Re: [Open Babel] Chirality and tetrahedral stereo configuration

> I remember Geoff fixed some of the problems related to chirality in in rings > (with the > distance geometry approach, I believe). Unfortunately, even with the latest > code from GIT No, there is a maddening bug with chiral constraints with the distance geometry builder. In principal, DG ca

Re: [Open Babel] SMART notation to select diamine molecule

>> From your suggestion, is there a way of counting functional group > occurrencies within obabel? With the command-line? No. But you can use C++ or Pybel to do that, e.g. http://baoilleach.blogspot.com/2007/07/pybel-hack-that-sd-file.html import pybel amine = pybel.Smarts("[N]") for mol in pyb

Re: [Open Babel] fillUC strict option in python bindings

I believe you want something of this sort (untested): fillUC = openbabel.OBOp.FindType("fillUC") fillUC.Do(myOBMol, "strict") --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu web: http://hutchison.chem

Re: [Open Babel] Unity3D + OpenBabel Crashing

> I'm having some trouble with some code I'm using in Unity with C#. While you may be using C#, the underlying code is still C++. It's quite clear that you have some atoms with NULL residues (i.e., they don't have residues set) and there are possibly some residues with NULL atoms. (Don't trust P

Re: [Open Babel] Problem assigning Partial Charges with OBChargeModel

27;d go to code. -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu web: http://hutchison.chem.pitt.edu/ > On Jun 20, 2016, at 2:37 PM, Marcelino Arciniega > wrote: > > Hi all, > > I am having proble

Re: [Open Babel] {Spam?} Re: Problem assigning Partial Charges with OBChargeModel

> if (mmffCharges && mmffCharges->ComputeCharges(mol)) { Practical Real-Life Debugging experience says "check each part of this && statement" and see which one of them is failing. So? Which one? Is the mmffCharges object not created? Or can it not compute charges? If it's not created, I'd mak

Re: [Open Babel] Open Babel descriptor export in text?

> I am quite new to open babel. I have some SDF files of thousands of molecules > and I would like to calculate some of their descriptors. It depends on what you want. For example: https://open-babel.readthedocs.io/en/latest/Command-line_tools/Rosetta.html obabel benzodiazepine.sdf.gz -otxt --ti

Re: [Open Babel] GAFF2 in babel?

> I don't know whether people would like to implement this new GAFF2 into > BABEL... Sure, although as David van der Spoel mentioned, there was a considerable effort in updating the parameters and typing recently. Personally, I'd push to see if the GAFF2 developers can set up a test

Re: [Open Babel] obminimize

> If i use: obminimize [-ff forcield] [-algorithm] to calculate the > minimized energy of a given ligand a don't always get the same results. (of > course I only compare results with the same ligande, same forcefield and same > algorithm with each other) I'm not quite sure I understand what y

Re: [Open Babel] obconformer

> it shows me that the best of the 250 randomly generatet conformation has an > energy at somewhere about 3.5 kcal/mol but after the minimization of this > conformation the energy converges at about 68.2 kcal/mol. I think you really need to provide us with the molecule before we can help you fu

Re: [Open Babel] Ligand Information losing during splitting of large dataset

First off, I *highly* recommend e-mailing the list (or using the forum post feature) since there are many people who can answer your question. I’m not entirely sure what you’re trying to do. You have one giant SD file, and you want a bunch of MOL2 files. OK, but how is the “ligand ID” present in

Re: [Open Babel] New Windows User having problems with Openbabel (not sure if the first posting worked)

t's not going to affect operation of the tools. Hope that helps, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu web: ht

Re: [Open Babel] Command line help for protonation

> Can you or anyone else think of what the problem may be? No. It would certainly help if you gave more information on what platform (OS) you're using and the version of Open Babel. -Geoff -- ___

Re: [Open Babel] Building a molecule ( with SMILES) along a given vector

> I'm trying to build ( by using SMILES) a molecule along a given vector. > I need to grow a polymeric chain (for example) along well-determined It's possible, although it might be easier to build the molecule, then translate and align the resulting 3D geometry. For example, you could take atom

Re: [Open Babel] Open Babel 2.3 unable to filter batch SDF files on basis of logP and ROTATABLE_BOND

> Thank you so much. Silicos-it solved it for me. But I think it is really > odd that they would include a function in the example of official > documentation that doesn't actually exist. The example indicates that the SD file has a field called ROTATABLE_BOND. It’s an example of using a property

Re: [Open Babel] OpenBabel for Python 3?

> I am fairly new at Python, and am trying to stick to the latest version. > Is it possible to install the Open Babel bindings for Python 3? Yes. I don't know about the pip packages (or Mint ones) but you can do this from source, e.g.: https://open-babel.readthedocs.io/en/latest/Installation/ins

Re: [Open Babel] OpenBabel for Python 3?

ect developers. Use -Wno-dev to suppress it. > > CMake Warning (dev) at test/CMakeLists.txt:171 (include): > Syntax Warning in cmake code at > > /home/john/openbabel/openbabel-2.3.2/cmake/modules/UsePythonTest.cmake:57:39 > > Argument not separated from preceding token b

Re: [Open Babel] BUG: Nitrogen chirality

There's currently no code to test for chiral nitrogens - the stereochemical analysis assumes all nitrogens can invert and are therefore non-chiral. Would you be willing to upload this example as a SMILES or Mol to the issue tracker for 2.4.1? http://github.com/openbabel/openbabel/issues Thanks!

[Open Babel] ANNOUNCE: Open Babel 2.4.0 Released

I'm pleased to announce that Open Babel 2.4.0 has finally been released. This release represents a major update and should be a stable upgrade, strongly recommended for all users. We intend to move to an annual major release every September, with bug fix releases as needed. A sample of major n

Re: [Open Babel] ANNOUNCE: Open Babel 2.4.0 Released

Ooh, sorry - I see it didn’t get into the docs. :-( You can just say: .. --gen3d fastest The levels are: fastest fast med or medium slow or better slowest or best The different levels correspond to different # of conformers and optimization steps. For example fastest will skip conformer genera

Re: [Open Babel] Java bindings for openbabel 2.4.0

My fault - I'll issue a 2.4.1 shortly (i.e., either today or tomorrow, US time). Thanks, -Geoff -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdo

Re: [Open Babel] status of OBDotNet

> It looks like OBDotNet hasn't received any attention for quite some time. I don't have the appropriate compilers, so it's really hard to make / update those packages. It's pretty easy to update, though. Make sure you have SWIG installed and then when building Open Babel, make sure CSHARP_BINDI

Re: [Open Babel] OBConversion in Open Babel version 2.4.1

> I want to use the Java Interface of OpenBabel, so i compiled it with > -DJAVA_BINDINGS=ON. > I include the generated openbabel.jar into my Java Project. My example Java > file contains something like that: ... > Apparently, the shared object has been found but the symbol > new_OBConversion__SW

Re: [Open Babel] MOPAC

> /usr/local/bin/obabel '/Users/Chris/Desktop/confs/temp1.sdf' -omop -xf > '/Users/Chris/Desktop/confs/temp1.mop’ The key problem is the use of the -xf flag. This is a way to set keywords in the MOPAC file by reading another file. (Useful for batch processing): obabel *.sdf -omop -xf “ke

Re: [Open Babel] add hydrogens appropriate for pH

> No matter how acid I set the pH aniline (pKa 4.6) is never protonated It's not a general model of pH-dependent protonation. It has a set of rules, particularly for amino acids. For more accurate pKa determination, you'll probably want semiempirical quantum calculations or a more complete mode

Re: [Open Babel] add hydrogens appropriate for pH

> I could add a few more but I thought it would be worth getting some feedback > first. Oh, I think there's some general interest in improved patterns. :-) -Geoff -- ___ OpenBa

Re: [Open Babel] Maintaining cis/trans after fragmentation

> trying to copy the bond property (IsUp or IsDown) and assign it to the new > bonds (bonds assign tot he dummy atoms). However I figured out that both > functions are returning False values. As Noel indicated, OBStereoFacade (and related classes) are used to track stereochemistry. The "Up/Down

Re: [Open Babel] g++ can't find "openbabel/obconversion.h"

> I installed openbabel on ubuntu using: sudo apt-get install openbabel > I get the error: fatal error: openbabel/obconversion.h: No such file or > directory Most Linux distributions do not install the headers or other development interfaces in the standard packages. You'll want to install open

Re: [Open Babel] g++ can't find "openbabel/obconversion.h"

t; the problem of a bunch of undefined references. > > Terminal IO: http://pastebin.com/raw/riDc7KQX > <http://pastebin.com/raw/riDc7KQX> > > Thanks again for your help! > > - James > > On Sun, Nov 20, 2016 at 4:26 PM, Geoffrey Hutchison > mailto:geoff.hutchi...@gma

Re: [Open Babel] OBConversion in Open Babel version 2.4.1

> So 3.0.8 should be working, right ? You'll need to make sure the entire bindings are re-built (e.g., with javac in this case). But yes, I suspect the problem is that there's an older version of the bindings present, using SWIG2. -Geoff

Re: [Open Babel] Dear all, QEq partial charge predicts all zero value. Any suggestions ?

Dear Peter, I haven't looked in detail into the QEq implementation, but these methods derive in part due to equalizing electronegativity across a molecule (or in your case, cluster). Since there does not seem to be a difference in electronegativity between any of the Au atoms, I don't believe t

Re: [Open Babel] add hydrogens appropriate for pH

> One pattern I can’t get to work is an aniline, I’ve tried various > permutations including I’d use the SMARTS match in the obabel command-line tool or even a depiction: obabel testMol.sdf -O out.svg -s “Nc1c1 red" -xu -d > TRANSFORM [N^3]c1c1 >> [N+:1]c1c1

Re: [Open Babel] Conformer Search vs. Conformer Generation

The weighted random rotor search does not generate an ensemble of conformers, no. It’s intended to find the lowest energy conformer. Hope that helps, -Geoff > On Jan 4, 2017, at 12:16 PM, kcpearce wrote: > > I am new to OpenBabel and I am trying to generate numerous conformers of a > certain c

Re: [Open Babel] rmsd problem

> I'm moderately new to openbabel. Since I need to align several ligands a > pivot conformation. The main pupose is to get rmsd values. Of course, lower > rmsds are preferred. Which tool is recommended, obfit or obrms? I'm looking > forward to your suggestion. Since you say you want to ali

Re: [Open Babel] Support information

> Does Openbabel latest version suppoprt GPU programming? No. What in particular are you interested in doing? -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu web: http://hutchison.chem.pitt.

Re: [Open Babel] Support information

practice, but no one has indicated particular bugs. If your question is "I'd like a GPU-accelerated Open Babel" then you'll need to find someone willing to do the work - I'm not sure how much speedup you'd get, since many operations are IO limited. -Geoff --- Prof. G

Re: [Open Babel] cif to pdb

Noel's point is that a CIF file (and a PDB) do not necessarily retain connectivity. > The reason why I am using Avogadro is that I want to add hydrogen atoms to > oxygen in a cif file obtained from x-ray with keeping symmetry. Is there > any suggestion how to do that? Not necessarily. The h

Re: [Open Babel] issue with cairo support / having problem drawing 2D molecules

> from homebrew/macports and compiling manually), include/depict/ is not > installed. If I copy this folder from the source code, I get some errors like > this which I think means I'm missing the libraries. Mac OS X does not use cairo (a Linux drawing library). If you don't have it installed,

Re: [Open Babel] issue with cairo support / having problem drawing 2D molecules

d > these missing ones. I don't know what was wrong with my openbabel > installation but I just don't seem to be able to get those depict.h related > files and libraries installed. > > On another note, I don't mind using SVG. But I can't find the documen

Re: [Open Babel] enriching catalog. seeking advice

> 1. Looking for a way to add global identifiers such as SDF/MOL, SMILE, MDL, > PubChem, etc.; Certainly we can look up every product in our catalog manually > and find that information even in wikipedia but what is the easiest and most > effective way to do it? I don't understand. Are you sayi

Re: [Open Babel] Orca file coordiniates are different from Chemcraft

> I've a orca .out file. If I open it in Chemcraft, the coordinates of first > atom is -0.008, -0.011, 0.953. > But when I open the same file in Open Babel and convert it to xyz the > coordinates of the same atom is 0.00771, 0.00999, 3.67056. It would really help to see the actual Orca file. -Ge

Re: [Open Babel] How to Install openbabel for Python 3.6 on macOS Sierra 10.12.3

> Is there any way that I install it for python 2.7 and then edit some > environment variable or something to change its binding to Python 3.5??? No, because C and C++ libraries such as Open Babel have to link to the appropriate version of libpython. Noel's question is "why not use Python 3.5" i

Re: [Open Babel] open babel source installation - issues

> 4 warnings generated. > 36 warnings generated. That’s not the actual error - those are warnings. Can you send the entire log of “make”? >> I assume, due to the paths not specified in MACOSX_RPATH for inchi and >> openbabel, that I’m having issues with the installation. I would usually go >>

Re: [Open Babel] Openbabel to work with optimize command in pymol

> I was trying to compile the openbabel (2.4.1) in my mac. both in bash and > tcsh the command Cmake is not found. My goal is to use optimize in pymol, for > which I need openbabel. Any pointer to solve this? Homebrew? % brew install open-babel http://brewformulas.org/OpenBabel Cheers, -Geoff

Re: [Open Babel] Positive values of Energy (python)

/virttxtjml/energy1.htm Hope that helps, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu web: http://hutchison.chem.pitt.edu/ > I've tried for several sets of conformers (X-ray, minimized, 2D), > various in

Re: [Open Babel] Including molecular charge when converting xyz to SMILES

> Is there a way to tell babel what the charge of the molecule in the xyz file > is? From the command-line? No. Even if there was, it’s not going to suddenly assign formal charges to your de-protonated functional groups. (Yes, as humans we can find the most likely places to put the negative c

Re: [Open Babel] Problem with gcc5 and above

>> If there is a way, in future versions, to change the stack >> limit in OpenBabel, I think it could be useful. > > Not really, even if there was a way: someone'll just try to load a > larger structure and hit the same thing again. Moreover, it's a type of denial of service attack on the underl

Re: [Open Babel] [OpenBabel-scripting] Help needed with OpenBabel in python3

Hi Nitish, The openbabel-scripting mailing list has been shut down - much easier to discuss on the general list, because many people are using Python for "general" use. :-) You tried "pip install openbabel" and it didn't work? What does "dir(openbabel)" say after running pip? For the "regular

Re: [Open Babel] having trouble generating .png picture in c++

> I'm trying to convert a SMILES string to a png picture using openbabel C++ > library. Here's a minimal code that says what I want to do. ... > This compiles and runs fine but it generates a png that's only a few bytes > and can't be open. I tried the same code with "png" replaced by "svg" and

Re: [Open Babel] (no subject)

> For now we are interested in consistency before "accuracy", which is another > subject. As a related note, we have tested several atom typing programs > (Knodle, I-interpret, Unicon and also Open Babel) and the perception of the > number of aromatic atoms typically differ in 10-20 % when analy

Re: [Open Babel] removing salts changes the structure and add bonds to heterocyclic compounds with nitrogen...

> I use babel to remove salts from smiles and I have encountered that babel > changes heterocyclic compounds with nitrogens, see example below. This will trigger aromaticity perception, but the structure is unchanged. > input: > C[C@H](CN1CCC(CC1)N2C(=O)Nc3cc(Cl)ccc23)NC(=O)c4cc5c5[nH]4.OC(=O

Re: [Open Babel] how to use CMAKE_PREFIX_PATH with openbabel

> Setting -DOPENBABEL2_INCLUDE_DIR and -DOPENBABEL2_LIBRARIES on the other hand > doesn't work. What should I set those to? > > cmake -DOPENBABEL2_INCLUDE_DIR=/home/davide/opt/include/openbabel-2.0/ > -DOPENBABEL2_LIBRARIES=/home/davide/opt/lib/ .. No, you want cmake -DOPENBABEL2_INCLUDE_DIR

Re: [Open Babel] Adding Hydrogens

> "-h" is misnamed, I'm afraid. It doesn't add hydrogens to fill > valencies, but rather converrts implicit to explicit hydrogens. You > can open in Avogadro and click "Build/AddHydrogens" to do this. Well, Avogadro will just call Open Babel. ;-) > Note to Geoff: would this be a useful 'op' or el

Re: [Open Babel] Submolecule from OBMol

> If it's a disconnected portion of the molecule, and you wanted to > write a smiles, there is a fragment option for the smiles writer that > you could use. It doesn't have to be a disconnected portion. That feature to the SMILES writer will take a bit mask for the fragment -- it can be any combi

Re: [Open Babel] Submolecule from OBMol

> I was wrong, the "F" option retains bonds' order and it even works for > aromatic atoms. > For future reference, to generate smiles of fragment by atom indices in > Python you can do: > idxs = [1,2,3,4] > mol.write('smi', opt={'F': ' '.join(map(str, idxs))}).strip() Yes, this method was from

Re: [Open Babel] Website down?

> I can't visit openbabel.org. It says site not found. Is it just me? My apologies. There was a server migration with my web host and the “site not found” page was apparently enough to convince scripts that the site was up. Should be all set now. -Geoff

Re: [Open Babel] modify molecules through internal coordinates

Sure. The API call would operate on an OBBond: http://openbabel.org/api/2.3/classOpenBabel_1_1OBBond.shtml#a62b38719673238813acc911788969922 > I'm trying to edit a molecule through internal coordinates like you would do > in a graphic editor. For example, I would like to change the bond length

Re: [Open Babel] Put atoms of target molecule in same order as reference

> I should probably add this feature. In the meanwhile, one way would be to > generate canonical labels and then shuffle the atoms of both into that order. Considering this seems to be a common problem, perhaps a Pybel example script is in order (e.g., read in two molecule files, assign the can

Re: [Open Babel] Put atoms of target molecule in same order as reference

> where you want the RMSD without alignment (but still need automorphisms for > the mapping). I realized that "obrms" does the mapping... -Geoff -- Check out the vibrant tech community on one of the world's most engaging

Re: [Open Babel] Pybel calcdesc

> I am attempting to begin using pybel/openbabel to calculate inchi strings on > the fly without having to write temporary files and use command line open > babel. Try this as a workaround: inchi = pybelmol.write(‘inchi’) smiles = pybelmol.write(‘can’) I’m wondering if there’s something subt

Re: [Open Babel] Pdbqt output missing protein side chains

Sorry - I saw that no one responded. I haven't used the PBQT format myself, but: r Output as a rigid molecule (i.e. no branches or torsion tree) So my guess is that the -xr is removing the side chain perhaps? -Geoff > On Aug 2, 2017, at 4:14 AM, David van der Spoel wrote: > > Hi, > > I

Re: [Open Babel] Substructure searching with multiple molecules

It's a little hard to give advice on your error without seeing the code. Can you post the code, e.g. via gist or Pastebin? Best regards, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu web:

Re: [Open Babel] Openbabel error in ReadFile

I think my first question is whether 3upo_protein.pdb exists in the directory. If so, can Open Babel read it on the command line? obabel 3upo_protein.pdb -O 3upo.mol2 # this will attempt to convert the PDB file to Mol2 -Geoff >> --receptor 3upo_protein.pdb\ >>

Re: [Open Babel] OpenBabel-discuss Digest, Vol 135, Issue 17

> I’m not sure if clustering is implemented in Openbabel, there are other > options. There is no clustering code directly in Open Babel because you can use a huge variety of packages to do clustering (e.g., using Python or R). As Chris mentions if you want to do it directly in the cheminformati

Re: [Open Babel] Confab not generating structures

e best cutoff will be, but something like this perhaps: obabel ~/Desktop/polymer.mol2 -O confs.mol2 --confab --conf 1 --verbose --ecutoff 1500 You can also look at other conformer generation options in Open Babel that ignore energy cutoffs.. -Geoff --- Prof. Geoffrey Hutchison Depar

Re: [Open Babel] Conversion SMILES to XYZ

That likely won't work, because in general the SMILES doesn't include hydrogens. If you want to follow double-bonds, I recommend converting to a file format with bonding information, e.g., SDF. Best regards, -Geoff > this is a question regarding the conversion of SMILES to xyz. I have to > ide

Re: [Open Babel] Building of non-parallel OpenBabel 2.4.1

> babel will use all cores of my machine. It is not optimal for small molecule > and, as a result, very slow. I do not believe the default installation has OpenMP enabled. Did you download the source or a binary? For which OS? Thanks and best regards, -Geoff --- Prof. Geoffrey Hut

Re: [Open Babel] Building of non-parallel OpenBabel 2.4.1

> I builded OpenBabel from sources on Ubuntu 14. You built with ENABLE_OPENMP on (which is off by default) so yes, it will use all the cores you have. cmake -DENABLE_OPENMP=OFF . # or ccmake . # in build directory # turn off ENABLE_OPENMP Hope that helps, -Geoff --- Prof. Geoffrey Hutchi

Re: [Open Babel] Adding readability to gaussian input files

> I noticed that gaussian input file (.com, .gjf) is not a readable format by > openbabel. I personally need this functionality quite a bit. Is this left out > intentionally? If not, I can add a new plugin for reading this format. If you're interested in attempting this, I'd be happy to give you

Re: [Open Babel] Adding readability to gaussian input files

> I was planning to just make the whole keywords a OBGenericData stored in > OBMol. For molecular specification section I plan to only read coordinates > and connectivity, if they are present, since those are enough to build a > molecule. Is this reasonable? There's some support already for wr

Re: [Open Babel] obminimize outputs only in pdb (multimolecule pdb)

The obminimize program does not have all the features of the obabel command. You can naturally convert a PDB file to SDF: obabel file.pdb -O file.sdf > I tried -osdf filename.sdf and it didn't work. How can I get it in sdf format? > Or how can I convert multimolecule pdb file to an sdf file? Yo

[Open Babel] Migrating from MediaWiki

Hi everyone, I’d like to modernize the Open Babel webpages, including migrating away from MediaWiki to Markdown / Jekyll. The idea behind the MediaWiki site was to enable anyone to edit. Unfortunately, unlike Wikipedia, we don’t have the same level of anti-spam resilience. So we had to move to

Re: [Open Babel] gen3d doesn't convert all compounds

> Are you able to provide files that show this? Or reduce it to single > compounds that are being eliminated that can be shared? Even if it’s only a subset, that would be helpful. I’m working on a distance geometry method that should offer increased range. Either way, having examples is crucial

Re: [Open Babel] Unable to match hydronium ions (H3O+) and H5O2+ using SMARTS

> atom by atom, and then call `ConnectTheDots()` to add bonds Not surprisingly, for a general-purpose library, Open Babel has a general-purpose bond perception algorithm. As you note, it will ensure oxygen atoms have a maximum of two bonds. This ensures PDB and other crystallography files with

Re: [Open Babel] How to handle rendering with overlaid hydrogen atoms

> Hello did anybody see the below email or was there an error? Just checking > as I've not posted to this forum before. >> I ran obabel on macOS installed with cairo through homebrew on a structure I >> downloaded in SDF format from PubChem. >> On PubChem, the 2D structure displayed is We saw

Re: [Open Babel] error: openbabel/babelconfig.h: No such file or directory

It seems like you downloaded a new version of Open Babel, but didn’t build it. Run cmake, make install before you link your code to the new version of the code. If you haven’t run cmake, there will not be a babelconfig.h header - it’s generated with the #define statements needed for your compute

Re: [Open Babel] Generating same conformers

It would be helpful to see the molecule. Certainly, I’d expect that you’d get more variety, but it’s possible you have some symmetric rotors that are not being picked up. -Geoff > On Nov 15, 2017, at 7:50 AM, MD Simulation > wrote: > > Hello, > > I'm using obabel random conformation generat

Re: [Open Babel] Generating same conformers

> Thanks for the reply. I've attached the structure, generated conformers and > a plot of the RMSD from structure 1. Looking at the plot, you get an > oscillatory behavior with the same "random" conformer being generated every > 12 structures. What OS are you using? My guess is that you have

Re: [Open Babel] Generating same conformers

> Does obabel sample dihedral angles from the input file, or does it sample > from the new dihedral angles? It samples from the initial geometry. What do you mean by "new dihedral angles?" The presumption of most conformer generation tools is that the set of rotatable bonds is fixed. -Geoff -

Re: [Open Babel] [EXTERNAL] Re: Problem Converting .cdx files using Pybel

> I have attached a new ChemDraw file with some generic structures in it. This > raises the same error I have seen with the other files. I have also included > a screenshot of the OpenBabel GUI conversion of the same .cdx file. I have seen this before (e.g., inside of Avogadro or other progra

Re: [Open Babel] Firefly dat output error

Hi, I'm not sure how well we cover GAMESS vs. Firefly formats. Please file a bug report with the file: http://github.com/openbabel/openbabel/issues <http://github.com/openbabel/openbabel/issues> Thanks and best regards, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry Un

Re: [Open Babel] [EXTERNAL] Problem Converting .cdx files using Pybel

> It seems that it’s not just a Jupyter Notebook problem. No, it's not. As I said, I've encountered this sometimes when using Open Babel inside of the Avogadro editor on a Mac. There's something different about reading the binary file inside another process (locale?) and I'm not sure what that

Re: [Open Babel] naming of pictures

> I would like to get an advise, if I can name the PNG image file with the name > of the formula in SDF. ... > And I need a PNG file ZINC40154034.png You can't do this directly with the obabel command-line program, but you can do this pretty easily in Python: http://open-babel.readthedocs.io/en

Re: [Open Babel] Best way to convert pdbqt to pdb

l. Best regards, -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/ -- Check out

Re: [Open Babel] Problems importing pybel on Mac

> I'm on a mac running 10.13.1 and I installed openbabel using homebrew. I’d ask the Homebrew folks, but my guess is that you’re either not using the right python: % which python Or, Homebrew is installing the Open Babel python packages into a directory that you’ll need to add to your Python p

Re: [Open Babel] Reading large coordinate files in C++ using Babel

> as an example you use this file (silica glass SiO2 with 3000 atoms in PDB > format, written using Babel): ... > Is this the reason why it is so slow for this kind of coordinates is because > Babel looking for bonds ? My guess, based on your example, is ring / aromaticity perception. In PDB, w

Re: [Open Babel] For some g09 log files pybel.readfile throws StopIteration error

>> Other g09 logs seem to have no problem. Can somebody shed light on what is >> missing. > > Gaussian files are a mess, not everything is supported. Maybe you can post a > full command line and the output you get from command line obabel to start > with. As David said, you'll need to post a fu

Re: [Open Babel] Atoms order in exported PDB

> The "--canonical" option of obabel can reorder atoms into a canonical order. > This can also be accessed through the API, e.g. through Pybel, via > _operations["canonical"]. Actually, I think the concern is that the atoms are not grouped by residue, e.g., all the hydrogens will end up at the

Re: [Open Babel] Openbabel - 2.3.2 with gcc 6.3 Compilation error

> I am trying to compile Openbabel – 2.3.2 with gcc 6.3. You're trying to compile a package from 2012 with a compiler from December 2016? Please try 2.4.1: https://sourceforge.net/projects/openbabel/files/latest/download It is,

Re: [Open Babel] how to convert

> I am wondering if you know a way to convert over 1000 outputs from mopac to > another format like sdf or mol ? each output is a molecule You don't mention what OS you use, but let's assume Linux or Mac - with a command-line: obabel *.out -osdf -m # convert all *.out files (MOPAC or otherwis

Re: [Open Babel] Problem of installing open-babel locally on Mac

ing object files from one source to any other Dropbox shares.) --- 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 May 7, 2018, at 5:16 PM, Tang, Dai wrote: > > Hi,

Re: [Open Babel] print UFF parameters

> Is there a way to print the UFF parameters for each molecule in database, or > even potential formula of each term such as valence, bonded or non-bonded, so > that I can use them for other MD / MC engines? Right now, you'd need to edit the source, e.g., src/forcefields/*uff.cpp By default, y

Re: [Open Babel] Displaying Titles for .smi to .png conversion

> I am hoping to convert a number of molecules in a .smi file to a single .png > file with all of the structures displayed: I dunno. I use a Mac, so the PNG format isn't very useful for me. But you can do this pretty easily with the SVG format and then use another program to convert from SVG to

Re: [Open Babel] Getting bond information

format will give bond information, e.g. Molfile / SDF. Even a PDB file will give BOND records on connected atoms. But if you want all that information, it's much easier to write a Python script and iterate through the bonds. -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry Un

Re: [Open Babel] obfit question

the-depiction-using-a-fixed-substructure <http://open-babel.readthedocs.io/en/latest/Command-line_tools/Rosetta.html#align-the-depiction-using-a-fixed-substructure> Hope that helps, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 ema

Re: [Open Babel] Open Babel Gasteiger partial charges and the -p option

We're not responsible for Autodock - you might want to contact them. As far as small molecules getting large total charges, that's a bug - can you give us an example and file it at: https://github.com/openbabel/openbabel/issues Thanks and best regards, -Geoff > On Jun 14, 2018, at 8:44 AM, Mich

Re: [Open Babel] Trouble converting .sdf files downloaded from PDB website

> I am facing a similar problem. I dowload ligands in sdf format from pdb > website. Can you give us particular examples? Particular links? Particular problems? What version of Open Babel are you using? What OS? Right now, I'd say "it works for me" because I've processed the entire LigandExpo f

Re: [Open Babel] Babel 1.05 on Android

We have no connection to that software and I doubt it has a well-defined license. I guess my question would be whether there's a particular reason to use that rather than a current version of Open Babel (e.g., 2.4.0)? -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry Universi

Re: [Open Babel] saving conformer coordinates from --confab

> obabel n-Pentane.xyz -O n-Pentane.sdf --confab --nconf 30 --writeconformers You don't mention what version of Open Babel you're using, so I can't verify that you're actually running confab. But it's not quite the right syntax - you're using features for the default conformer search methods…

Re: [Open Babel] Issues Maintaining Bond Order Through Conversion

> Is there an option that I haven’t included that can solve this problem, or is > this a bug that hasn’t been addressed? Any help would be appreciated. The two formats you mention don't store bond orders. (In particular XYZ only stores atoms - not even bond connections.) OB includes an algorith

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