Re: [Open Babel] Errors in file conversion

2025-02-12 Thread Noel O'Boyle
If you use the -e option, I think it will write out an empty SMILES with the title. Or was this something I didn't add in the end... On Wed 12 Feb 2025, 20:34 Chris Swain via OpenBabel-discuss, < openbabel-discuss@lists.sourceforge.net> wrote: > Hi, > > Many thanks for the prompt response, > Chee

Re: [Open Babel] retain identifier with InChI conversions

2023-07-07 Thread Noel O'Boyle
obabel -Hinchi lists the options. Read option 'n' will do it. obabel -:"InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3 Noel" -iinchi -osmi -an CCO Noel More importantly, do not convert InChIs to SMILES without understanding the caveats. InChI is not a storage format for chemical structures. Regards, Noel

Re: [Open Babel] Prevent addition of H during minimization

2023-03-31 Thread Noel O'Boyle
Hi Hetal, As I always comment, "OB is not adding hydrogens. The hydrogens are already there, just implicit." That is, your original MOL file is in fact Li(OH)2 (but you can't tell that unless you are familiar with the MOL file spec). How are you creating the input file? Is there a way to set the

Re: [Open Babel] extracting ligands from macromolecular structures

2023-03-04 Thread Noel O'Boyle
Also OBMol::CopySubstructure as described at https://baoilleach.blogspot.com/2018/05/when-all-you-want-is-ring.html and https://openbabel.github.io/api/3.0/classOpenBabel_1_1OBMol.shtml#a3271860ee44de0d38a27102c79913b1b . Should be quite a bit faster I would think. On Fri, 3 Mar 2023, 14:19 Richar

Re: [Open Babel] Explicit H as property

2023-02-22 Thread Noel O'Boyle
Indeed - Andrew's approach is all you can do at the moment. I've often thought it would be a useful option to add, and just a one or two line change to the C++ (just skip the part where the "organic subset" is treated as special). Regarding SMARTS, given that "CC" is also a valid SMARTS that would

Re: [Open Babel] Avoid sanitization

2023-02-22 Thread Noel O'Boyle
hermore, the SMILES that I use as input are already processed by a > chemical platform (called Vega), so for consistency sake I should not > modify the information. > > Il giorno dom 19 feb 2023 alle ore 18:32 Noel O'Boyle < > baoille...@gmail.com> ha scritto: > >&

Re: [Open Babel] Avoid sanitization

2023-02-19 Thread Noel O'Boyle
CN(CCNC(=O)c1cccn2c1nc1c1c2=O)C\t\n' > > Furthermore, can you explain me this: > > mol = pybel.readstring('smi', "O=C(NCCN(C)C)c12C(=O)c3c3(Oc12)") > sma = pybel.Smarts("c12Cc3c3(Oc12)") > sma.obsmarts.Match(mol.OBMol, True)

Re: [Open Babel] Avoid sanitization

2023-02-17 Thread Noel O'Boyle
Hi Thomas, OB does not sanitize molecules when reading from SMILES (or any other format). By default it writes aromatic SMILES though, but it sounds like you want Kekule SMILES - see the obabel -Hsmi for the list of options. In this case you want 'k': $ obabel -:"O=C1C=COC(=C1(O))C" -xk -osmi O=C

Re: [Open Babel] Writer Format - WLN Writer + Reader Functionality Expansion

2022-06-20 Thread Noel O'Boyle
I should add that I'm very much looking forward to this addition! On Mon, 20 Jun 2022, 15:21 Noel O'Boyle, wrote: > Hi Michael, > > Just submit a pull request. To do this, your code changes should made to a > fork of the project on github. We can then give feedback ther

Re: [Open Babel] Writer Format - WLN Writer + Reader Functionality Expansion

2022-06-20 Thread Noel O'Boyle
Hi Michael, Just submit a pull request. To do this, your code changes should made to a fork of the project on github. We can then give feedback there. Regards, Noel On Mon, 20 Jun 2022, 14:57 Michael Blakey via OpenBabel-discuss, < openbabel-discuss@lists.sourceforge.net> wrote: > Hi There, > >

Re: [Open Babel] Run obabel with n cpu cores?

2022-02-28 Thread Noel O'Boyle
See also using GNU parallel in combo with obabel. Some starting points on my blog and in comments: https://baoilleach.blogspot.com/2013/11/got-cpus-to-burn-put-em-to-work-with.html When I need to do this myself these days I just use multiprocessing and Python. On Mon, 28 Feb 2022 at 00:50, Franco

Re: [Open Babel] count chiral centers

2022-01-25 Thread Noel O'Boyle
See also the docs at https://open-babel.readthedocs.io/en/latest/Stereochemistry/stereo.html. On Mon, 24 Jan 2022 at 23:28, Richard Overstreet wrote: > You could do something like this in python. Not sure how reliable this is > but it is a start. This could also be ported over to c++ too. > > fr

Re: [Open Babel] openbabel python binding for macOS

2021-11-17 Thread Noel O'Boyle
If no one here knows, ask whoever is responsible for that package. On Mon, 15 Nov 2021, 20:03 Alan, wrote: > Hi there, > > Ok, > > brew install open-babel > > got me obabel, but I need the python openbabel. How to get it? > > thanks in advance > -- > Alan > __

Re: [Open Babel] Alternative to UsetPartialChargesPerceived() in 3.x

2021-09-16 Thread Noel O'Boyle
Hi Stefano, Most of the changes in 3.0 are described at https://open-babel.readthedocs.io/en/latest/UseTheLibrary/migration.html#molecule-atom-and-bond-flags. In short, OBMol::SetPartialChargesPerceived(false). The rationale for this change is described at https://github.com/openbabel/openbabel/pu

Re: [Open Babel] split multi-molecule structure into single-molecules

2021-08-28 Thread Noel O'Boyle
Hi Jan, Please don't use InChIs to store the structure, but rather as an identifier that can be derived from the structure. The easiest way to split the structure is to split on the dot in a SMILES string. If you have salt forms that you want to retain you'll have to do a bit more work to identif

Re: [Open Babel] Validating a SMILES string

2021-08-27 Thread Noel O'Boyle
Hi Anonymous, There is a one-line change source change that governs this behaviour, and it's one that I've changed in the past, and maybe it should be an option. If you have compiled Open Babel yourself, all you need to do is change "return true" to "return false" in the right place. The thing is

Re: [Open Babel] Hide "Open Babel Error" error messages in openbabel/python

2021-08-26 Thread Noel O'Boyle
Sorry. Just noticed you did this. To disable messaging entirely, try StopLogging(). On Thu, 26 Aug 2021, 15:24 Noel O'Boyle, wrote: > That code creates a new message handler. You want to get the existing > message handler and change the settings. It's at openbabel.obErrorLog. &g

Re: [Open Babel] Hide "Open Babel Error" error messages in openbabel/python

2021-08-26 Thread Noel O'Boyle
That code creates a new message handler. You want to get the existing message handler and change the settings. It's at openbabel.obErrorLog. On Thu, 26 Aug 2021, 14:07 , wrote: > > Hi, > > I want to use openbabel conversion in python like shown below. > But I do not want to get an error message

Re: [Open Babel] Adding Hydrogen During Confab

2021-08-23 Thread Noel O'Boyle
b, the outputs contain 28 atoms. I am not > familiar with SDF files, so do you have any suggestions as to where > something might be wrong? > > - Kevin > > On Mon, Aug 23, 2021 at 9:51 AM Noel O'Boyle wrote: > >> Which means that there is something wrong with your input

Re: [Open Babel] Adding Hydrogen During Confab

2021-08-23 Thread Noel O'Boyle
ect the issue. > > - Kevin > > On Wed, Aug 18, 2021 at 5:17 PM Noel O'Boyle wrote: > >> Ah OK. Try an sdf file, and then there will be no need for OB to guess >> anything. >> >> On Wed, 18 Aug 2021, 21:50 Kevin Skinner, wrote: >> >>> Hel

Re: [Open Babel] Adding Hydrogen During Confab

2021-08-18 Thread Noel O'Boyle
> > On Wed, Aug 18, 2021 at 3:47 PM Noel O'Boyle wrote: > >> Hi Kevin, >> >> Working as intended. The forcefields and QM calculations require explicit >> hydrogens to correctly calculate the energy. It's trivial to remove the H >> afterwards, but

Re: [Open Babel] Adding Hydrogen During Confab

2021-08-18 Thread Noel O'Boyle
Hi Kevin, Working as intended. The forcefields and QM calculations require explicit hydrogens to correctly calculate the energy. It's trivial to remove the H afterwards, but this would be a bit unusual so think it over. Regards, Noel On Wed, 18 Aug 2021 at 16:25, Kevin Skinner wrote: > Hello,

Re: [Open Babel] Library not loaded

2021-08-16 Thread Noel O'Boyle
If the formula excluded the Schrodinger code (there's an option to do this for this very reason) then the dependency goes away. On Tue, 17 Aug 2021, 01:28 Francois Berenger, wrote: > On 13/08/2021 00:29, Chris Swain via OpenBabel-discuss wrote: > > Hi, > > > > I’m sure I’ve seen mention of this

Re: [Open Babel] Turn off adding hydrogens

2021-04-25 Thread Noel O'Boyle
Based on this, your input SD file does not describe the deprotonated form. You should take a look at the spec for SDF regarding charged atoms and check your file against it. On Sun, 25 Apr 2021, 13:28 David van der Spoel, wrote: > On 2021-04-25 14:09, Peter Jarowski wrote: > > Hi David: > > > >

Re: [Open Babel] XYZ Atom Order

2021-02-04 Thread Noel O'Boyle
It's the order of the atoms in the OBMol's vector of OBAtoms. On Thu, 4 Feb 2021 at 12:54, Matt Bone wrote: > Dear OpenBabel, > > What determines the atom order in the XYZ files written by > OpenBabel/Avogadro? It appears there is some logical pattern behind it, but > I can't figure it out from

Re: [Open Babel] Prevent warning messages (Python, OB 3.1.0)

2020-12-19 Thread Noel O'Boyle
That creates a new message handler. You need to get hold of the existing one. It's something like obErrorLog. If you use dir() on ob, you will find the exact name. On Fri, 18 Dec 2020, 23:38 Stefano Forli, wrote: > Hi, > > I'm having a hard time disabling warning messages using the > OBMessageHa

Re: [Open Babel] problem installing python bindings

2020-12-03 Thread Noel O'Boyle
You'll need to install the latest OpenBabel. On Tue, 1 Dec 2020, 19:09 Rita Ortega, wrote: > Hello, > > I am tryint to install the python bindings to use pybel but I keep > gettin error messages. > > I reinstalled openbabel in the 2.3.1 version and I am using python 3.7 > version. I tried instal

Re: [Open Babel] mol.EndModify() and upgrade to ob3.0

2020-10-17 Thread Noel O'Boyle
Hi Simon, I'm finding it a bit confusing to work out what's going on here. If you could either provide the simplest possible self-contained example, or else describe what you want to do. At the back of my mind is the fact that molA += molB is how you add one molecule to another in Open Babel - it

Re: [Open Babel] Chirality perception

2020-10-12 Thread Noel O'Boyle
Hi Stefano, This is documented in the "0D structures" section: "if you wish to identify additional stereocenters whose stereo configuration is unspecified, ...then you may wish to trigger perception." The reason we don't do this by default is simply for speed. Regards, Noel On Mon, 12 Oct 2020 a

Re: [Open Babel] Failed to kekulize aromatic bonds | structure building

2020-07-14 Thread Noel O'Boyle
cause of that there is a data > discrepancy downstream, so I wonder what can I do to find out what is wrong > in my case. > > > > Best, > > Lukas > > > > *From: *Noel O'Boyle > *Date: *Tuesday, 14 July 2020 at 15:13 > *To: *Lukas Pravda > *Cc: *"

Re: [Open Babel] Failed to kekulize aromatic bonds | structure building

2020-07-14 Thread Noel O'Boyle
Before 3.0, aromaticity perception was performed as if the position of the hydrogens were unknown, and the hydrogens were inferred afterwards. This makes sense for structures from the PDB, but not for anything else (e.g. SMILES) where there were occasional errors and it was much slower than necessa

Re: [Open Babel] Python scripts, Open Babel and SMOG output

2020-06-21 Thread Noel O'Boyle
Hi Anthony, You're on the right track. "etab" is gone now, as you've found. "ob.GetAtomicNum(element)" is the replacement you're looking for. Looking through the code, I think it should work now. FYI, if you want to use Python 3 instead of Python 2, you may also need to replace "f.next()" with "n

Re: [Open Babel] Babel not recognised

2020-05-26 Thread Noel O'Boyle
The release notes at https://open-babel.readthedocs.io/en/latest/ReleaseNotes/ob300.html explain that 'babel' has been removed. - Noel On Mon, 25 May 2020 at 19:18, Tanya Jaiswal wrote: > Hello, > I downloaded the v2.3 of open babel earlier but without noticing it I > downloaded the v3.0 today

Re: [Open Babel] Openbabel and Python 3.8

2020-05-26 Thread Noel O'Boyle
It works fine on Linux if you have Swig 4.0. Just doesn't work on Windows. On Tue, 26 May 2020 at 13:10, Hongyi Zhao wrote: > Noel O'Boyle 于2020年5月26日周二 下午7:55写道: > > > > Those listed at https://pypi.org/project/openbabel/3.1.1/. > Unfortunately, we were not a

Re: [Open Babel] Openbabel and Python 3.8

2020-05-26 Thread Noel O'Boyle
t; Thanks! > > On Tue, May 26, 2020, 3:39 AM Noel O'Boyle wrote: > >> 3.8 is not supported on Windows. >> >> On Mon, 25 May 2020, 19:54 MD Simulation, >> wrote: >> >>> Hello, >>> >>> I followed the instructions to install O

Re: [Open Babel] Openbabel and Python 3.8

2020-05-26 Thread Noel O'Boyle
3.8 is not supported on Windows. On Mon, 25 May 2020, 19:54 MD Simulation, wrote: > Hello, > > I followed the instructions to install Openbabel using pip from: > > > https://open-babel.readthedocs.io/en/latest/UseTheLibrary/PythonInstall.html#windows > > > I'm using Python 3.8 and have installe

Re: [Open Babel] installing and importing openbabel

2020-05-17 Thread Noel O'Boyle
The current version of OB is 3.1.1, not 2.0. On Fri, 15 May 2020 at 16:13, Weise, David wrote: > Hi, > Try another method listed: > http://openbabel.org/wiki/Category:Macintosh > > I was able to do it on linux with conda. > > --David > > > David Weise > Linux Systems Admin > Penn Medicine Acade

Re: [Open Babel] cmake problems

2020-04-23 Thread Noel O'Boyle
Hi David, Can you provide the output from running Cmake on a clean build of Open Babel 3.0? What exact OS is this? - Noel On Wed, 22 Apr 2020, 19:17 Weise, David, wrote: > Hello Everybody, > I've been trying to compile openbabel for a hpc lsf environment. I'm > having a problem with cmake and

Re: [Open Babel] compiling python bindings for obabel 3.0

2020-04-20 Thread Noel O'Boyle
Yes 3.0. E.g. from https://github.com/openbabel/openbabel/releases On Thu, 16 Apr 2020 at 21:25, Bennion, Brian wrote: > Is there a later version than 2.3.1.tar.gz that I can download? > -- > *From:* Noel O'Boyle > *Sent:* Thursday, April 16, 2

Re: [Open Babel] compiling python bindings for obabel 3.0

2020-04-16 Thread Noel O'Boyle
If you use CMAKE_INSTALL_PREFIX=wherever, then the Python bindings will be installed locally, along with the rest of Open Babel. There is no need for Conda or pip, etc. Are you saying that this wouldn't work for you for some reason? To use it, you just need to set a couple of environment variables.

Re: [Open Babel] OpenBabel-discuss Digest, Vol 167, Issue 10

2020-04-16 Thread Noel O'Boyle
Hi Brian, (Note that it's a good idea to edit the subject when replying to a digest.) Let's get you set up with the Python bindings. Try it again from a clean build, and report what you find. Note that the 3.0 release requires that you have Swig and pass -DRUN_SWIG=TRUE (an oversight on our part)

Re: [Open Babel] Operating on multi molecule sdf files

2020-04-14 Thread Noel O'Boyle
Apart from --addoutindex I think that's right. I'm not sure how we would implement that in any case, though suggestions are welcome. Can you give a specific example of what you want to do? Where are these identifiers coming from? On the other hand, it's straightforward to do it from Python. As you

Re: [Open Babel] read molecules from xyz files and merge them

2020-04-10 Thread Noel O'Boyle
Just to add that "addh" and "removeh" don't add and remove hydrogens, they convert the hydrogens that are explicit in the molecular graph into implicit hydrogens. I appreciate that the names are misleading, but it's hard to change them at this point. To actually delete an explicit hydrogen, you nee

Re: [Open Babel] read molecules from xyz files and merge them

2020-04-09 Thread Noel O'Boyle
Use the Python keyword "next" on an iterator to get the next item: mol1 = next(pybel.readfile() You can add an OBMol to an existing one: m1 += m2 I'd recommend writing it out as SMILES at this point, just to check the structure: print(pybel.Molecule(m1).write("smi")) If the hydrogens are

Re: [Open Babel] compiling openbabel3 on Ubuntu 18.04

2020-04-05 Thread Noel O'Boyle
Hi Thomas, Just to take a step back, if you need to change the Python that CMake finds, the relevant CMake variables are (with example values): -DPYTHON_EXECUTABLE=/usr/bin/python3 -DPYTHON_INCLUDE_DIR=/usr/include/python3.5m -DPYTHON_LIBRARY=/usr/lib64/ libpython3.5m.so Regarding your question,

Re: [Open Babel] Filter options

2020-03-29 Thread Noel O'Boyle
Hi Chris, Sorry for the delay. The only detail is whatever you get when you type "obabel -L" and the name of the descriptor. To answer some of the questions, descriptors that return 'true' or 'false' are really filters, e.g. the "-s". They are handled by the same code that handles true descripto

Re: [Open Babel] Problems deleting a OBMol object

2020-03-07 Thread Noel O'Boyle
Conformer(i); > > OBff->Setup(*mol); > > OBff->GetCoordinates(*mol); > > energy = OBff->Energy(); > > if (OBff->GetUnit() == "kJ/mol"){ // Converting to > kcal/mol, if needed. > > ener

Re: [Open Babel] Other ob tools

2020-03-03 Thread Noel O'Boyle
> others can hopefully try out and provide feedback. Tools that are regularly > used and prove to be robust and useful could then be rolled into obabel. > > And no I don’t know of a process to do this. > > Cheers, > > Chris > > > On 2 Mar 2020, at 20:11, Noel O'

Re: [Open Babel] Other ob tools

2020-03-02 Thread Noel O'Boyle
It's not a popular opinion, but I think we should have a single robust executable. I've never used any of the others, and they are mostly untested. On Sat, 29 Feb 2020, 18:21 Chris Swain via OpenBabel-discuss, < openbabel-discuss@lists.sourceforge.net> wrote: > Hi, > > I’m working on an update to

Re: [Open Babel] Problems deleting a OBMol object

2020-03-01 Thread Noel O'Boyle
It would help us if you could provide the shortest possible (but complete) example code that exhibits the problem. As it is, you say the problem is when you delete the molecule, but there is no line that deletes the molecule. On Thu, 27 Feb 2020 at 16:19, Alessandro S. Nascimento < asnascime...@if

Re: [Open Babel] First steps with OpenBabel

2020-03-01 Thread Noel O'Boyle
atom.GetResidue() has the PDB information. for atom in ob.OBMolAtomIter(mol.OBMol): residue = atom.GetResidue() print("%d %s %s" % (residue.GetIdx(), residue.GetName(), residue.GetAtomID(atom))) Regarding addh(), I'm not sure what DSSP is. On Sun, 16 Feb 2020 at 15:40, Athanasios Anastas

Re: [Open Babel] Removal from Mail List

2020-02-05 Thread Noel O'Boyle
Hi Emmanuel, To unsubscribe, please follow the link at the bottom of every mailing list email. If this doesn't work, please let us know and we can do it from this end. Regards, - Noel On Wed, 5 Feb 2020 at 10:00, Emmanuel Adeyemi via OpenBabel-discuss < openbabel-discuss@lists.sourceforge.net> w

Re: [Open Babel] Python: Getting atomic forces after a FF optimization

2020-02-04 Thread Noel O'Boyle
Untested, but try "mol.GetData(ob.ConformerData)". I note that the value of ConformerData is 4 not 1. - Noel On Tue, 4 Feb 2020 at 00:10, Shiring, Stephen B wrote: > Hi all, > > > > I’m writing a Python script to screen a bunch of molecules, and for part > of that I would like to read in and op

Re: [Open Babel] Using Pybel to generate mopac input files

2020-01-07 Thread Noel O'Boyle
Sorry, FindType(). On Tue, 7 Jan 2020, 20:38 Markus Grimm via OpenBabel-discuss, < openbabel-discuss@lists.sourceforge.net> wrote: > Hi Noel, > > thank you very much! > > Unfortunately I got an error when I tried the FindPlugin() function. > > Code: > > > > > > > > > > > > > > > > *import pybel#

Re: [Open Babel] Using Pybel to generate mopac input files

2020-01-07 Thread Noel O'Boyle
Hi Markus, In the world of Open Babel, "gen3d" is an 'operation' rather than an input or output option. These are only triggered when using OBConversion::Convert, which is not very friendly for Python use (we should do something about this). Anyway, you just need to trigger the operation yourself

Re: [Open Babel] cmake and make Errors with OpenBabel Compiling

2020-01-07 Thread Noel O'Boyle
Hi Justice, It looks like CMake is not part of Xcode. You can just download and install it separately from https://cmake.org/download/. When you run this, it will create the Makefile that "make" will use. Regards, - Noel On Tue, 7 Jan 2020 at 14:24, Justice Calderon wrote: > To whom this may

Re: [Open Babel] Concatenate Smiles

2019-11-18 Thread Noel O'Boyle
Hi Markus, Concatenating SMILES strings may not be the best way to solve this problem. I would just create a bond between the two atoms from Python and set the charges to zero, and adjust hydrogens (if necessary). But since you asked...:-) $ obabel -:"O=C1CCC(=O)[N-]1" -xf 7 -osmi [N-]1C(=O)CCC1

Re: [Open Babel] Using Openbabel with a New Package

2019-11-04 Thread Noel O'Boyle
EL_DATADIR to the correct >> path when I use the conda package in Windows, unlike in Linux and Mac. This >> is a minor issue but It would be convenient if users do not need to mess >> with environment variables. >> >> >> >> Thanks for your help, >> >&

Re: [Open Babel] How to install pybel?

2019-11-04 Thread Noel O'Boyle
Yes - up to date documentation can be found at https://openbabel.github.io/docs/3.0/. Is it possible to do a redirect, Geoff? On Thu, 31 Oct 2019 at 22:58, Peng Yu wrote: > So the documentation > https://openbabel.org/docs/dev/UseTheLibrary/Python_PybelAPI.html#pybel-api > is outdated? Thanks. >

Re: [Open Babel] Strange behaviour with pdbqt format

2019-11-04 Thread Noel O'Boyle
"snap install openbabel" on ubuntu will install version 3.0. To run it, use openbabel.obabel. On Mon, 21 Oct 2019 at 13:33, Horacio Pérez Sánchez wrote: > Last Ubuntu version > Thanks > > On 10 Oct 2019, at 02:27, Geoffrey Hutchison > wrote: > > Is it possible to get the binary of the last deve

Re: [Open Babel] How to draw structure from SMILES?

2019-11-01 Thread Noel O'Boyle
The "brew info" is describing the new version, which appears to include cairo. Why not get rid of 2.4.1 and install 3.0.0, and see if that works? On Thu, 31 Oct 2019 at 23:03, Peng Yu wrote: > I got the following error. Do you know what is wrong? Thanks. > > $ obabel '-:C(=O)Cl' -O acidchloride.

Re: [Open Babel] Strange behaviour with pdbqt format

2019-10-03 Thread Noel O'Boyle
Have you tried the latest code? If the problem persists with the latest development code, could you please file a bug. Thanks, Noel On Wed, 18 Sep 2019 at 11:38, HORACIO EMILIO PEREZ SANCHEZ wrote: > Hi, >we are using Open Babel 2.4.1 and we have found a very strange > behaviour when con

Re: [Open Babel] Using Openbabel with a New Package

2019-10-02 Thread Noel O'Boyle
It took me a little while to figure it out, but try adding the following to your CMake file: add_definitions(-DUSING_DYNAMIC_LIBS) On Wed, 2 Oct 2019 at 12:34, Noel O'Boyle wrote: > I will try and get some time to look at this. My only thought at the > moment is that the Windows bu

Re: [Open Babel] Using Openbabel with a New Package

2019-10-02 Thread Noel O'Boyle
this issue > for Linux and Mac. > > > > Asim > > > > > > *From: *Asem Alenaizan > *Sent: *Friday, September 27, 2019 4:06 PM > *To: *Geoffrey Hutchison > *Cc: *Noel O'Boyle ; > openbabel-discuss@lists.sourceforge.net > *Subject: *RE: [Open Babe

Re: [Open Babel] Using Openbabel with a New Package

2019-09-27 Thread Noel O'Boyle
gt; > > The program can be compiled and linked correctly against openbabel, but I > cannot find the force field. > > I also tried with newer visual studios but had the same problem. > > > > Asim > > > > *From: *Noel O'Boyle > *Sent: *Thursday, Septem

Re: [Open Babel] Using Openbabel with a New Package

2019-09-26 Thread Noel O'Boyle
; > On Thu, Sep 26, 2019 at 3:52 PM Noel O'Boyle wrote: > >> When you compile Open Babel, do the binaries work? e.g. "obabel -: >> -omol --gen3d" >> >> Regarding 3.0 versus 2.4.1, the release is imminent. Whether you wait or >> not, is up to

Re: [Open Babel] Using Openbabel with a New Package

2019-09-26 Thread Noel O'Boyle
When you compile Open Babel, do the binaries work? e.g. "obabel -: -omol --gen3d" Regarding 3.0 versus 2.4.1, the release is imminent. Whether you wait or not, is up to you. - Noel On Thu, 26 Sep 2019 at 17:54, Asem Alenaizan wrote: > Hello, > > > > We are currently working on developing a

Re: [Open Babel] Error handling with smi file in pybel?

2019-09-11 Thread Noel O'Boyle
Hi Vin, By default the command-line application stops on error, a behavior that can be overridden by "-e". I have to say that this behavior drives me bananas. But anyway... I've just been trying to do the same through Python, but have been failing. Adding obconversion.AddOption("e", obconversion.

Re: [Open Babel] substructure search fails

2019-09-10 Thread Noel O'Boyle
Can you provide a single example of a molecule that it misses? We can then try to explain why or work out a solution. Regards, - Noel On Tue, 10 Sep 2019 at 13:33, Vaibhav Dixit wrote: > Dear Openbabel community, > I'm trying to extract all compounds from an sdf file which contain an OH > group

Re: [Open Babel] Smiles

2019-08-19 Thread Noel O'Boyle
Hi Markus, Only possible with the development version (available as snap for example). "-Hsmi" gives the output options, of which one is 'k': $ obabel -:c1c1 -osmi -xk C1C=CC=CC=1 - Noel On Mon, 19 Aug 2019 at 14:36, Markus Grimm via OpenBabel-discuss < openbabel-discuss@lists.sourceforge.n

Re: [Open Babel] obabel not drawing thick lines from command line

2019-08-02 Thread Noel O'Boyle
All output options must be preceded by "-x", so "-xt" in this case. On Thu, 25 Jul 2019 at 18:09, JacksonBurns wrote: > Hi everyone! > In the Open Babel GUI, I am able to move from .mol to .png and select the > "use thicker lines" options and everything works fine. > The issue is that I need to

Re: [Open Babel] [OpenBabel-Devel] PDB files with multiple bonds via CONECT

2019-08-02 Thread Noel O'Boyle
I'm on the fence. Usually I'd say avoid extensions by default, but this looks like a common extension that preserves information. But I can't really say as I don't deal with PDB files. But if you do go ahead with this, it's important that there is an option to turn it off in case it does cause prob

Re: [Open Babel] 3D Rendering of Molecules via POVRay

2019-06-24 Thread Noel O'Boyle
The pov file is intended as a starting point for the user. But you're right, rotating the molecule to be face-on as Avogadro does would be a good idea. - Noel On Mon, 24 Jun 2019, 22:27 Malte Frank Gerdes, wrote: > Hi, > > I'm trying to generate 3D Molecules via POVRay. The camera seems to not

Re: [Open Babel] calculate chemical descriptors from published paper

2019-05-14 Thread Noel O'Boyle
C2=CC(=O)CCC2(C3C1C4CCC5(C4(CC3)C)CCC(=O)O5)C') > for a in mol: > if a.OBAtom.IsInRing(): > print(f'{a.idx}, {a.atomicnum}, {a.cidx}') > > Can you provide further assistance? Thanks. > > > Best regards, > > > Spencer > > > Vào Th 2, 13 t

Re: [Open Babel] calculate chemical descriptors from published paper

2019-05-13 Thread Noel O'Boyle
Hi Spencer, To count the number of ring systems, simply find a ring atom that you have not yet visited (OBAtom.IsInRing()) and floodfill through all of the adjacent ring atoms via bonds that are in a ring. That's ring system 1. Repeat to find additional ring systems. In the reference you point to

Re: [Open Babel] Extract properties of mol2 molecules, along with properties ?

2019-05-03 Thread Noel O'Boyle
Looks like a Scitegic extension to a Tripos format. In theory we could add support but in the meanwhile, it might be better to see whether a Scitegic tool can be use to convert the file to an SDF file, for example, where Open Babel's property support is much stronger. - Noel On Thu, 2 May 2019 at

Re: [Open Babel] ​How to combine t​wo OB​Mol objects​ ​​in python?

2019-04-27 Thread Noel O'Boyle
Have you tried molA += molB? On Fri, 26 Apr 2019, 18:20 Lux QC, wrote: > Dear All, > > Greetings! > > What I want to do is to combine two molecules. > > I tried to combine two OBMol objects together, to obtain an OBMol object > which contains the coordinates of the two molecules. > > After check

[Open Babel] Information on breaking API changes in forthcoming 3.0 release

2019-04-27 Thread Noel O'Boyle
Hi there, As we work towards the next release, Geoff has asked me to put together some documentation on the API changes introduced that might affect your code: https://open-babel.readthedocs.io/en/latest/UseTheLibrary/migration.html This not a "What's New?" - that will have to be done separately

Re: [Open Babel] protonation using Python

2019-04-22 Thread Noel O'Boyle
all it from Python. > I was trying something like this: > > obConversion.AddOption("p", obConversion.GENOPTIONS, "3.0") > > That seems vaguely consistent with how to set the option from Python given > how the CLI option works, but unfortunately it doesn't se

Re: [Open Babel] ImportError: cannot import name 'OBElementTable' from 'openbabel' (unknown location)

2019-04-20 Thread Noel O'Boyle
The dev version will be 3.0. I've written up docs on the migration but am away from that computer right now. Looking at the Python tests ( https://github.com/openbabel/openbabel/blob/master/test/testbindings.py) I see: from openbabel import openbabel as ob ob.GetAtomicNum() o On Sat, 20 Apr 2019

Re: [Open Babel] protonation using Python

2019-04-15 Thread Noel O'Boyle
Hi Tim, Many of these options are just wrappers around API functions, so it's worthwhile taking a look at the API documentation. In this case, here's the link to the relevant docs: http://openbabel.org/api/2.3/classOpenBabel_1_1OBPhModel.shtml Regards, - Noel On Thu, 11 Apr 2019 at 16:11, Tim D

Re: [Open Babel] Contributed code for new file format

2019-02-21 Thread Noel O'Boyle
Hi Paul, Sounds great. It'd be definitely nice to have some test cases to ensure that it actually works as intended and will keep working. It's sound like you have some already. I can help integrate these if you wish. There is also information over at https://open-babel.readthedocs.io/en/latest/C

Re: [Open Babel] ImportError: DLL load failed

2019-02-14 Thread Noel O'Boyle
the python bindings: openbabel-python-1.8.py33.exe > > > > On Sun, Feb 10, 2019 at 5:15 AM Noel O'Boyle wrote: > >> I think it is a version problem. Can you paste in the exact file names of >> the files you downloaded? I note that you are using a 32-bit Python, and so >

Re: [Open Babel] Problem with ring detection

2019-02-14 Thread Noel O'Boyle
In Python, for example, call the IsInRing() method of an atom to find this out. On Sun, 27 Jan 2019 at 18:03, Tang, Dai wrote: > Hi, > > > I have a problem with the ring detection using Open Babel 2.4.1. My goal > is to know which carbon atoms (or other element) of a molecule belong to a > ring

Re: [Open Babel] ImportError: DLL load failed

2019-02-10 Thread Noel O'Boyle
I think it is a version problem. Can you paste in the exact file names of the files you downloaded? I note that you are using a 32-bit Python, and so you will need to ensure that you use the 32-bit Open Babel and bindings. - Noel On Thu, 7 Feb 2019 at 22:13, Tayeb Kakeshpour wrote: > Maybe this

Re: [Open Babel] install openbabel on pythonanywhere server

2019-01-28 Thread Noel O'Boyle
I don't know. For sure the "pip" won't work as it doesn't include the binaries, and the wheels we provide I think are just for Windows. For support, you should contact the developers of www.pythonanywhere.com - Noel On Sun, 27 Jan 2019 at 23:11, Spencer Trinh wrote: > Hi, > > I wanted to insta

Re: [Open Babel] Python 2.7.15 cannot find Open Babel 2.4.1

2019-01-11 Thread Noel O'Boyle
It wasn't able to find the module because PYTHONPATH was only set for the terminal in which you ran the export command. You will need to set it in your .bashrc (or equivalent) to enable it for all terminals. To see the current value from within the Python interpreter, do "import sys" and then "pri

Re: [Open Babel] changes to fingerprint generation, and FPS output

2019-01-10 Thread Noel O'Boyle
On Wed, 9 Jan 2019 at 20:23, Andrew Dalke wrote: > On Jan 9, 2019, at 15:45, Noel O'Boyle wrote: > > Making such an API addition adds a maintainence would commit us to > correctly maintaining the underlying information, and that's a maintainence > task I'm not

Re: [Open Babel] changes to fingerprint generation, and FPS output

2019-01-09 Thread Noel O'Boyle
s, - Noel On Tue, 8 Jan 2019, 15:40 Andrew Dalke > On Jan 7, 2019, at 14:10, Noel O'Boyle wrote: > > > > Can you clarify the requirement for bumping the version? That is, which > of the following is the invariant: > > 1. Any molecule represented in any format c

Re: [Open Babel] NxN Tanimoto similarity calculations/searches

2019-01-08 Thread Noel O'Boyle
Right now, the best approach is to use Andrew Dalke's chemfp. - Noel On Mon, 7 Jan 2019 at 15:12, John Hutchinson wrote: > Hello all, > > > > I have a list of ~4000 SMILES codes. For each substance, I want to > determine all the substances with Tanimoto similarity >70%. I generated a > fastsear

Re: [Open Babel] changes to fingerprint generation, and FPS output

2019-01-07 Thread Noel O'Boyle
l On Mon, 7 Jan 2019 at 13:10, Noel O'Boyle wrote: > Can you clarify the requirement for bumping the version? That is, which of > the following is the invariant: > 1. Any molecule represented in any format changes must create the same > fingerprint > 2. Any SMILES string must cr

Re: [Open Babel] changes to fingerprint generation, and FPS output

2019-01-07 Thread Noel O'Boyle
Can you clarify the requirement for bumping the version? That is, which of the following is the invariant: 1. Any molecule represented in any format changes must create the same fingerprint 2. Any SMILES string must create the same fingerprint 3. Any OBMol must create the same fingerprint Since yo

Re: [Open Babel] be removed from the list

2018-12-23 Thread Noel O'Boyle
There's a link at the bottom of every email. On Sun, 23 Dec 2018, 10:02 Yu Guo Hi, > > I want to be removed from the list of > openbabel-discuss@lists.sourceforge.net. Thank you! > > > Yu Guo > > ​ > > ___ > OpenBabel-discuss mailing list > OpenBabel-di

Re: [Open Babel] generate image dynamically

2018-12-22 Thread Noel O'Boyle
Sure. Have the html include an img with src pointing to an svg file, and have this request handled by flask which should return the svg file generated dynamically based on the url. The important step is that flask should set the mimetype correctly. On Sat, 22 Dec 2018, 19:22 Spencer Trinh Hi, > >

Re: [Open Babel] Open Babel installation on Mac

2018-12-21 Thread Noel O'Boyle
We are not the developers of iBabel. I see there is a "contact me" link over at https://www.macinchem.org/ibabel/. On Fri, 21 Dec 2018 at 13:02, Zabdiel Alvarado Martinez wrote: > Hello > I appreciate this very powerful tool that this team has designed, however, > I am new to Mac and have recent

Re: [Open Babel] atom mapped RXN file to PNG

2018-12-21 Thread Noel O'Boyle
Unfortunately, the PNG depiction doesn't depict reactions (as far as I know). On Fri, 21 Dec 2018 at 13:02, gpreciat wrote: > Hi all, > I'm trying to convert my database of RXN files into PNG files for faster > visualization. I have tried different commands in the terminal but so far > none has

Re: [Open Babel] Weighted rotor search in parallel

2018-12-21 Thread Noel O'Boyle
I'm afraid not. :-/ You could try one of the other approaches like the genetic algorithm, and see whether it progresses faster. On Wed, 12 Dec 2018 at 21:45, Michele Galasso wrote: > Hello everyone! > > > I am using the weighted rotor search implemented in Open Babel in order to > search for low

Re: [Open Babel] << ECFP4 in OpenBabel >>

2018-12-07 Thread Noel O'Boyle
some measurable global structural property related to a physical property of interest. - Noel On Fri, 7 Dec 2018 at 10:22, Noel O'Boyle wrote: > An ECFP4 implementation could use a single bit or a million bits. The > actual information that is being encoded is an element of a set

Re: [Open Babel] << ECFP4 in OpenBabel >>

2018-12-07 Thread Noel O'Boyle
An ECFP4 implementation could use a single bit or a million bits. The actual information that is being encoded is an element of a set of size of more than billions (I forget the details). So it's hashed to something manageable. The shorter the length, the more bit collisions (everything will collid

Re: [Open Babel] Math multiplication symbol in SMARTs

2018-11-24 Thread Noel O'Boyle
The source code for filter-it is open. Also it's documented. http://silicos-it.be.s3-website-eu-west-1.amazonaws.com/software/filter-it/1.0.2/filter-it.html#logs On Fri, 23 Nov 2018, 13:15 Leif Peterson I changed it to an X and might try x since results are off a little. some > compounds als

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