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
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
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
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
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 different
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
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 LNK2005:
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 http
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
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 it
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
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 software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation
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 H1A was not
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 that
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 based
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
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?
On 12/03/2013 11:28, Chris Swain wrote:
Message: 4
Date: Sun, 10 Mar 2013 21:02:41 +
From: Chris Morley c.mor...@gaseq.co.uk mailto:c.mor...@gaseq.co.uk
Subject: Re: [Open Babel] obabel and fingerprints
To: openbabel-discuss@lists.sourceforge.net
mailto:openbabel-discuss
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
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
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: Chris Morley c.mor...@gaseq.co.uk mailto:c.mor
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 the sdf
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 environment
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
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
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
On 17/12/2012 20:38, Geoffrey Hutchison wrote:
On Dec 17, 2012, at 2:52 PM, Kirk Simmons kirkasimm...@gmail.com 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
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.Convert();
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 to
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
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 reply. I was
November 2012 14:53, Chris Morley c.mor...@gaseq.co.uk
mailto:c.mor...@gaseq.co.uk wrote:
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
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 c.mor...@gaseq.co.uk
mailto:c.mor...@gaseq.co.uk wrote:
Scott
Your correct smiles
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 is
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
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 in the
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)[H])N([H])[H]
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
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
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
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 for
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 substring color 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
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 line
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 file
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 that the
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 can
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 nan
1
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
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 will do
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
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:
==
*** Open
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:
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 in one
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) ?
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 (and
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?
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
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 error
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_25000.fs
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 )
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.
On 09/12/2011 19:44, Noel O'Boyle wrote:
Or more succintly, with obabel 2.3.1 I have:
C:\Users\Noelobabel -:[Al]C#N -oinchi -xK -xX Recmet
==
*** Open Babel Warning in InChI code
#1 :Metal was disconnected
♥
1 molecule converted
...which is rather sweet,
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
-sB(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:
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
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
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 7
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
babel
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
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
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 all
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 Morleyc.mor...@gaseq.co.uk
wrote:
On 19/09/2011 09:32, Martin Guetlein wrote:
Hi,
I would like to do smarts matching
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 could use
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)
OB now
On 09/08/2011 17:08, pmaietta wrote:
I guess this is one of the most stupid question for an advanced user,
but I would like to know how to convert
an InChI to an InChI key. I read the help for the inchi format, but it's
not clear to me how to pass options to the program.
I'm using babel 2.2.3
On 05/08/2011 23:43, Andrew Dalke wrote:
I can't find this mentioned in the documentation so I thought I would
post it here in case others come across it in the future. Or so that
people can correct my misunderstanding.
OpenBabel plugin code seems to have changed with 2.3 . If I want
to
On 30/06/2011 01:23, A. Heifets wrote:
When I use FastSearch, the numbers added by addinindex seem to always
start from 1, unlike searching the original SDF. Am I doing it wrong?
$ obabel -isdf ./small_db.sdf -osmi --addoutindex --addinindex -sn1c1
On 27/05/2011 22:58, A. Heifets wrote:
I'm trying to follow http://openbabel.org/wiki/Tutorial:Fingerprints
and obabel -H fs on my data but I have some strange digressions from
the tutorial.
First, I'm not convinced that the index was built correctly (although
there were no error messages to
On 09/05/2011 10:19, Noel O'Boyle wrote:
I was going to say that this has been fixed in the development
version, but the dev version doesn't appear to have any stereobonds.
Any idea what's going on here Chris?
In the dev code you have to explicitly ask for wedges and hashes to be
generated
On 12/04/2011 17:58, carlos ortega wrote:
Greetings,
I try to use babel to convert a multifile SDF to several files MOL2,
I use this line:
babel -isdf *.sdf -omol2 *.mol2 -m
But the conversion put other name for the giles MOL2, and the file SDF has the
name for each file MOL2.
How I do
On 12/04/2011 20:00, carlos ortega wrote:
Greetings,
I used the line
babel *.sdf .mol2 -m
But, does not work.
It put one file mol2 and the name is the same for the file SDF.
Sorry, I misunderstood what you were doing. Use
babel mymultifile.sdf out.mol2 -m
which will produce
On 12/04/2011 20:31, carlos ortega wrote:
Thank you,
this line work fine.
But, is not possible put the name for each molecule that appear in the sdf
file?
I have about one million of molecules in the sdf file,
each one have its name in the sdf file, and is some tedious search one name
On 11/04/2011 09:20, Noel O'Boyle wrote:
I have the same on Win7. It looks like obenergy has suffered bit rot.
We have been trying to replace these executables with equivalent
options to obabel. See the section in the OB docs about adding a new
op (operation).
There already is an op --energy
On 05/04/2011 16:54, ariste...@cbm.uam.es wrote:
Hello, i'm unable to add a formula in a .sdf file with 2.3.0, is this
option broken with the new Open Babel release?
To add to the title, use
--append formula
To as a property, use
--add formula.
The parameter on --append and --add can be a
On 31/03/2011 08:44, Balaji Ramachandran wrote:
Dear sir/madam,
I am Balaji R currently working in Computational biology. I have a query
about OpenBabel version 2.3.0. windows version. Is there any way i can
convert Multiple files into other format files. It would be very kind of you
if you
On 16/03/2011 17:41, nms_uk wrote:
Dear all,
I'm using openbabel to compare 2 molfiles. It tells me that the 2 molfiles
has different sp3 stereochemistry.
When I display the molfiles, they look exactly the same.
I have 2 questions:
1- Can 2 molecules with different sp3 stereochemistry be similar
On 25/02/2011 13:30, Santi Villalba wrote:
A molecule created from a smiles string lacks explicit hydrogen
information, while hydrogens are there when reading from the pubchem
file. Explicit hydrogens are used when computing the fingerprints, and
so the substructures found differ in both
On 07/02/2011 12:05, Andrew Dalke wrote:
Can someone help me understand what's wrong with my searches?
% babel Compound_09425001_0945.sdf.fs results.sdf '-sN#Cc1c1C#N'
-at0.6
Segmentation fault
This is all with a version of Babel I compiled from version control (since I
want the
On 01/02/2011 07:12, Andrew Dalke wrote:
On Jan 31, 2011, at 8:15 PM, chakravar...@ncbs.res.in wrote:
I noticed that molecules such as Myristic acid and Palmitic acid have same
similarity score of 1,
...
I am thinking of modifying Tanimoto score to other coefficient's like
Kulczynski
On 26/01/2011 01:16, Craig A. James wrote:
On 1/25/11 3:33 PM, Andrew Dalke wrote:
On Jan 25, 2011, at 4:01 PM, Pascal Muller wrote:
Using pybel, I would like to generate a smarts with explicit H before
doing a substructure search.
...
scaffoldSmiles = mol.write(can)
scaffoldSmarts =
On 25/01/2011 02:47, chakravar...@ncbs.res.in wrote:
Dear Chris Morley,
I tried your technique of holding ctrl to input more than one file. It helps,
but,
I did not get desired output.
Here is my input and output.
Input
When there are only a small number of molecules, fpt format will give
you what you want; you are nearly there.
In the GUI, select sdf for the input format and ftp for the output.
Open the sdf file with the pattern molecule, then open the sdf file with
all the other molecules you want to
Dan
You can look for an exact match in a large dataset using fastsearch format.
Index the data file (which must not be compressed):
obabel datset.xxx -ofs
Do an exact structure search:
obabel dataset.fs -O out.yyy -s SMILES exact
where the SMARTS string can be replaced by a
On 13/01/2011 12:39, NGUYEN Thanh Binh wrote:
I have taken the database with SMILES from DIPPR. Now i want to use
C++ in order to read these structures SMILES and give me the result
with the number of the functions within it.
For example : i have a SMILES C=CCC. It means that we have a
kl. 15.29 skrev Chris Morley:
On 15/11/2010 12:17, Fredrik Wallner wrote:
Hi all!
I'm having some problems with SMART matching...
# This is the query I would like to have worked, without modifications
on either molecule or SMARTS
$ echo OCCOc1c1C=C1C(=O)NC(=S)NC1=O | obabel -ismi -ocan
On 15/11/2010 21:58, Noel O'Boyle wrote:
Hi Chris,
I think that right now it's not possible. The ability to access a
molecule's number would also be useful for filtering too.
On 15 November 2010 20:57, christophersw...@btconnect.com
christophersw...@btconnect.com wrote:
I have sdf that
On 15/11/2010 12:17, Fredrik Wallner wrote:
Hi all!
I'm having some problems with SMART matching...
# This is the query I would like to have worked, without modifications
on either molecule or SMARTS
$ echo OCCOc1c1C=C1C(=O)NC(=S)NC1=O | obabel -ismi -ocan
On 12/11/2010 17:57, JP wrote:
Hi there @OpenBabel,
A Friday evening tedious problem.
Can anyone tell me why the following mol file
LACMAD
ChemPy3D 0
31 32 0 0 1 0 0 0 0 0999 V2000
0.5638 11.85826.3019 N 0 0 0 0 0 0
On 09/11/2010 13:53, Andrew Dalke wrote:
I am willing to write documentation about this, about the list
of available plugins, the MACCS fingerprints, and how to handle
new fingerprint plugins.
Great!
I am also willing to write tests which cover these.
Even better!
I'll try to output the
On 08/11/2010 15:11, Andrew Dalke wrote:
In C++
std::string OBPlugin::ListAsString
(const char* PluginID, const char* param=NULL);
gives similar functionality, but I don't know whether it is exposed in
Python.
It seems I'm doing wrong. I can't find where the code uses
On 15/10/2010 10:13, Jean-Paul Ebejer wrote:
Hi there,
I am using Openbabel 2.2.3 (on Ubuntu) and get a dreaded segmentation
fault:
x...@yyy:~/test/1hvy$ obfit
1 - 100 of 119 matches
Mail list logo
