> this question is that after this process, the result is totally difference
> with the results of another software named Avogadro (use the same Ghemical
> force field for energy minimization).
> ...i want to figure out how the difference came out? should they be same
> since their use same for
On Dec 17, 2012, at 2:52 PM, Kirk Simmons 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 directories "data", "doc" and "examples".
What platform are you using?
> ANULENE is an aromatic molecule. To my surprise OpenBabel is giving C2 atom
> type to every carbon atom. Molecule is ~planar.
> Please help me out in rectifying the problem (if there is any).
So what is your question? Every atom should be sp2 carbon = C2.
Best regards,
-Geoff
--
> the atom type should be 'Car' as it is for Benzene molecule.
> thanx a lot
Your molecule is an 18 electron species -- Cyclooctadecanonaene or [18]annulene.
Open Babel does not consider annulenes above 14 atoms as aromatic. The limit is
in place, partly due to performance reasons, and partly be
It seems as if some of the wxWidgets install is causing problems. I suggest
re-running cmake and adding -DBUILD_GUI=FALSE
Hope that helps,
-Geoff
On Dec 26, 2012, at 3:35 PM, Vera Stehr wrote:
> Hello,
>
> I just tried to compile OpenBabel 2.3.2 today, but it fails with the
> following error
I have no idea if ChemSpider supports arbitrary options to Open Babel. There's
a ChemSpider support page:
http://www.chemspider.com/OpenBabel.asmx
> It gets a smiles from chemspider and then asks OpenBabel to convert it to a
> mol file. The problem is there are no 3D coordinates. I know that I h
es with a
few constraints. For many formats, this can be done (without the more
time-consuming bond order perception) automatically.
Alex, if you give us a bit more information, we can give you some example code.
Hope that helps,
-Geoff
---
Prof. Geoffrey Hutchison
Department of Chemistry
University
When running cmake, add:
cmake … -DBUILD_GUI=OFF
You can also run "ccmake ." in the build directory to change the settings --
look for "BUILD_GUI" naturally.
Hope that helps,
-Geoff
---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412)
one step
from the command-line. Either write a short script with Pybel, or save the
output from gen3d and *then* run the conformer search.
Hope that helps,
-Geoff
---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geo...@pitt
> I am trying to generate multiple conformation of small molecules. As a first
> step I am trying to minimize the molecule.
> However when I try to select the forcefield using
> OBForceField* pFF = OBForceField::FindForceField("MMFF94");
> if (!pFF->Setup(obmol1)){
...
> Replacing this with :
> i
> g++: -lopenbabel: linker input file unused because linking not done
This sounds like you are supplying -lopenbabel when you are compiling objects
before linking the binary. Assuming the binary links, there's no problem -- the
compiler is just telling you that you don't need -lopenbabel (e.g.,
> obminimize -ff MMFF94 -sd source.sdf > target.sdf
Indeed, we intentionally do not change the source file. I'd prefer to keep the
original coordinates around in case something strange happened during the
optimization or I wanted to do conformer searching, etc.
Cheers,
-Geoff
-
> obabel input -O output --conformer --nconf 50 --score rmsd
>
> - I seem to only get one conformer written to the output file. How can you
> produce multiple conformers?
If you're using the latest SVN / Git "master" development code, you want;
--writeconformers
> - Also, it would be great to s
> For some internal purposes, I wanted a combined openbabel/confab code
> base, so I merged them.
Thanks. Noel (cough, cough) said he'd do this ages ago. :-) Can you remind me
the differences that went into confab? I seem to remember that Noel thought I
might have some issues with certain chang
> I dug up old versions of tree.hh from Cadabra . Luckily, it actually
> has the exact same files as Confab, but with a GPLv2-compliant
> license. Since the author of Cadabra is the same person as the author
> of tree.hh, I think these files should be considered cleanly under
> GPLv2.
If the file
> Is there a way to calculate accessible surface area (ASA) or
> solvent-accessible surface area (SASA) or van der Waals Volume in OpenBabel
At the moment, no. I believe ChemKit, among other toolkits does allow this:
http://wiki.chemkit.org/Features
Hope that helps,
-Geoff
-
> My previous email didn't sound very enthusiastic. :-) But I am. All
> code contributions are much appreciated.
And there are a *lot* of Qt users for Open Babel. At one point there was a Qt
GUI.
http://kopenbabel.sourceforge.net
I don't know if it's maintained (the website looks old) but I mig
> hi.I wanted to know is how this article was composed or found a way to
> synthesize it?
That's not really our thing. We write software that helps people index,
convert, etc. chemicals. Your best bet is to find an organic synthesis forum.
A quick Google search suggested:
http://www.chemicalforu
impler tool that
> can fit this purpose? Any help would be greatly appreciated.
>
> Have a great day,
>
> Alex Gorbounov
>
>
> From: Alex Gorbounov
> To: Geoffrey Hutchison
> Sent: Tuesday, April 9, 2013 12:48 PM
> Subject: Re: [BlueObelisk-discuss] Dat
> But the issue that I am having is that the ConjugateGradients method doesn't
> actually change any coordinates, it seems not to be doing any actual
> minimization. The file I am using is a completely unminimized geometry so it
> cannot be that it is converging quickly I think.
The OBForceFiel
> seems that the most matching format of POSCAR that avogadro can offer is
> fractional format, therefore I have to convert fractional format to POSCAR
> format.
Open Babel and Avogadro will read POSCAR files directly. Also supported include
CIF, the free-form fractional, and a variety of other f
> But what I need is to export the coordinates to POSCAR. Does either
> openbabel or avogadro can export other coordinates to POSCAR files?
Yes. You just need to name the file POSCAR, and it should export in Vasp 5.x
format. Open Babel has a few options to control the formatting.
Hope that helps
> "the client that is using Open Babel must use OBConversion::ReadFile() to
> begin the conversion."
This is just saying that you can't use some forms of code in C++ or Python. The
command-line tools and Avogadro should handle things correctly to read / write
POSCAR.
I can vouch for this -- I h
Can you give us an example file or two? This would help us debug by reproducing
the problem.
Thanks very much,
-Geoff
On Apr 24, 2013, at 11:01 AM, Pascal Muller wrote:
> Hi,
>
> I have a little pybel script for generating Murcko scaffolds, which
> works well with 2.3.1, but fails on a few m
There's no problem. Build files were generated. Run "make" and continue with
the build.
Open Babel can be built on many systems with different libraries, etc. These
lines tell the build what parts of the code to include, e.g. How to scan
through directories for plugins.
Hope that helps,
Geoff
This version of Open Babel (2.0.2) was released in July 2006. It is not
supported. The latest version is 2.3.1:
http://openbabel.org/wiki/Install
Hope that helps,
-Geoff
--
Get 100% visibility into Java/.NET code with Ap
> I have come across some ChemDraw files (.cdx and .chm files) that I need to
> convert to images. I found the Open Babel project, and was able to opne the
> .cdx files just fine, but this program does not seem to support the older
> .chm files.
.chm files are really, really old. For many reas
> Does anybody know, if MMFF94 with OpenMP works in any bindings? It works fine
> in CLI, but bindings ignore that.
I suspect you may need to check the environment variables, etc. Certainly the
bindings would just be calling the C++ library anyway.
-Geoff
-
>I got following error message when compiling openbabael.
> Plz try to remove the error.
I'd re-run cmake and use -DBUILD_GUI=FALSE
Hope that helps,
-Geoff
--
AlienVault Unified Security Management
> molecules using open babel. The catch is: I wish I could loose accuracy as
> minimum as possible. I mean, I wish I could extract the two geometries from
> the fchk file keeping as many decimal digits as possible and then generate
> two new geometries with as many decimal digits as possible. How c
> The only issue that remains is the number of decimal places in the output
> geometry. I really could make use of few more digits. Any way to increase it?
If you're willing to re-compile, I'd just edit src/formats/xyzformat.cpp:
snprintf(buffer, BUFF_SIZE, "%-3s%15.5f%15.5f%15.5f\n",
> etab = ob.OBElementTable()
> etab.GetSymbol(6)
Although I can see some benefit for Pybel to have a wrapper to handle something
like atom.element and hide all this in something more "Pythonic".
(Noel, would you let me try doing this?)
-Geoff
--
> 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.
Well, if you or others have suggestions, I can try hacking those too. If you're
willing to rebuil
> All I can see in TFM is pybel.Molecule.addh() for "-h" -- is there way
> to get to the rest? Specifically, "-xa" and "-xi", as I can
> post-process the SVG to change the size and the background.
These are output options in the Python openbabel module (not accessible from
pybel, IIRC)
conv = ob
That's way cool.
> I would be honored to fold some of the code into open babel itself, although
> I admittedly don't know where it would go / if it's outside the project scope.
I've been trying to build up the "contrib" repository:
https://github.com/openbabel/contributed
Basically, you could f
> I think the actual criticism here is that there is no documented schema
> for this file format, but it seems the format is so trivial it's
> basically self-documenting...
>
> I think a more valid question would be whether there is a need for 101
> different chemical formats...
That was my orig
> 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 format
from an OBMol. Parsing a pile of differe
This isn't working because the Open Babel PDB code does not recognize space
groups at the moment.
-Geoff
On Jun 17, 2013, at 1:41 PM, Herbert Fruchtl
wrote:
> Dear all,
>
> I want to find all the atomic positions in a pdb file, not just the symmetry
> unique ones. I think the flag to do thi
> 1. Can I superimpose more than two molecules using OBFit? How would this be
> done if it is possible?
I'm not sure what you mean. The obfit program can take one scaffold and align
many molecules in a multi-molecule file.
I think you're asking if you can put say 3 fragments all on top of each
I don't use Ruby much, but I suggest you get in contact with the Rubabel people:
https://github.com/princelab/rubabel
On Jun 17, 2013, at 9:21 AM, he...@in-silico.ch wrote:
> I am trying to update our openbabel gem
> https://github.com/opentox/openbabel-gem because I cannot list or use
> descript
> Gaussian is an ab initio format and as such, does not have any notion of
> connectivity.
No, there's Geom=Connectivity. Among other things, it's useful for QM / MM
jobs. It just hasn't been a very high priority thing and at least in earlier
versions of the Gaussian website, there was no formal
> thanks for the info. Indeed I am aware that most of the time there is no
> notion of connectivity, but I ran into problems when using the
> geom=connectivity option. Right now the only work-around is not to use the
> geom=connectivity option in Gaussian with Openbabel written molecules.
Heh.
> I just noticed that the OpenBabel 3D builder gives different results
> on each run (see example below). Can I set a seed somehow?
Good question. At the moment, no. But that should be fairly easy to fix in the
development code by adding an OBBuilder::SetRandomSeed() method.
-Geoff
-
I don’t know much about Pipeline Pilot. People are, of course, welcome to sell
Open Babel binaries, provided the other parts of the GPL are met -- that is,
all source code is provided:
http://www.gnu.org/licenses/gpl-faq.html#DoesTheGPLAllowMoney
Obviously any modifications you make to the sourc
On Jul 24, 2013, at 5:25 AM, scott_m wrote:
> B(CP(C(C)(C)C)C(C)(C)C)(CP(C(C)(C)C)C(C)(C)C)C1=CC=CC=C1
MMFF94 does not have parameters for boron. Use UFF.
-Geoff
--
See everything from the browser to the database with
> I'm attempting to convert either .mol2 or .sdf to .smi from the zinc
> database.
I guess I'm not sure why you're doing this. ZINC provides SMILES too.
But I agree with David.. it'd help to know what file you're trying to convert,
and what version of Open Babel you're using. I assume on Windows
> That is wrong because arimatic atoms are missed.
> Anybody knows what could be the problem?
Looks like a bug. Can you post to the tracker with the file? I'm having trouble
copy/paste from your e-mail:
http://sourceforge.net/p/openbabel/bugs/
Thanks very much,
-Geoff
> While I like cartesian coordinates, I don't think cartesian cifs need to be
> supported in cases where a unit cell is specified. But this is just coming
> from my own experience- I've never seen people use cartesian cifs.
IIRC, the development code uses this heuristic -- if there is a unit cel
> Note that an output format is not used but something still has to be there.
> Writing the functionality as an output format -ocount as suggested by Noel
> would be clearer but I didn't find it easy to do.
I suspect the op will be slightly faster than an output format due to overhead.
-Geoff
olume between the box and the
molecule).
I suspect other people may find this useful. Should I code it up as a C++
command-line tool? (obvolume?)
Cheers,
-Geoff
#!/usr/bin/python
# Simple Monte Carlo estimation of VdW molecular volume (in A^3)
# by Geoffrey Hutchison
#
# Usage:
# volume.py
> What is the default model used to compute the partial charges?
Gasteiger. The mol2 output actually will say this.
> Is there a way to control which one to use?
Of course:
obabel --partialcharge MMFF94 …
obabel -L charges # gives a list of the installed charge models
Hmm, this needs to go i
Hi!
First off, I strongly suggest trying the development “master” from Git, which
has a number of improvements to CIF support.
> The following three points would need to be addressed:
> 1. Instead of Cartesian coordinates, fractional coordinates must be used in
> the .cif file.
> 2. The space-g
I definitely think this is a great idea. Personally, I'm a fan of Twirlymol
(https://github.com/baoilleach/twirlymol) but I think 2D depiction is also
really important here. Does iPython support SVG rendering?
-Geoff
> From: Patrick Fuller
> Subject: [openbabel] Interactive 3D IPython Renderi
> In /sources/openbabel/build/include/openbabel there was only one file -
> babelconfig.h. I manually copied all other files from
> /sources/openbabel/openbabel-2.3.2/include/openbabel/, was it the right
> idea?
Wait, what? Did you run "make install"?
> OBPlugin::List("forcefields"); also works,
> PS. in case anyone's wondering, no, a picture of a 1K+-atom molecule is
> not very useful. I just wanted to see what it'd look like.
No, it’s the 2D depiction that’s limited to 1000 atoms (SVG and PNG). Open
Babel core happily handles thousands of atoms with no problem.
If you have problems ex
> M CHG 2 3 1 6 -1
>
> is illegal. Is there a way to make openbabel understand this line?
What on earth is it trying to indicate?
It seems like you have a lot of non-standard SDF files. What is the source?
-Geoff
>> The SMILES parser has an explicit 1000-atom limit. It's unfortunate.
>
> So does the the inchi one -- I ran a couple more tests...
I'm willing to hear suggestions as far as SMILES and InChI limits, but I don't
even know if a 1000-atom SMILES would be particularly useful. That, plus the
pote
It's not a limit in *parsing*. It's a limit in *writing* the SMILES. Open Babel
will read in any length SMILES. At the moment, it stops before exporting a
molecule > 1000 atoms.
Since there's interest, I just committed a patch to the github "master" to
remove this limit. Please give me feedback
Indeed, Open Babel does support reading Dalton input files:
obabel -L formats
…
dalmol -- DALTON Input
So you can use -idalmol to specify the format as DALTON input format when
reading. The unit conversion will happen automatically.
Hope that helps,
-Geoff
--
>> ==
>> *** Open Babel Warning in InChI code
>> 2mal.pdb :Too many atoms
>
> If it's "too many to process" then it's an *error*. If it's a *warning*,
> then it's "a lot of atoms, processing may take a long time".
The issue is this .. we hand off the molecule to the
> So the .cif output from .castep files in OpenBabel is very close to useful,
> but some more changes are needed. I can provide examples, but the first
> decision that needs to be taken is where the space-group information is
> coming from: is it taken from the .cell file (i.e. a different file
The general answer to David's question is "no, but there's a lot of interest".
For example, not too long ago, Abe Heifets was asking about similar questions:
http://www.cs.toronto.edu/~lilien/lilien_projCSP.html
> I think you will find one or two reactions at Daniel Lowe's bitbucket
> account: ht
> Not really a contribution in answering the question, but I've been thinking
> about the potential uses of such an open-source database? Synthesis design?
> Virtual library enumeration? Any other ideas?
I'm interested in such a library also for teaching purposes. The idea would be
a website or
> (I would naively expect "CC" + "CCO" to produce "" and H2O, but
There are obviously multiple possible *chemical* things one could imagine. But
there’s no way code can or should make assumptions about chemical
transformations.
We do have a chemical transformation class for handling reactio
> has anyone already has experience with compiling OpenBabel 2.3.2 under OS X
> 10.9 (Maverick)?
I’m obviously compiling “master” but my laptop uses Mavericks and there’s no
problem.
Are you using boost? This should be un-necessary. Can you send me the
CMakeCache file from your build directory
I'd recommend trying Git master. I'm intending to make a 2.3.3 stable release
at some point, so I will try to track down the problem.
But as I said, I know that the latest development code compiles cleanly.
-Geoff
--
And
> I don't know if there's any real workaround for this (without changing the
> OpenBabel source). It could also be a bit of a challenge to change the
> OpenBabel code to work with this while keeping it compatible with older
> versions of MOPAC (such as the zoo of MOPAC 7 modifications that are
My suggestion would be to compile from the development "master". You can
download the source code through GitHub from here:
https://github.com/openbabel/openbabel/archive/master.zip
I believe this has been fixed. It would be helpful to know as we move towards a
2.3.3. bug-fix release.
Thanks v
> I came across a problem of converting XYZ to HIN format for imine
> compounds. In more detail, the double C=N bond in imine series is
> determined as a single bond. (As a result, atom typification for Merck
> force field is completely screwed up.)
The problem here is that the H-N-C bond angle is
On Nov 8, 2013, at 2:50 AM, David van der Spoel wrote:
> However even for good geometries OB has problems with bond orders
> sometimes as I pointed out the other day. Is there anything that can be
> done about that? Changing smiles?
Bond order perception is never going to be bullet-proof, part
I'll change the page. We now use cmake, so if you have already installed cmake,
you want:
CXXFLAGS='-g -O2 -msse3 -mfpmath=sse -fopenmp -lgomp' cmake [path to source]
I'm really not sure how the conversion can be successfully parallel using
OpenMP (i.e., the same computer). While there are some
I'm not sure what you want. You want to know that the most common isotope
(0) is, in fact, carbon 13 or something? I mean, you can round the exact
mass and this will give you the isotope. I can't think of a
counter-example. Can you?
-Geoff
On Wed, Nov 13, 2013 at 4:42 PM, Dimitri Maziuk wrote:
u
can't use Open Babel for that since we don't store or tabulate the
abundance of isotopes, only the isotopic masses and the mass for the most
common form.
Hope that helps,
-Geoff
On Wed, Nov 13, 2013 at 5:52 PM, Dimitri Maziuk wrote:
> On 11/13/2013 04:34 PM, Geoffrey Hutchison wr
> And, I got this error: "Can't locate object method "new" via package
> "Chemistry::Openbabel::OBOp" (perhaps you forgot to load
> "Chemistry::Openbabel::OBOp"?) at convert_iuphar.pl line 30." This is the
> same way I call OBConversion and OBMol, so I'm not sure why it's not working.
> Either
> I'm using version 2.2.3 of Open Babel.
I don't remember, but it's entirely possible OBOp is not included in the Perl
wrapper for that version. It's now over 4 years old.
The latest version is 2.3.2:
http://openbabel.org/wiki/Install
Hope that helps,
-Geoff
> Then I take 8 different inputs allegedly describing the same molecule
> and get 5 different outputs. According to David it's because the inputs
> are broken -- that doesn't surprise me.
Look, we all want software to be deterministic. But bugs are inevitable in
complex software, and there's a
> I don't think the problem is in OpenBabel, but I can't tell. RCSB says
> they're all describing the same molecule. OpenBabel says they aren't.
> Who should I trust and why? So I asked.
No, that's fine. We're happy that you ask these questions. :-) I'd rather know
if there's a bug in our softw
> make an isotope/mass vector a member of OBElement instead of its "mass
> Atomic mass (in amu)", but that's just me.)
The problem is that the full isotope table is fairly huge and rarely used.
Checking memory use, I see that in my programs, it's usually never even
initialized, while the element
> 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 GetPrevalentIsotope()
method? Why not just round the mass to an integer? I mean, if it's Uranium 235,
it's within 0.5 amu of 235.0.
-Geoff
--
> my $filename = $id . '.sdf';
> open (OUT, ">temp.sdf");
> print OUT @sdfdata;
> close OUT;
> $obConversion->ReadFile($obMol, "temp.sdf”);
This just seems weird. Even if you have a bunch of data, you don’t need to sa
> Thank you for the speedy replies. I attached an example 2D SDF file.
Well, you can verify for yourself that 3D generation works, e.g.:
% obabel ~/Desktop/CHEMBL100358.sdf --gen3d -O CHEMBL.sdf
# waiting.. .. ..
% cat CHEMBL.sdf
It works fine from the command-line.
Hope that helps,
-Geoff
-
If no title is set by the format, Open Babel will use the file name as a
default indicator of the origin.
Geoff
> On Nov 27, 2013, at 4:20 PM, "Noel O'Boyle" wrote:
>
> The molecule title is appended to the SMILES string in Open Babel's
> implementation of a SMILES file. When you write "smi" w
> Unless the output is svg in which case the title is "OBDepict".
I would call that a bug. I'll go fix it.
Thanks,
-Geoff
--
Rapidly troubleshoot problems before they affect your business. Most IT
organizations don't ha
PWSCF is a relatively new addition to the parser. So it's possible that it's a
new type of file that isn't read correctly. Can you send me an example file or
two?
Thanks very much,
-Geoff
On Dec 2, 2013, at 8:41 AM, Otto Kohulák wrote:
> Hello,
>
> Thank you all who are helping me with this
> Not sure if this helps at all. The whole issue is kind of confusing as
> again, the exact same code works when called from a simpler snippet that
> does not write results to a file and does not allow any options to be set.
When you say "does not allow any options to be set," do you mean the
OBC
> You're probably right, C also has to read therm, but other than recognizing
> the beginning and the end of the molecule it wouldn't do anything especially
> kekulization and bonding etc.
Actually no. Indeed this would be a useful "lazy" optimization, but is not
currently implemented this way.
On Dec 3, 2013, at 3:52 PM, Chris Morley wrote:
> In fact it is implemented this way for most common multi-molecule file
> formats. The molecules before the one specified by the -f option are
> skipped without being parsed. (The format's virtual SkipObjects()
> function is used.)
I stand corr
> inevitable will come down to applying the CIP rules. Do you disagree with
> that?
No, I disagree. Yes, there are implementations of the CIP rules in code.
Generally these are used when generating IUPAC names, and that's about it.
If I take a structure to a colleague to synthesize, I only need
> This only proves, that I really want to use it. Is the proof.py script
> working correctly for anybody (attached in previous mail)? It should ouptut
> molecules no. 5-10 out of 100 in proof.sdf
No, it doesn't work.
% python proof.py | wc
100 1001300
Hmm. Chris, any idea why this
> version contains a minimum at 0. I agree with OB implementation that this is
> not at all true but I want to know the origin of the expression you have
> used. One important feature that can be obtained in Rappé's formulation is
> that after taking the second derivative of the energy respect t
> And the one in Rappé's paper (after Towhee's correction):
> Triangular (UFF paper) -> K_ijk/9 ( 1 - cos(3t))
> Those two expressions are not equivalent. Even more they differ a lot. A
> simple plot would tell you that. They both have a minimum at 120 deg.
> Nevertheless Rappé's version contains
> OpenBabel crash more nicely with an error message rather than entering an
> infinite loop…
Right. Infinite loops are a clear bug, and "crash" certainly is too. I think
what you really mean is that it'll refuse to translate the CIF because there's
nothing in it.
Anyway, these are helpful - la
> I need to review and, in most cases, fix the SMILES chains coming out
> from OpenBabel for inorganic compounds (either manually or
> semiautomatically). I am also stuck to version 2.2.3 because versions
> newer than this perform worse for inorganic compounds.
If you can give some bug reports or
ince I can script the downloads.
As I said before, I really want to know of these types of bugs (inorganics, but
also any type of changes from one release to another).
Thanks,
Geoff
> On Dec 14, 2013, at 1:26 AM, mquiros wrote
> El 13/12/2013 22:16, Geoffrey Hutchison escribió:
>>>
> Does anyone know of a way of extracting xyz coords following symmetry
> operations from a cif file?
Sorry for the delayed reply. This is pretty easy. You want something like:
obabel file.cif -O file.xyz --fillUC strict
The “fillUC” will perform all defined symmetry operations to give the comp
>> babel -isdf 1.sdf -o mol2 2.mol2 --writeconformers --gen3D --nconf 4
>> --weighted
>
> The result, however, is a file name '4' instead of 2.mol2. If I remove the
> --nconf, i do get 2.mol2 (one conformation). Is that a bug or am I using the
> command incorrectly?
We highly recommend using
> Hope you are well. I'm trying to figure out how to install python bindings
> for Python 3. Is this functional yet?
Hi there!
Yes, Pybel has been compatible with Python 3 for a while now. What are your
problems installing the bindings?
Thanks,
-Geoff
> What is everyones opinion of fixing setup.py to be standalone and work with
> pypi and pip? I still think this would be the best path forward.
This would be great, see below.
> a. Compiling for Python should not require Cmake edits, especially with the
> excellent installers that are now ava
> I just tried to run the github pybel through Python3 on my Mac and got a
> UnicodeDecodeError in _getpluginnames. To fix, I replaced
>
Aha. Thanks, I've seen the same problem on my MacBook, but didn't really track
down the bug. It lead to un-reproducible errors when I was running a few
scrip
> Any interest in resurrecting the automated Mac build for the dashboard?
I didn't realize it stopped. I'll make a todo.
-Geoff
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