Re: [Open Babel] single sdf to multi pdbs conversion with compound names

On 25/10/2017 07:55, Sundar wrote: Can anyone help me convert a single input (multimolecular) sdf file into multiple pdb files with the molecule names (as seen in the sdf file) as their file names instead of consecutively numbered file names? Try: obabel manymols.sdf -O dummy.pdb --split Eac

Re: [Open Babel] "b" option in INOPTIONS in python

On 10/08/2017 08:16, devw wrote: The bond detection behavior has been acting up recently and as part of the problem solving process I've been trying to find any documentation whatsoever about this "b" option being set in INOPTIONS. To be more explicit, it's not for a particular format, it has an

Re: [Open Babel] Conversion : CML to SDF

Sebastian While reading CML files, OB ignores most elements and attributes it does not understand. But the element (for the SGroup) embedded within the main is not handled properly. I don't think there is an option to bypass this (see obabel -L cml). It seems this issue was recognized but no

Re: [Open Babel] error with obabel filter by SMARTS

The -s option is more restricted when used with the fs format. If you type obabel -L fs the documentation says: The search target is the parameter of the ``-s`` option and can be slightly extended SMILES (with ``[#n]`` atoms and ``~`` bonds) or the name of a file containing a molecule. This is

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

On 24/07/2014 17:06, Wallace Chan wrote: > Tim, > > Thanks for your reply. Yes, we have the canonical SMILES strings stored > as properties in our glass.sdf file. I tried to generate canonical SMILES > as the result, and they are different than ours. Thus, ours were > probably acquired using a diff

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

On 29/05/2014 13:53, ANKIT RUNGTA wrote: > Hi, > > I am trying to evaluate whether this software can help me compare two > chemical structures and find out whether they are same or similar. > > Any kind of support will be helpful. Using the command line, the easiest way to compare molecules is

Re: [Open Babel] Bindings - first and last molecule option

> On 2013-12-03 04:28, Maciek Wójcikowski wrote: >> You're probably right, C also has to read therm, but other than recognizing the beginning and the end of the molecule it wouldn't do anything especially kekulization and bonding etc. > On 03/12/2013 18:11, Geoffrey Hutchison wrote: > Actually no.

Re: [Open Babel] Open Babel & Boost.Log linking errors.

On 03/10/2013 11:33, Anton Simakov wrote: > Hi! > > I'm trying to use Boost.Log 2.0 in my project which is based on Open Babel. > I'm currently compiling at Windows with Visual C++ 2010 and linkage > fails with the following message > > libboost_log-vc100-mt-gd-1_54.lib(exceptions.obj) : error LNK2

Re: [Open Babel] Count Molecules

be clearer but I didn't find it easy to do. Chris /** opcount.cpp - Counts objects in files Copyright(C) 2013 by Chris Morley This file is part of the Open Babel project. For more information, see

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

With the obabel -s option you can specify the number of matches within a single molecule, e.g. find molecules with more than 2 benzene rings. Try obabel -L ops s for details. (Maybe obgrep's c option was originally going to do this?) Chris On 08/08/2013 09:43, Noel O'Boyle wrote: > Or just l

Re: [Open Babel] obabel: Converting sdf with multi-line properties

The fix is at Line 183 in obconversion.cpp: -static string title(_title); //potential problems in calling code with multiple molecules! +static string title; //static because returning a pointer to it +title =_title; //now assigned; previously initialized which caused problems with mu

Re: [Open Babel] SMILES, SMARTS, and PDB

On 05/07/2013 17:54, Brett T. Hannigan wrote: > I have a database of molecules in pdb files. I'd like to go through > each molecule and see if it has certain substructures, and if they do > identify which atoms are part of that substructure. So it's easy enough > to read the pdb file in, convert

Re: [Open Babel] Segmentation fault in inchi conversion

I think this is due to a bug in the stereo perception code which appeared in v2.3.2 . It has been mentioned before on this and the development list but a fix is not yet committed to the development code. Version 2.3.1 works ok for me. Incidentally, prefer obabel to the older babel. obabel is sa

Re: [Open Babel] vibrational info missing from g03 file

On 23/05/2013 17:18, Mathias Laurin wrote: > Dear all, > > > I have compiled Open Babel rev 5063 with Python bindings and no GUI on > Windows XP under MSYS/MinGW. > > > It seems that I am missing the vibrational data from Gaussian g03 files > now, although it was present under Open Babel 2.3.0. > >

Re: [Open Babel] Atom numbers

On 25/04/2013 23:39, Dimitri Maziuk wrote: > On 04/25/2013 05:00 PM, Chris Morley wrote: >> On 25/04/2013 21:52, Dimitri Maziuk wrote: >> >>> is there an option to display atom numbers on 2D drawing (png or svg, >>> using sdf for input)? E.g. MarvinView

Re: [Open Babel] Atom numbers

On 25/04/2013 21:52, Dimitri Maziuk wrote: > is there an option to display atom numbers on 2D drawing (png or svg, > using sdf for input)? E.g. MarvinView has a checkbox under View - Misc. > > Specifically, as a command line switch to [o]babel or pybel api call? There is for svg: use the -xi opti

Re: [Open Babel] Alias data in SD file

On 24/04/2013 12:40, Jean-Marc Nuzillard wrote: > Dear All, > > I am presently attempting to read an SD file with Alias data at the end > of molecule description > such as > ... > A5 > H1A > A6 > H1B > A7 > H1C > ... > that causes the printing of warning messages such as: > Alias H1

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

ugging. Chris /****** murcko.cpp - A OBOp for generation Murcko scaffolds Copyright (C) 2013 by Chris Morley This file is part of the Open Babel project. For more information, see <http://openbabel.org/> This program is free softwar

Re: [Open Babel] Similarity search / Open Babel Warning in ParseSmiles

On 10/04/2013 16:55, Pascal Muller wrote: > Dear all, > > I would like to find similar molecules within library and compute > Tanimoto coefficient. > > I'm right by assuming that, using -at0.0, I should retrieve all molecules? > > obabel library.fs -Smol.smi -ofpt -at0.0 > (version 2.3.2) > > But I

Re: [Open Babel] Confusion in similarity search

On 11/04/2013 15:45, Pascal Muller wrote: > Hi, > > In a similarity search, obabel consider another molecule than the > reference I'm giving. > > My library being test.smi: > > C1(=CC2=C(C(C(C2)(C#N)C#N)(CC(=O)C)C#N)C(=O)N)C(=O)NC(=O)S1 A > C1(=Cc2c(oc3c(cc(cc3)Br)c2=O)C(=O)N)C(=O)NC(=O)S1B >

Re: [Open Babel] ranking SD files

On 08/04/2013 15:14, Kareem Khoury wrote: > is it possible with Babel to re-order an sdf file based off of a data field > > I have an sdf file with a docking score data filed. > > i was looking at the --sort command but as far as i can tell it only > sorts based off of descriptors. You are right t

Re: [Open Babel] (no subject)

On 02/04/2013 10:20, Rajeev Roy wrote: > On 02/04/2013 07:51, Rajeev Roy wrote: > > I have a confusion regarding validity of descriptors appended by help of > > the plugin provided in openbabel. > I''m talking about accuracy of each descriptor. > > And at the same time I also included rotor (i.e

Re: [Open Babel] (no subject)

On 02/04/2013 07:51, Rajeev Roy wrote: > I have a confusion regarding validity of descriptors appended by help of > the plugin provided in openbabel. > Please help me in this regard. You need to be more specific. Is it the accuracy of a particular descriptor? Or the design of a new descriptor bas

Re: [Open Babel] (no subject)

On 28/03/2013 12:17, Pascal Muller wrote: > Hi, > >> Is there a way to append ROTATABLE_BOND as a descriptor in openbabel, If is >> there any then please help me. > > http://forums.openbabel.org/number-of-rotatable-bonds-td959206.html > > Should be easy to add the corresponding line in > openbabel-

Re: [Open Babel] Please can you help me with the following question...

It is better to ask questions on the openbabel mailing list - there are more people there to answer them. On 27/03/2013 03:21, EDGAR R wrote: > I am a chemistry student. I read about your work OpenBabel and I have > some questions: > > 1. What do the numbers OpenBabel Fingerprint Program? http://

Re: [Open Babel] obabel and fingerprints

On 12/03/2013 11:28, Chris Swain wrote: >> Message: 4 >> Date: Sun, 10 Mar 2013 21:02:41 +0000 >> From: Chris Morley mailto:c.mor...@gaseq.co.uk>> >> Subject: Re: [Open Babel] obabel and fingerprints >> To: openbabel-discuss@lists.sourceforge.net >> <m

Re: [Open Babel] obabel and fingerprints

On 10/03/2013 12:45, Chris Swain wrote: > I'm moving to use obabel rather than babel and I'm having a few problems > working out the syntax > > obabel /Users/swain/obsmiles.smiles -osmi -s "c1c1" -xt > > Gives a list of 907 molecule names > > I've created the fastsearch index > > obabel /Use

Re: [Open Babel] obminimize

On 28/02/2013 07:48, Оги Боги wrote: > Thank you guys for your answer. I tried what you said but the output is > not a sdf file. How to format it in order to obtain normal sdf file? An alternative way of accessing the same functionality is to use the --minimize op with obabel, which provides more

Re: [Open Babel] Fingerprints

On 14/02/2013 08:49, Saulė G. wrote: > Dear Sir or Madam, > I am using your products for a fast search of molecule in > DB//Crystallography Open Database ( http://www.crystallography.net/ ) . > I am using fingerprints and i really need to know > what means each bit. Is this information anywhere or

Re: [Open Babel] 2.3.2

On 12/02/2013 09:38, Chris Swain wrote: > > On 12 Feb 2013, at 07:32, > openbabel-discuss-requ...@lists.sourceforge.net > <mailto:openbabel-discuss-requ...@lists.sourceforge.net> wrote: > >> Message: 3 >> Date: Sun, 10 Feb 2013 19:40:53 + >> From: C

Re: [Open Babel] cannot open aromatic.txt

On 09/02/2013 03:14, JimJoyner wrote: > "...which you may not have intended..." > This was intended. > > "...but should not be catastrophic." > This was done and worked many times until this problem came up. > > "Possibly the environment variable BABEL_DATADIR has become corrupted." > I reset the e

Re: [Open Babel] 2.3.2

On 09/02/2013 20:04, Chris Swain wrote: > Hi > My main machine has OpenBabel 2.3.1 installed and this command works fine. > > ChrisMacbookPro:~ swain$ /usr/local/bin/obgrep -v -c "" > /Users/swain/Desktop/ChemicalStructures/acetophenones.sdf > 665 > The number being the number of molecules in

Re: [Open Babel] cannot open aromatic.txt

This is strange behaviour. The command line you showed would write text representation of fingerprints to C:\OUTPUTNAME.smi, which you may not have intended but should not be catastrophic. Possibly the environment variable BABEL_DATADIR has become corrupted. Try re-setting it (via the Control P

Re: [Open Babel] Deleting Residues and Atoms in Molecules

On 15/01/2013 11:07, mpillong wrote: > Hey everyone, > > I seem to be stuck again. What I want to do is a sliding window analysis > over the residues of a peptide. Currently, I implemented a for-loop that > creates a copy of the original molecule and with every run deletes all > residues outside of

Re: [Open Babel] How to Compile on Windows against the OpenBabel Library

It is a pity that writing your own C++ programs on Windows isn't easier, but until a simplified method is developed the best way is to download the whole project from SVN. (I use TortoiseSVN http://tortoisesvn.net.) You could checkout the 2.3.2 branch https://openbabel.svn.sourceforge.net/svnroo

Re: [Open Babel] Fw: Re: substructure search problem

It would be useful to show the molecules you expect to be matched and those which you expect not to be matched. But I suppose that you want to distinguish the molecules whose SMILES are c1c1N and c1c1N(C)C . The SMARTS c1c1N matches both these molecules but c1c1[NH2] or c1c1

Re: [Open Babel] Directory structure in install directory for OpenBabel

On 17/12/2012 20:38, Geoffrey Hutchison wrote: > > On Dec 17, 2012, at 2:52 PM, Kirk Simmons wrote: > >> Perhaps I am just confused, but I have recently downloaded and installed >> OpenBabel v2.3.2. I noticed that unlike the OpenBabel 2.3.1 and earlier >> installs there are no directories "data

Re: [Open Babel] duplicated molecules in an output file

On 10/12/2012 21:50, Sarah Rodriguez wrote: > Many thanks for the openbabel snapshot. I have now installed it. > Regarding my original question of how I might output the duplicated > molecules into a file, could you tell me what command i need to use or > how to modify the --unique command in order

Re: [Open Babel] substructure classification

On 09/12/2012 21:03, David van der Spoel wrote: > Thanks, I now use this which works: > > if (conv.SetOutFormat("fpt")) > { > conv.AddOption("f", OpenBabel::OBConversion::OUTOPTIONS, > "FP4"); > conv.AddOption("s"); > conv.Co

Re: [Open Babel] substructure classification

On 08/12/2012 21:32, David van der Spoel wrote: > On 2012-12-08 17:42, Noel O'Boyle wrote: >> C:\Users\Noel>obabel -:c1(Br)cc(Br)ccc1 -ofpt -xf fp4 -xs >>> >> Arylbromide Aromatic >> 1 molecule converted >> > Great, I can reproduce that. > Is there a simple way of getting this functionality fro

Re: [Open Babel] cmake trouble -- building the code in SVN trunk

Sarah I have made an OpenBabel snapshot with a Windows installer, which may be an easier option for you. This includes the mod to --unique you want to use, but also uncommitted code - it is essentially what is on my machine at present. Download and run http://gaseq.co.uk/OB/2-4-0/OpenBabel2.4.

Re: [Open Babel] database

On 05/12/2012 00:10, Sarah Rodriguez wrote: > Hi, > > I asked the earlier question: > > On 11/11/2012 04:01, Sarah Rodriguez wrote: > > Hello, > > I am wondering if I have 2 large databases that I want to compare the > > structures in, would I be able to do this in babel? > > Thanks for your rep

Re: [Open Babel] Smiles conversion problems with Ion and Zwitterion

esent the original cif molecule as a smiles string and from > there recreate the molecule with gen3d. The problem at the moment is > that the number of H atoms is changing. Any work around for this? > > On 4 December 2012 15:05, Chris Morley <mailto:c.mor...@gaseq.co.uk>> wrote: >

Re: [Open Babel] Smiles conversion problems with Ion and Zwitterion

ults in the addition of > H's. > > I've attached the cif file. > > Many thanks, > > Scott > > > On 30 November 2012 14:53, Chris Morley <mailto:c.mor...@gaseq.co.uk>> wrote: > > On 30/11/2012 12:03, scott_m wrote: > > Dear all,

Re: [Open Babel] Smiles conversion problems with Ion and Zwitterion

On 30/11/2012 12:03, scott_m wrote: > Dear all, > > The conversion of (S)-3-carboxy-2-(imidazol-3-ium-1-yl)propanoate from a > .cif file to .smi and subsequent generation of coordinates from the .smi > file results in the addition of an extra H to one of the ring C atoms. The > original cif formula

Re: [Open Babel] Tidying up files

Chris My apologies also for the slow response. OB will already read MDL files with abbreviations in the A (alias) line, like in the attached file. (But not in the S or R structures.) So obabel alias2.mol -O expanded2.mol -r will expand the abbreviations and also remove all disconnected mol

Re: [Open Babel] dbase filtering, then substructure search (in that order)

On 20/11/2012 08:03, Visvaldas K. wrote: > Dear all, > > I am trying to look for certain molecules in the sdf/fs database > containing certain fragments as substructure. The problem is my > fragments can be small (I am running a script to do multiple searches), > so I can get "too many candidates i

Re: [Open Babel] comparing databases

On 11/11/2012 04:01, Sarah Rodriguez wrote: > Hello, > I am wondering if I have 2 large databases that I want to compare the > structures in, would I be able to do this in babel? It depends what you mean by databases and compare. OpenBabel can find duplicate molecules (i.e. with the same structur

Re: [Open Babel] set bondlength

On 28/10/2012 00:06, rik1654 wrote: > Hi all > > I would like to have the svg image resized but the p option does not seem to > be working. The output always has the same size > > example > > obabel -:"C1=CC=CC(=C1C(=O)[H])N([H])[H]" -xu -p 10 -O /tmp/out.svg > > or > > obabel -:"C1=CC=CC(=C1C(=O)[

Re: [Open Babel] babel segvs on certain gaussian log files

On 17/10/2012 14:46, David van der Spoel wrote: > On 2012-10-17 15:15, David van der Spoel wrote: >> Hi, >> >> I've done some G2 calculations on small molecules using Gaussian, and >> each of these files contains 7 calculations. Babel crashes when trying >> to read this: >> >> % curl http://folding

Re: [Open Babel] Y-help

On 17/10/2012 02:32, 蓝鱼在嘴里 wrote: > Hi,all, > I know openbabel can generate four kinds of fingerprints,each has an > original > fragement library.If I just want to code a molecule's fingerprint use 0 > or 1 bit to > represent a fragament exist in the molecule or not,how can I do this? Is > there >

Re: [Open Babel] Data directory missing from Open Babel 2.3.1 Installation?

On 03/09/2012 13:30, Noel O'Boyle wrote: > H...not good. It sounds like OB 2.3.1 doesn't install on Win 7 > without admin priviledges. I need to check this somehow. If true, we'd > better sort it out for 2.3.2. > . > In the meanwhile, you can workaround this. I will send you off-list > the data

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

On 28/08/2012 16:58, Jaehong Shin wrote: > hello All, > > I am using openbael and have a quick question about the reference of > fingerprint implemented in openbabel. > I am just wondering if I can get the reference for the fingerprints FP2 > and FP3. Actually, I would like to have the description

Re: [Open Babel] OBConversion OUTOPTIONS characters

On 08/08/2012 20:15, Rob Smith wrote: > Is there a way (like obabel -L svg) to get the GENOPTIONS? I am > struggling to get the -s " " section to transfer > programmatically. The -s option is not part of SVGFormat and works on the internal OBMol object, so you can also see the color when it is ou

Re: [Open Babel] OBConversion OUTOPTIONS characters

On 07/08/2012 23:02, Rob Smith wrote: > Does anyone know of a comprehensive list of the OBConversion > OUTOPTIONS characters? I am trying to extend a ruby wrapper we are > developing for openbabel, and I'm having trouble locating the correct > characters to complete the translation of the command l

Re: [Open Babel] SDF tag

On 02/08/2012 10:17, Altyr wrote: > Hi all, > I'm a beginner with openbabel and I want to know how to have tag in a SDF > file. > I read the doc but I have not found what I was looking for. > Do I have to add it myself or there is a way to have them automatically > (especially the unique ID)? The

Re: [Open Babel] (no subject)

On 14/07/2012 12:41, Geoffrey Hutchison wrote: > >> I think I'm using the latter and other hydrogens are added, but not the one >> I mentioned. Using version 2.3. > > Ah. I just looked through the gen3d code to see why this is happening: > >>pmol->AddHydrogens(false, true); // Add some hydrog

Re: [Open Babel] (no subject)

On 11/07/2012 18:51, James Jack wrote: > > When I convert this to a 3D molfile with "add explicit H" checked in the > OpenBabel GUI or I try the same in code the OH seems to become O- (O > with a negative charge). > In the GUI you need to check "Add hydrogens (make explicit)" but have the editbox

Re: [Open Babel] Weighted-rotor search

On 13/07/2012 14:46, scott_m wrote: > Thanks for the reply but that doesn't seem to be working for me (code below). > If I just want to get a rough set of coordinates, what should I do? I see > that gen3d (see link below) does a weighted rotor search as part of the > process of making 3d coords but

Re: [Open Babel] Structure is not tanimoto similar to itself

On 09/07/2012 20:59, Jeff Janes wrote: > If I make a file foo.smi with just this in it: > > [N-]=[N+]=c1c(=O)ccc2=c1c(=O)c1c1c2=O > > And then make and use an index file: > > ~/openbabel/bin/obabel foo.smi -ofs > ~/openbabel/bin/obabel foo.fs -ocan -sfoo.smi -at5 -aa --title "" > > I find tha

Re: [Open Babel] File format

On 11/07/2012 22:33, andi wrote: >> Nope, it's not already in OB. Sorry. Seems like it should be easy to code. > Indeed it is. I'm not very familiar with OB protocols as to reading/writing > molecules. Can you point out somewhere I can to look before I start coding > things from scratch (Perhaps I

Re: [Open Babel] help

On 06/07/2012 16:18, Craig James wrote: > > > 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 >

Re: [Open Babel] computation of L5 not working via command line

On 06/06/2012 13:39, Martin Guetlein wrote: > Hi All, > > this is how I use openbabel to compute descriptors, L5 is not working, > though (openbabel version is 2.3.1). > > $obabel -:CCC -otxt --append MW -osmi > CCC 44.0956 > 1 molecule converted > $obabel -:CCC -otxt --append L5 -osmi > CCC

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

Craig's failing example works fine for me under Windows with both 2.3.1 and the development code. As he suggested, this inconsistency suggests that there is something not being initialized properly. The logic around the flag OB_TCHARGE_MOL is a bit tricky and so is a candidate, but I cannot see

Re: [Open Babel] obabel crash while removing salt (removing counter-ions)

The example files did not make it through to the mailing list. With SMILES it is probably safe to just copy them in to the text. (Don't do this for SDF files!) The -e option enables obabel to continue with the next molecule after an error, so if the crash is not too severe you may be able to g

Re: [Open Babel] Discuss about Fingerprints and Results

On 13/04/2012 13:02, Jochen Schreiber wrote: > Hello everybody, > > i have a dataset where i know (form a clustering) which compounds are in > which cluster. > > For example Cluster 55: With 16 Compounds. > > Now i want to start a similarity search on each compound in this cluster with > babel. I

Re: [Open Babel] Smirks and tautomers (mesomers)

On 27/03/2012 00:53, Samuele Sommariva wrote: The OpenBabel class OBChemTsfm that does the work here is rather old and is known to have bugs, as you have found. Wrapping it as an op was intended to make it easier to debug, but unfortunately this didn't happen and OBChemTsfm is still not very us

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

On 15/03/2012 00:01, Tony Cook wrote: > The Alias feature is for display. That is if you draw the structure from the > information in the SDF file (or any of the MDL formats) >you are supposed to use the alias name instead of the atomic symbol in the > drawing only. However for all other pur

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

On 12/03/2012 23:18, baratron wrote: > Hi all, > > I'm trying to find the quickest way to get ligands from the PDB website into > .mol2 format for use in another program. > If I run the OpenBabel program from command line, I get lots of > warning messages: > == > *** O

Re: [Open Babel] Chembl fs file

a) The parameter of the -s option has to be a SMILES string (or a filename) The ${...} syntax is not recognised. b) It is better to use obabel rather than babel because it is safer and more versatile. The syntax difference is very small ( -O before output filename). So this works for me: obab

Re: [Open Babel] Generating fs from sdf

On 02/03/2012 17:47, Björn Grüning wrote: > Hi Jochen, > > maybe you can explain what you want to do with it. We are running such > Setup in our lab using postgresql and pgchem and it works very well. > > The fs file from openbabel is smaller than the sdf file and as far as i > know the fs file sho

Re: [Open Babel] Generating fs from sdf

On 02/03/2012 15:23, Jochen Schreiber wrote: > Hello everybody, > > i have the completed pubchem compound sdf file on my file system an want to > to a smiliarity search on them. > > Can i execute babel with more then one input fs file or how is the way to do > the search? Put all the molecules i

Re: [Open Babel] SDF first line content

On 13/02/2012 15:22, Nina Jeliazkova wrote: > I've received recently several SDF files, containing various identifiers > and calculated descriptors in the first line of SDF records, as in the > example below. > Is it something OpenBabel generates (I would normally expect these values > as SDF tags)

Re: [Open Babel] MOL to PNG?

On 03/02/2012 16:56, KC soh wrote: > I read that openbabel can read png to mol but would it be possible to then > export the mol as png/svg/jpg formats? Is there somewhere i can find out > how to do it with the C++ implementation? Could you clarify what you are looking for? OpenBabel can read (a

Re: [Open Babel] Substructure search with .fs generated with FP3, FP4 and MACCS fingerprints

On 02/02/2012 19:15, David García Aristegui wrote: > Here are examples with .fs generated with the default fingerprint, FP2 > http://openbabel.org/docs/dev/Fingerprints/fingerprints.html > > Is different the way to do a substructure search in a .fs generated with > FP3, FP4 or MACCS fingerprints?

Re: [Open Babel] .sdf and .fs files (substructure search)

In making the .fs index you meant to write obabel 1.7_24.sdf -ofs In using it to look for three connected aliphatic carbons you can use obabel 1.7_24.fs -sCCC -Oresults.smi or obabel 1.7_24.sdf -ifs -sCCC -Oresults.smi and it is necessary for the data .sdf and the index files to be in

Re: [Open Babel] Substructure searching (large datasets) .sdf format doubt

On 11/01/2012 14:23, David García Aristegui wrote: > "First of all, you need to create a fastsearch index (see above). The > index is created with the following command: > > babel mymols.sdf -ofs" > > http://openbabel.org/docs/dev/Fingerprints/fingerprints.html > > Could you please tell me the diff

Re: [Open Babel] one input file - multiple output files

On 03/01/2012 16:29, Cyberbroker1 wrote: > > the -m option works good, but is there anypossibility to make the filename > the molecule name? There have been several requests for this, so I have added this capability. It is currently only in the development code, and is described a little more on

Re: [Open Babel] Problem with PUBCHEM properties

On 13/12/2011 13:26, Adebayo Adeniyi wrote: > I want to use open babel to append properties to sdf file and also to filter > a sdf file with the properties like: > CAT_NO > > PUBCHEM_CACTVS_HBOND_DONOR > PUBCHEM_CACTVS_HBOND_ACCEPTOR > > PUBCHEM_MOLECULAR_WEIGHT > PUBCHEM_XLOGP3 > > but i got an e

Re: [Open Babel] Need complementary information on FP2

On 16/12/2011 11:01, Marianne wrote: > Dear all, > > In order to have fingerprint of reactions, is it possible to make > fingerprint (FP2) difference between 2 (or more) compounds, ? (as daylight > finger print do in section 6.2.2 here > http://www.daylight.com/dayhtml/doc/theory/theory.finger.html

Re: [Open Babel] Similarity Searching in fs-File

On 16/12/2011 08:00, Jochen Schreiber wrote: > Hello guys, > > i think i have a problem with my syntax. > > I have an sdf-File then i make an mol-File with: babel input.sdf -omol > query.mol > > and then i want to search with the query-File against one fs-File: > > babel Compound_1_250

Re: [Open Babel] small molecule finger printing

On 10/12/2011 15:55, AKHILA wrote: > Am new to the concept of fingerprints..I would like to know wich finger > prints of the 3 types present in openbabel should be used if i want the > fingerprints of small molecules like methane,ethane etc. You haven't said what you wanted the fingerprints for. T

Re: [Open Babel] Babel Multiple Input Files

You haven't included the whole molecule - the bonds are missing. Try again. It would be better to attach files rather than pasting ttext into emails to avoid corruption. Chris On 12/12/2011 10:01, Jochen Schreiber wrote: > Hello, > > sry i havnt seen the posts. > > Here is the head output from

Re: [Open Babel] Using openbabel.py to generate InChIKey with reconnect metal option

On 09/12/2011 19:44, Noel O'Boyle wrote: > Or more succintly, with obabel 2.3.1 I have: > > C:\Users\Noel>obabel -:[Al]C#N -oinchi -xK -xX Recmet > == > *** Open Babel Warning in InChI code >#1 :Metal was disconnected > ♥ > 1 molecule converted > > ...which is rathe

Re: [Open Babel] Babel Multiple Input Files

On 08/12/2011 10:30, Jochen Schreiber wrote: > Hello, > > i have joined all sdf in one (join.sdf). > > Now i want to search: babel join.sdf resultadawd.sdf > -s"B(C1=CC(=CC=C1)N2C(=O)C3CC=C4C(C3C2=O)CC5=C(C4C6=C(C(=CC=C6)F)O)C(=O)C=C(C5=O)Br)(O)O" > > But i became the following output: > > ===

[Open Babel] Converting from compound names in OpenBabel

Reminded by a question on Blue Obelisk Exchange (http://blueobelisk.shapado.com/questions/converting-from-compound-name-to-chemical-structure), I have tweaked up some code to access the NIH Chemical Identifier Resolver from an input format in OpenBabel. There must be doubts as to whether this s

Re: [Open Babel] Openbabel Memory Usage

On 29/11/2011 09:35, icdi wrote: > Dear all, > > I know there is some memory restrict in the Openbabel when doing the > conversion. My question is can I enlarge the memory restrict to get my large > sdf file (contains 25000 molecules) converted? Now I can only convert 4057 > of them. On my Windows

Re: [Open Babel] InChI v 1.04 and CML to InChI conversion

On 04/12/2011 23:59, Ken Smith wrote: > I noticed that version 1.04 of the InChI software has removed the > capability to generate InChIs directly from CML. Does Openbabel > defer this functionality to the v 1.03 InChI code at the moment? Openbabel has never used the InChI software in the convers

Re: [Open Babel] Babel Multiple Input Files

On 05/12/2011 14:30, Noel O'Boyle wrote: > I don't know if Open Babel supports joining fs files, so joining the > sdf may be your only choice. Chris? > > On 5 December 2011 15:20, Jochen Schreiber wrote: >> One question: Sholud i join the fs Files or the sdf Files and create the fs >> File on the

Re: [Open Babel] Babel strange behaviour (.fs empty)

On 21/11/2011 14:43, David García Aristegui wrote: > http://openbabel.org/docs/dev/Fingerprints/fingerprints.html > > The following command works like a charm with Open Babel 2.3.0 (linux) > babel mymols.fs -ifs -sN#Cc1c1C#N results.smi > > But, if you forgot to define the smiles output file >

Re: [Open Babel] Feature request - transparent background when converting to svg

On 21/11/2011 09:12, JP wrote: > Brilliant, many thanks for this Chris. > > - How do you make your molecules in a grid like in your attached example? If more than one molecule is being output, they are automatically put in a square grid. You can also specify the number of rows or columns. This i

Re: [Open Babel] OpenBabel v 2.2.3 installer

On 20/11/2011 18:43, Kirk Simmons wrote: > Is the Win32 installer for OpenBabel v.2.2.3 still available? I think so: http://sourceforge.net/projects/openbabel/files/openbabel/2.2.3/ Chris -- All the data continuously gen

Re: [Open Babel] Pybel's 'FP4' fingerprint bug report

I have added this to bug #3431239 to which it seem be related. With its stereochemistry mol1 fails when making an FP4 fingerprint (lots of SMARTS matching). But without the stereochemistry it is ok. Chris On 31/10/2011 16:37, Mingyue Zheng wrote: > Hi all, > I found my python script unexp

Re: [Open Babel] smiles from SDF

See http://openbabel.org/wiki/--append , which says that the first character in the parameter of append is used as a delimiter between the entries. However getting this to work with a tab seems a bit problematical although this is platform dependent. Excel will also work with delimiters other

Re: [Open Babel] OBDotNet : OpenBabel.openbabel_csharpPINVOKE exception

On 05/10/2011 09:25, Brüngger Adrian wrote: > The value of the BABEL_DATADIR is as you suggest (and points to the correct > directory). I do see the warning messages only when I run the application > from within VS 2010 (debug mode). When I go to the bin/Debug/ dir (where the > executable and a

Re: [Open Babel] smarts matching using the command line

On 26/09/2011 11:50, Martin Guetlein wrote: > On Mon, Sep 19, 2011 at 11:23 AM, Martin Guetlein< > martin.guetl...@googlemail.com> wrote: > >> On Mon, Sep 19, 2011 at 11:04 AM, Chris Morley >> wrote: >>> On 19/09/2011 09:32, Martin Guetlein wrote: >>

Re: [Open Babel] smarts matching using the command line

On 19/09/2011 09:32, Martin Guetlein wrote: > Hi, > > I would like to do smarts matching with OpenBabel, and for some > reasons I am restricted to use the command line interface. > Is there an efficient way to match a range of smarts strings against a > dataset? > > What I found out is that I coul

Re: [Open Babel] Python, openbabel, generation of InChIs and InChIKeys for proton and protonated molecular hydrogen from SMILES

On 05/09/2011 19:27, Ken Smith wrote: In response to this, I have made a few changes to the way OpenBabel calculates InChI. > E.g. for a proton [H+], I get: > > InChI=1S/H/q+1 > (ASSFXGJQJOXDAB-UHFFFAOYSA-N) > > But I *think* I should be getting: > > InChI=1S/p+1 > (GPRLSGONYQIRFK-UHFFFAOYSA-N)

Re: [Open Babel] Reading CML bug

On 14/09/2011 14:18, Weerapong Phadungsukanan wrote: > Dear all, > > I found that if the white space characters are found before and not after > the root ending tag, babel will not be able to read the CML file properly > (even if they all represent the same molecule). Here is the command I used > t

Re: [Open Babel] SDF conversion test results

On 23/08/2011 11:29, Noel O'Boyle wrote: > I note that Chris has fixed some problems with metals, and we're down > to 146 failures. Some notes on this are below. (I was waiting to make sure the changes didn't cause mass test failure.) On 09/08/2011 13:39, Róbert Kiss wrote: > We recently did so

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