The name OBRing _path suggests that it's a circular traversal around the ring,
but the documentation doesn't formally say so. Are the atoms in a _path
actually a traversal, or an unordered collection? It's not obvious from
reading the code.
In other words, is there a bond between _path[n] and
Hi Vinay,
> could someone help me to eliminate the unwanted
> functional functional groups from the database. Using SMARTS! and the
> string which should be eliminated, this command gives the message, that
> i does not recognize the sequence. It may not recognise the parenthes
Hi Oscar,
> Usually, calculation softwares demand chemical structures be uploaded
> in individual files (one molecule per file). I´d like to know if
> OpenBabel can export this way from a file containing all structures.
If you type "babel -H" (help), you'll find this:
-m Produces multiple ou
Vinay M wrote:
> I tried this , but found a error message, could you help
>
> [r...@vcentos53 2.2.3]#
> bash: [CX3H][#6]: command not found
> bash: [CX3H2]: command not found
This isn't a problem with obgrep, it's because you're using a bash "shell"
program that executes the commands that you
Vinay M wrote:
> Can anyone help to know, how to convert from SMARTS to SMILES.
You can't. SMARTS is a superset of SMILES, and most SMARTS are not valid SMILES.
Perhaps if you explain why you need to do this, we might be able to suggest a
solution.
Craig
--
Vinay,
Thanks for your reply, i was using smiles to view the
structure, so few are in smarts. I just wanted to convert smiles to
smarts and smarts to smiles.
Ok, now that I know what you're doing, I can suggest a possible way to do it,
but it's not easy. Attached is a little P
Vinay,
> Thanks a lot, could you please send me the C or C++ code,
> since it deal with it a lot. I will follow those in perl and try. Thanks
> a lot.
You're welcome, but I can't do it in C or C++. It would take days to do the
same thing. Perl has very powerful string-handling f
Andreas Maunz wrote:
> Hi list,
>
> this is strictly speaking not an OB question: How can I match a SMARTS
> pattern with optional branch?
> Example: My compound is "C-C(-O)=C-C". The SMARTS expressions are
> s1="[#6]-[#6](-[#8])=[#6]" matches, as well as s2="[#6]-[#6]=[#6]".
> Since s2 is contain
Andreas Maunz wrote:
> Hello Craig,
>
> Craig A. James wrote on 11/16/2009 06:12 PM:
>> You may be able to do this using recursive SMARTS. In a recursive
>> SMARTS, an atom expression can itself be a whole SMARTS, ad infinitum.
>> And since an atom can be an OR li
Hi Paul,
> is there a way to include results from obchiral into the smiles strings
> generated by babel? One can highlight chiral atoms inside smiles using
> an asterisk when one does not wan't to give the absolute configuration.
>
> e.g. CCC*(C)(O)C(C)C, instead of c...@](C)(O)C(C)C or CC[C@@](C
Jean-Marc Nuzillard wrote:
> I am interested in 2D structure diagram generation from atom connectivity,
> as a part of LSD project (www.univ-reims.fr/LSD) for NMR-constrainted
> structure generation
> of small organic molecules.
>
> I have seen in previous posts to this mailing list that
> pybel.
Leonid,
> I was converting SDF molecules into canonical SMILES, but in my case,
> I would like to keep the correspondence between the (order of
> appearance) index of the SDF file atoms and the (order of appearance)
> index of the atoms in the newly created SMILES string.
>
> Would you say this i
Leonid Chepelev wrote:
> For some reason, the -xx option does not output the Z coordinate even
> though the coordinate is non-zero in my input.
Probably because I was in a hurry when I wrote it...
> Would it be easy for
> someone to change that, so that Z-coordinate is printed?
If you're in a h
On 3/11/10 7:44 AM, Andrew Voronkov wrote:
> I have several questions regarding OpenBabel usage.
> 1) Is it possible to compare two databases using obgrep, I mean if I have
> not only SMARTS pattern, but for example
> the datasets of ligands which I want to use against other dataset?
Are these
On 3/24/10 2:24 AM, David García Aristegui wrote:
> Same input file prop.smi (CCC), and in the examples of my user prop.smi
> is owned by "aristegui"
>
> With root:
>
> r...@thema:/tmp/test_dir_1# babel --gen3D -ismi prop.smi -osdf prop.sdf
> 1 molecule converted
> 1 info messages 55 audit log mess
Narendra,
On 3/25/10 12:32 PM, Polani, Narendra K wrote:
> Thank you for the information. The problem is fixed.
> I have another question, does the 'babel' stick to the bond order input of
> user or discards the bond order and forces assignment of
> bond orders based on the connectivity.
(You sh
On 4/13/10 5:02 AM, 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 parts of software b
One more thing...
On 4/13/10 9:48 AM, Craig A. James wrote:
> On 4/13/10 5:02 AM, 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 so
On 6/8/10 5:31 AM, Geoffrey Hutchison wrote:
> As Chris said, there is depiction in v2.3. It's evidently solid enough that
> Craig uses it for a service on eMolecules.com.
http://depict.emolecules.com
Craig
--
ThinkGeek
On 6/8/10 11:00 PM, Jérôme Pansanel wrote:
> Hi,
>
> This is an old thread, but the problem remains. I'm porting Mychem for MySQL
> 5.1, and it is not a piece of cake. MySQL has a new security 'feature' that
> requires to put the mychem library in the plugin directory
Postgres has the same require
On 7/7/10 11:20 AM, Tim Vandermeersch 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 molecules with the same title are
>>> the same.
>>
>> I've been thinking abou
On 7/21/10 5:39 PM, TJ O'Donnell wrote:
> In building a database of pubchem and other publicly available structures,
> I'm converting from molfile to isomeric cansmi. In several cases (about
> 7 per thousand)
> I get one cansmi from the molfile, but another when I ask for the cansmi
> of the
> resu
Hans,
> a client of us is looking for a tool to perform compound library
> enumerations by defining the building blocks and some general reaction
> schemes. The client has access to Pipeline Pilot in which this kind of
> stuff can be done, but for the particular project in mind it would be
> very
On 8/16/10 7:39 AM, eiso 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 equivalent would h
On 9/8/10 9:32 AM, Douglas Houston wrote:
> I realise I could potentially use SMILES as input but this doesn't
> work in some cases, e.g. 'C1=CC=CC=C1' is a benzene ring in SMILES
> format but according to the following link will not match benzene if
> it's used as a SMARTS string.
>
> http://www.
On 11/8/10 12:55 AM, Hans De Winter wrote:
> maybe a simple question but I couldn't figure it out: which OB C++
> method/class should I use to remove all stereochemical (implicit or
> explicit) information from a molecule? I want to modify the molecule
> in such way that stereochemistry is removed
You have several bonds with bond order zero, e.g. the first one.
Craig
On 11/12/10 9:57 AM, JP wrote:
> 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 0 0 0 0 0 0
> 1.452
On 11/17/10 5:35 PM, Imran Haque wrote:
> Hi,
>
> I have a large set of C++ molecule-manipulation libraries that
> internally use OpenBabel to handle molecule input and structure, and I'm
> trying to wrap them into a Python library using standard Python C API
> techniques. These routines work fine
On 11/22/10 2:51 PM, Geoffrey Hutchison wrote:
>> Is there a way in OpenBabel 2.3 to standardise the bonds in molecules in
>> such way that the bond orders are no longer dependent on the way the
>> molecule was entered? For example, the two smiles representations of the
>> indole ring, N1C=CC2=C
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 = pybel.Smarts(scaffoldSmiles)
>
>
> On Jan 26, 2011, at 11:54 AM, Chris Morley wrote:
> As may have been discussed here earlier, maybe this option should output
> explicit hydrogen as [H] rather than a hydrogen count on another atom.
> SMARTS [CH2] matches a C with exactly two Hs; SMARTS [H]C[H] will match a
> carbon with at lea
On 3/17/11 11:40 AM, andi wrote:
> Hey everyone, I am kind of new to openbabel, but I was wondering if there is
> a way to produce fragments given one or more molecules. And if not, anything
> close to what openbabel supports
>
> An example is like the one on the openbabel documention page at addre
On 3/19/11 8:33 AM, 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 would qualify as same
On 3/22/11 1:54 PM, Geoffrey Hutchison wrote:
>
> On Mar 16, 2011, at 1:39 AM, 討僖哓醜 wrote:
>
>> We develop the website with django under Windows. When I use
> django's runserver to run the site, pybel is working properly;
> while use apache+mod_wsgi to run the site, the following errors
On 3/23/11 6:06 AM, andi wrote:
> Hey Craig, the fragments that I need are indeed for similarity.
>
> Any thoughts?
Yes ... let us know when you figure it out!
Seriously, this is a hard problem. Many of the solutions in the past haven't
been well thought out.
Daylight's fingerprints were origi
On 3/24/11 9:10 AM, Douglas Houston wrote:
> Can anyone tell if if there's a way to get OpenBabel to output
> explicit hydrogens in smiles strings?
>
> I'm trying to define a hydroxymate group, which has a hydroxyl group,
> but the smiles I'm getting from OB at the moment doesn't seem to
> differe
On 3/24/11 9:39 AM, Douglas Houston wrote:
> I must be missing something really obvious. I tried the -h option but
> there are no hydrogens in the output.
>
> This is the command I'm using:
>
> babel -ipdb hydroxymate.pdb -osmi -h
>
> The help page says:
> Write Options e.g. -xt
> h Output exp
On 4/7/11 4:24 AM, Jalil Zerdani wrote:
> Dear fellow developers,
>
> I am actually developing a software to find the common structure between two
> molecules inspired from the "RASCAL" algorithm.
> I just happened to wonder if it would possible to use Open Babel to do so by
> using the command "
... etc.
Craig
#!/usr/bin/perl
#==
# FILE: split_sdf.pl
# AUTHOR: Craig A. James
# DESCRIPTION:
# Splits an MDL SD File into manageable-sized chunks.
#
#==
# Co
On 6/9/11 5:03 AM, nms_uk wrote:
> this must be very basic, but how do you use openbabel from command line to
> compare 2 InChI strings?
If both molecules are in the same file (say an SDF), do this:
babel file.sdf -o inchi | sort -u | wc -l
(that's a lowercase "L", not a digit 1 on wc).
If it
On 6/22/11 9:18 AM, Noel O'Boyle wrote:
>> I dont really understand this limitation, why should 4=aromatic be only used
>> for queries, its not ambigious like the others? (maybe its a typo, and it
>> should be '5 though 8' ;-) ).
>
> In general, it's not clear which bonds should be marked aromatic.
On 8/10/11 1:29 PM, DavidFlicker wrote:
> Hello,
>
> I just downloaded the NCI Natural Products Set II sdf file and I cannot get
> OpenBabel to convert it to any format.
>
> I get this error:
> ==
> *** Open Babel Warning in OpenBabel::MDLFormat::ReadMolecule
>WARNI
On 8/29/11 7:53 PM, budgerigar wrote:
> I think you give a very good suggestion. I should define my own atom type.
> There are much more work if if match the atom type between openbabel and
> opls-aa. I only need to define the atom type in
> http://towhee.sourceforge.net/forcefields/oplsaa.html and
On 9/13/11 12:41 AM, varunim...@gmail.com wrote:
> make 2>&1 | tee make.out
> make: *** No targets specified and no makefile found. Stop.
You need to give a lot more details than this. Were you trying to compile
OpenBabel, a program of your own, or something else entirely? Did you read the
in
On 9/29/11 10:38 AM, Noel O'Boyle wrote:
> "As far as I know in SMILES notation every double bond is specified
> with just ONE pair of slash/backslash"
>
> That's not quite correct. One pair of slashes is sufficient, but more
> may be used. Open Babel writes out as many as possible as it makes
> th
On 9/29/11 11:32 PM, green69 wrote:
> P.S. Please, do you know if it exist a document where I can found all the
> rules followed by openbabel for the SMILES canonization?
We have been planning to write such a paper for quite a while, but it's a lot
of work and we haven't found the time. The fil
On 10/12/11 7:53 AM, Chakravarthy Marella wrote:
> Hello,
>
> I am working on the problem of comparing SMILES strings based on
> alignment. In my research, I came across the following problem:
>
> Lets say there are two SMILES strings,
>
> SMILES 1: CC(=O)NC(C(CCC)O)CO
> SMILES
On 11/10/11 7:44 AM, David García Aristegui wrote:
> Hello, i'm reading about substructure and similarity searches...
> http://openbabel.org/docs/dev/Fingerprints/fingerprints.html
>
> "On larger datasets it is necessary to first build a fastsearch index.
> This is a new file that stores a database
On 11/16/11 3:55 AM, Ernst-Georg Schmid wrote:
>> InChI-Key are exactly done for exact searching.
>
> exactly, unlike different SMILES canonicalization implementations
> the InChI algorithm is standardized.
In my opinion, this is a common but incorrect criticism of SMILES. Variations
in canoni
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