from:"Axel Pahl"

Re: [Rdkit-discuss] SMARTS definition for basic nitrogen

2022-10-06 Thread Axel Pahl


Oh, indeed.
I did not think about that, thank you.

KR Axel

On 06.10.22 13:09, Jonas Bostrom wrote:


Hey Axel,

The Daylight SMARTS example page can also be a useful source:

https://www.daylight.com/dayhtml_tutorials/languages/smarts/smarts_examples.html

All the best

Jonas

*From:*Axel Pahl 
*Sent:* Thursday, 6 October 2022 12:10
*To:* RDKit Discuss 
*Subject:* [Rdkit-discuss] SMARTS definition for basic nitrogen

*[EXTERNAL MESSAGE]*



Dear RDKitters,

does someone have a good SMARTS definition for basic nitrogen
(aliphatic and aromatic), which they would be able to share?

My Google-fu is failing me.

Many thanks in advance.

Kind regards,
Axel


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Re: [Rdkit-discuss] SMARTS definition for basic nitrogen

2022-10-06 Thread Axel Pahl


Thank you, Wim, I will check out these, as well.

KR Axel

On 06.10.22 12:46, Wim Dehaen wrote:

Hi,
For an even simpler definition that works "well enough" for many cases
I have been using
"[NX3,NX2,nX2;!$(NC=O);!$(NS=O)]"
this excludes amides, nitro,nitroso, sulfonamide and pyrrole
nitrogens, but include aliphatic amines, anilines, pyridines,
hydroxylamines, imines etc
best wishes
wim

On Thu, Oct 6, 2022 at 12:12 PM Axel Pahl  wrote:

Dear RDKitters,

does someone have a good SMARTS definition for basic nitrogen
(aliphatic and aromatic), which they would be able to share?

My Google-fu is failing me.

Many thanks in advance.

Kind regards,
Axel

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Re: [Rdkit-discuss] SMARTS definition for basic nitrogen

2022-10-06 Thread Axel Pahl


Great!

Thanks a lot, Jan!

Kind regards, Axel

On 06.10.22 12:23, Jan Halborg Jensen wrote:

Hi Axel

Have a look at https://github.com/jensengroup/protonator

Best regards, Jan


On 6 Oct 2022, at 12.09, Axel Pahl  wrote:

Dear RDKitters,

does someone have a good SMARTS definition for basic nitrogen
(aliphatic and aromatic), which they would be able to share?

My Google-fu is failing me.

Many thanks in advance.

Kind regards,
Axel

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[Rdkit-discuss] SMARTS definition for basic nitrogen

2022-10-06 Thread Axel Pahl


Dear RDKitters,

does someone have a good SMARTS definition for basic nitrogen (aliphatic
and aromatic), which they would be able to share?

My Google-fu is failing me.

Many thanks in advance.

Kind regards,
Axel
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Re: [Rdkit-discuss] CalcNumAtoms import error

2022-07-14 Thread Axel Pahl


Hi Chris,
this might not be a great help, but it works for me on Ubuntu 22.04 with
RDKit 2021.09.5:

import rdkit
print(rdkit.__version__)
from rdkit import Chem
from rdkit.Chem.rdMolDescriptors import CalcNumAtoms
m = Chem.MolFromSmiles("c1c1C(=O)NC")
print(CalcNumAtoms(m))

Output:
2021.09.5
19

According to Github, it was only added to the C++ MolDescriptors module
in June 2021:
https://github.com/rdkit/rdkit/commit/53523a4a1106e4e3b1a69ff26d0510225019e35c

KR Axel

On 14.07.22 12:46, Chris Swain via Rdkit-discuss wrote:

Hi,

If I try

from rdkit.Chem.rdMolDescriptors import CalcNumAtoms

I get

cannot import name 'CalcNumAtoms' from 'rdkit.Chem.rdMolDescriptors'

I can import a range of other descriptors fine

Using Python 3.7.6 and RDKit 2020.09.1

Cheers

Chris


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Re: [Rdkit-discuss] Web-front end for PostgreSQL database with RDKit cartridge

2022-07-05 Thread Axel Pahl


Hi Charmaine,

coming from Python, for single page applications I can really recommend
Panel: https://panel.holoviz.org/
There is also a very nice OSS chemistry plugin (which I have not yet
tried myself): https://github.com/MarcSkovMadsen/panel-chemistry

Kind regards,
Axel

On 05.07.22 11:53, Charmaine Siu Man Chu wrote:


Hello,

I’ve set up a PostgreSQL chemical database with RDKit cartridge on a
Linux desktop as server but for the database to be searchable by
chemists, I would need to set up a web-front end with a user-friendly
UI for the database which I have no experience in.

Can anyone advise on what is the best way in setting this web-front
end up?

Regards,

Charmaine Chu



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Re: [Rdkit-discuss] conda spell to install rdkit?

2020-11-24 Thread Axel Pahl


Hi Dimitri,

my (tried & tested) "spell" to install RDKit via conda is the following
(on Linux):

    conda create -c conda-forge -n chem python=3.8 rdkit cairo cffi
pillow matplotlib

After activation of the environment,  finalize with a

    pip install cairocffi

The cairo- and ffi-related installs are recommended when you use the old
drawing code.

Kind regards,
Axel

On 24.11.20 21:46, dmaziuk via Rdkit-discuss wrote:

Hi all,

what is the magic spiel to install rdkit in miniconda these days? --
My container that worked a year ago now won't build because "my python
=3.8" and rdkit wants "<3.8.0a0".

This is miniconda3-lates on linux x64

TIA
Dimitri


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Re: [Rdkit-discuss] RDKit C wrappers?

2020-04-27 Thread Axel Pahl




On 27.04.20 10:18, Stephan Michels wrote:



Am 27.04.2020 um 09:58 schrieb Axel Pahl mailto:axelp...@gmx.de>>:

yes, I agree that manual wrapping would be a ton of work (and hard to
maintain).
My question was not necessarily with a concrete language in mind, but
since you are asking (;-)), I am really excited about the Swift
programming language lately. Open Source, nice syntax, developed by
Apple and endorsed by Google as the next generation platform for
machine learning ("Swift for Tensorflow",
https://tryolabs.com/blog/2020/04/02/swift-googles-bet-on-differentiable-programming/).


Unfortunately Swift doesn’t support C++ yet. I use RDKit in my Swift
projects by using an Objective-C Framework, where I wrap all necessary
classes, which I need. These wrappers are far from complete. But I get
my things done and it is cross compiled for x86 and arm.

Regards,
Stephan Michels


Dear Stephan,

thanks a lot, that is really interesting.
I am using Swift on Linux, so I guess Objective-C wrappers are not
usable for me?

Kind regards,
Axel



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Re: [Rdkit-discuss] RDKit C wrappers?

2020-04-27 Thread Axel Pahl


Hi Greg,

yes, I agree that manual wrapping would be a ton of work (and hard to
maintain).
My question was not necessarily with a concrete language in mind, but
since you are asking (;-)), I am really excited about the Swift
programming language lately. Open Source, nice syntax, developed by
Apple and endorsed by Google as the next generation platform for machine
learning ("Swift for Tensorflow",
https://tryolabs.com/blog/2020/04/02/swift-googles-bet-on-differentiable-programming/).

Thanks a lot for the link to the MinimalLib, that looks very
interesting, I will definitely have a look.

Kind regards,
Axel

On 27.04.20 09:43, Greg Landrum wrote:

Hi Axel,

Doing complete C wrappers around the C++ library would be a ton of
work - you'd have to simulate the object model on the C side, and
that's "not easy".

Doing a "full" wrapper for another programming language is almost
certainly best handled using SWIG (assuming it has bindings for the
language you are interested in).

An alternate approach would be to look at the MinimalLib: the library
that's used to generate the Javascript wrappers: it's based on the
idea of exposing a small number of useful functions instead of
supporting the full API:
https://github.com/rdkit/rdkit/tree/master/Code/MinimalLib

-greg


On Sun, Apr 26, 2020 at 9:47 PM Riccardo Vianello
mailto:riccardo.viane...@gmail.com>> wrote:

Hi Axel,

On Sun, Apr 26, 2020 at 6:21 PM Axel Pahl mailto:axelp...@gmx.de>> wrote:

is anyone aware of efforts for creating "bridging" C wrappers
for the RDKit?
This would make it easier to bind the toolkit to other
programming languages, in addition to Python and Java.

I'm not aware of any active/existing projects, but I've been also
thinking about this possibility in a couple of occasions.

Could the existing SWIG interface be perused for this?

as far as I know, this isn't (or at least wasn't) directly
possible. SWIG includes the core functionality required to
generate these wrappers, but C is not a supported target language.
Last time I checked a mostly functional but not ready to merge
GSoC branch existed, that was aimed at providing this feature, but
I am not sure it made any progress.

Best,
Riccardo


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Re: [Rdkit-discuss] RDKit C wrappers?

2020-04-27 Thread Axel Pahl


Hi Riccardo,

thanks for the information.

Yes, I think it would be quite useful, but I guess it would have to be
mostly auto-generated, otherwise it would be too much work (and hard to
maintain).
The GSoC SWIG 2012 branch does indeed not seem to have made it into
master (https://github.com/swig/swig/tree/gsoc2012-c/).

Kind regards,
Axel


On 26.04.20 21:44, Riccardo Vianello wrote:

Hi Axel,

On Sun, Apr 26, 2020 at 6:21 PM Axel Pahl mailto:axelp...@gmx.de>> wrote:

is anyone aware of efforts for creating "bridging" C wrappers for
the RDKit?
This would make it easier to bind the toolkit to other programming
languages, in addition to Python and Java.

I'm not aware of any active/existing projects, but I've been also
thinking about this possibility in a couple of occasions.

Could the existing SWIG interface be perused for this?

as far as I know, this isn't (or at least wasn't) directly possible.
SWIG includes the core functionality required to generate these
wrappers, but C is not a supported target language. Last time I
checked a mostly functional but not ready to merge GSoC branch
existed, that was aimed at providing this feature, but I am not sure
it made any progress.

Best,
Riccardo


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[Rdkit-discuss] RDKit C wrappers?

2020-04-26 Thread Axel Pahl


Dear all,

is anyone aware of efforts for creating "bridging" C wrappers for the RDKit?
This would make it easier to bind the toolkit to other programming
languages, in addition to Python and Java.

Could the existing SWIG interface be perused for this?

Kind regards,
Axel
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Re: [Rdkit-discuss] Synthetic Accessibility (SA) score

2020-04-01 Thread Axel Pahl


Hi Ganesh,

I guess the synthesis of a fragment can be quite different from the
synthesis of a whole molecule containing that fragment, so I don't know
if it is a valid assumtion that the SA scores of the fragments have to
add up to the SA score of the whiole molecule.

Kind regards,
Axel

On 01.04.20 12:34, Ganesh Shahane wrote:

Hi Axel,

Thank you for your response.

Yes, I tried to implement the aforementioned script. It works very
well on whole molecules.

However, I am trying to implement the script on fragments.
For example, if I have fragments: A, B and C that makes up a whole
molecule "ABC", then the sum of SA scores of the fragments should be
equal to SA score of the whole molecule.

Right now, the summation doesn't add up.

I was wondering if there is a correction that needs to be made to the
sum of SA scores such that it is equal to the SA score of the whole
molecule.

--
Best,
Ganesh


On Mon, Mar 30, 2020 at 4:30 PM Axel Pahl mailto:axelp...@gmx.de>> wrote:

Hi Ganesh,

are you aware that the SA Score IS implemented in RDKit:

https://github.com/rdkit/rdkit/tree/master/Contrib/SA_Score

Kind regards,
Axel



On 30.03.20 16:55, Ganesh Shahane wrote:

Dear RDKitters,

I am trying a to find a way to implement the SA score as a sum of
fragments contributions from this paper:

Ertl, Peter, and Ansgar Schuffenhauer. 2009. “Estimation of
Synthetic Accessibility Score of Drug-like Molecules Based on
Molecular Complexity and Fragment Contributions.” /Journal of
Cheminformatics/ 1 (1): 8.

For example, if I have three different fragments: A, B and C and
their respective SA scores, then the SA score of molecule "A+B+C"
should be the sum of all three fragment SA scores.

In practice though, the fragment SA scores do not add up.

I was wondering if anyone across the cheminformatics community
has successfully implemented this or a similar strategy?

--
Best,
Ganesh


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Re: [Rdkit-discuss] Synthetic Accessibility (SA) score

2020-03-30 Thread Axel Pahl


Hi Ganesh,

are you aware that the SA Score IS implemented in RDKit:

https://github.com/rdkit/rdkit/tree/master/Contrib/SA_Score

Kind regards,
Axel



On 30.03.20 16:55, Ganesh Shahane wrote:

Dear RDKitters,

I am trying a to find a way to implement the SA score as a sum of
fragments contributions from this paper:

Ertl, Peter, and Ansgar Schuffenhauer. 2009. “Estimation of Synthetic
Accessibility Score of Drug-like Molecules Based on Molecular
Complexity and Fragment Contributions.” /Journal of Cheminformatics/ 1
(1): 8.

For example, if I have three different fragments: A, B and C and their
respective SA scores, then the SA score of molecule "A+B+C" should be
the sum of all three fragment SA scores.

In practice though, the fragment SA scores do not add up.

I was wondering if anyone across the cheminformatics community has
successfully implemented this or a similar strategy?

--
Best,
Ganesh


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Re: [Rdkit-discuss] Interactive plots in Jupyter notebooks

2020-01-15 Thread Axel Pahl


Hi Chris,

i too, looked for this functionality in Plotly, but I was not able to
find it.
This is the reason I switched to bokeh / holoviews.

https://github.com/apahl/mol_frame/blob/68801e16af3cfb60f846c40f471d190cbe34748b/mol_frame/mol_frame.py#L949
and
https://github.com/apahl/mol_frame/blob/68801e16af3cfb60f846c40f471d190cbe34748b/mol_frame/mol_frame.py#L1214

Kind regards,
Axel

On 15.01.20 10:30, Chris Swain via Rdkit-discuss wrote:

Hi,

I've been looking at ways to produce interactive plots within a
Jupyter notebook and after trying a couple of options I used Plotly.
This seems fairly straight-forward to use and I can produce
interactive data frames, in addition to 2D and 3D scatterplots.

https://www.macinchem.org/blog/files/a5cc1afff58a411056af7b8d9b0011dd-2577.php

Whilst I can get text to appear when hovering over a data point I'd be
interested in ideas of how to get the structure displayed when you
mouse over a point.

Cheers,

Chris




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Re: [Rdkit-discuss] 答复: Non Round-trippable Molecule

2019-09-03 Thread Axel Pahl


Dear Hongbin,

kekulizing the Smiles does indeed work in this case, that's a good tip.

Thanks a lot.

KR Axel

On 03.09.19 11:26, Hongbin Yang wrote:


Hi Axel,

The format like "c11” is implicitly defining the bonds between
atoms and  the output of the “canonical” SMILES has redundant ring
labels (1 and 2) , which I think confused the parser and caused the
problem.

I have no idea whether it is a bug or whether it is true reason.

But try this to solve your problem.

smi = Chem.MolToSmiles(mol, kekuleSmiles=True)

You will get the explicit bonds in the SMILES and it can be read by
`MolFromSmiles`

COC1:C:C:C2:C:C:1OC1:C:C:C(:C:C:1)/C=C\\C1:C:C(:C(OC):C:C:1CCN(C)C)OC1:C(:C(CCN(C)C):C(OC):C(OC):C:1OC)/C=C\\2

Best,

Hongbin

*发件人: *Axel Pahl <mailto:axelp...@gmx.de>
*发送时间: *2019年9月3日16:45
*收件人: *RDKit Discuss <mailto:rdkit-discuss@lists.sourceforge.net>
*主题: *[Rdkit-discuss] Non Round-trippable Molecule

Hi,

I know that the RDKit makes no guarantees abount being able to
round-trip (Smiles -> Mol -> Smiles -> Mol) every molecule, but I
would like to know if there are any recommendations on how to handle
such cases.

In my current case the problem seems to lie in different aromatic
models for a large ring containing oxygen.

This is the code to reproduce the issue and there is also a more
illustrative Notebook
(https://gist.github.com/apahl/06e55f5965cb82bc43d2aafd8ee0d532):



from rdkit.Chem import AllChem as Chem
from rdkit.Chem import Draw
from rdkit.Chem import Descriptors as Desc
from rdkit.Chem.Draw import IPythonConsole

# RDKit can parse the original Smiles into a valid molecule.
mol =
Chem.MolFromSmiles("c12c(\C=C/c(ccc3OC)cc3Oc4ccc(cc4)\C=C/c(cc5O1)c(CCN(C)C)cc5OC)c(CCN(C)C)c(OC)c(OC)c2OC")
print(Desc.MolWt(mol))

# And parse it back into a Smiles.
smi = Chem.MolToSmiles(mol)
print(smi)  # ->
COc1ccc2cc1-o-c1ccc(cc1)/c=c\c1cc(c(OC)cc1CCN(C)C)-o-c1c(c(CCN(C)C)c(OC)c(OC)c1OC)/c=c\2

# But the Smiles generated by RDKit can not be parsed back into a
valid molecule.
tmp = Chem.MolFromSmiles(smi)
# -> RDKit ERROR: [10:39:41] Can't kekulize mol. Unkekulized atoms: 2
3 4 5 6 7 9 10 11 12 13 14 15 16 17 18 19 20 23 24 31 32 33 39 42 45 48 49



BTW, the JS Molecule Editor by Peter is also not able to round-trip
this molecule.

Many thanks in advance,
Axel

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[Rdkit-discuss] Non Round-trippable Molecule

2019-09-03 Thread Axel Pahl


Hi,

I know that the RDKit makes no guarantees abount being able to
round-trip (Smiles -> Mol -> Smiles -> Mol) every molecule, but I would
like to know if there are any recommendations on how to handle such cases.

In my current case the problem seems to lie in different aromatic models
for a large ring containing oxygen.

This is the code to reproduce the issue and there is also a more
illustrative Notebook
(https://gist.github.com/apahl/06e55f5965cb82bc43d2aafd8ee0d532):



from rdkit.Chem import AllChem as Chem
from rdkit.Chem import Draw
from rdkit.Chem import Descriptors as Desc
from rdkit.Chem.Draw import IPythonConsole

# RDKit can parse the original Smiles into a valid molecule.
mol =
Chem.MolFromSmiles("c12c(\C=C/c(ccc3OC)cc3Oc4ccc(cc4)\C=C/c(cc5O1)c(CCN(C)C)cc5OC)c(CCN(C)C)c(OC)c(OC)c2OC")
print(Desc.MolWt(mol))

# And parse it back into a Smiles.
smi = Chem.MolToSmiles(mol)
print(smi)  # ->
COc1ccc2cc1-o-c1ccc(cc1)/c=c\c1cc(c(OC)cc1CCN(C)C)-o-c1c(c(CCN(C)C)c(OC)c(OC)c1OC)/c=c\2

# But the Smiles generated by RDKit can not be parsed back into a valid
molecule.
tmp = Chem.MolFromSmiles(smi)
# -> RDKit ERROR: [10:39:41] Can't kekulize mol.  Unkekulized atoms: 2 3
4 5 6 7 9 10 11 12 13 14 15 16 17 18 19 20 23 24 31 32 33 39 42 45 48 49



BTW, the JS Molecule Editor by Peter is also not able to round-trip this
molecule.

Many thanks in advance,
Axel

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Re: [Rdkit-discuss] Understanding Coloring in Similarity Maps

2019-08-22 Thread Axel Pahl


Hi Sereina,

thanks a ton for the elaborate and very helpful explanation.

Kind regards,
Axel

On 22.08.19 12:23, Sereina wrote:

Hi Axel,

What is calculated in the function GetAtomicWeightsForModel() is the
difference between the probability value of the complete molecule
(“base probability”) and the probability value when the bits of a
certain atom are deleted.

In the cookbook (and based on a quick glance also in your code), the
probability of the active class is used as the measure for the
similarity maps (that’s defined in the getProba() helper function).
This means that any atom whose missing bits lead to an increase in the
probability to be active is colored green. If it leads to a decrease,
it gets colored pink.

Now if you have an inactive molecule then your base probability for
the active class is close to zero. In your cases it looks like nearly
all of the atoms in the molecule are necessary to make these molecules
be considered inactive. In other words, deleting any of green colored
atoms results in a higher probability to be active – although it might
still be below 50% (note that the color range is not standardized
globally but based on the largest difference observed in the molecule).

I hope this helps.

Best,
Sereina



On 22 Aug 2019, at 11:38, Axel Pahl mailto:axelp...@gmx.de>> wrote:

Dear fellow RDKitters,

I am experimenting with the classification example from the Cookbook
[1] using a RandomForestClassifier and Similarity Maps for visualization.
I need, however, some help with the interpretation of the coloring in
the similarity map.
In the attached example, the compounds were correctly predicted
("AC_Pred") as being inactive ("0") with a high probability.
But the corresponding similarity maps show mainly green areas,
indicating (in my understanding) a positive contribution to the
activity class, which should have lead to a different prediction.

What would be the correct interpretation of the coloring?
Many thanks in advance for any help.

Kind regards,
Axel

P.S.: The code is available in a repo [2], an example notebook can be
found in the tutorials folder.

[1] http://www.rdkit.org/docs/Cookbook.html#using-scikit-learn-with-rdkit
[2] https://github.com/apahl/mol_frame

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Re: [Rdkit-discuss] Spacing of dashes in downward wedge

2019-03-26 Thread Axel Pahl


Thanks a lot for the comprehensive answer,  Paolo.
This also explains why changing the DrawingOptions.dash parameter does
not change anything.

Kind regards,
Axel

On 26.03.19 16:12, Paolo Tosco wrote:


Dear Axel,

looking at rdkit/Chem/Draw/cairoCanvas.py it appears that the
DrawingOptions.dash parameter is ignored and dash is hardcoded to (3, 3).

Please apply the following changes if you wish the DrawingOptions.dash
to be honoured:

---
./third-party/Python/lib/python3.6/site-packages/rdkit/Chem/Draw/MolDrawing.py.orig
2019-03-26 15:05:54.371731743 +
+++
./third-party/Python/lib/python3.6/site-packages/rdkit/Chem/Draw/MolDrawing.py
2019-03-26 15:06:16.683144329 +
@@ -203,7 +203,7 @@
 if not dash:
   self.canvas.addCanvasPolygon(poly, color=color)
 elif self.drawingOptions.wedgeDashedBonds and
self.canvas.addCanvasDashedWedge:
-  self.canvas.addCanvasDashedWedge(poly[0], poly[1], poly[2],
color=color)
+  self.canvas.addCanvasDashedWedge(poly[0], poly[1], poly[2],
color=color, dash=dash)
 else:
   self.canvas.addCanvasLine(pos, nbrPos, linewidth=width * 2,
color=color, dashes=dash)

---
./third-party/Python/lib/python3.6/site-packages/rdkit/Chem/Draw/cairoCanvas.py.orig
2019-03-26 15:06:25.459913254 +
+++
./third-party/Python/lib/python3.6/site-packages/rdkit/Chem/Draw/cairoCanvas.py
2019-03-26 15:06:30.853771245 +
@@ -402,7 +402,7 @@
   def addCanvasDashedWedge(self, p1, p2, p3, dash=(2, 2), color=(0,
0, 0), color2=None, **kwargs):
 self.ctx.set_line_width(kwargs.get('linewidth', 1))
 self.ctx.set_source_rgb(*color)
-    dash = (3, 3)
+    #dash = (3, 3)
 pts1 = self._getLinePoints(p1, p2, dash)
 pts2 = self._getLinePoints(p1, p3, dash)

However, you might be disappointed as spacing between dashes may
become uneven (which is probably why spacing was hardcoded):

Cheers,
p.

On 03/26/19 11:20, Axel Pahl wrote:

Hi,

is there an option to set the spacing of the dashes in a downward
wedge bond using Draw.MolToImage()?
In the depiction I am currently getting (attached), the dashes are
very close to each other, I would like to increase the spacing.

Changing the values in the tuple `Draw.DrawingOptions.dash` does not
change the depiction for me.

Many thanks in advance.

Kind regards,
Axel




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[Rdkit-discuss] Spacing of dashes in downward wedge

2019-03-26 Thread Axel Pahl


Hi,

is there an option to set the spacing of the dashes in a downward wedge
bond using Draw.MolToImage()?
In the depiction I am currently getting (attached), the dashes are very
close to each other, I would like to increase the spacing.

Changing the values in the tuple `Draw.DrawingOptions.dash` does not
change the depiction for me.

Many thanks in advance.

Kind regards,
Axel
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Re: [Rdkit-discuss] [Announcement] 8th RDKit UGM in Hamburg, Germany

2019-03-15 Thread Axel Pahl


Hi,

looking very much forward to the UGM, thanks a lot for organizing it.
Are there any recommended hotels?

Kind regards,
Axel

On 15.03.19 15:29, Greg Landrum wrote:

Dear all,

This year's RDKit User Group Meeting will take place from 25-27 
September in Hamburg, Germany and is being hosted by Emanuel Ehmki at 
the University of Hamburg.


Registration for the RDKit UGM is free:
https://www.eventbrite.com/e/8th-rdkit-ugm-2019-tickets-58836131453

We will once again mostly stick to what has become a tried and true 
format:
Days 1 and 2: Talks, lightning talks, roundtable(s), discussion, 
poster sessions, and talktorials. For those who haven’t attended 
before, talktorials are somewhere between a talk and a tutorial, they 
cover something interesting done with the RDKit and include the code 
used to do the work. During the presentation you'll give an overview 
of what you did and also show the pieces of the code that are central 
to the work. The idea is to mix the science up with the tutorial aspects.


Day 3 will be a hackathon: those who choose to stay will spend an 
intense day working in small groups to produce useful artifacts: new 
bits of code, KNIME nodes, KNIME workflows, tutorials, documentation, 
Jupyter notebooks, etc. We will once again try to structure this a bit 
by collecting a bunch of ideas for things to work on in advance. In 
the past we have also done extended tutorials on Day 3; if there are 
volunteers to do tutorials and people interested in attending them, 
we'll repeat that this year as well.


Like last year there will be an optional training day on Tuesday (the 
24th). Daria Goldmann (KNIME) will offer a course on KNIME and the 
RDKit. We hope to also be able to offer an RDKit and Python course, 
but we're still finalizing the details on that. Space for both of 
these is limited, so we'll do separate registrations for them. We will 
send around registration links once we've got the logistics figured out.


There will also be, of course, social activities. We will be 
announcing more details about these later.


A more detailed announcement with additional information about place, 
hotels and logistics will follow soon.


We are looking for people who are willing to do presentations, 
talktorials or posters on the first two days. If you're interested in 
contributing, please send Greg and Emanuel an email.
Lighting talks don't need to be arranged too far in advance; we will 
start collecting the list of people interested in doing those shortly 
before the event.


Best Regards,
Greg and Emanuel


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Re: [Rdkit-discuss] no structure depiction in Jupyter notebook

2018-08-31 Thread Axel Pahl


Hi Andrew,

on Linux, using Anaconda, RDKit and Python 3.6, I always need to 
additionally install cairocffi via pip:


pip install cairocffi

Kind regards,
Axel

On 31.08.2018 15:05, Andrew Dalke wrote:

On Aug 31, 2018, at 11:58, Andrew Dalke  wrote:

I am unable to see an inline structure depiction in the Jupyter notebook, nor 
in the JupyterLab notebook, tested with both the Python 2 and Python 3 kernels, 
and rdkit.__version__ '2018.03.1'.

I've narrowed it down to the Cairo code.

I ran Draw._moltoimg manually, and the d2d.GetDrawingText() call returns b"".

If I do

   del Draw.rdMolDraw2D.MolDraw2DCairo

then the image generation code will fall back to MolToImage, and give me an 
inline depiction in the notebook.



Andrew
da...@dalkescientific.com



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[Rdkit-discuss] MPI Dortmund is looking for a Cheminformatics PostDoc

2018-08-07 Thread Axel Pahl


Dear fellow RDKitters,

the Max Planck institute of Molecular Physiology (department 4, Chemical 
Biology, Prof. Waldmann) is looking for a Cheminformatics PostDoc to 
work on two interesting projects in the highly relevant context of 
chemical biology.
For details, please have a look at the job posting 
(https://www.mpg.de/12151792/postdoctoral-position-in-cheminformatics).


Kind regards,

Axel
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Re: [Rdkit-discuss] Make chain atoms not match ring atoms

2018-06-30 Thread Axel Pahl


Hi Greg,

yes, I had a look at those flags and also at your blog post describing 
them, but indeed I thought that I could not achieve what I intended with them.

It would be awesome if that option could be added.

Kind regards,
Axel

Am 30. Juni 2018 11:06:20 schrieb Greg Landrum :

AdjustQueryParameters might also be worth looking into:
http://www.rdkit.org/Python_Docs/rdkit.Chem.rdmolops.AdjustQueryParameters-class.html

This may not do exactly what you want, but it’s pretty close. And adding 
“ring matches ring only” would be pretty easy to add


-greg

On Sat, 30 Jun 2018 at 10:44, Axel Pahl  wrote:
Paolo,

thanks a lot for this solution, I am going to use that.
Also, TIL that ^ is Python's XOR operator. Thanks for that, too ;-) !

Kind regards,
Axel


On 29.06.2018 10:49, Paolo Tosco wrote:

Dear Axel,
what about this:
https://gist.github.com/ptosco/26af473fc1f3129878ca86cb070afe3a
Cheers,
p.


On 06/29/18 08:04, Axel Pahl wrote:

Dear all,

my google-fu is failing is me.
Is it possible in substructure searches to have chain atoms NOT match ring 
atoms?


In essence, I would like the following example query for n-propane in 
cyclo-hexane to return False (currently it is returning True):


mol = Chem.MolFromSmiles("C1C1")
q = Chem.MolFromSmiles("CCC")
print(mol.HasSubstructMatch(q))  # ==> True

Many thanks in advance for your help.

Kind regards,
Axel



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Re: [Rdkit-discuss] Make chain atoms not match ring atoms

2018-06-30 Thread Axel Pahl


Paolo,

thanks a lot for this solution, I am going to use that.
Also, TIL that ^ is Python's XOR operator. Thanks for that, too ;-) !

Kind regards,
Axel

On 29.06.2018 10:49, Paolo Tosco wrote:


Dear Axel,

what about this:

https://gist.github.com/ptosco/26af473fc1f3129878ca86cb070afe3a

Cheers,
p.

On 06/29/18 08:04, Axel Pahl wrote:

Dear all,

my google-fu is failing is me.
Is it possible in substructure searches to have chain atoms NOT match 
ring atoms?


In essence, I would like the following example query for n-propane in 
cyclo-hexane to return False (currently it is returning True):


mol = Chem.MolFromSmiles("C1C1")
q = Chem.MolFromSmiles("CCC")
print(mol.HasSubstructMatch(q))  # ==> True

Many thanks in advance for your help.

Kind regards,
Axel


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Re: [Rdkit-discuss] Make chain atoms not match ring atoms

2018-06-29 Thread Axel Pahl


Hi, Steve,

thanks.
Is there no other possibiliy? Like setting a search option that non-ring 
should not match ring atoms?
The reason I am asking is that my query molecules come from an SD file, 
so converting them into Smarts would be difficult.


Kind regards,
Axel


On 29.06.2018 10:06, Stephen Roughley wrote:

Axel,

You need to use a SMARTS query:

q = Chem.MolFromSmarts("[CR0][CR0][CR0]")

Have a look at 
http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html


Steve

On 29 June 2018 at 08:04, Axel Pahl <mailto:axelp...@gmx.de>> wrote:


Dear all,

my google-fu is failing is me.
Is it possible in substructure searches to have chain atoms NOT
match ring atoms?

In essence, I would like the following example query for n-propane
in cyclo-hexane to return False (currently it is returning True):

mol = Chem.MolFromSmiles("C1C1")
q = Chem.MolFromSmiles("CCC")
print(mol.HasSubstructMatch(q))  # ==> True

Many thanks in advance for your help.

Kind regards,
Axel


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[Rdkit-discuss] Make chain atoms not match ring atoms

2018-06-29 Thread Axel Pahl


Dear all,

my google-fu is failing is me.
Is it possible in substructure searches to have chain atoms NOT match 
ring atoms?


In essence, I would like the following example query for n-propane in 
cyclo-hexane to return False (currently it is returning True):


mol = Chem.MolFromSmiles("C1C1")
q = Chem.MolFromSmiles("CCC")
print(mol.HasSubstructMatch(q))  # ==> True

Many thanks in advance for your help.

Kind regards,
Axel
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Re: [Rdkit-discuss] Errors with RDKit

2018-01-22 Thread Axel Pahl


Hi Carlos,


insert this in your loop:


if not mol: continue



Kind regards,

Axel


On 23.01.2018 03:59, Carlos Faerman wrote:


Hello,

My code is very simple:

suppl4 = Chem.SDMolSupplier("/Volumes/MyPassportForMac/chembl_23.sdf")

i = 0

for mol in suppl4:

smile = Chem.MolToSmiles(mol,isomericSmiles=True)

fingerpri = get_fp_rdkit(mol)

namenmol = mol.GetProp("_Name")

patron[namenmol]=fingerpri

print (i,namenmol,smile)

outfile.write('{} {} {}\n'.format(namenmol,smile,fingerpri))

i = i+1

I know that a few molecules in Chembl_23.sdf have wrong valences.

Is there a way to skip these molecules when these errors are found?


671231 CHEMBL1254908 
O=C(NCCN1CCC2(CC1)C(=O)NCN2c1(Cl)c1)c1cc2cc(F)ccc2[nH]1


[21:18:16] Explicit valence for atom # 35 N, 5, is greater than permitted

[21:18:16] ERROR: Could not sanitize molecule ending on line 48940986

[21:18:16] ERROR: Explicit valence for atom # 35 N, 5, is greater than 
permitted


Traceback (most recent call last):

File "calculate-fingerprints.py", line 23, in 

smile = Chem.MolToSmiles(mol,isomericSmiles=True)

Boost.Python.ArgumentError: Python argument types in

rdkit.Chem.rdmolfiles.MolToSmiles(NoneType)

did not match C++ signature:

MolToSmiles(RDKit::ROMol mol, bool isomericSmiles=False, bool 
kekuleSmiles=False, int rootedAtAtom=-1, bool canonical=True, bool 
allBondsExplicit=False, bool allHsExplicit=False)


 The "culprit" molecule seems to be

CHEMBL450200

-My question to this forum:

Please suggest a way to modify the code to skip the wrong molecule(s) 
instead of abruptly ending the run


Thank you,

Carlos Faerman



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Re: [Rdkit-discuss] RDKit and Google Summer of Code 2018

2018-01-15 Thread Axel Pahl


Dear RDKitters,

here is a project idea for GSoC 2018 (actually brought up by Greg during 
the Hackathon of RDKitUGM2016):


Project: RDKit lite

Brief explanation:
Create a minimal version of the RDKit that only contains basic 
functionality (like MolFrom/ToSmiles and substructure search 
capabilities, (...)) in order to make it easier to create bindings to 
the RDKit from other languages or to port the RDKit to other languages.


Expected results:
A minimal version of the RDKit that could be bound to from other 
languages like Go, Rust or Nim, would immensely enhance its reach by 
introducing cheminformatics capabilities to languages where this 
functionality is currently still missing or lacking.


Prerequisites: C, C++

Mentor: t.b.d.

Kind regards,
Axel

On 15.01.2018 08:09, Greg Landrum wrote:

Dear all,

We've been invited again to participate in the OpenChemistry 
application for Google Summer of Code.


In order to participate we need ideas for projects and mentors to go 
along with them.


The current list of RDKit ideas is being maintained here:
http://wiki.openchemistry.org/GSoC_Ideas_2018#RDKit_Project_Ideas

(Note: at the point that I'm pressing "send", that's still a copy of 
last year's project ideas).


If you're willing to be a mentor (please ask me about the ~5 
hours/week required here) or have ideas, please reply to this thread.


Best,
-greg


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Re: [Rdkit-discuss] rdkit

2017-07-05 Thread Axel Pahl

Hi Paul,

when using pillow and Python 2 I recommend to also install pycairo 
(avail. via conda install).

For Python 3 you would need cairo from conda and cairocffi from pip.
(http://rdkit.org/docs/Install.html#recommended-extras)

Kind regards,
Axel

On 05.07.2017 08:09, Paul Czodrowski wrote:

Dear Greg (and RDKitters),

good news is: I just re-ran “conda install -c rdkit rdkit”, and at 
least rdkit is working properly.

“import pillow” still does not work.

This is the output of “conda list”:

backports-abc 0.5   

backports.shutil-get-terminal-size 1.0.0 

bleach 2.0.0 

boost 1.56.0   py27_3rdkit

bzip2 1.0.6 vc9_3  [vc9]

certifi 2017.4.17 

colorama 0.3.9 

configparser 3.5.0 

decorator 4.0.11

entrypoints 0.2.3 

enum34 1.1.6 

freetype 2.5.5 vc9_2  [vc9]

functools32 3.2.3.post2   

html5lib 0.9   

idisplay  0.1.2 

ipykernel 4.6.1 

ipython 5.4.1 

ipython-genutils 0.2.0 

ipywidgets6.0.0

Jinja2 2.9.6 

jpeg 9bvc9_0  [vc9]

jsonschema 2.6.0 

jupyter 1.0.0 

jupyter-client 5.0.1 

jupyter-console 5.1.0 

jupyter-core 4.3.0 

libpng 1.6.27vc9_0  [vc9]

libtiff  4.0.6 vc9_3  [vc9]

MarkupSafe 1.0   

mistune 0.7.4 

mkl 2017.0.1  0

nbconvert 5.2.1   

nbformat 4.3.0 

notebook 5.0.0 

numpy 1.11.3   py27_0

olefile 0.44 py27_0

pandas0.20.1 np111py27_0

pandocfilters 1.4.1 

pathlib2 2.2.1 

pickleshare 0.7.4 

pillow 4.2.0py27_0

pip 9.0.1py27_1

prompt-toolkit 1.0.14

py3Dmol 0.6.3 

Pygments   2.2.0 

python 2.7.131

python-dateutil 2.6.0 

python-dateutil 2.6.0py27_0

pytz  2017.2py27_0

pyzmq 16.0.2

qtconsole 4.3.0 

scandir 1.5   

setuptools 27.2.0   py27_1

setuptools 36.0.1

simplegeneric 0.8.1 

singledispatch 3.4.0.3   

six 1.10.0   py27_0

six   1.10.0   

testpath 0.3.1 

tornado 4.5.1 

traitlets 4.3.2 

vs2008_runtime 9.00.30729.5054   0

wcwidth 0.1.7 

webencodings 0.5.1 

wheel 0.29.0   py27_0

widgetsnbextension 2.0.0 

win-unicode-console 0.5   

zlib 1.2.8 vc9_3  [vc9]

Best regards,

Paul

*Von:*Greg Landrum [mailto:greg.land...@gmail.com]
*Gesendet:* Mittwoch, 5. Juli 2017 06:33
*An:* Paul Czodrowski 
*Cc:* rdkit 
*Betreff:* Re: [Rdkit-discuss] rdkit

The fact that "import pillow" doesn't work is very suspicious.

Can you please be sure that pillow and the rdkit are both installed in 
the active environment by executing:

"conda list"

On Wed, Jul 5, 2017 at 5:50 AM, Paul Czodrowski 
> wrote:

Dear Greg (and RDKitters),

before it came to this error message, the conda installation of
rdkit was running properly.

I then did a “conda install pillow” in this conda installation,
which now results in this error.

BTW, “import pillow” shows:

ImportErrorTraceback (most recent call last)

in ()

> 1importpillow

ImportError: No module named pillow

“import rdkit” gives:

---

ImportErrorTraceback (most recent call last)

in ()

> 1importrdkit

c:\users\m163729\appdata\local\continuum\anaconda2\envs\rdkit_env\lib\site-packages\rdkit\__init__.pyin
()

  1try:

> 2from.rdBase importrdkitVersion as__version__

3exceptImportError:

  4   __version__ ='Unknown'

  5raise

ImportError: DLL load failed: Das angegebene Modul wurde nicht
gefunden.

BZW, “import PIL” works without any problems.

It does not make sense to me that a simple “conda install pillow”
screws up the

Re: [Rdkit-discuss] ipywidgets & py3Dmol

2017-06-20 Thread Axel Pahl


Hi Paul,

I just tried the example Notebook that you provided and it runs just as 
in Greg's blog post, i.e. with the interactive slider (see attached 
screenshot).

This is the configuration I used (in Anaconda):

python 3.5.3
rdkit 2017.03.2
notebook  5.0.0
ipywidgets6.0.0
py3Dmol   0.6.3

Kind regards,
Axel


On 20.06.2017 07:48, Paul Czodrowski wrote:


Dear RDKitters,

When trying to re-run Greg’s wonderful blog entry about the py3Dmol 
integration 
(https://rdkit.blogspot.de/2016/07/using-ipywidgets-and-py3dmol-to-browse.html 
), I’m getting a different behavior (check the attachment with a 
screenshot and the jupyter notebook).


Any help would be appreciated.

Cheers,
Paul

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Re: [Rdkit-discuss] generating scaffold trees

2017-03-31 Thread Axel Pahl

Hi Markus,

to my knowledge, there is no implementation in RDKit available yet.

Kind regards,
Axel

On 31.03.2017 16:55, Markus Metz wrote:

Dear Axel and all:

I have come across an older discussion about Ansgar Schuffenhauer's
work on scaffolds:

Axel Pahl
<http://www.mail-archive.com/search?l=rdkit-discuss@lists.sourceforge.net=from:%22Axel+Pahl%22>
Fri, 22 May 2015 04:39:33 -0700
<http://www.mail-archive.com/search?l=rdkit-discuss@lists.sourceforge.net=date:20150522>

Dear RDKitters,

has someone used the RDKit to generate scaffold trees from molecules as
described in this paper:
Schuffenhauer, A., Ertl, P., Roggo, S., Wetzel, S., Koch, M. A.,
Waldmann, H., J. Chem. Inf. Model. 2007, 47, 47-58
I know that this is possible with ScaffoldHunter and that there is a
Pipeline Pilot component for it, but being able to do it in RDKit would
fit especially well in my workflow...

Kind regards and have a nice weekend,
Axel
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Has there been any update regarding this matter?
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Re: [Rdkit-discuss] scaffold distance algorithm

2017-03-28 Thread Axel Pahl

Well, I guess this means no.
That leaves more fun for me... :-P

-Axel

On 23.03.2017 09:38, Axel Pahl wrote:
> Dear fellow RDKitters,
>
> has someone by any chance tried to implement in RDKit the scaffold
> distance algorithm by Jürgen Bajorath et al. (and would be willing to
> share some code)?
>
> Li, R.; Stumpfe, D.; Vogt, M.; Geppert, H.; Bajorath, J.
> Development of a Method to Consistently Quantify the Structural Distance
> Between Scaffolds and to Assess Scaffold Hopping Potential
> J. Chem. Inf. Model. 2011, 51, 2507
> DOI: 10.1021/ci2003945
>
> Best regards,
> Axel
>
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[Rdkit-discuss] scaffold distance algorithm

2017-03-23 Thread Axel Pahl

Dear fellow RDKitters,

has someone by any chance tried to implement in RDKit the scaffold 
distance algorithm by Jürgen Bajorath et al. (and would be willing to 
share some code)?

Li, R.; Stumpfe, D.; Vogt, M.; Geppert, H.; Bajorath, J.
Development of a Method to Consistently Quantify the Structural Distance 
Between Scaffolds and to Assess Scaffold Hopping Potential
J. Chem. Inf. Model. 2011, 51, 2507
DOI: 10.1021/ci2003945

Best regards,
Axel

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Re: [Rdkit-discuss] Find out if a molecuole object was generated from smiles or smarts

2016-11-07 Thread Axel Pahl


Thanks, Greg.

This is exactly what I was looking for.

KR Axel

On 07.11.2016 15:18, Greg Landrum wrote:
Brian is exactly right: atoms (or bonds) constructed from SMARTS will 
have queries, and so HasQuery() will return True. This is not true of 
atoms (or bonds) that are constructed from SMILES.


-greg


On Mon, Nov 7, 2016 at 2:23 PM, Brian Kelley <fustiga...@gmail.com 
<mailto:fustiga...@gmail.com>> wrote:


I would try checking:

atom.HasQuery()

I expect the smarts molecules have this property by default and
smiles don't.  Greg can confirm, and I can double check later today.


Brian Kelley

> On Nov 7, 2016, at 7:57 AM, Paul Emsley
<pems...@mrc-lmb.cam.ac.uk <mailto:pems...@mrc-lmb.cam.ac.uk>> wrote:
>
    >> On 07/11/2016 12:37, Axel Pahl wrote:
>>
>> amongst other options, I can generate an RDKit mol object by one of
>> these two ways:
>>
>> mol1 = Chem.MolFromSmiles()
>> mol2 = Chem.MolFromSmarts()
>>
>> Is there a possibility to detect for a given mol object whether
it was
>> generated from Smiles or Smarts?
>
> Not obviously to me.
>
> Perhaps you can do something like this at creation time:
>
> mol2.SetProp('origin', 'SMARTS')
>
> then use mol.GetProp('origin') when you need to do the test
(inside a try/except KeyError).
>
> Paul.
>
>
>

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[Rdkit-discuss] Find out if a molecuole object was generated from smiles or smarts

2016-11-07 Thread Axel Pahl

Dear all,

amongst other options, I can generate an RDKit mol object by one of 
these two ways:

mol1 = Chem.MolFromSmiles()
mol2 = Chem.MolFromSmarts()

Is there a possibility to detect for a given mol object whether it was 
generated from Smiles or Smarts?

Many thanks in advance.

Kind regards,
Axel

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Re: [Rdkit-discuss] OCEAN: Our Target Prediction Paper (including Source Code)

2016-09-27 Thread Axel Pahl


Hi Paul,

very interesting, thanks a lot for sharing!
Looking forward to the presentation at the UGM!

Kind regards,
Axel

On 27.09.2016 06:13, Paul Czodrowski wrote:


Dear RDKitters,

Our target prediction method – fully based on RDKit – has become online:

OCEAN: *O*ptimized *C*ross r*EA*ctivity estimatio*N*

http://pubs.acs.org/doi/abs/10.1021/acs.jcim.6b00067

The source code can be found here:

https://github.com/rdkit/OCEAN

We will give a talk as well an hands-on workshop at the upcoming RDKit 
UGM end of October.


Cheers,

Guido & Paul

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Re: [Rdkit-discuss] bond length in 2D structure drawing

2016-09-19 Thread Axel Pahl


Hi Greg,

thanks a lot.
That is exactly what I was looking for!

RDKit rules!

Kind regards,
Axel


On 19.09.2016 09:35, Greg Landrum wrote:

Hi Axel,

It's probably most straightforward to use the function 
AllChem.TransformMol() to scale the coordinates.
Here's an example of applying the function to scale all the 
coordinates by a factor of 2:


In [1]: from rdkit import Chem

In [2]: from rdkit.Chem import rdMolTransforms

In [5]: from rdkit.Chem import AllChem

In [6]: import numpy

In [7]: tm = numpy.zeros((4,4),numpy.double)

In [8]: for i in range(3): tm[i,i] = 2.

In [9]: tm[3,3] = 1.

In [10]: m = Chem.MolFromSmiles('C1CCC1')

In [11]: AllChem.Compute2DCoords(m)
Out[11]: 0

In [12]: print(Chem.MolToMolBlock(m))

 RDKit  2D

  4  4  0  0  0  0  0  0  0  0999 V2000
1.0607   -0.0. C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.   -1.06070. C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.06070.0. C   0  0  0  0  0  0  0  0  0  0  0  0
0.1.06070. C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  1  1  0
M  END


In [13]: AllChem.TransformMol(m,tm)

In [14]: print(Chem.MolToMolBlock(m))

 RDKit  2D

  4  4  0  0  0  0  0  0  0  0999 V2000
2.1213   -0.0. C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.   -2.12130. C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.12130.0. C   0  0  0  0  0  0  0  0  0  0  0  0
0.2.12130. C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  1  1  0
M  END


In your case, assuming that the bond length in the drawings is 1.0A, 
you would use a scale factor of 1.5 (that's on line [8] above).


Best,
-greg


On Mon, Sep 19, 2016 at 8:41 AM, Axel Pahl <axelp...@gmx.de 
<mailto:axelp...@gmx.de>> wrote:


Dear fellow RDKitters,

I have an SD file with 2D molecules generated by another
Cheminformatics
toolkit (yes, there are others! ;-) ).
When I depict them with RDKit (with Draw.MolToImage()) they look very
condensed with too short bonds and just appear not right.
When I re-generate the coordinates by using Compute2DCoord(), the
structure drawings do look great, but RDkit re-calculates all
coordinates and the orientation of the whole molecule is
completely changed.
Can I avoid this, keep the original orientation of the molecules and
just do something like "apply drawing settings" or "use standard bond
lengths" to a molecule?

Many thanks in advance.

Kind regards,
Axel



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[Rdkit-discuss] bond length in 2D structure drawing

2016-09-19 Thread Axel Pahl

Dear fellow RDKitters,

I have an SD file with 2D molecules generated by another Cheminformatics 
toolkit (yes, there are others! ;-) ).
When I depict them with RDKit (with Draw.MolToImage()) they look very 
condensed with too short bonds and just appear not right.
When I re-generate the coordinates by using Compute2DCoord(), the 
structure drawings do look great, but RDkit re-calculates all 
coordinates and the orientation of the whole molecule is completely changed.
Can I avoid this, keep the original orientation of the molecules and 
just do something like "apply drawing settings" or "use standard bond 
lengths" to a molecule?

Many thanks in advance.

Kind regards,
Axel


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Re: [Rdkit-discuss] Some feedback from the Sheffield Cheminformatics Conference

2016-07-07 Thread Axel Pahl


Hi Greg,

that is great news, honest congratulations and thanks for sharing.
And just wait for the big event coming up end of october! Then 100% of 
the talks will cover the RDKit!


Kind regards,
Axel

On 07.07.2016 09:20, Greg Landrum wrote:

Dear all,

I was at the Sheffield Cheminformatics conference earlier this week 
(along with several people from this list) and I was really struck by 
the number of talks and posters that are using the RDKit. By my rough 
count the RDKit was used for about 1/3 of the talks and a similar 
fraction of the posters.


This of course, makes me smile rather broadly (Christian, Nadine, and 
Sereina had to suffer through this while we were waiting at the 
airport ;-) ) but a big part of the reason for this success is the 
engagement and activity of the RDKit community. So I figured I'd share 
so that those of you who weren't in Sheffield also get the chance to 
grin about it.


We're having an impact... that's really cool. Thanks! and congrats! :-)

-greg



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Re: [Rdkit-discuss] conda build of Release_2016_03_2 failed on Ubuntu 16.04.

2016-06-28 Thread Axel Pahl


Hi Riccardo,

thanks, I found the problem. As suspected it was related to conda and 
had nothing to do with RDKit 
(https://github.com/conda/conda/issues/2212#issuecomment-228277548).


Many thanks for your help.

Kind regards,
Axel

On 27.06.2016 22:44, Riccardo Vianello wrote:

Hi Axel,

thanks a lot for your help, using the development branch and the
Release_2016_03_2 git tag in rdkit/meta.yaml worked.
I now get a strange error in anaconda when actually trying to
install the package (Error: Invalid version spec: ==), but that
seems to be unrelated to RDKit (there is already an issue on
anaconda github).
My understanding was that the preferred way to install the RDKit
was via anaconda (RDKit was the reason I started using anaconda),
is that still correct?


I'm not exactly sure about the commands you used, but I'm afraid I 
wasn't able to reproduce the described problem using conda 4.1.4 and 
conda-build 1.21.2 on my fedora box. In case the error persisted, 
could you please provide some additional context?


Best regards,
Riccardo



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Re: [Rdkit-discuss] Generation of stereo-isomers

2015-09-25 Thread Axel Pahl


Hi Soren,

maybe this function which enumerates racemates with one stereocenter 
into the corresponding enantiomers might help:


def enum_racemates(sdf_list_or_file, find_only=True, mol_id="molid"):
"""returns: result_sdf::list, racemic_molids::list
find_only==True:  return new sdf as list which contains all the 
racemates of the input sdf.
find_only==False: return new sdf as list with ALL input structures, 
where the racemates are
  replaced by their two enantiomers. The returned 
sdf is always

  equal in size or larger as the input sdf.
Multiple stereo centers are not yet handled.
In the new sdf the molids are no longer unique and should be reassigned
(remove molid and run calc_props(sdf))."""

result_sdf = Mol_List()
racemic_molids = []

if not isinstance(sdf_list_or_file, list) and 
sdf_list_or_file.atEnd(): # sdf is file

print("  * file object is at end, please reload.")
return None

for mol in sdf_list_or_file:
first_undefined = False
chiral_centers  = Chem.FindMolChiralCenters(mol, 
includeUnassigned=True)


if chiral_centers:
first_center= chiral_centers[0][0]
first_undefined = chiral_centers[0][1] == "?"

if first_undefined:
racemic_molids.append(int(mol.GetProp(mol_id)))
if find_only:
result_sdf.append(mol)
continue

else:
mol1 = Chem.Mol(mol)
mol2 = Chem.Mol(mol)
mol1.GetAtomWithIdx(first_center).SetChiralTag(Chem.rdchem.ChiralType.CHI_TETRAHEDRAL_CW)
mol2.GetAtomWithIdx(first_center).SetChiralTag(Chem.rdchem.ChiralType.CHI_TETRAHEDRAL_CCW)
result_sdf.append(mol1)
result_sdf.append(mol2)

else:
if not find_only: # return ALL mols
result_sdf.append(mol)

return result_sdf, racemic_molids

Please also have a look at this post 
http://sourceforge.net/p/rdkit/mailman/message/32390126/ and Toby's 
answer which pointed me in the right direction.


Kind regards,
Axel

On 24.09.2015 23:17, Soren Wacker wrote:

Hi,

is it possible with RDKit to generate all stereoisomers of a given 
compound?


If not, is anyone working on it?

If not, how difficult would it be / what would be the best way to 
implement such a function.


best regards

Soren


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Re: [Rdkit-discuss] generating scaffold trees

2015-09-02 Thread Axel Pahl

Hi Nick,

are there any news on this?
It would still be very interesting.

Kind regards,
Axel
(and a great UGM to all attendees!)

On 22.05.2015 17:31, Nicholas Firth wrote:
> We have an as yet unpublished method which is similar (but performs better) 
> implemented in RDKit. However we use MOE for the scaffold tree. It would be 
> quite easy to implement in RDKit , but I have a thesis to write!
>
> My suggestion would be to ask Nathan to write up the paper and then give you 
> guys the code.
>
> Best,
> Nick
>
> Nicholas C. Firth | PhD Student | Cancer Therapeutics
> The Institute of Cancer Research | 15 Cotswold Road | Belmont | Sutton | 
> Surrey | SM2 5NG
> T 020 8722 4033 | E nicholas.fi...@icr.ac.uk | W www.icr.ac.uk | Twitter 
> @ICRnews
>
> 
> From: George Papadatos [gpapada...@gmail.com]
> Sent: 22 May 2015 16:27
> To: Axel Pahl
> Cc: RDKit Discuss
> Subject: Re: [Rdkit-discuss] generating scaffold trees
>
> Hi all,
>
> Coincidentally, we had a chat about this with James the other day.
> Maybe the good colleagues at the ICR have implemented this already with 
> RDKit? Nick?
>
> Cheers,
>
> g
>
>
> On 22 May 2015 at 13:38, Axel Pahl <axelp...@gmx.de<mailto:axelp...@gmx.de>> 
> wrote:
> Dear RDKitters,
>
> has someone used the RDKit to generate scaffold trees from molecules as
> described in this paper:
> Schuffenhauer, A., Ertl, P., Roggo, S., Wetzel, S., Koch, M. A.,
> Waldmann, H., J. Chem. Inf. Model. 2007, 47, 47-58
>
> I know that this is possible with ScaffoldHunter and that there is a
> Pipeline Pilot component for it, but being able to do it in RDKit would
> fit especially well in my workflow...
>
> Kind regards and have a nice weekend,
> Axel
>
>
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Re: [Rdkit-discuss] create a mol from core and mol fragments

2015-07-03 Thread Axel Pahl

Nicholas,

thanks a lot for the code, I will definitely look into it.

Kind regards,
Axel

On 03.07.2015 09:19, Nicholas Firth wrote:
 Hi Axel,

 I was sure there was something in the core that did this but I can't seem to 
 find it now! I have a function that uses isotope labelled dummy atoms to 
 attach fragments if it's of any use? As with most the code I write, it 
 doesn't have the greatest error handling, or rational use of deepcopy.

 def connectAllFragsIsomeric(molList):
  numFrags = len(molList)
  isotopeList = []
  allIsos = []
  # This loop is to make a list of molecules along with which isotopes 
 they contain
  # so I can keep track of where which R-Groups are later
  for i in range(numFrags):
  molList[i] = processToIsomericMol(molList[i])
  for atom in molList[i].GetAtoms():
  isotope = atom.GetIsotope()
  if(isotope):
  isotopeList.append(isotope)
  allIsos.append(isotope)
  molList[i] = [molList[i], deepcopy(isotopeList)]
  del isotopeList[:]

  allIsos.sort()
  allIsos = list(set(allIsos))

  for i in allIsos:
  reactantIdx = []
  # Find two fragments with the labeled R-group
  for j in range(len(molList)):
  if(i in molList[j][1]):
  reactantIdx.append(j)
  # Sanity check that there are only two frags with the same R-group
  if(len(reactantIdx) != 2):
  print 'Too many fragments with a R-groups numbered with %i' % i
  exit()
  rxn = 
 AllChem.ReactionFromSmarts('[a,A:1]-[%i*:2].[a,A:3]-[%i*:4][a,A:1]-[a,A:3].[%i*:2][%i*:4]'
  % (i, i, i, i))
  ps = rxn.RunReactants((molList[reactantIdx[0]][0], 
 molList[reactantIdx[1]][0]))
  newMol = ps[0][0]
  newIsos = list(set(molList[reactantIdx[0]][1]) | 
 set(molList[reactantIdx[1]][1]))
  newIsos.remove(i)
  molList.append([newMol, newIsos])
  del molList[reactantIdx[1]]
  del molList[reactantIdx[0]]
  return molList



 Best,
 Nick

 Nicholas C. Firth | PhD Student | Cancer Therapeutics
 The Institute of Cancer Research | 15 Cotswold Road | Belmont | Sutton | 
 Surrey | SM2 5NG
 T 020 8722 4033 | E nicholas.fi...@icr.ac.uk | W www.icr.ac.uk | Twitter 
 @ICRnews

 
 From: Axel Pahl [axelp...@gmx.de]
 Sent: 03 July 2015 07:27
 To: RDKit Discuss
 Subject: [Rdkit-discuss] create a mol from core and mol fragments

 Dear fellow RDKitters,

 I use ReplaceCore and GetMolFrags to create a 2D SAR table:


 tmp = Chem.ReplaceCore(mol, core_mol, labelByIndex=True)

 frag_mols = list(Chem.GetMolFrags(tmp, asMols=True))


 Is it also possible to do the reverse? Create a new molecule from the core 
 and two fragments?
 I would like to fill the gaps in the SAR table and calculate some properties 
 for these molecules.

 Kind regards,
 Axel

 The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company 
 Limited by Guarantee, Registered in England under Company No. 534147 with its 
 Registered Office at 123 Old Brompton Road, London SW7 3RP.

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 the message is received by anyone other than the addressee, please return the 
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[Rdkit-discuss] create a mol from core and mol fragments

2015-07-03 Thread Axel Pahl


Dear fellow RDKitters,

I use ReplaceCore and GetMolFrags to create a 2D SAR table:

tmp = Chem.ReplaceCore(mol, core_mol, labelByIndex=True)

frag_mols = list(Chem.GetMolFrags(tmp, asMols=True))

Is it also possible to do the reverse? Create a new molecule from the 
core and two fragments?
I would like to fill the gaps in the SAR table and calculate some 
properties for these molecules.


Kind regards,
Axel
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[Rdkit-discuss] RDKit Tools for the IPython Notebook

2015-07-02 Thread Axel Pahl


Dear fellow RDKitters,

the RDKit community is always so helpful that I wanted share back two 
functions that I use in the IPython Notebook from which I thought that 
they could be of use to others, as well.


- show_table:
Display a list of molecules in a table with molecule properties as columns.
When an ID property is given, the table becomes interactive and 
compounds can be selected.
I know that this can be also done with PandasTools but that might be 
overkill in some situations. Also the table from Pandas is not 
interactive to my knowledge.


- jsme:
Display Peter Ertl's Javascript Melecule Editor to enter a molecule 
directly in the IPython notebook (how cool is that??)


If you are interested, please have a look at the GitHub 
https://github.com/apahl/rdkit_ipynb_tools repo and the example 
http://nbviewer.ipython.org/github/apahl/rdkit_ipynb_tools/blob/master/rdkit_ipynb_tools.ipynb 
notebook.


Kind regards,
Axel
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Re: [Rdkit-discuss] generating scaffold trees

2015-05-23 Thread Axel Pahl

That would be awesome.
Kind regards,
Axel

On 22.05.2015 17:31, Nicholas Firth wrote:
 We have an as yet unpublished method which is similar (but performs better) 
 implemented in RDKit. However we use MOE for the scaffold tree. It would be 
 quite easy to implement in RDKit , but I have a thesis to write!

 My suggestion would be to ask Nathan to write up the paper and then give you 
 guys the code.

 Best,
 Nick

 Nicholas C. Firth | PhD Student | Cancer Therapeutics
 The Institute of Cancer Research | 15 Cotswold Road | Belmont | Sutton | 
 Surrey | SM2 5NG
 T 020 8722 4033 | E nicholas.fi...@icr.ac.uk | W www.icr.ac.uk | Twitter 
 @ICRnews

 
 From: George Papadatos [gpapada...@gmail.com]
 Sent: 22 May 2015 16:27
 To: Axel Pahl
 Cc: RDKit Discuss
 Subject: Re: [Rdkit-discuss] generating scaffold trees

 Hi all,

 Coincidentally, we had a chat about this with James the other day.
 Maybe the good colleagues at the ICR have implemented this already with 
 RDKit? Nick?

 Cheers,

 g


 On 22 May 2015 at 13:38, Axel Pahl axelp...@gmx.demailto:axelp...@gmx.de 
 wrote:
 Dear RDKitters,

 has someone used the RDKit to generate scaffold trees from molecules as
 described in this paper:
 Schuffenhauer, A., Ertl, P., Roggo, S., Wetzel, S., Koch, M. A.,
 Waldmann, H., J. Chem. Inf. Model. 2007, 47, 47-58

 I know that this is possible with ScaffoldHunter and that there is a
 Pipeline Pilot component for it, but being able to do it in RDKit would
 fit especially well in my workflow...

 Kind regards and have a nice weekend,
 Axel


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 Registered Office at 123 Old Brompton Road, London SW7 3RP.

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[Rdkit-discuss] generating scaffold trees

2015-05-22 Thread Axel Pahl

Dear RDKitters,

has someone used the RDKit to generate scaffold trees from molecules as 
described in this paper:
Schuffenhauer, A., Ertl, P., Roggo, S., Wetzel, S., Koch, M. A., 
Waldmann, H., J. Chem. Inf. Model. 2007, 47, 47-58

I know that this is possible with ScaffoldHunter and that there is a 
Pipeline Pilot component for it, but being able to do it in RDKit would 
fit especially well in my workflow...

Kind regards and have a nice weekend,
Axel


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Re: [Rdkit-discuss] install rdkit cartridge

2015-04-24 Thread Axel Pahl

Dear Tim,

please take a look at this README in your installation:
your RDKit folder/Code/PgSQL/rdkit/README

It essentially boils down to this:
cd $RDBASE/Code/PgSQL/rdkit
$ make
$ sudo make install
$ make installcheck

(only the second step has to be performed as root)

Kind regards,
Axel

On 04/24/2015 01:33 PM, Tim Dudgeon wrote:
 How to install RDKit cartridge?
 The instructions here show how to use it, but not how to install it.
 http://www.rdkit.org/docs/Cartridge.html

 I have RDKit and PostgreSQL installed from the corresponding Debian
 packages, but alas no cartridge :-(

 Tim

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Re: [Rdkit-discuss] install rdkit cartridge

2015-04-24 Thread Axel Pahl

The instructions below appliy to the RDKit installation from source and 
are probably not applicable to the Debian package, sorry for generating 
confusion.

Kind regards,
Axel

On 04/24/2015 02:24 PM, Axel Pahl wrote:
 Dear Tim,

 please take a look at this README in your installation:
 your RDKit folder/Code/PgSQL/rdkit/README

 It essentially boils down to this:
 cd $RDBASE/Code/PgSQL/rdkit
 $ make
 $ sudo make install
 $ make installcheck

 (only the second step has to be performed as root)

 Kind regards,
 Axel

 On 04/24/2015 01:33 PM, Tim Dudgeon wrote:
 How to install RDKit cartridge?
 The instructions here show how to use it, but not how to install it.
 http://www.rdkit.org/docs/Cartridge.html

 I have RDKit and PostgreSQL installed from the corresponding Debian
 packages, but alas no cartridge :-(

 Tim

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Re: [Rdkit-discuss] getting stereo info from bonds

2014-08-22 Thread Axel Pahl


Dear Micha,



have you considered using the commandline tool molconvert that is part of MarvinSketch, which can do just that (and many other things):



molconvert mol mol.mrv -o mol.mol



It should be under bin/ in the Marvin installation



for batch processing you can e.g. use a small shell script:

for f in *.mrv; do
 echo  converting f...

 BN=(basename f .mrv)
 molconvert mol f -o BN.mol
done



Hope, this helps.



Kind regards,

Axel






 A question I have is why you want to access the bond wedging.

This is very good question so I will begin with answering this. Im
writing a module, which converts *mrv files to molfiles, both ways. In
my case, the original mrv file looks like this:

cmlMDocumentMChemicalStructmolecule molID=m1atomArrayatom
id=a1 elementType=C x2=-3.1249866416667733
y2=-0.5015733293207466/atom id=a2 elementType=C
x2=-4.458533297665067 y2=-1.2715733231607467/atom id=a3
elementType=C x2=-4.458533297665067 y2=-2.81175997750592/atom
id=a4 elementType=C x2=-3.1249866416667733
y2=-3.58175997134592/atom id=a5 elementType=C
x2=-1.7912533190033066 y2=-2.81175997750592/atom id=a6
elementType=C x2=-1.7912533190033066
y2=-1.2715733231607467/atom id=a7 elementType=C
x2=-0.45751999633984003 y2=-0.5013866626555733/atom id=a8
elementType=O x2=-0.45751999633984003
y2=1.0384266583592534/atom id=a9 elementType=C
x2=0.87583999299328 y2=-1.2713866564955734/atom id=a10
elementType=C x2=0.87583999299328
y2=-2.8113866441755735//atomArraybondArraybond atomRefs2=a1
a2 order=2/bond atomRefs2=a2 a3 order=1/bond atomRefs2=a3
a4 order=2/bond atomRefs2=a4 a5 order=1/bond atomRefs2=a5
a6 order=2/bond atomRefs2=a6 a1 order=1/bond atomRefs2=a6
a7 order=1/bond atomRefs2=a7 a9 order=1/bond atomRefs2=a9
a10 order=1/bond atomRefs2=a7 a8
order=1bondStereoW/bondStereo/bond/bondArray/molecule/MChemicalStruct/MDocument/cml

Its easy to spot, that the last bond have additional tag -
bondStereo with value W. Looking at this specification
http://download.accelrys.com/freeware/ctfile-formats/ctfile-formats.zip,
page 50 I can see that this can be translated into 1 in 4th field in
bond block and the field is called bond stereo, the same as mrvs
bond tag - this is the actual reason why Ive used term stereo in my
email. So the resulting molfile looks like this:




10 10 0 0 0 0 0 0 0 0999 V2000
-1.6741 -0.2687 0. C 0 0 0 0 0 0 0 0 0 0 0 0
-2.3885 -0.6812 0. C 0 0 0 0 0 0 0 0 0 0 0 0
-2.3885 -1.5063 0. C 0 0 0 0 0 0 0 0 0 0 0 0
-1.6741 -1.9188 0. C 0 0 0 0 0 0 0 0 0 0 0 0
-0.9596 -1.5063 0. C 0 0 0 0 0 0 0 0 0 0 0 0
-0.9596 -0.6812 0. C 0 0 0 0 0 0 0 0 0 0 0 0
-0.2451 -0.2686 0. C 0 0 0 0 0 0 0 0 0 0 0 0
-0.2451 0.5563 0. O 0 0 0 0 0 0 0 0 0 0 0 0
0.4692 -0.6811 0. C 0 0 0 0 0 0 0 0 0 0 0 0
0.4692 -1.5061 0. C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0 0 0 0
2 3 1 0 0 0 0
3 4 2 0 0 0 0
4 5 1 0 0 0 0
5 6 2 0 0 0 0
6 1 1 0 0 0 0
6 7 1 0 0 0 0
7 9 1 0 0 0 0
9 10 1 0 0 0 0
7 8 1 1 0 0 0
M END

Now imagine I only have this molfile and I want to convert it back to
*mrv. I dont want to write my own parser for molfiles when I know
that RDKit can already parse it. But I need to extract this bond
stereo information from within RDKit somehow.

Now when you say that this 1 or W value corresponds to bond
direction, Im guessing that direction can store only two values: up
and down so 1 and 6 (W and H in marvin terms). So what about
other values which this field can have, If for example I have this
molfile:



10 10 0 0 0 0 0 0 0 0999 V2000
-1.6741 -0.2687 0. C 0 0 0 0 0 0 0 0 0 0 0 0
-2.3885 -0.6812 0. C 0 0 0 0 0 0 0 0 0 0 0 0
-2.3885 -1.5063 0. C 0 0 0 0 0 0 0 0 0 0 0 0
-1.6741 -1.9188 0. C 0 0 0 0 0 0 0 0 0 0 0 0
-0.9596 -1.5063 0. C 0 0 0 0 0 0 0 0 0 0 0 0
-0.9596 -0.6812 0. C 0 0 0 0 0 0 0 0 0 0 0 0
-0.2451 -0.2686 0. C 0 0 0 0 0 0 0 0 0 0 0 0
-0.2451 0.5563 0. O 0 0 0 0 0 0 0 0 0 0 0 0
0.4692 -0.6811 0. C 0 0 0 0 0 0 0 0 0 0 0 0
0.4692 -1.5061 0. C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0 0 0 0
2 3 1 0 0 0 0
3 4 2 0 0 0 0
4 5 1 0 0 0 0
5 6 2 0 0 0 0
6 1 1 0 0 0 0
6 7 1 0 0 0 0
7 9 1 0 0 0 0
9 10 1 0 0 0 0
7 8 1 4 0 0 0
M END

So 4 instead of 1, how I will get this information from RDKit?

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