not loaded: @rpath/libcairo.2.dylib Referenced from: /Users/spoel/GG/openbabel-dev/install/lib/openbabel/3.1.1/acesformat.so Reason: image not found It does find the OB libraries, but not those OB is linked to. Any clue what I am doing wrong in terms of cmake etc.? % cmake --version cmake version 3.18.2 Thanks! -- David van der Spoel, Ph.D., Professor of Biology Uppsala University. http://virtualchemistry.org ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] script bindings / Use of EXTERN in headers
Den 2020-05-01 kl. 19:50, skrev Geoffrey Hutchison: As part of the 3.0.1 release process, I spun up a new build bot on Github to generate /all/ the script bindings. - At the moment, the R binding is broken - open to suggestions on how to fix / build it - The Ruby binding is broken because EXTERN evokes a macro in a Ruby header to issue warnings I'd like to switch use of EXTERN in the Open Babel headers to OB_EXTERN with the 3.1 release. For 3.0.1, we'll have to drop the Ruby bindings. Is extern still needed for anything with modern c++ compilers? Thoughts? -Geoff ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel -- David van der Spoel, Ph.D., Professor of Biology Uppsala University. http://virtualchemistry.org ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] Why are there plugins?
Den 2020-01-08 kl. 15:18, skrev Noel O'Boyle:
If you delete all of the plugins you don't want, this will speed things
up for you.
Alternatively, if you make a static build (I forgot the precise
invocation), then the plugins are compiled in rather than loaded
dynamically.
cmake -DBUILD_SHARED=OFF indeed solves my problems, thanks!
However it would be good to discuss the rationale for plugins and
whether the (complex) implementation serves its purpose.
I don't have time right now to go into why plugins are a great idea, but
hopefully the suggestions above will sort out your immediate problems.
Regards,
- Noel
On Wed, 8 Jan 2020 at 13:51, David van der Spoel <mailto:sp...@xray.bmc.uu.se>> wrote:
Hi,
I am trying to debug some code that links to OpenBabel and wonder why
there are plugins for everything?
In theory one could load only the plugins needed and in that way save
startup time and memory. However in OB, once you load one plugin all
plugins are loaded (one by one, making it slow).
So is there any rationale for these or should we phase them out?
Cheers,
--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
___
OpenBabel-Devel mailing list
OpenBabel-Devel@lists.sourceforge.net
<mailto:OpenBabel-Devel@lists.sourceforge.net>
https://lists.sourceforge.net/lists/listinfo/openbabel-devel
--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
___
OpenBabel-Devel mailing list
OpenBabel-Devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-devel
[OpenBabel-Devel] Why are there plugins?
Hi, I am trying to debug some code that links to OpenBabel and wonder why there are plugins for everything? In theory one could load only the plugins needed and in that way save startup time and memory. However in OB, once you load one plugin all plugins are loaded (one by one, making it slow). So is there any rationale for these or should we phase them out? Cheers, -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] Hydrogen management bug
Den 2019-11-26 kl. 13:58, skrev Noel O'Boyle:
The "M CHG" line looks dubious. It states that there is a single
charge, a +5 charge on atom 1. What is the source of this SDF file?
Emacs :(
Regards,
- Noe
On Tue, 26 Nov 2019 at 12:12, David van der Spoel <mailto:sp...@xray.bmc.uu.se>> wrote:
Den 2019-11-26 kl. 13:06, skrev Noel O'Boyle:
> Hi David,
>
> Can you provide the input file?
Attached, thanks for looking into this.
>
> Regards,
> - Noel
>
> On Tue, 26 Nov 2019 at 09:50, David van der Spoel
mailto:sp...@xray.bmc.uu.se>
> <mailto:sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se>>> wrote:
>
> Den 2019-11-26 kl. 10:12, skrev Noel O'Boyle:
> > An SDF file describes the number of hydrogens on each
atom. Open
> Babel
> > is neither adding nor removing them. AddHydrogens() is just
> making them
> > explicit.
> Unfortunately, no. The structure below has 7 hydrogens and
one charge
> but obprop adds one H and 4 (!) charges.
>
> % obprop 2-aminoguanidinium.sdf
> name 2-aminoguanidinium.sdf 1
> formula CH8N4+
>
>
>
>
>
> OpenBabel11261907103D
>
> 12 11 0 0 0 0 0 0 0 0999 V2000
> -1.5988 -0.6139 0.0135 N 0 0 0 0 0 0 0 0
0 0 0 0
> -0.4655 1.3957 -0.0077 N 0 0 0 0 0 0 0 0
0 0 0 0
> 0.7405 -0.6123 0.0118 N 0 0 0 0 0 0 0 0
0 0 0 0
> 1.9392 0.1153 0.0724 N 0 0 0 0 0 0 0 0
0 0 0 0
> -0.4481 0.0607 0.0074 C 0 0 0 0 0 0 0 0
0 0 0 0
> -1.6144 -1.6250 0.0385 H 0 0 0 0 0 0 0 0
0 0 0 0
> -2.4894 -0.1345 0.0041 H 0 0 0 0 0 0 0 0
0 0 0 0
> -1.3186 1.9349 -0.0175 H 0 0 0 0 0 0 0 0
0 0 0 0
> 0.4173 1.8753 -0.1389 H 0 0 0 0 0 0 0 0
0 0 0 0
> 1.9696 0.6569 0.9451 H 0 0 0 0 0 0 0 0
0 0 0 0
> 2.7365 -0.5322 0.1048 H 0 0 0 0 0 0 0 0
0 0 0 0
> 0.8109 -1.6139 -0.1611 H 0 0 0 0 0 0 0 0
0 0 0 0
> 1 6 1 0 0 0 0
> 2 8 1 0 0 0 0
> 4 3 1 0 0 0 0
> 4 11 1 0 0 0 0
> 4 10 1 0 0 0 0
> 5 1 1 0 0 0 0
> 5 2 1 0 0 0 0
> 5 3 1 0 0 0 0
> 7 1 1 0 0 0 0
> 9 2 1 0 0 0 0
> 12 3 1 0 0 0 0
> M CHG 1 1 5
> M END
>
> >
> > Regards,
> > - Noel
> >
> > On Tue, 26 Nov 2019 at 06:50, David van der Spoel
> mailto:sp...@xray.bmc.uu.se>
<mailto:sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se>>
> > <mailto:sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se>
<mailto:sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se>>>> wrote:
> >
> > Hi,
> >
> > I was trying to use obprop on an SDF file, but found
out that
> it adds
> > one hydrogen to my compound that should not be there.
I then
> went to
> > look at the code and removed these two lines
> > if (!mol.HasHydrogensAdded())
> > mol.AddHydrogens();
> > recompiled and installed.
> > Lo and behold, the bug is still there! That is, upon
reading
> an SDF
> > file
> > the library already adds a hydrogen that shouldn't be
there.
> >
> > What to do about this?
> > Replace
> > conv.Read(&mol, &ifs);
> > by a new call
> > conv.ReadAndDoNotModifyMyCompound(&mol, &ifs);
> >
> > Other suggestions?
> >
> > --
> > David van der Spoel, Ph.D., Professor of Biology
> > Head of Department, Cell & Molecular Biology, Uppsala
University.
> > Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
> > http://www.icm.uu.se
Re: [OpenBabel-Devel] Hydrogen management bug
Den 2019-11-26 kl. 13:06, skrev Noel O'Boyle:
Hi David,
Can you provide the input file?
Attached, thanks for looking into this.
Regards,
- Noel
On Tue, 26 Nov 2019 at 09:50, David van der Spoel <mailto:sp...@xray.bmc.uu.se>> wrote:
Den 2019-11-26 kl. 10:12, skrev Noel O'Boyle:
> An SDF file describes the number of hydrogens on each atom. Open
Babel
> is neither adding nor removing them. AddHydrogens() is just
making them
> explicit.
Unfortunately, no. The structure below has 7 hydrogens and one charge
but obprop adds one H and 4 (!) charges.
% obprop 2-aminoguanidinium.sdf
name 2-aminoguanidinium.sdf 1
formula CH8N4+
OpenBabel11261907103D
12 11 0 0 0 0 0 0 0 0999 V2000
-1.5988 -0.6139 0.0135 N 0 0 0 0 0 0 0 0 0 0 0 0
-0.4655 1.3957 -0.0077 N 0 0 0 0 0 0 0 0 0 0 0 0
0.7405 -0.6123 0.0118 N 0 0 0 0 0 0 0 0 0 0 0 0
1.9392 0.1153 0.0724 N 0 0 0 0 0 0 0 0 0 0 0 0
-0.4481 0.0607 0.0074 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.6144 -1.6250 0.0385 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.4894 -0.1345 0.0041 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.3186 1.9349 -0.0175 H 0 0 0 0 0 0 0 0 0 0 0 0
0.4173 1.8753 -0.1389 H 0 0 0 0 0 0 0 0 0 0 0 0
1.9696 0.6569 0.9451 H 0 0 0 0 0 0 0 0 0 0 0 0
2.7365 -0.5322 0.1048 H 0 0 0 0 0 0 0 0 0 0 0 0
0.8109 -1.6139 -0.1611 H 0 0 0 0 0 0 0 0 0 0 0 0
1 6 1 0 0 0 0
2 8 1 0 0 0 0
4 3 1 0 0 0 0
4 11 1 0 0 0 0
4 10 1 0 0 0 0
5 1 1 0 0 0 0
5 2 1 0 0 0 0
5 3 1 0 0 0 0
7 1 1 0 0 0 0
9 2 1 0 0 0 0
12 3 1 0 0 0 0
M CHG 1 1 5
M END
>
> Regards,
> - Noel
>
> On Tue, 26 Nov 2019 at 06:50, David van der Spoel
mailto:sp...@xray.bmc.uu.se>
> <mailto:sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se>>> wrote:
>
> Hi,
>
> I was trying to use obprop on an SDF file, but found out that
it adds
> one hydrogen to my compound that should not be there. I then
went to
> look at the code and removed these two lines
> if (!mol.HasHydrogensAdded())
> mol.AddHydrogens();
> recompiled and installed.
> Lo and behold, the bug is still there! That is, upon reading
an SDF
> file
> the library already adds a hydrogen that shouldn't be there.
>
> What to do about this?
> Replace
> conv.Read(&mol, &ifs);
> by a new call
> conv.ReadAndDoNotModifyMyCompound(&mol, &ifs);
>
> Other suggestions?
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Head of Department, Cell & Molecular Biology, Uppsala University.
> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
> http://www.icm.uu.se
>
>
> ___
> OpenBabel-Devel mailing list
> OpenBabel-Devel@lists.sourceforge.net
<mailto:OpenBabel-Devel@lists.sourceforge.net>
> <mailto:OpenBabel-Devel@lists.sourceforge.net
<mailto:OpenBabel-Devel@lists.sourceforge.net>>
> https://lists.sourceforge.net/lists/listinfo/openbabel-devel
>
--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
___________
OpenBabel-Devel mailing list
OpenBabel-Devel@lists.sourceforge.net
<mailto:OpenBabel-Devel@lists.sourceforge.net>
https://lists.sourceforge.net/lists/listinfo/openbabel-devel
--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
2-aminoguanidinium.sdf
Description: chemical/molfile
___
OpenBabel-Devel mailing list
OpenBabel-Devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] Hydrogen management bug
Den 2019-11-26 kl. 10:12, skrev Noel O'Boyle:
An SDF file describes the number of hydrogens on each atom. Open Babel
is neither adding nor removing them. AddHydrogens() is just making them
explicit.
Unfortunately, no. The structure below has 7 hydrogens and one charge
but obprop adds one H and 4 (!) charges.
% obprop 2-aminoguanidinium.sdf
name 2-aminoguanidinium.sdf 1
formula CH8N4+
OpenBabel11261907103D
12 11 0 0 0 0 0 0 0 0999 V2000
-1.5988 -0.61390.0135 N 0 0 0 0 0 0 0 0 0 0 0 0
-0.46551.3957 -0.0077 N 0 0 0 0 0 0 0 0 0 0 0 0
0.7405 -0.61230.0118 N 0 0 0 0 0 0 0 0 0 0 0 0
1.93920.11530.0724 N 0 0 0 0 0 0 0 0 0 0 0 0
-0.44810.06070.0074 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.6144 -1.62500.0385 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.4894 -0.13450.0041 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.31861.9349 -0.0175 H 0 0 0 0 0 0 0 0 0 0 0 0
0.41731.8753 -0.1389 H 0 0 0 0 0 0 0 0 0 0 0 0
1.96960.65690.9451 H 0 0 0 0 0 0 0 0 0 0 0 0
2.7365 -0.53220.1048 H 0 0 0 0 0 0 0 0 0 0 0 0
0.8109 -1.6139 -0.1611 H 0 0 0 0 0 0 0 0 0 0 0 0
1 6 1 0 0 0 0
2 8 1 0 0 0 0
4 3 1 0 0 0 0
4 11 1 0 0 0 0
4 10 1 0 0 0 0
5 1 1 0 0 0 0
5 2 1 0 0 0 0
5 3 1 0 0 0 0
7 1 1 0 0 0 0
9 2 1 0 0 0 0
12 3 1 0 0 0 0
M CHG 1 1 5
M END
Regards,
- Noel
On Tue, 26 Nov 2019 at 06:50, David van der Spoel <mailto:sp...@xray.bmc.uu.se>> wrote:
Hi,
I was trying to use obprop on an SDF file, but found out that it adds
one hydrogen to my compound that should not be there. I then went to
look at the code and removed these two lines
if (!mol.HasHydrogensAdded())
mol.AddHydrogens();
recompiled and installed.
Lo and behold, the bug is still there! That is, upon reading an SDF
file
the library already adds a hydrogen that shouldn't be there.
What to do about this?
Replace
conv.Read(&mol, &ifs);
by a new call
conv.ReadAndDoNotModifyMyCompound(&mol, &ifs);
Other suggestions?
--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
___
OpenBabel-Devel mailing list
OpenBabel-Devel@lists.sourceforge.net
<mailto:OpenBabel-Devel@lists.sourceforge.net>
https://lists.sourceforge.net/lists/listinfo/openbabel-devel
--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
___
OpenBabel-Devel mailing list
OpenBabel-Devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-devel
[OpenBabel-Devel] Hydrogen management bug
Hi, I was trying to use obprop on an SDF file, but found out that it adds one hydrogen to my compound that should not be there. I then went to look at the code and removed these two lines if (!mol.HasHydrogensAdded()) mol.AddHydrogens(); recompiled and installed. Lo and behold, the bug is still there! That is, upon reading an SDF file the library already adds a hydrogen that shouldn't be there. What to do about this? Replace conv.Read(&mol, &ifs); by a new call conv.ReadAndDoNotModifyMyCompound(&mol, &ifs); Other suggestions? -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
[OpenBabel-Devel] FindForceField returns nullptr
Hi, I am using a patched version of OB with the force field code to do atomtyping. My code is simply like this: std::string forcefield = "gaff"; auto *ff = OpenBabel::OBForceField::FindForceField(forcefield); it works fine on some installations (both Linux and Mac) but on other Linux boxes it does not work. The code is installed somewhere in my homedirectory. Environment variable BABEL_DATADIR or BABEL_LIBDIR have no effect as far as I can tell. Any clues? Cheers, -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] Algorithm for FF atomtypes
Den 2019-10-18 kl. 23:04, skrev Geoffrey Hutchison: How about Gaussian log files? It works with those as well. Somehow there bond orders are derived correctly as well although no such information is extracted from the log files. Are you saying that PDB is giving you different information than the Gaussian files? If so, I'd be curious to see some files. -Geoff I've uploaded a file to my work webserver http://folding.bmc.uu.se/diethyl-sulfate-3-oep.log.gz Using the master branch, freshly updated and built: % obenergy -ff GAFF diethyl-sulfate-3-oep.log.gz 3 os NO 4 s6 NO 5 os NO 6 o NO 7 o NO Now, using pdb: % obabel -ig09 diethyl-sulfate-3-oep.log.gz -opdb -O test.pdb 1 molecule converted % obenergy -ff GAFF test.pdb 3 os NO 4 s6 NO 5 os NO 6 oh NO 7 oh NO (note that no hydrogens are added but the atomtype changes). Possibly related to this is that conversion to sdf seems to have changed for this compound from version 2.4.1 to master (3.0). The double bonds S=O have disappered, however there is another change in the sixth column after the element symbol: % diff ds2.4.1.sdf ds3.0dev.sdf 10,11c10,11 < 0.00011.2905 -1.2428 O 0 0 0 0 0 0 0 0 0 0 0 0 <-0.00021.29051.2428 O 0 0 0 0 0 0 0 0 0 0 0 0 --- > 0.00011.2905 -1.2428 O 0 0 0 0 0 1 0 0 0 0 0 0 >-0.00021.29051.2428 O 0 0 0 0 0 1 0 0 0 0 0 0 29c29 < 4 7 2 0 0 0 0 --- > 4 7 1 0 0 0 0 32c32 < 6 4 2 0 0 0 0 --- > 6 4 1 0 0 0 0 To make things more complicated the charges generated are different for the two SDF file as well... Sorry for the long message! -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] Algorithm for FF atomtypes
Den 2019-10-18 kl. 20:37, skrev Noel O'Boyle:
With pdb files we have to guess the bond orders. With sdf files, we
don't. There shouldn't be any other difference.
How about Gaussian log files? It works with those as well.
Somehow there bond orders are derived correctly as well although no such
information is extracted from the log files.
On Fri, 18 Oct 2019, 18:52 David van der Spoel, <mailto:sp...@xray.bmc.uu.se>> wrote:
Hi,
it seems that the algorithm for determining bonds and atomtypes depends
on the input file, is that correct?
When I run
obenergy -ff GAFF file.pdb
I get different bonds then when I run
obenergy -ff GAFF file.sdf
Since the atomtyping is done based on smarts I wonder whether different
algorithms are used for generating smarts depending on the input file?
Alternatively, tips for debugging this, where to look in the code,
would
be appreciated.
Cheers,
--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
___
OpenBabel-Devel mailing list
OpenBabel-Devel@lists.sourceforge.net
<mailto:OpenBabel-Devel@lists.sourceforge.net>
https://lists.sourceforge.net/lists/listinfo/openbabel-devel
--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
___
OpenBabel-Devel mailing list
OpenBabel-Devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-devel
[OpenBabel-Devel] Algorithm for FF atomtypes
Hi, it seems that the algorithm for determining bonds and atomtypes depends on the input file, is that correct? When I run obenergy -ff GAFF file.pdb I get different bonds then when I run obenergy -ff GAFF file.sdf Since the atomtyping is done based on smarts I wonder whether different algorithms are used for generating smarts depending on the input file? Alternatively, tips for debugging this, where to look in the code, would be appreciated. Cheers, -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] C++11 requirement for 3.0 release (and going forward)?
Den 2019-09-11 kl. 17:59, skrev Geoffrey Hutchison: There are a few patches and pull requests asking for C++11 support in Open Babel. My main question is when we "pull the plug" on older compilers. Pro - drop older compilers for 3.0 since we're dropping a bunch of backwards compatibility Con - we're changing a lot of other stuff, let older compilers still use OB-3.0 From what I can tell, gcc-4.8 supports C++11 going back to mid-2013, but I'm not sure what distros have older compilers (e.g., CentOS). For reference, GROMACS is moving to C++14 with the upcoming 2020 release. C++11 has not caused us any issues. But there will be tons of new warnings :) Thoughts? -Geoff (My personal feeling is that we force C++ support for 3.0 and going forward.) ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] PDB files with multiple bonds via CONECT
Den 2019-07-29 kl. 22:11, skrev Geoffrey Hutchison: David Koes has contributed a pull request that fixes a bunch of file handling errors via round-trip testing. One thing he's implemented is to bring back writing PDB files with multiple bond orders via repeated CONECT records. Before I consider the rest of the patch, I want to know opinions on this. It's been a few years since OB reverted to "standard" PDB output and omitted only one CONECT per bond connection. This matches the practice of the PDB itself, although the "bond order" practice is fairly wide-spread. David feels strongly that OB should default to write files with bond order information. I can't find the threads of previous discussion, which suggests some of it was in the SourceForge bug tracker - I can't find anything pro or con from that discussion, only that it was eventually decided to stick with one CONECT per bond. - Do you favor single CONECT records? - Do you favor bond order information? - What do you feel are pro or cons? I'd like an open discussion. If it's possible, I know many people expect PDB files to support bond orders. What would be the drawback? Will other programs crash when they read a pdb file where the same CONECT is stated twice? I would love to have accurate bond orders in .sdf files (and also location of charged groups) but do not know what the status is. I mention these things since last time I checked (4 years ago) determining border was not very accurate (10% error rate). -Geoff ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] Can not find force field
Den 2018-10-01 kl. 17:23, skrev Geoffrey Hutchison: Hi, we are trying to implement the babel force field code into gromacs but face a weird problem. In summary, we copied the relevant lines from obenergy.cpp: … However this does not help when using the above statement in gromacs. Anything we have forgotten? My guess, without having time to look at the code this morning, is that plugins are not being loaded. Try initializing an OBConversion object. This forces plugin loading. -Geoff The plugins are loaded, but not the force fields. We already have a conv object before that but I will play with it more. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
[OpenBabel-Devel] Can not find force field
Hi, we are trying to implement the babel force field code into gromacs but face a weird problem. In summary, we copied the relevant lines from obenergy.cpp: auto *ff = OpenBabel::OBForceField::FindForceField(forcefield); The practically same code works in obenergy but not in our code, the problem is that the force field can not be found. In order to make obenergy work, environment variables have to be set: BABEL_DATADIR=/usr/local/share/openbabel BABEL_LIBDIR=/usr/local/lib/openbabel/2.4.90/ However this does not help when using the above statement in gromacs. Anything we have forgotten? -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
[OpenBabel-Devel] Getting rid of all warnings
Hi, I mentioned in an earlier thread it would be good to get rid of all warnings in order to make it easier to find real issues. I started with a little patch https://github.com/openbabel/openbabel/pull/1862, I guess this is the preferred way of proceeding? Cheers, -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] Modest Proposal - Gen3D won't do conformer searching
Den 2018-06-15 kl. 01:20, skrev Geoffrey Hutchison: Hi, One of the GSoC projects this summer is an improved fragment-based coordinate generation method. While that's going, I've been reading a lot of papers on 3D coordinate generation. As near as I can tell, no other program attempts to do a conformer search as part of the 3D generation. Everyone just generates one 3D geometry and then lets people do conformer searching on top if they choose. Some of the papers (e.g. Pierre Baldi) compare to Open Babel and then say that babel is slow - but that's because a lot more work is performed. I'd like to change --gen3d to default to creating a geometry. Optionally, geometry optimization can be performed, but the conformer searching will be separate: --gen3d # default: will only create a geometry --gen3d=opt # will perform MMFF or UFF optimization on the geometry I think for many uses, this will provide much faster performance. From your description above it is the conformer searching that makes it slow, so why not make that optional rather than the optimization? In addition it would be nice if the 3D generation would not crash every once in a while (at least it does in Avogadro). I guess due to numerical issues. Thoughts? Concerns? -Geoff -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] Proposal to require test cases
Den 2018-04-17 kl. 07:51, skrev Noel O'Boyle:
To avoid digressing, absolutely we would like to do this and have the
technical means to enforce...once we reduce the warnings. I did a
certain amount already this year. Once a particular type of warning is
eliminated we can add it as a requirement using gcc's treat warnings as
errors. But we're not there yet. Like Geoff says, we encourage people to
help.
If there's some other way this can be enforced on a patch by patch basis
(e.g. controlling for an increase in warnings), I'd be interested to
hear. Maybe you can point me to the relevant person over at Gromacs.
The GROMACS system uses gerrit https://www.gerritcodereview.com/ for
reviewing code and jenkins for building in the background
https://jenkins.io/index.html
As far as I understand this is not entirely trivial to maintain, but
once it is set up it works nicely.
- Noel
On Tue, 17 Apr 2018, 05:18 David van der Spoel, <mailto:sp...@xray.bmc.uu.se>> wrote:
Den 2018-04-16 kl. 22:46, skrev Dominik 'Rathann' Mierzejewski:
> On Monday, 16 April 2018 at 20:20, David van der Spoel wrote:
>> Den 2018-04-16 kl. 17:36, skrev David Koes:
>>> I didn't chime in since I thought it was obviously a good idea.
>>> However, I strongly agree that the process of creating a test
case needs
>>> to be as simple and documented as possible. I had a test case
with my
>>> last pull request, but it required a fair amount of poking
around to
>>> figure out how to best implement it (and this experience
prompted the
>>> GSoC project).
>>>
>>> Also, test cases may not make sense for some pull requests (e.g.
>>> documentation).
>>
>> Agree tests are a must.
>>
>> How about making warning-free code a must?
>
> Warning-free under which compiler (and version)? GCC adds new
warnings
> in every release.
Under all compilers. Obviously we can only fix the warnings we are
getting.
We have this policy in http://www.gromacs.org and it is enforced
automatically by the robot that verifies patches. No patches that
produce warnings on any platform (Linux, Mac, Windows) will be accepted.
>
> Regards,
> Dominik
>
--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
___
OpenBabel-Devel mailing list
OpenBabel-Devel@lists.sourceforge.net
<mailto:OpenBabel-Devel@lists.sourceforge.net>
https://lists.sourceforge.net/lists/listinfo/openbabel-devel
<https://lists.sourceforge.net/lists/listinfo/openbabel-devel>
--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
___
OpenBabel-Devel mailing list
OpenBabel-Devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] Proposal to require test cases
Den 2018-04-16 kl. 22:46, skrev Dominik 'Rathann' Mierzejewski: On Monday, 16 April 2018 at 20:20, David van der Spoel wrote: Den 2018-04-16 kl. 17:36, skrev David Koes: I didn't chime in since I thought it was obviously a good idea. However, I strongly agree that the process of creating a test case needs to be as simple and documented as possible. I had a test case with my last pull request, but it required a fair amount of poking around to figure out how to best implement it (and this experience prompted the GSoC project). Also, test cases may not make sense for some pull requests (e.g. documentation). Agree tests are a must. How about making warning-free code a must? Warning-free under which compiler (and version)? GCC adds new warnings in every release. Under all compilers. Obviously we can only fix the warnings we are getting. We have this policy in http://www.gromacs.org and it is enforced automatically by the robot that verifies patches. No patches that produce warnings on any platform (Linux, Mac, Windows) will be accepted. Regards, Dominik -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] Proposal to require test cases
- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsdm.link%2Fslashdot&data=01%7C01%7Cdkoes%40pitt.edu%7C4ac34c6b0120470e14fe08d5a363bb6b%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=83icsxpRpixLc17l6uM2q9vYFc9lbjP2pD35KIIhnvE%3D&reserved=0 ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fopenbabel-devel&data=01%7C01%7Cdkoes%40pitt.edu%7C4ac34c6b0120470e14fe08d5a363bb6b%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=9hu%2BMd5JtcoV4n1TJa62THT9OAayd1nbLd0eTCvDZKs%3D&reserved=0 -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
[OpenBabel-Devel] Output of charge to sdf file or inchi
Hi, I am reading a lot of Gaussian output files and added the following line to src/formats/gaussformat.cpp: mol.SetTotalCharge(total_charge); where total_charge is extracted from the log file. However, this is not printed to a .sdf file if I generate one, and not either to an InChI, e.g. using: % obabel -ig09 1-butyl-3-methylimidazolium-g4.log.gz -o inchi InChI=1S/C8H15N2/c1-3-4-5-10-7-6-9(2)8-10/h6-8H,3-5H2,1-2H3 1 molecule converted Any idea what code I should check to implement this? Cheers, -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] Reading molecular coordinates in standard orientation
On 20/06/17 18:32, Mohammad Mehdi Ghahremanpour wrote: Hello OpenBabel developers, Greetings! I am coding to read the coordinates from gaussian log file using OpenBabel libraries. Having the coordinates, I calculate molecular electric moments up to quadrupoles. To compare my results to QM, particularly for quadrupoles, I need to have the "Standard Orientation” as Gaussian does Population analysis in the Standard Orientation. My question is that when I use OpenBabel to extract the coordinate, does it return the Standard Orientation? You can try to use GetConformers to access all the coordinates that Gaussian prints, however it is only of either the standard orientation or of the input orientation. This you can check by comparing to the log file manually for a few cases. http://openbabel.org/dev-api/classOpenBabel_1_1OBMol.shtml#a5246a44bf82aa31c2f428665db94bfb8 Thanks, Mohammad -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] OB API/ABI changes
x27;s a bit weird about adding optional parameters, e.g. >>>> bool Build(OBMol &mol); >>>> becomes >>>> bool Build(OBMol &mol, bool stereoWarnings = true); >>>> >>>> This isn't an API issue, since a program build to the first will still >>>> recompile. This is an ABI problem, but we've never been too concerned about >>>> that from 2.x to 2.y. >>>> >>>>> I have a few comments to make regarding some of the changes, but will do >>>>> that separately. >>>> >>>> >>>> I'm obviously interested in the feedback. It's also useful to make sure >>>> that source documentation was added. >>>> >>>> Thanks, >>>> -Geoff >>> >>> >>> >>> -- >>> What NetFlow Analyzer can do for you? Monitors network bandwidth and >>> traffic >>> patterns at an interface-level. Reveals which users, apps, and protocols >>> are >>> consuming the most bandwidth. Provides multi-vendor support for NetFlow, >>> J-Flow, sFlow and other flows. Make informed decisions using capacity >>> planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e >>> ___ >>> OpenBabel-Devel mailing list >>> OpenBabel-Devel@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/openbabel-devel >>> >> >> -- >> >> Stefano Forli, PhD >> >> Assistant Professor of Integrative >> Structural and Computational Biology, >> Molecular Graphics Laboratory >> >> Dept. of Integrative Structural >> and Computational Biology, MB-112A >> The Scripps Research Institute >> 10550 North Torrey Pines Road >> La Jolla, CA 92037-1000, USA. >> >> tel: +1 (858)784-2055 >> fax: +1 (858)784-2860 >> email: fo...@scripps.edu >> http://www.scripps.edu/~forli/ > > -- > What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic > patterns at an interface-level. Reveals which users, apps, and protocols are > consuming the most bandwidth. Provides multi-vendor support for NetFlow, > J-Flow, sFlow and other flows. Make informed decisions using capacity > planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e > ___ > OpenBabel-Devel mailing list > OpenBabel-Devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-devel > -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] OB API/ABI changes
>> I'm obviously interested in the feedback. It's also useful to make sure >>> that source documentation was added. >>> >>> Thanks, >>> -Geoff >> >> -------------- >> What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic >> patterns at an interface-level. Reveals which users, apps, and protocols are >> consuming the most bandwidth. Provides multi-vendor support for NetFlow, >> J-Flow, sFlow and other flows. Make informed decisions using capacity >> planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e >> ___ >> OpenBabel-Devel mailing list >> OpenBabel-Devel@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/openbabel-devel >> > -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] Hard, Slow, or Tricky Kekule structures
On 06/04/16 21:58, Geoffrey Hutchison wrote: >> A bit off topic but it would be great if a new kekulizer had an option to >> preserve existing hydrogens. This is the only blocker to applying the >> respective valence models on reading for smiles and molfile. It also of >> course makes the problem a lot easier. > > That’s a given, actually. I’ve sat down and thought out the aromaticity > detection and Kekule code and how to explain it to CS undergrads. While I’m > sure there will be some initial bugs, I think the results will be strong. > > The base concept will be to keep atoms as-is when specified and apply bit > masks as constraints. That is, there will be a pass to remove atoms/nodes and > edges from the graph for Kekule assignment (e.g., aromatic S in thiophene or > -NH in pyrrole). > > I also have the beginnings of an aromaticity detection code that does not use > SSSR or LSSR assignments - simply doing a BFS path to count electrons, > inspired by recent discussion on OpenSMILES. > > The students also seem eager to attempt a more efficient, likely OpenMP > enabled ConnectTheDots implementation. > > Again, I’m looking for a good test set. I have 200 molecules on which OB fails to find the double bonds (at least when we tested 2 years ago: tested by looking at them one by on Avogadro). The files are derived from Gaussian which in addition to the atoms gives the total charge and multiplicity. It would be great if some/most of these can be fixed! http://folding.bmc.uu.se/OB-BondOrderProblems.zip David. > > -Geoff > -- > ___ > OpenBabel-Devel mailing list > OpenBabel-Devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-devel > -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
[OpenBabel-Devel] OBMol::EndModify
Hi, I'm debugging the workings of the above. In the file formats/gaussformat.cpp we are calling mol.SetTotalCharge(charge); however, down the line the function mol.EndModify(); is called which resets the charge. Without this call however the atomtype perception does not work well. Question therefore is how can I change the total charge of an OBMol? -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] Many test exception on Mac OSX with -DCMAKE_BUILD_TYPE=Debug
On 08/02/16 15:46, Geoffrey Hutchison wrote: >> if I compiled OB with -DCMAKE_BUILD_TYPE=Debug on my mac (OSX Mavericks, >> gcc 4.9) many tests fail with > > Why are you using gcc-4.9 on Mavericks? I don't think that's a supported > compiler. > > I don't have a problem compiling with Debug or Release using Apple Clang. In > principal, it's fine, but if you're trying to figure out a subtle bug, I'd > use the stock compiler. > > -Geoff > Because clang does not support OpenMP. But I will retry with clang. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] Many test exception on Mac OSX with -DCMAKE_BUILD_TYPE=Debug
On 08/02/16 14:37, David Lonie wrote:
> No idea what's happening there, but you can run ctest with -V to see
> the process output for the failing tests.
Thanks, that helps a bit. Now I get
5: Test command: /Users/spoel/GG/openbabel-dev/build/bin/test_runner
"aligntest" "5"
5: Environment variables:
5: BABEL_DATADIR=/Users/spoel/GG/openbabel-dev/openbabel/data
5: LD_LIBRARY_PATH=/Users/spoel/GG/openbabel-dev/build/lib
5: Test timeout computed to be: 1500
5: test_runner(86947,0x7fff7af0f310) malloc: *** error for object
0x105d64950: pointer being freed was not allocated
5: *** set a breakpoint in malloc_error_break to debug
5/150 Test #5: test_align_5 .***Exception:
Other 6.48 sec
Then debugging that I find it breaks at
165 //Return true if non-empty line read, false if empty line
read or eof or error
166 bool OBDefine::ReadLine(istream& ifs, string& ln, bool
removeComments)
167 {
-> 168 if(getline(ifs, ln))
169 {
170 if(removeComments)
171 {
(lldb) p ifs
error: incomplete type 'istream' (aka 'basic_istream >') where a complete type is required
note: forward declaration of 'basic_istream >'
error: 1 errors parsing expression
(lldb) p ln
(string) $0 = {}
Nothing obviously wrong here.
>
> 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 tests fail with
>>4/150 Test #4: test_align_4 .***Exception: Other
>>6.57 sec
>> Start 5: test_align_5
>> 5/150 Test #5: test_align_5 .***Exception:
>> Other 6.78 sec
>> Start 6: test_automorphism_1
>> 6/150 Test #6: test_automorphism_1 ..***Exception:
>> Other 6.46 sec
>> Start 7: test_automorphism_2
>>
>> Using the normal Release build type all tests pass. Any idea?
>> (I compiled it like that in order to debug a particular test).
>>
>> On Linux the build_type has no influence on the tests.
>>
>> Cheers,
>> --
>> David van der Spoel, Ph.D., Professor of Biology
>> Dept. of Cell & Molec. Biol., Uppsala University.
>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
>> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
>>
>> --
>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>> Monitor end-to-end web transactions and take corrective actions now
>> Troubleshoot faster and improve end-user experience. Signup Now!
>> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
>> ___
>> OpenBabel-Devel mailing list
>> OpenBabel-Devel@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/openbabel-devel
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
--
Site24x7 APM Insight: Get Deep Visibility into Application Performance
APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
Monitor end-to-end web transactions and take corrective actions now
Troubleshoot faster and improve end-user experience. Signup Now!
http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
___
OpenBabel-Devel mailing list
OpenBabel-Devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-devel
[OpenBabel-Devel] Many test exception on Mac OSX with -DCMAKE_BUILD_TYPE=Debug
Hi, if I compiled OB with -DCMAKE_BUILD_TYPE=Debug on my mac (OSX Mavericks, gcc 4.9) many tests fail with 4/150 Test #4: test_align_4 .***Exception: Other 6.57 sec Start 5: test_align_5 5/150 Test #5: test_align_5 .***Exception: Other 6.78 sec Start 6: test_automorphism_1 6/150 Test #6: test_automorphism_1 ..***Exception: Other 6.46 sec Start 7: test_automorphism_2 Using the normal Release build type all tests pass. Any idea? (I compiled it like that in order to debug a particular test). On Linux the build_type has no influence on the tests. Cheers, -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] bondtyp.txt
On 05/02/16 20:09, Geoffrey Hutchison wrote: > Strange. Can you send the bondtyp.txt or post it on GitHub? > > Thanks, > -Geoff Is it possible to run a test in the debugger? > >> On Feb 5, 2016, at 9:54 AM, Mohammad Mehdi Ghahremanpour >> wrote: >> >> Hello, >> >> I defined some new bond types in bondtyp.txt file and the compilation was >> done successfully and obenergy also worked well. >> For instance, it recognizes the atom type for hypervalent phosphorous in >> different molecules more accurate. >> However, the test number 38 related to test_gzip_1 failed afterward. >> >> >> Start 38: test_gzip_1 >> 38/145 Test #38: test_gzip_1 ..***Failed0.27 sec >> >> Any comments? >> >> Cheers, >> Mohammad >> -- >> Site24x7 APM Insight: Get Deep Visibility into Application Performance >> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month >> Monitor end-to-end web transactions and take corrective actions now >> Troubleshoot faster and improve end-user experience. Signup Now! >> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140___ >> OpenBabel-Devel mailing list >> OpenBabel-Devel@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/openbabel-devel > > > -- > Site24x7 APM Insight: Get Deep Visibility into Application Performance > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month > Monitor end-to-end web transactions and take corrective actions now > Troubleshoot faster and improve end-user experience. Signup Now! > http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 > ___ > OpenBabel-Devel mailing list > OpenBabel-Devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-devel > -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] Generating SMARTS format
On 20/01/16 10:59, Fredrik Wallner wrote: > Hi, > > What is the file format of the input structure? Converting from SMILES to > SMARTS isn’t really necessary since all SMILES are valid SMARTS and can be > put into the query directly. For other, more advanced queries you could > always try to convert to SMILES with the options -xn (to suppress name) and > -xh 1 (to suppress the addition of implicit hydrogens on aromatic nitrogens, > needs a value i.e. the ”1”, but it can be anything). > > Regardless of how you prepare the SMARTS, I can really recommend > http://smartsview.zbh.uni-hamburg.de to visualize the result to make sure you > got the correct structure. > Thanks for the tip! The issue at hand is to debug GAFF atomtype generation and therefore to see which SMARTS match the atomtype. To do this we have added a print statement to forcefieldGAFF.cpp that shows how the program cycles over the list of smarts in gaff.prm until it converges, e.g. using a Gaussian log file as input: % obenergy -ff GAFF pyridine.log Atom X-1 smart [*] Atom X-2 smart [*] Atom X-3 smart [*] Atom X-4 smart [*] Atom X-5 smart [*] Atom X-6 smart [*] Atom X-7 smart [*] Atom X-8 smart [*] Atom X-9 smart [*] Atom X-10 smart [*] Atom X-11 smart [*] Atom ha-2 smart [#1X1] Atom ha-4 smart [#1X1] Atom ha-6 smart [#1X1] Atom ha-8 smart [#1X1] Atom ha-10 smart [#1X1] Atom hc-4 smart [#1X1][CX4] Atom c3-3 smart [#6X4] Atom c2-1 smart [#6X3] Atom c2-5 smart [#6X3] Atom c2-7 smart [#6X3] Atom c2-9 smart [#6X3] Atom cc-7 smart [#6X3;R](=*)-*=* Atom cc-9 smart [#6X3;R](=*)-*=* Atom n2-11 smart [#7X2] Atom n1-11 smart [#7X2](=*)=* Atom n1-11 smart [#7X2](=*)=* > Kind regards, > Fredrik >> 18 jan. 2016 kl. 16:43 skrev Stefano Forli : >> >> Hi Mohammad, >> when I had to do it myself, I used the CACTVS web service at NIH: >> >> >> http://cactus.nci.nih.gov/chemical/structure/[YOUR-SMILES-HERE]/file?format=smarts >> >> Not very straightforward, but you can automate the process using some >> scripting (bash, python?). >> Hope this helps, >> >> S >> >> -- >> >> Stefano Forli, PhD >> >> Assistant Professor of Integrative >> Structural and Computational Biology, >> Molecular Graphics Laboratory >> >> Dept. of Integrative Structural >> and Computational Biology, MB-112F >> The Scripps Research Institute >> 10550 North Torrey Pines Road >> La Jolla, CA 92037-1000, USA. >> >> tel: +1 (858)784-2055 >> fax: +1 (858)784-2860 >> email: fo...@scripps.edu >> http://www.scripps.edu/~forli/ >> >> From: Mohammad Mehdi Ghahremanpour [ghahramanpou...@gmail.com] >> Sent: Monday, January 18, 2016 6:55 AM >> To: openbabel-devel@lists.sourceforge.net >> Subject: [OpenBabel-Devel] Generating SMARTS format >> >> Hi, >> >> I am updating gaff.prm file by defining new SMARTS format to support all >> GAFF atom types for different molecules. >> Is there any routine or function in the code which generates SMARTS from a >> given molecular structure as the output or even as the stderr? >> >> >> Cheers, >> Mohammad >> >> >> >> -- >> Site24x7 APM Insight: Get Deep Visibility into Application Performance >> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month >> Monitor end-to-end web transactions and take corrective actions now >> Troubleshoot faster and improve end-user experience. Signup Now! >> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140 >> ___ >> OpenBabel-Devel mailing list >> OpenBabel-Devel@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/openbabel-devel >> >> >> -- >> >> -- >> Site24x7 APM Insight: Get Deep Visibility into Application Performance >> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month >> Monitor end-to-end web transactions and take corrective actions now >> Troubleshoot faster and improve end-user experience. Signup Now! >> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140 >> ___ >> OpenBabel-Devel mailing list >> OpenBabel-Devel@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/openbabel-devel > > > -- > Site24x7 APM Insight: Get Deep Visibility int
Re: [OpenBabel-Devel] Bonds for unusual valencies
On 11/01/16 16:56, Geoffrey Hutchison wrote: >> for a number of ions, like hydronium (H3O+) and perchlorate (ClO4-) OB >> does detect all bonds. > > I would assume you mean “does not” detect all bonds. Indeed. > > The maximum number of bonds for a particular element is defined in > data/elements.txt (i.e. OBElement::MaxBonds() > http://openbabel.org/dev-api/classOpenBabel_1_1OBElement.shtml) > > I’m not sure I’d “fix it” on a general basis, since OBMol::ConnectTheDots() > is likely to recognize many spurious bonds. Instead, I’d probably set up some > level of separate perception routine. For example, in PDB files, these are > often residues and they have their own bond detection code. > > -Geoff > I implemented a call to ConnectTheDots but it does not add any more bonds. According to the documentation for this routine "This method adds single bonds between all atoms closer than their combined atomic covalent radii, then "cleans up" making sure bonded atoms are not closer than 0.4A and the atom does not exceed its valence. It implements blue-obelisk:rebondFrom3DCoordinates. " In other words, it may add the bond and then remove it again :( -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140 ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] Bonds for unusual valencies
On 11/01/16 15:42, Craig James wrote: > It would be helpful if you could be very specific. Are you reading a > file, or creating a molecule via a C++ program? What sort of output are > you looking at, a particular file (like SMILES, SDF, or PDB)? The best > way is to give a concrete example with sample files that will allow > others to repeat your results. Sorry about that. Reading a gaussian log file at http://folding.bmc.uu.se/images/hydronium.log then babel -ig09 hydronium.log -osdf h3o.sdf In this file only two O-H bonds are made even though the geometry is fine. > > Regards, > Craig > > On Mon, Jan 11, 2016 at 6:02 AM, David van der Spoel > mailto:sp...@xray.bmc.uu.se>> wrote: > > Hi, > > for a number of ions, like hydronium (H3O+) and perchlorate (ClO4-) OB > does detect all bonds. Is this determined by input files (like > bondtyp.txt) or by the code itself? Suggestions for how I can fix it? > > Cheers, > -- > David van der Spoel, Ph.D., Professor of Biology > Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. > sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se> > http://folding.bmc.uu.se > > > -- > Site24x7 APM Insight: Get Deep Visibility into Application Performance > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month > Monitor end-to-end web transactions and take corrective actions now > Troubleshoot faster and improve end-user experience. Signup Now! > http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140 > ___ > OpenBabel-Devel mailing list > OpenBabel-Devel@lists.sourceforge.net > <mailto:OpenBabel-Devel@lists.sourceforge.net> > https://lists.sourceforge.net/lists/listinfo/openbabel-devel > > > > > -- > - > Craig A. James > Chief Technology Officer > eMolecules, Inc. > - -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140 ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
[OpenBabel-Devel] Bonds for unusual valencies
Hi, for a number of ions, like hydronium (H3O+) and perchlorate (ClO4-) OB does detect all bonds. Is this determined by input files (like bondtyp.txt) or by the code itself? Suggestions for how I can fix it? Cheers, -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140 ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] (no subject)
On 29/12/15 23:00, Stefano Forli wrote: > Hi, > aiming at the 2.4 release, I've proposed a patch for the function > OBAtom::IsHbondAcceptor(), which is a bit more fine-grained than the current > one, which is essentially based only on the element, see here: > >https://github.com/openbabel/openbabel/pull/244 > > The goal was to provide results more accurate for small organic molecules > (i.e., drug-like, fragments, etc...) so my tests were mainly based on > molecules like these. > Geoff suggested to check also for possible effects of this change on the > force field typing (which, *hopefully* should be non-existent) so it would be > great if anybody with a bit more experience on the matter could take a look. > > Thanks! > > S > *any* force field typing, or a specific one? -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] 2.4 Release - Scheduling & Future Plans
On 14/12/15 22:07, Geoffrey Hutchison wrote: > Dear everyone, > > The 2.4 release was long-delayed, in part due to other (job-related) > obligations, but I’d like to get a push and some planning. > > I’m proposing the following schedule for the 2.4 release: > > - 31 January 2016 - Create 2.4 “release branch” (i.e., only critical > bug-fixes, documentation, etc. will be merged) > - 15 February 2016 - Target Date > > That gives us several weeks to incorporate any remaining changes, e.g.: > - New EEM charge model from J. Cheminf. (patch submitted, pending revision) > - New Distance Geometry coordinate creation (partially incorporated - needs > stereochemistry fixes) > > Please let me know if there are particular patches, features, and/or bugs to > target. > We will prepare a patch to gaff.prm and friends to get more reliable atom type assignments. > My goal is that we can begin to target a ~6 month schedule to release new > major versions (2.5, 2.6, 2.7, etc.) > > Thoughts? Suggestions? Any plans to run all the code through clang --analyze? For instance: % clang -I../include -I../../openbabel/include --analyze ../../openbabel/src/mol.cpp ../../openbabel/src/mol.cpp:4257:32: warning: Called C++ object pointer is null bestbond->SetBondOrder(bestbond->GetBondOrder()-1); ^~~~ 1 warning generated. I'd be happy to help, however in some cases it may require someone with more in-depth knowledge to fix the issues. > -Geoff > -- > ___ > OpenBabel-Devel mailing list > OpenBabel-Devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-devel > -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
[OpenBabel-Devel] Linking openbabel-dev formats
Hi, still having problems linking my code to OpenBabel, now getting this error: CMakeFiles/alexandria_objlib.dir/gauss_io.cpp.o: In function `read_babel(char const*, OpenBabel::OBMol*)': /home/spoel/GG/alexandria/gromacs/src/programs/alexandria/gauss_io.cpp:107: undefined reference to `OpenBabel::OBConversion::SetInFormat(char const*, bool)' CMakeFiles/alexandria_objlib.dir/gauss_io.cpp.o: In function `gmx_molprop_read_babel(char const*, alexandria::MolProp&, char*, char*, char*, char*, int, int, char const*)': The link command looks like this (due to tons of cmake): /opt/openmpi/bin/mpic++ -msse2 -std=c++11 -Wundef -Wextra -Wno-missing-field-initializers -Wl,-rpath,/home/spoel/GG/alexandria/gromacs/build/lib:/opt/sqlite/lib:/home/spoel/GG/openbabel-dev/install/lib -Wpointer-arith -Wall -Wno-unused-function -g -fno-inline -L/home/spoel/openbabel-dev/install/lib -L/home/apps/lib64 -L/home/apps/lib -L/opt/sqlite/lib CMakeFiles/alexandria.dir/alexandria.cpp.o (more c++ object files) CMakeFiles/alexandria_objlib.dir/tune_pol.cpp.o -o ../../../bin/alexandria -rdynamic ../../../lib/libgromacs.so.2.0.0 -lcln -lsqlite3 -ldl -lrt -lm -fopenmp -lz -lopenbabel -lfftw3f -lxml2 -lz -lfftw3f -lxml2 Any clues? -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
[OpenBabel-Devel] Conflict with system locale.h
Hi, I'm trying to compile a gromacs variant dependent on openbabel but am getting trouble because system c++ files include openbabels version of locale.h. I'm pretty sure I'm doing something wrong, but wouldn't it make sense anyhow to rename locale.h in OB to oblocale.h or something like that? Cheers, -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Go from Idea to Many App Stores Faster with Intel(R) XDK Give your users amazing mobile app experiences with Intel(R) XDK. Use one codebase in this all-in-one HTML5 development environment. Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs. http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140 ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] git version of OB broken?
On 15/07/15 19:29, Geoffrey Hutchison wrote: >> Forget this for now, it may be an apple issue anyway as it does work on >> Linux contrary to what I stated earlier. > > I'm using Mac / Clang and can't reproduce this. I know David Koes also > develops on Mac. > > Did you run "make install" on Mac? Have you tried clang instead of gcc-4.8? > > -Geoff > clang indeed solves the problem, thanks! -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Don't Limit Your Business. Reach for the Cloud. GigeNET's Cloud Solutions provide you with the tools and support that you need to offload your IT needs and focus on growing your business. Configured For All Businesses. Start Your Cloud Today. https://www.gigenetcloud.com/ ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
[OpenBabel-Devel] pull request problem
Hi, my pull request has errors in the appveyor that I don't understand. Clues appreciated! https://github.com/openbabel/openbabel/pull/200 Thanks, -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Don't Limit Your Business. Reach for the Cloud. GigeNET's Cloud Solutions provide you with the tools and support that you need to offload your IT needs and focus on growing your business. Configured For All Businesses. Start Your Cloud Today. https://www.gigenetcloud.com/ ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] git version of OB broken?
On 12/07/15 14:32, David van der Spoel wrote: > Hi, > > I compiled a fresh OB clone but get SEGV on a number of programs, > including babel. > % babel -ig98 decane-g4.log -osdf koko.sdf > Segmentation fault Forget this for now, it may be an apple issue anyway as it does work on Linux contrary to what I stated earlier. > > and > > % valgrind !! > valgrind babel -ig98 decane-g4.log -osdf koko.sdf > ==27734== Memcheck, a memory error detector > ==27734== Copyright (C) 2002-2012, and GNU GPL'd, by Julian Seward et al. > ==27734== Using Valgrind-3.8.1 and LibVEX; rerun with -h for copyright info > ==27734== Command: babel -ig98 decane-g4.log -osdf koko.sdf > ==27734== > ==27734== Invalid write of size 1 > ==27734==at 0x3DF1C0E35A: _dl_signal_error (in /lib64/ld-2.12.so) > ==27734==by 0x3DF1C0E4D9: _dl_signal_cerror (in /lib64/ld-2.12.so) > ==27734==by 0x3DF1C0A319: _dl_lookup_symbol_x (in /lib64/ld-2.12.so) > ==27734==by 0x3DF1C0E03F: _dl_fixup (in /lib64/ld-2.12.so) > ==27734==by 0x3DF1C14804: _dl_runtime_resolve (in /lib64/ld-2.12.so) > ==27734==by 0x40A41A: main (babel.cpp:318) > ==27734== Address 0x7feff6a80 is not stack'd, malloc'd or (recently) free'd > ==27734== > ==27734== Invalid read of size 8 > ==27734==at 0x3DF1C1721D: __longjmp (in /lib64/ld-2.12.so) > ==27734==by 0x6163656400383966: ??? > ==27734==by 0x6F6C2E34672D656D: ??? > ==27734==by 0x6664736F2D0066: ??? > ==27734==by 0x6664732E6F6B6F6A: ??? > ==27734==by 0x70733D52455354FF: ??? > ==27734==by 0x4E474F4C006C656E: ??? > ==27734==by 0x656F70733D454D40: ??? > ==27734==by 0x2F3D454D4F48006B: ??? > ==27734==by 0x6F70732F656D6F67: ??? > ==27734==by 0x3D48544150006C64: ??? > ==27734==by 0x70732F656D6F682E: ??? > ==27734== Address 0x7feff6a88 is not stack'd, malloc'd or (recently) free'd > > > Happens on both Linux and OSX with gcc >= 4.8 > Clues? > -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Don't Limit Your Business. Reach for the Cloud. GigeNET's Cloud Solutions provide you with the tools and support that you need to offload your IT needs and focus on growing your business. Configured For All Businesses. Start Your Cloud Today. https://www.gigenetcloud.com/ ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] git version of OB broken?
On 13/07/15 10:35, Noel O'Boyle wrote: > Can you provide a test case? http://folding.bmc.uu.se/decane-g4.log.gz > > On 12 July 2015 at 13:32, David van der Spoel wrote: >> Hi, >> >> I compiled a fresh OB clone but get SEGV on a number of programs, >> including babel. >> % babel -ig98 decane-g4.log -osdf koko.sdf >> Segmentation fault >> >> and >> >> % valgrind !! >> valgrind babel -ig98 decane-g4.log -osdf koko.sdf >> ==27734== Memcheck, a memory error detector >> ==27734== Copyright (C) 2002-2012, and GNU GPL'd, by Julian Seward et al. >> ==27734== Using Valgrind-3.8.1 and LibVEX; rerun with -h for copyright info >> ==27734== Command: babel -ig98 decane-g4.log -osdf koko.sdf >> ==27734== >> ==27734== Invalid write of size 1 >> ==27734==at 0x3DF1C0E35A: _dl_signal_error (in /lib64/ld-2.12.so) >> ==27734==by 0x3DF1C0E4D9: _dl_signal_cerror (in /lib64/ld-2.12.so) >> ==27734==by 0x3DF1C0A319: _dl_lookup_symbol_x (in /lib64/ld-2.12.so) >> ==27734==by 0x3DF1C0E03F: _dl_fixup (in /lib64/ld-2.12.so) >> ==27734==by 0x3DF1C14804: _dl_runtime_resolve (in /lib64/ld-2.12.so) >> ==27734==by 0x40A41A: main (babel.cpp:318) >> ==27734== Address 0x7feff6a80 is not stack'd, malloc'd or (recently) free'd >> ==27734== >> ==27734== Invalid read of size 8 >> ==27734==at 0x3DF1C1721D: __longjmp (in /lib64/ld-2.12.so) >> ==27734==by 0x6163656400383966: ??? >> ==27734==by 0x6F6C2E34672D656D: ??? >> ==27734==by 0x6664736F2D0066: ??? >> ==27734==by 0x6664732E6F6B6F6A: ??? >> ==27734==by 0x70733D52455354FF: ??? >> ==27734==by 0x4E474F4C006C656E: ??? >> ==27734==by 0x656F70733D454D40: ??? >> ==27734==by 0x2F3D454D4F48006B: ??? >> ==27734==by 0x6F70732F656D6F67: ??? >> ==27734==by 0x3D48544150006C64: ??? >> ==27734==by 0x70732F656D6F682E: ??? >> ==27734== Address 0x7feff6a88 is not stack'd, malloc'd or (recently) free'd >> >> >> Happens on both Linux and OSX with gcc >= 4.8 >> Clues? >> >> -- >> David van der Spoel, Ph.D., Professor of Biology >> Dept. of Cell & Molec. Biol., Uppsala University. >> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. >> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se >> >> -- >> Don't Limit Your Business. Reach for the Cloud. >> GigeNET's Cloud Solutions provide you with the tools and support that >> you need to offload your IT needs and focus on growing your business. >> Configured For All Businesses. Start Your Cloud Today. >> https://www.gigenetcloud.com/ >> ___ >> OpenBabel-Devel mailing list >> OpenBabel-Devel@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/openbabel-devel -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Don't Limit Your Business. Reach for the Cloud. GigeNET's Cloud Solutions provide you with the tools and support that you need to offload your IT needs and focus on growing your business. Configured For All Businesses. Start Your Cloud Today. https://www.gigenetcloud.com/ ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] git version of OB broken?
It seems the error below was introduced by this commit according to git bisect commit d34579511061a09ac7ea873294fa85c3eaff875e Author: dkoes Date: Sun Jun 14 15:21:05 2015 -0400 On 12/07/15 14:32, David van der Spoel wrote: > Hi, > > I compiled a fresh OB clone but get SEGV on a number of programs, > including babel. > % babel -ig98 decane-g4.log -osdf koko.sdf > Segmentation fault > > and > > % valgrind !! > valgrind babel -ig98 decane-g4.log -osdf koko.sdf > ==27734== Memcheck, a memory error detector > ==27734== Copyright (C) 2002-2012, and GNU GPL'd, by Julian Seward et al. > ==27734== Using Valgrind-3.8.1 and LibVEX; rerun with -h for copyright info > ==27734== Command: babel -ig98 decane-g4.log -osdf koko.sdf > ==27734== > ==27734== Invalid write of size 1 > ==27734==at 0x3DF1C0E35A: _dl_signal_error (in /lib64/ld-2.12.so) > ==27734==by 0x3DF1C0E4D9: _dl_signal_cerror (in /lib64/ld-2.12.so) > ==27734==by 0x3DF1C0A319: _dl_lookup_symbol_x (in /lib64/ld-2.12.so) > ==27734==by 0x3DF1C0E03F: _dl_fixup (in /lib64/ld-2.12.so) > ==27734==by 0x3DF1C14804: _dl_runtime_resolve (in /lib64/ld-2.12.so) > ==27734==by 0x40A41A: main (babel.cpp:318) > ==27734== Address 0x7feff6a80 is not stack'd, malloc'd or (recently) free'd > ==27734== > ==27734== Invalid read of size 8 > ==27734==at 0x3DF1C1721D: __longjmp (in /lib64/ld-2.12.so) > ==27734==by 0x6163656400383966: ??? > ==27734==by 0x6F6C2E34672D656D: ??? > ==27734==by 0x6664736F2D0066: ??? > ==27734==by 0x6664732E6F6B6F6A: ??? > ==27734==by 0x70733D52455354FF: ??? > ==27734==by 0x4E474F4C006C656E: ??? > ==27734==by 0x656F70733D454D40: ??? > ==27734==by 0x2F3D454D4F48006B: ??? > ==27734==by 0x6F70732F656D6F67: ??? > ==27734==by 0x3D48544150006C64: ??? > ==27734==by 0x70732F656D6F682E: ??? > ==27734== Address 0x7feff6a88 is not stack'd, malloc'd or (recently) free'd > > > Happens on both Linux and OSX with gcc >= 4.8 > Clues? > -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Don't Limit Your Business. Reach for the Cloud. GigeNET's Cloud Solutions provide you with the tools and support that you need to offload your IT needs and focus on growing your business. Configured For All Businesses. Start Your Cloud Today. https://www.gigenetcloud.com/ ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
[OpenBabel-Devel] git version of OB broken?
Hi, I compiled a fresh OB clone but get SEGV on a number of programs, including babel. % babel -ig98 decane-g4.log -osdf koko.sdf Segmentation fault and % valgrind !! valgrind babel -ig98 decane-g4.log -osdf koko.sdf ==27734== Memcheck, a memory error detector ==27734== Copyright (C) 2002-2012, and GNU GPL'd, by Julian Seward et al. ==27734== Using Valgrind-3.8.1 and LibVEX; rerun with -h for copyright info ==27734== Command: babel -ig98 decane-g4.log -osdf koko.sdf ==27734== ==27734== Invalid write of size 1 ==27734==at 0x3DF1C0E35A: _dl_signal_error (in /lib64/ld-2.12.so) ==27734==by 0x3DF1C0E4D9: _dl_signal_cerror (in /lib64/ld-2.12.so) ==27734==by 0x3DF1C0A319: _dl_lookup_symbol_x (in /lib64/ld-2.12.so) ==27734==by 0x3DF1C0E03F: _dl_fixup (in /lib64/ld-2.12.so) ==27734==by 0x3DF1C14804: _dl_runtime_resolve (in /lib64/ld-2.12.so) ==27734==by 0x40A41A: main (babel.cpp:318) ==27734== Address 0x7feff6a80 is not stack'd, malloc'd or (recently) free'd ==27734== ==27734== Invalid read of size 8 ==27734==at 0x3DF1C1721D: __longjmp (in /lib64/ld-2.12.so) ==27734==by 0x6163656400383966: ??? ==27734==by 0x6F6C2E34672D656D: ??? ==27734==by 0x6664736F2D0066: ??? ==27734==by 0x6664732E6F6B6F6A: ??? ==27734==by 0x70733D52455354FF: ??? ==27734==by 0x4E474F4C006C656E: ??? ==27734==by 0x656F70733D454D40: ??? ==27734==by 0x2F3D454D4F48006B: ??? ==27734==by 0x6F70732F656D6F67: ??? ==27734==by 0x3D48544150006C64: ??? ==27734==by 0x70732F656D6F682E: ??? ==27734== Address 0x7feff6a88 is not stack'd, malloc'd or (recently) free'd Happens on both Linux and OSX with gcc >= 4.8 Clues? -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Don't Limit Your Business. Reach for the Cloud. GigeNET's Cloud Solutions provide you with the tools and support that you need to offload your IT needs and focus on growing your business. Configured For All Businesses. Start Your Cloud Today. https://www.gigenetcloud.com/ ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
[OpenBabel-Devel] Building manual page
Hi, how do I get OB to generate man and html pages based on the source code for a new tool? Cheers, -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Don't Limit Your Business. Reach for the Cloud. GigeNET's Cloud Solutions provide you with the tools and support that you need to offload your IT needs and focus on growing your business. Configured For All Businesses. Start Your Cloud Today. https://www.gigenetcloud.com/ ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
[OpenBabel-Devel] Is obconformer the same as confab ?
Hi, I read the paper from 2011 by Neil and other OB gurus "Confab - Systematic generation of diverse low- energy conformers". Is this functionality available in the normal OB development code? I would like to be able to call a function to yield the real number of accessible conformers, rather than 3^N where N is the number of rotatable bonds. obconformer gives the number N but 3^N overestimates the real number of course. Or should we just run obconformer and use an energy treshold on the resulting conformations? Thanks, -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports and Dashboards with Interactivity, Sharing, Native Excel Exports, App Integration & more Get technology previously reserved for billion-dollar corporations, FREE http://pubads.g.doubleclick.net/gampad/clk?id=190641631&iu=/4140/ostg.clktrk ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] Generating symmetry number for a molecule
On 2015-02-09 19:12, Geoffrey Hutchison wrote: >> 1) Is this correct? Shouldn't it be Td? > > It will depend on the coordinates. The code is really "brute force" and > doesn't always pick up full symmetry. > > We'd love to have better symmetry perception code, but everything I've seen > is either Java or Fortran. These codes would need porting. > How much code would be involved? >> 2) Can I extract the symmetry number based on the point group? Or is >> there another way? In order to compute rotational entropy of molecules the rotational symmetry number sigma_rot must be known, as it contributes significantly, by -R ln sigma For instance we have a bunch of Gaussian calculations where this is incorrect. For methane the symmetry number is 12. which yields a correction of ~ -20 J/mol K. We have to apply this for ~2000 molecules so automation is needed. > > What do you mean by the "symmetry number?" Do you mean the order of the point > group? > > Thanks, > -Geoff > -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Dive into the World of Parallel Programming. The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] Thermochemistry
On 2015-02-05 15:47, Noel O'Boyle wrote: > Could you use "--" for options where the keyword is more than one > letter, and "-" only for those with a single letter? > Sure! Any suggestions for the important question: >> >> However it would be extremely helpful if someone can give me a pointer >> as to how to use OB to get the symmetry number! >> >> Thanks, -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Dive into the World of Parallel Programming. The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] Thermochemistry
I now made a program obthermo that works like this: % obthermo methane-g3-298.log obthermo - extract thermochemistry data from quantum chemistry logfiles Found symmetry number 1 in methane-g3-298.log DeltaHform(0K) -16.2427kcal/mol DeltaHform(298.149K)-18.1592kcal/mol DeltaSform(298.149K)-14.5067 cal/mol K DeltaGform(298.149K) -13.834kcal/mol S0(298.149K) 49.3317 cal/mol K However, the symmetry number is wrong, therefore: % obthermo -symm 12 methane-g3-298.log obthermo - extract thermochemistry data from quantum chemistry logfiles Found symmetry number 1 in methane-g3-298.log Changing symmetry number to 12 Applying rotational entropy correction Srot -4.93802 Applying correction to free energy T Srot DeltaHform(0K) -16.2427kcal/mol DeltaHform(298.149K)-18.1592kcal/mol DeltaSform(298.149K)-19.4448 cal/mol K DeltaGform(298.149K)-15.3063kcal/mol S0(298.149K) 44.3937 cal/mol K That seems to work, so I will prepare a patch for this. However it would be extremely helpful if someone can give me a pointer as to how to use OB to get the symmetry number! Thanks, -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Dive into the World of Parallel Programming. The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
[OpenBabel-Devel] Generating symmetry number for a molecule
Hi, I have an OBMol object and want to extract the symmetry number for it. My code now has the following lines: // Check for symmetry OBPointGroup obPG; obPG.Setup(mol); const char *pg = obPG.IdentifyPointGroup(); when running this with methane as an input the code prints returns "Cs". Two questions: 1) Is this correct? Shouldn't it be Td? 2) Can I extract the symmetry number based on the point group? Or is there another way? -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Dive into the World of Parallel Programming. The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
[OpenBabel-Devel] Thermochemistry
Hi, I have previously contributed some code to extract thermochemistry data from Gaussian log files, now my group are considering extending that somewhat. The data are gathered when reading a Gaussian log file containing the right information and stored in .sdf files. However it might be useful to simply print it on the terminal (there would be 8 results from a calculation). I assume this is not appreciated if one runs obabel for file conversion. Does this seem like a reasonable target for an "obthermo" program? One would run it like % obthermo file.log and it would print the relevant numbers to the screen. Or should such functionality be implemented in another tool? Thanks, -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Dive into the World of Parallel Programming. The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] one discrepancy between developer version of open babel and the stable version in atom types
On 2014-10-24 14:20, Mohammad Mehdi Ghahremanpour wrote: > Hi Geoff, > > If you remember my previous emails, the developer version often makes > mistake in assigning SP2-conjugated double bonds in the ring systems. > SP2-conjugated double bond should be cc-cd, but the developer version > sometimes assigns cc-cc that is incorrect. > > I compared the mol.cpp file between the developer master version and > V-2-3-2 version. They are different, particularly in void > OBMol::PerceiveBondOrders(). I compared these two files for this method > and saw that the sections of Pass5 and Pass6 are different. Pass 5 > checks for aromatic rings and assigns bonds, and Pass 6 assings > remaining bond types ordered by electronegativity. Pass 6 also > recognizes possible SP2-hybrid atoms. > > That would be great if you could have look at the void > OBMol::PerceiveBondOrders(). It may be useful to debug this problem. > We will try to find the issue which I suspect is in mol.cpp using git bisect. > Cheers! > Mohammad > > > >> On Oct 23, 2014, at 1:59 AM, Geoffrey Hutchison >> mailto:geoff.hutchi...@gmail.com>> wrote: >> >> Atom typing for force fields is not done through the internal type >> translation. For fidelity, it is done by the force field code itself. >> >> I haven't had time to look at code changes, but I suspect there have >> been GAFF patches since 2.3.2. >> >> Geoff >> >> On Wednesday, October 22, 2014, David van der Spoel >> mailto:sp...@xray.bmc.uu.se>> wrote: >> >> >> >> On 22 okt 2014, at 15:21, Geoffrey Hutchison >> > wrote: >> >> >> I am using the developer version in my programs, I have to use >> that, please help me understand why the developer version of >> openbabel has problem to match cc and cd atom types. >> > >> > The difference is that I noticed v2.3.2 was still using the >> Ghemical force field as the default, which isn't a good thing. You >> definitely want atom typing and energies from MMFF94, which is >> what's used in the developer "master" version. >> > >> > Hope that helps, >> >> We are using Gaff. But openbabel uses an internal type first, right? >> > -Geoff >> > >> > >> > >> >> -- >> > Comprehensive Server Monitoring with Site24x7. >> > Monitor 10 servers for $9/Month. >> > Get alerted through email, SMS, voice calls or mobile push >> notifications. >> > Take corrective actions from your mobile device. >> > http://p.sf.net/sfu/Zoho >> > ___ >> > OpenBabel-Devel mailing list >> > OpenBabel-Devel@lists.sourceforge.net >> > https://lists.sourceforge.net/lists/listinfo/openbabel-devel >> >> >> -- >> ___ >> OpenBabel-Devel mailing list >> OpenBabel-Devel@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/openbabel-devel >> >> -- >> ___ >> OpenBabel-Devel mailing list >> OpenBabel-Devel@lists.sourceforge.net >> <mailto:OpenBabel-Devel@lists.sourceforge.net> >> https://lists.sourceforge.net/lists/listinfo/openbabel-devel > -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] one discrepancy between developer version of open babel and the stable version in atom types
On 22 okt 2014, at 15:21, Geoffrey Hutchison wrote: >> I am using the developer version in my programs, I have to use that, please >> help me understand why the developer version of openbabel has problem to >> match cc and cd atom types. > > The difference is that I noticed v2.3.2 was still using the Ghemical force > field as the default, which isn't a good thing. You definitely want atom > typing and energies from MMFF94, which is what's used in the developer > "master" version. > > Hope that helps, We are using Gaff. But openbabel uses an internal type first, right? > -Geoff > > > -- > Comprehensive Server Monitoring with Site24x7. > Monitor 10 servers for $9/Month. > Get alerted through email, SMS, voice calls or mobile push notifications. > Take corrective actions from your mobile device. > http://p.sf.net/sfu/Zoho > ___ > OpenBabel-Devel mailing list > OpenBabel-Devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-devel -- ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] Smarts & GAFF blues / Kekulization
On 2014-03-08 22:21, Paul van Maaren wrote:
> I had a look at it too, the following hack seems to work for all types
> of imidazolium ions.
>
> In gaussformat.cpp I moved mol.SetTotalCharge(charge) close to the
> location where the charge is extracted from the Gaussian file and in
> kekulize.cpp I added the following:
>
> diff --git a/src/kekulize.cpp b/src/kekulize.cpp
> index dedf371..e5f7841 100644
> --- a/src/kekulize.cpp
> +++ b/src/kekulize.cpp
> @@ -515,6 +515,9 @@ namespace OpenBabel
> int idx;
> OBAtom *atom;
> OBBond *bond;
> +int charge;
> +
> +charge = _totalCharge;
>
> // Figure out which atoms are in this ring system and whether or not
> each
> // atom can donate an electron.
> @@ -532,6 +535,13 @@ namespace OpenBabel
> atomState[idx] = DOUBLE_PROHIBITED;
> if (DEBUG) { cout << "atom " << idx << " rejected NR3 double bonds
> " << endl; }
> }
> +
> + if (atom->IsNitrogen() && atom->GetFormalCharge() == 0 &&
> atom->GetValence() == 3 && charge > 0) {
> +atomState[idx] = DOUBLE_ALLOWED; // It has an electron it can
> donate, because of the total charge
> + charge--;
> +if (DEBUG) { cout << "atom " << idx << " rejected NR3 double bonds
> overruled by totalcharge " << endl; }
> + }
> +
>
> And I get:
>
> babel -ig03 1-ethyl-3-methylimidazolium3-esp.log.gz -osmi
> c1n(ccn1C)CC
>
Any further insights?
Are we on the right track here or should this be handled differently?
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
--
Learn Graph Databases - Download FREE O'Reilly Book
"Graph Databases" is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/13534_NeoTech
___
OpenBabel-Devel mailing list
OpenBabel-Devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] Smarts & GAFF blues / Kekulization
On 2014-03-07 22:16, Geoffrey Hutchison wrote: > I'm sorry, it's been a very hectic few weeks and I have not had much time for > e-mail, much less coding. > No worries, that's life. > As you suspect the problem is not with GAFF or SMARTS but the aromatic > detection and Kekulization of the molecules. > > I'm not 100% certain where the problem is. The first question is this.. > you're going from Gaussian and asking for bond detection. If you translate > from the Gaussian output to SDF, do you think the bond orders (e.g., double > bonds) are assigned correctly? > There should be an additional double bond N=C (on either of the N), so the answer is no. One of the ring carbons is detected as c3 and the whole ring designated AL (aliphatic?). > Next off, it seems like the problems are with charged molecules. Is the > positive charge assigned at all to one of the nitrogens? > > If not, if you take an SDF file and assign the positive charge, does that > aromatize correctly (e.g, when saved to SMILES the lower case letters appear). > Positive charge does not help, and adding the extra double bond in addition to that does not help either. > Basically the question is where in the chain is the bug occurring. For > example, if I take that file, I see this as a SMILES: > [CH]1N(C=CN1C)CC 1-ethyl-3-methylimidazolium3-esp.log.gz > > So I see the double bond appear, but not the charges.. This is how to break > down the problem — what part of the translation is failing? > > -Geoff > -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Subversion Kills Productivity. Get off Subversion & Make the Move to Perforce. With Perforce, you get hassle-free workflows. Merge that actually works. Faster operations. Version large binaries. Built-in WAN optimization and the freedom to use Git, Perforce or both. Make the move to Perforce. http://pubads.g.doubleclick.net/gampad/clk?id=122218951&iu=/4140/ostg.clktrk ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] Smarts & GAFF blues / Kekulization
On 2014-03-05 22:30, David van der Spoel wrote: > Dear list, > > we're struggling with getting OB to produce the right gaff atom parameters. > > We start from a Gaussian log file > (http://folding.bmc.uu.se/1-ethyl-3-methylimidazolium3-esp.log.gz). > Then, using > > obabel -ig09 1-ethyl-3-methylimidazolium3-esp.log.gz -omol2 koko.mol2 > > we find the ring atom types are not aromatic. Alternatively using > > obenergy -ff GAFF 1-ethyl-3-methylimidazolium3-esp.log.gz > we can see that the incorrect atom types for the ring atoms are produced. > > Incidentally, we have fixed some minor things in gaff.prm, but dealing > with aromatics is harder. Meddling with gaff.prm does not solve it. In > addition, the gaussformat.cpp file explicitly sets the total charge of > the molecule (all the way at the end, I may have added this previously), > but this is apparently not used in kekulizing. > > mol.SetTotalCharge(charge); > > Any clue would be appreciated, but it seems there are errors in smarts > parsing code as well as in gaff.prm > > A correct sdf generated by open eye software can be found at the pubchem > site here: > http://pubchem.ncbi.nlm.nih.gov/vw3d/vw3d.cgi?cmd=crtvw&reqid=1553910336500617460# > > Cheers, > Any pointers to where to start fixing this? I'm happy to do some programming, but it seems the problems lie deeper in the code than in forcefieldgaff.cpp. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Subversion Kills Productivity. Get off Subversion & Make the Move to Perforce. With Perforce, you get hassle-free workflows. Merge that actually works. Faster operations. Version large binaries. Built-in WAN optimization and the freedom to use Git, Perforce or both. Make the move to Perforce. http://pubads.g.doubleclick.net/gampad/clk?id=122218951&iu=/4140/ostg.clktrk ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
[OpenBabel-Devel] Smarts & GAFF blues
Dear list, we're struggling with getting OB to produce the right gaff atom parameters. We start from a Gaussian log file (http://folding.bmc.uu.se/1-ethyl-3-methylimidazolium3-esp.log.gz). Then, using obabel -ig09 1-ethyl-3-methylimidazolium3-esp.log.gz -omol2 koko.mol2 we find the ring atom types are not aromatic. Alternatively using obenergy -ff GAFF 1-ethyl-3-methylimidazolium3-esp.log.gz we can see that the incorrect atom types for the ring atoms are produced. Incidentally, we have fixed some minor things in gaff.prm, but dealing with aromatics is harder. Meddling with gaff.prm does not solve it. In addition, the gaussformat.cpp file explicitly sets the total charge of the molecule (all the way at the end, I may have added this previously), but this is apparently not used in kekulizing. mol.SetTotalCharge(charge); Any clue would be appreciated, but it seems there are errors in smarts parsing code as well as in gaff.prm A correct sdf generated by open eye software can be found at the pubchem site here: http://pubchem.ncbi.nlm.nih.gov/vw3d/vw3d.cgi?cmd=crtvw&reqid=1553910336500617460# Cheers, -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Subversion Kills Productivity. Get off Subversion & Make the Move to Perforce. With Perforce, you get hassle-free workflows. Merge that actually works. Faster operations. Version large binaries. Built-in WAN optimization and the freedom to use Git, Perforce or both. Make the move to Perforce. http://pubads.g.doubleclick.net/gampad/clk?id=122218951&iu=/4140/ostg.clktrk ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
[OpenBabel-Devel] gaff.prm
Hi, we're testing generating atom types for GAFF using OB and will compare the results with Antechamber as well. There are some issues that turned up like sulphur atoms not being recognized and getting atom type X (e.g. in the thiophene C4H4S ring structure). Is anybody still working on this stuff? Or should we just try to fix it as best we can and upload a new version of the file? Cheers, -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments & Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
[OpenBabel-Devel] License
Hi, I have a somewhat selfish question: as a GROMACS core developer I proposed to the developers to start using OpenBabel for file I/O of common formats in our software. However, as of version 4.6, gromacs is licensed under the LGPL, rather than GPL v2 which it was before, and what OpenBabel still is. In the case that GROMACS code is linked to by a closed source program (e.g. a commercial viewer) then it is not allowed to link to OpenBabel anymore, right? In principle we could use system calls to get a subset of the functionality, but that is not a great solution. Have the OpenBabel developers considered moving to LGPL? Regards, -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60133471&iu=/4140/ostg.clktrk ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] Proposal to deprecate babel
On 2013-05-11 19:30, Noel O'Boyle wrote: > While at the ACS a month ago I met some power users of Open Babel and > was surprised to hear that they are still using the babel executable > instead of obabel. > >>From this I assume that only a small number of people have moved to > using obabel. In my mind, babel has been deprecated for some years and > I have made zero attempt to create plugin options compatible with it. > There simply aren't enough letters in the alphabet to register all the > option parameters necessary, as evidenced by the current LPMD plugin's > warning messages (I'll sort this out). > > So I propose we officially forget about registering option parameters > and add a message to babel along the lines of: > > """Deprecation notice: The babel executable you are running is > deprecated and may be removed in a future release of Open Babel. You > should used the obabel executable instead. obabel has more features > and works much better. For more information on using obabel, type > "obabel -H" """ > > Ok, so maybe we won't remove 'babel' in a future release (though I > recommend aliasing babel to obabel in a few years), but it's time to > start encouraging users to switch. The "works much better" line is > lame, but whatever it takes :-) Keeping the two side by side just adds to the confusion. Is there any functionality in babel that is not in obabel, and can not be ported easily? That would really be the only reason to keep it. > > - Noel > > -- > Learn Graph Databases - Download FREE O'Reilly Book > "Graph Databases" is the definitive new guide to graph databases and > their applications. This 200-page book is written by three acclaimed > leaders in the field. The early access version is available now. > Download your free book today! http://p.sf.net/sfu/neotech_d2d_may > ___ > OpenBabel-Devel mailing list > OpenBabel-Devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-devel > -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. This 200-page book is written by three acclaimed leaders in the field. The early access version is available now. Download your free book today! http://p.sf.net/sfu/neotech_d2d_may ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] types.txt
On 2013-04-30 10:43, David van der Spoel wrote: > On 2013-04-26 21:22, Geoffrey Hutchison wrote: >>> I assume it works like this that OB determines the atom type to be HO (H >>> bound to O). >> >> No, no. This file is like a big translation dictionary. It says "if an atom >> type comes in from a PCModel file with atom type X," that's equivalent to .. >> well, everything on that row. Obviously, this need not be a one to one >> mapping. HO is a particularly good example, since I think PCModel has the >> "MMX" force field and separates between different types of HO hydrogens -- >> sorry I can't find the MMX atom type list right now. >> >> So we could, in principal, have the internal atom types as a superset of all >> atom types, but I think this is a bit crazy. >> >> If you want the internal atom typing rules, see data/atomtyp.txt >> (particularly EXTTYP). >> >> Hope that helps, >> -Geoff >> > Thanks for pointing that out. This means in practice that OB can not > distinguish between all those atomtypes that are used in random > packages, right? > > It would still be useful to have a textual description of each OB atom > type, what information there is in atomtyp.txt is not very descriptive. > > Let me just expand on why I am interested in this: we are busy developing a new force field, and would like to use the OB types as the basis, to be translated to new force field atom types, which would need to be a subset of these types. On a side note, it seems that a number of Nitrogen atom types have atomnumber 6 (or maybe Rar and R are carbons anyway?) Rar 6 0 62 1 C C 3 C 2 R.ar 33 C C 2 1 C.0 26 1 R 6 0 62 1 C C 3 C 2 R. 33 C C 2 1 C.0 26 1 Nr 6 0 62 8 C C 3 C 2 Nr. 33 C C 2 1 C.0 26 8 -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET Get 100% visibility into your production application - at no cost. Code-level diagnostics for performance bottlenecks with <2% overhead Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap1 ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] types.txt
On 2013-04-26 21:22, Geoffrey Hutchison wrote: >> I assume it works like this that OB determines the atom type to be HO (H >> bound to O). > > No, no. This file is like a big translation dictionary. It says "if an atom > type comes in from a PCModel file with atom type X," that's equivalent to .. > well, everything on that row. Obviously, this need not be a one to one > mapping. HO is a particularly good example, since I think PCModel has the > "MMX" force field and separates between different types of HO hydrogens -- > sorry I can't find the MMX atom type list right now. > > So we could, in principal, have the internal atom types as a superset of all > atom types, but I think this is a bit crazy. > > If you want the internal atom typing rules, see data/atomtyp.txt > (particularly EXTTYP). > > Hope that helps, > -Geoff > Thanks for pointing that out. This means in practice that OB can not distinguish between all those atomtypes that are used in random packages, right? It would still be useful to have a textual description of each OB atom type, what information there is in atomtyp.txt is not very descriptive. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET Get 100% visibility into your production application - at no cost. Code-level diagnostics for performance bottlenecks with <2% overhead Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap1 ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] types.txt
On 2013-04-26 11:17, Noel O'Boyle wrote: > It's always good to link changes in the code to specific bugs that > need fixing. It may be useful to see whether you identify such cases > here before you spend time on this. If you decide to go ahead, I would > suggest that you add some test cases to ensure that existing correct > behaviour is retained. Wouldn't you agree it is a bug that an OB atom type has an undefined mapping to other force fields? > > - Noel > > On 26 April 2013 09:08, David van der Spoel wrote: >> On 2013-04-26 07:36, David van der Spoel wrote: >>> On 2013-04-26 05:38, Geoffrey Hutchison wrote: >>>>> I'm looking at types.txt and wondering whether not the internal >>>>> representation of atom types (INT) should be unique? Now there are three >>>>> HO, two H, three C3 etc. >>>> >>>> IIRC, the issue is that some programs have different distinctions. For >>>> example PCModel (PCM) separates between multiple HO types. >>>> >>>> Now that's not saying it's perfect. I think I did a "sort -u" at one >>>> point, because people kept adding to the bottom and there would be >>>> duplicate entries, etc. So if you spot good simplifications, please >>>> suggest them. >>>> >>> I assume it works like this that OB determines the atom type to be HO (H >>> bound to O). Now you can in principle subdivide this into different HO, >>> depending on what the O is bound to. However if you don't use different >>> names for these HO (HO1, HO2 etc.) then the information gets lost, right? >>> >>> I would suggest that >>> 1) no double internal names should be allowed >>> 2) a description of each atom type should be included in the file >> >> How about the following file format: >> # Comment text >> # More Comment text >> # Internal|Description|FF1|FF2| >> H|Generic hydrogen|H1|H3|... >> HO|Hydrogen bound to oxygen|HO1|HP|... >> >> where the internal names are unique (and this should be enforced). >> >> I'm happy to implement it, so please let me know if there are grave >> objections. >>> >>> >>>> For example, I don't remember the difference between MM2 "H" type 5 and >>>> type 28. We could certainly separate these. >>>> >>>> -Geoff >>>> >>> >>> >> >> >> -- >> David van der Spoel, Ph.D., Professor of Biology >> Dept. of Cell & Molec. Biol., Uppsala University. >> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. >> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se >> >> -- >> Try New Relic Now & We'll Send You this Cool Shirt >> New Relic is the only SaaS-based application performance monitoring service >> that delivers powerful full stack analytics. Optimize and monitor your >> browser, app, & servers with just a few lines of code. Try New Relic >> and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr >> ___ >> OpenBabel-Devel mailing list >> OpenBabel-Devel@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/openbabel-devel -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Try New Relic Now & We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, & servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] types.txt
On 2013-04-26 07:36, David van der Spoel wrote: > On 2013-04-26 05:38, Geoffrey Hutchison wrote: >>> I'm looking at types.txt and wondering whether not the internal >>> representation of atom types (INT) should be unique? Now there are three >>> HO, two H, three C3 etc. >> >> IIRC, the issue is that some programs have different distinctions. For >> example PCModel (PCM) separates between multiple HO types. >> >> Now that's not saying it's perfect. I think I did a "sort -u" at one point, >> because people kept adding to the bottom and there would be duplicate >> entries, etc. So if you spot good simplifications, please suggest them. >> > I assume it works like this that OB determines the atom type to be HO (H > bound to O). Now you can in principle subdivide this into different HO, > depending on what the O is bound to. However if you don't use different > names for these HO (HO1, HO2 etc.) then the information gets lost, right? > > I would suggest that > 1) no double internal names should be allowed > 2) a description of each atom type should be included in the file How about the following file format: # Comment text # More Comment text # Internal|Description|FF1|FF2| H|Generic hydrogen|H1|H3|... HO|Hydrogen bound to oxygen|HO1|HP|... where the internal names are unique (and this should be enforced). I'm happy to implement it, so please let me know if there are grave objections. > > >> For example, I don't remember the difference between MM2 "H" type 5 and type >> 28. We could certainly separate these. >> >> -Geoff >> > > -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Try New Relic Now & We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, & servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] types.txt
On 2013-04-26 05:38, Geoffrey Hutchison wrote: >> I'm looking at types.txt and wondering whether not the internal >> representation of atom types (INT) should be unique? Now there are three >> HO, two H, three C3 etc. > > IIRC, the issue is that some programs have different distinctions. For > example PCModel (PCM) separates between multiple HO types. > > Now that's not saying it's perfect. I think I did a "sort -u" at one point, > because people kept adding to the bottom and there would be duplicate > entries, etc. So if you spot good simplifications, please suggest them. > I assume it works like this that OB determines the atom type to be HO (H bound to O). Now you can in principle subdivide this into different HO, depending on what the O is bound to. However if you don't use different names for these HO (HO1, HO2 etc.) then the information gets lost, right? I would suggest that 1) no double internal names should be allowed 2) a description of each atom type should be included in the file > For example, I don't remember the difference between MM2 "H" type 5 and type > 28. We could certainly separate these. > > -Geoff > -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Try New Relic Now & We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, & servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] types.txt
On 2013-04-25 09:45, David van der Spoel wrote: > Hi, > > I'm looking at types.txt and wondering whether not the internal > representation of atom types (INT) should be unique? Now there are three > HO, two H, three C3 etc. > > Cheers, > And is there a description of each of the types somewhere? -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Try New Relic Now & We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, & servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
[OpenBabel-Devel] types.txt
Hi, I'm looking at types.txt and wondering whether not the internal representation of atom types (INT) should be unique? Now there are three HO, two H, three C3 etc. Cheers, -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Try New Relic Now & We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, & servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] Bug in obabel on Mac when input and output formats match
On 2013-04-09 03:28, Marcus D. Hanwell wrote: > Hi, > > We are using obabel to perform geometry optimizations etc on the > command line, and we are hitting a bug that seems to only present > itself on the Mac. If the input and output formats are the same then > the operation fails, for example, > > obabel -icml -ocml --minimize --log --ff UFF > > That is using standard in/out, but it also seems to happen when using > files. This works as expected on Linux and Windows, are we diverging > from expected use too much or is this a bug. This is the same in 2.3.2 > and master, using 10.6.8 and GCC 4.2.1. > > The full output is below, compared with using xyz as the output (we > could of course work around this issue by using different formats). > There is a SMARTS error I just noticed too, but that seems unrelated > to this bug on the Mac. > > $ obabel -icml ethane.cml -ocml --minimize --log --ff UFF > == > *** Open Babel Error in RegisterOptionParam >The number of parameters needed by option "t" in The LPMD file > format. differs from an earlier registration. > == > *** Open Babel Error in SMARTSError >SMARTS Error: > [#6+:1](~N:2)(~N:3)* > ^ > > > A T O M T Y P E S > > IDX TYPE RING > 1 H_ NO > 2 C_3 NO > 3 H_ NO > 4 H_ NO > 5 C_3 NO > 6 H_ NO > 7 H_ NO > 8 H_ NO > > S E T T I N G U P C A L C U L A T I O N S > > SETTING UP BOND CALCULATIONS... > SETTING UP ANGLE CALCULATIONS... > SETTING UP TORSION CALCULATIONS... > SETTING UP OOP CALCULATIONS... > SETTING UP VAN DER WAALS CALCULATIONS... > > C O N J U G A T E G R A D I E N T S > > STEPS = 2500 > > STEP n E(n) E(n-1) > > 1 2.378 4.699 > 4 1.069 1.069 > CONJUGATE GRADIENTS HAS CONVERGED > 0 molecules converted > > $ obabel -icml ethane.cml -oxyz --minimize --log --ff UFF > == > *** Open Babel Error in RegisterOptionParam >The number of parameters needed by option "t" in The LPMD file > format. differs from an earlier registration. > == > *** Open Babel Error in SMARTSError >SMARTS Error: > [#6+:1](~N:2)(~N:3)* > ^ > > > A T O M T Y P E S > > IDX TYPE RING > 1 H_ NO > 2 C_3 NO > 3 H_ NO > 4 H_ NO > 5 C_3 NO > 6 H_ NO > 7 H_ NO > 8 H_ NO > > S E T T I N G U P C A L C U L A T I O N S > > SETTING UP BOND CALCULATIONS... > SETTING UP ANGLE CALCULATIONS... > SETTING UP TORSION CALCULATIONS... > SETTING UP OOP CALCULATIONS... > SETTING UP VAN DER WAALS CALCULATIONS... > > C O N J U G A T E G R A D I E N T S > > STEPS = 2500 > > STEP n E(n) E(n-1) > > 1 2.378 4.699 > 4 1.069 1.069 > CONJUGATE GRADIENTS HAS CONVERGED > 8 > Ethane > H 1.17997 -0.003101.00769 > C 0.76583 -0.02288 -0.02125 > H 1.161440.85024 -0.57962 > H 1.10906 -0.95033 -0.52388 > C -0.765820.022910.02127 > H -1.16141 -0.850540.57913 > H -1.109180.950090.52435 > H -1.179890.00361 -1.00770 > 1 molecule converted > > -- > Precog is a next-generation analytics platform capable of advanced > analytics on semi-structured data. The platform includes APIs for building > apps and a phenomenal toolset for data science. Developers can use > our toolset for easy data analysis & visualization. Get a free account! > http://www2.precog.com/precogplatform/slashdotnewsletter > ___ > OpenBabel-Devel mailing list > OpenBabel-Devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-devel > Interesting, it seems to be something with writing cml. I'm using trunk but I get: [artemisia:~/tmp] % obabel -isdf ethanol.sdf -ocml ethanol.cml == *** Open Babel Error in OpenAndSetFormat Cannot open ethanol.cml and then all the output is dumped on the terminal instead (it does do the minimization as requested). So it seems something goes wrong opening a cml file for writing. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -
Re: [OpenBabel-Devel] What's new in OB?
On 2013-03-27 22:04, Craig James wrote: > > > Reinis Danne mailto:rei4...@gmail.com>>wrote: > > > I think it was the thread where I mentioned I'm working on > > kekulization algorithm using graph theory (maximum matching). It > > has been quite some time when I last looked at that code and it > > is not yet usable. > > > I don't know if this overlaps with your work, but I spent a fair amount > of time on the aromaticity-detection algorithm and improved it by orders > of magnitude. See the comment in kekulize.cpp around line 887 -- copied > below. > > Craig > > NEW ANALYSIS methods: rely on LSSR methods to only target one ring. > Works much faster on fullerens, graphene, etc. > > Recursive function to find a sensible kekule assignment of single and > double bonds for an aromatic ring system. > > Very large aromatic ring systems can be very computationally difficult. > In theory, there are 2^N ways to try assigning single/double to assign > bonds (where N is the number of bonds in the aromatic system). For > large molecules such as fullerenes, this number (e.g. 2^60) exceeds all > computing power in the world. > > To avoid this, three strategies are used. > > 1. The algorithm proceeds by assigning bonds to each complete ring > from the LSSR, rather than treating the whole aromatic system. > That reduces the complexity to roughly O(2^R) where R is the number > of rings in the LSSR. > > 2. Each time a ring is completed (a trial assignment of > single/double), the whole tentative assignment is checked for > sensibility. If any atom has all of its bonds assigned, but > still has a leftover electron, then the assignment fails before a > lot more work is invested. (Atoms connected to bonds that haven't > been examined yet are ignored during this test.) > > 3. When one ring is finished, the next ring is selected by finding the > one "most connected" to previously-considered rings. Say, for > example, we're working on a fullerene and have just finished one > ring. The second ring will be one that's adjacent to the first > ring (one of its bonds is already assigned). Now for the third > ring, we can pick one that's in a "corner" of the first two, that > is, a ring that has TWO bonds already assigned. > > Strategy #3 means that the completed area of the ring system (the bonds > we've already assigned) will tend to have a "minimal perimeter", and any > atom that has one bond assigned will quickly have all of its bonds > assigned. That means that strategy #2 can be used as early as possible > to detect bond assignments that can never work, long before the entire > aromatic system has been examined. Strategy #1 means that we can > typically assign alternating single/double bonds correctly to any > particular ring on the first try. > > Together, these three strategies together mean that even very large > aromatic systems are typically solved in milliseconds. Great that a number of solutions are being worked on. At least for Carbon based molecules one can relatively easy filter out errors by counting the sum of bond orders on the bonds to each carbon (although there are pathetic cases like carbon monoxide). I would rather not get bond orders from the algorithm than incorrect ones. It is my impression that the total charge on molecules is not (always) taken into account, even if it is present from e.g. quantum chemistry files. > > > > > -- > Own the Future-Intel® Level Up Game Demo Contest 2013 > Rise to greatness in Intel's independent game demo contest. > Compete for recognition, cash, and the chance to get your game > on Steam. $5K grand prize plus 10 genre and skill prizes. > Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d > > > > ___ > OpenBabel-Devel mailing list > OpenBabel-Devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-devel > -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Own the Future-Intel® Level Up Game Demo Contest 2013 Rise to greatness in Intel's independent game demo contest. Compete for recognition, cash, and the chance to get your game on Steam. $5K grand prize plus 10 genre and skill prizes. Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] What's new in OB?
On 2013-03-14 13:57, Geoffrey Hutchison wrote: >> Is there a RESP module in OB? I have code that does this rather well, >> the only thing that does not work exactly as it should is symmetry >> detection (to find atoms that should have the same charge because of >> symmetry). > > There is not a RESP module. If you have code you'd like to contribute, I > suspect it would be *highly* used. My analysis is that the vast majority of > citation for Open Babel come through Gasteiger charges. :-) > >> I have previously asked some questions here about bond-order/atom type >> detection and we are now going through a dataset of ~2000 molecules >> manually to see whether double bonds generated by OB are in the right >> place. There a few systems, in particular with five-rings, where >> problems occur. It seems to me that these errors can be detected >> relatively easy (just looking for C with 3 bonds would help). > > If you can get me a set of such mistakes, I can certainly adjust the bond > order code. I've put a zip file with a bunch of more or less pathetic cases on http://folding.bmc.uu.se/OB-BondOrderProblems.zip Some common themes are hetero rings, fused rings with odd number of carbons, isocyano groups etc. Thanks for looking into this. > >> Somebody here said he was working on a complete new algorithm for this >> purpose > > I haven't seen such a thread. I wrote the majority of the existing code, > based on Roger Sayle's "Cruft to Content" talk which you can find online. > > I've followed the literature and haven't found anything which appears > dramatically better. > > -Geoff > -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Own the Future-Intel® Level Up Game Demo Contest 2013 Rise to greatness in Intel's independent game demo contest. Compete for recognition, cash, and the chance to get your game on Steam. $5K grand prize plus 10 genre and skill prizes. Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] What's new in OB?
On 2013-03-13 22:15, Noel O'Boyle wrote: > Hey all, > > I'm thinking about giving a CINF flash talk at the Spring ACS on > "What's new and cooking in OB". > > It's somewhat rough, but here are the items I have so far. I've gone > through the commit logs, but there seems to be a bias towards features > I've added (!) so I'd appreciate if you could let me know if you can > think of anything missing: > > == > What's new in OB 2.3.2? > > InChified SMILES and Universal SMILES > > Smiles options: > R do not reuse bond closure symbols > o output in user specified order > F generate SMILES for a fragment > > Asciiformat and Painterformat > Improved PNG depiction quality, and added all the options currently > available for SVG > Multimolecule PNGs > Access the stereo from Python > Andy Lang's new MP descriptor > > --highlight highlight substructures in depictions > enable easier debugging of group contribution descriptors > improved stereo perception from 2D wedge and hash bonds > > SVG highlight option - highlight molecule if condition is met > > What's under development? I've added some stuff to extract enthalpy of formation from gaussian files, and still working to improve that functionality. Is there a RESP module in OB? I have code that does this rather well, the only thing that does not work exactly as it should is symmetry detection (to find atoms that should have the same charge because of symmetry). I have previously asked some questions here about bond-order/atom type detection and we are now going through a dataset of ~2000 molecules manually to see whether double bonds generated by OB are in the right place. There a few systems, in particular with five-rings, where problems occur. It seems to me that these errors can be detected relatively easy (just looking for C with 3 bonds would help). Somebody here said he was working on a complete new algorithm for this purpose and therefore it might not be worthwhile to fix the old one, or what do you think? > > Speed up ring algorithms. > New strict SMILEs parser > Find duplicate molecules (--unique) > MDLBench mdlvalence > == > > - Noel > > -- > Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > http://p.sf.net/sfu/appdyn_d2d_mar > ___ > OpenBabel-Devel mailing list > OpenBabel-Devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-devel > -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_mar ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] GitHub Migration
On 2013-03-01 00:16, Geoffrey Hutchison wrote: > Noel pointed out to me that the migration to the "new" SourceForge tracker, > etc. did weird things to SVN. That is, the SourceForge code browser points at > the "migrated" SVN, but the old SVN repository still exists. And all of us > have been using it. > >> One thing I've found is that each project has a new SVN repo, which is not >> kept in sync with the old one. In other words, people (myself included) have >> been commiting to the old SVN repo for Open Babel, but the commits since Oct >> have not been moving across to the new one. See >> https://sourceforge.net/p/openbabel/code/commit_browser >> >> As usual, there is no info or warning about this at SF (that I could see). I >> assume that at some point the old SVN will be killed by SF, so I guess >> either we should all move across or else make the move to git. > > So I just pulled the plug. In principal, you cannot write to the SVN > repository at SourceForge anymore. > > If you'd like to access and/or write changes, you'll need to use GitHub. This > means that some of you will probably need to go create a GitHub account (very > painless) and point your SVN at a new location: > > https://github.com/blog/1178-collaborating-on-github-with-subversion > > svn co --depth empty https://github.com/openbabel/openbabel > cd openbabel; svn up trunk > … > # Done! > > Better yet, you might consider trying Git. I'm happy to provide some > tutorials and/or howtos on the mailing list, and there are really nice GUIs > from GitHub: > http://mac.github.com > http://windows.github.com > 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). > I realize this is a pain, but keeping the SVN at SourceForge is a problem > waiting to happen. I'll try to facilitate a mirroring system for the > now-read-only repository at SF.net. > > -Geoff > -- > Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > http://p.sf.net/sfu/appdyn_d2d_feb > ___ > OpenBabel-Devel mailing list > OpenBabel-Devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-devel > -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] Heuristic for selecting best forcefield?
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 included for backwards-compatibility -- it was much > easier to implement than MMFF94. > >> * Is GAFF particularly good at any systems that the others handle poorly? > > It's the "Generalized Amber Force Field." It should be fairly good with > proteins, but I don't think it's been tuned for speed as much as MMFF94 and > UFF have been. > Speed? Should make no difference at all. Lennard Jones + Coulomb on point charges. It is rather not for proteins (that is regular Amber) but for small (organic) ligand molecules. > -Geoff > -- > Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > http://p.sf.net/sfu/appdyn_d2d_jan > ___ > OpenBabel-Devel mailing list > OpenBabel-Devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-devel > -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_jan ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] Heuristic for selecting best forcefield?
On 2013-02-04 16:24, David Lonie wrote: > 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 pure organics, say only C, H, O, N, S > * MMFF94 is good for dynamics > * UFF is good for non-organics > > This is mostly inline with the documentation on the avogadro wiki: > > http://avogadro.openmolecules.net/wiki/Tutorials:Force_fields > > My big questions are: > > * Are there cases where MMFF94s should be preferred to Ghemical? > * Is GAFF particularly good at any systems that the others handle poorly? > > Comments, corrections, suggestions are welcome! I would always prefer a well-defined modern force field based on published work. MMF94 is relatively old so GAFF would be my preferred one for cases that are supported. Is there a publication describing Ghemical? My group provides a database of small molecule topologies that have been tested with GAFF (and OPLS/AA) at http://virtualchemistry.org/. This is still relatively small, but the main point is that this kind of tests are available for the popular force fields. How about support for macromolecules? > > Thanks, > Dave > > > -- > Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > http://p.sf.net/sfu/appdyn_d2d_jan > > > > ___ > OpenBabel-Devel mailing list > OpenBabel-Devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-devel > -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_jan ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] Bzip2 format support
On 2013-01-17 18:20, Kirill Okhotnikov wrote: > Dear Babel Developers, > > I decided to implement bzip2 pack/unpack functionality in open-babel > (#91 bzip2 compression/decompression). > > I'm new in openbabel, so I want to discuss some things. > > 1) I decided to go for boost iostreams library. They have compressed > gzip/bzip2 support in similar way, like implemented now in obabel. I > think, that it will be good idea to have boost library to be required by > the project (connected permanently). Some other boost libraries can be > useful. For example, Program Options, Geometry, RegExp. In the future > developers can easily use this powerful well known library. I'm not sure that most developers would vote for an obligatory boost library. Isn't it quite hard to compile on uncommon platforms? Optional might be OK though, what do other people think? > > 2) Compressed stream is not supported tellg/seekg functions. So, some > formats cannot be read. What should I do with it? May be add a property > to format plug-in, that the format is not supported compressed streams. Exit with a comprehensible warning makes most sense. For the Gaussian format I implemented support for gzipped files by using normal C++ I/O operations (rather than the old workaround that was in place). Why wouldn't that work with bzip? > > 3) Can somebody help me to compile and test the system under MS Windows? > > > Best, > Kirill Okhotnikov. > > > > -- > Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, > MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current > with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft > MVPs and experts. ON SALE this month only -- learn more at: > http://p.sf.net/sfu/learnmore_122712 > ___ > OpenBabel-Devel mailing list > OpenBabel-Devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-devel > -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnmore_122712 ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] Python compile failure on trunk with OBFreeGridPoint
On 2012-12-12 22:02, Maciek Wójcikowski wrote:
> I have simmilar problem building Trunk on CentOS 5:
>
> CMakeFiles/bindings_python.dir/python/openbabel-python.cpp.o: In
> function `_wrap_new_OBFreeGridPoint__SWIG_0':
> /mnt/lustre/home/maciek/openbabel/openbabel-svn/scripts/python/openbabel-python.cpp:20526:
> undefined reference to `OpenBabel::OBFreeGridPoint::OBFreeGridPoint()'
> CMakeFiles/bindings_python.dir/python/openbabel-python.cpp.o: In
> function `_wrap_delete_OBFreeGridPoint':
> /mnt/lustre/home/maciek/openbabel/openbabel-svn/scripts/python/openbabel-python.cpp:20557:
> undefined reference to `OpenBabel::OBFreeGridPoint::~OBFreeGridPoint()'
> collect2: ld returned 1 exit status
>
This is fixed by https://sourceforge.net/p/openbabel/patches/60/
Maybe one of the core developers can have a look at it and add it to trunk?
>
> cmake 2.9.10.2, Python 2.7, swig 2.0.8, eigen 2+3 rest is stock.
>
>
> Pozdrawiam, | Best regards,
> Maciek Wójcikowski
> mac...@wojcikowski.pl <mailto:mac...@wojcikowski.pl>
>
>
>
> 2012/11/22 David van der Spoel <mailto:sp...@xray.bmc.uu.se>>
>
> On 2012-11-22 10:33, Noel O'Boyle wrote:
> > I've a problem compiling the Python bindings on trunk with MSVC
> due to
> > a recent addition to the codebase:
> >
> > 2>openbabel-python.obj : error LNK2019: unresolved external symbol
> > "__declspec(dllimport) public: __thiscall
> > OpenBabel::OBFreeGridPoint::OBFreeGridPoint(void)"
> > (__imp_??0OBFreeGridPoint@OpenBabel@@QAE@XZ) referenced in function
> > __wrap_new_OBFreeGridPoint
> > 2>openbabel-python.obj : error LNK2019: unresolved external symbol
> > "__declspec(dllimport) public: __thiscall
> > OpenBabel::OBFreeGridPoint::~OBFreeGridPoint(void)"
> > (__imp_??1OBFreeGridPoint@OpenBabel@@QAE@XZ) referenced in function
> > __wrap_delete_OBFreeGridPoint
> >
> > OBFreeGridPoint is in generic.h and appears to have the necessary
> > OBAPI incantation. Any ideas?
> >
> > I note in passing that OBFreeGrid (a different class) doesn't seem to
> > have the same ctor and dtor as the other OBGenericData
> subclasses. I'm
> > not sure of the significance of this...
>
> My bad I guess.
> The constructor and destructor are not defined anywhere. Adding {} in
> the generic.h file for both should fix that.
>
> >
> > - Noel
> >
> >
>
> --
> > Monitor your physical, virtual and cloud infrastructure from a single
> > web console. Get in-depth insight into apps, servers, databases,
> vmware,
> > SAP, cloud infrastructure, etc. Download 30-day Free Trial.
> > Pricing starts from $795 for 25 servers or applications!
> > http://p.sf.net/sfu/zoho_dev2dev_nov
> > ___
> > OpenBabel-Devel mailing list
> > OpenBabel-Devel@lists.sourceforge.net
> <mailto:OpenBabel-Devel@lists.sourceforge.net>
> > https://lists.sourceforge.net/lists/listinfo/openbabel-devel
> >
>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205
> .
> sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se>
> http://folding.bmc.uu.se
>
>
> --
> Monitor your physical, virtual and cloud infrastructure from a single
> web console. Get in-depth insight into apps, servers, databases, vmware,
> SAP, cloud infrastructure, etc. Download 30-day Free Trial.
> Pricing starts from $795 for 25 servers or applications!
> http://p.sf.net/sfu/zoho_dev2dev_nov
> ___
> OpenBabel-Devel mailing list
> OpenBabel-Devel@lists.sourceforge.net
> <mailto:OpenBabel-Devel@lists.sourceforge.net>
> https://lists.sourceforge.net/lists/listinfo/openbabel-devel
>
>
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
--
LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial
Remotely access PCs and mobile devices and provide instant support
Improve your efficiency, and focus on delivering more value-add services
Discover what IT Professionals Know. Rescue delivers
http://p.sf.net/sfu/logmein_12329d2d
___
OpenBabel-Devel mailing list
OpenBabel-Devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] mmff94 test fail
On 2012-12-10 15:44, Geoffrey Hutchison wrote: >> The SSSR of buckyball has changed. Can I just update the energy in the >> appropriate test file? > > Yes. You can do that manually or run ffmff94 -g to re-generate the test file. > By the way is there an instruction somewhere how to add tests to the repository? -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
[OpenBabel-Devel] reply-to list as default?
Hi, wouldn't it make sense to make the default for replying to a list message to reply to the list rather than the sender? The volume on the list is rather moderate, and it helps to archive discussions in full. Cheers, -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Keep yourself connected to Go Parallel: TUNE You got it built. Now make it sing. Tune shows you how. http://goparallel.sourceforge.net ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
[OpenBabel-Devel] Fwd: Re: failed tests in trunk
On 2012-11-29 20:04, Tim Vandermeersch wrote: > Hi, > > I recently added the smiley test, this is still experimental and I have > to check it on more platforms etc. So don't worry about this one. > > I have no idea why the MMFF94 test fails though. I assume you were not > wroking on the force field code? No I'm not... I wonder how one can check the output? I'd like to make some gaussian processing tests. > > Tim > > On Thu, Nov 29, 2012 at 7:49 PM, David van der Spoel > mailto:sp...@xray.bmc.uu.se>> wrote: > > Hi, > > I ran the tests in the latest trunk and got > > The following tests FAILED: > 14 - smiley_Test (Failed) > 37 - ffmmff94_Test (Failed) > > any clue? > > -- > David van der Spoel, Ph.D., Professor of Biology > Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205 > . > sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se> > http://folding.bmc.uu.se > > > -- > Keep yourself connected to Go Parallel: > VERIFY Test and improve your parallel project with help from experts > and peers. http://goparallel.sourceforge.net > ___ > OpenBabel-Devel mailing list > OpenBabel-Devel@lists.sourceforge.net > <mailto:OpenBabel-Devel@lists.sourceforge.net> > https://lists.sourceforge.net/lists/listinfo/openbabel-devel > > -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Keep yourself connected to Go Parallel: TUNE You got it built. Now make it sing. Tune shows you how. http://goparallel.sourceforge.net ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
[OpenBabel-Devel] failed tests in trunk
Hi, I ran the tests in the latest trunk and got The following tests FAILED: 14 - smiley_Test (Failed) 37 - ffmmff94_Test (Failed) any clue? -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Keep yourself connected to Go Parallel: VERIFY Test and improve your parallel project with help from experts and peers. http://goparallel.sourceforge.net ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] Python compile failure on trunk with OBFreeGridPoint
On 2012-11-22 10:33, Noel O'Boyle wrote:
> I've a problem compiling the Python bindings on trunk with MSVC due to
> a recent addition to the codebase:
>
> 2>openbabel-python.obj : error LNK2019: unresolved external symbol
> "__declspec(dllimport) public: __thiscall
> OpenBabel::OBFreeGridPoint::OBFreeGridPoint(void)"
> (__imp_??0OBFreeGridPoint@OpenBabel@@QAE@XZ) referenced in function
> __wrap_new_OBFreeGridPoint
> 2>openbabel-python.obj : error LNK2019: unresolved external symbol
> "__declspec(dllimport) public: __thiscall
> OpenBabel::OBFreeGridPoint::~OBFreeGridPoint(void)"
> (__imp_??1OBFreeGridPoint@OpenBabel@@QAE@XZ) referenced in function
> __wrap_delete_OBFreeGridPoint
>
> OBFreeGridPoint is in generic.h and appears to have the necessary
> OBAPI incantation. Any ideas?
>
> I note in passing that OBFreeGrid (a different class) doesn't seem to
> have the same ctor and dtor as the other OBGenericData subclasses. I'm
> not sure of the significance of this...
My bad I guess.
The constructor and destructor are not defined anywhere. Adding {} in
the generic.h file for both should fix that.
>
> - Noel
>
> --
> Monitor your physical, virtual and cloud infrastructure from a single
> web console. Get in-depth insight into apps, servers, databases, vmware,
> SAP, cloud infrastructure, etc. Download 30-day Free Trial.
> Pricing starts from $795 for 25 servers or applications!
> http://p.sf.net/sfu/zoho_dev2dev_nov
> ___
> OpenBabel-Devel mailing list
> OpenBabel-Devel@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-devel
>
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
--
Monitor your physical, virtual and cloud infrastructure from a single
web console. Get in-depth insight into apps, servers, databases, vmware,
SAP, cloud infrastructure, etc. Download 30-day Free Trial.
Pricing starts from $795 for 25 servers or applications!
http://p.sf.net/sfu/zoho_dev2dev_nov
___
OpenBabel-Devel mailing list
OpenBabel-Devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-devel
[OpenBabel-Devel] Gaussian coordinate reading
Hi, in the gaussformat.cpp file the atomic coordinates are read from either Input orientation: or Standard orientation: in practice the last occurrence of either is used. These coordinates are very different (rotated and translated). I would think both might be of interest however there is no mechanism to control which coordinates one gets. Or is there? -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
[OpenBabel-Devel] Patch for Gaussian stuff uploaded.
http://sourceforge.net/p/openbabel/patches/59/ -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] convert obmol to inchi in C++
On 2012-11-14 17:36, Chris Morley wrote:
> On 14/11/2012 16:02, David van der Spoel wrote:
>> Hi,
>>
>> if I have an existing OBMol object, is there a simple way to get an
>> InChi from it in C++ without rereading the file?
>>
>> Thanks,
>>
>
> OBMol mol;
> ...
> OBConversion conv;
> conv.SetOutFormat("inchi");
> std::string s = conv.WriteString(&mol);
close but no cigar:
InChI=1S/H2O/h1H2
should be
InChI=1S/H2O/h1H2
and
InChI=1S/C2H6OS/c1-4(2)3/h1-2H3
should be
InChI=1S/C2H6OS/c1-4(2)3/h1-2H3
Can I just chop off the last 5 characters? Looks like a line feed or so.
>
> Chris
>
> --
> Monitor your physical, virtual and cloud infrastructure from a single
> web console. Get in-depth insight into apps, servers, databases, vmware,
> SAP, cloud infrastructure, etc. Download 30-day Free Trial.
> Pricing starts from $795 for 25 servers or applications!
> http://p.sf.net/sfu/zoho_dev2dev_nov
> ___
> OpenBabel-Devel mailing list
> OpenBabel-Devel@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-devel
>
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
--
Monitor your physical, virtual and cloud infrastructure from a single
web console. Get in-depth insight into apps, servers, databases, vmware,
SAP, cloud infrastructure, etc. Download 30-day Free Trial.
Pricing starts from $795 for 25 servers or applications!
http://p.sf.net/sfu/zoho_dev2dev_nov
___
OpenBabel-Devel mailing list
OpenBabel-Devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-devel
[OpenBabel-Devel] convert obmol to inchi in C++
Hi, if I have an existing OBMol object, is there a simple way to get an InChi from it in C++ without rereading the file? Thanks, -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] Extracting energy data from OBMol
On 2012-11-13 12:15, Chris Morley wrote:
> On 12/11/2012 17:50, David van der Spoel wrote:
>> Hi,
>>
>> I have now implemented the extraction of G2/3/4 energies from Gaussian
>> files, e.g.
>>
>> % babel -ig98 water-g3.log.gz -oinchi
>> DHf(0K) = -56.778415 kcal/mol.
>> DHf(298.15K) = -59.838414 kcal/mol.
>> InChI=1S/H2O/h1H2
>> 1 molecule converted
>> 11 audit log messages
>>
>> Now my question is what to do with the result?
>>
>> So far I've used:
>>
>> OBPairData (set attribute and value)
>> OBMol.SetData(PairData)
>>
>> since each calculation yields at least two values (Delta H_form at 0K
>> and 298.15K) this seemed to be the most flexible way. Then
>>
>> OBPairData obpd = OBMol.GetData("DHf(0K)") would get the appropriate
>> data struct from a molecule. Is this a suitable way?
>
> OBPairData is a good place for single items because they can be
> automatically output as properties in sdf or cml files (without
> programming).
Cool, that works instead.
>
G4
>
-56.694956
>
-59.754956
>
> It would also be possible to make a descriptor DHf(T) with T as a
> parameter, although I doubt this is of sufficiently general interest.
>
In practice we don't have experimental data at any other T than 298.15K
which makes it difficult.
> Is the code available?
>
Soon. I'm also including ESP points with new class based on OBGrid, but
for this I need to find out how to add an instance of OBGrid to a molecule.
> Chris
>
>
> --
> Monitor your physical, virtual and cloud infrastructure from a single
> web console. Get in-depth insight into apps, servers, databases, vmware,
> SAP, cloud infrastructure, etc. Download 30-day Free Trial.
> Pricing starts from $795 for 25 servers or applications!
> http://p.sf.net/sfu/zoho_dev2dev_nov
> ___
> OpenBabel-Devel mailing list
> OpenBabel-Devel@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-devel
>
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
--
Monitor your physical, virtual and cloud infrastructure from a single
web console. Get in-depth insight into apps, servers, databases, vmware,
SAP, cloud infrastructure, etc. Download 30-day Free Trial.
Pricing starts from $795 for 25 servers or applications!
http://p.sf.net/sfu/zoho_dev2dev_nov
___
OpenBabel-Devel mailing list
OpenBabel-Devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-devel
Re: [OpenBabel-Devel] Quadrupole, ESP and more
On 2012-11-12 21:43, Geoff Hutchison wrote: >> I just noticed that multipoles higher than dipole are not read in from >> Gaussian log files, and neither are ESP points! > > These are relatively new data. I added the support (e.g., quadrupoles) in the > core library, but not complete implementations. > > So yes, if you're willing to add support, people will use it. ESP, you > probably want to add as an OBGridData type. > In fact OBGridData will not work, since not all the points are on a regular grid. I'd rather need a vector of double x,y,z,potential; -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov ___ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
