Re: [Open Babel] Converting pdbqt to sdf

, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl czw., 11 mar 2021 o 09:46 Eduardo Mayo napisał(a): > Hi OpenBabels users, > Nice to join the community. > I would like to convert pdbqt file to sdf file without using openbabel > itself. I mean why should my project has another dep

Re: [Open Babel] Access OBElementTable from C# binding OBDotNet.dll

openbabel namespace, so you need to import it as follows: > from openbabel import openbabel Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl niedz., 10 lis 2019 o 15:23 Yang, Chengxi napisał(a): > Hi Openbabel Team, > > I noticed that you have removed t

Re: [Open Babel] Adding hydrogens before docking

Hi, This is highly dependent on docking software. Autodock Vina requires only polar hydrogens, but others will differ. Best, Maciek sob., 3 lis 2018, 11:28: Noel O'Boyle napisał(a): > You need to add all hydrogens. I have never understood why those options > are provided. > > On Thu, 1 Nov

Re: [Open Babel] Help with generation of atom names in mol2 format

residue to whatever you want via res.SetName('BLAH') Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2018-01-18 23:57 GMT+01:00 Antonio Jesus Banegas Luna < ajbane...@alu.ucam.edu>: > Hello all, > > I'm a newby in obabel and I need a bit of help. &g

Re: [Open Babel] Define origin for ECFP2 fingerprints

OBMolAtomBFSIter is buggy and does not work correctly with disconnected molecular parts, which will happen with proteins ( https://github.com/openbabel/openbabel/issues/1639). Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2017-10-16 15:27 GMT+02:00 Marcos Vinicius Da Silva

Re: [Open Babel] Submolecule from OBMol

| Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2017-06-19 17:19 GMT+02:00 Maciek Wójcikowski <mac...@wojcikowski.pl>: > No worries :) I planned to do Chem.FindAtomEnvironmentOfRadiusN() and > Chem.PathToSubMol() in RDKit, but the function you've suggested is also > fe

Re: [Open Babel] Submolecule from OBMol

No worries :) I planned to do Chem.FindAtomEnvironmentOfRadiusN() and Chem.PathToSubMol() in RDKit, but the function you've suggested is also feasible. @Geoff - the smiles fragment does not perserve any bond information from what I've tested so far. Pozdrawiam, | Best regards, Maciek

Re: [Open Babel] Submolecule from OBMol

---- Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2017-06-19 15:53 GMT+02:00 Noel O'Boyle <baoille...@gmail.com>: > This would be a useful API function. > > If it's a disconnected portion of the molecule, and you wanted to > write a smiles, there is a fragmen

Re: [Open Babel] Submolecule from OBMol

The last BeginModify should be EndModify. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2017-06-19 16:39 GMT+02:00 Maciek Wójcikowski <mac...@wojcikowski.pl>: > I'm trying to get back the ECFP environments, most preferably as smiles. > So it's lite

[Open Babel] Submolecule from OBMol

Hi all, Quick question: I have OBMol and want to create a sub-molecule from a subset of atoms given by atom/bond indices. Is there a clever way to do it in OpenBabel? I'm aware that I can make a copy and prune the unwanted atoms ;) Pozdrawiam, | Best regards, Maciek Wójcikowski mac

Re: [Open Babel] Error when using compound.draw() in pybel installed by conda - PNG depiction support not found.

I've rebuilt the Python 2.7 packages for Windows (the rest is still compiling), and the PNG should work now. Update openbabel package to 2.4.1 py27_3: `conda install -c openbabel openbabel`. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2017-05-31 13:16 GMT+02:00

Re: [Open Babel] Error when using compound.draw() in pybel installed by conda - PNG depiction support not found.

this issue and try to support PNG files. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2017-05-31 11:06 GMT+02:00 Hongbin Yang <yanyangh...@163.com>: > Hi， > > I installed openbabel via `conda install -c openbabel openbabel`. > > I wanted to d

Re: [Open Babel] About pybel module installation

Hello, What you need is openbabel package not pybel: "pip install openbabel" See https://pypi.python.org/pypi/openbabel Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2017-04-06 1:23 GMT+02:00 Phuong Do <phuongdo@gmail.com>: > Hello, > &

Re: [Open Babel] How to Install openbabel for Python 3.6 on macOS Sierra 10.12.3

Hello, Python 3.6 support is not there yet. It should be added soon. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2017-02-13 5:31 GMT+01:00 i4hashmi <i4has...@hotmail.com>: > I am using Python for making a script to work with some chemical structures &g

Re: [Open Babel] MOPAC

Babel is deprecated in 2.4, maybe that's messing with your app? Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2016-11-15 12:45 GMT+01:00 Chris Swain <sw...@mac.com>: > Hi, > > Thanks, that works fine. > > Chris > > On 15 Nov 20

Re: [Open Babel] Problem with Pybel installation for Anaconda

Hi, Indeed for some reason InCHI is not built on windows. I'll have to fix it, stay tuned for updates. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2016-10-15 9:30 GMT+02:00 Noel O'Boyle <baoille...@gmail.com>: > I can't comment on the anaconda parts,

Re: [Open Babel] Question about file conversion

uot;, like "c1c1 benzene" Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2016-05-09 4:35 GMT+02:00 Brendan M. O'Boyle <bmobo...@caltech.edu>: > Hello, > > I am trying to use OpenBabel and iBabel to convert SMILES strings into sdf > files for

Re: [Open Babel] generating conformers with open babel

Hello, I think that Confab is available only in current development branch. Check "obabel -L confab" to see if it's there. If not then you'd have to use conda or compile it yourself. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2016-05-03 12:14 GMT+02:0

Re: [Open Babel] set the atom type in python interface

lig.atoms] Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2016-04-13 19:13 GMT+02:00 Yun Ding <ydi...@lsu.edu>: > Dear all, > > > I would like to get the SYB type of the atom using the python interface, > however, it always gives the INT type,

Re: [Open Babel] problem with residue detection

Hi, Add "-xl" to the command line (which ignores the residues for mol2). Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2016-04-11 19:08 GMT+02:00 Fredy Quevedo <maquevedo@gmail.com>: > Dear all: > > I am having some problem with the

Re: [Open Babel] PAINS filtering

. (although currently it uses Rajarshi's SMARTS definition). I have to update those to Greg's revised version. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2016-03-15 18:54 GMT+01:00 Stefano Forli <fo...@scripps.edu>: > About that, a while ago I had compi

Re: [Open Babel] pdf export

oddt.virtualscreening import virtualscreening as vs pipeline = vs() pipeline.load_ligands('sdf', 'ampc/actives_final.sdf.gz') pipeline.write_csv('ampc_docked.csv') Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2016-01-22 14:17 GMT+01:00 Chris Swain <sw...@mac.

Re: [Open Babel] azoxy

-oddt.docking.AutodockVina Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2016-01-05 12:14 GMT+01:00 Stefano Forli <fo...@scripps.edu>: > Hi Stefano, > the problem with the PDBQT format is that connectivity is implicit and > bond order is lost. > If your atom coo

Re: [Open Babel] splitting molecule file - the hard case

te that m is an OBMol object, so to get pybel molecule you need to initiate it via Molecule class: for m in mol.OBMol.Separate(): > print pybel.Molecule(m) Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2015-11-10 16:59 GMT+01:00 Filip Stefaniak <stef

Re: [Open Babel] access all properties from mol2 file

Got it. OpenBabel currently does not support @TRIPOSCOMMENT, where the data sit from Gold. You can save docked conformations as SDF file and normalize them. There is no other solution, as Gold embeds SDF style variables in @TRIPOSCOMMENT. Pozdrawiam, | Best regards, Maciek Wójcikowski mac

Re: [Open Babel] access all properties from mol2 file

Hi, Currently only UCSF Dock-style data fields are supported in mol2 files, and you have to specify -ac or -xc option to read/write it from/to a file. Can you give example of such mol2? Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2015-04-30 17:16 GMT+02:00 Hitesh

Re: [Open Babel] Compressed pybel.Outputfile output

. Otherwise Stefano's solution is the one you go for. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2015-04-25 0:45 GMT+02:00 Matthew Lardy mla...@gmail.com: Hi Stefano, That worked! Thanks! Matthew On Fri, Apr 24, 2015 at 3:34 PM, Stefano Forli fo...@scripps.edu

Re: [Open Babel] MACCS key 44

Hello Andrew, I created pull request on github [ https://github.com/openbabel/openbabel/pull/96] Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2014-10-20 15:14 GMT+02:00 Andrew Dalke da...@dalkescientific.com: Hi all, Open Babel's MACCS definitions derive

Re: [Open Babel] Generating a diverse set of conformers

Hi, Is the input molecule flexible? It would be much easier to test if you could sent it to the list. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2014-05-07 11:19 GMT+02:00 Fredrik Wallner fred...@wallner.nu: Continue by running obabel -L formats and obabel

Re: [Open Babel] running Open Babel in parallel / distributed mode

| parallel -P 8 log 2 error.log (or 21 if someone prefers joint log) Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2014-02-04 11:58 GMT+01:00 Francois Berenger beren...@riken.jp: On 2/4/14, 6:28 PM, Noel O'Boyle wrote: It would be nice to see some explicit examples

Re: [Open Babel] missing obabel executable when compiling by sources on HPC

I think you should build with SHARED = True and append correct directory to LD_LIBRARY_PATH, which probably should look like: export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:~/openbabel/openbabel-2.3.2-install/lib Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2014/1/15

Re: [Open Babel] Bindings - first and last molecule option

, then it should work. Unfortunately I struggle to find the spot. Tried to add it to ReadFile, but it does not work. Any better ideas? Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2013/12/5 Geoffrey Hutchison geoff.hutchi...@gmail.com This only proves, that I

Re: [Open Babel] Bindings - first and last molecule option

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 Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2013/12/3 Chris Morley c.mor

Re: [Open Babel] Bindings - first and last molecule option

the beginning and the end of the molecule it wouldn't do anything especially kekulization and bonding etc. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2013/12/3 Dimitri Maziuk dmaz...@bmrb.wisc.edu On 2013-12-03 04:28, Maciek Wójcikowski wrote: Hello, I'd

[Open Babel] Openbabel and Lone Pairs

/*, as in mol2/sdf, atom types and ignore them. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl -- November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable

Re: [Open Babel] Can we just copy the compiled files to another account ?

Hi, You also have to copy the bash variables you've set. Have you done that? There is no reason it shouldn't work, unless you've configured it right. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2013/10/30 Zhengyh swanboi...@gmail.com Greetings, I compiled

Re: [Open Babel] Can't make it work on a Redhat X64 platform!

Hi, Besides PYTHON_PATH please try adding the directory with openbabel.so.4 to $LD_LIBRARY_PATH Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2013/10/25 Zhengyh swanboi...@gmail.com Greetings, I was compiling the openbabel 2.3.1 version with binding for Python

Re: [Open Babel] Which is the function in API doing the same thing as --join

Hi, Have you tried mol1 += mol2? I use it for joining proteins with ligands, but should work in any case. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2013/10/25 Zhengyh swanboi...@gmail.com Hello, Thank you all who are helping me with this openbabel. We use

Re: [Open Babel] create a database with openbabel

Hello, The other choice, if you prefer MySQL, is Mychem http://mychem.sourceforge.net/. But I'd say neither of them is easy to use for unexperienced user (unless you have at least some DB knowledge). Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2013/8/22 Steffen

Re: [Open Babel] SMILES, SMARTS, and PDB

be (although it's the most error prone). Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2013/7/8 Brett Hannigan godot_gil...@yahoo.com Unfortunately, I don't think that's quite what I need. The obabel filter command will look at the given pdb and then output the entire pdb

Re: [Open Babel] SMILES, SMARTS, and PDB

You could also look into ProDy, if you use PDB files. http://www.csb.pitt.edu/prody/reference/atomic/flags.html#term-hetero Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2013/7/8 Maciek Wójcikowski mac...@wojcikowski.pl I think you need custom code. For python

Re: [Open Babel] SMILES, SMARTS, and PDB

lecture: http://openbabel.org/wiki/FastSearch Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2013/7/5 Brett T. Hannigan bret...@mail.med.upenn.edu I have a database of molecules in pdb files. I'd like to go through each molecule and see if it has certain

Re: [Open Babel] python api question

Hello, Sure - try atom.atomicnum (pybel) or OBAtom.GetAtomicNum() (openbabel). It returns atomic number of element (fe. C - 6). Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2013/6/5 Dimitri Maziuk dmaz...@bmrb.wisc.edu Hi all, I'm after the atom (element

Re: [Open Babel] python api question

If you realy need symbol of an element in automated fassion, then there is OBElementTable.GetSymbol( atomicnum ) that you can use. http://openbabel.org/dev-api/classOpenBabel_1_1OBElementTable.shtml#a18907ad1590deb926b43c4f08cac9405 Pozdrawiam, | Best regards, Maciek Wójcikowski mac

Re: [Open Babel] python api question

Yes. etab = ob.OBElementTable() etab.GetSymbol(6) Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2013/6/5 Dimitri Maziuk dmaz...@bmrb.wisc.edu On 2013-06-05 02:54, Maciek Wójcikowski wrote: If you realy need symbol of an element in automated fassion

Re: [Open Babel] Atom numbers again, this time from python

to pass empty value, since None is reserved for options without value. You could look into that in pybel.py file. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2013/6/5 Dimitri Maziuk dmaz...@bmrb.wisc.edu Hi everyone, one more python question: I'm trying to do

[Open Babel] PHP bindings

and molecules depiction. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.plhttps://mail.google.com/mail/u/0/?view=cmfs=1tf=1to=mac...@wojcikowski.pl -- Precog is a next-generation analytics platform

Re: [Open Babel] openbabel + confab

Try cherry-picking a commit. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2013/3/18 Noel O'Boyle baoille...@gmail.com Hi David, Can you put all of the Confab-related code on a branch so I can get at them without pulling the other unrelated code on your master

Re: [Open Babel] obminimize

Try: obminimize -ff MMFF94 -sd source.sdf target.sdf Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2013/2/27 Оги Боги alchemist...@abv.bg Hi guys, I am trying to use obminimize under 64bit windows 7 in order to minimize geometry of molecules inside

[Open Babel] Residue support in Pybel

it's a good idea would it be possible to add it to trunk? PS. How is github/git integration going? Github repo seams to be forgotten since initial sync somewhere in October 2012... Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.plhttps://mail.google.com/mail/u/0/?view=cmfs

Re: [Open Babel] Problem with --gen3D Open Babel 2.3.1

Have you tried it with OB 2.3.2? Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2013/1/20 David García Aristegui ariste...@cbm.uam.es OK, is an open bug http://sourceforge.net/p/openbabel/bugs/833/ Hello, i'm trying to assign 3D coordinates to this SMILES

Re: [Open Babel] Problem with --gen3D Open Babel 2.3.1

631 6944641 7044651 1 molecule converted Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2013/1/20 David García Aristegui ariste...@cbm.uam.es OK, in the News section of the Openbabel main page is announced 2011-10-17 Open Babel

[Open Babel] OB binginds segfault on EL5

on the same set of compounds. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.plhttps://mail.google.com/mail/u/0/?view=cmfs=1tf=1to=mac...@wojcikowski.pl -- Keep yourself connected to Go Parallel

Re: [Open Babel] Copy format in Pybel

That was just a proof of concept piece of code. I wanted to process some molecules and try to leave them intact. Thanks for information. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2012/11/8 Geoffrey Hutchison geo...@pitt.edu Is pybel suppose to support 'copy

[Open Babel] Copy format in Pybel

Is pybel suppose to support 'copy' format? I try to make it work, but it generates empty string. Proof of concept: mol = pybel.readstring(smi, c1=CC=CC=c1) mol.write('copy') '' I'm on latest SVN openbabel + CentOS 6. Pozdrawiam, | Best regards, Maciek Wójcikowski mac

Re: [Open Babel] OpenBabel to split multimol2 file but without changing bond types?

Have you tried copy output format? -ocopy Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2012/10/4 Juliette Pradon pra...@ccdc.cam.ac.uk Hello, I am using OpenBabel to split a multimol2 file into separate mol2 files (i.e. one mol2 file per compound). I use

Re: [Open Babel] Openbabel in Python in concurrent processes

Oh, I forgot to mention that. I use CentOS and ScientificLinux 6, both HVM. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2012/7/20 Craig James cja...@emolecules.com Did you see this article? You didn't say what Linux you are using, but if it's Ubuntu, this may

[Open Babel] Openbabel in Python in concurrent processes

? Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers

Re: [Open Babel] Openbabel in Python in concurrent processes

intensive computing. I must say that I'm pretty disappointed with those results, although it's quite obvious... Out of curiosity I'm going to rerun the tests on KVM and probably on OpenVZ to see how it goes there. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2012/7/20

Re: [Open Babel] Weighted-rotor search

Hello, You should use: ff.GetCoordinates(mol) Where ff is your OBForceField class and mol is OBMol. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2012/7/13 scott_m js...@cam.ac.uk That's great, many thanks for the help. One other thing, I mentioned pybel

[Open Babel] Perl bindings in current SVN

] Błąd 1 make[1]: *** [scripts/CMakeFiles/bindings_perl.dir/all] Błąd 2 To clarify, given cmake command build 2.3.1 version without problem. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl -- Live

Re: [Open Babel] Perl bindings in current SVN

successfully 1.x. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2012/5/31 Maciek Wójcikowski mac...@wojcikowski.pl It worked. The failing line was: /usr/bin/c++ -fPIC -O2 -g -O2 -g -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc

Re: [Open Babel] Perl bindings in current SVN

I was wrong. something went wrong and SWIG wasnt recognized at all. I'm looking for another problem. Do you have any Idea where first to look? Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2012/5/31 Maciek Wójcikowski mac...@wojcikowski.pl Apparently it seams

Re: [Open Babel] Perl bindings in current SVN

='-lresolv -lnsl -ldl -lm -lcrypt -lutil -lpthread -lc'; Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2012/5/31 Noel O'Boyle baoille...@gmail.com Yes - I doublechecked. The latest SWIG still fails. What I can do is add in the output of perl -V:perllibs. This solves

[Open Babel] pybel + ouput options

Hello everyone, Is it possible to set conversion options in pybel? I couldn't find any information about it. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl -- Live Security Virtual Conference

Re: [Open Babel] Energy Minimization of complex of two molecules

Have you tried H1 + H2? Actually this wasn't working for me in perl, but it's supposed to be working in Python. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl W dniu 23 kwietnia 2012 13:52 użytkownik Чугунов Антон batc...@yandex.runapisał: Dear Open Babel users

Re: [Open Babel] [Chimera-users] UCSF Dock mol2 files

Maybe @TRIPOSCOMMENT would be a better place for them? http://tripos.com/data/support/mol2.pdf Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl W dniu 4 kwietnia 2012 20:08 użytkownik Conrad Huang con...@cgl.ucsf.edunapisał: Our approach to file formats in Chimera

Re: [Open Babel] PHP binding

If you set that up it would be nice. What kind of test scripts do you need? Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl W dniu 3 kwietnia 2012 02:40 użytkownik Geoff Hutchison ge...@geoffhutchison.net napisał: On Apr 2, 2012, at 5:34 PM, mwojcikowski wrote

Re: [Open Babel] UCSF Dock mol2 files

see dock6/src/dock/library_file.cpp it seams fairy simple and always uses ##. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl W dniu 3 kwietnia 2012 21:13 użytkownik Scott Brozell sbroz...@rci.rutgers.edu napisał: Hi, This is a good suggestion. But before

Re: [Open Babel] Difficulty appending OBMols in Perl (Was OBForceField in Perl)

; # doesn't work, throws error $mol3 - add($mol1); # this does what above should. ### print Mol3 step two: .$mol3-NumAtoms().\n; Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl W dniu 28 marca 2012 16:48 użytkownik Noel O'Boyle baoille...@gmail.comnapisał: Can you

Re: [Open Babel] OBForceField in Perl

- SetLogToStdOut(1); $pFF - SetLogLevel(2); # We pass the constraints as argument for Setup() $pFF - Setup($mol, $constraints); # Perform the actual minimization, maximum 1000 steps $pFF-SteepestDescent(1000); Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl W dniu 26

[Open Babel] OBForceField in Perl

to not initializing Forcefield properly, but I've did my best and failed to do so. Can anyone post an example of correct part of perl script with FF? Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl