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
% e
1.5291886255562557,
- -0.7244637238690441,
- 0.8189433858796095
+ 2.313816216007316,
+ 0.669250157347277,
+ 2.4146659588503769,
+ 4.189331679349326,
+ 4.052466878708012,
+
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 document
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 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,
>
>
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
t 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
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
w
ttps://lists.sourceforge.net/lists/listinfo/openbabel-devel
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När du har kontakt med oss på Uppsala universitet med e-post så innebär det att
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e.
Thanks,
Mohammad
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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 v
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
the code.
Cheers,
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Uppsala University.
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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
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!
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s?
-Geoff
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http://virtualche
l 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
slow).
So is there any rationale for these or should we phase them out?
Cheers,
--
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Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
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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
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, skre
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 i
, 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?
--
Davi
her
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,
--
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Head of Department, Cell & Molecular Bi
rry for the long message!
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lthough 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 ru
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,
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Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596
sts.sourceforge.net
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Box 596, SE-75124 Uppsala, Sweden. Phone: +4618
ago) determining
border was not very accurate (10% error rate).
-Geoff
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will play with it more.
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forgotten?
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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,
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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:
>> D
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 proces
tes, Slashdot.org! http://sdm.link/slashdot
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, 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?
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iling list
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Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http:/
ourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/openbabel-devel
>>>
>>
>> --
>>
>> Stefano Forli, PhD
>>
>> Assistant Professor of Integrative
>> Structural and Computational Biology,
>> Molecular Graphics Lab
> that source documentation was added.
>>>
>>> Thanks,
>>> -Geoff
>>
>> --------------
>> What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
>&g
el mailing list
> OpenBabel-Devel@lists.sourceforge.net
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>
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does not work well.
Question therefore is how can I change the total charge of an OBMol?
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Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.sehttp://folding.
7;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.
--
Davi
'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
test).
On Linux the build_type has no influence on the tests.
Cheers,
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Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.u
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> Mo
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 m
> 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 inpu
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 & M
ge 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?
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ome cases it may require someone with
more in-depth knowledge to fix the issues.
> -Geoff
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lopenbabel -lfftw3f -lxml2 -lz
-lfftw3f -lxml2
Any clues?
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Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.seh
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
-
gt; Did you run "make install" on Mac? Have you tried clang instead of gcc-4.8?
>
> -Geoff
>
clang indeed solves the problem, thanks!
--
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Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala
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, Swed
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
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,
>> inclu
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
y 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?
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Hi,
how do I get OB to generate man and html pages based on the source code
for a new tool?
Cheers,
--
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Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se
rs, 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,
--
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or ~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
>
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emely 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. Ph
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,
--
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"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?
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Box 596, 75124 Upp
print the relevant numbers to the screen.
Or should such functionality be implemented in another tool?
Thanks,
--
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Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc
gt;> 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 p
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
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 trac
harges.. This is how to break
> down the problem — what part of the translation is failing?
>
> -Geoff
>
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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
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,
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this
stuff? Or should we just try to fix it as best we can and upload a new
version of the file?
Cheers,
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Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.s
OpenBabel developers considered moving to LGPL?
Regards,
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Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
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h_d2d_may
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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 &qu
; 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 ato
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, Da
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, thr
(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. W
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 o
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,
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Box 5
ist
> 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
® Level Up Game Demo Contest 2013
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>
>
>
> __
. 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
>
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> 2012/11/22 David van der Spoel <mailto:sp...@xray.bmc.uu.
e how to add tests to the
repository?
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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
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,
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David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell &a
> 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,
>
>
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?
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David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sw
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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.u
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.u
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,
>
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
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.
ary, 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
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