Hi,
I can't reproduce this. The order of fragments should be canonical (the
algorithm takes this into account). What is the original source of the
OBMol that gives a different result?
For example, the following SMILES all convert to the same canonical form:
ClCCl.O.[Cl-]
O.ClCCl.[Cl-]
O.[Cl-].Cl
Hi,
This patch [1] can be used to specify a timeout. The example molecule takes
60 seconds on my computer.
[1]
https://github.com/timvdm/openbabel/commit/117b2e510c3c174e08d4e5dee71314e69ba126ea
Tim
On Tue, Feb 21, 2017 at 3:33 PM, Noel O'Boyle wrote:
> Your structure is messed up (multiple
Hi,
Unfortunatly this is not possible out-of-the-box.
The SMILES format uses the default timeout (5 seconds) for calculating the
canonical code (specified in include/openbabel/canon.h). Changing the call
in src/formats/smilesformat.cpp from
CanonicalLabels(&mol, symmetry_classes, canonical_order
Hi,
It looks like it can't find the template ring templates. You can set the
BABEL_DATADIR environment variable to fix this. This should result in
better coordinates.
Tim
On Feb 26, 2016 14:22, "Moshe Ben-zion" wrote:
> I would greatly appreciate some help with my problem.
>
> I am not a linux
Hi,
OBMol::GetGIVector considers the following properties:
* graph theoretical distance
* heavy valence
* aromaticity
* ring membership (boolean)
* atomic number
* implicit valence
OBGraphSymPrivate::GetGIVector considers two additional properties:
* heavy bond sum (see graphsym.cpp, I think No
Hi,
I assume you have canonical SMILES strings in glass.sdf stored as titles or
properties. Correct me if this is incorrect. If so, it depends on what
program was used to create these canonical SMILES strings. If you used
openbabel for this, you can convert the molecules in result.smi to
openbabel
) functions: These are getter functions
following the convention used in Qt and many other projects. It might be a
good idea to briefly clarify this on the quick reference card though.
Thanks for the feedback.
Tim
Che
/helium-manual
* Quick reference card:
http://moldb.net/Helium%200.2%20Quick%20Reference%20Card.pdf
* Performance enhancements: relevant cycles, canonicalization, ...
*New features: 2D depictions, aromaticity, ...
* Experimental windows binary python module for python 2.7
Kind regards,
Tim
Hi,
FYI, Helium support this by default. For example, the following python
script illustrates this:
from helium import *
SMILES = Smiles()
mol1 = Molecule()
if not SMILES.read('[NH3][CH2][C](=O)=O', mol1):
print SMILES.error()
exit()
mol2 = Molecule()
if not SMILES.read('[NH3][CH2]C(=O
Hi,
I'd like to announce the first release of Helium, a lightweight informatics
toolkit. This first release is far from a complete toolkit, especially
compared to OpenBabel. However, the aim of this first release is to let
people know about the project and get some initial feedback. The main page
Hi,
While testing the changes to correctly canonicalize multi-fragment SMILES,
I noticed the same problem and it seems to only occur for multi-fragment
molecules. I reported this on the openbabel-devel mailing list with title "More
multi-fragment canonical SMILES tests". I'm not sure where things
tch on a few million molecules and
compare the results to get a better view (with more confidence) of what
would actually change.
Tim
On Mon, Feb 17, 2014 at 6:41 PM, Tim Vandermeersch <
tim.vandermeer...@gmail.com> wrote:
> Hi,
>
> Are there any examples of disconnected SMILES that hav
Hi,
Are there any examples of disconnected SMILES that have this problem? IIRC,
a canonical code is created for each fragment individually and these are
later sorted to create the entire canonical order. A quick look at the code
confirms this but I'll try to test some cases tonight to see if this
Yes, this is due to the fact that SWIG doesn't expose nested classes. I've
fixed this for python so this should hopefully also be possible for java.
On Thu, Dec 5, 2013 at 10:15 PM, Yoel wrote:
> Thanks Noel
>
> On 5 December 2013 16:12, Noel O'Boyle wrote:
> > ...and in relation to this, I've
The ability to determine CIP rules is a nice feature to have but not really
necessary for most cheminformatics applications. If someone donates this
code it would certainly be considered a valuable addition. I rewrote most
of the sterochemistry code for OB a few years ago and never got around to
im
Hi,
IIRC, I got the same error (i.e. tr1/memory header not found) once when I
tried to compile with the c++11 standard. Does clang use c++11 as default
standard on OSX10.9?
Tim
On Thu, Oct 31, 2013 at 4:18 PM, Hans De Winter wrote:
> Geoff,
>
> even the master gives me the same issue:
>
> Her
Hi,
On Tue, Jul 23, 2013 at 12:07 AM, Noel O'Boyle wrote:
> My own 2c is that we should remove the randomness. I think it's the
> wrong solution to the problem, and sweeps the problem under the
> carpet. There should be no need for it.
IIRC, the randomness comes from the need to to have a vect
rally cleaner code. That is,
> molecule["atoms"]["C1"]["location"] is easier to understand than
> molecule["elements"]["coords"]["3d"][0]. In that regard, I completely
> agree with him.
>
> While i somewhat agree with Dim
On Thu, Jun 6, 2013 at 10:50 PM, Dimitri Maziuk wrote:
> On 06/06/2013 03:13 PM, Tim Vandermeersch wrote:
> > Hi,
> >
> > The OpenChemsitry project also uses JSON (
> > http://wiki.openchemistry.org/Chemical_JSON).
>
> Not criticizing your effort, specifically,
Hi,
The OpenChemsitry project also uses JSON (
http://wiki.openchemistry.org/Chemical_JSON). I'm also using json for a
project I'm working on although I don't use it yet to store molecules. If a
consensus could be reached it might be a valuable format to work with on
the web.
Tim
On Thu, Jun 6,
Hi,
The reason for canonicalizing the fragments seperatly is to determine their
position in the smiles. It was not intended to be used as your example
illustrates. However, I think the canonical codes should be the same. It
might be the case that the smiles format does something that causes a
diff
Hi,
The FP2 fingerprint is a path-based hashed fingerprint. First, all paths
(i.e. no branches) up to 7 atoms in the molecule are enumerated. A
canonical value for each path is then computed (this is an integer value).
Finally these values are hashed using a prime number (1021 for the 1024 bit
FP2
Hi,
On Wed, Oct 17, 2012 at 12:57 PM, Reinis Danne wrote:
> On Wed, Oct 17, 2012 at 11:04:55AM +0200, Fredrik Wallner wrote:
>> If you build up the molecule from within OpenBabel, chances
>> are that that molecule will be possible to describe as a
>> SMILES string which is valid SMARTS.
>
> This,
Hi,
On Tue, Oct 16, 2012 at 7:05 PM, J Birch wrote:
> Is there any know SMART output format for Open Babel? If not Open Babel, and
> other chemistry development kit?
OpenBabel does not currently support this. The main reason for this is
that OB currently does not manipulate read SMARTS express
Hi,
On Tue, Oct 16, 2012 at 7:41 PM, J Birch wrote:
> Is there an algorithm that will fragment a molecule finding all 'fragments',
> not 'paths' in the given molecule within a certain size, say 3-7? I am not
> sure if Fingerprinting does this.
Subgraph enumeration algorithms do this. See Andr
On Wed, Aug 29, 2012 at 4:55 PM, 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 is also: http://ope
Hi Igor,
On Mon, Aug 27, 2012 at 11:17 PM, Igor Filippov
wrote:
> I'd like to pitch in about the changes in aromaticity perception - it
> looks like the more recent version of OB (2.3.1) is not recognizing one
> of the rings in the attached image as aromatic. I set atomic numbers for
> Z and D to
Hi,
On Tue, Aug 21, 2012 at 9:38 AM, Alejandro Speck Planche
wrote:
> Dear colleagues
> My name is Alejandro. I've been using it several times OpenBabel program
> (version 2.3.1) for conversion to multiple molecular formats. Right now I'm
> particularly interested in how to print the atoms and /
On Mon, Aug 20, 2012 at 4:12 PM, Tim Vandermeersch
wrote:
> On Mon, Aug 20, 2012 at 4:08 PM, Tim Vandermeersch
> wrote:
>> On Mon, Aug 20, 2012 at 3:18 PM, Igor Filippov
>> wrote:
>>> Noel,
>>>
>>> Thank you - could you give just a few lines example
On Mon, Aug 20, 2012 at 4:08 PM, Tim Vandermeersch
wrote:
> On Mon, Aug 20, 2012 at 3:18 PM, Igor Filippov
> wrote:
>> Noel,
>>
>> Thank you - could you give just a few lines example how to do this?
>> I looked at the suggested header file and I'm still stump
On Mon, Aug 20, 2012 at 3:18 PM, Igor Filippov
wrote:
> Noel,
>
> Thank you - could you give just a few lines example how to do this?
> I looked at the suggested header file and I'm still stumped :(
The code to set an atom's tetrahedral stereochemistry to unknown goes
something like this:
#inclu
HI,
On Thu, Aug 9, 2012 at 12:01 AM, Jeff Janes wrote:
> On Wed, Aug 8, 2012 at 5:49 AM, Noel O'Boyle wrote:
>> I fixed the Eigen2 problem with a cast. Hopefully it still works for Eigen3.
>
> I've verified revision 4976 against Eigen2
>
> but against Eigen 3 it now fails with:
>
> [ 82%] Buildi
Hi,
On Wed, Aug 8, 2012 at 10:32 AM, Noel O'Boyle wrote:
> On 6 August 2012 19:14, Tim Vandermeersch wrote:
>> Hi,
>>
>> On Mon, Aug 6, 2012 at 12:24 PM, Noel O'Boyle wrote:
>>> Even more unforunately, it's not possible to access most of the stereo
Hi,
On Mon, Aug 6, 2012 at 12:24 PM, Noel O'Boyle wrote:
> Even more unforunately, it's not possible to access most of the stereo
> functionality from anything but C++. This is due to the use of nested
> classes for the stereo config, which we realised after-the-fact is not
> supported by SWIG. I
Hi,
On Tue, Jul 31, 2012 at 11:50 PM, Igor Filippov [Contr]
wrote:
> Answering my own email - it seems if I surround lines 303 and 304 in
> tools/obabel.cpp with:
>
> #if defined(USING_DYNAMIC_LIBS)
> ...
> #endif
>
> I will get everything compiling nicely in MinGW.
> Would it be possible to com
Hi,
On Tue, Jul 31, 2012 at 7:22 PM, Alessandro Nascimento
wrote:
> Hi OB folks,
> I am brand new to OpenBabel and I`m trying to learn how to use the
> conformerSearch in OB. However, I am finding some odd results and
> would like to hear from you about hints on how to generate multiple
> conform
vector conformers;
> rotamers.ExpandConformerList(mol,
> conformers);//mol.GetConformers());
> mol.SetConformers(conformers);
>
> cout << mol.NumConformers() << endl;
>
> What am I doing wrong?
>
> Thanks
>
>
> On Wed, Jul 25,
Hi,
Based on src/conformer.cpp:
OBMol mol; // read a molecule...
OBRototList rotorList
rotorList.Setup(mol);
if (!rotorList.Size()) { // only one conformer
return;
}
// create some random rotor keys
RotorKey rotorKey(rotorList.Size() + 1, 0); // indexed from 1
On Thu, Jul 12, 2012 at 6:40 PM, Chris Swain wrote:
> 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?
I'm currently working on improving the algorithm for fastsearch like
operat
Hi,
On Thu, Jun 28, 2012 at 11:25 PM, Jeff Janes wrote:
> >From page 35 of the pdf docs for 2.3.1, it has:
> =
> The parameter of the -s option in these examples is actually SMARTS,
> which allows a richer matching specification,
> if required. It does mean that the aromaticity of atoms and b
On Wed, Jun 20, 2012 at 12:03 PM, Noel O'Boyle wrote:
run two instances of OBForceFieldMMFF94 are being created. I would
like
to understand why is that, because I thought only one was necessary
and
therefore I am confused about this.
>>>
>>> I don't know. You'd need to run
Hi,
The problem is that all vdw and electrostatic pairs are precomputed in
the current implementation. Setting cut-off values doesn't change
this. To make the OB force fields work with large amounts of atoms,
the non-bonded pairs should be detected dynamically.
Tim
On Wed, May 16, 2012 at 6:17 P
Hi,
On Thu, Mar 8, 2012 at 9:30 PM, Fouad Ballout wrote:
> Hi there,
>
> I have problems with generating conformers for a particular molecule using
> openbabel. Following the openbabel documentation I've used the following
> command line
>
> obabel input.xyz -O output.xyz --conformer --systematic
Hi,
On Tue, Feb 21, 2012 at 8:01 AM, Steffen Neumann wrote:
> Hi,
>
> I haven't looked at the patch in detail,
> nor do I have any say in the OpenBabel steering,
> nor any idea of the OpenBabel code philosophy,
> so this is just my 2c:
>
> On Mon, 2012-02-20 at 20:53 +0100, Paolo Tosco wrote:
> .
Hi,
On Mon, Feb 20, 2012 at 8:08 PM, andi wrote:
> Hi all,
> I have two structures and when I perform OBIsomorphismMapper I get some
> unexpected results, and I wanted to double check my interpretation.
>
> When i do OBIsomorphismMapper on the two molecules( see images below), i
> expect the m
Hi,
On Sat, Nov 26, 2011 at 8:14 PM, Eric Jang wrote:
> Hello,
> I am trying to port the GAFF force field from data/gaff.dat and
> data/gaff.prm to be read by another program (TINKER). However the parameter
> file of GAFF looks quite different than from MMFF94 or any of the other
> force fields.
Hi,
On Sun, Nov 20, 2011 at 11:59 PM, Kirk Simmons wrote:
>
>> I am trying to search a fast search indexed database and getting an Open
>> Babel error "Cannot read the SMILES string". My input smiles is:
>> NC(=O)C(c1a1)c2a2. Does someone see an issue here?
This is not a valid smiles
Hi,
On Tue, Aug 2, 2011 at 10:47 PM, Noel O'Boyle wrote:
> On 2 August 2011 14:08, Pascal Muller wrote:
>> Hi,
>>
> I would to know the number of bonds between two atoms within a molecule
> (i.e. the shortest path).
>>
You're looking for a breadth-first search (BFS)
You just n
Hi,
On Mon, Jun 27, 2011 at 4:03 PM, Marianne wrote:
> Hello
>
> I am new to using the openbabel API and really exciting to use OB. I have an
> existing C++ program in MSVC2008, I would like to use some of the functions
> in Openbabel (Isomorphism).
>
> I followed the instructions on the website
On Wed, Mar 23, 2011 at 9:06 PM, andi wrote:
> Ahh I see. So to make sure I understand this correctly, the number of bits
> masked, is the number of atoms for possible consideration for the matching.
The mask determines which atoms are to be part of the query. An empty
mask means all atoms are pa
On Wed, Mar 23, 2011 at 7:15 PM, andi wrote:
> I have two molecules, ethane and pentane. Whenever I query ethane onto
> pentane, it works, but not the other way around, even when I specify the
> masking bit to 2.
>
> OBQuery* query = QueryAtom::CompileMoleculeQuery(pentane,2);
This doesn't work b
Hi,
On Sun, Mar 20, 2011 at 12:30 AM, andi wrote:
> I guess i spoke too soon. For some reason it cannot find the object from
> where I'm calling it from. It says
>
>
>
> "QueryAtom::QueryAtom()", referenced from:
> Molecules::loadFPMoleculesWithContentsOfFile(char const*)
> in Molecule.o
> ld: sy
Hi,
On Sat, Mar 19, 2011 at 10:47 PM, andi wrote:
> I see, I'm pretty close to getting it to work, but I'm having a little
> trouble with the CompileMoleculeQuery as I'm still learning C++.
>
> Instead of inserting code, i've inserted a screenshot, this way it's much
> readable...
You also need
Hi,
On Sat, Mar 19, 2011 at 4:33 PM, andi wrote:
> Hey everyone, I'm having this issue that whenever I try and do isomorphism
> between two structures such as cyclo-pentane and pentane, or benzene ring
> and hexane it gives a match between the two structures. From a graph point
> of view, they wo
On Mon, Jan 31, 2011 at 10:28 AM, SALDANA MIRANDA Diego
wrote:
> Hi,
>
> I would like to know if there is an article or a page explaining the
> conversion to canonical SMILES in detail, I would like to reference it in an
> article.
There is no paper describing the algorithm in detail (yet). Howev
Hi,
On Wed, Dec 15, 2010 at 3:58 AM, Gert Thijs wrote:
> Hello,
>
> I am encountering some unexpected results with OBPairTemplate. I am
> trying to add a double value to a molecule and write in an SD file. To
> do this, I am using the OBPairTemplate class instead of the
> OBGenericData, such that
On Thu, Oct 21, 2010 at 1:35 AM, Tim Vandermeersch
wrote:
> On Wed, Oct 20, 2010 at 4:29 PM, Igor Filippov [Contr]
> wrote:
>> Tim,
>>
>>> I'll take a look since it is an important format to support. This
>>> should be the last major issue for static bui
On Wed, Oct 20, 2010 at 4:29 PM, Igor Filippov [Contr]
wrote:
> Tim,
>
>> I'll take a look since it is an important format to support. This
>> should be the last major issue for static building though.
>>
>
> Great - thank you! Could the static_plugins.o be also compiled into
> libopenbabel.a by d
On Tue, Oct 19, 2010 at 5:28 PM, Igor Filippov [Contr]
wrote:
>
>>
>> static_plugins.cpp only contains a few formats since including all
>> formats in a single cpp file can take a long time/memory to compile.
> True, but piece-meal inclusion with flags such as WITH_COMMON_FORMATS seems a
> very r
you have a static inchi library, you should be able to
include the inchi OB formats and link against it.
> Igor
>
>
>
>
> On Mon, 2010-10-18 at 16:09 -0400, Tim Vandermeersch wrote:
>> On Mon, Oct 18, 2010 at 9:49 PM, Igor Filippov [Contr]
>> wrote:
>> > Tim,
> 27% tests passed, 41 tests failed out of 56
>
> Far cry from 100% "PASS" on dynamically linked babel.
No, the tests don't work for static builds yet. Only the babel
executable with all plugins.
> Igor
>
> On Mon, 2010-10-18 at 14:59 -0400, Tim Vandermeersch wro
taticCMakeFiles/myexe.dir/myexe.cpp.o -o myexe -rdynamic
/usr/local/lib/libopenbabel.so.4.0.0 -lm -ldl -lz -Wl,-Bstatic
-Wl,-rpath,/usr/local/lib:
> Igor
>
>
> On Sat, 2010-10-16 at 10:23 -0400, Tim Vandermeersch wrote:
>> On Fri, Oct 15, 2010 at 11:40 PM, Igor Filippov [Contr]
On Fri, Oct 15, 2010 at 11:40 PM, Igor Filippov [Contr]
wrote:
> It builds nicely on Fedora 12, x64 system.
> Some points:
>
> 1) When building with -DBUILD_SHARED=no one needs to make sure static
> zlib exists somewhere (libz.a) otherwise the error message which cmake
> gives is somewhat confusin
Hi,
On Mon, Oct 4, 2010 at 4:59 PM, Geoffrey Hutchison
wrote:
>> For Murcko framework generation using pybel, I would like to reset the
>> stereochemistry. Even after hydrogen deletion, the E/Z stereochemistry
>> is conserved. Is there any way to reset the stereo?
>
> Well, if you're using Python
On Sun, Sep 26, 2010 at 7:22 PM, Steffen Neumann wrote:
> Hi,
>
> I tried to investigate this, but my C++ is quite rusty,
> so unless somebody else is on this SMARTS problem,
> could anyone point me what to look for ?
The problem seems to be the explicit closure bond at the end of the
SMARTS. The
2010/9/24 Dmitry Osolodkin :
> On 09/24/2010 04:08 PM, Tim Vandermeersch wrote:
>>>> babel --canonical somefile.mol2 somefile_can.mol2
>>>
>>> It doesn't work. Atom order remains the same as in input files. Using
>>> the latest development version or
2010/9/24 Dmitry Osolodkin :
> Hi Tim,
>
> On 09/24/2010 02:20 PM, Tim Vandermeersch wrote:
>> If you are willing to try the development version, you can
>> canonicalize the atom order for any format using:
>>
>> babel --canonical somefile.mol2 somefile_can.mol
Hi,
2010/9/23 Dmitry Osolodkin :
> Hello OpenBabel developers and users,
>
> probably you could help me with a simple problem. I have two molecules
> (attached) to compute all-atom RMSD between them; they are same at all
> except the position in the space (docking result and a cocrystal
> structur
On Mon, Aug 23, 2010 at 6:37 PM, Igor Filippov
wrote:
> This created a static library libopenbabel.a but it looks like the
> modules for different formats are still dynamic - i.e. smilesformat.so.
>
> My use of "--disable-dynamic-modules" was to compile all the different
> file formats into a sing
On Mon, Aug 23, 2010 at 6:06 PM, Geoffrey Hutchison
wrote:
>> What is the equivalent of the option "--disable-dynamic-modules" in
>> configure script for cmake?
>
> cmake [...] -DBUILD_SHARED=OFF
This alone doesn't do very much.
I recently made some changes to the build system to get static
com
On Tue, Aug 17, 2010 at 1:16 PM, Eiso AB wrote:
>
> hi,
>
> I'm looking for some convenient standard atom naming scheme that I
> could use for assigning (1H) NMR resonances on a large set of compounds.
>
> Preferably, atoms that are topologically similar and/or are chemically
> and or magnetically
gt;> > R4
>> > A 11
>> > R3
>> > A 14
>> > R2
>> > A 16
>> > R1
>> >
>> > Corrected -
>> >
>> > A 8
>> > R5
>> > A 10
>> > R4
>> > A 11
>>
On Fri, Jul 23, 2010 at 8:56 PM, TJ O'Donnell wrote:
> I've successfully compiled the cpp code and built the .so's using
> the current subversion source, but ran into a problem making the
> python bindings. The error (python setup.py build in
> openbabel/scripts/python)
> is that openbabel.py is
On Mon, Jul 12, 2010 at 6:30 PM, Igor Filippov
wrote:
> Is there any way to set atomic labels in openbabel to non-existent
> elements - i.e. X, Y, R1, R2, R3... ?
>
> So far I see only SetAtomicNum to specify atom type, but nothing to set
> the atomic label to something like "R1".
You can use Ali
On Thu, Jul 8, 2010 at 10:13 AM, Noel O'Boyle wrote:
> On 8 July 2010 08:08, Hans De Winter wrote:
>>> On Wed, Jul 7, 2010 at 6:54 PM, Geoffrey Hutchison
>>> wrote:
>
> isomorph code (identity checking), so in the meanwhile we would have
> to specify a convention such as all molecule
s welcome.
Tim
> -seth
>
>
> On Tue, Apr 20, 2010 at 5:06 PM, Tim Vandermeersch
> wrote:
>> Hi,
>>
>> Here is my own attempt at an openbabel webservice:
>> http://openbabel.selfip.org/ It runs on some spare hardware here at
>> home so I don't
On Wed, Jul 7, 2010 at 6:54 PM, Geoffrey Hutchison
wrote:
>> isomorph code (identity checking), so in the meanwhile we would have
>> to specify a convention such as all molecules with the same title are
>> the same.
>
> I've been thinking about this for a while. The easiest detection is that:
> a)
or
bonds explicitly.
C1-C2-C3-C4-C5-C6-C7-C8
Suggestions?
Tim
> You guys rock.
>
> Cheers,
> Chris.
>
> On Wed, Jun 30, 2010 at 9:14 AM, Tim Vandermeersch
> wrote:
>> On Wed, Jun 30, 2010 at 6:05 AM, Geoffrey Hutchison
>> wrote:
>>>> I edited "sr
On Wed, Jun 30, 2010 at 6:05 AM, Geoffrey Hutchison
wrote:
>> I edited "src/forcefield.cpp", adding this line:
>> rl.SetFixAtoms(_constraints.GetFixedBitVec());
>
> Well, that's not quite kosher, since the constraints will return a temporary
> variable, and SetFixAtoms wants a reference. It's e
Hi,
On Tue, Jun 8, 2010 at 7:11 PM, Graham Ball wrote:
> Hi Folks,
>
>
>
> A quick question – is there any way to freeze atoms during a minimization or
> conformation search e.g., obconformer routine?
Yes, for minimization this is possible. I don't think it is currently
possible for the conforme
On Tue, Jun 8, 2010 at 12:06 AM, Rob Soe wrote:
> Hi,
> Thanks a lot for the suggestions.
>
> I have this plan that I am trying to work out. I am planning to use
> OBSetData() and use SetAttribute() to set a string (converted from a float
> number that I want to associate the molecule with).
>
> H
On Wed, May 12, 2010 at 5:23 PM, macc_200 wrote:
> Hi,
> I have installed openbabel 2.2.3 on an ubuntu 10.04 machine via the apt
> installer but I am having problems substructure searching an indexed
> database viz:
> > babel VS_Library_full.fs -ifs -s'N#Cc1c(Cl)1' results.smi
> =
Hi,
Here is my own attempt at an openbabel webservice:
http://openbabel.selfip.org/ It runs on some spare hardware here at
home so I don't know how the performance will be. It's not meant as a
complete API yet since there are only 3 apps but the main page has
instructions for contributors... :-)
On Tue, Apr 13, 2010 at 5:27 PM, Noel O'Boyle wrote:
> On 13 April 2010 13:02, Christian Meisenbichler
> wrote:
>> Is someone interested in creating an openbabel web service?
>
> It sounds like you are! :-)
>
> But seriously, it's a great idea. I've never gotten around to doing it
> myself, but w
Hi,
On Tue, Apr 13, 2010 at 2:02 PM, Christian Meisenbichler
wrote:
> Is someone interested in creating an openbabel web service?
>
> Let me explain what I mean by that. I Just recently got convinced by
> the idea of software as a service and the practical elegance of
> knitting together various
On Tue, Mar 30, 2010 at 11:10 PM, Ning Shen wrote:
> Hi, I am using swig wrapper of [openbabel][1](written in C++, and supply a
> python wrapper through swig)
>
> Below i just use it to read a molecule structure file and get the unitcell
> property of it.
> import pybel
> for molecule in pybel.rea
3D -ismi
>> > prop.smi
>> > > -osdf prop.sdf
>> > >
>> > > babel: cannot read input format!
>> > > Open Babel 2.2.0 -- Jul 17 2008 -- 11:53:19
>> > > Usage: babel [-i] [-o]
>> > > Try -H option for more information.
>
of OB installed?
Does "/usr/bin/babel -H" produce the same results as "/usr/local/bin/babel -H"?
Does /usr/local/bin versus /usr/bin have the same priority for user &
root? (i.e. are they in the same order in PATH env. var.)
> Best regards.
>
> El mar, 23-03-2010 a l
Hi,
On Tue, Mar 23, 2010 at 7:29 PM, David García Aristegui
wrote:
> Hello, i have a strange problem with non-root users and OpenBabel, and
> tested with two different versions of the program:
>
> Open Babel 2.2.3 -- Jan 18 2010
> Open Babel 2.2.0 -- Jul 17 2008
>
> OB is installed in a PC with U
Hi,
On Wed, Feb 17, 2010 at 4:08 PM, sam moors wrote:
> Hi,
>
> I'm trying to compile the example code on this page:
>
> http://openbabel.org/wiki/Developer:Cpp_Tutorial
>
> but I get errors during compilation with this command (the header files
> are installed in /home/sam/progs/openbabel-2.2.3/
On Tue, Nov 10, 2009 at 4:21 PM, Tim Vandermeersch
wrote:
> On Fri, Nov 6, 2009 at 11:43 PM, Rob Soe wrote:
>> Hi all,
>>
>> I have been reading quite a lot for this MSVCR80.dll error and here is what
>> I found at:
>>
>> http://www.instant-registry-fixes
On Fri, Nov 6, 2009 at 11:43 PM, Rob Soe wrote:
> Hi all,
>
> I have been reading quite a lot for this MSVCR80.dll error and here is what
> I found at:
>
> http://www.instant-registry-fixes.org/why-do-i-keep-receiving-msvcr80dll-missing-errors/
>
> "If an application is unable to reach the dll in
On Wed, Oct 14, 2009 at 4:36 PM, Fredrik Wallner wrote:
> Without patches, people should be able to pipe the output through babel such
> that Geoff's original command would be obminimize ... | babel -ipdb out.mol2
That's probably the best solution for now. In the future using the
input file forma
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