Re: [Open Babel] How to disable output stream in openbabel library?

Try: obErrorLog.StopLogging(); And/or you may need to use SetOutputLevel() . Craig On Sat, Aug 29, 2020 at 9:23 AM Wang, Jiyao (NIH/NLM/NCBI) [E] via OpenBabel-discuss wrote: > Hi,

Re: [Open Babel] How to disable output stream in openbabel library?

; > Thanks! > > > > Jiyao > > > > *From:* Craig James > *Sent:* Saturday, August 29, 2020 1:01 PM > *To:* Wang, Jiyao (NIH/NLM/NCBI) [E] > *Cc:* openbabel-discuss@lists.sourceforge.net > *Subject:* Re: [Open Babel] How to disable output stream in openbabel

Re: [Open Babel] Similarity search

ese compounds is important, you might want to start with eMolecules' free downloads database: https://downloads.emolecules.com Best, Craig > On Sun, 29 Dec, 2019, 11:59 Craig James, wrote: > >> >> >> On Fri, Dec 27, 2019 at 7:48 AM suyash pant >> wrote: >>

Re: [Open Babel] Similarity search

On Fri, Dec 27, 2019 at 7:48 AM suyash pant wrote: > Hello sir/mam > I hope You are doing well > I am writing this mail, as I am facing certain problem with doing the > similarity search using "Openbable" > I have a zinc dataset for lead like and drug like molecules. Unfortunately > I am not able

Re: [Open Babel] Openbabel issue

You'll get meaningful help if you can include the exact command that you are using, and include a test file that causes the problem. With the information you've provided, there isn't enough information for anyone to help you. Craig On Sun, Apr 14, 2019 at 5:26 PM Aljawharah A. Alqathama < aaqath.

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

See attached Perl program. If you can run a Perl program, it does exactly what you need, and a few more things too. Craig On Thu, Jan 31, 2019 at 12:03 PM gehtalles wrote: > I got a massive SDF file with some 300k structures I need to split into > smaller files > > I tried > > babel infile.sdf -

Re: [Open Babel] Math multiplication symbol in SMARTs

See: http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html Look at the first section, "4.1 SMARTS Atomic Primitives" section. Both "x" and "X" are valid, but not with spaces. Craig On Tue, Nov 20, 2018 at 9:21 AM Leif Peterson < outlook_ea1c3adb71ba7...@outlook.com> wrote: > I am usin

Re: [Open Babel] Openbabel 2.4.1 reading MOL file with radicals failed

The problem is that there is no "correct" answer to your question. The specifications for the MOL format doesn't include a clear definition of the assumed valence of each atomic element. So when you specify 5 hydrogens in the file instead of six, but no "M RAD" line, does it mean it's a radical? Or

Re: [Open Babel] Aromaticity

Here's a detail about Daylight's aromaticity detection that you might not be able to deduce by looking at results. (This is not a trade secret; Dave described this in public at several MUG meetings.) 1. Read the SMILES, SDF, or other format into an object. 2. Deduce the orbital configuration of EV

Re: [Open Babel] extract a single compound from a multimolecular sdf

This is really easy to do with a scripting language like Perl. Attached is a tar with two files: - SDF.pm, a general-purpose SDF parser (it can read files, standard input, or from an array) - sdf_filter.pl, which does exactly what you're looking for. Extract the two files to a directory

Re: [Open Babel] Conversion SMILES to XYZ

I second Geoff's recommendation: It's not a good idea to use the order of atoms in a SMILES for anything. For your problem, consider this: N(O=N(O)CC)C1CCC(Cl)C=1Br It's really not reasonable to try to analyze the string to figure out which atoms are connected to the double bond, unless

Re: [Open Babel] OpenSMARTS specification (?)

It would be nice to have the OpenSMILES and OpenSMARTS pages link to each other. Or even put them on one web site. Craig On Fri, Jun 30, 2017 at 2:12 AM, Noel O'Boyle wrote: > That was at opensmarts.org. We (the broader Blue Obelisk community) > should probably move it to github. The source is

Re: [Open Babel] Erroneous molecule from MDL file

On Wed, Jun 15, 2016 at 3:22 PM, cgram wrote: > Hi, > > I have this MDL file (I removed the header): > > *12 11* 0 0 0 0 0 0 0 0999 V2000 > With 12 atoms and 11 bonds, this structure can't be right if it has a ring in it. It would have to have 12 bonds. Craig > 0.0.

Re: [Open Babel] Open Babel question about convertion object

On Fri, Feb 12, 2016 at 6:49 AM, Dziamski, Olgierd < olgierd.dziam...@psychogenics.com> wrote: > Hi Forum members, > > I am the software developer at Psychogenics Inc. We are using Open Babel > for our drug discovery research and C# library to call the Open Babel API. > In order to convert smiles

Re: [Open Babel] OpenBabel+OpenACC/OpenMp

This is a very general question that might best be asked on a C++ forum or a forum devoted to GPU programming. My understanding is that you can't just compile regular C++ code for a GPU. It has to be written very specifically for the GPU with an understanding of how the GPU works. Craig On Tue,

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

Caitlin Steiner wrote: > I was wondering if there was a way to load a mass amount of CAS numbers to > generate chemical structures? > > You can upload moderately large lists by clicking on the "Upload a File" button on www.emolecules.com. The list is limited to 10,000 CAS numbers. You may also be

Re: [Open Babel] Multiple files conversion

You can also break it down like this (assuming the files have numeric names): for d in 0 1 2 3 4 5 6 7 8 9; do for f in $d*; do ... done done Craig On Sat, Jun 27, 2015 at 11:16 AM, Matthew Baumgartner wrote: > Actually it does work, I tested it (on ubuntu 14.04). > > #make a ton of e

Re: [Open Babel] Notation for fusion in SMARTS and identify the sequence of substructure in target molecule

The problem you have is actually quite difficult to solve in general. The example you gave illustrates why: it is "obvious" to a chemist's eye how the molecule was built, but the knowledge that the chemist has is very difficult to capture in a C++ program. Here is a suggestion for an algorithm. Be

[Open Babel] OBMol::GetGIVector versus OBGraphSymPrivate::GetGIVector

I found an odd thing with c1c1[N+](=O)[O-]. When I call OBMol::GetGIVector(), it says that the two oxygen atoms have the same symmetry classes. But OBGraphSym says they're in different symmetry classes. Why are there two of these? They both seem to do the same thing, but slightly differently.

Re: [Open Babel] MACCS key 44

On Tue, Oct 21, 2014 at 6:12 AM, John May wrote: > > That's all I know about that key definition. > > Likewise - I’ve seen in a few places but not aware if it’s truly correct. > > Extending OB SMARTS to handle component level grouping shouldn’t be too > much work. The parser just needs to label t

Re: [Open Babel] chirality and SMARTS pattern matching

On Tue, Jul 8, 2014 at 2:05 PM, Stefano Forli wrote: > Hi all, > I'm having an issue with SMARTS pattern matching and chirality. > I'm trying to recognize one specific chiral configuration, but I get > unexpected answers, > see the following example: > -- > #!/usr/bin/

Re: [Open Babel] Building with Perl

Jeff, On Mon, May 26, 2014 at 5:34 PM, Jeff Janes wrote: > I've succeeded in building Chemistry::OpenBabel, but only with great > difficulty and a lot of random flailing around. I decided to go back and > take it step by step to figure out what is going on. > Even after compiling it, I was ne

Re: [Open Babel] substructure search using molecule as query

On Thu, May 8, 2014 at 8:27 AM, Andrew Dalke wrote: > On May 8, 2014, at 5:02 PM, Craig James wrote: > >> Is there any way I can ask Open Babel to generate a query which only > considers the atom element number, and not the aromaticity? Better yet, if > it considers the atom e

Re: [Open Babel] substructure search using molecule as query

On Thu, May 8, 2014 at 5:34 AM, Andrew Dalke wrote: > I want to evaluate the effectiveness of Open Babel's substructure screen > fingerprint. > [...] > I want to use the molecule as a query, and find all matches, then generate > the fingerprint for the query and the targets and do a substructure

Re: [Open Babel] Bond order in canonical SMILES

> It would be nice if I had the ability to write (canonical) SMILES strings > without any bond order information, as a "round trip" to another format > (say, .xyz with gen3D) may cause this information to be lost and I end up > with different strings for the same molecule. For example, > [NH3][CH2

Re: [Open Babel] SDF to PDB

On Tue, Mar 18, 2014 at 9:19 AM, Daniel Rodriguez Elvira < d_r_elv...@hotmail.com> wrote: > > > Craig, > You are right, I should be more specific, sorry. I installed the apt just > fine, but when I type babel example.sdf example.pdb the following message > appears: > > Cannot open CID_969516.sdf

Re: [Open Babel] SDF to PDB

Hi Daniel, Can you be more specific than "just won't work"? Like, it won't install? It won't run? It runs but doesn't give the right answer? It runs but gives an error message? If you can tell us exactly what you're doing, what happened, and what you expected to happen (and attach relevant file

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

On Fri, Feb 14, 2014 at 12:03 PM, Geoffrey Hutchison < geoff.hutchi...@gmail.com> wrote: > > 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 some

Re: [Open Babel] Openbabel broken molecules

On Tue, Dec 10, 2013 at 5:24 PM, rpordeus wrote: > Hi, openbabel is presenting the problem when I convert several molecules. > Pdb. Sdf. The molecules are all broken. Can someone help me with this > problem? > What does "The molecules are all broken" mean? What error message did you get? What

Re: [Open Babel] stereo config question

On Wed, Dec 4, 2013 at 5:27 AM, Yoel wrote: > Thanks Noel, > > Sure I agree and thanks for answering the original question. For > Dimitri and I that are looking for assigning R and S your original > answer was also the correct one since this winding property bears no > relation to R/S because the

Re: [Open Babel] stereo config question

Hi Yoel, On Tue, Dec 3, 2013 at 7:44 PM, Yoel wrote: > Hum! I’m pretty confident with what I know but the issue here is that > you answer isn’t contributing to clarifying the question. The question > is how to we determine the chirality of a centre regardless of how you > may choose to represent

Re: [Open Babel] stereo config question

On Tue, Dec 3, 2013 at 1:11 PM, Yoel wrote: > Craig, > > Thanks a lot for this. I do not know the smile notation in details > however as a chemist I’m pretty sure I understand chirality. If I > understood your article I see that explains how chirality is > represented in smile notations but I sti

Re: [Open Babel] stereo config question

ferent form but these are the general rules. > > > > I hope it helps. > > No it doesn't, sorry. > > I have a message from Craig James here: > http://forums.openbabel.org/stereo-config-td4656861.html that says it's > based on "local connectivity around a

Re: [Open Babel] (no subject)

On Mon, Dec 2, 2013 at 5:41 AM, Otto Kohulák wrote: > > babel -i pwscf pw.out -o xyz out.xyz > > the result is always: > > 0 molecules converted > 2 audit log messages > Can you convert from or to other formats? For example, can you do this? echo "CCO" | obabel -i smi -o sdf By the way, the

Re: [Open Babel] smiles output includes input filename

On Wed, Nov 27, 2013 at 1:13 PM, Dimitri Maziuk wrote: > On 11/27/2013 02:47 PM, Igor Filippov wrote: > > It is documented in the Daylight specs (the main authority on SMILES): > > http://www.daylight.com/dayhtml/doc/convert/ > > > > > >- When converting to SMILES, isomeric SMILES, SMARTS or S

Re: [Open Babel] Issue when using Java API in Netbeans

On Thu, Nov 21, 2013 at 6:09 AM, beginner_ wrote: > After each run of a script/application the project needs to be cleaned an > recompiled. If I do not recompile I get following error: > > /Error: Could not find or load main class Files.OpenBabel-2.3.2 > Java Result: 1/ > > The same application r

[Open Babel] Fwd: Openbabel system library compiled for Centos

On Thu, Nov 21, 2013 at 6:26 AM, Rajesh wrote: > Thanks James and Dimitri for your quick reply. > > Upon installation, I have compiled and executed OBTest.java to validate > java > binding. Unfortunately, it said "Benzene has 0 atoms" even after preloading > libopenbabel.so > > [root@localhost li

Re: [Open Babel] Fwd: stereo config

On Wed, Nov 20, 2013 at 11:12 AM, Dimitri Maziuk wrote: > On 11/18/2013 06:56 PM, Craig James wrote: > > >> For L-Alanine: > >> > >> PC: InChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m0/s1 > >> PDB: InChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,

Re: [Open Babel] Openbabel system library compiled for Centos

On Tue, Nov 19, 2013 at 7:17 AM, H Rajesh wrote: > Dear All, > > > > Currently we are developing a Java application in Cent OS, and facing > difficulty to integrate Openbabel API: > > *.* > > *Error received while compiling the Sample Test code* > > Exception in thread "main" java.lang.Unsati

[Open Babel] Fwd: stereo config

As a rule, you should always include all input files you use. Otherwise we can't say much about the output you provided. On Mon, Nov 18, 2013 at 4:09 PM, Dimitri Maziuk wrote: > On 11/16/2013 11:40 AM, Dimitri Maziuk wrote: > > > I guess now I'll have to come up with a different test plan. > > So

Re: [Open Babel] Smiles for diphosphorus

at the SMILES spec says. Craig > > Best wishes, > > Scott > > > On 8 November 2013 15:17, Craig James wrote: > >> On Fri, Nov 8, 2013 at 3:52 AM, scott_m wrote: >> >>> Hi all, >>> >>> When I use gen3d with P#P I get a molecule with two hyd

Re: [Open Babel] Smiles for diphosphorus

On Fri, Nov 8, 2013 at 3:52 AM, scott_m wrote: > Hi all, > > When I use gen3d with P#P I get a molecule with two hydrogens. Should it > not > be the diphosphorus molecule with chemical formula P2? Using [P]#[P] > produces the desired result but I wanted to find out why gen3d does this. > Differe

Re: [Open Babel] bug in SMILES generation

On Wed, Nov 6, 2013 at 11:13 PM, Francois Berenger wrote: > obabel test.mol2 -Oref.smi > and > obabel test.mol2 -Otest.sdf > obabel test.sdf -Ocurr.smi > > will create some different SMILES string in the .smi files. > Not all different, bu some will differ > > for example these 2 simles are suppos

Re: [Open Babel] cmake errors regarding perl bindings

On Tue, Nov 5, 2013 at 7:26 AM, Dimitri Maziuk wrote: > On 2013-11-05 08:34, Craig James wrote: > > > I don't know if it's something specific to OpenBabel, or a more general > > problem with C/C++. I have to believe it's OpenBabel, because I know > > lots

Re: [Open Babel] cmake errors regarding perl bindings

On Mon, Nov 4, 2013 at 12:30 AM, Anil Kumar wrote: > Sorry to re-post -- is there a work around for this? > I found a patch for this but, when I cut/paste that patch into > cmakelist.txt, it did not make any difference. The link to the patch I > refer to is here

Re: [Open Babel] open-source chemical reactions?

We have looked a number of times over the years at various sources of reaction data that we might make available as part of eMolecules. We've never found anything useful. The entire patent system is wide open, but extracting meaningful reactions from it is almost impossible due to the deliberate v

Re: [Open Babel] molecule too large

On Tue, Oct 8, 2013 at 10:27 AM, Dimitri Maziuk wrote: > On 10/08/2013 11:35 AM, Geoffrey Hutchison wrote: > > > I'm willing to hear suggestions as far as SMILES and InChI limits, > > but I don't even know if a 1000-atom SMILES would be particularly useful. > That, plus the potential for overwhelm

Re: [Open Babel] molecule too large

On Fri, Oct 4, 2013 at 2:35 PM, Dimitri Maziuk wrote: > So is SMILES output supposed to handle > 1000 atoms and the fact that it > doesn't is a bug? > > The SMILES parser has an explicit 1000-atom limit. It's unfortunate. Craig

Re: [Open Babel] M-block problem

There are only 30 atoms in this molecule, but the "M CHG" line is referencing atom 31. Craig On Fri, Oct 4, 2013 at 1:53 PM, Mezei, Mihaly wrote: > To follow up on my query a while ago (thanks, Craig James for a quick > answer): > > When issued the command > > ]

Re: [Open Babel] Convert a DImer pdb to Mol2

You need to provide a detailed, exact description of the steps you are using, exactly what goes wrong, and include the files you are using. Are you using other programs besides OpenBabel? Is the problem with OpenBabel or the other programs? The more information you can give, the better your chan

Re: [Open Babel] generate obMol from smiles

Rafel, Valgrind often reports uninitialized-variable errors and off-by-one array index errors in system libraries. In the valgrind output you provided, the error is in libz, the gzip-compression system library. This has nothing to do with OpenBabel, and is probably a harmless warning. Craig O

Re: [Open Babel] obgrep - aromaticity / kekule + molecule name bug

On Thu, Aug 8, 2013 at 12:38 AM, Pascal Muller wrote: > Hi all, > > > With file.smi being > C1=CC=CC=C1 single-double > c1c1 aro > c1c1N > > obgrep C1=CC=CC=C1 file.smi > gives no output. But in my opinion, all 3 molecules should be matched. > No, the query string is a SMARTS, not a SMILE

Re: [Open Babel] Licensing Openbabel

Peter, On Tue, Jul 23, 2013 at 8:03 AM, Peter Schmidtke wrote: > Hi Geoff, > > Pipeline Pilot could do indeed independent calls to openbabel binaries. > We would not use the C++ API and link to libopenbabel, but rather fork a > shell that calls opebabel via this shell with the appropriate environ

Re: [Open Babel] obgrep doesn't work on .sdf

On Tue, Jun 11, 2013 at 2:34 AM, Pascal Muller wrote: > Dear all, > > Usually, I use obgrep (Open Babel 2.3.2) with smiles files, but today I > tried with an sdf - and it doesn't work. There is no match, and no error > message (e.g. > obgrep 'C' methane.sdf > gives no output, as if there were no m

Re: [Open Babel] Open Babel in the browser

On Fri, Jun 7, 2013 at 10:25 AM, Patrick Fuller wrote: > A SMILES contains exactly the same information as the atom/bond lists in a > much more compact form. If you want to avoid the aromaticity problem, just > use Kekule form, which makes it virtually identical to any other connection > table for

Re: [Open Babel] Open Babel in the browser

On Thu, Jun 6, 2013 at 2:11 PM, Patrick Fuller wrote: > Tim, > > I think Dimitri's point is that all the references are implicitly defined > by list indices, rather than explicit keys. For example, something like > > { > "atoms": { > "C1": { "element": "C", "location": [ 0.230811, 0.3

Re: [Open Babel] Open Babel in the browser

Regarding using JSON as a new file format... This discussion has focussed on the syntax of JSON, but completely overlooks the real problem with ALL chemical file formats: how do you handle all of the cases where a simple connection-table ("ball and stick") doesn't capture reality? Things like aro

Re: [Open Babel] openbabel2.3.2 install error

On Tue, May 21, 2013 at 2:21 AM, benniu2004 wrote: > Dear everyone, > > When I tried to install the openbabel 2.3.2 on my PC (ubuntu11.10 64bit), > after "$ cmake ../openbabel-2.3.2", there were four files (CMakeCache.txt > CMakeFiles cmake_install.cmake Makefile) were created. End here, > ever

Re: [Open Babel] Stripping stereochemistry in Perl

On Sat, May 11, 2013 at 5:24 PM, Jeff Janes wrote: > > I am using perl with Chemistry::OpenBabel for canonicalizing some smiles > strings, using this construct: > > $obConversion->SetInAndOutFormats("smi", "can") > > Is there something I can change the "can" to so that it will strip out the > ste

Re: [Open Babel] Bug 2.3.1 vs 2.3.2 (mol.OBMol.DeleteAtom?)

Hi Noel, On Thu, May 9, 2013 at 1:33 PM, Noel O'Boyle wrote: > I'm going to edit DeleteAtom so that any Stereo object containing the > deleted atom is invalidated but all other stereos remain unchanged. > While you're in there, if you spot a simple way to fix this problem (e.g. invalidating the

Re: [Open Babel] canonicalization of disconnected SMILES

On Tue, Apr 16, 2013 at 12:04 PM, Jeff Janes wrote: > > > I'm using Open Babel 2.3.2 to canonicalize some SMILES strings. > > I thought that each fragment of a disconnected SMILES would be > canonicalized separately (which I believe agrees what what is explained in > http://openbabel.org/dev-api/

Re: [Open Babel] What's New and Cooking in Open Babel?

Nice! Craig On Thu, Apr 11, 2013 at 1:39 PM, Noel O'Boyle wrote: > I presented a short talk at the recent ACS meeting describing what's > new and under development in Open Babel. You can check it out at: > > http://baoilleach.blogspot.com/2013/04/talk-on-open-babel-at-new-orleans-acs.html > > Re

Re: [Open Babel] Coordinates for atoms using their internal atom index

(Repeat ... forgot to cc the list on the first try.) On Tue, Apr 9, 2013 at 1:20 PM, Roy wrote: > Hi, > > I want to access the coordinate for a group of atoms that I have searched > using SMARTS pattern. I store the atom indexes (atomno=atom->GetIdx(); ) in > std::vector< std::vector > groups; >

Re: [Open Babel] obabel hangs upon H addition

On Mon, Mar 25, 2013 at 4:29 PM, Ling Chan wrote: > Hello folks, > > obabel freezes when I tried to add hydrogens to a molecule. > > Upon typing > obabel input.mol -h -o mol -O output.mol > obabel hangs, and there are only 3 lines in the output file (output.mol). > > However, > obabel input.m

Re: [Open Babel] 5-membered ring SMARTS matching problem

On Fri, Mar 22, 2013 at 1:25 AM, Noel O'Boyle wrote: > One thing you could try is rather than use SMARTS to write some code > to check for membership of the LSSR. I've never really looked into > this, but it may be what you are looking for. > Another possibility: it looks trivially easy to chang

Re: [Open Babel] substructure search problem

On Fri, Jan 4, 2013 at 4:25 AM, shanghq...@hotmail.com < shanghq...@hotmail.com> wrote: > ** > Dear All, > > I am using Openbabel to search substructure in my database. I found > that when I converted the following two Kekule SMILES (1,2) generated > by Chemdraw to aromatic form with Openbabel, I

[Open Babel] New OpenSMILES specification posted

Thanks to Tim, there is a new version of the OpenSMILES specification, in both HTML and PDF formats: http://www.opensmiles.org Tim did a great deal of reformating with nice style sheets, and there is a whole new section on stereo centers. I'm leaving on vacation so I haven't had time to review

Re: [Open Babel] Intro to using Open Babel

Very nice ... thanks for doing this. Things like this should be available in the OB documentation as a resource for those starting new projects or trying to make a presentation to their management. Craig On Tue, Dec 4, 2012 at 3:31 AM, Noel O'Boyle wrote: > Hi all, > > Here are some introducto

Re: [Open Babel] Invalid memory access during OBConversion.WriteFile()

Your email had no messages in it ... see below. Craig On Mon, Dec 3, 2012 at 6:51 AM, mpillong wrote: > Hey everyone, > > I am currently running OpenBabel on a MacOSX 10.6.8 in Eclipse with Java. > Recently, I encountered the following exception during using the > WriteFile() > Method in OBConv

Re: [Open Babel] Adding Hydrogens not working

he CIF format has more information about the bonds between crystallographic units (I'm not familiar with the CIF format), there's not much you can do. Craig > > Best wishes, > > Scott > > On 8 September 2012 19:49, Craig James wrote: >> >> On Sat, Sep 8, 2012

Re: [Open Babel] FP2 reference and description for fingerprints

On Wed, Aug 29, 2012 at 7:55 AM, Igor Filippov [Contr] wrote: > Wow - I never realized there are API documentation for 2.3.x branch - > thank you Chris! I just always went through the front page - > openbabel.org and didn't know there is backdoor to the more recent docs. There's a really fast way

Re: [Open Babel] OBConversion OUTOPTIONS characters

On Tue, Aug 7, 2012 at 3:02 PM, Rob Smith <2robsm...@gmail.com> wrote: > Does anyone know of a comprehensive list of the OBConversion > OUTOPTIONS characters? This is a bit of a hack, but... for format in `babel -H | tail -n +16 | egrep -v '^[- A-Z]' | sed -e 's/ .*//'` ; do echo "---

Re: [Open Babel] Adding hydrogens in right order

On Tue, Jul 31, 2012 at 6:12 AM, Чугунов Антон wrote: > Dear open babel users, > I'm adding hydrogens in python script using pep.OBMol.AddHydrogens(False, > True, 7) function (where pep is pybel molecule). But after saving this to > PDB file I've got a problem: all hydrogens are written AFTER all

Re: [Open Babel] Openbabel in Python in concurrent processes

least Xen) for > memory intensive computing. I must say that I'm pretty disappointed with > those results, although it's quite obvious... > > Out of curiosity I'm going to rerun the tests on KVM and probably on > OpenVZ to see how it goes there. > > Pozdrawi

Re: [Open Babel] Openbabel in Python in concurrent processes

On Fri, Jul 20, 2012 at 2:16 AM, Maciek Wójcikowski wrote: > Hi, > I'm doing some scripting in Python to minimize ligands and want to run > them concurrently on SMP server (many processes, one core per proc.). The > problem that I hit is that when I run one instance, process take 100% CPU > and ru

Re: [Open Babel] about usage of openBabel

Ozgun, On Thu, Jul 19, 2012 at 8:18 PM, ozgun bursali wrote: > I am a computer engineering student from Turkey and I am doing my > internship right now in Arizona State University. As a part of my work I > need to convert mol files to inchi files. I searched in google and read > many articles abo

Re: [Open Babel] help

On Thu, Jul 5, 2012 at 3:06 AM, 蓝鱼在嘴里 <807409...@qq.com> wrote: > Hello， > I want to understand the fingerprint type of FP2 in Openbabel,where can I > find the information?For example,"0616<670>",I know which fragment it > represents,but for "0 6 5 6 5 6 1 6 <936>",I do not know.So where can I > f

Re: [Open Babel] Open Babel on Google Plus

int of contact for people who want to keep up to > date with these, as well as posts by others (e.g. Chris Swain, Jan Jensen's > students), recent papers and so forth. > > - Noel > > On 20 May 2012 00:32, Craig James wrote: > >> On Sat, May 19, 2012 at 12:00 PM, Noel

Re: [Open Babel] Open Babel on Google Plus

On Sat, May 19, 2012 at 12:00 PM, Noel O'Boyle wrote: > Hi there, > > Open Babel now has a page on Google Plus thanks to Björn Grüning. It's at > the easily-remembered URL of > https://plus.google.com/u/0/b/103351679221702862791/ > > Bits of news related to Open Babel will be posted there from ti

Re: [Open Babel] REAL FIX: Atom charge lost in 2.3.x SDF-to-SMILES conversion

ig > > Best regards, > Paolo > > On 05/18/2012 01:53 AM, Craig James wrote: > > Hi Paolo, > > I think you (and the original author) have mixed up the size of the > structures with the length of the string. There's no need to do a sizeof() > or to define a

Re: [Open Babel] REAL FIX: Atom charge lost in 2.3.x SDF-to-SMILES conversion

Hi Paolo, I think you (and the original author) have mixed up the size of the structures with the length of the string. There's no need to do a sizeof() or to define a constant OB_ATOM_TYPE_LENGTH. Here's what I think is needed ... it's actually simpler than the original. Just use strcpy() inste

Re: [Open Babel] Atom charge lost in 2.3.x SDF-to-SMILES conversion

; It could be that I'm completely wrong, since I don't have a comprehensive > picture of the way OB works, I'm just telling you about my experience, so > maybe someone can find a better patch than mine (which works, though :-) > > Cheers, > p. > > > On 05/17/201

Re: [Open Babel] Atom charge lost in 2.3.x SDF-to-SMILES conversion

#x27;m way beyond my area of familiarity with the OB code. Paolo's patch is a workaround, but this is a pretty serious bug in the OBAtom::operator=. Craig On Thu, May 17, 2012 at 9:38 AM, Craig James wrote: > > > On Thu, May 17, 2012 at 9:04 AM, Chris Morley wrote: > >>

Re: [Open Babel] Atom charge lost in 2.3.x SDF-to-SMILES conversion

d applied your patch, and the problem is fixed. Thanks very much! Craig > > p. > > > On 05/17/2012 06:38 PM, Craig James wrote: > > > > On Thu, May 17, 2012 at 9:04 AM, Chris Morley wrote: > >> Craig's failing example works fine for me under Windows with

Re: [Open Babel] Atom charge lost in 2.3.x SDF-to-SMILES conversion

rmal charge: -2, spin mult: 0 smilesformat: atom 1: formal charge: 2, spin mult: 0 smilesformat: atom 2: formal charge: 0, spin mult: 0 smilesformat: atom 3: formal charge: 0, spin mult: 0 smilesformat: atom 4: formal charge: 0, spin mult: 0 I'll keep digging... but if anyone recalls making a

Re: [Open Babel] Atom charge lost in 2.3.x SDF-to-SMILES conversion

ou do SDF-to-SDF, it doesn't lose the charge. Thanks, Craig On Wed, May 16, 2012 at 4:44 PM, Craig James wrote: > Here's another problem in 2.3.x that's not in 2.2.x. I realize these are > bogus molecules, but it illustrates a serious problem. > > $ echo "[Fe+2][Fe-2

Re: [Open Babel] Atom charge lost in 2.3.x SDF-to-SMILES conversion

nefit from that? It also includes a small patch > on "A T O M T Y P E S" logging that I had left behind previously. > > Best regards, > Paolo > > > On 05/17/2012 01:44 AM, Craig James wrote: > > Here's another problem in 2.3.x that's not in 2.2.x. I

[Open Babel] Atom charge lost in 2.3.x SDF-to-SMILES conversion

Here's another problem in 2.3.x that's not in 2.2.x. I realize these are bogus molecules, but it illustrates a serious problem. $ echo "[Fe+2][Fe-2].[Fe+2].[Fe-2]" | babel -i smi -o can [Fe-2][Fe+2].[Fe-2].[Fe+2] Everything looks good -- charges are maintained. Now go through the SDF forma

Re: [Open Babel] libopenbabel.so versions

On Mon, Apr 23, 2012 at 3:20 PM, Michael Banck wrote: >> I'm (finally) moving to the latest version of OpenBabel.  I discovered >> that after compiling, the .so version number is still >> libopenbabel.so.4 -- the same name as OpenBabel 2.2.x.  By my >> understanding of .so libraries, this means Op

[Open Babel] libopenbabel.so versions

I'm (finally) moving to the latest version of OpenBabel. I discovered that after compiling, the .so version number is still libopenbabel.so.4 -- the same name as OpenBabel 2.2.x. By my understanding of .so libraries, this means OpenBabel 2.3.1 is 100% ABI compatible with code compiled against Ope

Re: [Open Babel] problem with aromaticity

On Tue, Apr 17, 2012 at 7:56 AM, Noel O'Boyle wrote: > Well, Geoff, if you're going to be working on this I've recently been > subjecting ChEMBL to some canonicalisation tests, and can supply a good few > more test cases. I'll wrap them up and email them to you off list tomorrow. Would it be poss

Re: [Open Babel] SMILES & SMARTS

On Mon, Mar 19, 2012 at 2:58 AM, Fredrik Wallner wrote: > No, Geoff is right. Taken from the Daylight manual at > http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html > > All SMILES expressions are also valid SMARTS expressions, but the > semantics changes because SMILES describes molecu