Re: [Open Babel] Help with "obminimize: cannot read input/output format!" error

I think you’re mixing up “obminimize” which is a specific tool, and “obabel” which can convert, etc. I’d suggest something like: obabel {input_file} -O {output_file} -opdbqt --minimize -sd -ff GAFF -h Best, -Geoff On Aug 8, 2023 at 2:24:21 PM, Lock Meister wrote: > Hi, > > I was trying to r

[Open Babel] Help with "obminimize: cannot read input/output format!" error

Hi, I was trying to run Obminimize to convert SDF files that I converted from SMILE strings into PDBQT files, and when I run the code that I have to loop it with a perl script with multiple files, I'm constantly getting this error: "obminimize: cannot read input/output format!" I was wondering if

Re: [Open Babel] help with installation

cember 3, 2021 05:06 To: Artur Hermano Subject: Re: [Open Babel] help with installation It's all about in which environment you did install openbabel. In macOS for example, using brew, only the python shipped by brew will see the openbabel module, not even a virtual env from this very same

[Open Babel] help with installation

Hello OpenBabel users, I've been having issues with OpenBabel and thought I might use some help from more experienced users. My main problem is that I have (apparently) installed OpenBabel succesfully, but other softwares cannot access it. For example, when I try to run a programm that uses Ope

[Open Babel] open babel help

Hi Dear, I am an open babel user, I have a small problem regarding uploading files to Open Babel, some times I have a molecule worked in a txt file and I wanted to convert to PDB files but at that time it cannot convert to the corresponding file or it cannot upload that txt file, so how can you he

Re: [Open Babel] Help on SMILES format

> I had to generate a 3D molecule from SMILES to xyz. But i have noticed that, > 'sometimes', if i give a SMILES input for a cyclic molecule, ('c1c1' for > benzene) and convert it into xyz (3d) coordinates and take the data to > visualize in Avogadro, it is not showing a cyclic molecule at a

Re: [Open Babel] Help on SMILES format

Dear all, I had to generate a 3D molecule from SMILES to xyz. But i have noticed that, 'sometimes', if i give a SMILES input for a cyclic molecule, ('c1c1' for benzene) and convert it into xyz (3d) coordinates and take the data to visualize in Avogadro, it is not showing a cyclic molecule at al

Re: [Open Babel] Help on SMILES format

> I am using Openbabel GUI on windows. I am converting SMILES to xyz format > using 'generate 3D coordinates' option. Everything is looking fine (viewing > in gui.svg viewer in firefox) as expected. I'm not sure why you're generating 3D coordinates to view a 2D format (SVG). > But when i am

[Open Babel] Help on SMILES format

I am using Openbabel GUI on windows. I am converting SMILES to xyz format using 'generate 3D coordinates' option. Everything is looking fine (viewing in gui.svg viewer in firefox) as expected. But when i am taking the output xyz data to view in other molecular editors like GaussView or Avogadro, it

Re: [Open Babel] Help

While it's easy for you to hack the mol2format.cpp code - I have never seen more than 3-4 decimal places in a mol2 file. I've looked for the format specification, but it doesn't seem to be online. How much is it changing the dihedral angles? -Geoff --- Prof. Geoffrey Hutchison Department of Ch

[Open Babel] Help

Hi, I am working with xyz files but I need to convert many .xyz to .mol2. I used babel *.xyz - omol2 -m but the mol2 file round in the 4 decimal number and I need all the decimals that came from the .xyz file. This is important because it changes some dihedral angles. Thank you for your time a

[Open Babel] help installing pybel

hello, I'm trying to install pybel on windows, I follow the instruction but when I write import pybel the following lines appear: >>> import pybel Traceback (most recent call last): File "", line 1, in File "C:\Python32\lib\site-packages\pybel.py", line 52, in import openbabel as ob Fil

Re: [Open Babel] Help using Pybel in Microsoft Visual Studio and from within batch file

> My second question is regarding running python programs in command line, > have you ever tried to run the python program that imports pybel from inside > a batch file? For me this throws an error "ModuleNotFoundError: No module > named pybel". One way or another, the environment is different. Wh

[Open Babel] Help using Pybel in Microsoft Visual Studio and from within batch file

Hi, I have so far been able to build the openbabel solution in Debug mode with Python bindings enabled. I see that the openbabel-2.dll and openbabel.py have been built in the Debug folder inside the "bin" folder. The Debug folder in the "src" folder also contains two library files named "openbabel

Re: [Open Babel] Help with compiling the language bindings

If you want to install on a Linux system, I find the conda installer the easiest way. First, you need to install anaconda, then, you can install openbabel simply using the command in the following link: https://anaconda.org/openbabel/openbabel -Tayeb Tayeb Kakeshpour Graduate Research Assistant

[Open Babel] Help with compiling the language bindings

Hi there, I am very new to all of this, and am looking for help with the install. I followed the instructions on the page below: http://openbabel.org/wiki/Install_(source_code) specifically the section on Installing globally with root ac

Re: [Open Babel] Help

On Tue, May 29, 2018 at 8:42 AM, Haddadi Kiandokht wrote: > Hello! > > There might be different smiles for a compound due to existence of > tautomers. I need to convert canonical smiles of a compound to all possible > smiles of its tautomers. > > I dig into tautomer.h library and tried to obtain

[Open Babel] Help

Hello! There might be different smiles for a compound due to existence of tautomers. I need to convert canonical smiles of a compound to all possible smiles of its tautomers. I dig into tautomer.h library and tried to obtain all possible tautomer smiles of a compound but the algorithm just out

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

Thanks Maciek, that's exactly what I need. Best, Antonio El 19/01/2018 a las 10:38, Maciek Wójcikowski escribió: Hi Antionio, OpenBabel generates new labels, unless there are already OBResiude info on that. You can set it to whatever you want with OBResiude.SetAtomID(). Checkout the script

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

Hi Antionio, OpenBabel generates new labels, unless there are already OBResiude info on that. You can set it to whatever you want with OBResiude.SetAtomID(). Checkout the script below: import pybel > ob = pybel.ob > mol = pybel.readstring('smi', 'c1c1') > res = ob.OBResidue() > for atom in ob

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

Hello all, I'm a newby in obabel and I need a bit of help. I use obabel to convert a file from sdf to mol2 format because another program requires such conversion. The conversion is fine, and I get something like this (I only show the ATOM block): @ATOM   1 C   0.5825   -1.4943   

[Open Babel] HELP about -k option

I using the command obabel t.sdf -O t.gjf -m -k "opt" in Linux to convert a sdf file to multiple gaussian gjf files. yes it works, but it was always got "Unable to translate keywords!" in the first line in gjf files. I also try obabel t.sdf -O t.gjf -m -k"opt" also try obabel t.sdf -O t.gjf -m -k

Re: [Open Babel] Help to conversion format cif_to_pdb

Ok Thanks for the interest Now, i need to convert the format, only and it's necessary that it has the best fidelity possible with the original structure I think it's openbabel can't help me I'm going to research more 2014-04-15 19:09 GMT-03:00 Dimitri Maziuk : > On 04/15/2014 03:59 PM, Wellisson

Re: [Open Babel] Help to conversion format cif_to_pdb

On 04/15/2014 03:59 PM, Wellisson Gonçalves wrote: > Sorry but i don't understand your answer OpenBabel deals with molecules. PDB deals with studies of crystal structures, extended (with varying degree of success) to structures obtained from EM, NMR, and other methods. The "study" includes much

Re: [Open Babel] Help to conversion format cif_to_pdb

Sorry but i don't understand your answer What's OBMol and what can it do ? in fact babel in openbabel don't translate the file completely it's omits a lot of information. I don't worried about this The point is how different and reliable it is 2014-04-15 14:14 GMT-03:00 Dimitri Maziuk : > On 04/

Re: [Open Babel] Help to conversion format cif_to_pdb

On 04/14/2014 08:51 AM, David Hall wrote: > Can you explain what parts of the file are not compatible that you are > looking at? Residue numbering? Temperature Factors? Testing briefly, it > appears the coordinates agree, so knowing that fields you are looking to > preserve would be useful. SEQRES

Re: [Open Babel] Help to conversion format cif_to_pdb

Can you explain what parts of the file are not compatible that you are looking at? Residue numbering? Temperature Factors? Testing briefly, it appears the coordinates agree, so knowing that fields you are looking to preserve would be useful. -David On Sat, Apr 12, 2014 at 3:20 PM, Wellisson Gonç

Re: [Open Babel] Help to conversion format cif_to_pdb

I know about that But i don't get compile I receive a lot of compilation errors But a find a other tool http://sw-tools.pdb.org/apps/CIFTr/index.html It's very simple But i'm developing a bioinformatics tool using C++ with QT for platforms linux, MAC OS X and windows It's necessary to me put a f

Re: [Open Babel] Help to conversion format cif_to_pdb

On 4/12/2014 2:20 PM, Wellisson Gonçalves wrote: > A use the executable babel with parameters > babel -icif '4POQ.cif' -opdb '4POQ_cif_to_pdb.pdb' > > And i received the file that not compatible with the original file. > > I know becouse i downloaded the original file in website 4POQ.pdb and > It

[Open Babel] Help to conversion format cif_to_pdb

Hello This is the first message for the group I'm studying Bioinformatics and i need a help about the format convertion cif to pdb Recently the pdb.org changed the submition format But a have a aplication that works with pdb file A use the executable babel with parameters babel -icif '4POQ.cif' -

Re: [Open Babel] Help please

> 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

[Open Babel] Help please

hi.I wanted to know is how this article was composed or found a way to synthesize it? Or if you can find me.'m Grateful. Acetic acid 2a,7,10-trimethyl-3-oxo-2,2a,3,4,4a,5,6,7,7a,8,10b,10c-dodecahydro-naphtho[2,1,8-cde]azulen-5-yl ester

Re: [Open Babel] help in using molprint2D

It's not possible, and the code will have to be rewritten to allow an arbitary number of layers. In the meanwhile, you may want to check out my implementation in Python: http://baoilleach.blogspot.co.uk/2008/07/calculate-circular-fingerprints-with.html On 12 November 2012 16:15, green69 wrote: >

[Open Babel] help in using molprint2D

Hi everybody, I'm running Open Babel 2.3.1 in GNU/LinuxDebian OS. I'm interested in using molprint2D fingerprints. As described in openbabel manual the following command should gives the list of molprint2D fingerprint for each molecule: /obabel -ismi test.smi -ompd/ As described in manual the fo

Re: [Open Babel] help

On 06/07/2012 16:18, Craig James wrote: > > > On Thu, Jul 5, 2012 at 3:06 AM, 蓝鱼在嘴里 <807409...@qq.com > > wrote: > > Hello， > I want to understand the fingerprint type of FP2 in Openbabel,where > can I find the information?For example,"0616<670>",I know which >

Re: [Open Babel] help

On Thu, Jul 5, 2012 at 3:06 AM, 蓝鱼在嘴里 <807409...@qq.com> wrote: > Hello， > I want to understand the fingerprint type of FP2 in Openbabel,where can I > find the information?For example,"0616<670>",I know which fragment it > represents,but for "0 6 5 6 5 6 1 6 <936>",I do not know.So where can I > f

[Open Babel] help

Hello?? I want to understand the fingerprint type of FP2 in Openbabel,where can I find the information?For example,"0616<670>",I know which fragment it represents,but for "0 6 5 6 5 6 1 6 <936>",I do not know.So where can I find the instruction. If there is someone know,please tell me.Thanks!--

Re: [Open Babel] Help: everything compile well... But no results

Hi, On Mon, Jun 27, 2011 at 4:03 PM, Marianne wrote: > Hello > > I am new to using the openbabel API and really exciting to use OB. I have an > existing C++ program in MSVC2008, I would like to use some of the functions > in Openbabel (Isomorphism). > > I followed the instructions on the website

[Open Babel] Help: everything compile well... But no results

Hello I am new to using the openbabel API and really exciting to use OB. I have an existing C++ program in MSVC2008, I would like to use some of the functions in Openbabel (Isomorphism). I followed the instructions on the website and built the windows-vc2008 and then tried to add the sample code

Re: [Open Babel] Help with FastSearch

On May 27, 2011, at 11:58 PM, A. Heifets wrote: > I'm trying to follow http://openbabel.org/wiki/Tutorial:Fingerprints > and obabel -H fs on my data but I have some strange digressions from > the tutorial. Are you interested in trying out my new chemfp package? http://code.google.com/p/chem-fing

Re: [Open Babel] Help with FastSearch

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

Re: [Open Babel] Help with FastSearch

On 27/05/2011 22:58, A. Heifets wrote: > I'm trying to follow http://openbabel.org/wiki/Tutorial:Fingerprints > and obabel -H fs on my data but I have some strange digressions from > the tutorial. > > First, I'm not convinced that the index was built correctly (although > there were no error messag

[Open Babel] Help with FastSearch

Hello Babelers, I'm trying to follow http://openbabel.org/wiki/Tutorial:Fingerprints and obabel -H fs on my data but I have some strange digressions from the tutorial. First, I'm not convinced that the index was built correctly (although there were no error messages to imply that it failed). If

Re: [Open Babel] help - segmentation fault with Pybel on Mac OS x

> 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

[Open Babel] help - segmentation fault with Pybel on Mac OS x

Hi 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: >> im

Re: [Open Babel] Help regarding structure searching

Hi, It depends upon your database system. If you are using: - mysql: see mychem -> http://mychem.sourceforge.net - postgresql: see pgchem -> http://pgfoundry.org/projects/pgchem You can also find further informations on the ChemiSQL website (you will see another project that are not using Open B

[Open Babel] Help regarding structure searching

Hi I wanted to check if this software can work with a database. What we are trying to get to is structure searching from our database. We have a j2ee based application and our clients should be able to give smiles etc in the website and search for them in the our database. How will this softwa