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,
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
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
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
re, 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:
>
>> It
g('smi', "O=C(NCCN(C)C)c12C(=O)c3c3(Oc12)")
> sma = pybel.Smarts("c12Cc3ccccc3(Oc12)")
> sma.obsmarts.Match(mol.OBMol, True)
> False
>
> Thank you again
> Thomas
>
> Il giorno ven 17 feb 2023 alle ore 18:37 Noel O'Boyle <
> baoille...@g
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
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 there.
>
&g
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,
>
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,
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.
>
>
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
>
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
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
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
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.
>
> On
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
confab, 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. Or
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:
>>
>>> H
>
> 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 this would
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,
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
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:
> >
> >
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
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
>
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
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
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
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: *"openbabel-
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
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
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
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 able
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 Openba
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
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
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
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,
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
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
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
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
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
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
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
;
>
> OBff->GetCoordinates(*mol);
>
> energy = OBff->Energy();
>
> if (OBff->GetUnit() == "kJ/mol"){ // Converting to
> kcal/mol, if needed.
>
> energy = energy/4.18;
>
>
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'Boyle wr
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
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 <
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
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>
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
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#
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
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
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
BABEL_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,
>>
>&
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.
"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
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
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
> 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 Babel] Using Op
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, September 2
;
> 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 you.
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
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",
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
>
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 <
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
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
:
> 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 thg 5, 2019 vào lúc 09:45 Noel O'Boyle <
> baoille...@gmail.com>
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
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
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
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
hon.
> 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 seem to work.
>
>
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
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
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
>> you
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
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
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
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
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 willing to take on.
>
, 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 changes must create the same
> fi
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
>
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 create the s
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
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
>
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,
>
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
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
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
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 o
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
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
You need to look at the definition in the original reference; you won't be
able to reproduce the model unless you use the same definitions.
I'm pretty sure that it doesn't involve 3d structures or partial charge
calculations. Think about how you would identify hydrophobic atoms given a
molecular
It's probably a capital X4 without spaces messed up by the journal. What's
the ref?
On Tue, 20 Nov 2018, 17:21 Leif Peterson <
outlook_ea1c3adb71ba7...@outlook.com wrote:
> I am using OB and SmartsPattern fetching in 2D compounds, and need to
> fetch a published SMARTS which looks like the
Have you tried the development version? This has been rewritten.
On Fri, 16 Nov 2018, 00:19 Stefano Forli Hi,
>
> I've found a series of molecules that trigger what looks like a bug but I
> want to make sure there isn't something clearly wrong with the structures,
> before reporting it.
>
> The
.
Regards,
- Noel
On Thu, 15 Nov 2018 at 15:56, Bennion, Brian wrote:
> https://github.com/harryjubb/openbabel_python_docker/issues/1
>
> This is the same issue that I am observing. So I dont think that I should
> submit another report.
>
> Brian
>
>
>
>
> On November
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