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

tereo 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: geo...@pitt.edu web: https://hutchisonlab.org/ ___

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

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

Re: [Open Babel] Errors while Building openbabel

t; started with my contributions to openbabel > > On Fri, Nov 3, 2023 at 3:12 AM Geoffrey Hutchison < > geoff.hutchi...@gmail.com> wrote: > >> The MAE parser has some definite issues. >> >> Try running “ccmake” to turn off WITH_MAEPARSER or run “cma

Re: [Open Babel] Errors while Building openbabel

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 wrote: > Hello everyone, > I am Dhruv, a third year Computer Engineering undergrad from Mumbai, > India.

[Open Babel] Open Babel website

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:

Re: [Open Babel] Desprotonated Molecules

ust 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 Hutch

Re: [Open Babel] Openbabel installation error and python version compatibility

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: geo...@pitt.edu twitter: @ghutchis web: https://hutchisonlab.org/ ___ Open

Re: [Open Babel] OpenBabel SMILES to XYZ conversion

. obabel -:'CCC.C=O' -O test.xyz —gen3d See attached. Best, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu twitter: @ghutchis web: https://hutchisonlab.org/ On Jul 25, 2023 at 1:58:18 PM, Alan Liška wrote: > D

Re: [Open Babel] problem with pip install

The pip recipe is to build the openbabel python bindings from source. That requires that openbabel has been built and installed from source before you run the pip build. Personally, I’d suggest using mamba-forge and their openbabel package. Best, -Geoff On Jul 31, 2023 at 5:04:11 AM, Tim

Re: [Open Babel] Issues compiling OpenBabel-2.4.1 on MacOS

I doubt you can do this. Open Babel 2.4.1 was from 2016 or so? Compilers have changed. The current version of Open Babel is 3.1.1 and it definitely compiles on my Mac. You can install with homebrew or conda, etc. if you don’t want to compile yourself. -Geoff --- Prof. Geoffrey Hutchison

Re: [Open Babel] Issues compiling OpenBabel-3.1.1 on Linux

GCC 4.8.2 is known to be problematic with C++ and is also an ancient compiler. https://www.gnu.org/software/gcc/gcc-4.8/ The original release was in 2013 (10 years ago). Please install a more recent version of GCC / G++ Best regards, -Geoff On Jun 8, 2023 at 1:34:12 PM, Alessandro S.

Re: [Open Babel] 2048 fingerprints

d bit length. Hope that helps, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu twitter: @ghutchis web: https://hutchisonlab.org/ ___ OpenBabel-discuss mailing list OpenBabel-discu

Re: [Open Babel] unable to read CIF

> > When running this code no errors are thrown but the molecule seems to > empty (molwt is zero). > Can anyone tell if this is a problem with OBabel or with the CIF files > that have been generated? > This CIF file is weird. I tried loading it in CCDC Mercury, which I consider the “gold

Re: [Open Babel] indexing atoms in png file

.")[0] # save a PNG - change the scale to meet your needs cairosvg.svg2png( bytestring=svg, scale=3.0, write_to=name+".png" ) Best, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu twitter:

Re: [Open Babel] converting many smiles to many mol

in the standard output stream. Try, for example: % obabel test.smi -O output.mol --gen3d -m % ls *.mol # lists a bunch of output1.mol, output2.mol, etc. Hope that helps, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu twi

Re: [Open Babel] Convert sodium chloride from pdb to sdf

The element symbols on the right should be in positions 77-78, or 3 positions to the right. When they’re present, they take precedence over the atom name columns, because deciphering Na = sodium vs. Na = nitrogen alpha is a pain. Also, for what it’s worth, these should definitely be HETATM not

Re: [Open Babel] PDB to PDBQT failed to kekulize aromatic bonds error

> > Not sure if this is relevant, but the PDB file was predictively generated > on AlphaFold. > Do you think you can share the file or something similar from AlphaFold? Usually bond orders are inferred in PDB files from the residue information. I don’t think I’ve seen actual files from

Re: [Open Babel] Regarding converting MTI and many others types of files to PDB

rrently using similar program to Match but I do not possess any kind of > database so do you have any solution for this issue? Thanks for replying. > ------ > *From:* Geoffrey Hutchison > *Sent:* Monday, January 9, 2023 10:48 AM > *To:* Наранбилэ

Re: [Open Babel] Regarding converting MTI and many others types of files to PDB

--- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu twitter: @ghutchis web: https://hutchisonlab.org/ On Jan 8, 2023 at 9:07:34 PM, Наранбилэгт Нацагдорж < naranbileg...@mas.ac.mn> wrote: > Those are the examples and I have

Re: [Open Babel] Errors when installing openbabel

Open Babel 2.3.1 is exceedingly old. You are running into problems with a newer compiler from Ubuntu 18.04 and older C++ syntax. The current version of Open Babel is 3.1.1 - you can likely install packages directly from Ubuntu or conda-forge. Hope that helps, -Geoff --- Prof. Geoffrey

Re: [Open Babel] Error in "from openbabel import pybel"

Use `conda install -c conda-forge openbabel` — like many packages, we have migrated to use the conda-forge infrastructure. Hope that helps, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu twitter: @ghutchis web

Re: [Open Babel] Writer Format - WLN Writer + Reader Functionality Expansion

Hi Michael, I just wanted to check in. If submitting through GitHub is too much trouble, I'm sure Noel or I could help create the patches, etc. if you can send the code. Thanks, -Geoff > On Jun 16, 2022, at 3:56 AM, Michael Blakey via OpenBabel-discuss > wrote: > > Hi There, > > I have

Re: [Open Babel] Crash Software

> I have problems in Windows, when I generate 3d coordinates the program > crashes. Please I need help. It would help a lot if you could be a bit more specific: - What version of Windows you are using - What version of Open Babel you have installed - What molecules you are trying to generate 3d

Re: [Open Babel] Question for Openbabbel installation with Python

ders from a Gaussian file. The warning shows up when the bond orders are not automatically detected. Best regards, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu twitter: @ghutchis web: https://hutchis

Re: [Open Babel] Writer Format - WLN Writer + Reader Functionality Expansion

> Just submit a pull request. To do this, your code changes should made to a > fork of the project on github. We can then give feedback there. If you're not sure of this, GitHub has a guide to getting started and the "GitHub flow" https://docs.github.com/en/get-started/quickstart/github-flow

Re: [Open Babel] --splitinto

No, it means that you need to use a *newer* version of Open Babel. The current version is 3.1.1. If you use Linux, your distribution likely has newer packages. Best regards, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo

Re: [Open Babel] Question for Openbabbel installation with Python

change to: from openbabel import openbabel Hope that helps, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu twitter: @ghutchis web: https://hutchisonlab.org/ > I would need some precision of the installation of

Re: [Open Babel] Include OpenBabel into R package

dings, but you may find it easier to use ChemMineR / ChemineOB e.g https://www.bioconductor.org/packages/2.14/bioc/html/ChemmineOB.html https://github.com/girke-lab/ChemmineOB <https://github.com/girke-lab/ChemmineOB> Hope that helps, -Geoff --- Prof. Geoffrey Hutchison Department of

Re: [Open Babel] Garbled 3D structures from Python

> But instead of that, using mol.make3D() gives the garbled structures with > interlocked rings. I'll take a look at the Pybel code. I thought it pretty much did the same thing as the OBOp. (The code certainly looks like it's doing the same thing..) -Geoff

Re: [Open Babel] Garbled 3D structures from Python

> I'm having problems when generating 3D molecules using the Python bindings. > This may be a result of the molecule containing charges, but I'm not certain > about this. I haven't seen that problem (interlocking rings) in a long time. Are you sure your Python bindings are using OB 3.1? You

Re: [Open Babel] Residue information lost

> I've been trying to generate molecules programatically in Python when I found > a buggy behavior. When you're creating molecules programmatically, you need to make sure you set the perception flags. In your case, OBAtom calls: OBResidue *OBAtom::GetResidue() { OBMol *mol =

Re: [Open Babel] Operating on multi molecule sdf files

> After reading the docs I think that adding individual properties to > individual molecules in a multi molecule sdf files is probably not possible? > I have an sdf file with 500k molecules and I would like to add a little > unique identifier that isn’t a supported descriptor to each molecule

Re: [Open Babel] read molecules from xyz files and merge them

> >> m1 = mol1.OBMol > >> m2 = mol2.OBMol You'll want to count the number of atoms in each molecule before you do the addition. > >> m1 += m2 > >>#merging the two molecules > >> m1.AddBond(1,2,1)

Re: [Open Babel] Poor CML to LMPDAT Conversion

> I have a CML file that I'm trying to convert to a LMPDAT format. The > conversion appears to work, … Considering I don't know many people using LMPDAT it would really help to know what the "correct" (e.g. your version) would look like. I know that Albert wrote the code as a quick example that

[Open Babel] If someone had time on their hands (now) …

As many of you may know, Open Babel is participating in Google Summer of Code 2020. The last two years, we've been lucky to have Naruki working on the fragment-based builder in 3.0 as well as improvements in the not-quite-finished distance geometry builder. If you know of students who might be

Re: [Open Babel] How to convert inchikey to other formats?

> PS: there is an unpractical way though: compute the inchikey of all possible >molecules, until you hit the key that you were looking for. There are several 'resolvers' out there for InChi Keys. https://cactus.nci.nih.gov/blog/?tag=inchikey-resolver

Re: [Open Babel] Compute Tanimoto coefficients from Spectrophore fingerprints?

> Can Euclidean distances for Spectrophores be computed directly in obabel or > obspectrophores?=' Chris Swain was recently asking a similar question. Silicos contributed the code - and has since disbanded. At the moment, I don't see code for that, although I'd be happy to help guide someone

Re: [Open Babel] Problems deleting a OBMol object

> I haven't had a chance to test this but it looks like you're deleting > pointers that you shouldn't be. Only call "delete" if there is a > corresponding "new". The general rule is that you shouldn't delete pointers > returned by Open Babel API calls, unless the documentation explicitly states

Re: [Open Babel] How to install openbabel on Mac OS X?

> $ brew install open-babel > Warning: open-babel 3.0.0 is already installed and up-to-date > To reinstall 3.0.0, run `brew reinstall open-babel` … > $ pip3 install -U openbabel > Collecting openbabel > Using cached openbabel-2.4.1.tar.gz (74 kB) This is a bad idea. I haven't looked to see if

Re: [Open Babel] Python: Getting atomic forces after a FF optimization

> I’m writing a Python script to screen a bunch of molecules, and for part of > that I would like to read in and optimize a geometry using OpenBabel’s > ForceField methods subjected to a couple constraints. I would like to obtain > the resulting forces for each atom from the optimization to use

Re: [Open Babel] CMAKE_BUILD_TYPE=Debug compile flags

> I noticed (after several hours) that when compiling in Release mode functions > get mangled in a different manner than when compiling in Debug mode. E.g.: Yes. We don't set how a C++ compiler handle function names. That's a standard handled by the compilers. But in any case, you can use a

Re: [Open Babel] Help on SMILES format

m a debugging perspective because it gives us nothing to test, debug and improve. If you have a specific example with OB-3.0, please submit the bug report and example SMILES to https://github.com/openbabel/openbabel/issues Thanks and best regards, -Geoff --- Prof. Geoffrey Hutchison Departmen

Re: [Open Babel] Help on SMILES format

mple of the SMILES, the SVG and the XYZ file? Thanks very much, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu twitter: @ghutchis web: https://hutchison.chem.pitt.edu/ ___

Re: [Open Babel] xyz oscillating canonical

> I tried this with mdl mol files and here the result is as expected (all files > identical), > so this might occur with xyz files only, but since no warning is issued when > combining > xyz files and the --canonical flag this is rather dangerous.. I'm not sure where you would give such a

Re: [Open Babel] UFF periodic boundary condition

> In case it's working, how can I make use of it? I am now trying to compute > energy of a periodic, crystalline structure, where I "manually" create bonds > across the PBC, but this results in disaster. Removing the bonds across the > PBC makes it better, but I have no clue whether it's

Re: [Open Babel] Openbabel join in Python

> Specifically I want to take as input a protein pdb file, and a small molecule > as sdf input, then output a pdb containing both structures. That's pretty easy: from openbabel import pybel protein = next(pybel.readfile("pdb", "filename.pdb")) print(len(protein.atoms)) small =

Re: [Open Babel] OpenBabel-discuss Digest, Vol 160, Issue 16

> I have a related bug. Just downloaded OpenBabel-3.0.0-x86.exe from GitHub but > it was generating corrdinates with too many digits. Excerpt from PDBQT file > overflowing the coords mask: I'd suggest filing a bug with an example file. I'm not entirely sure what to do because the problem isn't

Re: [Open Babel] converting .cdx files containing reaction schemes to .rxn

> for example, the reaction scheme gets messed up - reagents over the reaction > arrow are lost, and some reactants become completely altered. Without example files, it's impossible to know what's happening. I suggest posting an example file and a bug report to:

Re: [Open Babel] Alignment Question

I think you'll need to write a script because you want more than just standard alignment. Take a look at obfit.cpp or other alignment scripts and then you can delete the atoms not in the match. -Geoff > My ultimate goal is to take molecule A, align it to molecule B and then > "delete" all

Re: [Open Babel] Openbabel3 import error in python

> But, when i am trying to import openbabel within the python, it shows the > import error. I would guess that you either have multiple versions of Python on your computer, or at least multiple versions of the Open Babel bindings. Have you installed previous versions of the OB bindings? If

Re: [Open Babel] issues reading recent gamess output for charge

> However, a collaborator sent us source code that for some version of obabel > that actually reads the output Patches are always welcome. :-) > The issue at this point is that it fails to read the charge data of the > molecule correctly IF the log file contains hessian data where there are >

Re: [Open Babel] How to suppress messages from obabel?

> $ obabel '-:C(=O)Cl' -O /tmp/acidchloride.png > 1 molecule converted This is sent to the standard error, you can do: obabel '-:C(=O)Cl' -O /tmp/acidchloride.png 2>/dev/null Hope that helps, -Geoff ___ OpenBabel-discuss mailing list

Re: [Open Babel] How to draw structure from SMILES?

> Although there are many online tools (e.g., PubChem sketcher) to draw > structure from SMILES You can generate 2D depictions as mentioned in the docs: https://open-babel.readthedocs.io/en/latest/Depiction/depiction.html

Re: [Open Babel] How to install pybel?

> This one does seem to be the same the above one. > https://pypi.org/project/pybel You want: https://pypi.org/project/openbabel/ Or: https://anaconda.org/conda-forge/openbabel See

Re: [Open Babel] Getting 3d coordinates from mol object

> This gives me a pybel molecule. > I was wondering if it is possible to turn this into an OBMol object? Yes. You can get an OBMol object as an attribute from Pybel molecules like this: mol.OBMol https://open-babel.readthedocs.io/en/latest/UseTheLibrary/Python_PybelAPI.html#pybel.Molecule >

[Open Babel] ANNOUNCE: Open Babel 3.0.0 Released

I'm pleased to announce the release of Open Babel 3.0.0 [finally]: This release represents a major update and is strongly recommended for all users. It also removes deprecated components and breaks the API in a few places. For information on migrating from the previous version, please see:

Re: [Open Babel] Strange behaviour with pdbqt format

> Is it possible to get the binary of the last development version? Or only the > source? We are currently building binaries of 3.0 - what platform do you use? -Geoff ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net

Re: [Open Babel] Heuristic to convert .xyz to SMILES

> Thank you for the extremely detailed answer, that is exactly what I was > looking for! Beyond Andrew's great answer - PerceiveBondOrders code is based on Roger Sayle's "Cruft to Content" talk: https://www.daylight.com/meetings/mug01/Sayle/m4xbondage.html

Re: [Open Babel] Confab limit dihedral angles to rotate

> Is there a way to "freeze" some dihedral angles so they are not rotated when > generating conformers? Or, just as good, a way to specify which dihedrals to > rotate? Not from the automated conformer routines at the moment (although it could be done with some coding). If you want to scan

Re: [Open Babel] [OpenBabel-Devel] Default force field option for --gen3d

> Depending on the scenario, I would consider either vacuo (1) or water (80) to > be good > choices, but 4 is a 'close enough approximation' of 1. There are a variety of papers suggesting that the effective dielectric constant inside a peptide is ~4.0. Most organic solvents are ~2-2.3 epsilon.

[Open Babel] Default force field option for --gen3d

While it's possible to change the force field with the -gen3d option, most people don't. I think for 3.0 it might be nice to: - Use MMFF94s (i.e., the one with planar aromatic nitrogens) - Use a default dielectric constant of ~4.0 In my testing #1 helps a bit - and #2 at least doesn't hurt when

Re: [Open Babel] Some questions about conformation optimization

by default - but whether it needs further optimization depends on your needs. My research group, for example, typically does density functional or other quantum chemical calculation - so a MMFF94 geometry is only a starting point. Hope that helps, -Geoff --- Prof. Geoffrey Hutchison Department

Re: [Open Babel] OpenBabel-discuss Digest, Vol 160, Issue 16

Indeed small differences in XYZ coordinates, distances, etc. are not meaningful, although certainly a structure can shift slightly from a true optimum (all gradients are essentially zero) with rounding. On the other hand, not every file format supports arbitrary precision (e.g., 8 decimals or

Re: [Open Babel] Help

While it's easy for you to hack the mol2format.cpp code - I have never seen more than 3-4 decimal places in a mol2 file. I've looked for the format specification, but it doesn't seem to be online. How much is it changing the dihedral angles? -Geoff --- Prof. Geoffrey Hutchison Department

Re: [Open Babel] obtain bond order from smiles string seems wrong?

ly matches the diagram (e.g., atoms 5-6 are a double bond, etc.) Hope that helps, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu twitter: @ghutchis web: https://hutchison.chem.pitt.edu/ > On Aug 26, 2019, at 11:4

Re: [Open Babel] gamess input and output not compatible with obabel supported formats?

> [bennion1@czvnc2 ATBJOBS]$ /usr/gapps/bbs/TOSS-3/bin/obabel -igamess > 317358/1/qm.inp -osdf -O test > 0 molecules converted This just looks like that kind of GAMESS input is not supported by the reader. It's hard to devise a general input reader. As far as the output, nothing should

Re: [Open Babel] Weird regression in chemdraw handling between 2.3.2 and 2.4.90

contiguous fragment (strip salts)" Hope that helps, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu twitter: @ghutchis web: https://hutchison.chem.pitt.edu/ > On Aug 23, 2019, at 1:03 PM, Fant, Andrew (NIH/NIDA) [

Re: [Open Babel] converting certain molecules to 3D

> Because that's how it works. If I have a 2D alanine SDF and I "convert" to > 3D, I may get D-Alanine or I may get L-Alanine. If I'm working with > biomolecules, D-Alanine is not the one I want. That would only happen if your 2D structure doesn't have any stereochemical (wedge/hash)

Re: [Open Babel] OPENBABEL on Android - license request

> maybe you remember - some time ago I asked you about details of similar > program - BABEL (I attached the correspondence below). Now, because the > compilation of static OPENBABEL build for Android was successful, I would > like to ask you, if I could upload the recent OPENBABEL binaries /

Re: [Open Babel] converting certain molecules to 3D

> I'm interested in converting to 3D only the 2D molecules in a batch where 2D … > using obabel in a python script. Could you help me please? If you're looking through molecules using Pybel, you can do something like this: https://gist.github.com/ghutchis/0766478cc9bc1c00f623ce560954b8c1

Re: [Open Babel] converting certain molecules to 3D

> If there's stereochemistry in any of your 2D molecules, you're not > guaranteed to get the right 3D conformer from the conversion. What? Why do you say that? -Geoff ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net

Re: [Open Babel] PDB files with multiple bonds via CONECT

> Just a note: PDB has stopped accepting X-ray structures in .pdb format a > while back, and is going to stop accepting .pdb NMR structures soon. I.e. > what you are discussing is a dead format essentially. Sadly, as far as users are concerned PDB has become an informal interchange format, so

[Open Babel] PDB files with multiple bonds via CONECT

David Koes has contributed a pull request that fixes a bunch of file handling errors via round-trip testing. One thing he's implemented is to bring back writing PDB files with multiple bond orders via repeated CONECT records. Before I consider the rest of the patch, I want to know opinions on

Re: [Open Babel] Downloading Pybel

> Today I downloaded OpenBabel by using conda and was trying to impliment the > modules to help me write code; however, when I wrote import pybel into my > interpreter, it gave ValueError: not enough values to unpack (expected 2, got > 1). After that I went into the pybel module itself to try

Re: [Open Babel] Force field selection in tools

> In other words, in a number of tools the force field is hardcoded which seems > unnecessary. Would this be worthwhile to fix? Often, the tools directory has been thought of more as a set of examples - not so much as independent codes for people to use. (Many of these have "ops" from babel)

Re: [Open Babel] making wedge & hashed bonds

> We are using Open Babel to convert smile files into mol file but for > stereocenters it generate only one wedge or one hashed bond. We would prefer > to have both wedge and hashed bonds like in Cram convention. I'm not sure I understand what you're asking. If a molecule requires both types of

Re: [Open Babel] Pybel error

> I am running into a problem where I cannot import my pybel module into my > python script. Installing Open Babel does not mean that you've installed the Python module. My personal suggestion is to use conda (which is indicated in your Python version) conda install -c openbabel openbabel

Re: [Open Babel] Compression using Python API

>> Ahh, look like I read the pybel code wrong. >> When I get confused about the OB API, I look there first to see how Noel did >> it. >> Here's the relevant code: ... >> So, try obConversion.GENOPTIONS ? Yes, we need to add some additional examples to the Python docs, but this should work.

Re: [Open Babel] Open babel selfstarts

> One thought do you have a plugins or indexing agents that might be indexing > any molecular files on your hard drive? The process for Spotlight indexing is "mds' .. in the case of ChemSpotlight, it doesn't launch anything that's named 'obabel' although it's certainly possible other programs

Re: [Open Babel] Open babel selfstarts

I can't think of any reason installing a package would automatically run obabel periodically. But we're not responsible for the homebrew package, so I'd check the package maintainer and file a bug/issue. -Geoff > On Apr 3, 2019, at 6:42 AM, anrozina via OpenBabel-discuss > wrote: > > I

Re: [Open Babel] questions about new install on Windows 10

> Does it matter what version of Python and OpenBabel I install? You should be able to install Pybel with any version of Python after 3.3 (i.e., it works just fine with 3.7.x - I know from personal experience). Hope that helps, -Geoff ___

Re: [Open Babel] information loss while using Open Babel

> I've been trying to use Open Babel (windows) to perform a file conversion > from a log file (Gaussian) to a Tinker xyz file, while demanding the > conversion to work with MM3 atom types. The problem began with trying to > convert an ordinary primary amide (expecting atom type 9 in return) log

Re: [Open Babel] Disabling additional molecule generation in Obabel

> How to 'disable' obabel from generating 3 molecules for tryphtophan while > running the following? > obabel trp.sdf -O trp.1.sdf Your file has more than one molecule. If you want the 2nd, then you'd use the "first" and "last" filters: obabel trp.sdf -O trp.1.sdf -f 2 -l 2 Hope that helps,

Re: [Open Babel] Contributed code for new file format

with a polarizable charge model.) Thanks again, it's a big help. -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu twitter: @ghutchis web: https://hutchison.chem.pitt.edu/ > On Mar 5, 2019, at 3:34 PM, Paul Becherer wr

Re: [Open Babel] Contributed code for new file format

> Looking at it again now, it seems that the charges from Open Babel's QEq > often have the wrong sign or are simply unreasonably large. I have no idea > what causes that, as I only had a cursory look at the code. But it looks as > if there's more going on than just the additional

Re: [Open Babel] Contributed code for new file format

> We could not really find hard guidelines for coding standards, or what kinds > of tests are desired, so I'd appreciate any feedback on that. The code in the > patch is based on the exampleformat.cpp template and was further developed by > two colleagues and myself at Culgi. We presently test

Re: [Open Babel] SDF file - meta data ignored on conversion

You want to use the "copy" format: https://openbabel.org/docs/dev/FileFormats/Copy_raw_text.html e.g. obabel infile.sdf -O outfile.sdf -ocopy -f 1 -l 1000 Hope that helps, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492

Re: [Open Babel] Some questons

> I’ve been looking at a web based CDXML to png/gif/jpeg converter that so we > are able to display the molecular structures directly to the website. But I’m > having a really hard time to find anything like this and our time is so > limited. Personally, I'd suggest SVG output, which is a

Re: [Open Babel] Open Babel installation for PyMOL Optimize

> I am trying to install Open Babel to use the Optimize plugin for PyMOL. I > used Homebrew to install Open Babel with Python bindings (brew install > open-babel --with-python@2) which seemed to run successfully. However, when I > try to run import openbabel in python, I get the following

Re: [Open Babel] Help using Pybel in Microsoft Visual Studio and from within batch file

> My second question is regarding running python programs in command line, > have you ever tried to run the python program that imports pybel from inside > a batch file? For me this throws an error "ModuleNotFoundError: No module > named pybel". One way or another, the environment is different.

Re: [Open Babel] << ECFP4 in OpenBabel >>

> Using OpenBabel, I got a file with the information that the fingerprint is a > 6040 bits set and got hexadecimal numbers. > Using PyBioMed, which is based in RDKIT, I got a binary string of 1024 bits, > very different from that obtained with OpenBabel. The RDKit binary string will be "folded"

Re: [Open Babel] how to transform the cif format of the nonstandard amino acid to pdb format

t your concerns. -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu twitter: @ghutchis web: https://hutchison.chem.pitt.edu/ ___ OpenBabel-discuss mailing list OpenBabel-d

Re: [Open Babel] abstracting xyz help

In general, Open Babel will extract frames of a Gaussian calculation into separate conformers, so --writeconformers should work for you. That said, you might also want to look at http://cclib.github.io/ obabel gaussian.out -O .xyz -m --writeconformers # should work -Geoff --- Prof. Geoffrey

Re: [Open Babel] Math multiplication symbol in SMARTs

> The source code for filter-it is open. Also it's documented. I can't remember if there's a more official version, but there are several mirrors, e.g. https://github.com/UnixJunkie/filter-it/tree/master/filters For future Google searches, Francois has a nice backup of all of the Silicos-it

Re: [Open Babel] OpenBabel Knime node

so plenty of SDF fixes (thanks to Noel) in the development mainline. -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu twitter: @ghutchis web: https://hutchison.chem.pitt.edu/___

Re: [Open Babel] Generation 3D structure algorithm

> My current conversion: .cdx -> .xyz using make3D. And after this, checking > image from .xyz using chemcraft. And for big structures it looks not enough > good. It would really help to have actual structures (e.g., both ChemDraw and XYZ) to understand what you mean by "not good enough."

Re: [Open Babel] Bounce action notification

> corresponding to said covalent graph (meaning if valence angle ABC is used > to embed a point there is a bond AB and a bond BC). I would like to compare > the efficiency of my code with openbabel. Is there a piece of code that > traverses the covalent graph and gives vertices cartesian

Re: [Open Babel] (no subject)

> i conveted sdf to pdf format > how to save from babel the pdf format. thank you I'm not entirely sure what you want to do. PDF is a printed document. Do you mean PDB? Best regards, -Geoff ___ OpenBabel-discuss mailing list

Re: [Open Babel] Multiple ligand energy minimization, write to single mol2

> Chimera's Viewdock can input a mol2 file containing many ligands, and > determine minimum binding energy for a specific receptor's pocket for each > ligand. Can OB perform energy minimization of ligands in batch mode (loop) > and then export all ligands to a single mol2 file? Sure. % cat

Re: [Open Babel] Aromatic bonds

> Thanks for comments. When I print out files from Avogadro that we use for > input to our program, the atoms are in a given sequence. After going through > OpenBabel, the atom numbering and sequence is totally different from the > files that were read as evidenced by the numbering that

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