[Rdkit-discuss] gromacs force field and topology from SMILES

2016-10-14 Thread Rafal Roszak 
Dear all,

1. I want to generate gromacs topology with force field parameters
from SMILES. RDKit has two FFs so this should be easy task at least for
this two force fields. Bond and angle parameters can be simply take
from Get*BondStretchParams and Get*StretchBendParams, but vdW and
torsian parameters are not so obvious.
-) How to assign vdW params to atoms? How can I extract this from rdkit?
-) How to convert result of Get*TorsionParams (Inversion and OopBend) to
something which can be used by gromacs? (I know, it is not strictly
question about RDKit)

2. It think I found bug in MMFF implementation:

>>> acetona=Chem.AddHs(Chem.MolFromSmiles('[CH2-]C(=O)C') )
>>> AllChem.MMFFHasAllMoleculeParams(acetona)
True
>>> acetmm=AllChem.MMFFGetMoleculeProperties(acetona)
>>> sumch=0
>>> for i in range( len(acetona.GetAtoms()) ):
...  sumch+=acetmm.GetMMFFPartialCharge(i)
... 
>>> round(sumch,2)
0.0
>>> for i in range( len(acetona.GetAtoms()) ):
...  sumch+=acetmm.GetMMFFFormalCharge(i)
... 
>>> round(sumch,2)
0.0

The molecule is anion but sum of formal or partial charge is zero. In
my opinion it is not currect result :) The same behaviour I also
observed for other exotic C-anion.


Regards,

Rafał

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Re: [Rdkit-discuss] gromacs force field and topology from SMILES

2016-10-14 Thread Paolo Tosco 
Dear Rafal,

answers below.

On 10/14/16 13:53, Rafal Roszak wrote:
> Dear all,
>
> 1. I want to generate gromacs topology with force field parameters
> from SMILES. RDKit has two FFs so this should be easy task at least for
> this two force fields. Bond and angle parameters can be simply take
> from Get*BondStretchParams and Get*StretchBendParams, but vdW and
> torsian parameters are not so obvious.
> -) How to assign vdW params to atoms? How can I extract this from rdkit?
The RDKit currently returns has two Get*VdWParams() functions which 
retrieve the vdW parameters for a specific *pair* of atoms, i.e. after 
the {MMFF, UFF} combination rules have been applied. I can add getters 
for the raw per-atom vdW parameters; I'll let you know once they are 
implemented.
> -) How to convert result of Get*TorsionParams (Inversion and OopBend) to
> something which can be used by gromacs? (I know, it is not strictly
> question about RDKit)
I am not myself a Gromacs user and I don't know about the Gromacs 
topology format, so I am afraid I can't help with this one.
>
> 2. It think I found bug in MMFF implementation:
>
 acetona=Chem.AddHs(Chem.MolFromSmiles('[CH2-]C(=O)C') )
 AllChem.MMFFHasAllMoleculeParams(acetona)
> True
 acetmm=AllChem.MMFFGetMoleculeProperties(acetona)
 sumch=0
 for i in range( len(acetona.GetAtoms()) ):
> ...  sumch+=acetmm.GetMMFFPartialCharge(i)
> ...
 round(sumch,2)
> 0.0
 for i in range( len(acetona.GetAtoms()) ):
> ...  sumch+=acetmm.GetMMFFFormalCharge(i)
> ...
 round(sumch,2)
> 0.0
>
> The molecule is anion but sum of formal or partial charge is zero. In
> my opinion it is not currect result :) The same behaviour I also
> observed for other exotic C-anion.
>
The MMFF force field does not have parameters for carbanions nor for 
carbocations, so AllChem.MMFFHasAllMoleculeParams() should return False. 
Thanks for reporting this; I'll file a bug and fix it as soon as I have 
a bit of time.

Best,
Paolo
> Regards,
>
> Rafał
>
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[Rdkit-discuss] Issues with rdkit and postgresql cartridge conda installation

2016-10-14 Thread Danes, Larson 
Hello all,


First and foremost, please excuse any inaccuracies as I am new to the world of 
Cheminformatics. I'll start with some background on my issue. I've got a MySQL 
database with chemical information such as CASRNs, Annotation Class, and SMILE 
strings. I have a web app currently in development that takes a list of CASRNs 
as input and performs an enrichment analysis on those chemicals. The goal is to 
now take a SMILE string as input, query the rdkit postgresql database (which 
will consist of a table with rows that have CASRNs and SMILE strings) to find 
any chemicals that match the input SMILE string over a set threshold. These 
chemicals CASRNs will then become the input for enrichment and the rest of the 
app will be agnostic toward how the CASRNs were obtained.


I suppose I should say this: if the description above isn't something rdkit is 
suited for and I'm totally off base, please let me know! As I stated earlier, 
I'm new to this realm.


Anyway, the issues I'm facing currently involve the installation of rdkit and 
the postgresql cartridge. I should say, I've tried this on both Windows 7 and 
Windows 10 (work desktop in 7 and laptop is 10). So, the first question I have 
is when running the command

conda install -c https://conda.binstar.org/rdkit rdkit-postgresql

I'm faced with a "PackageNotFoundError". Conda then suggests maybe I meant 
"rdkit-postgresql: postgresql". So, I run

conda install -c https://conda.binstar.org/rdkit postgresql

which seems to install just fine. My question is simply, is this ok? Do i 
specifically need the "rdkit-postgresql" package? I searched anaconda.org for 
the rdkit-postgresql package and found it. It said it could be installed with

   conda install -c rdkit rdkit-postgresql=2016.03.4

but this resulted in a similar error. I was wondering if it was possibly a 
platform difference, because anaconda.org shows the package as "linux-64".


I'd also just like to mention a few other issues I was (seemingly) able to work 
around, but I would still like to mention them as they may provide context for 
my next question. The path to the rdkit bin folder for me is 
"C:\Users\Larson\Anaconda3\envs\my-rdkit-env\Library\bin" while the 
documentation specifies it should follow the "[conda 
folder]/envs/my-rdkit-env/bin" convention. Perhaps it's a change in the 
directory structure that hasn't been updated in the documentation? Next, to 
actually start the postgresql server the command I had to use was

   C:\Users\Larson\Anaconda3\envs\my-rdkit-env\Library\bin\pg_ctl -D 
path/to/db/data -l logfile start

as opposed to

   [conda folder]/envs/my-rdkit-env/bin/postgres -D 
/folder/where/data/should/be/stored

as outlined in the documentation.


And I believe that brings us to my current issue/question. In the 
documentation, it specifies to create a database you should do the following:

   createdb my_rdkit_db

psql my_rdkit_db

# create extension rdkit;

The first two lines I can get through just fine, but the "create extension" 
command gives me a file not found error, with the file in question being 
"rdkit.control". I searched the rdkit github page and found one such file and 
copied it to the appropriate location 
("C:\Users\Larson\Anaconda3\envs\my-rdkit-env\Library\share\extension", I 
believe). After doing so I got a new error that I can't replicate at the 
moment, but it was another file not found error and the file it was looking for 
was "rdkit--3.5.sql" I'm fairly sure. I could not find any such file on github, 
which is what prompted me to create this post.


Please let me know if I'm doing anything incorrectly or anything else that 
might help. I will also do my best to provide any clarification if necessary.


Thanks very much for your time,


Larson Danes
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[Rdkit-discuss] where to find I-State of atoms

2016-10-14 Thread Guillaume GODIN 
?Dear All,


I'm looking for the definition & values of the atomic "I-State" used in Dragon 
for RDF, MORSE descriptors.


Do you have a source for those physical descriptors ?


best regards,

Dr. Guillaume GODIN
Principal Scientist
Chemoinformatic & Datamining
Innovation
CORPORATE R&D DIVISION
DIRECT LINE +41 (0)22 780 3645
MOBILE  +41 (0)79 536 1039
Firmenich SA
RUE DES JEUNES 1 | CASE POSTALE 239 | CH-1211 GENEVE 8
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[Rdkit-discuss] windows 32 shared library

2016-10-14 Thread Steven Combs 
Has anyone compiled rdkit into a 32bit shared library dll?

Steven Combs
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Re: [Rdkit-discuss] where to find I-State of atoms

2016-10-14 Thread Giuseppe Marco Randazzo 
This book >>> http://onlinelibrary.wiley.com/book/10.1002/9783527613106 <<< 
that look like a bible.

Best regards,

GMR





> On 14 Oct 2016, at 19:28, Guillaume GODIN  
> wrote:
> 
> ​Dear All,
> 
> I'm looking for the definition & values of the atomic "I-State" used in 
> Dragon for RDF, MORSE descriptors.
> 
> Do you have a source for those physical descriptors ?
> 
> best regards,
> 
> Dr. Guillaume GODIN
> Principal Scientist
> Chemoinformatic & Datamining
> Innovation
> CORPORATE R&D DIVISION
> DIRECT LINE +41 (0)22 780 3645
> MOBILE  +41 (0)79 536 1039
> Firmenich SA
> RUE DES JEUNES 1 | CASE POSTALE 239 | CH-1211 GENEVE 8
> 
> 
> **  
> DISCLAIMER  
> This email and any files transmitted with it, including replies and forwarded 
> copies (which may contain alterations) subsequently transmitted from 
> Firmenich, are confidential and solely for the use of the intended recipient. 
> The contents do not represent the opinion of Firmenich except to the extent 
> that it relates to their official business.  
> ** 
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> engaging tech sites, SlashDot.org ! 
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> 
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss 
> 

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Re: [Rdkit-discuss] gromacs force field and topology from SMILES

2016-10-14 Thread Daniel Seeliger 
Hi Rafal,

as far as I know the MMFF is not compatible with any contemporary MD 
forcefield. The usual way to generate topologies for ligands is the generalised 
amber forcefield (GAFF). What you need are ambertools (http://ambermd.org/ 
) and acpype (https://github.com/t-/acpype 
). As input you need a mol2 file of your ligand 
which you can generate with the rdkit from smiles. Make sure to add hydrogens 
and the protonation state you want. Partial charges can either be computed with 
AM1-BCC or Gaussian (RESP). 
Acpype can generate topologies for Amber or Gromacs. In either case you should 
use an amber forcefield for the protein (I guess you want to run a simulation 
of a complex).

I recommend to check the structure after minimisation, especially if you’re 
attempting to generate a topology for a molecule which is not common (e.g. a 
transition state) since GAFF sometimes assigns incorrect angle and dihedral 
parameters.

Best,
Daniel


> On 14 Oct 2016, at 15:12, Paolo Tosco  wrote:
> 
> Dear Rafal,
> 
> answers below.
> 
> On 10/14/16 13:53, Rafal Roszak wrote:
>> Dear all,
>> 
>> 1. I want to generate gromacs topology with force field parameters
>> from SMILES. RDKit has two FFs so this should be easy task at least for
>> this two force fields. Bond and angle parameters can be simply take
>> from Get*BondStretchParams and Get*StretchBendParams, but vdW and
>> torsian parameters are not so obvious.
>> -) How to assign vdW params to atoms? How can I extract this from rdkit?
> The RDKit currently returns has two Get*VdWParams() functions which 
> retrieve the vdW parameters for a specific *pair* of atoms, i.e. after 
> the {MMFF, UFF} combination rules have been applied. I can add getters 
> for the raw per-atom vdW parameters; I'll let you know once they are 
> implemented.
>> -) How to convert result of Get*TorsionParams (Inversion and OopBend) to
>> something which can be used by gromacs? (I know, it is not strictly
>> question about RDKit)
> I am not myself a Gromacs user and I don't know about the Gromacs 
> topology format, so I am afraid I can't help with this one.
>> 
>> 2. It think I found bug in MMFF implementation:
>> 
> acetona=Chem.AddHs(Chem.MolFromSmiles('[CH2-]C(=O)C') )
> AllChem.MMFFHasAllMoleculeParams(acetona)
>> True
> acetmm=AllChem.MMFFGetMoleculeProperties(acetona)
> sumch=0
> for i in range( len(acetona.GetAtoms()) ):
>> ...  sumch+=acetmm.GetMMFFPartialCharge(i)
>> ...
> round(sumch,2)
>> 0.0
> for i in range( len(acetona.GetAtoms()) ):
>> ...  sumch+=acetmm.GetMMFFFormalCharge(i)
>> ...
> round(sumch,2)
>> 0.0
>> 
>> The molecule is anion but sum of formal or partial charge is zero. In
>> my opinion it is not currect result :) The same behaviour I also
>> observed for other exotic C-anion.
>> 
> The MMFF force field does not have parameters for carbanions nor for 
> carbocations, so AllChem.MMFFHasAllMoleculeParams() should return False. 
> Thanks for reporting this; I'll file a bug and fix it as soon as I have 
> a bit of time.
> 
> Best,
> Paolo
>> Regards,
>> 
>> Rafał
>> 
>> --
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>> engaging tech sites, SlashDot.org ! 
>> http://sdm.link/slashdot 
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>> 
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss 
>> 
> 
> 
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[Rdkit-discuss] Solved! (was, Re: Fwd: Jupyter renders only from the outermost level?)

2016-10-14 Thread Peter S. Shenkin 
In an earlier thread, I reported that I could not get Jupyter to render
except from the outermost level of the notebook. For instance, the
following code would not render Benzene:

--
from rdkit import Chem
from rdkit.Chem import rdDepictor
from rdkit.Chem.Draw import rdMolDraw2D
from rdkit.Chem.Draw import IPythonConsole
from IPython.display import SVG, display

m = Chem.MolFromSmiles("c1c1")

def render_mol(m):
rdDepictor.Compute2DCoords(m)
drawer = rdMolDraw2D.MolDraw2DSVG(400, 200)
drawer.DrawMolecule(m)
drawer.FinishDrawing()
svg = drawer.GetDrawingText().replace('svg:','')
SVG(svg)

render_mol(m)
--

Googling around for something else, I accidentally found out how to make
this work. Namely, replace the last line in render_mol() with:

display(SVG(svg))

In other words, use the IPython.display.display function. This function
will render to the screen from anywhere in your notebook code. You'll note
I have imported it in the above excerpt.

The suggestion at the time was to use MolsToGridImage(), which is a great
facility, but it might not always be what you want. So I was happy to find
this.

-P.
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Re: [Rdkit-discuss] Issues with rdkit and postgresql cartridge conda installation

2016-10-14 Thread Greg Landrum 
Hi Larson,

On Fri, Oct 14, 2016 at 6:17 PM, Danes, Larson  wrote:
>
> First and foremost, please excuse any inaccuracies as I am new to the
world of Cheminformatics. I'll start with some background on my issue. I've
got a MySQL database with chemical information such as CASRNs, Annotation
Class, and SMILE strings. I have a web app currently in development that
takes a list of CASRNs as input and performs an enrichment analysis on
those chemicals. The goal is to now take a SMILE string as input, query the
rdkit postgresql database (which will consist of a table with rows that
have CASRNs and SMILE strings) to find any chemicals that match the input
SMILE string over a set threshold. These chemicals CASRNs will then become
the input for enrichment and the rest of the app will be agnostic toward
how the CASRNs were obtained.
>
>
> I suppose I should say this: if the description above isn't something
rdkit is suited for and I'm totally off base, please let me know! As I
stated earlier, I'm new to this realm.

The basic flow you describe: search a database for molecules similar to a
query and retrieve the results is definitely right inline with what the
RDKit cartridge can do.

> Anyway, the issues I'm facing currently involve the installation of rdkit
and the postgresql cartridge. I should say, I've tried this on both Windows
7 and Windows 10 (work desktop in 7 and laptop is 10). So, the first
question I have is when running the command
>

This is the problem from which all the others stem: We don't currently
provide conda builds of the rdkit-postgresql cartridge for any systems
other than 64bit linux. There hasn't been a lot of demand for this and it's
a non-zero amount of work to set things up, so it hasn't happened.

Do you have access to linux? The cartridge should work fine on a VM running
on your windows machine (using virtual box) or using the new "Bash on
Windows" subsystem in Windows 10 (
https://msdn.microsoft.com/en-us/commandline/wsl/about?f=255&MSPPError=-2147217396
)

-greg
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Re: [Rdkit-discuss] windows 32 shared library

2016-10-14 Thread Greg Landrum 
Hi Steven,

On Fri, Oct 14, 2016 at 8:32 PM, Steven Combs 
wrote:

> Has anyone compiled rdkit into a 32bit shared library dll?
>
>
It should be possible. What are you trying to do?

-greg
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Re: [Rdkit-discuss] where to find I-State of atoms

2016-10-14 Thread Greg Landrum 
Guillaume,

I've been using this chapter from the Handbook of Chemoinformatics for the
3D descriptors:
http://michem.disat.unimib.it/chm/download/materiale/geometrical_descriptors.pdf

Section 2.6 has a discussion of the MoRSE descriptor, along with a
definition of the I values.

Is there sufficient info there for you?

-greg


On Fri, Oct 14, 2016 at 8:41 PM, Giuseppe Marco Randazzo <
gmranda...@gmail.com> wrote:

> This book >>> http://onlinelibrary.wiley.com/book/10.1002/9783527613106
> <<< that look like a bible.
>
> Best regards,
>
> GMR
>
>
>
>
>
> On 14 Oct 2016, at 19:28, Guillaume GODIN 
> wrote:
>
> ​Dear All,
>
> I'm looking for the definition & values of the atomic "I-State" used in
> Dragon for RDF, MORSE descriptors.
>
> Do you have a source for those physical descriptors ?
>
> best regards,
>
> *Dr. Guillaume GODIN*
> Principal Scientist
> Chemoinformatic & Datamining
> Innovation
> CORPORATE R&D DIVISION
> DIRECT LINE +41 (0)22 780 3645
> MOBILE  +41 (0)79 536 1039
> Firmenich SA
> RUE DES JEUNES 1 | CASE POSTALE 239 | CH-1211 GENEVE 8
>
>
> **
> DISCLAIMER
> This email and any files transmitted with it, including replies and
> forwarded copies (which may contain alterations) subsequently transmitted
> from Firmenich, are confidential and solely for the use of the intended
> recipient. The contents do not represent the opinion of Firmenich except to
> the extent that it relates to their official business.
> **
> 
> --
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> engaging tech sites, SlashDot.org ! http://
> sdm.link/slashdot___
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>
>
> 
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[Rdkit-discuss] gromacs force field and topology from SMILES

2016-10-14 Thread Daniel Seeliger 
Hi Rafal,

as far as I know the MMFF is not compatible with any contemporary MD
forcefield. The usual way to generate topologies for ligands is the
generalised amber forcefield (GAFF). What you need are ambertools (
http://ambermd.org/) and acpype (https://github.com/t-/acpype). As input
you need a mol2 file of your ligand which you can generate with the rdkit
from smiles. Make sure to add hydrogens and the protonation state you want.
Partial charges can either be computed with AM1-BCC or Gaussian (RESP).
Acpype can generate topologies for Amber or Gromacs. In either case you
should use an amber forcefield for the protein (I guess you want to run a
simulation of a complex).

I recommend to check the structure after minimisation, especially if you’re
attempting to generate a topology for a molecule which is not common (e.g.
a transition state) since GAFF sometimes assigns incorrect angle and
dihedral parameters.

Best,
Daniel


On 14 Oct 2016, at 15:12, Paolo Tosco > wrote:

Dear Rafal,

answers below.

On 10/14/16 13:53, Rafal Roszak wrote:

Dear all,

1. I want to generate gromacs topology with force field parameters
from SMILES. RDKit has two FFs so this should be easy task at least for
this two force fields. Bond and angle parameters can be simply take
from Get*BondStretchParams and Get*StretchBendParams, but vdW and
torsian parameters are not so obvious.
-) How to assign vdW params to atoms? How can I extract this from rdkit?

The RDKit currently returns has two Get*VdWParams() functions which
retrieve the vdW parameters for a specific *pair* of atoms, i.e. after
the {MMFF, UFF} combination rules have been applied. I can add getters
for the raw per-atom vdW parameters; I'll let you know once they are
implemented.

-) How to convert result of Get*TorsionParams (Inversion and OopBend) to
something which can be used by gromacs? (I know, it is not strictly
question about RDKit)

I am not myself a Gromacs user and I don't know about the Gromacs
topology format, so I am afraid I can't help with this one.


2. It think I found bug in MMFF implementation:

acetona=Chem.AddHs(Chem.MolFromSmiles('[CH2-]C(=O)C') )
AllChem.MMFFHasAllMoleculeParams(acetona)

True

acetmm=AllChem.MMFFGetMoleculeProperties(acetona)
sumch=0
for i in range( len(acetona.GetAtoms()) ):

...  sumch+=acetmm.GetMMFFPartialCharge(i)
...

round(sumch,2)

0.0

for i in range( len(acetona.GetAtoms()) ):

...  sumch+=acetmm.GetMMFFFormalCharge(i)
...

round(sumch,2)

0.0

The molecule is anion but sum of formal or partial charge is zero. In
my opinion it is not currect result :) The same behaviour I also
observed for other exotic C-anion.

The MMFF force field does not have parameters for carbanions nor for
carbocations, so AllChem.MMFFHasAllMoleculeParams() should return False.
Thanks for reporting this; I'll file a bug and fix it as soon as I have
a bit of time.

Best,
Paolo

Regards,

Rafał


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Re: [Rdkit-discuss] where to find I-State of atoms

2016-10-14 Thread Guillaume GODIN 
Thanks Greg & Marco,


so after reading a little around the Dictionary + 3D descriptors pdf... I-State 
are in fact "E-state" and are available in rdkit in python 
(https://github.com/rdkit/rdkit/tree/master/rdkit/Chem/EState) as fingerprint 
per atom.


I will look at it.

Best regards,

Dr. Guillaume GODIN
Principal Scientist
Chemoinformatic & Datamining
Innovation
CORPORATE R&D DIVISION
DIRECT LINE +41 (0)22 780 3645
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De : Greg Landrum 
Envoyé : samedi 15 octobre 2016 06:00
À : Guillaume GODIN; rdkit-discuss@lists.sourceforge.net
Objet : Re: [Rdkit-discuss] where to find I-State of atoms

Guillaume,

I've been using this chapter from the Handbook of Chemoinformatics for the 3D 
descriptors:
http://michem.disat.unimib.it/chm/download/materiale/geometrical_descriptors.pdf

Section 2.6 has a discussion of the MoRSE descriptor, along with a definition 
of the I values.

Is there sufficient info there for you?

-greg


On Fri, Oct 14, 2016 at 8:41 PM, Giuseppe Marco Randazzo 
mailto:gmranda...@gmail.com>> wrote:
This book >>> http://onlinelibrary.wiley.com/book/10.1002/9783527613106 <<< 
that look like a bible.

Best regards,

GMR





On 14 Oct 2016, at 19:28, Guillaume GODIN 
mailto:guillaume.go...@firmenich.com>> wrote:

?Dear All,

I'm looking for the definition & values of the atomic "I-State" used in Dragon 
for RDF, MORSE descriptors.

Do you have a source for those physical descriptors ?

best regards,

Dr. Guillaume GODIN
Principal Scientist
Chemoinformatic & Datamining
Innovation
CORPORATE R&D DIVISION
DIRECT LINE +41 (0)22 780 3645
MOBILE  +41 (0)79 536 1039
Firmenich SA
RUE DES JEUNES 1 | CASE POSTALE 239 | CH-1211 GENEVE 8


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