Hi everyone,
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?
TIA
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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 has a checkbox under View - Misc.
>>
>> Specifically, as a c
On 4/26/2013 2:49 AM, Chris Morley wrote:
> It's hardwired in line 247 in src/depict/depict.cpp if you are in a
> position to recompile. I'll change it to "teal" for the future.
I can, however, a) I'm not yet sure I need to and b) I can also
post-process the svg.
Dima (I'd change it to '-xi [co
Hi all,
I'm after the atom (element) type letter. What I get from pybel's
atom.type or atom.OBAtom.GetType() are O3, O2, C3, C2, etc. Is there a
function or property that returns just O's and C's?
TIA,
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On 2013-06-05 02:54, Maciek Wójcikowski wrote:
> If you realy need symbol of an element in automated fassion, then there
> is OBElementTable.GetSymbol( atomicnum ) that you can use.
>
> http://openbabel.org/dev-api/classOpenBabel_1_1OBElementTable.shtml#a18907ad1590deb926b43c4f08cac9405
So it's ex
Noel, would you let me try doing this?)
While you're at it & if you feel like it, things like
atom.isotope = property( OBAtom.GetIsotope(), OBAtom.SetIsotope() )
(not to be taken literally, obviously ;) would be more "pythonic", too.
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the SVG to change the size and the background.
TIA
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try and figure out SVGFormat
and OBPainter and the rest of them...
bardzo dziekuje
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was right) and I didn't
even notice myself until the picture popped up with black background.
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quot; or "license" for more information.
>>> import pybel
>>> print sorted( pybel.informats )
['CONFIG', ...
...
... 'yob']
What do you get?
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d at least the table of elements,
the table of bond "numbers" (might as well use names), and atoms encoded
as (element, index) pairs. Connections as (atom1, atom2, bond) tuples
and 3d coordinates as (x, y, z) tuples.
One of the particularly annoying things about pubchem is nowhere in
th
ns more information: I can urlopen the sdf into OBMol
and get all sorts of data out. Except for the name -- the only way I can
get to the word "ethane" is by generating and inchi string and querying
our own ligand database... but only if the molecule is a PDB ligand.
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7;re
doing X-ray crystals you see bonds but you have to deal with multiple
conformers. And so on.
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On 2013-06-06 22:13, Geoffrey Hutchison wrote:
>> Although I'm starting to think that json is such a simple format
>> that
it could do without a strict chemical specification. Getting json out of
an OBMol is <5 lines of code
>
> My concern is the opposite. It's always easy to write to an
> arbitrar
Except for attributes: if you have bad xml, like instead of 1C, then it
isn't.
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associative array, string, number, boolean.
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include
std::stringstream out;
OBConversion obc;
obc.SetOutStream( out );
...
out.str() returns std::string and out.str().c_str() will give you
null-terminated char array (aka c-style string).
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]
sdf = "%s/%s" % (self._workdir, filename)
print >> sys.stderr, sdf
self._obmol = pybel.readfile( "sdf", sdf, opt={"canonical":None}).next()
The 'else' fork works. In both cases the filename is logged as (e.g.)
/var/tmp/bm30/92802.sdf and it is the sam
the state between wsgi
invocations I tried changing the readfile call to
list( pybel.readfile( "sdf", sdf, opt = { "canonical" : None } ) )
and returning list[0] -- no dice, still the same error.
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it is.
Thank you. It was a unicode,
pybel.readfile("sdf", sdf.encode("ascii"), opt={ "canonical" : None } )
does the trick.
(The problem with unicode in python, "print sdf" won't tell you what you
need to know. Only "print type( sdf )" will
; i.e. -aT (read title only).
python:
cnt = 0
for mol in readfile( ... ) : cnt += 1
print cnt, "molecules"
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signa
exit... }
pOutFormat = Conv.FormatFromExt(OutputFileName.c_str());
...
Standard getopt should allow "-o count" as well as "-ocount" IIRC.
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atoms
here.)
8-core/16GB RAM, linux centos 6.3 x86_64, openbabel 2.3.2 built from source.
Thx
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atom tables etc. But the error message suggests that it's
openbabel core that's limited to 1K atoms.
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100% CPU.
> If you have problems exporting a PDB as, say, XYZ please file a bug
report and if possible post the file.
http://www.rcsb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=2MAL
So is SMILES output supposed to handle > 1000 atoms and t
On 10/04/2013 05:01 PM, Craig James wrote:
> The SMILES parser has an explicit 1000-atom limit. It's unfortunate.
So does the the inchi one -- I ran a couple more tests...
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Des
;> import pybel
>>> File "C:\Python33\lib\site-packages\pybel.py", line 69, in
>>> informats = _formatstodict(_obconv.GetSupportedInputFormat())
I think you should first figure out your python: is it 3.3 or 2.7?
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the job's started from the GUI
-- or at least popping up a dialog box saying "are you sure you wanna do
this?". And even then I'd say the issue is memory usage: these days you
probably have at least 3 more cores for other stuff, so as long as OB
doesn't gobble up all the RAM i
applied to inchi & smiles? It's an interesting exercise,
but I'd say if you're a user in need of an actual picture with more than
2-3 dozen atoms, use pymol.
(Disclaimer: I'm programmer, not a chemist)
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*** Open Babel Warning in InChI code
2mal.pdb :Too many atoms
==
*** Open Babel Error in InChI code
InChI generation failed
0 molecules converted
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ot of atoms, processing may take a long time".
> ==
> *** Open Babel Error in InChI code
> InChI generation failed
So what's the error? The obvious assumption is "too many atoms", but is
it really the case?
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how our code can better handle that case.
According to grep there are error codes in ichierr.h. Also,
ichisize.h:#define MAX_ATOMS 1024
Some day in my copious free time I might try to to rebuild w/ that set
to maxint or something... In the meantime canonical SMILES without the
1000-atom limit s
On 2013-10-25 04:33, Fredrik Wallner wrote:
> Hi,
>
> Wouldn't this be good to have exposed directly in pybel? Seems a bit
> non-intuitive to have to add the OBMols…
To a programmer it's plenty intuitive. What's not intuitive to this
programmer is if a and b have more than one possible binding s
t;H12" ), b.lose( "O1H1" ), then I agree: "a + b" is not very
intuitive.
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On 10/25/2013 11:55 AM, Dimitri Maziuk wrote:
> On 10/25/2013 10:11 AM, Igor Filippov wrote:
>> I don't think it does.
>> I could be wrong but I think one has to create a bond from somewhere in
>> mol1 to somewhere in mol2 explicitly.
>
> Now if "+" does
On 10/25/2013 01:15 PM, Fredrik Wallner wrote:
> Well, I was referring to the fact that
> a += b won't work, but a.OBMol += b.OBMol will. That isn't intuitive to me...
Ah. Yes, pybel should override the __add__().
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OBMol to be something that creates a bond whereas
OBMol + OBMol = (OBMol, OBMol) is a set of disjoint molecules, no
strings attached.
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ing this carbon and this metal more or less
together...
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October Webinars: C
On 2013-10-30 19:38, Francois Berenger wrote:
>
> Honestly, to deploy things in a cluster, you should rather use
> the packaging system of your Linux distro.
>
> If you are really forced to work with the source code
> of something, try to create the binary .rpm or .deb from
> the sources in order t
On 2013-11-05 08:34, Craig James wrote:
> I don't know if it's something specific to OpenBabel, or a more general
> problem with C/C++. I have to believe it's OpenBabel, because I know
> lots of projects use libraries written in C++ linked to executables
> written in C.
Generally speaking it requ
/or initialization code, so the classes aren't initialized properly.
Interesting... makes me sooo happy I don't do that sort of thing anymore. ;)
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Hi guys,
one for the next release wishlist: is it possible to expose bonds as an
iterable, similar to atoms?
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On 2013-11-12 00:55, Fredrik Wallner wrote:
> Hi,
>
> Since pybel doesn’t have a ”bond-concept” at the moment, I suppose
> it needs to be defined first.
Hm. I find I have to get to OBMols and OBAtoms all the time anyway, I
expect bond will be no different. So I'd skip pybel.Bond and just go for
Hi all,
is there a way to find the number of "isotope 0"? I'm not seeing
anything suitable in isotope table.
TIA
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ate, or round as in
"round(2.675, 2) gives 2.67 instead of the expected 2.68"?
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( 7 )
...
>>> mol.OBMol.EndModify()
>>> mol.molwt
31.9987999
>>>
>>> mol.OBMol.BeginModify()
>>> for atom in mol.atoms :
... if atom.OBAtom.IsCarbon() : atom.OBAtom.SetIsotope( 5 )
...
>>> mol.OBMol.EndModify()
>>> mol.molwt
31
rbon() : atom.OBAtom.SetIsotope( i )
... mol.OBMol.EndModify()
... print i, ":", mol.molwt
... del mol
...
9 : 41.0298367
8 : 40.036475
7 : 31.9988
6 : 31.9988
5 : 31.9988
4 : 31.9988
>>>
And with the same code:
21 : 53.04814
22 : 54.056
23 : 31.9988
24 : 31.9988
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Dimitri
On 2013-11-14 06:43, David Hall wrote:
> I'm unsure why you make comments saying that you doubt isotope.txt is
> not where information about isotopes lives for openbabel.
I was confused by 31.9988 and the fact that setting carbon isotope to 7
didn't throw an (e.g.) ArrayOutOfBounds. I then reali
On 11/14/2013 09:54 AM, Dimitri Maziuk wrote:
> Yeah well. I saw that OBIsotopeTable looks like there must be one per
> element and I saw one "isotab" extern global and grep didn't show when
> or where it's initialized. Those things put together didn't make se
d if their ligand file is put
together from several processing streams and their atom list doesn't
exactly match their inchi. But getting 4 different inchi strings for
allegedly the same molecule doesn't sound right to me.
Am I missing something?
TIA
-
On 2013-11-16 10:21, David Hall wrote:
...
> Of those strings, only "SMILES_CANONICAL CACTVS" specify two
> stereochemical centers. The ones without canonical in their name don't
> specify any stereochemistry at all. I'm pretty sure those never specify
> any stereochemistry in the entire ligand exp
On 2013-11-16 03:27, Noel O'Boyle wrote:
> Can you be a bit more specific with your question? After reading your
> email twice I can't figure out exactly what the problem is.
>
> (I note in passing that PDB files are the worst possible way of
> storing chemical data as they typically do not contain
On 2013-11-17 12:34, Geoffrey Hutchison wrote:
> It doesn't take a cheminformatics specialist to realize these strings are
> different:
Well, as I understand it, one of the problems with smiles is you can
start your graph at any atom. Which gives you any number of different
smiles string for t
t;Prevalent" if
you can think of a better word. (All I could think of along the lines of
"NaturalAbundance" was too long for my liking.)
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--- openbabel-2.3.2.orig/include/openbabel/data.h 2010
re should be no perceptible difference in runtime, typically a tight
loop like this would be optimized to run out of cache.
Rounding doubles, on the other hand, comes with the possibility that the
nearest representable value to 238.050788 is actually within
0.49003849 amu of 238.00 and will round
On 11/18/2013 03:20 PM, Dimitri Maziuk wrote:
> On 11/18/2013 03:07 PM, Geoffrey Hutchison wrote:
>>> In the meantime, here's the patch -- feel free to rename "Prevalent" if
>>
>> I think my big question is why you do the loop in the
> GetPrevalentIsotop
On 11/16/2013 11:40 AM, Dimitri Maziuk wrote:
> I guess now I'll have to come up with a different test plan.
So I downloaded both "2D" and "3D" SFDs for L- and D-Alanine from
PubChem, ran them through my scripts and compared to the original and to
chem. comps in li
Someone familiar with OB's stereo perception (Geoff?)
-- is there a way to get 'R' and 'S' labels from one of the *Stereo classes?
Also, is there a way to find E and Z labels for a bond? -- I could use
those, too.
TIA
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On 2013-11-19 03:09, Noel O'Boyle wrote:
> We neither have R/S perception nor E/Z.
OK, thanks.
Dima
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ttp://openbabel.org/dev-api/classOpenBabel_1_1OBEnergyConformerScore.shtml#_details
OBEnergyConformerScore is "Since: 2.3", so if you compiled with 2.3.1
and are running with with 2.2.3, "undefined symbol:
_ZTVN9OpenBabel22OBEnergyConformerScoreE" sounds about right.
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Dimitri Maziu
s1/i4+1
>>
>
> Are you saying there is a problem, or is this just interesting for some
> reason?
I'm saying I had a bug in my script: I was not resetting the nitrogen
after calculating N15 isotopic mass.
Now if only OB stereo could do R/S and E/Z, I wouldn't have to al
items are nullable so I don't have to fill them in if the data is
not available. However, if it is obtainable, I want it.
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depends". If you install
java-1.7.0-openjdk, then yes, it's 1.7. Some of the packages depend on
openjdk-1.6 and some other pull in gcj-1.4.
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Hi guys,
> $ /share/linux/openbabel-2.3.2/bin/obabel -i pdb -o smi SB3_model.pdb
> C(=O)([C@@H]1N1C(=O)C(=O)C(CC)(C)C)O[C@H](CCc1c1)c1c1
> SB3_model.pdb
> 1 molecule converted
Should "\tSB3_model.pdb" be there? Is that part of SMILES specification?
Tha
and_expo/EHN.pdb
You have been warned."
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On 11/27/2013 03:45 PM, Geoffrey Hutchison wrote:
> If no title is set by the format, Open Babel will use the file name as a
> default indicator of the origin.
Unless the output is svg in which case the title is "OBDepict".
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On 2013-11-27 20:06, Craig James wrote:
> Likewise, OpenBabel can (optionally) write a name after the SMILES. But
> that's just a feature of OpenBabel, not SMILES.
Is it possible to turn the option off, then? My problem with "val =
Molecule.write( "smi" ).split()[0]" is that when something goes
On 2013-12-03 04:28, Maciek Wójcikowski wrote:
> Hello,
>
> I'd like to ask, if it's somehow possible to use first [-f] and last
> [-l] options via python bindings?
last = list(mols)[-1] ? -- I haven't tried myself. I suspect even in c++
you still have to actually read them all in to get random a
structure/object with a winding property that
> has two possible values: clockwise and anticlockwise. These are R ans S to
> me!
They print "clockwise" for both L-alanine and D-alanine so they are R
and S as long as you don't mind your ALA turning into DAL.
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the
front, I need to turn the spanner one way and if I'm looking from the
back I need to turn it the other way. What I don't know is how you can
tell rectal from withershins when you don't know which way you're looking.
I'm confused.
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have a message from Craig James here:
http://forums.openbabel.org/stereo-config-td4656861.html that says it's
based on "local connectivity around a single atom or bond". Please
define "atomic numbers" in terms of "local connectivity around a single
atom or bond".
Ho
but I still don’t see how do you know
> what chirality to represent starting from a mol file lets say. I
> thought that was what Dimitri was asking.
Thank you Yoel. Yes, my problem is, if I knew where R/S & E/Z are
already I wouldn't be asking OB to find them for me.
--
D
On 2013-12-03 22:28, Geoffrey Hutchison wrote:
> Craig's point is not that CIP is impossible, but rather from a
practical implementation side, it's easier to use other local stereo
designations. I might be wrong, but the codes that I can think of with
CIP implementations are all commercial, and as
oop_ line -- although in practice it'd be
hard to find one that doesn't.
Another issue is that in STAR (CIF) all whitespace is equal so what you
normally see in mmCIF files is just pretty-printing:
_name value
_name value
loop_
name_
name_
name_
value value value
Just FYI
--
molecule, and its value may be like
"1, 3, 7". Because they had a mix of 3 conformers in the sample.
On top of which there are a few tentacles hiding just under the surface
when it comes to parsing STAR formats like CIF. Keywords inside values
being one.
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Hi guys,
I was asked to pull 2D drawing coordinates for a molecule (don't ask).
Are those easily obtainable? -- Quick look around OBDepict wasn't
helpful. I'm guessing not & I'm better off reading the source SDF and
just copying what's in there.
TIA
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On 01/03/2014 06:19 PM, Dimitri Maziuk wrote:
> Hi guys,
>
> I was asked to pull 2D drawing coordinates for a molecule (don't ask).
Scratch that, I got it: they're there until you run make3D().
Apologies for the noise.
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On 1/4/2014 12:48 PM, S Joshua Swamidass wrote:
> The problem with the current cmake approach, though, is that it ignores
> the standard python installation mechanism using setuptools. Therefore..
It's a systemic problem. It's not just eggs or pypis, it's jars, debs,
cpans, dmgs, and the list go
ndif(BUILD_SHARED) was supposed
to be about 10 lines above where it is now?
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On 4/12/2014 2:20 PM, Wellisson Gonçalves wrote:
> A use the executable babel with parameters
> babel -icif '4POQ.cif' -opdb '4POQ_cif_to_pdb.pdb'
>
> And i received the file that not compatible with the original file.
>
> I know becouse i downloaded the original file in website 4POQ.pdb and
> It
PDB entry is probably hard enough (e.g. what do you do with
NMR structure with 50 models and REMARK 210 BEST REPRESENTATIVE
CONFORMER IN THIS ENSEMBLE : 19,23,42).
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rt all of
that information between 2 PDB formats: it's not what it's for.
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---
) )
NOTE: elt.lower() can be "xx"
HTH,
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about SF
spam/moderation mechanisms?
Thx
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"Accelerate Dev Cycles w
on is, is it possible to get a sane layout with all
hydrogens added?
And a wish list one: rather than generating a garbage picture, how about
aborting when there are no 2D coordinates?
(I've another one coming)
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t; na_1.svg
> bin/obabel -h --gen2d --title "" -xb none -xi -xa -xP1200 -ismi -osvg na.smi
> -O na_2.svg
See attached.
The question here and in the previous one: what's up with Na?
TIA,
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Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.bmr
On 05/21/2014 11:36 AM, Noel O'Boyle wrote:
> 40Kb max. Zip 'em and resend.
Got it, thanks.
(all together now: "640K should be enough for everyone")
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Dimitri Maziuk
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BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
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$';
count
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815
-- and we don't import their "compound" chem. comps into our database.
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Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
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ion.
>>>> import sys
>>>> sys.path.append( "/share/linux/openbabel-2.3.2/lib" )
>>>> import pybel
>>>> import openbabel
>>>> mol = pybel.readfile( "sdf",
>>>> "/share/dmaziuk/projects/metabolomics/71080.
D-alanine.
Whereas
pybel.readfile( "sdf", ... ) -> mol.write( format = "svg", ... )
works fine for the same molecules.
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Dimitri Maziuk
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BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
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On 10/23/2014 05:51 PM, ftorazyne wrote:
> raise ValueError("%s is not a recognised Open Babel format" % format)
> ValueError: smi is not a recognised Open Babel format
Have you tried "readstring(sorted(pybel.informats[-16]..." -- or
whatever its index is?
--
portal to asgard and brain-eating alien zombies
start pouring in.)
Index-based accesses should work though. Try
for i in len( pmol.atoms ) :
... use pmol.atoms[i] ...
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Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
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t's one of the side-effects of garbage collection they don't tell you
about unless you're a Comp.Sci. student.
If you use a garbage-collected language as front-end to
non-garbage-collected library code, all bets are off.
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Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-
u'll have to figure it out from there.
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Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
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___
quot;.
Like I said, I don't know of any software that will do what you want. In
5A05.cif the first row of _struc_conn table is
covale1 covale ? H GLC . C1 ? ? ? 1_555 H BGC . O4 ...
which I believe means there's a covalent bond between GLC C1 and BGC O4.
ICBW,
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Dimitri Maziuk
Pro
On 2015-11-18 05:05, Alexandre Fassio wrote:
> For example, a cellobiose can be represented as two glucoses (GLCs). Thus,
> it is difficult to know without a previous knowledge, which ligand is
> represented by these two GLCs.
>
> In another case, I had a PDB with 8 ligands covalently bonded and I
On 2015-11-19 05:28, Alexandre Fassio wrote:
> Right, it's true. But, for example, if I have 8 ligands covalently bonded I
> would like to consider these 8 ligands as it were only one ligand and search
> on the mmCIF dictionary for a ligand that represents the 8 ligands together.
> Because by sear
On 11/19/2015 10:17 AM, Dimitri Maziuk wrote:
> I think our best option
--^^^
That was supposed to be "your"
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Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
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