> How can I tell what version of OpenBabel I have installed? Is there
> a command I can run?
babel -v # gives version info
babel -H # gives the full help text
> When a new version comes out, do I have to uninstall the old version
> before installing the new one? How DO I uninstall it if I d
> Anyone knows what is the period of OBRandom? I am trying to simulate
> a long-time system, so I want to know that. Is it 2^32?
It's not that great of a random number generator. (We'll be replacing
it in the future.)
My suggestion? If you want a good random generator in C++, use boost:
http:
> I am struggling with the geometry optimization routine "obminimize"
> within Open Babel. It works perfectly, but I wonder how I can put
> the resulting structure back into a *.mol2 file, since the result
> only appears in the command window.
You can redirect output to the terminal, e.g.:
On Oct 12, 2009, at 2:00 AM, sourceforge@dfgh.net wrote:
> But the terminal output geometry from obminimize is always in PDB
> format, isn't it?!
Good point. :-)
I'm happy to add an output format flag to obminimize. If people want
patches, I'd be glad to send them -- but it otherwise woul
I am very proud to announce the availability of Avogadro 1.0.
Avogadro is a free, open source, cross-platform molecular editor
designed for flexible use in computational chemistry, molecular
modeling, bioinformatics, materials science, and related areas.
Packages are available for Mac OSX,
> One more thing, why do we have two different codes obprop and
> obrotamer, is it possible to include print rotatable bonds by
> running obprop , can we do that.
The definition of rotatable bonds is slightly different. The obprop
program uses a general rule -- think of it as indicating the
> Also, I noticed that babel -V returns :"Open Babel 2.2.1 -- Mar 1
> 2009
> -- 19:20:41" instead of 2.2.3
Please run the following commands:
uname -a
which babel
ls -l /usr/local/bin/babel
I'm obviously surprised that you had problems with the Mac package,
since I compile it the same wa
> OpenBabel can export this way from a file containing all structures.
Yes, usually. I could give you an example if you told me a bit more
about the specifics of the formats involved. But let's take this for
an example:
babel file.sdf -xk "#n B3LYP/6-31G* Opt" -ocom -m
That should split the
> Thanks for your reply, i was using smiles to view the
> structure, so few are in smarts. I just wanted to convert smiles to smarts
> and smarts to smiles.
SMILES is a subset of SMARTS, so any SMILES string can be used as a SMARTS. The
reverse is not true. I can design many SMAR
> I have tested a few RXN files on Openbabel GUI on Windows but 0 result has
> been output. One of the RXN file is attached.
RXN format is definitely supported for reaction conversion (e.g., to CML
reaction formats). What exactly are you trying to do in the GUI?
Thanks,
-Geoff
; John Evans Professor
>
> Department of Chemistry and Biochemistry
> University of Denver
> FW Olin Hall 202
> 2190 E. Iliff Ave
> Denver, CO 80208
> 303-871-2995
> FAX 303-871-2254 (chem)
>
>
>
&
> According to Openbabel's wiki this format is following the specification of
> Symyx CTFile at http://www.symyx.com/downloads/public/ctfile/ctfile.jsp. But
> I have observed it does not.
I perhaps should adjust the wiki to point out that the CTFile specification has
changed repeatedly. I haven
On Nov 20, 2009, at 1:00 PM, Andrew Dalke wrote:
> But OB only generates a warning for them, which seems acceptable.
> (Though it would be nice to also know the line number of the problem.)
I think we can arrange line numbers in the warning. :-)
> Also, your suggestion "It would be more appli
Great! I just added it to the list of Open Babel projects.
I hope you'll find some interested users, it certainly fits in with a number of
interesting projects.
Best regards,
-Geoff
--
Let Crystal Reports handle the repo
> Could anyone help me to get energy minimal value for more than 2
> decimal places, i need atleast 5 decimal places. For example
I highly doubt the molecular mechanics energies have more than 2-3 decimal
places of accuracy in either the model or implementation. (Yes, the
implementati
> Does anyone have any experience with converting molecular files to the povay
> format?
There is a "babel31.inc" file which should be placed somewhere in your PovRay
installation. This processes spheres vs. ball-and-stick, etc.
If you can't find yours in the installed Open Babel, you can get i
> How else could one identify which atoms in a nucleic acid residue are
> backbone, sugar or purine/pyrimidine?
The code is a little strange -- I hadn't looked at it before. The real work is
happening in residue.cpp::GetAtomIDNumber() which processes the properties
based on the atom labels.
I d
> When typing "make" on the terminal, I got some error messages as follows:
>
> make[3]: *** [forcefieldghemical.lo] Error 1
The problem is that the key error would be on the 3-4 lines above this, so we
cannot know for sure the problem. It would also help to know what Linux
distribution you ar
> Jolotium is no longer a correct name but the Russians may still prefer it for
> political reasons or something. Maybe it's worth adding it to
> OBElementTable?
> Again, I think it would be more of a political statement than a useful
> feature. :)
Open Babel generally doesn't keep the full
> generated by babel? One can highlight chiral atoms inside smiles using
> an asterisk when one does not wan't to give the absolute configuration.
There is currently no option to do this. The code could be modified, but I'm
not sure which software would accept the resulting SMILES.
Traditionally
>> I have seen in previous posts to this mailing list that
>> pybel.readstring("smi", "CCO").draw() would do the job for ethanol.
>>
>> My questions are:
>> Which is the algorithms that works beyind the scenes? depict?
>
> The ab-initio 2D coordinates are generated by the MCDL algorithm by Trepal
> Somebody told me that openbabel can get the hybridization of a molecule.
> Anybody can tell me how I can get it?
I'm not quite sure what you mean by "hybridization of a molecule." I assume you
mean, hybridization of atoms in the molecule.
Yes, you can write a simple program to get the hybridi
On Jan 26, 2010, at 12:20 PM, Robert DeLisle wrote:
> you get a different bonding pattern. See attached. It appears that babel is
> having issues with the bonding pattern (due to aromaticity detection?) of the
> tricycle.
This is clear. I'm sorry, since I'm a bit late coming into this. Can s
> Then I recognized the OBFieldForce class (example used in the obenergy tool)
> and I got rather large energy values in kJ/mol for molecules of at most 240
> amu. Finally I built in the energy minimizing step (using the
> pFF->ConjugateGradients(1)), but only the energy values of small
> m
> As far as I can tell, using a weighted rotor search calculates the energy
> for the scorings but doesn't do minimization.
It's useful to start with a pre-minimized structure, but yes, a weighted rotor
search will do some number of steepest descent optimization steps for each
generated conform
> appearance) index of the SDF file atoms and the (order of appearance)
> index of the atoms in the newly created SMILES string.
This would no longer be a canonical SMILES -- it would be a "regular" SMILES,
where there may be several SMILES strings with different ordering.
There are ways to crea
> babel -isdf yournoncanonicalsdf.sdf -osmi yoursmilesfile.smi -xcx
>
> The -xc part should output canonical smiles, and -xx gives me the
> X-coordinate of the atoms in the order they appear in the canonical
> SMILES string. Is this usage safe/correct? Is the canonicalization
> algorithm in -osmi
> I'm trying to get canonical smiles generation to work properly and someone
> recommended I install the SVN version of openbabel. I used svn to download
> the source, but there was no configure file included and I was therefore
> unable to proceed. Please help.
The "trunk" development versio
> I'm trying to design a calculator for use with ASE (Atomic Simulation
> Environment: https://wiki.fysik.dtu.dk/ase/) which uses openbabel to get
> energies using UFF and ghemical (for now). For this, I have a couple of
> questions.
Two quick notes, since I see Noel answered some of the other que
> Forces on individual atoms will do just fine. I didn't find them in the
> documetation, however. Can you give me a pointer?
Some information is in the OBForceField class with GetCoordinates()
http://openbabel.org/api/2.2.0/classOpenBabel_1_1OBForceField.shtml#8be38bcae14834b6849d777e19885955
Yo
> 1) Is it possible to compare two databases using obgrep, I mean if I have
> not only SMARTS pattern, but for example
> the datasets of ligands which I want to use against other dataset?
It sounds like you want to perform some sort of "diff" between two databases?
That's an interesting use,
Well, if you're having problems, please submit a bug report, and attach the
file that's causing the error.
https://sourceforge.net/tracker/?atid=428740&group_id=40728&func=browse
Thanks very much,
-Geoff
On Mar 22, 2010, at 1:43 PM, tejal.s...@chem-is-try.com wrote:
> Respected sir,
>
> I am
> We are looking to pointers/examples, explaining atom hybridization matching
> "^" , implemented in OpenBabel . Is there additional information to the one
> found at http://openbabel.org/wiki/SMARTS page?
I suspect your question is "how do you determine hybridization?" The rules are
given in
> I have installed openbabel version openbabel-2.2.2 locally on my linux
> system. There were no errors after installation.
What version of Linux are you using? Do you know what compiler version you are
using?
Thanks very much,
-Geoff
---
TJ
> Also, it appears the residue names DA, DC, DG, DT and DU are commonly used in
> pdb files.
> I think these are the deoxy versions of A, C, G, T, U.
> Is there any chance of getting these processed properly and maybe adding
> those to OBResidueIndex namespace?
Yes, the DA, DC, DG, DT, and D
n
Babel developers:
http://avogadro.openmolecules.net/
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/
--
Downlo
> I have done some coding on the basis of your suggestion. My present code
> gives me the Molecular Weight and Number of bonds present in SMILES. Now I
> want to know other vital information like how many rings, double bonds and
> triple bonds are present in SMILES. My code is as:
...
>> FO
> Where does OpenBabel store atom names? I realize not all formats have
> named atoms, but some (e.g. PDB) do, and I'm not sure where in the
> OBAtom/OBMol/other objects I can find this info.
For PDB-related formats, these are stored in the OBResidue:
http://openbabel.org/api/2.2.0/classOpenBabe
does not work with modern compilers.
The latest release is 2.2.3.
Best regards,
-Geoff
---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geo...@pitt.edu
web: http://hutc
On May 19, 2010, at 6:22 AM, Gleb Sitnikov wrote:
> Hello! I am compiling latest (thru svn) OpenBabel code with wxWidgets on
> OpenSolaris 2009.06. I got this file "src/CMakeFiles/openbabel.dir/flags.make"
...
> Did you note "-mt;-D_REENTRANT"? The fact is OpenSolaris doesn't support -mt
> flag
> I faced a problem when I wanted to configure openbabel-2.0.2
...
> I recently installed Ubuntu 10.04 - could this be a problem?
If you installed Ubuntu, you can install the Ubuntu openbabel package. The
latest source version is 2.2.3.
Cheers,
-Geoff
> You need create an OBPairData (a subclass of OBGenericData), and apply
> it to the molecule using OBMol.SetData. I usually grep the OpenBabel
> source for examples of things.
There are also working examples in the API documentation, e.g. (see the
Detailed Description):
http://openbabel.org/api
Chris and Noel have made comments already, and I generally agree with them. I
have only added comments where I felt it was needed.
> SMILES support is good, although it doesn't have support for stereochemistry
> around double bonds. Excepting this lack, canonicalization is also good and
> wide
On Jun 8, 2010, at 10:43 AM, Andrew Dalke wrote:
> On the topic of documentation quality (which Geoff asked about), how does one
> find this out?
> Go to http://openbabel.org/wiki/Develop and there's mention of FP2, FP3 and
> FP4 but not MACCS fingerprints.
Point taken.
> (BTW, what's the rea
On Jun 8, 2010, at 11:20 AM, Andrew Dalke wrote:
>> There is automatic recognition of which of several computational
>> chemistry programs a .out and .log files came from.
>
> My understanding of the format support, admittedly incomplete, is that one
> specifies the format, and that's mapped t
On Jun 8, 2010, at 11:24 AM, Robert DeLisle wrote:
> If/when you fix it, please post back what you did so that others can benefit.
...
> "This application has failed to start because MSVCR80.dll was not found.
> Re-installing the application may fix this problem."
The other possible issue is th
> I have about 50 MOPAC Z-matrix files for which I need 2d
> representations for publication.
Here's one easy way -- without needing to install anything else. I'm assuming
you can use a Linux box with bash, or something similar. I use "curl" but
"wget" can also work here with slightly different
> If not, would it be possible to add it to the python interface? That
> would be very helpful to check if certain features are present or not if
> a script is run on another machine.
Sorry for the delay. For the development version ("trunk") I added a function
for this, which will be incorpora
> I edited "src/forcefield.cpp", adding this line:
> rl.SetFixAtoms(_constraints.GetFixedBitVec());
Well, that's not quite kosher, since the constraints will return a temporary
variable, and SetFixAtoms wants a reference. It's easy to fix, though.
> Hopefully this is an appropriate place to po
> g++ -Wall -L/home/athri/openbabel-2.2.3/src/.libs/
> -I/home/athri/openbabel-2.2.3 ./ex-1.cpp -o ex1
...
> The compiler does not find mol.h [“openbabel/mol.h: No such file or
> directory"]
Well, if you want the header, you'd need something like:
g++ -Wall -I/home/athri/openbabel-2.2.3/includ
> I am doing a conversion of a multi-mol2 file to the individual mol2 files
> with openbabel (openbabel –imol2 $.mol2 -omol2 $.mol2 –m) and in the course
> of the conversion I receive the warning message “no hcounts”.
Sorry, I just saw this message myself. It's a warning when Open Babel is
perc
> isomorph code (identity checking), so in the meanwhile we would have
> to specify a convention such as all molecules with the same title are
> the same.
I've been thinking about this for a while. The easiest detection is that:
a) The number of atoms is the same
b) The element list is the same (a
On Jul 12, 2010, at 12:45 PM, Tim Vandermeersch wrote:
>> So far I see only SetAtomicNum to specify atom type, but nothing to set
>> the atomic label to something like "R1".
>
> You can use AliasData for this.
See src/formats/mdlformat.cpp for an exact example.
Hope that helps,
-Geoff
---
> I am using OBMol->GetMapList to get the occurrences of fragments in
> molecules. I'm not to sure that everything works correctly, though.
...
> obconversion.ReadString(mol, "C1(N=C(NC(C)C)N=C(N=1)OC)NC(C)C");
...
> smartsPattern.Init( "N" );
The SMARTS pattern "N" matches only non-aromatic nitro
> downloaded through SVN (20 July 2010), fails to assign correct atom
> types to pyridinium ion; namely, aromaticity is not perceived, and all
In what form are you importing the molecule? SMILES? PDB? If there is no
assigned formal charge to the pyridinium nitrogen, then there is no guaranteed
ding them as starting from a
> SMILES string?
I believe SDFile would work just fine.
Best regards,
-Geoff
---
Prof. Geoffrey Hutchison
Assistant Professor, Department of Chemistry
University of Pittsburgh
http://hutchison.chem.pitt.edu/
Office:
> For example, if I read in a mol2 into OB and wish to delete a carbon atom,
> replace it with an oxygen and re-write that into a new file (that has all the
> carbon’s extra hydrogens deleted and in general a chemically correct
> molecule). Something in those lines.
>
I think that would be som
> I've attached an example sdf file with 20 structures, all of which show this
> behaviour.
> I hope someone can take a look and see if I'm doing something odd or how I
> might correct this.
As Craig said, you're not doing anything odd. Breaking ties is tough, and this
type of testing really tax
I always flag a few e-mails for upcoming releases. Do you still want to propose
a different ordering for FindAngles / OBMolAngleIter?
-Geoff
On Apr 23, 2009, at 5:35 PM, Iordan Hristov wrote:
>> The Open Babel "FindAngles" method doesn't work like you're expecting.
>> Instead, it starts at the
ope that helps,
-Geoff
---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geo...@pitt.edu
web: http://hutchison.chem.pitt.edu/
--
The Palm PDK Hot Apps Program offers
> You didn't say whether you are using the subversion trunk or not - it
> sounds like you aren't. See http://openbabel.org/wiki/CMake for
> information on checking and compiling the development code.
Or if you think the PDBQT format is close to ready, you can also send it to
Noel or myself and we
On Aug 17, 2010, at 11:43 AM, Brian Smith wrote:
> get is why openbabel is picking up these libraries at all the e...
> definitions are in /usr/local/include/zlibemboss.h and the EMBOSS zlib
> library is /usr/local/lib/libezlib*, so why should they ever be found by
> openbabel?
Well, that's m
> that are in the openbabel docs directory which uses dioxin as an example
> as well as one Ive tried. Ive got the babel31.inc file being found by
> povray, I was wondering if there was anything else I needed to do?
Generally no. Are you sure there are lights?
-Geoff
-
> What is the equivalent of the option "--disable-dynamic-modules" in
> configure script for cmake?
cmake [...] -DBUILD_SHARED=OFF
Hope that helps,
-Geoff
--
This SF.net email is sponsored by
Make an app they can't li
> It turns out that I have v4 of the dylibs
Do you have Open Babel installed anywhere else? You mentioned MacPorts. Did you
install OB at any point using MacPorts? I'd check /opt for a "v3" dylib.
Something is picking that up.
Hope that helps,
-Geoff
> openbabel command line, it would seem that the results are different
> from those obtained with the AddHydrogens() method embedded in the pybel
> library, with the correctforpH option.
Well yes, if you're comparing AddHydrogens() with and without correctForPH,
then the results are different.
> conversion works, but the inchikey WriteString() command that
> immediately follows gives the inchi string, not the inchikey. (yes, i'm
> using SetOptions("K",conv.OUTOPTIONS)).
It would be incredibly helpful if you could post the actual code.
Thanks very much,
-G
On Sep 9, 2010, at 1:53 PM, Michael Lerner wrote:
> gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386
> -isysroot /Developer/SDKs/MacOSX10.5.sdk
> -I/Library/Frameworks/Python.framework/Versions/6.2/include
> -I/usr/local/include -I../../include
> -I/Library/Frameworks/
On Sep 15, 2010, at 11:31 PM, hao wang wrote:
> warning:Problem reading a MDL file
> cannot read creator/dimension line line
Well, you clearly have a non-standard MDL file. Open Babel does its best to
translate it, but it wants you (the user) to understand it's not a standard MDL
file. Persona
> Can you teach me how to add hydrogen for each molecule by babel?(I know how
> add this for only one molecule) I have many molecules. I want to know a batch
> way.thankyou!
> How to write the command line for this problem?
Well, if you're using the command-line and you have one file with multip
> Create a list? :) I'll need to google and find an exemple to copy
> paste... hope to find some code easy to understand.
There's plenty of code in src/mol.cpp, for example for deleting hydrogens:
OBMol *mol;
OBAtom *atom;
vector::iterator i;
vector delatoms;
for (atom = mol.
> For Murcko framework generation using pybel, I would like to reset the
> stereochemistry. Even after hydrogen deletion, the E/Z stereochemistry
> is conserved. Is there any way to reset the stereo?
Well, if you're using Python, there's an easy way to reset the stereochemistry
of a SMILES. Just
Dear Paolo,
> atom types and/or MMFF94 charges. Included is a test.sdf file which
> triggers the misassignments, so you may test yourself the results before
> and after the cure.
Thanks very much! This is a big help. We're also trying to track down some
strange mis-assignments of atom types in c
> preliminary random rotor search. If this distance in the input structure is
> close (~0.1Å) to the constraint requirement, things turn out fine, but things
> go badly wrong when it's not close; the molecule basically blows up, and
> other curiosities occur, such as the CG optimization being bo
On Oct 6, 2010, at 9:42 AM, françois Bagaïni wrote:
> But When I fit the Nterminal ends of both molecules (initial conformer and
> the result of the program), the C-terminal end is not superimposed. It looks
> as if minimization can't deal with geometrical constraints. What's wrong in
> my prog
, we will be working on fixing up the documentation the website, etc.
Let us know what you think -- we look forward to a good release on Oct. 23rd.
Thanks,
-Geoff
---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geo...@pitt.edu
web: http
Yes, this would definitely be a bug, although I can see that it's ionizing an
alpha-beta unsaturated ketone.
But I would ask you to try with 2.2.99 / 2.3.0 rc1, since this will shortly be
the newest stable version and has a lot of fixes over 2.2.3.
Thanks,
-Geoff
On Oct 12, 2010, at 10:55 AM,
On Oct 21, 2010, at 12:13 PM, JP wrote:
> A colleague of mine and myself noticed this 'interesting' behaviour earlier
> on today - and I thought I'd drop you an email to get your feedback on this.
Mol2 has this strange feature that carboxylates are evidently supposed to be
marked with "aromati
) unless I hear some obvious flaw
in rc2.
Thanks very much for all the hard work and contributions,
-Geoff
---
Prof. Geoffrey Hutchison
Assistant Professor, Department of Chemistry
University of Pittsburgh
http://hutchison.chem.pitt.edu/
Office: (412) 648-0492
ports, 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/
--
Nokia and AT&T prese
t can handle de novo molecular
design and fused aromatic ring systems. (evil grin)
Thanks for any suggestions,
-Geoff
---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geo...@pitt.edu
web: http://hutchiso
o have some level of screening against truly challenging
targets.
Thanks,
-Geoff
---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geo...@pitt.edu
web: http://hutchison.ch
ow what the problem
is. Certainly the '-r' option should work to run StripSalts.
Can you send us part of the SDF? If it's a secret, feel free to e-mail me
personally.
Thanks very much,
-Geoff
---
Prof. Geoffrey Hutchison
Assistant Professor, Department of Chemistry
University of Pit
> I was wondering if there is a way to set up constraints that can be used when
> OBConformerSearch generates candidate solutions for the GA. Specifically, I
> would like to set up 3 pairs of dihedrals that I know to be symmetric from
> experimental data & distance between two non-bonded atoms t
> generate EEM charges via the OB API? I did a quick Java implementation
> and the results weren't too encouraging, so I was hoping to check
> another implementation
Good question. I was thinking of creating an EEM charge model, which I just
added to trunk. I have a test set of a few thousand org
> Is there a way in OpenBabel 2.3 to standardise the bonds in molecules in such
> way that the bond orders are no longer dependent on the way the molecule was
> entered? For example, the two smiles representations of the indole ring,
> N1C=CC2=C1C=CC=C2 and N1C=CC2=CC=CC=C12,
First off, I need
> Is there a way in OpenBabel 2.3 to standardise the bonds in molecules in such
> way that the bond orders are no longer dependent on the way the molecule was
> entered? For example, the two smiles representations of the indole ring,
> N1C=CC2=C1C=CC=C2 and N1C=CC2=CC=CC=C12, lead to differences
On Nov 22, 2010, at 6:24 PM, Craig A. James wrote:
> It appears that OpenBabel retains the original single/double bond assignment
> and uses that to determine aromaticity of the remaining part of the molecule
> after atoms are deleted. But depending on the original Kekule assignment of
> bonds
>
>>> babel -isdf test1000.sdf -osdf test1000_nofrags.sdf -r
>>>
>>> I get 997 of the following errors, and only 3 molecules converted:
>>>
>>> *** Open Babel Error in DoTransformations
>>> Error executing an option
To get back to Douglas's question, it's a non-obvious bug in the transformatio
> 2. How is it decided? If this is through OBRotorRules, where should I be
> looking to take a look at it.
Take a look at tools/obrotamer.cpp for some example code. It uses both
OBRotorRules and OBRotorList.
> 3. This does not seem like a list of "allowed" torsional values, because when
> I us
> I have noticed that the Pybel library doesn't support that similarity search,
> but that openbabel.py should. But cannot use the FindSimilar() method because
> of the type of the arguments. So basically my question is:
> Is there a way to use the method FindSimilar() with Python? I think SWIG
> when substructure matching C[C@@H](O)C(O)=O and c...@h](O)C(O)=O, both
> match vice versa. Is that intended behavior?
No, that would definitely be a bug. I assume you're using v2.3.0?
-Geoff
--
Increase Visibility of
On Nov 30, 2010, at 12:33 PM, ariste...@cbm.uam.es wrote:
> Please, could you tell me the proper flag to import/export PDBQT files?
-ipdbqt for input and -opdbqt for output.
If the files have an extension of .pdbqt, it should also be automatically
recognized without a flag.
Hope that helps,
-
On Nov 30, 2010, at 10:21 AM, Igor Filippov [Contr] wrote:
> I would be very interested in this too, if it's possible in a general
> case.
There is not currently a mechanism to do this.
The code in kekulize.cpp would need to be changed -- right now, it terminates
once it's found a successful K
> I'll have a look into it - I'll keep you updated.
I'll point out that the kekulize.cpp code is hairy, in part because we don't
wish to break old API. (Fortunately that will change now.)
In the 2.3 code, look for expandKekulize() and instead of "return true", you'll
want to save that bond assi
> I have prepared one more patch (attached) against the latest SVN OpenBabel.
> With this patch the mighty OpenBabel can correctly assign MMFF94 types of ALL
> of the 761 structures of the CCL.NET MMFF validation suite starting from the
> original .mol2 file! Before this patch I had to use a MOL
> I've never seen this before, but it looks like libopenbabel is now
> printing warning messages on stderr:
> ==
> *** Open Babel Warning in CreateCisTrans
> Error in cis/trans stereochemistry specified for the double bond
If you don't like to see warnings, you can ea
> Browsing openbabel-2.3.0/src/charges seems to confirm that
> 'none' is not a charge option.
> Is there another way to ignore the charges ?
At the moment, not from the user utilities, no. I just added a "none" option to
the development trunk.
> 'input_file' - use the charges already in the in
> I installed openbabel-2.3.0 on my centOS system following the instruction
> using cmake. The compilation seems fine, no errors. But when I
...
> Is it a bug with the compilation?
Well, it would help a lot to know what version of CentOS and the g++ compiler
you are using. Some older versions o
> The following informations could be useful:
> 1) I exported the file directly from Material Studio
> 2) The problem seemsto be size dependent, i.e. conversion works if I cut
> down the structure to 150 atoms
I suspect this isn't a specific problem with "car" format, rather with
bond/aromaticit
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