openbabel-discuss  

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• Re: [Open Babel] OpenBabel-discuss Digest, Vol 217, Issue 4 Chris Swain via OpenBabel-discuss
• [Open Babel] Errors in file conversion Chris Swain via OpenBabel-discuss
  • Re: [Open Babel] Errors in file conversion Geoffrey Hutchison
  • Re: [Open Babel] Errors in file conversion Chris Swain via OpenBabel-discuss
  • Re: [Open Babel] Errors in file conversion Noel O'Boyle
  • Re: [Open Babel] Errors in file conversion Andrew Dalke
• [Open Babel] Mychem v2.0.0 Jerome Pansanel
• [Open Babel] Angle constraints not applied during OBForceField optimization Overstreet, Richard E via OpenBabel-discuss
• [Open Babel] How to get source code for UFF and MMFF84 minimization Srdjan Pusara
  • Re: [Open Babel] How to get source code for UFF and MMFF84 minimization Andrew Dalke
• [Open Babel] Errors and problems in 3 D structure generation Raghav, Darpan - (draghav)
• [Open Babel] Openbabel filtering a list of conformers I L
• [Open Babel] Assistance Needed with Modifying Molecules in Python Script Álex Balogh via OpenBabel-discuss
  • Re: [Open Babel] Assistance Needed with Modifying Molecules in Python Script Geoffrey Hutchison
• [Open Babel] Custom force field to OB? David van der Spoel
  • Re: [Open Babel] Custom force field to OB? Geoffrey Hutchison
  • Re: [Open Babel] Custom force field to OB? David van der Spoel
• [Open Babel] How to include names in the output files? Masse
• [Open Babel] Tautomerization Sivani Baskaran via OpenBabel-discuss
• [Open Babel] Errors while Building openbabel Dhruv J
  • Re: [Open Babel] Errors while Building openbabel Geoffrey Hutchison
  • Re: [Open Babel] Errors while Building openbabel Geoffrey Hutchison
• [Open Babel] Open Babel website Geoffrey Hutchison
• [Open Babel] Desprotonated Molecules María Virginia Chaulet
  • Re: [Open Babel] Desprotonated Molecules Geoffrey Hutchison
• [Open Babel] Problem adding non-polar hydrogens whilst converting from pdbqt to pdb Anthony Nash via OpenBabel-discuss
• [Open Babel] Openbabel use error during a software runtest Gupta, Tulika
• [Open Babel] Openbabel compile error Gupta, Tulika
• [Open Babel] Help with "obminimize: cannot read input/output format!" error Lock Meister
  • Re: [Open Babel] Help with "obminimize: cannot read input/output format!" error Geoffrey Hutchison
• [Open Babel] Openbabel installation error and python version compatibility Gupta, Tulika
  • Re: [Open Babel] Openbabel installation error and python version compatibility Geoffrey Hutchison
• [Open Babel] OpenBabel SMILES to XYZ conversion Alan Liška
  • Re: [Open Babel] OpenBabel SMILES to XYZ conversion Geoffrey Hutchison
  • Re: [Open Babel] OpenBabel SMILES to XYZ conversion Alan Liška
  • [Open Babel] OpenBabel SMILES to XYZ conversion, update Alan Liška
• [Open Babel] problem with pip install Tim Dudgeon
  • Re: [Open Babel] problem with pip install Geoffrey Hutchison
• [Open Babel] retain identifier with InChI conversions Sivani Baskaran via OpenBabel-discuss
  • Re: [Open Babel] retain identifier with InChI conversions Francois Berenger
  • Re: [Open Babel] retain identifier with InChI conversions Noel O'Boyle
• Re: [Open Babel] Issues compiling OpenBabel-2.4.1 on MacOS Geoffrey Hutchison
  • Re: [Open Babel] Issues compiling OpenBabel-2.4.1 on MacOS Chuhong Wang
• [Open Babel] Issues compiling OpenBabel-3.1.1 on Linux Alessandro S. Nascimento via OpenBabel-discuss
  • Re: [Open Babel] Issues compiling OpenBabel-3.1.1 on Linux Geoffrey Hutchison
  • Re: [Open Babel] Issues compiling OpenBabel-3.1.1 on Linux Alessandro S. Nascimento via OpenBabel-discuss
• [Open Babel] ConstruQt Webinar Peter Jarowski
• [Open Babel] Openbabel installing problem Pratyajit Mohapatra
• [Open Babel] 2048 fingerprints Covell, David (NIH/NCI) [E] via OpenBabel-discuss
  • Re: [Open Babel] 2048 fingerprints Geoffrey Hutchison
• [Open Babel] unable to read CIF Tim Dudgeon
  • Re: [Open Babel] unable to read CIF Geoffrey Hutchison
• [Open Babel] indexing atoms in png file MD Simulation
  • Re: [Open Babel] indexing atoms in png file Geoffrey Hutchison
• [Open Babel] converting many smiles to many mol Mohammad Goodarzi
  • Re: [Open Babel] converting many smiles to many mol Geoffrey Hutchison
• [Open Babel] Problem with openbabel package installation in python Mohammad Amin Ghanavati
• [Open Babel] Helps me María Virginia Chaulet
• [Open Babel] Prevent addition of H during minimization Hetal Patel
  • Re: [Open Babel] Prevent addition of H during minimization Noel O'Boyle
• [Open Babel] Convert sodium chloride from pdb to sdf David van der Spoel
  • Re: [Open Babel] Convert sodium chloride from pdb to sdf Michael Brunsteiner via OpenBabel-discuss
  • Re: [Open Babel] Convert sodium chloride from pdb to sdf Geoffrey Hutchison
• [Open Babel] extracting ligands from macromolecular structures Tim Dudgeon
  • Re: [Open Babel] extracting ligands from macromolecular structures Richard Overstreet
  • Re: [Open Babel] extracting ligands from macromolecular structures Noel O'Boyle
  • Re: [Open Babel] extracting ligands from macromolecular structures Tim Dudgeon
• [Open Babel] Explicit H as property Thomas
  • Re: [Open Babel] Explicit H as property Andrew Dalke
  • Re: [Open Babel] Explicit H as property Thomas
  • Re: [Open Babel] Explicit H as property Noel O'Boyle
• [Open Babel] Avoid sanitization Thomas
  • Re: [Open Babel] Avoid sanitization Noel O'Boyle
  • Re: [Open Babel] Avoid sanitization Thomas
  • Re: [Open Babel] Avoid sanitization Noel O'Boyle
  • Re: [Open Babel] Avoid sanitization Thomas
  • Re: [Open Babel] Avoid sanitization Noel O'Boyle
• [Open Babel] OB install with pip (Google Colab) Alessandro S. Nascimento via OpenBabel-discuss
• [Open Babel] Warning in Perceiving Bond Order from mmcif files Ibrahim Roshan Kunnakkattu
• [Open Babel] splitting into pdbqt files Siavoush Dastmalchi via OpenBabel-discuss
• [Open Babel] PDB to PDBQT failed to kekulize aromatic bonds error Ilinca Flacau
  • Re: [Open Babel] PDB to PDBQT failed to kekulize aromatic bonds error Geoffrey Hutchison
• Re: [Open Babel] pythonbinding for openbabel3.1.1 and python 3.11.1 David van der Spoel
• [Open Babel] Converting from pdb to pdbqt Ilinca Flacau
  • Re: [Open Babel] Converting from pdb to pdbqt Francois Berenger
• Re: [Open Babel] Regarding converting MTI and many others types of files to PDB Geoffrey Hutchison
  • Re: [Open Babel] Regarding converting MTI and many others types of files to PDB Geoffrey Hutchison
• [Open Babel] Thread usage for make3D() Tim Dudgeon
• [Open Babel] add hydrogens appropriate for PH using Pybel #MENG ZHENYU# via OpenBabel-discuss
  • Re: [Open Babel] [EXTERNAL] add hydrogens appropriate for PH using Pybel Vincent Scalfani
  • Re: [Open Babel] [EXTERNAL] add hydrogens appropriate for PH using Pybel #MENG ZHENYU# via OpenBabel-discuss
• [Open Babel] create cif or POSCAR file Deependra Shah
  • Re: [Open Babel] create cif or POSCAR file Andrew Dalke
• [Open Babel] Iterate and convert .smi to multiple .png Azman, Adam
  • Re: [Open Babel] Iterate and convert .smi to multiple .png Chris Swain via OpenBabel-discuss
• Re: [Open Babel] Errors when installing openbabel Geoffrey Hutchison
• [Open Babel] PDBQT to SDF with correct 3D structure also as an input Mandar Kulkarni
• [Open Babel] Error in "from openbabel import pybel" Will
  • Re: [Open Babel] Error in "from openbabel import pybel" Geoffrey Hutchison
• [Open Babel] Energy value when converting from g16 to xyz Corrado Bacchiocchi
• [Open Babel] Writer Format - WLN Writer + Reader Functionality Expansion Michael Blakey via OpenBabel-discuss
  • Re: [Open Babel] Writer Format - WLN Writer + Reader Functionality Expansion Noel O'Boyle
  • Re: [Open Babel] Writer Format - WLN Writer + Reader Functionality Expansion Noel O'Boyle
  • Re: [Open Babel] Writer Format - WLN Writer + Reader Functionality Expansion Geoffrey Hutchison
  • Re: [Open Babel] Writer Format - WLN Writer + Reader Functionality Expansion Andrew Dalke
  • Re: [Open Babel] Writer Format - WLN Writer + Reader Functionality Expansion Geoffrey Hutchison
  • Re: [Open Babel] Writer Format - WLN Writer + Reader Functionality Expansion m.k.blakey--- via OpenBabel-discuss
  • Re: [Open Babel] Writer Format - WLN Writer + Reader Functionality Expansion m.k.blakey--- via OpenBabel-discuss
  • Re: [Open Babel] Writer Format - WLN Writer + Reader Functionality Expansion m.k.blakey--- via OpenBabel-discuss
• [Open Babel] Crash Software Hola, soy José Luis Morán!
  • Re: [Open Babel] Crash Software Geoffrey Hutchison
• [Open Babel] --splitinto Siavoush Dastmalchi via OpenBabel-discuss
  • [Open Babel] --splitinto Siavoush Dastmalchi via OpenBabel-discuss
  • Re: [Open Babel] --splitinto Tru Huynh
  • Re: [Open Babel] --splitinto Siavoush Dastmalchi via OpenBabel-discuss
  • Re: [Open Babel] --splitinto Geoffrey Hutchison
  • Re: [Open Babel] --splitinto Siavoush Dastmalchi via OpenBabel-discuss
• [Open Babel] Installation of openbabel3 with python Antonio Jesús Banegas Luna
• [Open Babel] Question for Openbabbel installation with Python Quentin Delobelle
  • Re: [Open Babel] Question for Openbabbel installation with Python Geoffrey Hutchison
  • Re: [Open Babel] Question for Openbabbel installation with Python Quentin Delobelle
  • Re: [Open Babel] Question for Openbabbel installation with Python Geoffrey Hutchison
  • Re: [Open Babel] Question for Openbabbel installation with Python Francois Berenger
• [Open Babel] Error calculating descriptor jiangshan
  • Re: [Open Babel] Error calculating descriptor Fredrik Wallner
• [Open Babel] Include OpenBabel into R package Gindea Macarovici Nikita
  • Re: [Open Babel] Include OpenBabel into R package Geoffrey Hutchison
• [Open Babel] convert SMILE to Mol Mohammad Goodarzi
  • Re: [Open Babel] convert SMILE to Mol Francois Berenger
  • Re: [Open Babel] convert SMILE to Mol Richard
  • Re: [Open Babel] convert SMILE to Mol Mohammad Goodarzi
• [Open Babel] Change PDB Beta column during write Richard
• Re: [Open Babel] SDF to Structure Matrix Chris Swain via OpenBabel-discuss
  • Re: [Open Babel] SDF to Structure Matrix Rudy Richardson
• [Open Babel] SDF to Structure Matrix? Rudy Richardson
  • Re: [Open Babel] SDF to Structure Matrix? Christopher Mayer-Bacon
  • Re: [Open Babel] SDF to Structure Matrix? Rudy Richardson
• [Open Babel] Run obabel with n cpu cores? Rudy Richardson
  • Re: [Open Babel] Run obabel with n cpu cores? Richard Overstreet
  • Re: [Open Babel] Run obabel with n cpu cores? Rudy Richardson
  • Re: [Open Babel] Run obabel with n cpu cores? Francois Berenger
  • Re: [Open Babel] Run obabel with n cpu cores? Noel O'Boyle
  • Re: [Open Babel] Run obabel with n cpu cores? Rudy Richardson
  • Re: [Open Babel] Run obabel with n cpu cores? Rudy Richardson
• [Open Babel] Convert SMILES to SDF with a property from the name line? Rudy Richardson
  • Re: [Open Babel] Convert SMILES to SDF with a property from the name line? Andrew Dalke
  • Re: [Open Babel] Convert SMILES to SDF with a property from the name line? Rudy Richardson
• [Open Babel] Error Writer.hpp not found Miguel Quirós Olozábal
• [Open Babel] charges when generating mol2 format Tim Dudgeon
• [Open Babel] energy and minimisation from Python Tim Dudgeon
• [Open Babel] Python API GetParameters Richard Overstreet
• [Open Babel] count chiral centers Jan Hummel via OpenBabel-discuss
  • Re: [Open Babel] count chiral centers Richard Overstreet
  • Re: [Open Babel] count chiral centers Noel O'Boyle
  • Re: [Open Babel] count chiral centers Stefano Forli via OpenBabel-discuss
• [Open Babel] ValueError when testing Python bindings in Windows cmayerb1
• [Open Babel] obabel 3.x Alan
• [Open Babel] Failed to kekulize aromatic bonds Lorenzo Bernacchia
• [Open Babel] Identical Fingerprints for three compounds Wolcott, Chris (NIH/NCI) [C] via OpenBabel-discuss
  • Re: [Open Babel] Identical Fingerprints for three compounds Francois Berenger
  • Re: [Open Babel] Identical Fingerprints for three compounds Wolcott, Chris (NIH/NCI) [C] via OpenBabel-discuss
  • Re: [Open Babel] Identical Fingerprints for three compounds Andrew Dalke
  • Re: [Open Babel] Identical Fingerprints for three compounds Wolcott, Chris (NIH/NCI) [C] via OpenBabel-discuss
  • Re: [Open Babel] Identical Fingerprints for three compounds Francois Berenger
  • Re: [Open Babel] Identical Fingerprints for three compounds Wolcott, Chris (NIH/NCI) [C] via OpenBabel-discuss
• [Open Babel] Apple silicon Chris Swain via OpenBabel-discuss
• [Open Babel] getting error Md Umar
• [Open Babel] help with installation Artur Hermano
  • Re: [Open Babel] help with installation Artur Hermano
• [Open Babel] SetTorsion screws up molecule Simon Dürr via OpenBabel-discuss
• [Open Babel] openbabel python binding for macOS Alan
  • Re: [Open Babel] openbabel python binding for macOS Noel O'Boyle
• [Open Babel] Warnings using --gen3D Francesca Magarotto - francesca.magarot...@studio.unibo.it
• [Open Babel] Conversion SMILES to mol2 Francesca Magarotto - francesca.magarot...@studio.unibo.it
  • Re: [Open Babel] Conversion SMILES to mol2 Andrew Dalke
  • [Open Babel] R: Conversion SMILES to mol2 Francesca Magarotto - francesca.magarot...@studio.unibo.it
• Re: [Open Babel] Garbled 3D structures from Python Geoffrey Hutchison
  • Re: [Open Babel] Garbled 3D structures from Python Tim Dudgeon
  • Re: [Open Babel] Garbled 3D structures from Python Stefano Forli via OpenBabel-discuss
  • Re: [Open Babel] Garbled 3D structures from Python Tim Dudgeon
  • Re: [Open Babel] Garbled 3D structures from Python Geoffrey Hutchison
• [Open Babel] In Windows, use PHP to call Openbabel for help jackzhang via OpenBabel-discuss
• [Open Babel] Residue information lost Stefano Forli via OpenBabel-discuss
  • Re: [Open Babel] Residue information lost Geoffrey Hutchison
  • Re: [Open Babel] Residue information lost Stefano Forli via OpenBabel-discuss
• [Open Babel] Question regarding your software Evgeny Akkuratov
  • Re: [Open Babel] Question regarding your software Francois Berenger
• [Open Babel] Alternative to UsetPartialChargesPerceived() in 3.x Stefano Forli
  • Re: [Open Babel] Alternative to UsetPartialChargesPerceived() in 3.x Noel O'Boyle
  • Re: [Open Babel] Alternative to UsetPartialChargesPerceived() in 3.x Stefano Forli
• [Open Babel] NetCharge from mol2 doesn't match expected value Vaibhav Dixit
• [Open Babel] obabel -imol2 file.mol2 -oxyz -O file.xyz -h Fredrik Haeffner
  • [Open Babel] Fwd: obabel -imol2 file.mol2 -oxyz -O file.xyz -h Fredrik Haeffner
  • Re: [Open Babel] Fwd: obabel -imol2 file.mol2 -oxyz -O file.xyz -h David van der Spoel
• [Open Babel] changing size when creating an svg? TheoKinDB
• [Open Babel] split multi-molecule structure into single-molecules Jan Hummel via OpenBabel-discuss
  • Re: [Open Babel] split multi-molecule structure into single-molecules Noel O'Boyle
• [Open Babel] Random seeds in --gen3d? (followup) theokindb
• [Open Babel] Validating a SMILES string theokindb
  • Re: [Open Babel] Validating a SMILES string Noel O'Boyle

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