On Jan 19, 2011, at 9:36 AM, Hu, Xin (NIH/NHGRI) [C] wrote:
> Hi Geoff,
> I use CentOS 5.5 and gcc 4.1.2. Should I try other version?
IIRC, GCC 4.1 was the buggy version.
https://www.centos.org/modules/newbb/viewtopic.php?topic_id=25519
Hope that helps,
-Geoff
---
>> cmake ../openbabel-2.3.0
>> -DCMAKE_INSTALL_PREFIX=/home/hux6/Program/openbabel-install/
>> make -j4
>> make -install
>
> CMake Error at src/cmake_install.cmake:41 (FILE):
> file INSTALL cannot find file
> "/home/hux6/Program/openbabel-install/lib/libopenbabel.so.4.0.0" to
> install.
There
On Jan 20, 2011, at 1:59 PM, Hu, Xin (NIH/NHGRI) [C] wrote:
>> There must be some other earlier error. CMake is telling you that it cannot
>> find the file to install.
Do you see any errors when you run "make?"
Best regards,
-Geoff
--
> If the charges in the input file are all zero then the output file
> will contain nonzero gasteiger partialcharges.
Hmm. That would be a bug. I'll take a look.
-Geoff
--
Special Offer-- Download ArcSight Logger for FRE
Please make sure to CC the list in your messages. I'm not the only one who can
answer your questions, and I definitely have times when I'm quite busy.
> Here are more error message from "make install"
...
> file INSTALL cannot find file
> "/home/hux6/Program/openbabel-install/lib/libopenbabel.s
> Just out of curiosity - did the Molcore project fly eventually?
We're in the planning/initial stages. Getting 2.3 out the door took a lot of
work, and usually there's a bit of a lull as contributors take care of other
things (e.g., family, work, etc.).
Anyone interested in helping with MolCor
> But when I use OBAlign, and compile my program, I get an error saying it
> cannot find 'Eigen/Core'.
When you compile your own programs, you need to include flags to the compiler
to find headers, for example:
g++ -I/path/to/eigen -I/usr/local/include/openbabel-2.0 ..
Hope that helps,
-Geoff
itaut.o definition of common _pn_tRankForSort (size
> 16)
> /usr/libexec/gcc/i686-apple-darwin8/4.0.1/libtool: internal link edit command
> failed
First off, I would suggest that you make sure you have the latest CMake and
XCode tools installed. What version are you using?
Best regar
Can you send me (off-list) the result of running "make VERBOSE=1"?
Thanks very much,
-Geoff
--
The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE:
Pinpoint memory and threading errors before they hap
> But, sadly, all binary packages in repositories are for 2.2.3 version (even
> for 11.04 Ubuntu) and they are unusable :(
Well, I think you should request a package upgrade. :-) I believe the problem
is that the current Ubuntu package maintainer has been busy at a new job.
But we're glad to kno
.4.zip/download
At the very least, you could install the binary and then use the pre-compiled
libinchi:
cmake -DOPENBABEL_USE_SYSTEM_INCHI=true [other options]
Hope that helps,
-Geoff
---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
emai
> Is there a way to install Open Babel on a Solaris 10 Server from binaries or
> if it can be compiled from the source code provided ?
I don't know of any Solaris binaries, but if you have g++ installed, it should
be easy to compile from source.
Best regards,
-Geoff
> ligands in which my SMARTS pattern appears multiple times -- Its not
> clear to me how obfit decides where to do the overlay.
If multiple atom sets match in the *reference*, all such atoms are used as a
reference. If there are multiple matches in the "moving" ligand, obfit will
find the best
On Feb 18, 2011, at 11:43 AM, christophersw...@btconnect.com wrote:
> Is it possible to get the obminimize tool to output anything other than pdb
> file format?
Yes. Supply a '-o[ext]' flag. This works with v2.2 or later. Come to think of
it, *you* asked for the feature! :-)
Cheers,
-Geoff
--
ain atom
types. Otherwise Open Babel has to "perceive" bond orders and without hydrogens
to complete the valence, we have to base hybridization on bond lengths and
angles. It's good, but not fool-proof.
Best regards,
-Geoff
---
Prof. Geoffrey Hutchison
Departm
> I have managed to compile OpenBabel with the python bindings on my Mac by
> following the instructions on the OpenBabel website. OpenBabel works fine
> form the command line, and I can import pybel into python. However whenever
> I try to use pybel I get a segmentation error For example:
Y
> I am trying to install openbabel on my workstation (linux system), but
> everytime I try I got an error, I had a go with both the stable version and
> last version of openbabel available at website, both of them give me the same
> error, Here is the error, please any kind of help would be appr
> It gave me this time another error, by the way, I am a user not the
> administrator. But I defined the path to cmake and boost. Here is the last
> error:
> Workstation2/scratch/openbabel-2.3.0/include/openbabel/xml.h:176: undefined
> reference to `xmlTextWriterStartElement'
> CMakeFiles/cdxml
ut
depending on your structure, that may not work either.
The Qeq and QTPIE methods will assign charges to every element, although they
are not necessarily as reliable as Gasteiger or MMFF94 as a predictor of the
molecular electrostatic potential.
Hope that helps,
-Geoff
---
Prof. Geoffrey Hut
On Mar 13, 2011, at 3:57 AM, qiancheng shen wrote:
> smarts = pybel.Smarts([F,Cl,Br,I]C1=CC=CC=C1)
> matched_list = smarts.findall(sdf)
> /**End**/
> Can't find any matched molecule.
Right. Because that SMARTS says to match a molecule with a bunch
> I went in src/formats/mol2format.cpp, line 226...
> added this line after "if ( !elemno ) {" :
> cout << mol.GetTitle();
> and modified the error message to be sure that the modification is
> taken in account (simply modified "Mol2" in "mol2").
Well, for one, there's no "endl" for that cout, so
> Let me know when it's done, I'll try to download & compile again :)
Give it a try. The 2.3.90 version number at least indicates that it's trunk.
The new error message should also give the offending atom type, rather than a
generic complaint.
-Geoff
On Mar 16, 2011, at 5:45 AM, Pascal Muller wrote:
> The formula given by babel 2.3.90 (yesterday build) for a charged molecule, eg
...
> C16H18N3O2+
Yes, that's the idea. I think there's also some idea that it could be more like
[C16H18N3O2]+, etc.
This means that species like NO3- will give a
On Mar 19, 2011, at 3:09 PM, nms_uk wrote:
> What about when it says they have different double bond stereochemistry?
Double bond stereochemistry refers to cis vs. trans (or E vs. Z) isomers around
a double bond.
Hope that helps,
-Geoff
-
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 occurred:
> Traceback:
> File "D:\Python\lib\site-packages\
> Is there a way to get the atomic type(symbol C for Carbon, N for Nitrogen
> etc..) without the extra information?
You're looking for:
etab.GetSymbol(atom->GetAtomicNum())
This turns the atomic number into the element symbol using the element table.
Cheers,
-Geoff
> aromatic, it checks out, however when I create the same molecule manually,
> it no longer detects the bonds as aromatic.
If you're adding atoms and bonds programmatically, you should wrap the
modifications with:
mol.BeginModify();
// make changes
mol.EndModify();
The EndModify() call will res
On Apr 4, 2011, at 4:31 AM, qiancheng shen wrote:
> Thank you very much!! But all these tools are not suitable for me..Any
> other ideas?
You also asked on CCL.net and several people also pointed you to the NIH
Chemical Resolver. Noel's link pointed out that Cinfony and Webel can provide
> The files like ghemical.prm are located in the standard folder :
> /usr/local/share/openbabel (and also in /usr/local/share/openbabel/2.3.0
> If I launch, for example, obminimize in the terminal I see all the
> forcefields and the program work well.
I'd make sure that Xcode is finding the rig
I'm happy to announce the release of an updated version of the ChemSpotlight
tool for Mac OS X 10.5 or later.
ChemSpotlight is a Spotlight metadata importer plugin for Mac OS X, which reads
common chemical file formats using the Open Babel chemistry library. Spotlight
can then index and search
On Apr 5, 2011, at 11:44 AM, Igor Filippov [Contr] wrote:
> 6. CIR
> what's wrong with CIR?
Indeed. Noel even indicated open source tools which allow batch access to CIR.
Cheers,
-Geoff
--
Xperia(TM) PLAY
It's a maj
> translate coordinates, according to the formula introduced in the
> International Tables for Crystallography (2006, Vol. B, chapter 3.3), the
> results are different from those that your program gives.
Throughout the development of Open Babel, this is one area that has always made
me a little a
> cmake ../openbabel-2.3.0b2 -DPYTHON_BINDINGS=ON -DPERL_BINDINGS=ON
> -DJAVA_BINDINGS=ON -DEIGEN2_INCLUDE_DIR=/usr/local/include/eigen2
Why are you using an old version of Open Babel? The latest release is 2.3.0 -
final, not beta2. Not to mention that at some point fairly soon, there will be
a
On Apr 21, 2011, at 10:00 AM, remy d1 wrote:
> obgrep -c 'Cc1nnc(C)[nH]1' sdf-1-3500-match-triazole-result1.sdf
> 0
The main problem is the use of the explicit 'H' in the pattern. In your
structure, the "lone" nitrogen (i.e., not the nn motif) has a carbon bond. A
SMARTS pattern with an "H" re
> I am dusting off my 3D geometry as I speak to do this 'the hard way', but
> wondered if there was something I was missing...
I hadn't realized, but yes there isn't a defined API for setting angles -- in
the code itself, it's all done "the hard way" with sines and cosines.
You can certainly ge
On May 28, 2011, at 9:48 AM, Chris Morley wrote:
> This limitation is not documented and needs to be. There also needs to
> be a warning when preparing the index when the datafile is found to be
> too large. And, of course, the deficiency needs to be eliminated by
> changing the structure of t
> and then the structure.pdb file is completely empty. The same thing happens
> with Quantum Espresso files, although that's less unexpected since running
> babel -H doesn't list Quantum Espresso as a suitable format (even though the
> website claims the code can read these files).
What versio
> use the SetFactor method with different values and I found out that
> constraints were more likely to be respected completely (the processing time
> also increases) if I used SetFactor with a high value before adding any
> constraints. Can anybody explain to me if this is correct?
Yes, that's
> i want to know absolute R/S configurations at this stereo center. if you have
> module
> implementing CIP rule, it will be uselful. thanks.
We do not have an implementation of CIP rules. Yes, it would be useful, but
it's been less pressing than making sure the rest of the stereochemistry engin
> Sorry if this problem is obvious to the experts but I can’t get OB to compile
Well, you got it to compile, but as you noticed, the tests didn't all pass.
What version of gcc are you using?
"gcc -v"
CentOS has had a buggy version of g++.
-Geoff
> The files *does
> not* cause segfault with the latest checkout, so please ignore my
> question. It's already handled. Thank you!
No sweat. Obviously, we like to track down every crash.
-Geoff
--
All of the data gener
Yes, you have the infamous buggy gcc-4.1.
Try:
yum install gcc44 gcc44-c++
Hope that helps,
-Geoff
On Jun 28, 2011, at 11:27 AM, Mike Lipkin, BioFocus wrote:
> Thanks for the reply,
>
> I am using gcc 4.1.2
>
> Currently I have openbabel 2.2.3 installed and two programs using it
> (I don't
On Jun 29, 2011, at 8:36 PM, Ruggero Gabbrielli wrote:
> Hi, I don't sem to be able to add hydrogen to a graphene patch. Is this a
> known issue?
Can you define the problem? It takes a long time? It completes, but doesn't add
H atoms where you expect? What version of OB are you using? What OS?
On Jul 5, 2011, at 3:07 PM, Ricardo Righetto wrote:
> am an Avogadro/Open Babel user and I'd like to add a cif==>xyz conversion
> functionality in a MATLAB/OCTAVE program we develop at our lab (
> http://megacell.lnls.br ). It would be really valuable for us to provide this
> support. Of cours
> I am attaching a copy of a file I tried to convert to POV, I built the
> molecule in Avogadro.
Sorry, I missed some of the discussion here, but if you built the molecule in
Avogadro, why don't you save the POV-Ray file from Avogadro? These files should
be self-contained.
Cheers,
-Geoff
-
> I commited yesterday a patch to the svn tree, so that missing cell angle
> values will be interpreted as 90° - with an OB warning.
Great, thanks! I'll make sure this gets into v2.3.1.
-Geoff
--
10 Tips for Better Web Se
lps,
-Geoff
---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geo...@pitt.edu
web: http://hutchison.chem.pitt.edu/
--
Magic Quadrant for Content-Aware Data Loss Preventi
> After you pointed out that it's not finding cmake.exe, I realized that I'm
> using cmake 2.8 so I just changed the 2.6 for 2.8 in the 64-bit build bat
> file and it worked. Nevertheless I got a couple unresolved externals when I
> tried to compile. These are:
> _imp_FreeStructFromINCHI
> _imp_
> FNK_ideal.pdb contains a full set of CONECT records; is there some way that I
> can get babel to use only those records and not add extra bonds based on
> atomic proximity? I see the -ac option to ignore CONECT records, but that's
> not what I want.
You want -ab to ignore the perceived bondi
On Jul 28, 2011, at 12:57 PM, Thomas Womack wrote:
> Thanks, but I'm afraid that leaves all the bonds marked as being of order 1
> and all the atoms as SP3-hybridised; is there a way that I can use the
> perceived bond orders on the assumption that the CONECT records get the
> topology right?
On Jul 29, 2011, at 7:31 PM, Jimmy G Lafontaine Rivera wrote:
> I have one more question. Is there anyway to differentiate between a ketone
> and an aldehyde in a substructure search?
Sure. See, for example:
http://www.daylight.com/dayhtml_tutorials/languages/smarts/smarts_examples.html#GROUP
> 1) there are structures that have information in labels. So sometimes the
> stereochemistry at a particular center is is given by a dummy atom nearby
> with a label 'R' or 'S'.
I think this is a perfect example of how "standard formats" quickly become
complicated by "in practice usage." If y
On Sep 15, 2011, at 8:33 AM, Noel O'Boyle wrote:
> I understand what you're saying, but that is on purpose. The library
> API is geared towards converting files, rather than returning string
> representations for further processing.
There is, of course OBConversion::WriteString(&mol, true), whic
> Actually, I used WriteString() when I got that extra newline character:
>
> my $inchi = $obinchi->WriteString($obmol);
my $inchi = $obinchi->WriteString($obmol, true); # trim final whitespace
Hope that helps,
-Geoff
> Indeed
> babel svgError.sdf svgError.svg
> --> Segmentation fault
Strangely, I don't get a segfault, but I do get a hang:
#2 0x0001001434df in OpenBabel::TSimpleMolecule::getBond
(this=0x1041f8000, index=61) at mcdlutil.cpp:1618
#3 0x000100161312 in OpenBabel::TSimpleMolecule::bondsOv
On Oct 5, 2011, at 4:31 AM, green69 wrote:
> Please, does anybody know if there is a way to calculate the partial charges
> independently from those of input file?
The command you used would generate Gasteiger charges. If the input file
already has Gasteiger charges, the result will be the same
> I have noticed that some smiles codes give odd results when converted to a
> mol2 file. For example when I convert NC(Cc1ccc(cc1)O)C(=O)O
> tyrosine_100_0_n_3601_10 to mol2 I get:
The first column is an atom label -- Open Babel recognizes that you supplied a
tyrosine residue, so it uses the st
On Oct 7, 2011, at 11:32 AM, Elliott Rapp wrote:
> Geoff,
>
> Yes it does. I turned residue off (output ignores residue information) but I
> noticed that it still numbers the individual atoms (i.e. C2, C3, O2, O3,
> instead of just C,C,O,O). Is there any way to turn that off?
These aren't
cture, and features of the toolkit.
Thanks to Noel M. O'Boyle, Michael Banck, Craig A. James, Chris Morley, and Tim
Vandermeersch!
-Geoff
---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geo...@pitt.edu
web: http://hutchiso
mitted feedback, bug reports, and code.
Cheers,
-Geoff
---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geo...@pitt.edu
web: http://hutchison.chem.pitt.edu/
--
All t
On Nov 14, 2011, at 4:14 AM, Hassan Thomas Mamdani wrote:
> CMake Error at cmake/modules/FindEigen2.cmake:32 (file):
> file Internal CMake error when trying to open file:
> ~/tools/eigen/Eigen/src/Core/util/Macros.h for reading.
> ...
> Everything else is fine, the only other warning in the o
On Nov 17, 2011, at 1:22 PM, Andrew Dalke wrote:
> # In Open Babel 2.3.0, OBConversion() must be called before trying to
> # find any plugin. This was not needed in earlier releases.
> ob.OBConversion()
There's a patch under discussion that would eliminate this for 2.4. Basically,
we switched f
> 1. is it possible to generate the full set of rotamers ( any specified
> amount) rather then one with the lowest energy? If ansew to my question is
> yes, then HOW Can I ask f.e about structures of top 100?
> 2. by default. this program calculates # of rotatable bonds and # of
> rotamers
> Hello, i'm installing the 2.3.1 release.
...
> /home/aristegui/openbabel-2.3.1/include/openbabel/obutil.h:85: error:
> âgettimeofdayâ was not declared in this scope
> make[2]: *** [src/CMakeFiles/openbabel.dir/alias.o] Error 1
> make[1]: *** [src/CMakeFiles/openbabel.dir/all] Error 2
> make: ***
> But babel reports "1 molecule", see below
> Please advise,
This is more of a wording question. "1 molecule converted" really means "I read
in one molecular system 'record', where a record may contain more than one
fragment."
Obviously the latter is a little too long to print easily. :-)
Hope
> Specifically, I was wondering if there is an example of how to use
> OBConformerSearch from Python (and is there a way how to use this directly
> from the command line?).
Sorry the documentation isn't online -- we should definitely fix that. It's
easy to use from the command-line:
obabel -L
On Dec 9, 2011, at 12:12 PM, Geoffrey Hutchison wrote:
> As of yet, no. That could be done new scoring function (e.g., minenergy)
> which determines the energy after some minimization. It's a good idea.
OK, that seemed like an easy task, so SVN trunk now has "min" as a s
> Very cool! :-) I'd be for having this in Open Babel. In fact, I think
> you should also consider it as an output format.
Indeed, this would be a nice test of "roundtripping" names. :-)
> Regarding the specifics, I'm just wondering whether the format should
> be renamed to include the word "web"
This e-mail has been long delayed. As 2011 draws to a close, Open Babel is over
10 years old! At this point, it's used by over 40 open source projects,
downloaded over 200,000 times, and been used in over 400 academic papers. And
of course, there have been 15 releases and dozens of contributors.
> IMHO, OBv3 goals have been set some time ago and many of them are completed
> now, so its completion
> should be pursued first since its easier and faster to work with the
> existing code, especially when most of the functionality is already
> there. That should be v3. MolCore could come later a
r major release, v4, etc.). That's our numbering scheme.
> In our university we have a course on opensource and I'm considering to
> use that as an excuse to do some OB programming next semester :)
Glad to hear it. We'd be happy to provide any guidance or pointers needed.
> I get one big file with multiple Molecules within. The file will look
> something like this:
>
>
>
> Heptane
>
Well, the biggest problem I see is that as you've written it, it isn't any
particular format supported by Open Babel. CML would probably be the best, and
it does support multiple
> the -m option works good, but is there anypossibility to make the filename
> the molecule name?
IIRC, the answer is still "no, but it's fairly easy to do"
http://sourceforge.net/mailarchive/forum.php?thread_name=BANLkTimwxP%3DkUsu%3DDDn9yr6j2UShL852ig%40mail.gmail.com&forum_name=openbabel-discu
On Dec 28, 2011, at 2:24 PM, Prashanth Athri wrote:
> I was wondering if there is an 'optimal' path to do the following using OB
> C++ library:
> 1. Read protein (PDB -- well formatted)
> 2. Mutate one residue with another at specific points (say I have a vector of
> OBMol's with all amino acid
> i will need to have a format suitable for RMG (reaction mechanism
> generator).
> The format that RMG needs looks like that:
I think you'll need to ask the RMG folks how they input data. While I know they
use Open Babel, there is no "RMG format" in Open Babel.
Best regards,
-Geoff
---
> obfit '(c1c1).(c2c2)' mol1.sdf mol2.sdf
Open Babel does not support the '.' operator in SMARTS. So obfit can't support
fitting multiple fragments at once.
Hope that helps,
-Geoff
--
RSA(R) Conference 2012
Mar 2
> I would like to calculate the energy of a molecule (using the mmff94 force
> field). I do *not* want to do minimization, just read off the energy value
> programatically.
>
> I see that there is an "energy" attribute in pybel -- but the documentation
> at
> http://openbabel.org/docs/dev/Use
abel will preserve a comment in a different format (e.g., Mol2)
and store that into an SDF. It attempts to retain such data, although to a
human, it's obvious that these are separate tags.
That's my guess as to the origin of the first line comments in your files.
Hope that helps,
-Geoff
> Im asking because I am using CDK and OpenBabel, and I am suffering of
> interoperability problems, because both tools have different ways of
> defining aromaticity.
There is no unified aromaticity model in chemistry. I'm not sure the
aromaticity algorithm in Open Babel is publishable, and even
> I have a thought about mol2 files form Dock program, which contain
> additional information in commentary (###). Those information is being lost
> during openbabel operations, which is a pity. I'd like to propose a in/out
> option for mol2 for Dock'ed mol2's to read/write compatible information f
ult, since InChI intentionally
uses a "canonical ordering" of the atoms, which will almost definitely not
match the PDB file.
If that's not what you're trying to do, could you be a bit more specific about
your goals?
Thanks very much,
-Geoff
---
Prof. Geoffrey Hutchison
Department o
> Let me start with a little more background on the problem. I am using Pybel
> to extract the information I need about a set of ~875 PAH molecules
> (including alkyl substituted and radical PAHs).
...
> "signature" of an error is typically that a C atom is labelled as sp3
> hybridized when it o
> And in that python file, when I typed "import openbabel" then it didn't work.
> However when I typed "import openbabel" in python command line or run a
> python file with openbabel, it didn't call error.
> It works very well.
Well, I'm not an expert at ajax, but I suspect the server's error log
> Fingerprints are 1D therefore similarity search is 1D. To my knowledge there
> is no shape similarity search in OB.
The Spectrophore techniques are shape dependent.
http://openbabel.org/docs/current/Fingerprints/spectrophore.html
-Geoff
-
set of bonded atoms defined by atom numbers you supply -- you really don't care
about the SMARTS matching feature of obrotate at all, correct?
If so, I'd suggest you just hack obrotate.cpp to your needs. I don't have time
tonight, but it's not a huge ordeal.
-Geoff
---
nd suitable to scripting -- use SetLogFile() and set
the log level using SetLogLevel(). The OBFF_LOGLVL_HIGH level should give each
component of the forcefield energy.
If you have a reasonable suggestion for API to query this, I'm open to it.
Hope that helps,
-Geoff
---
Prof. Geoffrey Hutc
> I followed your advise. After editing the CMakeCache.txt and adding the
> compiler flags OpenMP is working for me. However, I would like to avoid
> this additional step by adding some conditional compilation lines to the
> CMakeLists.txt
This seems reasonable, since OMP_NUM_THREADS is needed
On Jun 20, 2012, at 4:26 PM, My Th wrote:
> IMHO this should be wrapped in a cmake flag to enable/disable during
> configuration so it can be explicitly turned on/off as needed, not just
> rely on automagick feature discovery.
My apologies -- I had the same thought earlier today. In SVN trunk, y
> I think I'm using the latter and other hydrogens are added, but not the one I
> mentioned. Using version 2.3.
Ah. I just looked through the gen3d code to see why this is happening:
> pmol->AddHydrogens(false, true); // Add some hydrogens before running MMFF
So if you're using code, you wa
othing
ff.SteepestDescent(1500, 1.0e-4)
ff.WeightedRotorSearch(250, 25)
ff.ConjugateGradients(2500, 1.0e-6)
# now we've updated the coordinates internal to the ff object
> ff.GetCoordinates(mol)
Hope that helps,
-Geoff
---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (
> Dens_A number*(occupation number)
> (total nr. of points)
If you're willing to work from the SVN trunk and compile a new binary of Open
Babel, I can definitely hack that.
-Geoff
---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel:
> Having problems compiling latest source code for Openbabel on Mac OS X
> (Lion). Don't think the error is a Mac issue, but I'll let you judge...
> Cmake and make output below.
This was just posted to openbabel-devel. A recent commit (r4990) broke things.
I'll make sure it's fixed later toda
Himalayan Bioresource Technology)
> Council of Scientific and Industrial Research,
> Palampur, Himachal Pradesh,
> India-176061.
>
>
---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geo...@pitt.edu
web: http://hutchison.chem.p
On Oct 9, 2012, at 1:58 PM, David van der Spoel wrote:
> So is there any defined plan for what goes into 2.4 and when it should
> be ready?
...
> I can live with a development version as well (trunk?) for a while but
> since we're considering linking openbabel in with gromacs at some stage
> (
Hi,
It's much better to e-mail the openbabel-discuss mailing list, since there are
many people who can potentially answer your question. But I'm not sure what
your question is. It sounds like you want to know for each compound how many of
these SMARTS (fingerprints) match? Is that correct?
Bes
> Is pybel suppose to support 'copy' format? I try to make it work, but it
> generates empty string.
No, the copy format relies on the C++ stream code. But why would you need it?
In Python, you *have* the original file or string.
So I'm a bit confused.
-Geoff
Can you be a bit more specific? Are you trying to use the command-line
interface? If so, what version of Open Babel are you using? Older versions will
only save one conformer.
Thanks very much,
-Geoff
On Nov 5, 2012, at 9:01 AM, Ioanna Kalvari wrote:
> Hello,
>
> I am trying to generate confo
est_unitcell
> [100%] Built target test_unitcell
So "make" went through to 100%. Just run "make install" and you're in business.
Hope that helps,
-Geoff
---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0
> I got a cmake inside of Cygwin and another one for Windows 7 itself. ... I
> could try uninstalling the Windows CMake.
This is certainly possible. IIRC, Cygwin tries to grab commands from the
Windows path.
-Geoff--
L
> Ah perfect perfect! Thanks so much! Your response time is amazing, you
> ought to sleep sometime, its 1:35am PST!
Noel is amazing, but he has the advantage of being in the UK. :-)
-Geoff
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