I resolved to write a small object to be sure that the essential set of data
I was mostly interested in (i.e., atom and bond indices) is preserved when
copying the molecule.
It's far from elegant (just starting fiddling with OB), but it does the job
for me.
There's a placeholder for copying also
iate any input on the matter.
Thanks!
Stefano
[1]
http://blueobelisk.shapado.com/questions/which-openbabel-dev-version-methods-should-be-used-for-altering-stereochemistry
[2]
http://www.filewatcher.com/p/openbabel-2.3.0.tar.gz.14321281/openbabel-2.3.0/doc/guide/_sources/UseTheLibrary/PythonExa
he
> following code:
> config.winding = 2 if config.winding == 1 else 1
> ts.SetConfig(config)
> So replacing config.Invert() with these two lines will make your example work
> at least…
>
> Kind regards,
> Fredrik
> 18 jun 2014 kl. 03:45 skrev Stefano Forli :
>
>
the opposite in the molecule and p1,
p2, the
script finds matches.
Am I missing something, maybe?
Advices will be much appreciated.
Thanks
S
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Staff Scientist
Molecular Graphics Laboratory
Dept. of Integrative Structural
and Computational Biology, MB-112F
The
ime myself right now). I'm pretty
> sure I
> implemented this. A quick test is:
>
> obabel -:"'F[C@H](Br)Cl" -s "'F[C@@H](Br)Cl" -osmi
>
> ...should be "0 molecules converted"
>
> - Noel
>
>
> On 9 July 2014 00:
nvolving OBPairData, but there is no "_atom_site_label"
> found for my
> molecule.
>
> Just trying to find out where that information is stored.
> Any help would be appreciated.
>
> Cheers,
> --Jim
>
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Stefano Forli, PhD
Staff Scientist
Molecular Gra
C@@H](Br)Cl" -osmi
>
> ...should be "0 molecules converted"
>
> - Noel
>
>
> On 9 July 2014 00:16, Craig James <mailto:cja...@emolecules.com>>
> wrote:
>
> On Tue, Jul 8, 2014 at 2:05 PM, Stefano Forli <mailto:fo...@scripps.edu>> wr
orm
the actual transformation.
Unfortunately, I had not much luck in finding documentation on the matter, so
any
suggestions will be more than welcome.
Thanks,
S
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Staff Scientist
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Dept. of Integrative Structural
and Computational Biology
hon object to apply a RXN transformation to a
> series of
> molecules.
> In particular, I'm peeking at the RXN format source (rxnformat.cpp) to
> populate an
> OBReaction() object but then I don't know how to tie it to the OBChemTsfm
> class to perfo
C
...
As far as I can tell, there isn't much in the documentation (but I'll be happy
to be proved wrong!)
Any help will be appreciated.
Not sure if it makes a difference, but I'm using Python.
Stefano
[1] http://deposit.rcsb.org/adit/docs/pdb_atom_format.html#ATOM
ums.openbabel.org/Using-RXN-with-OBReaction-and-OBChemTsfm-Python-td4657628.html
[2] http://www.rdkit.org/docs/GettingStartedInPython.html#chemical-reactions
--
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Dept. of Integrative Structural
and Computational Biology, MB-
, then
one is
created (and named "LIG").
It seems like a bug to me, but I want to be sure I'm not missing anything
before reporting
it...
Thanks,
S
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Staff Scientist
Molecular Graphics Laboratory
Dept. of Integrative Structural
and Computation
ators shouldn't have side-effects. To
> directly perceive, uses OBChainsParser.
>
> - Noel
>
> On 3 October 2014 02:15, Stefano Forli wrote:
>> Hi,
>> I'm a little bit puzzled by the behavior of the following code:
>>
>> import
),
print facade.GetTetrahedralStereo(idx-1).IsSpecified()
===
Basically, for both molecules, the two methods return always False and True
(atom's and
facade's methods, respectively).
Any help would be very much appreciated.
S
--
Stefano Forli, PhD
Staff Scientist
Molecu
s, but this
> was never done.
>
> - Noel
>
> On 20 November 2014 20:37, Stefano Forli wrote:
>> Hi,
>>
>> I'm trying to find a robust method to identify if chirality is specified or
>> not in a
>> molecule, i.e.:
>>
>>OC[C@H]1O
[1] http://baoilleach.blogspot.com/2012/12/intro-to-open-babel.html
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Staff Scientist
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Dept. of Integrative Structural
and Computational Biology, MB-112F
The Scripps Research Institute
10550 North Torrey Pines Road
La Jolla, CA 92037-1000, USA.
r/c%2B%2B/mcs-cliquer
>
> Cheers,
> -Geoff
>
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Staff Scientist
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.
full conformational search?
Thanks,
S
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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
ained in this way.
Is there any word from developers on the matter?
Stefano
[1] http://sourceforge.net/p/openbabel/bugs/710/
--
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and Computational Biology, MB-112F
The Scripps Research Inst
that chirality is
not perceived (uncomment the last line to test it).
Is this expected, or there is a way to perceive it properly?
Thanks,
S
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and Computational Biology, MB-112F
The S
at the winding. The refs are
> in a different order in each case.
>
> Regards,
> - Noel
>
>
> On 17 February 2015 at 00:53, Stefano Forli wrote:
>> Hi,
>>
>> I can't understand the way in which chiral winding is handled by OpenBabel.
>> I
et the opposite chirality.)
The docs are at
http://openbabel.org/api/2.3/structOpenBabel_1_1OBTetrahedralStereo_1_1Config.shtml
- Noel
On 17 February 2015 at 19:13, Stefano Forli wrote:
Noel,
thanks for the clarification.
It makes sense now, but it means that I'm using the wrong tool for what I
want to
__
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>
>
>
>
> --
> --Nathan Pimental,
> --Peppertree Labs
Buffalo
> The State University of New York
> Department of Chemical and Biological Engineering
> 205 Furnas Hall
> Buffalo, NY 14260
> Ph no- 716-262-5115
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and Computational Biology
gt;
>
> --
> 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
> th
,' which is
invalid in SMILES
==
*** Open Babel Error in ObtainTarget
Cannot read the SMILES string
0 molecules converted
--
(note: I've escaped some characters in the pattern to avoid shell errors).
Thanks,
S
--
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ES
> which is then refined using SMARTS:
>
> obabel index.fs -omol2 -sSMILES -an |
> obabel -imol2 -O first.smi -sSMARTS
>
> Chris
>
> On 21/03/2015 21:52, Stefano Forli wrote:
>> I think there's an error either in the documentation or in the
>>
Hi all,
Is there any way to access the functionalities in obtautomer using Python?
Thanks,
S
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The Scripps Research Institute
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same coordinates and elements (but no bonds).
Is there any other step to do other than BeginModify()/EndModify() to be applied to the
molecule to achieve the same results I would get by reading a file?
Thanks!
S
--
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Staff Scientist
Molecular Graphics Laboratory
Dep
re compatible
> with
> pybel.Outputfile?
>
> Thanks in advance!
> Matthew
--
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and Computational Biology, MB-112F
The Scripps Research Institute
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m not sure what would be the way
to prevent it. Is this a bug or something that nobody should ever do (and it should be
added to the documentation)?
Thanks!
S
--
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Staff Scientist
Molecular Graphics Laboratory
Dept. of Integrative Structural
and Computational Biology, M
On 04/28/2015 04:50 PM, Stefano Forli wrote:
>
>> Now, I understand that a segFault shouldn't happen, but I'm not sure
>> what would be the way to prevent it. Is this a bug or something that
>> nobody should ever do (and it should be added to the documentation)?
>
>
ect
> the training
> as soon as possible.
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The Scripps Research Institute
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t
what I can tell, all textual descriptors [1] are missing.
Also, I was interested in understanding what 'smarts' and 's' descriptors
actually mean,
but I can't find any documentation on the matter other than this [1].
Advice is welcome.
Thanks,
S
[1] http://open-babel.
reate IDs only when the compound is seen
> often as you said.
>
> Thanks.
>
>
>
>
> --
> View this message in context:
> http://forums.openbabel.org/Problem-in-converting-a-PDB-file-to-MOL2-tp4659035p4659061.html
> Sent from the General discussion mailing list archive at Nabble.com.
>
>
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Molec
been some discussion in the mailing list about similar
problems using PDB files as well.
My advice is to manually correct the issues, hoping you don't have too many
files to process.
Best,
S
--
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Assistant Professor of Integrative
Structural and Computational Biology,
rogen is still there, somewhere.
Is this a bug or am I doing something wrong?
Thanks,
S
--
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Assistant Professor of Integrative
Structural and Computational Biology,
Molecular Graphics Laboratory
Dept. of Integrative Structural
and Computational Biology, MB-112F
Mark Driver
>>
>> PhD student
>>
>> University of Cambridge
>>
>> ------
>> Transform Data into Opportunity.
>> Accelerate data analysis in your applications with
>> Intel D
5111&iu=/4140
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Mo
that OBChemTsfm is indeed the one to use to perform
chemical
transformations, while OBReaction holds only the information about it.
I suspect I'm doing something wrong, but I can't figure out what it is.
Any advice on the matter?
Thanks!
S
[1] http://www.daylight.com/meetin
-td4657949.html
On 03/25/2016 05:57 AM, Noel O'Boyle wrote:
> We don't support smirks. See
> http://baoilleach.blogspot.co.uk/2012/08/transforming-molecules-intowellother.html?m=1
>
> On 24 Mar 2016 9:33 p.m., "Stefano Forli" <mailto:fo...@scripps.edu>>
I think both are feasible and I think we can supply some pointers. The
> problem has been one of "too many things and not enough cooks" rather than
> anything else.
>
> As you say, both have been requested many times. :-)
>
> Cheers,
> -Geoff
>
--
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well most of the times. Problems arise with molecules like
"CC1[NH+]1C", in which nitrogen has as a tetrahedral configuration defined,
but the
carbon (C1) doesn't.
Is there a better way to deal with chirality and avoid this issue?
Thanks,
S
--
Stefano Forli, PhD
list of all problematic molecules you
> come across (well, one example of each type) so that a future
> developer can fix this.
>
> Regards,
> - Noel
>
> On 27 April 2016 at 01:29, Stefano Forli wrote:
>> Hi all,
>>
>> I'm trying to enumerate all ena
31938128;j
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Structural
Brian,
not sure if related, but I had a similar issue a while ago, take a look here:
https://sourceforge.net/p/openbabel/mailman/message/32893219/
Maybe it helps,
S
--
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Assistant Professor of Integrative
Structural and Computational Biology,
Molecular Graphics
nvert directly the MOPAC output (which is supported)
into Mol2, and see if the proper charges are kept.
S
--
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Assistant Professor of Integrative
Structural and Computational Biology,
Molecular Graphics Laboratory
Dept. of Integrative Structural
and Computational Biology, MB
wrong, please correct
> the training
> as soon as possible.
>
>
> --
>
>
>
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forge.net
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>
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The Scripps Research Institute
10550 North Tor
k out the vibrant tech community on one of the world's most
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(apologies: this was a reply to the discussion
Re: [Open Babel] Put atoms of target molecule in same order as reference
clicked on the wrong email).
On 07/24/2017 09:59 AM, Stefano Forli wrote:
We've been using this method [1] from an old post in Noel's blog, and it was
quite
-
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ogens with this code bit me several times already, so if anybody has advice on
how to prevent the crash or improve the code, it would be appreciated.
Thanks
S
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Assistant Professor
Dept. of Integrative Structural
and Computational Biology, MB-112A
The Scripps Research
priotein.gpf -l 3upo_priotein.glg
autodock4 -p ligcovalent_3upo_protein.dpf -l
ligcovalent_3upo_protein.dlg
The output generated at each step of the process is available in the
directory '3upo_test/output'.
pr
ol2 guanine.mol2 -p 9 -omol2 -O guanine_after.mol2
Any advice would be welcome.
Thanks,
S
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Assistant Professor
Dept. of Integrative Structural
and Computational Biology, MB-112A
The Scripps Research Institute
10550 North Torrey Pines Road
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ve up (and use other toolkits, alas).
S
p.s. apologies for the repeated emails on the subject, but our spam filter was making a
mess and I couldn't see my own posts to the list
Regards,
- Noel
On 1 February 2018 at 00:16, Stefano Forli mailto:fo...@scripps.edu>>
wrote:
g out calls for Google Summer of Code at the moment; maybe this
is a possible project for a student.
On 1 February 2018 at 18:27, Stefano Forli mailto:fo...@scripps.edu>>
wrote:
Thanks for the clarification.
On 02/01/2018 12:43 AM, Noel O'Boyle wrote:
Actually, I
d back the data I need to the
C part.
save_babel_molecule_details (atoms, lot, coords);
free (lot);
free (coords);
mol.Clear();
return 0;
}
else
{
// Error reading file
return 1;
}
}
else
{
// Error with this form
hdot
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gs:
>>> *list(ssr[0])*# print for the first ring for example
[6, 5 , 2, 1, 3, 0]
>>> *len(ssr)*# or print the number of rings
3
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C1=O)2
ZINC00119428
1 molecule converted
I don't think in this form the 4-pyridone is aromatic, but I still think
there's something wrong with the way the valence information is lost when
parsing the structures.
Any clues?
Thanks,
S
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Assistant Professor
ic, but I still think
> there's something wrong with the way the valence information is lost when
> parsing the structures.
>
> Any clues?
>
> Thanks,
>
> S
> --
>
> Stefano Forli, PhD
>
> Assistant Professor
>
n documented anywhere?
>>
>>
>>
>>
>>
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>
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ogspot.com/2020/02/
[2] https://open-babel.readthedocs.io/en/latest/Stereochemistry/stereo.html
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s the best way to do so with babel?
Thanks.
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tel: +1 (858)784-2055
email: fo...@scripps.ed
I'm curious if anyone ever attempted to detect topicity using OpenBabel (or
other tools, for that matter).I feel it might be one of those non-trivial
problems, maybe worth writing a separate algorithm altogether.
Thanks,
S
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)F")
try:
# not available anymore in OB3
print(mol.IsChiral(), "IsChiral()")
except:
pass
facade = ob.OBStereoFacade(mol, True)
for a in ob.OBMolAtomIter(mol):
idx = a.GetId()
print(idx, a.IsChiral(), "IsChiral()")
print(idx, facade.HasTetrahedralSter
s can make sense, in the perspective of forcing to
keep the information in the input.
An interesting behavior worth reporting in the docs.
Thanks,
S
On 10/10/20 11:27 PM, Stefano Forli wrote:
Hi all,
we've been looking at migrating our OB2 code to OB3 and we have found differences in ho
,
This is documented in the "0D structures" section: "if you wish to identify
additional stereocenters whose stereo configuration is unspecified, ...then you may wish to trigger
perception." The reason we don't do this by default is simply for speed.
Regards,
Noel
On
OBMol::PerceiveBondOrders
...
I have tried the following code to suppress the messages with no success (I've
stopped the logging after trying changing the output level):
ob_log = ob.OBMessageHandler()
ob_log.SetOutputLevel(0)
ob_log.StopLogging()
Suggestions are welcome.
S
--
Stefano
Hi Noel,
that worked! For the record, this is the code:
-
from openbabel import openbabel as ob
ob.obErrorLog.SetOutputLevel(0)
-
Thank you much for the help!
Happy holidays,
Best,
S
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and
eforge.net/lists/listinfo/openbabel-discuss
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rogen
with 5 connections.
Interestingly, when parsing the OB atom type of the nitrogen is set to "N3+",
so at some point in the chemical perception, this is detected correctly. Yet, if there's
an easy way to fix this I couldn't find it.
This seems like a bug to me.
Any advice?
Th
hod
OBMol::UnsetPartialChargesPerceived()
The method is still listed in the comments in molchrg.cpp, but it's not in the
OBMol anymore.
I've tried looking for alternatives, possibly using the OBMol::UnsetFlag()
method, but no luck.
Any suggestions?
Thank you!
S
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ssibly using the OBMol::UnsetFlag()
method, but no luck.
Any suggestions?
Thank you!
S
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riggered by the bindings or it's a different problem.
Also, a while back [1] I reported a behavior that might be related to
this bug.
Thanks,
S
[1] https://sourceforge.net/p/openbabel/mailman/message/32894918/
--
Stefano Forli, PhD
Associate Professor
Dept. of Integrative Structura
tChainsPerceived(false) in advance on the original OBMol to avoid
copying the residues (and then reset it afterwards), or else call it on the new
OBMol so that residue information will be reperceived (when requested).
Hope that helps,
-Geoff
--
Stefano Forli, PhD
Associate Professor
De
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--
Stefano Forli, PhD
Associate Professor
Dept. of Integrative Structural
and Computational Biology, MB-112A
Scripps Rese
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