[Open Babel] building openbabel-3.0.0 with python 3 bindings on Ubuntu 18.04

I've managed to build openbabel 3 with bindings to python 3 on a local install. Everything went smooth. This is my cmake command: cmake ../openbabel-3.0.0 -DCMAKE_INSTALL_PREFIX=~/WORKSPACE/OpenBabel/openbabel-3.0.0_INSTALL -DPYTHON_BINDINGS=ON -DRUN_SWIG=ON Still, after setting the PYTHONPATH:

Re: [Open Babel] building openbabel-3.0.0 with python 3 bindings on Ubuntu 18.04

ok, fixed. I was using the wrong path. I've probably lost the last part of the path somewhere... Il giorno gio 2 apr 2020 alle ore 18:16 Thomas ha scritto: > I've managed to build openbabel 3 with bindings to python 3 on a local > install. Everything went smooth. > This

Re: [Open Babel] compiling openbabel3 on Ubuntu 18.04

try with "from openbabel import openbabel" instead, I get a different error: "ImportError: cannot import name 'openbabel'" Il giorno gio 2 apr 2020 alle ore 12:19 Thomas ha scritto: > Hi there, > I'm trying to compile the latest openbabel 3 on my Ubunu 18.

[Open Babel] Avoid sanitization

nwanted sanitizations are the addition of Hs if I generate the molecule from SMILES fragments (partial SMILES) Thank you Thomas ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] Avoid sanitization

1C=CC=CC=1C2=O)C\t\n' mol.write(opt={'c':True}) 'CN(CCNC(=O)c1cccn2c1nc1c1c2=O)C\t\n' Furthermore, can you explain me this: mol = pybel.readstring('smi', "O=C(NCCN(C)C)c12C(=O)c3c3(Oc12)") sma = pybel.Smarts("c12Cc3c3(Oc12)") s

Re: [Open Babel] Avoid sanitization

2Cc3c3(Oc12)" -osmi > 0 molecules converted > $ obabel -:"O=C(NCCN(C)C)c12C(=O)c3c3(Oc12)" -s > "c12Cc3c3(Oc12)" -osmi -aa > O=C(NCCN(C)C)c12C(=O)c3c3Oc12 > > Regards, > Noel > > > > On Fri, 17 Feb 2023 at 18:50, Thomas wr

[Open Babel] Explicit H as property

I am including OpenBabel as an alternative chemical library in a software that uses RDKit, but I'm missing some functions. Is it possible to get SMILES with explicit hydrogens as a "property" of another atom? For example from the SMILES "CC" I'd like to get '[CH3][CH3]' instead of '[H]C(C([H])([H]

Re: [Open Babel] Explicit H as property

mind. Thank you Il giorno mer 22 feb 2023 alle ore 11:12 Andrew Dalke < da...@dalkescientific.com> ha scritto: > On Feb 21, 2023, at 19:23, Thomas wrote: > > Is it possible to get SMILES with explicit hydrogens as a "property" of > another atom? > > For example fro

[Open Babel] Is there a way to get babel to believe *only* CONECT records in input PDB

records, but that's not what I want. Yours sincerely, Thomas Womack (Global Phasing) -- Got Input? Slashdot Needs You. Take our quick survey online. Come on, we don't ask for help often. Plus, you'll get a cha

[Open Babel] Naming auto-added hydrogens

I'm using babel as part of a process for producing dictionaries for crystallographic refinement software. The formats for such dictionaries refer to atoms by their names, and so it's very slightly annoying that the output from babel hydrogenation calls all the added hydrogens 'H'. Is there a w

[Open Babel] mol2 problem

On 23 Jan 2012, at 12:29, Douglas Houston wrote: > Hi all, > > I wonder if anyone can help me work out what's going on here. I'm trying to > convert a PDB file of ADP (from structure 3ATV) to mol2 format and add > hydrogens. The first step seems to work fine: > > babel -ipdb 3ATV_ADP.pdb -omol

[Open Babel] Different structures, same InChI key

The two attached PDB files differ in that one has a hydrogen on N17 and the other doesn't. But, with openbabel-2.3.1, I get the same InChI key twomack@fs1:~/projects/grade-inchi-2% obabel 4PC.grade_PDB_ligand.pdb -oinchi -xK GPLPRFCWPJTQND-IVZWLZJFSA-

[Open Babel] Why doesn't this work?

If I have a file glycerol.smi containing HOCC(OH)COH and issue % obabel glycerol.smi -osmiles -xK 0 molecules converted % obabel -V Open Babel 2.3.1 -- Jan 25 2012 -- 15:40:47 then it doesn't produce an INCHI key. If I remove the hydrogens from the SMILES string, it does. I think there shou

Re: [Open Babel] 3d coordinate generation with 'nan' coordinates

On 5 May 2012, at 13:40, Ferenc Szalai wrote: > Hi, > > I attached a structure in 2d mol file. If I try to generate 3d > coordinates for this structure ether using obgen or the pybel > interface I get result with invalid coordinates ('nan') and a lot of > warning messages which are stats the some

[Open Babel] mol2 files with charged atoms

The CSD has a fair number of structures with a big charged aromatic moiety and a counter-ion, things like the attached TUDTES.mol2 Using SVN 4747, I'm not seeing charges when I convert to SMILES - I get OCCn1c(=O)n(C)c2c(c1=O)n(C)cn2C.I out of obprop, where I would expect OCCn1c(=O)n(C)c2c(c1

[Open Babel] Announcement - R interface for OpenBabel

eOB. Best, Thomas -- Thomas Girke Institute for Integrative Genome Biology (IIGB) University of California Riverside, CA 92521 E-mail: thomas.gi...@ucr.edu Personal Site: http://girke.bioinformatics.ucr.edu -- DreamFact

[Open Babel] install of open babel for pymol under window 10 - BABEL_DATADIR issues??

ib\PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "C:\Users\Thomas\AppData\Roaming\pymol\startup\optimize.py", line 52, in set_conf_search conf_search(selection, forcefield, conf_method, nsteps1, conformers, lowest_conf) File "C:\Users\T

Re: [Open Babel] install of open babel for pymol under window 10 - BABEL_DATADIR issues??

Thanks Noel - looking at the PyMol Mailing list, it looks like this already happened... and the author of the post concludes this is an Open Babel issue, not a Pymol issue :-) https://sourceforge.net/p/pymol/mailman/message/33031324/ Will try again tonight... many thanks Thomas On 15 July 2016

Re: [Open Babel] install of open babel for pymol under window 10 - BABEL_DATADIR issues??

Hi Eric I contacted Osvaldo cc d on this (he wrote Optimize) and he kindly offered some help - but I never managed to get optimize to run Am traveling now but will have a look again next week Best Thomas On Saturday, 10 September 2016, eolmon wrote: > Dear Thomas, > > I am having

[Open Babel] sdf to mol2 converter issue with aromatics

44 94 1 96 97 45 95 1 98 46 47 ar 99 46 96 1 100 47 48 ar 101 47 97 1 102 48 98 1 @SUBSTRUCTURE 1 UNK 1 GROUP 0 0 ROOT -- == Dr Thomas E

[Open Babel] 4th Advanced in silico Drug Design workshop in Olomouc

chemoinformatic tasks and win prizes. http://fch.upol.cz/en/research/conferences-workshops/4add/ Please feel free to share this information to those who can be interested in participation in such event. Thank you. With kind regards, Thomas Evangelidis

[Open Babel] ImportError: cannot import name 'OBElementTable' from 'openbabel' (unknown location)

e' is missing. Was this table really removed, and if yes, how can I adapt my code below to work with the latest version? I thank you in advance. Thomas from openbabel.openbabel import OBElementTable > > # ELEMENT TABLE TO DETERMINE VDW AND COVALENT BONDS > et = OBElementTable() > # C

[Open Babel] multi-molecule sdf is converted to multi-MODEL pdbqt

w can I instruct OpenBabel to write a multi-molecule pdbqt file? I am not sure if the flag '--canonical' has any effect. I have heard that sometimes it fixes some random change in the atom order especially in structures with a high number of rotatable bonds and many symmetric groups. I tha

[Open Babel] help - segmentation fault with Pybel on Mac OS x

Hi I have managed to compile OpenBabel with the python bindings on my Mac by following the instructions on the OpenBabel website. OpenBabel works fine form the command line, and I can import pybel into python. However whenever I try to use pybel I get a segmentation error For example: >> im

[Open Babel] problem with Eigen2 while compiling on Mac Lion

Hi I tried to compile Open Babel on my Mac so I could have the Python bindings, but I'm running into problems with Eigen2. When I compile without reference to Eigen, the configuration completes without errors, but when I include the –DEIGEN2_INCLUDE_DIR I get the following error: … -- Looking

Re: [Open Babel] problem with Eigen2 while compiling on Mac Lion

mer immédiatement par courriel, effacer l'original sans en conserver de copie et ne pas en dévoiler le contenu ni utiliser l¹information pour quelque fin que ce soit. On 14/11/2011 16:12, "Geoffrey Hutchison" wrote: > >On Nov 14, 2011, at 4:14 AM, Hassan Thomas Mamdan