Re: [Open Babel] [OpenBabel-scripting] question about pybel for python 3.x

> 1. Possibly this could be detected by seeing what libraries are installed in > the openbabel install Indeed. Many of these things should already be set in the babelconfig.h header, which should be trivially parseable by Python. If something is missing, let me know and I can change CMake to ad

Re: [Open Babel] [OpenBabel-scripting] question about pybel for python 3.x

> 1. Possibly this could be detected by seeing what libraries are installed in > the openbabel install Indeed. Many of these things should already be set in the babelconfig.h header, which should be trivially parseable by Python. If something is missing, let me know and I can change CMake to ad

Re: [Open Babel] Pybel on Python3 + Mavericks

It looks like all of the weird strings are coming through ops/loader.cpp and plugindefines.txt. I have not been able to find the root cause of the problem or a workaround. -Geoff -- Rapidly troubleshoot problems before t

Re: [Open Babel] Pybel on Python3 + Mavericks

> Can you figure out a minimal plugindefines.txt that still causes the problem? Good point. I'm now seeing that the main issue is with SMARTS descriptors. I'll see if I can find the problems later tonight. Thanks, -Geoff ---

Re: [Open Babel] Pybel on Python3 + Mavericks

> I have the problem with clang 5.0.0 on Mac OS X 10.9.1 Mavericks. > There is no problem with clang 4.2.0 on Mac OS X 10.7.5 Lion. Incidentally, GCC is no longer included with the developer tools. I can't reproduce this with Apple-provided GCC 4.2.x on Mac OS 10.7.x Lion either. It's also possi

Re: [Open Babel] missing obabel executable when compiling by sources on HPC

> i get a linker error concerning the babel executable: > .. > /opt/cray/craype/2.01/bin/CC -O2 -g -DNDEBUG -O2 -g ... > /usr/bin/ld: attempted static link of dynamic object > `../lib/libopenbabel.so.4.0.2' > collect2: error: ld returned 1 exit status When you re-ran cmake, did you remove every

Re: [Open Babel] Are the pqr lines created by Open Babel in fixed format?

> I'd like to know if I can parse them in my software almost like regular > PDB lines (i.e. assuming a fixed format for each field). I'm not sure what you mean by a "fixed format" for each field. -Geoff -- WatchGuard Di

Re: [Open Babel] Are the pqr lines created by Open Babel in fixed format?

> Probably "fixed-width" format, at least that's how I read it. In that case.. Yes. Here's the format (in code): > snprintf(buffer, BUFF_SIZE, "%s%5d %-4s %-3s %c%4d%8.3f%8.3f%8.3f > %11.8f%8.3f %2s \n", > het?"HETATM":"ATOM ", > i, >

Re: [Open Babel] Tversky_ref and Tversky_db

> Could we have them in open babel in addition to Tanimoto? My suggestion would be to submit a feature request: http://sourceforge.net/p/openbabel/feature-requests/ Thanks, -Geoff -- Managing the Performance of Cloud-Bas

Re: [Open Babel] Openbabel build failing on Mac OS

> The git version seems to compile without issues. Maybe we should release a > new version to deal with this? I will work to get the next releases (2.3.3 particularly, but also 2.4.0) going soon. I have unfortunately been backlogged with a number of pressing issues, including grant proposal su

Re: [Open Babel] Multimolecule canonical SMILES

> I have a number of multimolecular complexes that I'm converting into > canonical SMILES. Some of these molecules are carbon monoxide, and I am > noticing that sometimes they are written as [C]=O, and sometimes as O=[C]. > > Is the expected behavior of canonical SMILES - or should it instead

Re: [Open Babel] Bug

> I am new here and I found a bug, where can i report it? A lot of people post thorough discussions on the mailing list. That's fine, although the best place for bug reports is the tracker: https://sourceforge.net/p/openbabel/bugs/ Please try to give as much information as possible, like the ve

Re: [Open Babel] fingerprinting

> I'm trying to generate some fingerprints for some drug molecules and > everytime I try to run the commands listed on your wiki/tutorial site it just > tells me it cant open the file? Can you tell us the exact commands you're using and the exact error messages? Thanks, -Geoff --

Re: [Open Babel] [OpenBabel-Devel] Multimolecule canonical SMILES

> This is actually a pretty bad thing. But it may not be that easy to fix, and > would result in a major change to the SMILES that OpenBabel produces (very > unfortunate, as it requires large databases to be completely > re-canonicalized). As far as I can tell, the code is still there.. As far

Re: [Open Babel] calculate faradaic efficiency

> I am try learn, so my first question, what is the first i should do when try > to calculate faradaic efficiency? Interesting question, but I'm not sure this is the right forum or even what you might want for faradaic efficiency? Of some sort of molecular electrochemical reaction? My suggest

Re: [Open Babel] IsHetAtom

> Starting from a pybel.Atom, it seems I have to do > a.OBAtom.GetResidue().IsHetAtom(a.OBAtom) Yes, it seems like it's asking for a shortcut. If you're willing to go through Git, I'm about to push a new method to atom.h which will then propagate through the SWIG bindings to Python. bool

Re: [Open Babel] about silk structure..

ry much, -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 Feb 19, 2014, at 9:20 AM, Baki Aksakal wrote: > I am trying to obtain the coordinates, angles, and dihedrals and so

Re: [Open Babel] obgen and other programs

st/Command-line_tools/babel.html#generating-conformers-for-structures obabel ligand.babel.smi -O ligand.babel.sdf --gen3d --conformer --nconf 20 --weighted Hope that helps, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu

Re: [Open Babel] Filtering by functional groups question

> I am quite new to Obabel, and I am trying to filter out diamines and > polyamines from group of amines in .smi format. > As final result I would like to have a group of mono-amines.., My suggestion would be to add a SMARTS descriptor to plugindefines.txt (you don’t mention what OS you’re usin

Re: [Open Babel] Two smi conversion problems

1. When converting a sdf file (see attached) for carbon monoxide to smiformat I get the following smi result:[C-]#[OH]The SDF says it came through Open Babel.. presumably from some other format. It gives formal charges:M  CHG  2   1  -1   2   1This gives a -1 charge to the carbon and +1 to the oxyg

Re: [Open Babel] Two smi conversion problems

> Thanks for the reply, the sdf file was actually produced from a smiles string > using gen3d. OK, I guessed that, but what was the original SMILES? And what version of Open Babel are you using? The current development code roundtrips: [C-]#[O+] -> SDF -> [C-]#[O+] Thanks, -Geoff--

Re: [Open Babel] Hi, about install the poltype and python bindings on ubuntu system

> I success intalled the gdma 2.8.12.2, openbabel 2.3.3, cmake 2.8.12.2 and > tinker 6.3.2, when I install poltype and python bindings, I met some problem! This is not the right place to ask. We don't develop poltype. A quick Google search turns up: http://water.bme.utexas.edu/wiki/index.php/Sof

Re: [Open Babel] openbabel

Hi Matt, The best place to send Open Babel questions is to the mailing list. Otherwise, you get stuck in my overfull e-mail box which I tend to ignore. I'm afraid I don't know much about Ruby, the OB gem, or Heroku. However, I do know that others on the list do know about this (e.g., there's no

[Open Babel] Spam holdup

l spam. Subscribe to the list if you want to ask a question.. Otherwise, how will you follow the discussion? Thanks and best regards, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu web: http://hut

Re: [Open Babel] MACCS fingerprint

> I am using OpenBabel program to calculate the 166 bits MACCS fingerprint for > some coumponds and got a result with 256 bits in API after convert > hexadecimal to binary. By default, the fingerprints are "folded" to certain bit lengths. http://open-babel.readthedocs.org/en/latest/FileFormats/

Re: [Open Babel] Error with inchi dependents

I would suggest getting the latest development version from GitHub, e.g. https://github.com/openbabel/openbabel/archive/master.zip Hope that helps, -Geoff -- "Accelerate Dev Cycles with Automated Cross-Browser Testing -

Re: [Open Babel] addFragment

> The multiple fragments are coming from different OBMol objects already > established where I'm also doing some rotation and translation. What is the > best way to combine these multiple fragments to a single OBMol object for the > minimization? You'll want to make sure the coordinates of the

Re: [Open Babel] Is it possible to change forcefield when using --gen3d?

> Just a quick santity check, but does either obabel --gen3d or obgen work? > In my hands both are giving seg faults starting from smiles. What is weird > is that --gen2d is working fine. They work just fine for me, but if you're getting segfaults, I'd definitely like some example SMILES. >

Re: [Open Babel] Conversion to SVG

Noel, Did we ever get instructions on how to add 2D templates for the MCDL code? I'd think something like a c60 is destined to cause problems with programatic layout. (Indeed, I know that ChemDraw and other depiction codes have special cases for these.) Thanks, -Geoff On May 8, 2014, at 5:47

Re: [Open Babel] Couting all substructures

Sorry for the delayed reply.. my e-mail got confused and I didn't notice until now. obgrep -c http://openbabel.org/wiki/Obgrep Hope that helps, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu web:

Re: [Open Babel] MMFF94 forcefield phenol atom typing

you think there would be radically different results? Thanks, -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 Apr 14, 2014, at 9:00 AM, Toby Wright wrote: > Hi, > >

Re: [Open Babel] Question about Conformer Search

> Glancing over the source I found "minenergy" and "minrmsd" to be > implemented but the respective command-line parameter ignored. Is > there any particular reason for this? They were crashing for me. Certainly if you're willing to test them, I'd be happy to try a patch. > "--converge #" ou

Re: [Open Babel] openbabel wiki

> Is there a way to declare myself a human? (My wiki user name is "Jeff Janes") Yes, you send a message like this to humans, and we literally add you to the "humans" group. (I'm not joking.) We've had such a problem with wiki spam, it comes to this. > Also, that page contains a link to > http

Re: [Open Babel] Building with Perl

> I never had the time nor the expertise to investigate and solve all the > compiler/linker/dynaloader issues. I just needed something that works year > after year. If you get Chemistry::OpenBabel to compile, link and actually > execute, that would be a good thing. I've never figured out why Pe

Re: [Open Babel] trying to implement chemical structure matching

> I am trying to evaluate whether this software can help me compare two > chemical structures and find out whether they are same or similar. Well, I'm not exactly sure what you want, but yes there are ways to detect identical molecules or compute similarity: http://openbabel.org/docs/current/Com

Re: [Open Babel] Broken svg #1

> And a wish list one: rather than generating a garbage picture, how about > aborting when there are no 2D coordinates? When are there ever no 2D coordinates? My big question for you is why you want to show all the hydrogens. This really complicates the 2D layout, since there are a lot of things

Re: [Open Babel] Convert double bond type

> Is there a way to automatically convert undefined double bond stereo to > trans? This is for display purposes only as undefined double bonds (C=C) > will be displayed in the used tool as crossed double bond, eg like an X but > users prefer to see them displayed as trans. There are ways to do thi

Re: [Open Babel] Broken svg #1

>> When are there ever no 2D coordinates? > > e.g. SMILES input. Depiction to SVG will automatically generate 2D coordinates. Now you may not like them, but the -gen2d flag should give you the same 2D coordinates and depiction as not specifying this. > Yes it does and yes there are. The attach

Re: [Open Babel] Getting Compile time Error For Android Installation

Can you send {BUILD_DIR} / include/openbabel/babelconfig.h Clearly the OBMCDL #define isn't set properly. Thanks, -Geoff On Jun 29, 2014, at 2:10 PM, Amit Pal wrote: > Hi folks, > > I was trying to compile OpenBabel code for generating shared library. I > followed http://openbabel.org/wiki

Re: [Open Babel] -bash: /usr/local/bin/babel: No such file or directory

> I am trying to use Ibabel on a Mac version 10.9.3. I downloaded the .zip file > from here: > http://www.macinchem.org/ibabel/ibabel3.php That doesn't install Open Babel itself. It's just an interface. See: http://openbabel.org/wiki/Get_Open_Babel Hope that helps, -Geoff ---

Re: [Open Babel] Getting Compile time Error For Android Installation

> After that i got an Error i..e Android.mk is trying to find ops.cpp which is > not present. To solve this i removed ops.cpp from Android.mk and build again. If you don't have ops.cpp, then you don't have a complete current version. (And BTW, why are you using 2.3.0, which is old?) Simply leav

Re: [Open Babel] Which data format is best for getting adjacency matrix?

> - Adjacency matrix or adjacency list for each graph > - Label information for each node in a graph (for labeled graphs) > - Class (+1/-1) information for each graph for classification > > I've found some datasets in .mol and .sdf formats (for example, Bursi > dataset: http://cheminformatics.org

Re: [Open Babel] chirality and SMARTS pattern matching

No, the devel version Noel mentioned is on GitHub: http://github.com/openbabel Hope that helps, Geoff On Wednesday, July 9, 2014, Stefano Forli wrote: > Hi, > > thanks for the replies. > > Craig, I think I understood what you meant with the incomplete chiral > description and it > makes sense w

Re: [Open Babel] Forcefields in Static Executable

> First of all, I'm getting a lot of warnings of "Cannot initialize database" > and "Cannot perform atom type translation: table cannot find requested > types." This doesn't seem to be the problem though, because the atom > conversions do seem to be working right. > > I think the problem invol

Re: [Open Babel] Add comments to output file

> But I would like to add comments, e.g. REMARK lines in the .pdb file These are set using OBPairData, so you'd want to add "REMARK" as the key and then the comments. For example with Pybel: http://openbabel.org/docs/dev/UseTheLibrary/Python_PybelAPI.html#pybel.MoleculeData mol = readfile(…..).

Re: [Open Babel] Conversion of SMILES to SMARTS String

A valid SMILES string is generally a SMARTS. It might not be the best possible SMARTS, but we do have a set of tests for SMILES to match themselves as SMARTS. Hope that helps, -Geoff -- Want fast and easy access to all th

Re: [Open Babel] mol2 writer adds residue number to residue name

Sorry, I missed your patch. It looks great, although I wonder if there should be some logic to look for a number at the end of the residue name. If present, the default would be not to number? Thoughts? Thanks, -Geoff > In case anybody is willing I have attached a patch. This introduces a > n

Re: [Open Babel] error on installation

> I am attempting to install the latest version of openbabel (obtained using > subversion) on a machine running Mac OS X L 10.4.10. I am following the > instructions here: Open Babel no longer uses subversion. The latest code is available on GitHub: http://github.com/openbabel/openbabel (If

Re: [Open Babel] Applying reactions in obabel

> I can find documentation and examples on reading reactions in one format and > saving them to a different one using obabel or language bindings, but I can't > find anything for applying a reaction SMARTS to a molecule and obtaining the > result. You want the OBChemTsfm class: http://openbabel

Re: [Open Babel] (no subject)

> I have a problem with Openbabel after updating my Ox to 10.9. Unfortunately, when you update a Mac, the contents of /usr/local (i.e., programs you installed like Open Babel) are not migrated. I *think* this will change with Yosemite - my test laptop seems OK. So you will need to re-install O

Re: [Open Babel] Problems with babel

ick minimization. Further minimization may still be useful. > * I'm having issues with gen3D, it gives me error messages with "steplength", > I forget the exact wording but what does steplength do? That's a warning that the initial rough geometry was a bit weird. It&#

Re: [Open Babel] MACCS key 44

> I created pull request on github > [https://github.com/openbabel/openbabel/pull/96 > ] And it's merged. Thanks both to Andrew and Maciek. :-) -Geoff-- Comprehensive Serv

Re: [Open Babel] MACCS key 44

> Extending OB SMARTS to handle component level grouping shouldn’t be too much > work. The parser just needs to label the components of the pattern. The > matcher can then check this post match (same as stereochem is implemented) by > labelling the connected components. Awesome. Let me know if

Re: [Open Babel] tape41 to molden format

ny format. So no orbital information would be translated. I don't know if it supports ADF tape41 format, but I suggest looking at the cclib project (http://cclib.github.io) which definitely reads a wide variety of QM data. Hope that helps, -Geoff --- Prof. Geoffrey Hutchison Departmen

Re: [Open Babel] Maximum common substructure (MCS) with OpenBabel

> This tool used to be somewhere in the contrib section of openbabel, the > source code is very compact and should be easy to > understand/use/modify. Indeed, it's here: https://github.com/openbabel/contributed/tree/master/c%2B%2B/mcs-cliquer Cheers, -Geoff

Re: [Open Babel] Openbabel and Anaconda

> Has anybody successfully compiled openbabel with python bindings that work > with Anaconda python > distribution (python 2.6)? Sure, there's no problem. You just need to make sure that Cmake is picking up the correct python and python libraries bef

[Open Babel] Library Generation & Stereo-isomer Enumeration

edback about suggested properties, features, bugs, etc. as we go. --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu web: http://hutchison.chem.pitt.edu/

Re: [Open Babel] Substructure Search(Pybel): why results are different from what I see

com/dayhtml_tutorials/languages/smarts/ 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/ ---

Re: [Open Babel] Chirality and winding

> We have an idea what to add to get around this (distance geometry), > but no-one has done it yet. I'm fairly close, but I'm still doing testing to make sure it's robust. If anyone would like to test, I can put a branch up on GitHub. -Geoff --

Re: [Open Babel] accessing and manipulating GAFF atom types?

> I was wondering if there is currently a mechanism to read out and > manipulate GAFF atom types. You can get out the atom types, e.g. http://openbabel.org/api/2.3/classOpenBabel_1_1OBForceField.shtml#aa41fd7cce6a9cf2e56ca603de7fbc507 At the moment, it is not possible to manipulate them. Suggesti

Re: [Open Babel] pybel/openbabel and use of confab

> The operations are aimed at use from the command-line and so I would > recommend using Python's subprocess. Well, I think you can employ them in Python directly. This is untested, but something like this would work: >> confab = openbabel.OBOp.FindType("confab") >> confab.Do(myOBMol, "options")

Re: [Open Babel] pybel/openbabel and use of confab

tions can > do this. > > Cheers, > Ryan > > -Original Message- > From: Geoffrey Hutchison [mailto:geoff.hutchi...@gmail.com] > Sent: Wednesday, February 25, 2015 3:24 PM > To: Noel O'Boyle > Cc: Renslow, Ryan S; openbabel-discuss@lists.sourceforge.net > Sub

Re: [Open Babel] MACCS key 44

> Looks like that might have been fixed.. the parser will throw an error on the > dot but actually parses and matches it okay if component grouping is > specified. The component grouping isn’t actually checked but the disconnected > query matches as expected. Might take a closer look this weeken

Re: [Open Babel] Openbabel python binding

I *strongly* recommend contacting the openbabel mailing list rather than me personally. My e-mail box is horrendous. In this case, I suspect you either have multiple versions of Python installed, or the active python is not able to load the _openbabel.so correctly. I usually see this sort of er

Re: [Open Babel] Getting into openbabel development

Ugh. Sorry, I don't think you got my reply. The cyclobutadione "bug" is a broader one with Kekulization. The problem is that if aromaticity is not detected, the Kekule code should attempt to derive approximate alternating double bond structures. The code is in kekule.cpp, but it's definitely a

Re: [Open Babel] Substructure Search(Pybel): why results are different from what I see

> [#6]~1~[#6]~[#6]~2~[#6]~[#6]~[#6]~[#6]~[#6]~2~[#6]~1 Alternatively, if you open compounds in Avogadro, there is a "Select SMARTS" which can also help debugging patterns. -Geoff -- Dive into the World of Parallel Progra

Re: [Open Babel] obabel convert problem

Please don't write to me directly. There are many other users and developers and in most cases, your message will simply get buried in my e-mail box. Without hydrogen atoms on the PDB file, the bond perception algorithm must "guess" (i.e. perceive) bond orders. If you know something about the b

Re: [Open Babel] mac mavericks - openbabel trouble with python3

I think you'll need to be more detailed when you say that you can't import openbabel with Python. What is the exact error message? -Geoff > On Apr 2, 2015, at 6:50 AM, lansana Camara wrote: > > Hey, > > i try to install openbabel with python3. I get also python2.7. > In a terminal window i t

Re: [Open Babel] Problem with gen3D keyword

>I get the xyz coordinates, but I also get a warning message: > WARNING: too small "scale" at Newton2NumLineSearch This is a minor warning from the geometry optimization. (Clearly I need to hide this.) > I need to grow the four alkyl chains of the structure. Why don't you create the methy

Re: [Open Babel] Problem with gen3D keyword

The warnings are simply indicating that in the geometry optimization, the coordinates at that step were a bit rough and the gradient is high. They can be ignored. No, conformational search won't help here. -Geoff > Geoff, I'll try Avogadro, but my initial plan was to get the coordinates the >

Re: [Open Babel] perl api

> After updating my release to the master I've found that this code doesn't > work anymore, inparticular the line: > What version of SWIG do you have on your system? -Geoff-- One dashboard for servers and applications

Re: [Open Babel] GAFF in Open Babel

> It will not replace a Nitrogen by an Oxygen but it could be quite wrong. > In addition I have no idea how partial charges are computed. At the moment, it appears to use Gasteiger charges unless other charges have been set (e.g., by importing from a Gaussian file). -Geoff -

Re: [Open Babel] Partial charge on OSX system

> I would like to use openbabel to generate the partial charge of my > molecules. I could use the mmff partial charge method. But I still need to > use qeq method. But it shows system could not find qeq. What version of Open Babel did you install? Can you give more specifics on "shows system

Re: [Open Babel] Partial charge on OSX system

t; Hi Geoffrey, > > I am sorry disturbing you again. > > Could you please let me know how did you download and install your openbabel? > I tried using linux version and I got the qeq. But the openbabel didn't work. > Could you please give me the link or procedure

Re: [Open Babel] Atom types depend on the input file format

> * with ./Typing.exe 10gs_ligand.sdf, the 4th atom is of type "o" (which is > the good type) > * with ./Typing.exe 10gs_ligand.xyz, the 4th atom is of type "os" While I can't comment on the particular files, an XYZ file has no bonding information whatsoever. While the bond perception in OB is f

Re: [Open Babel] [Avogadro-Discuss] Question about CAS numbers

hem. E-mail me if you'd like more details. Cheers, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu web: http://hutchison.chem.pitt.edu/--

Re: [Open Babel] atom types force field

> I need to get the atom types from molecules. I am using a Python/PyMOL > script. I have the following code Sorry, I realized no one got back to you. Here's code that should work http://openbabel.org/api/2.3/classOpenBabel_1_1OBForceField.shtml#aa41fd7cce6a9cf2e56ca603de7fbc507 def get_atom_typ

Re: [Open Babel] Segmentation fault

> I am getting segmentation faults from openbabel on a few small molecules when > trying to convert from .mol2 format (either to .smi or to .sdf). The version > we have is Open Babel 2.3.90, from Nov, 2014, on a linux server. Appreciate the report, but it works fine for me on the latest develop

Re: [Open Babel] ligand conformation search

> Steric clashes should be filtered out, but you might have to tweak the filter > in > the source. At least I had to do that for very big molecules. What was your tweak? This seems like an important patch for others. Thanks very much, -Geoff -

Re: [Open Babel] Determination of partial charges - no difference between force fields?

> forcefield calculations. In order to copy the internal charges to your > external object "mol" you need to call ff.GetPartialCharges(mol). (see Keep in mind that only MMFF94 uses a partial charge model. UFF has no partial charge model, and GAFF uses Gasteiger charges if nothing else is availa

Re: [Open Babel] Endless run for a particular SMILES

> I can reproduce this in 2.3.2. But it is fixed on the current (unreleased) > version of the code from github. Yes, I definitely need to push 2.4.0 out the door. This week, I'm pretty swamped with a grant proposal, but am aiming for November. -Geoff -

Re: [Open Babel] why forcefielduff correct angles when calculate energy?

> modified?after doing this the energy is far different from VASP result,why I’m not sure why you’d be concerned that UFF (a classical method) has a different energy than VASP (a quantum method). Moreover, the current force field implementation in Open Babel does not use periodic boundary condit

Re: [Open Babel] Problem in converting a PDB file to MOL2

> Indeed, we've tried the SDF and it is a good option. However, some small > ligands have covalent bonds with other small ligands and by using the SDF > format we won't able to detect it correctly. Can you give us some concrete examples of what you mean? -Geoff --

Re: [Open Babel] alternative FF?

> I would like to do minimization for protein/ligand complex. I am just > wondering, is it possible to introduce Amber99SB or latest Amber14SB FF > for my protein and GAFF for the ligand? For that, your best bet is to use Amber. -Geoff --

Re: [Open Babel] Question for open babel

> I read your paper on topic of Open Babel: An open chemical toolbox. This is > an excellent paper and program. However, After I used your programme (Open > Babel for mac) to converting amino acid sequences to smile format.after > that, program showed this message " 31 audit log messages".Wha

Re: [Open Babel] PDB to SMILES

> -problems with bond order (e.g. it makes non-aromatic ring out of aromatic > one) > -problems with charges (e.g. it converts charged group like NH3+ to radical > NH3); Can you post the PDB file? Since PDB does not usually contain bond orders, Open Babel needs to perceive aromaticity, etc. and

Re: [Open Babel] pdf export

> Apologies the title should be sdf export. But there is sdf.. do you mean csv (i.e., spreadsheet)? > It would be useful to have options for the delimiter. It is possible the > content may contain commas, so options for tab or pipe might be useful and/or > putting quotes around text. > Not ever

Re: [Open Babel] Confab Usage

> I can't seem to activate Confab on Openbabel 2.3.90 on Ubuntu: Are you sure you *have* confab? You need the Eigen library installed to build confab: > [ghutchis@geoffh-desktop] openbabel: babel -L confab > One of the ops > confabConfab, the diverse conformer generator > Typical usage: oba

Re: [Open Babel] OpenBabel+OpenACC/OpenMp

> I wanted to ask if anyone has any experience with GPU programming using C++. > I wanted to know about general procedure/ approach . because all the codes > that i am compiling on GPU are failing. This really is not the correct forum for this. If you’re interested in compiling Open Babel with

Re: [Open Babel] convert SDF format to MM3

> I cannot find the MM3 format as an output option. Is there a way to access it > or perhaps an equivalent (identical) format under another name? The Tinker format assigns MM3 atom types. If this doesn’t match the MM3 file format, it’s probably pretty similar. -Geoff --

[Open Babel] Open Chemistry in Google Summer of Code

Open Babel (and OpenChemistry) has been accepted into the Google Summer of Code for 2016: https://summerofcode.withgoogle.com/organizations/6290185763422208/ http://wiki.openchemistry.org/GSoC_Ideas_2016 If you are a student and interested in doing open chemistry software development this summe

Re: [Open Babel] java library dll error on 64-bit windows

> So is there a version for 64-bit platforms? No, not at the moment. -Geoff -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Moni

Re: [Open Babel] Tanimoto similarity calculation with Java library

>OBFingerprint fprinter = OBFingerprint.FindFingerprint("FP2"); >OBVectorData fp = vectorUnsignedInt(); // ??? this is the part > I could not integrate from python > OBVectorData fp2 = vectorUnsignedInt(); // ??? it gives an > error saying vectorU

Re: [Open Babel] 1-substituted adamantane InChIKeys

> On Mar 9, 2016, at 11:53 AM, John M wrote: > I think this is pretty easy to explain but just to clarify, you converted > SMILES to SDF/CML with 3D coordinates? If you're input didn't have > stereochemistry before this conversion it will always have it defined after. > A simpler example of but

Re: [Open Babel] PAINS filtering

> I am able to filter my SDF file using one SMARTS pattern at a time, but I > was wondering if OB provides a simple way of filtering all PAINS in one go. At the moment, no. But if someone posts the set of SMARTS patterns, it’s easy to add this as a filter to plugindefines.txt. -Geoff ---

Re: [Open Babel] PAINS filtering (mirix)

> Have a look at http://www.macinchem.org/reviews/pains/painsFilter.php This reminds me that we should integrate the Silicos tools into the main OB distribution. Thanks, -Geoff -- Transform Data into Opportunity. Acceler

Re: [Open Babel] OBChemTsfm and OBReaction

> If there's indeed some general interest, and developers think it's feasible, > even if in > the long run, I would be happy to work on it. Oh, I think both are feasible and I think we can supply some pointers. The problem has been one of "too many things and not enough cooks" rather than anyt

Re: [Open Babel] Python scripting internal coordinates

> I would like to generate a new set of coordinates for a molecule by > modifying the internal coordinates. > > When I convert the new molecule to gzmat or fh, some of the internal > coordinates atom definition are modified. Sure. The default CartesianToInternal method will do re-ordering if it t

Re: [Open Babel] unable to run babel command after installation centOS 6

> I think there is a delay in my responses getting accepted and viewed by > members of the group. If you are not a member of the mailing list or are sending an e-mail from a different e-mail address, your message will have to be moderated. -Geoff

Re: [Open Babel] OpenBabel-discuss Digest, Vol 119, Issue 5

> ​​babel -igamin xyz.out -igamin xyz.​i​np -f 22​ I don't know what kind of file xyz.out is, but I doubt that it's a GAMESS input. Try: obabel xyz.out -O xyz.inp -f 22 -ogamin Usually the ".out" format code is smart enough to figure out the kind of file you hand it. Best regards, -Geoff-

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