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From: Andrew D. <da...@da...> - 2024-09-11 12:57:33
|
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. |
From: Srdjan P. <srd...@ho...> - 2024-09-11 09:16:22
|
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. |
From: Raghav, D. - (draghav) <dr...@ar...> - 2024-07-22 23:26:28
|
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 |
From: I L <lim...@gm...> - 2024-05-30 10:07:37
|
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 |
From: Geoffrey H. <geo...@gm...> - 2024-02-27 17:25:06
|
> > 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/ |
From: Álex B. <ale...@br...> - 2024-02-26 15:33:10
|
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 |
From: David v. d. S. <dav...@ic...> - 2024-01-15 20:25:07
|
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 >> >> >> _______________________________________________ >> OpenBabel-discuss mailing list >> Ope...@li... >> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > > 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 |
From: Geoffrey H. <geo...@gm...> - 2024-01-15 20:22:03
|
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 > |
From: David v. d. S. <dav...@ic...> - 2024-01-15 19:57:53
|
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 |
From: Masse <moh...@gm...> - 2023-12-05 09:28:51
|
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 |
From: Sivani B. <siv...@ng...> - 2023-11-13 09:43:39
|
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. |
From: Geoffrey H. <geo...@gm...> - 2023-11-04 16:20:10
|
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 >>> >> |
From: Geoffrey H. <geo...@gm...> - 2023-11-02 21:42:22
|
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 > |
From: Dhruv J <dhr...@gm...> - 2023-11-02 18:00:37
|
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 |
From: Geoffrey H. <geo...@gm...> - 2023-10-24 20:58:47
|
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 |
From: Geoffrey H. <geo...@gm...> - 2023-09-21 01:51:58
|
> > I'm a PhD student. In my research, I'm using Obabel and have a problem > with this. After converting the molecules to physiological pH, deprotonated > molecules are not obtained in phosphate groups. > I’m not sure if I understand. Basically, you want a tool that’s going to adjust protonation for all functional groups? That’s not what Open Babel does .. it has a set of rules, particularly for amino acids. At the moment, you may want to look at Dimorphite: https://github.com/durrantlab/dimorphite_dl/blob/master/README.md Hope that helps, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: ge...@pi... twitter: @ghutchis web: https://hutchisonlab.org/ |
From: María V. C. <vir...@gm...> - 2023-09-20 15:59:54
|
I'm a PhD student. In my research, I'm using Obabel and have a problem with this. After converting the molecules to physiological pH, deprotonated molecules are not obtained in phosphate groups. Is there a solution for this? Does a script exist for this? I hope that somebody can help me. Virginia |
From: Alan L. <ala...@jh...> - 2023-08-26 17:00:37
|
Dear Geoff, in line with my previous letter (please see below - mailer-daemon returned it to me several days after sending, so I don´t know if you received it), I updated the OpenBABEL binaries in our apps. The most recent versions should work better. The installers and full sources are available in the corresponding Google Play links and in Github repositories. ... -------- Originalnachricht -------- Betreff: Re: [Open Babel] OpenBabel SMILES to XYZ conversion Datum: 2023-08-11 16:43 Von: Alan Liška <ala...@jh...> An: Geoffrey Hutchison <geo...@gm...> Kopie: ope...@li... Dear Geoff, thank you for the answer. I´m happy that the most recent versions of Open Babel can handle structures consisting of multiple fragments quite well. However, I found out that in the case of planar fragments like cyclopentadienyl rings in ferrocene obabel -:'[CH-]1C=CC=C1.[CH-]1C=CC=C1.[Fe+2]' -O test.xyz --gen3d or benzene molecules obabel -:'c1ccccc1.c1ccccc1' -O test.xyz --gen3d the resulting XYZ structure still contains both moieties located in the same positions (overlapping). Concerning our Android applications, we appreciate Open Babel a lot, as it makes the first (input) part of the quantum chemical calculations fast and comfortable. In most cases, the user can define the desired structure (to be calculated) easily by the IUPAC name, which is converted by OPSIN to SMILES, and subsequentely by Open Babel to XYZ in background. Thus, generating an input file takes few taps on the phone/tablet touch screen instead of complicated drawing atom by atom. Our applications enable performing typically semiempirical calculations natively in the mobile device (offline) which is nowadays possible due to the sufficient computational power of a typical hardware employed in almost any smartphone. As for your question, our source code repositories already contain the GUI inside. Generally, the Android app sources are distributed as whole Android Studio project which can be easily compiled to create the installer identical to that one which can be accessed in the Google Play Store. You can find the most relevant parts as follows: -Java source files (individual functions and their connectivity) /app/src/main/java/name/of/the/app/ -graphical and resource files (defining the graphical layout and styles employed in each app screen - that is maybe the answer for your request) /app/src/main/res/layout/ and /app/src/main/res/drawable/ -other files needed in the application (as the data files for Open Babel) /app/src/main/assets/ -precompiled binary stuff (binaries - executables and libraries which run on the UNIX core of Android = in the case of Open Babel it is the obabel binary) /app/src/main/jniLibs/[architecture= arm, aarch64, x86, x86_64 - the installer picks the one which is matching the device processor and OS architecture automatically]; executables in this folder have to be saved under the lib-XXX-.so names although they are not libraries - like obabel is renamed here to libobabel.so although it is a static executable (due to Google Android policy) I also updated the info on Open Babel sources inside of the app - the sourceforge entry was removed. I´m looking forward to hearing from you. Best, Alan Am 2023-08-03 20:55, schrieb Geoffrey Hutchison: > Dear Alan, > > While I don’t quite understand the purpose of converting molecules > on an Android phone, of course you can use Open Babel as you wish. > > A few concerns, however: > > * You mention Open Babel 2.3.1, which is at this point ancient. > * I would not indicate the SourceForge page as it is no longer used. > * Since you are directly using GPLv2 code (Open Babel), you must > include a link to the source code (your whole app). I don’t see the > code for the GUI? > > You mention a potential issue with multiple fragments, which doesn’t > seem to be an issue with the current versions, e.g. > > obabel -:'CCC.C=O' -O test.xyz [1] —gen3d > > See attached. > > Best, > -Geoff > > --- > Prof. Geoffrey Hutchison > Department of Chemistry > University of Pittsburgh > tel: (412) 648-0492 > email: ge...@pi... > twitter: @ghutchis > web: https://hutchisonlab.org/ |
From: Anthony N. <dis...@go...> - 2023-08-24 09:54:11
|
Dear OpenBabel mailing list, I'm using OpenBabel 3.1.1 and the Python to C++ bindings to load pdbqt files and convert them to pdb with explicit hydrogens. Unfortunately, I can't add nonpolar hydrogens using OpenBabel. I can do this using Autodock's PMV GUI as a test and comparison, so my concern is not the underlying molecule. In the python bindings, I've tried combinations of AddHydrogens(), AddNewHydrogens(), AddPolarHydrogens(), AddNonPolarHydrogens(), checking the OBMol.NumAtoms() each time, and nothing changes. In the OpenBabel GUI I've loaded the pdbqt files and tried combinations of "Add hydrogens (make explicit)", "Add hydrogens to nonpolar atoms only", and "Adds hydrogens to polar atoms only". Nothing changes the pdb output. Note: There is one polar-hydrogen present which can be removed and added back. Ultimately, I must determine why the Python bindings aren't adding hydrogens. Using the GUI was a sanity check. I've included for you below a copy & paste of a pdbqt file. Many thanks for your help. REMARK VINA RESULT: -8.009 0.000 0.000 REMARK INTER + INTRA: -11.923 REMARK INTER: -10.819 REMARK INTRA: -1.105 REMARK UNBOUND: -1.105 REMARK Name = ZINC000004125379 REMARK x y z vdW Elec q Type REMARK _______ _______ _______ _____ _____ ______ ____ ROOT ATOM 1 C LIG 1 -7.551 101.695 50.079 0.00 0.00 -0.030 A ATOM 2 C LIG 1 -7.837 101.486 48.730 0.00 0.00 +0.090 A ATOM 3 C LIG 1 -9.147 101.402 48.306 0.00 0.00 +0.030 A ATOM 4 C LIG 1 -10.180 101.524 49.216 0.00 0.00 -0.050 A ATOM 5 C LIG 1 -9.907 101.732 50.562 0.00 0.00 +0.130 A ATOM 6 C LIG 1 -11.610 101.431 48.746 0.00 0.00 +0.100 C ATOM 7 C LIG 1 -8.592 101.813 50.998 0.00 0.00 +0.120 A ENDROOT BRANCH 1 13 ATOM 8 C LIG 1 -3.446 102.767 52.833 0.00 0.00 +0.240 A ATOM 9 N LIG 1 -2.257 102.405 52.445 0.00 0.00 -0.250 NA ATOM 10 N LIG 1 -2.330 101.778 51.323 0.00 0.00 -0.230 NA ATOM 11 C LIG 1 -3.581 101.712 50.944 0.00 0.00 +0.080 A ATOM 12 S LIG 1 -4.712 101.147 49.709 0.00 0.00 +0.190 S ATOM 13 C LIG 1 -6.145 101.786 50.535 0.00 0.00 +0.170 A ATOM 14 N LIG 1 -5.709 102.349 51.619 0.00 0.00 -0.250 NA ATOM 15 N LIG 1 -4.348 102.331 51.887 0.00 0.00 -0.340 N BRANCH 8 17 ATOM 16 C LIG 1 -3.372 102.687 55.311 0.00 0.00 +0.060 C ATOM 17 C LIG 1 -3.777 103.522 54.095 0.00 0.00 +0.160 C ENDBRANCH 8 17 ENDBRANCH 1 13 BRANCH 5 18 ATOM 18 N LIG 1 -10.956 101.853 51.480 0.00 0.00 -0.620 N ATOM 19 H LIG 1 -11.561 102.610 51.427 0.00 0.00 +0.410 HD BRANCH 18 20 ATOM 20 C LIG 1 -11.124 100.921 52.438 0.00 0.00 +0.510 C ATOM 21 S LIG 1 -10.962 99.261 52.056 0.00 0.00 -0.470 S BRANCH 20 22 ATOM 22 N LIG 1 -11.419 101.297 53.699 0.00 0.00 -0.640 N ATOM 23 H LIG 1 -12.344 101.330 53.991 0.00 0.00 +0.410 HD ATOM 24 C LIG 1 -10.431 101.629 54.553 0.00 0.00 +0.530 C ATOM 25 O LIG 1 -9.272 101.589 54.186 0.00 0.00 -0.380 OA BRANCH 24 26 ATOM 26 C LIG 1 -10.754 102.041 55.932 0.00 0.00 -0.180 A ATOM 27 C LIG 1 -10.619 103.376 56.316 0.00 0.00 +0.070 A ATOM 28 C LIG 1 -10.922 103.754 57.607 0.00 0.00 +0.000 A ATOM 29 C LIG 1 -11.361 102.814 58.524 0.00 0.00 +0.080 A ATOM 30 C LIG 1 -11.500 101.489 58.153 0.00 0.00 -0.010 A ATOM 31 C LIG 1 -11.205 101.095 56.861 0.00 0.00 +0.170 A ATOM 32 F LIG 1 -11.341 99.801 56.499 0.00 0.00 -0.110 F ENDBRANCH 24 26 ENDBRANCH 20 22 ENDBRANCH 18 20 ENDBRANCH 5 18 TORSDOF 6 *Dr Anthony Nash PhD MRSC MSc MSc BSc* Computational Chemistry Consultant Warwick, United Kingdom |
From: Gupta, T. <t....@uc...> - 2023-08-14 17:35:33
|
Hi I am trying to install Theodore and when I am doing test run some of the tests are failing stating that it could not openbabel. However, in my python 3.10.9 virtual environment, I already have openbabel-3.1.1 as can be seen from below images: [cid:f76557dd-c1fd-4ccf-92a7-31d91020772d] [cid:2820bbe4-0b49-4f4a-8a23-df51ee90530b] Any help in this regard would be greatly appreciated. thanks Dr Tulika Gupta, PhD Dept. of Chemistry University College London 20, Gordon St. London, UK WC1H 0AJ e-mail t....@uc... -------------------------------------------------------------------------------- |
From: Alan L. <ala...@jh...> - 2023-08-11 14:43:19
|
Dear Geoff, thank you for the answer. I´m happy that the most recent versions of Open Babel can handle structures consisting of multiple fragments quite well. However, I found out that in the case of planar fragments like cyclopentadienyl rings in ferrocene obabel -:'[CH-]1C=CC=C1.[CH-]1C=CC=C1.[Fe+2]' -O test.xyz --gen3d or benzene molecules obabel -:'c1ccccc1.c1ccccc1' -O test.xyz --gen3d the resulting XYZ structure still contains both moieties located in the same positions (overlapping). Concerning our Android applications, we appreciate Open Babel a lot, as it makes the first (input) part of the quantum chemical calculations fast and comfortable. In most cases, the user can define the desired structure (to be calculated) easily by the IUPAC name, which is converted by OPSIN to SMILES, and subsequentely by Open Babel to XYZ in background. Thus, generating an input file takes few taps on the phone/tablet touch screen instead of complicated drawing atom by atom. Our applications enable performing typically semiempirical calculations natively in the mobile device (offline) which is nowadays possible due to the sufficient computational power of a typical hardware employed in almost any smartphone. As for your question, our source code repositories already contain the GUI inside. Generally, the Android app sources are distributed as whole Android Studio project which can be easily compiled to create the installer identical to that one which can be accessed in the Google Play Store. You can find the most relevant parts as follows: -Java source files (individual functions and their connectivity) /app/src/main/java/name/of/the/app/ -graphical and resource files (defining the graphical layout and styles employed in each app screen - that is maybe the answer for your request) /app/src/main/res/layout/ and /app/src/main/res/drawable/ -other files needed in the application (as the data files for Open Babel) /app/src/main/assets/ -precompiled binary stuff (binaries - executables and libraries which run on the UNIX core of Android = in the case of Open Babel it is the obabel binary) /app/src/main/jniLibs/[architecture= arm, aarch64, x86, x86_64 - the installer picks the one which is matching the device processor and OS architecture automatically]; executables in this folder have to be saved under the lib-XXX-.so names although they are not libraries - like obabel is renamed here to libobabel.so although it is a static executable (due to Google Android policy) I also updated the info on Open Babel sources inside of the app - the sourceforge entry was removed. I´m looking forward to hearing from you. Best, Alan Am 2023-08-03 20:55, schrieb Geoffrey Hutchison: > Dear Alan, > > While I don’t quite understand the purpose of converting molecules > on an Android phone, of course you can use Open Babel as you wish. > > A few concerns, however: > > * You mention Open Babel 2.3.1, which is at this point ancient. > * I would not indicate the SourceForge page as it is no longer used. > * Since you are directly using GPLv2 code (Open Babel), you must > include a link to the source code (your whole app). I don’t see the > code for the GUI? > > You mention a potential issue with multiple fragments, which doesn’t > seem to be an issue with the current versions, e.g. > > obabel -:'CCC.C=O' -O test.xyz [1] —gen3d > > See attached. > > Best, > -Geoff > > --- > Prof. Geoffrey Hutchison > Department of Chemistry > University of Pittsburgh > tel: (412) 648-0492 > email: ge...@pi... > twitter: @ghutchis > web: https://hutchisonlab.org/ > > On Jul 25, 2023 at 1:58:18 PM, Alan Liška <ala...@jh...> > wrote: > >> Dear OpenBabel developers, >> >> me and my friend Veronika Ruzickova focus at porting professional >> open-source chemistry codes to Android. Already in the past, we >> published the standalone OpenBabel app >> (https://play.google.com/store/apps/details?id=cz.jh.openbabel). >> Recently, we have published 3 new free apps: >> PHREEQC plus >> https://play.google.com/store/apps/details?id=cz.p >> https://github.com/alanliska/PHREEQC-plus >> DFTB+ >> https://play.google.com/store/apps/details?id=cz.jh.dftb >> https://github.com/alanliska/DFTB >> XTB >> https://play.google.com/store/apps/details?id=cz.jh.xtb >> https://github.com/alanliska/XTB >> where we utilized your OpenBabel binary for SMILES to XYZ >> translation. >> Because we plan to upgrade also some other similar apps, it is >> highly >> probable that we integrate OpenBabel there as well. >> Inside of each app as well as in the individual package >> descriptions, we >> cited your software as follows: >> >> * OPENBABEL >> Ref.: N M O'Boyle, M Banck, C A James, C Morley, T Vandermeersch, >> and G >> R Hutchison. "Open Babel: An open chemical toolbox." J. Cheminf. >> (2011), >> 3, 33. DOI:10.1186/1758-2946-3-33 >> The Open Babel Package, version 2.3.1 http://openbabel.org >> (accessed Oct 2011) >> Source code: http://openbabel.org/wiki/Main_Page, >> https://github.com/openbabel/openbabel, >> https://sourceforge.net/projects/openbabel/ >> >> Please let me know if you would like to enhance the reference to >> you, or >> specify the citation in a more detailed way. >> Thank you :-). >> >> My second question concerns the SMILES to structure conversion in >> case >> of molecular complexes, i.e. entities which contain the dot '.' >> between >> the individual parts. OpenBabel seems to place all the separated >> molecules in the same cartesian origin which makes the conversion of >> >> type >> >> obabel -ismi File-with-smiles.smi -oxyz --gen3D (where SMILES could >> be >> anything like "CCC.C=O") >> >> useless, as the resulting XYZ file describes a bundle of atoms >> coming >> from both overlapping structures, often collided together. Of >> course, >> the desired separation distance is generally unambiguous. On the >> other >> hand, I could imagine that there would be a function to define the >> distance of both molecular centres manually e.g. in form of a >> switch. >> Don´t you consider to implement something like that in the future >> versions of OpenBabel? Thanks in advance for the answer. >> >> Sincerely, >> >> Alan >> >> -- >> RNDr. Alan Liška, Ph.D. >> Ústav fyzikální chemie J. Heyrovského AV ČR, v.v.i. / J. >> Heyrovský >> Institute of Physical Chemistry of the CAS, v.v.i. >> Dolejškova 3/2155, 18223 Praha 8 >> Česká republika / Czech Republic >> >> _______________________________________________ >> OpenBabel-discuss mailing list >> Ope...@li... >> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > > Links: > ------ > [1] http://test.xyz |
From: Geoffrey H. <geo...@gm...> - 2023-08-10 17:27:33
|
I think you’re mixing up “obminimize” which is a specific tool, and “obabel” which can convert, etc. I’d suggest something like: obabel {input_file} -O {output_file} -opdbqt --minimize -sd -ff GAFF -h Best, -Geoff On Aug 8, 2023 at 2:24:21 PM, Lock Meister <mei...@gm...> wrote: > Hi, > > I was trying to run Obminimize to convert SDF files that I converted from > SMILE strings into PDBQT files, and when I run the code that I have to loop > it with a perl script with multiple files, I'm constantly getting > this error: "obminimize: cannot read input/output format!" > > I was wondering if there might be any reason for this as I'm not very > experienced with coding or open babel, and have attached my code and an > example .sdf file that I have. I'm on the most updated Open babel there is, > and Ive made sure to correctly place the files in the respective folders. > > I was wondering maybe if there was anything that I'm doing wrong that you > guys could point out that I've unsuccessfully been able to perform? > > > Cheers, > Locke > > _______________________________________________ > OpenBabel-discuss mailing list > Ope...@li... > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > |
From: Gupta, T. <t....@uc...> - 2023-08-10 14:31:24
|
Dear Team I am trying to build latest version of openbabel on my OS: Debian7 I am using Python-3.10.9 and swig-4.1.1 While initial cmake command : cmake ../. -DPYTHON_EXECUTABLE=/usr/local/bin/python3.10 -DSWIG_EXECUTABLE=/usr/local/custom-swig/bin/swig -DPYTHON_BINDINGS=ON -DRUN_SWIG=ON -DBUILD_GUI=ON -DCMAKE_INSTALL_PREFIX=/usr/local/custom-openbabel -DCMAKE_BUILD_TYPE=DEBUG -DCMAKE_C_COMPILER=/opt/gcc/8.5.0/bin/gcc -DCMAKE_CXX_COMPILER=/opt/gcc/8.5.0/bin/g++ ended successfuly. When I tried to make, it ended up with error (last lines are below): [cid:667f9db1-fcc8-4cf8-8632-66edbac1149a] Please advise. thanks Dr Tulika Gupta, PhD Dept. of Chemistry University College London 20, Gordon St. London, UK WC1H 0AJ e-mail t....@uc... -------------------------------------------------------------------------------- |
From: Lock M. <mei...@gm...> - 2023-08-08 18:24:40
|
Hi, I was trying to run Obminimize to convert SDF files that I converted from SMILE strings into PDBQT files, and when I run the code that I have to loop it with a perl script with multiple files, I'm constantly getting this error: "obminimize: cannot read input/output format!" I was wondering if there might be any reason for this as I'm not very experienced with coding or open babel, and have attached my code and an example .sdf file that I have. I'm on the most updated Open babel there is, and Ive made sure to correctly place the files in the respective folders. I was wondering maybe if there was anything that I'm doing wrong that you guys could point out that I've unsuccessfully been able to perform? Cheers, Locke |
From: Geoffrey H. <geo...@gm...> - 2023-08-08 15:39:22
|
> > I am facing issue in terms of installing openbabel latest version. Kindly > let me know which openbabel version is compatible with python-3.10.9 in > terms of bindings. > If you wish to install Python bindings, we *highly* recommend you use conda-forge, e.g. conda install -c conda-forge openbabel Also with regards to latest version installation I am facing erroe while > using compiler intel/2015.6: > I have never used an Intel compiler, but it looks as if you are missing required packages. A search for your error yields: https://stackoverflow.com/questions/44773296/libstdc-so-6-version-glibcxx-3-4-20-not-found Best regards, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: ge...@pi... twitter: @ghutchis web: https://hutchisonlab.org/ |