On 9/21/2019 11:28 AM, Geoffrey Hutchison wrote:
On the other hand, not every file format supports arbitrary precision
(e.g., 8 decimals or more) - there's not much that babel can do about
that, except by suggesting other formats with better suitability.
OTGH I've seen lots of numbers
On 8/6/2019 8:16 PM, Geoffrey Hutchison wrote:
If there's stereochemistry in any of your 2D molecules, you're not
guaranteed to get the right 3D conformer from the conversion.
What? Why do you say that?
Because that's how it works. If I have a 2D alanine SDF and I "convert"
to 3D, I may get
If there's stereochemistry in any of your 2D molecules, you're not
guaranteed to get the right 3D conformer from the conversion.
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On 7/29/2019 4:53 PM, Stefano Forli wrote:
... PDB files ...
Just a note: PDB has stopped accepting X-ray structures in .pdb format a
while back, and is going to stop accepting .pdb NMR structures soon.
I.e. what you are discussing is a dead format essentially.
Dima
On 4/6/2019 3:04 AM, moritz.be...@gmail.com wrote:
Thanks for the hint to use conda. However, maybe alpine-glibc is the
wrong base image? You snuck a /bin/bash in there and when I change that
to /bin/sh or /bin/ash I get a lot of errors upon importing pybel.
That image is for a service
On 4/2/19 7:42 PM, Dimitri Maziuk via OpenBabel-discuss wrote:
sorry, too much trimming:
> FROM frolvlad/alpine-glibc
> RUN echo 'export PATH=/opt/anaconda/bin:$PATH' >
> /etc/profile.d/anaconda.sh && \
> wget --quiet \
> https://repo.continuum.io/miniconda/Minicon
h && \
wget --quiet \
https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh \
-O ~/anaconda.sh && \
/bin/bash ~/anaconda.sh -b -p /opt/anaconda && \
rm ~/anaconda.sh
ENV PATH /opt/anaconda/bin:$PATH
RUN conda install -y -c rdkit rdkit
me python hacking to make it do what OP wants, if that's an
option I can post the code (and, more importantly, answer questions
about it).
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De
usubscribe person@gmail"
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mplate as or something. Maybe inside
s or cells. You'll have to play with it.
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On 12/28/18 6:03 AM, Spencer Trinh wrote:
> ... The xml file generated was thru Outputfile() and thus a file path
> is required. How to generate as a string?
For the 3rd time: pybel.Molecule.write()
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PS I haven't looked at SVG specs too closely: anyone knows what is does
with multiple "..." elements in the same file?
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XML file should have one XML declaration up top.
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(Repost with a catchy Subject)
Noel, Geoff,
this sounds like a bug:
On 12/23/18 2:52 PM, Spencer Trinh wrote:
>
> output=pybel.Outputfile('svg',filename='testsvg.svg',opt={'u':None,'C':None})
> for name,mol in mols.items():
> mol.removeh()
> mol.title=name
> output.write(mol)
> output.close()
Noel, Geoff,
this sounds like a bug:
On 12/23/18 2:52 PM, Spencer Trinh wrote:
>
> output=pybel.Outputfile('svg',filename='testsvg.svg',opt={'u':None,'C':None})
> for name,mol in mols.items():
> mol.removeh()
> mol.title=name
> output.write(mol)
> output.close()
> ... The svg file itself has
t; : None, "b" : "none", "i" : None } )
However, laying multiple images out on a grid is a different question. I
would recommend re-posting your question with a better subject, like
"how to draw multiple SVGs on a grid".
Merry Christ
On 5/24/2018 4:10 AM, Julian Kerr wrote:
Any babel command returning the bond information will work for me (not
just converting to a file format).
if your source is mmCIF, all you need to do is look at _chem_comp_bond
table.
Dima
isk quotas etc.
To the OP: if that's the case, get a linux machine with root access.
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y
MOL/SDFs were generated from PDBs with zero information loss, I wouldn't
expect anything from them.
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unning obminimize, too, if one's willing to pay for that. Or
just "for i in *.mol ; do nohup obminimize ... & ; done"
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On 2016-12-25 12:50, ishan wrote:
> Hi Pranav,
>
> Thanks for the reply, that seems to be a nice trick, I will try it. But One
> question still remains whether it is inherently possible in openbabel.
'''
High Throughput Computing is a computing paradigm that focuses on the
efficient execution of
; executable. The latter requires a
"static" library that some linux distribution vendors and/or package
maintainers no longer provide.
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r off
with shared memory (OpenMP) rather than strict message passing (MPI).
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D
5057 before atom reordering produces an OK
picture, in it the atoms are in a different order.
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alatis_output_Structure3D_CID_5057.sdf
Description: application/vnd.kinar
si
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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m_flag in the ligand mmCIF, but
that one's an even worse mess. :(
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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
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
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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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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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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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?
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= svg, ... )
works fine for the same molecules.
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Meet PCI DSS 3.0
/openbabel-2.3.2/lib )
import pybel
import openbabel
mol = pybel.readfile( sdf,
/share/dmaziuk/projects/metabolomics/71080.sdf ).next()
mol.removeh()
svg = mol.write( format = svg, opt = { b : none } )
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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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: elt.lower() can be xx
HTH,
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CONFORMER IN THIS ENSEMBLE : 19,23,42).
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not what it's for.
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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's
to be about 10 lines above where it is now?
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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
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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under the surface
when it comes to parsing STAR formats like CIF. Keywords inside values
being one.
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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
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
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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/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.
How is it different from the pikiwedia's explanation of CIP?
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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.
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.
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Rapidly troubleshoot problems before they affect your business. Most
, as a programmer I'm really dealing with specifically smiles,
or inchi -- I'm dealing with pybel.Molecule.write(), OBFormat, and
formats section of the docs. There's nothing there about there being a
part of smiles that's unique ID in daylight and trailing garbage
from dusk till dawn.
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-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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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 also use
rdkit...
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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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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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the lines of
NaturalAbundance was too long for my liking.)
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--- openbabel-2.3.2.orig/include/openbabel/data.h 2010-10-09 21:05:12.0 -0500
+++ openbabel-2.3.2/include/openbabel/data.h 2013-11-14 14:14
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
inchi strings for
allegedly the same molecule doesn't sound right to me.
Am I missing something?
TIA
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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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:
... if atom.OBAtom.IsCarbon() : atom.OBAtom.SetIsotope( 5 )
...
mol.OBMol.EndModify()
mol.molwt
31.9987999
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)
... 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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Hi guys,
one for the next release wishlist: is it possible to expose bonds as an
iterable, similar to atoms?
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aren't initialized properly.
Interesting... makes me sooo happy I don't do that sort of thing anymore. ;)
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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 to
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
of disjoint molecules, no
strings attached.
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On 10/25/2013 02:11 PM, Igor Filippov wrote:
a molecule is a thing with atoms and bonds.
Hmmm, no salts? No organometalics?
I didn't say you have to define bond as (e.g.) peptide-only. As long
as you know something's holding this carbon and this metal more or less
together...
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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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.
==
*** 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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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 should work for me.
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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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should first figure out your python: is it 3.3 or 2.7?
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.)
8-core/16GB RAM, linux centos 6.3 x86_64, openbabel 2.3.2 built from source.
Thx
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. But the error message suggests that it's
openbabel core that's limited to 1K atoms.
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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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(OutputFileName.c_str());
...
Standard getopt should allow -o count as well as -ocount IIRC.
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;
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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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
arbitrary
for attributes: if you have bad xml, like atom
idx=1 id=C/ instead of atomidx1/idxidC/id/atom, then it
isn't.
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,
associative array, string, number, boolean.
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)
['CONFIG', ...
...
... 'yob']
What do you get?
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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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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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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 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
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
--
Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison
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 command line switch to [o]babel or pybel
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