openbabel-discuss — Discussion on Open Babel and development

[Open Babel] ANN: chemfp 5.0

[Andrew D. <da...@da...>]

Hello Open Babel users,

  I've released chemfp 5.0, my Python package for cheminformatics
fingerprint generation, search, and analysis. You can install it on
Linux-based OSes using:

    python -m pip install chemfp -i https://chemfp.com/packages/

(Append "--upgrade" if you have already installed it.)

For a description of the changes since 4.2 see

  https://chemfp.com/docs/whats_new_in_50.html .

The highlights are:

 • Update the FPB format to handle over 1 billion fingerprints.
 
 • New chemfp shardsearch command-line tool which does similarity
    search across multiple target files and merges the result.
   - Tested with the 977 million structures in GDB-13
 
 • New chemfp simhistogram / chemfp simhist command-line tool and
    corresponding chemfp.simhistogram() high-level API function
    to create a histogram of similarity scores.
 
 • Initial support for count fingerprints:
   - new text-based FPC format based on the FPS format
   - rdkit2fpc tool which uses RDKit's sparse fingerprint generators
   - fpc2fps tool with various method to convert sparse count
       fingerprints to binary fingerprints
 
 • Fast implementations of the 4860-bit Klekota-Roth fingerprint
    for the OpenEye and RDKit toolkits.

Chemfp supports all of the Open Babel fingerprints and input
file formats.

Cheers,
 
				Andrew Dalke
				da...@da...
--
Have useful but old in-house cheminformatics software in need of refurbishment?
No one left knows how it works or has the time? Perhaps I can help. Contact me.

Re: [Open Babel] OpenBabel-discuss Digest, Vol 217, Issue 4

[Chris S. <sw...@ma...>]

Thanks everyone, lots for me to explore

Cheers

Chris

> On 13 Feb 2025, at 12:39, ope...@li... wrote:
> 
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> Today's Topics:
> 
>   1. Re: Errors in file conversion (Andrew Dalke)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Wed, 12 Feb 2025 22:34:50 +0100
> From: Andrew Dalke <da...@da...>
> To: Chris Swain <sw...@ma...>
> Cc: Open Babel <ope...@li...>
> Subject: Re: [Open Babel] Errors in file conversion
> Message-ID: <296...@da...>
> Content-Type: text/plain;	charset=us-ascii
> 
> On Feb 11, 2025, at 10:06, Chris Swain via OpenBabel-discuss <ope...@li...> wrote:
>> I want to convert some very large sdf files to SMILES.  I know that some structures will fail to convert.
>> 
>> Is it possible to do the conversion creating two files, one containing the valid SMILES and another file containing the records that failed to convert? Either as a sdf file or simply a text file containing the title of molecules.
> 
> Since Geoff commented that it wasn't possible directly in Open Babel, I'll suggest an alternative.
> 
> Chemfp supports multiple cheminformatics toolkits. To make things easier for me and for chemfp users, I've implemented a "toolkit" wrapper API for consistent molecule I/O across the supported toolkits.
> 
> This includes a "text" toolkit which knows just enough about SMILES and SD files to read the records as text blocks, with no need for a chemistry toolkit. This was designed to get access to the original record in order to, for example, preserve the exact input atom order and aromaticity, or to add a note like "could not process file" to an SD data item.
> 
> For chemfp's Open Babel SDF reader wrapper, I added an option to choose to use Open Babel to read the molecules (this is the default), or to use chemfp's text-based parser to identify the records, and then have Open Babel parse the record to get the molecule.
> 
> Chemfp's wrapper API also has a way to pass in the error handler to use when Open Babel fails to parse a record, eg, to ignore the problem and keep processing, or to stop processing immediately.
> 
> I'm pretty sure you can use the following, with some filename changes, to extract the records you mentioned.
> 
> import sys
> 
> from chemfp.io import ErrorHandler
> from chemfp import openbabel_toolkit as T
> 
> # Create a user-defined error handler which writes
> # the failing record to the specified file object.
> class SaveErrors(ErrorHandler):
>    def __init__(self, outfile):
>        self.outfile = outfile
> 
>    # Called whenever there is an error.
>    # The "location" object (always present for file I/O)
>    # when used with the "chemfp" implementation stores the
>    # current record in ".record", as a byte string.
>    def error(self, msg, location=None, extra=None):
>        assert location is not None
>        sys.stderr.write(f"ERROR: {msg}\n")
>        self.outfile.write(location.record)
> 
> with open("errors.sdf", "wb") as err_file:
>    with T.read_molecules(
>            "chembl_33.sdf.gz",
>            # have the chemfp wrapper use chemfp to tokenize SDF
>            # records instead of letting Open Babel parse everything.
>            reader_args = {"implementation": "chemfp"},
>            # Specify a user-defined error handler
>            errors = SaveErrors(err_file),
>            ) as reader:
>        with T.open_molecule_writer("dest.smi") as writer:
>            with reader.location.progress_bar() as progress_bar:
>                writer.write_molecules(progress_bar(reader))
> 
> This is a bit slower than using Open Babel's native reader, though I don't recall how much.
> 
> If the input is gzip compressed, then you can get a bit extra performance by off-loading the decompression to gzip, rather than use chemfp's own gzip reader, by setting the environment variable CHEMFP_GZIP to "gzip", like this:
> 
>  env CHEMFP_GZIP=gzip python chemfp_converter.py
> 
> If you do that, the progress bar will switch from the current read position / total input file size, to showing the number of records processed per second.
> 
> Best regards,
> 
> 					Andrew
> 					da...@da...
> 
> 
> 
> 
> 
> 
> ------------------------------
> 
> 
> 
> ------------------------------
> 
> Subject: Digest Footer
> 
> _______________________________________________
> OpenBabel-discuss mailing list
> Ope...@li...
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> ------------------------------
> 
> End of OpenBabel-discuss Digest, Vol 217, Issue 4
> *************************************************

Re: [Open Babel] Errors in file conversion

[Andrew D. <da...@da...>]

On Feb 11, 2025, at 10:06, Chris Swain via OpenBabel-discuss <ope...@li...> wrote:
> I want to convert some very large sdf files to SMILES.  I know that some structures will fail to convert.
> 
> Is it possible to do the conversion creating two files, one containing the valid SMILES and another file containing the records that failed to convert? Either as a sdf file or simply a text file containing the title of molecules.

Since Geoff commented that it wasn't possible directly in Open Babel, I'll suggest an alternative.

Chemfp supports multiple cheminformatics toolkits. To make things easier for me and for chemfp users, I've implemented a "toolkit" wrapper API for consistent molecule I/O across the supported toolkits.

This includes a "text" toolkit which knows just enough about SMILES and SD files to read the records as text blocks, with no need for a chemistry toolkit. This was designed to get access to the original record in order to, for example, preserve the exact input atom order and aromaticity, or to add a note like "could not process file" to an SD data item.

For chemfp's Open Babel SDF reader wrapper, I added an option to choose to use Open Babel to read the molecules (this is the default), or to use chemfp's text-based parser to identify the records, and then have Open Babel parse the record to get the molecule.

Chemfp's wrapper API also has a way to pass in the error handler to use when Open Babel fails to parse a record, eg, to ignore the problem and keep processing, or to stop processing immediately.

I'm pretty sure you can use the following, with some filename changes, to extract the records you mentioned.

import sys

from chemfp.io import ErrorHandler
from chemfp import openbabel_toolkit as T

# Create a user-defined error handler which writes
# the failing record to the specified file object.
class SaveErrors(ErrorHandler):
    def __init__(self, outfile):
        self.outfile = outfile
    
    # Called whenever there is an error.
    # The "location" object (always present for file I/O)
    # when used with the "chemfp" implementation stores the
    # current record in ".record", as a byte string.
    def error(self, msg, location=None, extra=None):
        assert location is not None
        sys.stderr.write(f"ERROR: {msg}\n")
        self.outfile.write(location.record)

with open("errors.sdf", "wb") as err_file:
    with T.read_molecules(
            "chembl_33.sdf.gz",
            # have the chemfp wrapper use chemfp to tokenize SDF
            # records instead of letting Open Babel parse everything.
            reader_args = {"implementation": "chemfp"},
            # Specify a user-defined error handler
            errors = SaveErrors(err_file),
            ) as reader:
        with T.open_molecule_writer("dest.smi") as writer:
            with reader.location.progress_bar() as progress_bar:
                writer.write_molecules(progress_bar(reader))

This is a bit slower than using Open Babel's native reader, though I don't recall how much.

If the input is gzip compressed, then you can get a bit extra performance by off-loading the decompression to gzip, rather than use chemfp's own gzip reader, by setting the environment variable CHEMFP_GZIP to "gzip", like this:

  env CHEMFP_GZIP=gzip python chemfp_converter.py

If you do that, the progress bar will switch from the current read position / total input file size, to showing the number of records processed per second.

Best regards,

					Andrew
					da...@da...

Re: [Open Babel] Errors in file conversion

[Noel O'B. <bao...@gm...>]

If you use the -e option, I think it will write out an empty SMILES with
the title. Or was this something I didn't add in the end...

On Wed 12 Feb 2025, 20:34 Chris Swain via OpenBabel-discuss, <
ope...@li...> wrote:

> Hi,
>
> Many thanks for the prompt response,
> Cheers
> Chris
>
> On 12 Feb 2025, at 20:19, Geoffrey Hutchison <geo...@gm...>
> wrote:
>
> I don’t think at the moment, we have something that copies any entries
> with errors. It’s a useful idea.
>
> -Geoff
>
> On Feb 11, 2025 at 4:06:09 AM, Chris Swain via OpenBabel-discuss <
> ope...@li...> wrote:
>
>> Hi,
>>
>> I want to convert some very large sdf files to SMILES.  I know that some
>> structures will fail to convert.
>>
>> Is it possible to do the conversion creating two files, one containing
>> the valid SMILES and another file containing the records that failed to
>> convert? Either as a sdf file or simply a text file containing the title of
>> molecules.
>>
>> Cheers
>>
>> Chris
>>
>> _______________________________________________
>> OpenBabel-discuss mailing list
>> Ope...@li...
>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>
>
> _______________________________________________
> OpenBabel-discuss mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>

Re: [Open Babel] Errors in file conversion

[Chris S. <sw...@ma...>]

Hi,

Many thanks for the prompt response,
Cheers
Chris

> On 12 Feb 2025, at 20:19, Geoffrey Hutchison <geo...@gm...> wrote:
> 
> I don’t think at the moment, we have something that copies any entries with errors. It’s a useful idea.
> 
> -Geoff
> 
> On Feb 11, 2025 at 4:06:09 AM, Chris Swain via OpenBabel-discuss <ope...@li... <mailto:ope...@li...>> wrote:
>> Hi,
>> 
>> I want to convert some very large sdf files to SMILES.  I know that some structures will fail to convert.
>> 
>> Is it possible to do the conversion creating two files, one containing the valid SMILES and another file containing the records that failed to convert? Either as a sdf file or simply a text file containing the title of molecules.
>> 
>> Cheers
>> 
>> Chris
>> 
>> _______________________________________________
>> OpenBabel-discuss mailing list
>> Ope...@li... <mailto:Ope...@li...>
>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] Errors in file conversion

[Geoffrey H. <geo...@gm...>]

 I don’t think at the moment, we have something that copies any entries
with errors. It’s a useful idea.

-Geoff

On Feb 11, 2025 at 4:06:09 AM, Chris Swain via OpenBabel-discuss <
ope...@li...> wrote:

> Hi,
>
> I want to convert some very large sdf files to SMILES.  I know that some
> structures will fail to convert.
>
> Is it possible to do the conversion creating two files, one containing the
> valid SMILES and another file containing the records that failed to
> convert? Either as a sdf file or simply a text file containing the title of
> molecules.
>
> Cheers
>
> Chris
>
> _______________________________________________
> OpenBabel-discuss mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>

[Open Babel] Errors in file conversion

[Chris S. <sw...@ma...>]

Hi,

I want to convert some very large sdf files to SMILES.  I know that some structures will fail to convert.

Is it possible to do the conversion creating two files, one containing the valid SMILES and another file containing the records that failed to convert? Either as a sdf file or simply a text file containing the title of molecules.

Cheers

Chris

[Open Babel] Mychem v2.0.0

[Jerome P. <j.p...@pa...>]

Dears,

After a break in development, I'm pleased to announce the release of the 
latest version of Mychem (v2.0.0). Mychem is an extension for MySQL 
adding new chemical SQL functions. This new version supports OpenBabel 
v3.0.0 and higher, as well as the latest versions of MySQL and MariaDB. 
GitHub Actions is now used to run CMake-based tests, consolidating the 
quality of code pushed to the repository.

The code can be found on:
https://github.com/mychem/mychem-code

It is also published on Zenodo:
https://zenodo.org/records/14786457

Best,

Jérôme

[Open Babel] Issue with Molecule Partitioning During PDB to PDBQT Conversion in Open Babel

[Mengyan C. <ca...@bc...>]

Dear Obabel Community,

I have encountered an issue while using Open Babel to convert molecular
structures from PDB to PDBQT format. It seems that during the conversion
process, Open Babel is partitioning the input molecules. This behavior is
unexpected, as the input files are correctly formatted and contain single,
unified molecules.

Here is the command I used for the example file that I attached below:

   -

   obabel 1rpu_model1_Protein_Model_1.pdb -O
1rpu_model1_Protein_Model_1_obabel.pdbqt -xr -p 7.4 --partialcharge
eem


The output file 1rpu_model1_Protein_Model_1_obabel.pdbqt contains multiple
TER records. My understanding is that TER marks the end of a chain or a
fragment, but in this case, it seems to indicate that molecules are being
divided into separate fragments instead of remaining unified.

Could you please clarify the following:

   1. What exactly does the presence of these excess TER records signify in
   this context?
   2. Would it be appropriate to simply remove the excess TER records?

I would greatly appreciate any guidance or recommendations you could
provide.

Thank you for your attention to this matter. I look forward to your advice.

Best regards,
Mengyan Cao

[Open Babel] Angle constraints not applied during OBForceField optimization

[Overstreet, R. E <ric...@pn...>]

All,

I am having trouble with forcefield constraints in OpenBabel regardless of the potential selected or size of the factor the angle always converges to an unconstrained minima. See the minimal example with carbon dioxide below:

from openbabel import openbabel

obConversion = openbabel.OBConversion()
obConversion.SetInFormat("smi")
mol = openbabel.OBMol()

obConversion.ReadString(mol, "C(=O)=O")

builder = openbabel.OBBuilder()
builder.Build(mol)

constraints = openbabel.OBFFConstraints()
constraints.AddAngleConstraint(2,1,3,float(178.0))
constraints.SetFactor(1e10)

ff = openbabel.OBForceField.FindForceField("gaff")
ff.Setup(mol, constraints)

ff.ConjugateGradients(10000, 1.0e-6)
ff.GetCoordinates(mol)

print(mol.GetAngle(mol.GetAtom(2),mol.GetAtom(1),mol.GetAtom(3)))

This always converges to:

$ python angle_demo.py
179.9743765482302

Any help would be appreciated. I am running Open Babel 3.1.0

Thanks,
Richard Overstreet

Re: [Open Babel] How to get source code for UFF and MMFF84 minimization

[Andrew D. <da...@da...>]

Hi Srdjan,

  The Open Babel source code is available at https://github.com/openbabel/openbabel . 

Use the green button labeled "<> Code" to get the source code either through the git version control tool, or as a zip file.

The UFF implementation is also available through the web interface at https://github.com/openbabel/openbabel/blob/master/src/forcefields/forcefielduff.cpp 

				Andrew
				da...@da...

P.S.
  For those who only follow the Open Babel list, the author sent a similar email to the RDKit mailing list and seems to have not edited it fully for the new context. I've done that too.


> On Sep 11, 2024, at 11:16, Srdjan Pusara <srd...@ho...> wrote:
> 
> Hello,
> 
> I have noticed that openbabel can return atom UFF/MMFF94 atom types, and knowing atom types is first step to compute energy or do energy minimization. However, I am still trying to find a table with all parameters and how these equations were implemented.
> 
> I have also noticed that Rdkit can return force field parameters between group of atoms (bond_params = rdForceFieldHelpers.GetUFFBondStretchParams(mol, 6, 1),angle_params = rdForceFieldHelpers.GetUFFAngleBendParams(mol, 0, 1, 2) etc).
> 
>   I would like to ask is it possible to find source code how these interaction terms were implemented? I understand that these equations can be implemented by reading original paper(s), but it would be helpful to access the source code od Openbabel where these interaction terms are already implemented.  In addition, I have noticed that original UFF paper has some small errors or typos, so having already implemented source code would help.

[Open Babel] How to get source code for UFF and MMFF84 minimization

[Srdjan P. <srd...@ho...>]

Hello,

I have noticed that openbabel can return atom UFF/MMFF94 atom types, and knowing atom types is first step to compute energy or do energy minimization. However, I am still trying to find a table with all parameters and how these equations were implemented.

I have also noticed that Rdkit can return force field parameters between group of atoms (bond_params = rdForceFieldHelpers.GetUFFBondStretchParams(mol, 6, 1),angle_params = rdForceFieldHelpers.GetUFFAngleBendParams(mol, 0, 1, 2) etc).

  I would like to ask is it possible to find source code how these interaction terms were implemented? I understand that these equations can be implemented by reading original paper(s), but it would be helpful to access the source code od Openbabel where these interaction terms are already implemented.  In addition, I have noticed that original UFF paper has some small errors or typos, so having already implemented source code would help.


  Thanx for help in advance.

[Open Babel] Errors and problems in 3 D structure generation

[Raghav, D. - (draghav) <dr...@ar...>]

Hi,

The goal of my project is to screen a huge database containing thousands of ligand molecules against my protein of interest. For this, I am using the Enamine database (https://enamine.net/) as a ligand repository. As a default, the database allows us to download the ligands in one single large file in .sdf format. The important thing is that all these ligands are in 2D geometry and not in 3D. Now I was trying to convert the .sdf file into .pdbqt file with 3D geometry using Open Babel 3.1.0. For this purpose, I have been using the following workflow:

Obabel -isdf EnamineLigands.sdf -O *.sdf --split.  (this is to split the large sdf file into individual sdf files)

Then, obabel -isdf *.sdf -opdbqt -O *.pdbqt --gen3D (to convert sdf to pdbqt in 3D at the same time)

When I execute this I constantly get the following error message in the terminal

*** Open Babel Error  in Do
  3D coordinate generation failed
==============================
*** Open Babel Warning  in CorrectStereoAtoms
  Could not correct 2 stereocenter(s) in this molecule (Spironolactone)
  with Atom Ids as follows: 12 19
Warning: Stereochemistry is wrong, using the distance geometry method instead

Now, when distance geometry method is used by the software it gets stuck for hours and even days. Currently I am only working on a small dataset of ~ 1000 ligands and things are stuck for the last 2 days.

I need help from the experts and developers. I hope I can get a work around this problem.

Many thanks for reading my mail.

Best regards

[Open Babel] Openbabel filtering a list of conformers

[I L <lim...@gm...>]

Hi all,
             This is similar to a question/issue posted on https://github.com/openbabel/openbabel/issues/2274 which was left unanswered.
I basically am conducting a conformer searching and then want to use the MM force field energy to rank the conformers, filter them out and take the best x (say 10).
What i have done thus far is :
#generate a number of conformers
obabel A_conformer.sdf -O confs.sdf --confab --conf 100000
#Numerous ways to get output energy based on MM fields

  1.
obenergy -ff MMFF94s confs.sdf
  2.
obabel confs.sdf -otxt --energy --append "Energy"

But none of this really saves the energy to (say be brought into avogadro to be ranked)
I tried to use
obabel Am_confs.sdf -osmi --filter "Energy < XXXX"
to see if that will filter but I dont think it recognises Energy
Im kind of struck on exactly how I can conduct the filtering process above and would appreciate if someone could guide me on where I'm making mistakes. I'm clearly misusing some of the functions and hope someone could help me out here. Appreciate any help on this matter.

Best regards,
Ingso

Re: [Open Babel] Assistance Needed with Modifying Molecules in Python Script

[Geoffrey H. <geo...@gm...>]

>
> I either start from SMILES and/or add atoms and bonds to an obmol object.
> I can change the tetrahedral stereochemistry of the molecules with ease,
> but I can't seem to do it for cis/trans isomers.
>
…

> I tried to change the configuration of the OBStereoFacade for the bond in
> question, but it did nothing.
> I tried rotating the atoms around the bond and minimizing the
> molecule, but nothing.
>


If you start from a SMILES string, you can easily change the stereoisomers
around a double bond by changing the ‘/‘ or ‘\’ characters as needed.

If you’re modifying the underlying coordinates, you will need to make sure
stereo is re-perceived from the 3D coordinates, as indicated in the manual:
https://open-babel.readthedocs.io/en/latest/Stereochemistry/stereo.html#stereo-perception


"If operations are performed on the molecule that require stereo is be
reperceived, then OBMol::SetChiralityPerceived(false) should be called.”

Best regards,
-Geoff

---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: ge...@pi...
web: https://hutchisonlab.org/

[Open Babel] Assistance Needed with Modifying Molecules in Python Script

[Álex B. <ale...@br...>]

Dear development team,

I am writing to seek assistance with a challenge I've encountered while
working on a Python script for creating and modifying molecules.
I either start from SMILES and/or add atoms and bonds to an obmol object.
I can change the tetrahedral stereochemistry of the molecules with ease,
but I can't seem to do it for cis/trans isomers.
As is understood from the documentation there is no implementation for
changing the stereochemistry of either double bonds or square planar
molecules, just query on the stereochemistry of the molecules, but I tried
the following:
I tried to change the configuration of the OBStereoFacade for the bond in
question, but it did nothing.
I tried rotating the atoms around the bond and minimizing the molecule, but
nothing.

I would greatly appreciate any help in this matter!
If this functionality is not supported, could you recommend another
library/program that I could use?

Thank you very much for your time and assistance.

Best wishes,
Álex Kálmán Balogh
Ale...@br...
Staff Scientist
www.brianqc.com

Re: [Open Babel] Custom force field to OB?

[David v. d. S. <dav...@ic...>]

On 2024-01-15 21:21, Geoffrey Hutchison wrote:
> Dear David,
>
> Of course we are happy to have an updated forcefield - I’m sure others
> will use it.
Ok, I will try and start with the GAFF stuff.
>
> Out of curiosity, does this include the polarizable electrostatics or
> does it just use whatever partial charges are assigned already?
The part of the code that I refer to would onlybe for atomtyping. The
force field code is not implemented in OpenBabel, but it would be
relatively easy to to implement charge generation.

>
> Thanks and best regards,
> -Geoff
>
> ---
> Prof. Geoffrey Hutchison
> Department of Chemistry
> University of Pittsburgh
> tel: (412) 648-0492
> email: ge...@pi...
> web: https://hutchisonlab.org/
>
>
> On Jan 15, 2024 at 2:41:00 PM, David van der Spoel
> <dav...@ic...> wrote:
>> Dear devs,
>>
>> my group have worked on implementing a better representation of the GAFF
>> atomtypes, as well as our own set of atomtypes for the upcoming
>> Alexandria force field. We updated the gaff.prm file and added a new
>> .prm file and forcefieldalexandria.cpp/h files. The code is available
>> from https://github.com/dspoel/openbabel
>>
>> Is there any interest to include any of this into the main openbabel
>> repository? I would then port my changes to the latest openbabel and
>> submit a pull-request.
>>
>> 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
>>
>>
>> _______________________________________________
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>> Ope...@li...
>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
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> känner igen avsändaren och vet att innehållet är säkert.
> CAUTION: Do not click on links or open attachments unless you
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--
David van der Spoel, Ph.D.,
Professor of Computational Molecular Biophysics
Uppsala University.
http://virtualchemistry.org









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Re: [Open Babel] Custom force field to OB?

[Geoffrey H. <geo...@gm...>]

 Dear David,

Of course we are happy to have an updated forcefield - I’m sure others will
use it.

Out of curiosity, does this include the polarizable electrostatics or does
it just use whatever partial charges are assigned already?

Thanks and best regards,
-Geoff

---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: ge...@pi...
web: https://hutchisonlab.org/


On Jan 15, 2024 at 2:41:00 PM, David van der Spoel <
dav...@ic...> wrote:

> Dear devs,
>
> my group have worked on implementing a better representation of the GAFF
> atomtypes, as well as our own set of atomtypes for the upcoming
> Alexandria force field. We updated the gaff.prm file and added a new
> .prm file and forcefieldalexandria.cpp/h files. The code is available
> from https://github.com/dspoel/openbabel
>
> Is there any interest to include any of this into the main openbabel
> repository? I would then port my changes to the latest openbabel and
> submit a pull-request.
>
> 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-discuss mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>

[Open Babel] Custom force field to OB?

[David v. d. S. <dav...@ic...>]

Dear devs,

my group have worked on implementing a better representation of the GAFF
atomtypes, as well as our own set of atomtypes for the upcoming
Alexandria force field. We updated the gaff.prm file and added a new
.prm file and forcefieldalexandria.cpp/h files. The code is available
from https://github.com/dspoel/openbabel

Is there any interest to include any of this into the main openbabel
repository? I would then port my changes to the latest openbabel and
submit a pull-request.

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

[Open Babel] How to include names in the output files?

[Masse <moh...@gm...>]

I have 3400 files in canonical smiles format and I use "obabel -ismi
drug-smiles/* -opdb -O drug-pdb/*.pdb" to convert my SMILES to pdb file.
First, is this the correct way of converting? and second, I would like to
have the name of the drug included in the pdb file, how should I do that?
example:

BALSALAZIDE.smile   > O=C(O)CCNC(=O)c1ccc(/N=N/c2ccc(O)c(C(=O)O)c2)cc1


output is:


COMPND    UNNAMED

AUTHOR    GENERATED BY OPEN BABEL 3.1.1

HETATM    1  O   UNL     1       0.000   0.000   0.000  1.00  0.00
  O

HETATM    2  C   UNL     1       0.000   0.000   0.000  1.00  0.00
  C

HETATM    3  O   UNL     1       0.000   0.000   0.000  1.00  0.00
  O

HETATM    4  C   UNL     1       0.000   0.000   0.000  1.00  0.00
  C

HETATM    5  C   UNL     1       0.000   0.000   0.000  1.00  0.00
  C

HETATM    6  N   UNL     1       0.000   0.000   0.000  1.00  0.00
  N

HETATM    7  C   UNL     1       0.000   0.000   0.000  1.00  0.00
  C

HETATM    8  O   UNL     1       0.000   0.000   0.000  1.00  0.00
  O

HETATM    9  C   UNL     1       0.000   0.000   0.000  1.00  0.00
  C

HETATM   10  C   UNL     1       0.000   0.000   0.000  1.00  0.00
  C

HETATM   11  C   UNL     1       0.000   0.000   0.000  1.00  0.00
  C

HETATM   12  C   UNL     1       0.000   0.000   0.000  1.00  0.00
  C

HETATM   13  N   UNL     1       0.000   0.000   0.000  1.00  0.00
  N

HETATM   14  N   UNL     1       0.000   0.000   0.000  1.00  0.00
  N

HETATM   15  C   UNL     1       0.000   0.000   0.000  1.00  0.00
  C

HETATM   16  C   UNL     1       0.000   0.000   0.000  1.00  0.00
  C

HETATM   17  C   UNL     1       0.000   0.000   0.000  1.00  0.00
  C

HETATM   18  C   UNL     1       0.000   0.000   0.000  1.00  0.00
  C

HETATM   19  O   UNL     1       0.000   0.000   0.000  1.00  0.00
  O

HETATM   20  C   UNL     1       0.000   0.000   0.000  1.00  0.00
  C

HETATM   21  C   UNL     1       0.000   0.000   0.000  1.00  0.00
  C

HETATM   22  O   UNL     1       0.000   0.000   0.000  1.00  0.00
  O

HETATM   23  O   UNL     1       0.000   0.000   0.000  1.00  0.00
  O

HETATM   24  C   UNL     1       0.000   0.000   0.000  1.00  0.00
  C

HETATM   25  C   UNL     1       0.000   0.000   0.000  1.00  0.00
  C

HETATM   26  C   UNL     1       0.000   0.000   0.000  1.00  0.00
  C

CONECT    1    2    2

CONECT    2    1    1    3    4

CONECT    3    2

CONECT    4    2    5

CONECT    5    4    6

CONECT    6    5    7

CONECT    7    6    8    8    9

CONECT    8    7    7

CONECT    9    7   26   26   10

CONECT   10    9   11   11

CONECT   11   10   10   12

CONECT   12   11   13   25   25

CONECT   13   12   14   14

CONECT   14   13   13   15

CONECT   15   14   24   24   16

CONECT   16   15   17   17

CONECT   17   16   16   18

CONECT   18   17   19   20   20

CONECT   19   18

CONECT   20   18   18   21   24

CONECT   21   20   22   22   23

CONECT   22   21   21

CONECT   23   21

CONECT   24   20   15   15

CONECT   25   12   12   26

CONECT   26   25    9    9

MASTER        0    0    0    0    0    0    0    0   26    0   26    0

END

[Open Babel] Tautomerization

[Sivani B. <siv...@ng...>]

Hello,

I am looking for an opensource tautomerization tool. I saw that in the release notes for 3.1.0 there was mention of a "Fixed tautomer code" and in 2.1.1 about "tautomer standardization" but I can't find any documentation regarding it in https://open-babel.readthedocs.io/.

I know of the Cactus Tautomerizer (https://cactus.nci.nih.gov/cgi-bin/tautomerize.tcl) but I am looking to run this process on a large number of chemicals (100K+). I'm also aware both CDK and RDKit have tautomerizer options.

Is tautomerization is a feature in openbabel? If so, where I can find more information?

Thanks,
Sivani

P.S. - thanks to those who provided assistance with a previous ask on InChI conversions!
The confidentiality or integrity of this message can not be guaranteed following transmission on the Internet. The addressee should be aware of this before using the contents of this message.

Re: [Open Babel] Errors while Building openbabel

[Geoffrey H. <geo...@gm...>]

 You can run “ctest” to run the tests.

In these particular cases, there is little difference between the data
types - these warnings do not show up with other compilers.

-Geoff



On Nov 4, 2023 at 7:44:45 AM, Dhruv J <dhr...@gm...> wrote:

> Hello,
> How can I know if I have built openbabel correctly, because now I am not
> getting error but am getting warnings instead
> ```
> C:\Users\dhruv\Desktop\openbabel\openbabel\test\../src/rand.cpp(329,21):
> warnin
> g C4244: 'return': conversion from '__int64' to 'int', possible loss of
> data [C
> :\Users\dhruv\Desktop\openbabel\build\test\test_runner.vcxproj]
> C:\Users\dhruv\Desktop\openbabel\openbabel\test\../src/rand.cpp(335,15):
> warnin
> g C4244: 'return': conversion from '__int64' to 'int', possible loss of
> data [C
> :\Users\dhruv\Desktop\openbabel\build\test\test_runner.vcxproj]
>
>   Generating Code...
>   test_runner.vcxproj ->
> C:\Users\dhruv\Desktop\openbabel\build\bin\Debug\test_
>   runner.exe
>   Building Custom Rule
> C:/Users/dhruv/Desktop/openbabel/openbabel/CMakeLists.tx
> ```
>
> Also, can you please suggest any of the issues from which I can get
> started with ....my contributions to openbabel
>
> On Fri, Nov 3, 2023 at 3:12 AM Geoffrey Hutchison <
> geo...@gm...> wrote:
>
>> The MAE parser has some definite issues.
>>
>> Try running “ccmake” to turn off WITH_MAEPARSER or run “cmake
>> -DWITH_MAEPARSER=OFF”
>>
>> Hope that helps,
>> -Geoff
>>
>> On Nov 2, 2023 at 2:00:12 PM, Dhruv J <dhr...@gm...>
>> wrote:
>>
>>> Hello everyone,
>>> I am Dhruv, a third year Computer Engineering undergrad from Mumbai,
>>> India. I am a data science and Machine learning enthusiast. I am interested
>>> in contributing to OpenBabel (I am aware of python and C++) but am very new
>>> to Open Source. I am trying to build openbabel from source in windows but I
>>> am encountering some errors
>>>
>>> C:\Users\dhruv\Desktop\openbabel\build\bin\Debug\maeparser.dll : fatal
>>> error LNK1120: 33 unresolved externals
>>> [C:\Users\dhruv\Desktop\openbabel\build\external\maeparser-v1
>>> .2.3\maeparser\maeparser.vcxproj]
>>> Generating atomizationenergies.h
>>>   Generating atomtyp.h
>>>   Generating bondtyp.h
>>>   Generating phmodeldata.h
>>>   Generating resdata.h
>>>   Generating ringtyp.h
>>>   Generating spacegroups.h
>>>   Generating torlib.h
>>>   Generating types.h
>>>   Building Custom Rule
>>> C:/Users/dhruv/Desktop/openbabel/openbabel/data/CMakeLists.txt
>>>
>>> I am running the build process from the terminal using cmake --build
>>> command.
>>> Can anyone please help me to solve this problem?
>>>
>>> Also Can anyone provide me with a beginner friendly issue so I can start
>>> contributing to openbabel.
>>> Thank you very much
>>>
>>> _______________________________________________
>>> OpenBabel-discuss mailing list
>>> Ope...@li...
>>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>>
>>

Re: [Open Babel] Errors while Building openbabel

[Geoffrey H. <geo...@gm...>]

 The MAE parser has some definite issues.

Try running “ccmake” to turn off WITH_MAEPARSER or run “cmake
-DWITH_MAEPARSER=OFF”

Hope that helps,
-Geoff

On Nov 2, 2023 at 2:00:12 PM, Dhruv J <dhr...@gm...> wrote:

> Hello everyone,
> I am Dhruv, a third year Computer Engineering undergrad from Mumbai,
> India. I am a data science and Machine learning enthusiast. I am interested
> in contributing to OpenBabel (I am aware of python and C++) but am very new
> to Open Source. I am trying to build openbabel from source in windows but I
> am encountering some errors
>
> C:\Users\dhruv\Desktop\openbabel\build\bin\Debug\maeparser.dll : fatal
> error LNK1120: 33 unresolved externals
> [C:\Users\dhruv\Desktop\openbabel\build\external\maeparser-v1
> .2.3\maeparser\maeparser.vcxproj]
> Generating atomizationenergies.h
>   Generating atomtyp.h
>   Generating bondtyp.h
>   Generating phmodeldata.h
>   Generating resdata.h
>   Generating ringtyp.h
>   Generating spacegroups.h
>   Generating torlib.h
>   Generating types.h
>   Building Custom Rule
> C:/Users/dhruv/Desktop/openbabel/openbabel/data/CMakeLists.txt
>
> I am running the build process from the terminal using cmake --build
> command.
> Can anyone please help me to solve this problem?
>
> Also Can anyone provide me with a beginner friendly issue so I can start
> contributing to openbabel.
> Thank you very much
>
> _______________________________________________
> OpenBabel-discuss mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>

[Open Babel] Errors while Building openbabel

[Dhruv J <dhr...@gm...>]

Hello everyone,
I am Dhruv, a third year Computer Engineering undergrad from Mumbai, India.
I am a data science and Machine learning enthusiast. I am interested in
contributing to OpenBabel (I am aware of python and C++) but am very new to
Open Source. I am trying to build openbabel from source in windows but I am
encountering some errors

C:\Users\dhruv\Desktop\openbabel\build\bin\Debug\maeparser.dll : fatal
error LNK1120: 33 unresolved externals
[C:\Users\dhruv\Desktop\openbabel\build\external\maeparser-v1
.2.3\maeparser\maeparser.vcxproj]
Generating atomizationenergies.h
  Generating atomtyp.h
  Generating bondtyp.h
  Generating phmodeldata.h
  Generating resdata.h
  Generating ringtyp.h
  Generating spacegroups.h
  Generating torlib.h
  Generating types.h
  Building Custom Rule
C:/Users/dhruv/Desktop/openbabel/openbabel/data/CMakeLists.txt

I am running the build process from the terminal using cmake --build
command.
Can anyone please help me to solve this problem?

Also Can anyone provide me with a beginner friendly issue so I can start
contributing to openbabel.
Thank you very much

[Open Babel] Open Babel website

[Geoffrey H. <geo...@gm...>]

Unfortunately, as part of a routine hosting update (e.g., my provider
changed DNS) the openbabel.org website is currently down.

It’s not clear from the logs why the site remains down.

I’m going to take the opportunity to cleanup a new website based on Noel
O’Boyle’s excellent docs: https://open-babel.readthedocs.io/en/latest/

If you have particular feedback as to the site (e.g., API docs for old
versions), please let me know.
(All the files are intact, it’s just stuck in a redirect loop for no
obvious reason.)

If you’d like to help, I will be going off of
https://github.com/openbabel/openbabel.github.io
(Although I may switch from Jekyll to Spinx + Markdown, since Noel’s docs
are already formatted.)

Best,
-Geoff