[Open Babel] Interesting Paper

Just came across this paper in a journal I don't normally read. http://www.almob.org/content/5/1/9 Results In this paper, we present a method which efficiently finds all fingerprints in a database with Tanimoto coefficient to the query fingerprint above a user defined threshold. The method i

Re: [Open Babel] OpenBabel

/acetophenones.sdf -ofpt > > The easiest way to search the list is to search > http://forums.openbabel.org either using the search box or via google > (e.g. site:forums.openbabel.org similarity search smiles) > > - Noel > > On 1 February 2012 11:30, Chris Swain

[Open Babel] OpenCL

I've just seen a demo of the impact of running applications on the GPU and it does seem for some operations you can get striking performance gains. Would it be worth considering porting openbabel to OpenCL? Chris -- Liv

Re: [Open Babel] OpenCL

Thanks for the input Geoff. The example I saw was a proprietary similarity search, I've no idea if a similar increase is speed would be possible for fastsearch? Cheers, Chris On 12 Jul 2012, at 13:16, Geoff Hutchison wrote: >> I've just seen a demo of the impact of running applications on the

[Open Babel] Tidying up files

Hi, I often end up editing files using a text editor because they contain features that are not compatible with other programs. In particular removing salts and/or solvents and expanding fragment labels e.g TMS, t-butyl etc. Would it be possible to do this within openbabel, perhaps an "obtidy"

Re: [Open Babel] Tidying up files

Hi, Here is a list of abbreviations I have compiled over the years. Ac, Ace, Acetate, Acetyl, Acyl AcAc acetoacetyl ACN = acetonitrile Ad = 1-adamantyl Alloc, AOC = allyoxycarbonyl All, Allyl Bam = benzamidomethyl BDMS = biphenyldimethylsilyl BOC, Boc, t-boc = t-butoxycarbonyl BOM = benzyloxymet

Re: [Open Babel] Tidying up files

Hi, I never knew this option existed, as far as I can tell it is not mentioned on the wiki and it does not appear when you type babel -H It does look as if it could be exactly what I want ;-) Cheers ChrisS On 30 Nov 2012, at 14:53, openbabel-discuss-requ...@lists.sourceforge.net wrote: > Mes

Re: [Open Babel] substructure classification

> > > -- > > Message: 2 > Date: Sat, 08 Dec 2012 14:51:44 +0100 > From: David van der Spoel > Subject: [Open Babel] substructure classification > To: openbabel-discuss@lists.sourceforge.net > Message-ID: <50c345f0.4070...@xray.bmc.uu.se> > Content-Type: text/plain; c

[Open Babel] 2.3.2

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 the sdf file. I've been playing around with OpenBa

Re: [Open Babel] 2.3.2

] 2.3.2 > To: openbabel-discuss@lists.sourceforge.net > Message-ID: <5117f7c5.9000...@gaseq.co.uk> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > On 09/02/2013 20:04, Chris Swain wrote: >> Hi >> My main machine has OpenBabel 2.3.1 installed and th

Re: [Open Babel] 2.3.2

co.uk> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > 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

[Open Babel] obabel and fingerprints

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 /Users/swain/obsmiles.smiles -ofs this created /Users/swain/

Re: [Open Babel] obabel and fingerprints

t=flowed > > 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 >> >>

[Open Babel] ElementalDB

I just thought you might find this interesting. Searching a 1.2M structure database on your iPad. http://www.macinchem.org/reviews/dotmatics/elementalTech.php Cheers. Chris -- Own the Future-Intel(R) Level Up Game Demo

[Open Babel] Count Molecules

Hi, Is there a way to simply count the number of molecules in a file? Cheers Chris -- Get 100% visibility into Java/.NET code with AppDynamics Lite! It's a free troubleshooting tool designed for production. Get down to c

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

obgrep used to guess the file type based on the extension but it does not seem to work now. Chris On 8 Aug 2013, at 10:30, openbabel-discuss-requ...@lists.sourceforge.net wrote: > Message: 2 > Date: Thu, 8 Aug 2013 09:59:54 +0200 > From: Pascal Muller > Subject: Re: [Open Babel] Fwd: obgrep doe

Re: [Open Babel] Count Molecules

> If it is for a mol2 file, you could do > fgrep -c "@ATOM" > > > If you are on Windows, open a DOS prompt and substitute > "fgrep -c" above with "find /c". > > etc. etc. > > > Ling > > > From: Chris Swain >

Re: [Open Babel] open-source chemical reactions? (David Koes)

Have you had a look at the ChemSpider Synthetic Pages? http://cssp.chemspider.com Organic Syntheses are available online but I don't know if you can get access to the database. Chris -- October Webinars: Code for Perfor

[Open Babel] Conversion to SVG

Hi, I’ve been comparing a couple of different molecule viewers including the SVG output from openbabel. One file that seems to cause problems is the SVG display of buckyball (file attached). Whilst the conversion does eventually take place it can take a long time on older machines (running M

Re: [Open Babel] Generating a diverse set of conformers (Douglas Houston)

> > Message: 2 > Date: Wed, 7 May 2014 05:45:46 -0700 (PDT) > From: Douglas Houston > Subject: Re: [Open Babel] Generating a diverse set of conformers > To: openbabel-discuss@lists.sourceforge.net > Message-ID: <1399466746210-4657403.p...@n4.nabble.com> > Content-Type: text/plain; charset=us-asc

Re: [Open Babel] error by installing open babel for mac

Hi Allassane, If you are setting up a Mac for Cheminformatics I wrote a detailed “How to” here that uses HomeBrew. http://www.macinchem.org/reviews/cheminfo/cheminfoMac.php Cheers, Chris---

Re: [Open Babel] PLIP - An Open Babel related project (Nathan Pimental)

Website also works beautifully on my iPad and iPhone. Really nice work. Chris -- One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Pe

[Open Babel] Results from Fastsearch

Hi, /usr/local/bin/obabel' '/Users/username/Desktop/MyFile.fs' -osmiles -S'Fc1cc2NCCc2cc1' -at1 -aa returns Cc1ccc(NCCc2c(cc(cc2[N+](=O)[O-])[N+](=O)[O-])[N+](=O)[O-])cc1 MLS000590224-01 0.536585 With a tab between SMILES and ID, and a space between ID and Tanimoto score. It might be better

[Open Babel] Flagging Potential Aggregators

Hi, I just thought I’d mention a Vortex script I’ve written (http://www.macinchem.org/reviews/vortex/tut29/scripting_vortex29.php ) for flagging potential aggregators in a high-thougput screen, it is written in Jython (http:

[Open Babel] iBabel

Hi, I’ve just released a new version of iBabel. Full details here. http://www.macinchem.org/ibabel/iBabel3_6.php Cheers, Chris -- ___ OpenBabel-discuss mailing list OpenBabel-

[Open Babel] pdf export

Hi, Is there an output format that can be used to convert an sdf file to delimited text, such that the output contains SMILES, molecule name and any fields within the sdf? Ideally with the first row of the file being the titles off the fields? Cheers, Chris -

Re: [Open Babel] pdf export

Apologies the title should be sdf export. A couple of additional comments. 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 every record in a sdf will have all

Re: [Open Babel] pdf export

csv('ampc_docked.csv') > > > > Pozdrawiam, | Best regards, > Maciek Wójcikowski > mac...@wojcikowski.pl <mailto:mac...@wojcikowski.pl> > > 2016-01-22 14:17 GMT+01:00 Chris Swain mailto:sw...@mac.com>>: > Apologies the title should be sdf exp

Re: [Open Babel] PAINS filtering (mirix)

Have a look at http://www.macinchem.org/reviews/pains/painsFilter.php Cheers Chris > On 15 Mar 2016, at 12:10, openbabel-discuss-requ...@lists.sourceforge.net > wrote: > > Send OpenBabel-discuss mailing list submissions to > openbabel-discuss@lists.sourceforge.net > > To subscribe or uns

Re: [Open Babel] : PAINS filtering

If you are planning to annotate very large data sets it might be worth looking at Vortex. http://macinchem.org/reviews/vortex/tut24/scripting_vortex24.php Pains matching PubChem 67M structures took under 4 hours. Chris > > Message: 6 > Date: Tue, 15 Mar 2016 10:54:11 -0700 > From: Stefano Fo

Re: [Open Babel] SMARTS question

Hi, I notice that you have defined the five-membered ring SMARTS with aromatic atoms, I’ve sometimes found unexpected behaviour with the definition of aromatic systems with small heterocyclic rings, especially if tautomeric forms are possible. Cheers, Chris Dr Chris Swain BA MA (Cantab

Re: [Open Babel] Question about file conversion

You need to have the SMILES string(s) in a plain text file. It should look like this c1c1 c1c1F C1C1 (=O)Cl and ideally you should name it something like myfile.si or myfile.smiles Enter the path to the file in the input file field. Cheers, Chris > > Message: 1 > Date: Sun, 8

Re: [Open Babel] Unable to import pybel in Python

Hi, I’ve written a page on installing cheminformatics tools on a Mac, here http://www.macinchem.org/reviews/cheminfo/cheminfoMac.php Cheers, Chris > On 8 Jul 2016, at 13:05, openbabel-discuss-requ...@lists.sourceforge.net > wrote: >

Re: [Open Babel] SMARTS question

Hi, I think Noel’s suggestion is correct. I use SMARTSviewer to work out SMARTS queries. http://smartsview.zbh.uni-hamburg.de Cheers Chris > > Message: 2 > Date: Mon, 12 Sep 2016 10:01:10 +0100 > From: "Noel O'Boyle" > Subject: Re: [Open Babel] SMARTS

[Open Babel] MOPAC

A user of iBabel reported that they could not convert sdf files to MOPAC (.mop) . I checked using the command line /usr/local/bin/babel '/Users/Chris/Desktop/confs/temp1.sdf' -omop -xf '/Users/Chris/Desktop/confs/temp1.mop’ and /usr/local/bin/obabel '/Users/Chris/Desktop/confs/t

Re: [Open Babel] MOPAC

Hi, Thanks, that works fine. Chris > On 15 Nov 2016, at 11:06, Pascal Muller wrote: > > Hi, > > > A user of iBabel reported that they could not convert sdf files to MOPAC > (.mop) . > > I checked using the command line > > /usr/local/bin/babel '/Users/Chris/Desktop/confs/temp1.sdf'

Re: [Open Babel] MOPAC

Thanks Geoff. > On 15 Nov 2016, at 20:18, Geoffrey Hutchison > wrote: > >> /usr/local/bin/obabel '/Users/Chris/Desktop/confs/temp1.sdf' -omop -xf >> '/Users/Chris/Desktop/confs/temp1.mop’ > > > The key problem is the use of the -xf flag. This is a way to set keywords in > the MOPAC f

[Open Babel] add hydrogens appropriate for pH

Hi, I’ve been experimenting with the add hydrogens appropriate for pH and I get a couple of curious results obabel -:"NC(=N)c1c1" -osmi -p 7.4 N[C+](=N)c1c1 Should this be [NH3+]C(=N)c1c1 Similarly obabel -:"NC(=N)Nc1c1" -osmi -p 7.4 N[C+](=N)Nc1c1 Should this be [NH3+]C(=

Re: [Open Babel] add hydrogens appropriate for pH

Thanks Geoff, I don't suppose the rules are in a user editable form? Cheers Chris Sent from Chris's iPhone > On 18 Nov 2016, at 00:01, Geoffrey Hutchison > wrote: > >> No matter how acid I set the pH aniline (pKa 4.6) is never protonated > > It's not a general model of pH-dependent protonat

Re: [Open Babel] add hydrogens appropriate for pH

Hi, Ok, I’ll have a look and see what I can contribute. Cheers, Chris > The (de)protonation rules are stored as a list of transformation using SMARTS > format in a file called /phmodel.txt/inside the /data/ directory. Such file > is editable but as Geoff suggested is not trivial to carefully en

Re: [Open Babel] add hydrogens appropriate for pH

Here are a few suggestions Changed #imidazole: note pKa=7.0 #if you uncomment this, also uncomment the seedcharge statement below #TRANSFORM [nD2:1]1c[nH]cc1 >> [n+:1]1c[nH]cc1 7.0 To include N-alkylimidazoles TRANSFORM [nD2:1]1c[nH,#6^3]cc1 >> [n+:1]1c[nH,#6^3]cc1

Re: [Open Babel] add hydrogens appropriate for pH

Hi, I’ve added a few more patterns and after some coaching from Matt added them to GitHub. One pattern I can’t get to work is an aniline, I’ve tried various permutations including #aniline TRANSFORM [N^3]c1c1 >> [N+:1]c1c1 4.6 Nc1c1 >>[ N+:1]c1c1

[Open Babel] Abbreviations and syperatoms

Cheers Chris Dr Chris Swain BA MA (Cantab) PhD CChem FRSC Macs in Chemistry sw...@mac.com http://www.macinchem.org -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDo

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

Might be useful? http://stackoverflow.com/questions/31561309/cmake-warnings-under-os-x-macosx-rpath-is-not-specified-for-the-following-targe Chris---

[Open Babel] Maximum size of files

I just tried to create a fastsearch index for a large file containing several million structures and I get this error. *** Open Babel Error in WriteChemObject The datafile must not be larger than 4GB Is there a limit in the number of structures that can be handled? Or would it be better to s

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

Hi, I’m not sure if clustering is implemented in Openbabel, there are other options. I’ve compared some here https://www.macinchem.org/reviews/clustering/clustering.php Cheers Chris > > > --

Re: [Open Babel] Conversion SMILES to XYZ (Volker Settels)

Hi Out of curiosity how are you planning to do the conformational search? Most tools I'm aware of would be expected to treat double bonds appropriately Chris > > Today's Topics: > > 1. Re: Conversion SMILES to XYZ (Volker Settels) > > > ---

[Open Babel] Bioconda

Hi, The bioconda channel is a Conda channel (https://bioconda.github.io/ ) providing bioinformatics related packages for Linux and Mac OS. Looking through the packages it is clear there it already contains a number of chemistry packages including Openbabel.

[Open Babel] Just FYI

Hi, Seasons greetings, just thought I’d let you know that iBabel has now been downloaded 2000 times https://www.macinchem.org/blog/files/e3f4babd10f41291d46a8ef1782839d4-2233.php Cheers, Chris

Re: [Open Babel] using Open Babel for virtual library generation

Hi, It depends on the transformations you want to undertake. I did a very quick library build about 20 years ago using SMILES strings. Just have dummy atoms with unique letters where you want to add functional groups then just do a text find and replace with the desired SMILES of the building b

[Open Babel] Augmented Reality

Hi, I was recently asked to help create an AppleScript droplet to automate creation of .obj and .mtl files using Jmol https://www.macinchem.org/applescript/generateARmodel.php Given the interest in augmented/virtual reality I was wond

Re: [Open Babel] Open Babel installation on Mac

Hi, Did you install OpenBabel first? iBabel is just a GUI. Chris > On 21 Dec 2018, at 21:39, openbabel-discuss-requ...@lists.sourceforge.net > wrote: > > Message: 2 > Date: Thu, 20 Dec 2018 23:33:52 -0500 > From: Zabdiel Alvarado Martinez mailto:zalva...@umd.edu>> > To: openbabel-disc...@list

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

Once implemented I’d be delighted to publicise it. One of the things I’ve been trying to do is encourage people to not reinvent the wheel and use existing cheminformatics libraries. https://www.macinchem.org/reviews/scientificsoftware/toolkits.php

Re: [Open Babel] Open babel selfstarts

Is it obabel or Obabel? One thought do you have a plugins or indexing agents that might be indexing any molecular files on your hard drive? Chris ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/

Re: [Open Babel] SMILES to PNG and then PNG to SMILES? (Fredrik Wallner)

I guess you have seen https://cactus.nci.nih.gov/osra/ Chris___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

[Open Babel] Openbabel join in Python

Using the command line it is possible to join (using -j) multiple input files into a single output file. Is it possible do this using Openbabel in a python jupyter notebook? Specifically I want to take as input a protein pdb file, and a small molecule as sdf input, then output a pdb containing

[Open Babel] Other ob tools

Hi, I’m working on an update to iBabel, and was hoping to clear out the tools tab particularly as I’m not sure if some are now supported with OpenBabel 3.0 Looking through the directory of openbabel tools that are installed we have obconformer equiv to obabel --conformer obdistgen (generate

Re: [Open Babel] Other ob tools

I've never used any of the others, and they are mostly untested. > > On Sat, 29 Feb 2020, 18:21 Chris Swain via OpenBabel-discuss, > <mailto:openbabel-discuss@lists.sourceforge.net>> wrote: > Hi, > > I’m working on an update to iBabel, and was hoping to clear out

Re: [Open Babel] Other ob tools

blem is that > people find it easier to add new executables, rather than spending a bit of > time figuring out how to add a plugin for obabel. > > Regards, > - Noel > > On Tue, 3 Mar 2020 at 07:52, Chris Swain <mailto:sw...@mac.com>> wrote: > Hi, > > It

[Open Babel] 2D or 3D

Hi, Is there a way to tell, using the command line, if a file contains a 2D or 3D structure? Cheers Chris ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] 2D or 3D

ugh wrote: > > What kind of file? > > Can you open it in a text editor and see if it contains geometric > coordinates? Or do you need an automated process? > > On Fri, Mar 6, 2020, 10:16 PM Chris Swain via OpenBabel-discuss > <mailto:openbabel-discuss@lists.sourcefo

[Open Babel] obspectrophore

One of the tools is to calculate spectrophores Described in details here. https://open-babel.readthedocs.io/en/latest/Fingerprints/spectrophore.html I’ve tried this and this gives the following output ID_02

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

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

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

> On Mon, Mar 16, 2020 at 12:40 PM Chris Swain <mailto:sw...@mac.com>> wrote: > Hi, > > As far as I can tell whilst it is possible to create the spectrophores in > open babel, that is all. It looks an interesting approach and it would be > useful to have a tool that d

[Open Babel] Filter options

Hi I’m looking at the —filter option and as I read the docs the available descriptors are and I’ve added, in brackets, a comment/question/guess about options for filtering based on the descriptors. Does anyone know if these are described in detail anywhere, otherwise I guess I’ll be spending a

[Open Babel] New release of iBabel

Hi, I’ve released an update to iBabel the Mac OSX GUI for OpenBabel. The announcement is here https://www.macinchem.org/blog/files/787e168c3da2597f0abb075706ffe98b-2605.php? And on Twitter here https://twitter.

Re: [Open Babel] [OpenBabel-Devel] If someone had time on their hands

Great idea Geoff, One thing that would be useful is better handling of fields within sdf files, I’d like to be able to convert an sdf to a tab delimited text file with the fields within the sdf as column headers, with the SMILES string as the first column. Cheers Chris > On 27 Mar 2020, at

Re: [Open Babel] [OpenBabel-Devel] If someone had time on their hands

In theory could work for any file format that had “tagged” information, XML, JSON etc. Cheers Chris > On 27 Mar 2020, at 13:22, Rudy Richardson wrote: > > Interesting idea, Chris. Perhaps the same thing could be done for Mol2 files. > > > > On Fri, Mar 27, 2020 at 9:

[Open Babel] 3D structure generation

Hi, I’m generating 3D structures, using -gen3D, from 2D structures in an sdf file containing >100,000 records. This works perfectly in the vast majority of cases, however there are a handful of molecules where the 3D coordination failed. In these cases the 2D structure is copied the output fil

[Open Babel] Shape-it

Hi, Has anyone used the slices-it tools with the latest version of OpenBabel? http://silicos-it.be.s3-website-eu-west-1.amazonaws.com/software/software.html Documentation mentions version 2.3 Cheers, Chris___

[Open Babel] Library not loaded

Hi, I’m sure I’ve seen mention of this error in the past but I can’t find it. An iBabel user has installed openbabel using home-brew on a Mac and they report this error Dyld: Library not loaded: Usr/local/opt/boost/lib/libbost_iostreams-mt.dylib Referenced from :/usr/local/bin/obabel Reason ima

[Open Babel] Apple silicon

Hi, The Mac users might find this of interest, I’ve started comparing my new MacBook Pro M1 max with my Intel machine. https://www.macinchem.org/reviews/MacBooks/m1macbookpromax.php Cheers Chris ___ OpenBabel-discuss mailing list OpenBabel-discuss@l

Re: [Open Babel] SDF to Structure Matrix

Hi, Might be worth looking at https://github.com/cbouy/mols2grid Chris > > Message: 1 > Date: Thu, 31 Mar 2022 15:24:57 -0400 > From: Rudy Richardson > To: babel > Subject: [Open Babel] SDF to Structure Matrix? > Message-ID: > > Content-Type: text/p

Re: [Open Babel] Iterate and convert .smi to multiple .png

Hi, Something like /Users/username/miniconda3/bin/obabel -ismiles '/Users/chrisswain/Desktop/SampleFiles/test.smiles' -opng-O '/Users/cusename/Desktop/SampleFiles/test'.png -m Seems to work for first structure but subsequent images seem broken? Cheers, Chris _