Re: [Rdkit-discuss] Building RDKit on Windows. Only static libraries produced? How to make the Python wrapper work?

[Joos Kiener]

Hi Ernst-Georg,

maybe you are running into the same issue as I was:

https://github.com/rdkit/rdkit/discussions/6148#discussioncomment-5450102

You have to explicitly tell python where the dlls are:

os.add_dll_directory(r"C:\path\to\rdkit\lib")

before importing rdkit.

>From python documentation:

DLL dependencies for extension modules and DLLs loaded with ctypes
 on Windows
are now resolved more securely. Only the system paths, the directory
containing the DLL or PYD file, and directories added with
add_dll_directory()
 are
searched for load-time dependencies. *Specifically, PATH and the current
working directory are no longer used, and modifications to these will no
longer have any effect on normal DLL resolution*.

Best Regards,

Joos


>
> -- Forwarded message --
> From: pgchem pgchem 
> To: "rdkit-discuss@lists.sourceforge.net" <
> rdkit-discuss@lists.sourceforge.net>
> Cc:
> Bcc:
> Date: Wed, 10 May 2023 16:32:31 +0200 (CEST)
> Subject: [Rdkit-discuss] Building RDKit on Windows. Only static libraries
> produced? How to make the Python wrapper work?
> Hello all,
>
> I'm currently trying to build RDKit 2023_03_1 on Windows 11 with Visual
> Studio 2022 Community. The building itself works:
>
> - No errors during the build
> - I get a working extension against PostgreSQL 15.2
> - I get working static libraries for Visual Studio (RDGeneral.lib etc.)
> - I get a rdkit package for Python 3.10
>
> BUT this does not work:
>
> from rdkit import Chem
>
> Traceback (most recent call last):
> File "", line 1, in 
> File "C:\RDKit\lib\site-packages\rdkit\__init__.py", line 6, in 
> from . import rdBase
> ImportError: DLL load failed while importing rdBase: The specified module
> could not be found.
>
> I am pretty sure, that the environment is ok, I have checked with the
> dependency walker that rdBase.pyd sees everything it needs.
>
> However, when I take a look at the rdkit package from PyPI, there are a
> lot of *.dlls. while my build only produces static libraries (*.lib).
>
> When I compare the sizes of rdBase.pyd from PyPI and mine, mine is much
> larger, so I assume that it also is statically linked - so it should work?,
> but it doesn't.
>
> Any pointers to what I am doing wrong here?
>
> This is my cmake command:
>
> c:/cmake/bin/cmake -DRDK_BUILD_PYTHON_WRAPPERS=ON
> -DBOOST_ROOT=C:/Devel/RDBuild/boost -DRDK_BUILD_CAIRO_SUPPORT=ON
> -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_AVALON_SUPPORT=ON
> -DRDK_BUILD_PGSQL=ON -DPostgreSQL_ROOT="C:\PostgreSQL\15"
> -DRDK_INSTALL_INTREE=OFF -DCMAKE_INSTALL_PREFIX=c:/RDKit
> -DEIGEN3_INCLUDE_DIR=C:/Devel/RDBuild/eigen3
> -DFREETYPE_INCLUDE_DIRS=c:/Devel/RDbuild/freetype/include
> -DFREETYPE_LIBRARY="c:/Devel/RDBuild/freetype/release
> dll/win64/freetype.lib" -DZLIB_INCLUDE_DIR=c:/Devel/RDBuild/zlib/include
> -DZLIB_LIBRARY=c:/Devel/RDBuild/zlib/libz.lib
> -DCAIRO_INCLUDE_DIRS=c:/Devel/RDBuild/cairo/include
> -DCAIRO_LIBRARIES=c:/Devel/RDBuild/cairo/lib/x64/cairo.lib
> -DRDK_BUILD_FREETYPE_SUPPORT=ON -DRDK_BUILD_COMPRESSED_SUPPLIERS=ON
> -G"Visual Studio 17 2022" -A x64 ..
>
> and the MSBuild command:
>
> & "C:\Program Files\Microsoft Visual
> Studio\2022\Community\MSBuild\Current\Bin\MSBuild.exe"
> /p:Configuration=Release INSTALL.vcxproj
>
> best regards
>
> Ernst-Georg
>
>
>
> -- Forwarded message --
> From: Ernst-Georg Schmid 
> To: "rdkit-discuss@lists.sourceforge.net" <
> rdkit-discuss@lists.sourceforge.net>
> Cc:
> Bcc:
> Date: Thu, 11 May 2023 14:35:23 +0200
> Subject: Re: [Rdkit-discuss] Building RDKit on Windows. Only static
> libraries produced? How to make the Python wrapper work?
> Am 10.05.2023 um 16:32 schrieb pgchem pgchem:
> > I'm currently trying to build RDKit 2023_03_1 on Windows 11 with Visual
> > Studio 2022 Community. The building itself works:
> > - No errors during the build
> > - I get a working extension against PostgreSQL 15.2
> > - I get working static libraries for Visual Studio (RDGeneral.lib etc.)
> > - I get a rdkit package for Python 3.10
> > BUT this does not work:
> > from rdkit import Chem
> > Traceback (most recent call last):
> > File "", line 1, in 
> > File "C:\RDKit\lib\site-packages\rdkit\__init__.py", line 6, in 
> > from . import rdBase
> > ImportError: DLL load failed while importing rdBase: The specified
> > module could not be found.
>
> Hello again,
>
> I have managed to build the shared objects also by now. I had to carve
> this out of the azure pipelines, apparently it only works correctly if
> you build like there, i.e. using cmake instead of MSBuild directly.
>
> E.g.
>
> C:\CMake\bin\cmake --build . --config=Release --target install
>
> instead of
>
> & "C:\Program Files\Microsoft Visual
> Studio\2022\Community\MSBuild\Current\Bin\MSBuild.exe"
> /p:Configuration=Release INSTALL.vcxproj (as the RDKit Book says)
>
> But the rdkit Python package still throws 

Re: [Rdkit-discuss] molecule sizing in MolsToGridImage

[Joos Kiener]

Hi Peter,

the change is most likely due to the update to the Drawing code in 2020.09.

I think the issue is that somewhere in the 100 mols you are drawing there
is a very large molecule compared to the others. It seems the new drawing
code then adjusts all molecules to the size of the smallest molecule hence
making all of them look tiny. This works fine when working with similar
sized molecules (series?) but of course becomes an issue when some are
larger than others. Personally I think the better approach is to shrink too
big images rather than making them all same-sized

You can try to just draw the first couple molecules to check if this is
true (looks like that on my side).

One can see the same behavior when using a drawer directly (drawing first
16 mols / first 2 rows)

drawer = rdMolDraw2D.MolDraw2DCairo(1600, 400, 200, 200)
opts = drawer.drawOptions()
opts.prepareMolsBeforeDrawing = True
drawer.DrawMolecules(mols[:16])
drawer.FinishDrawing()
IPython.display.Image(drawer.GetDrawingText())

That generates pretty much the same output as MolsToGridImage.
Here with the drawer the issue for me is that certain size options seem to
be ignored just so that everything is same-sized, most notably
fixedBondLength.

Hope that helps.

Best Regards,

Joos

-- Forwarded message --
> From: "Peter St. John" 
> To: RDKit Discuss 
> Cc:
> Bcc:
> Date: Thu, 25 Feb 2021 13:42:49 -0700
> Subject: [Rdkit-discuss] molecule sizing in MolsToGridImage
> Hi RDKit users,
>
> With rdkit 2020.03.3, MolsToGridImage had more reasonable molecule sizes:
> [image: Screen Shot 2021-02-25 at 1.39.46 PM.png]
>
> With rdkit 2020.09.4, the default drawing parameters seem to shrink the
> molecules by default in MolsToGridImage:
> [image: Screen Shot 2021-02-25 at 1.37.38 PM.png]
>
> Is there a make the individual molecules larger in MolsToGridImage?
> subImgSize just seems to increase the padding between molecules.
>
> Thanks!
> -- Peter
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Re: [Rdkit-discuss] RDKit ElasticSearch Plugin

[Joos Kiener]

Hi Naomi,

I once played around a bit with this idea using the Lucene-based RDKit
example as guidance. However what that code does inside Lucene and hence my
"adaption" inside elastic search is only the fingerprint screening part.
For the actual subgraph-match the data then has to be sent to the
caller/client and doesn't run inside elastic search and means one must
manipulate the elastic search results (hit count, paging,...) before
finally returning to the end user application. Simply said, not a very
usable but very hacky solution.

Even ignoring that part, it wasn't very fast either. That could be due to
many things like only having 1 machine for ES (my machine, no cluster) and
not being an expert in ES anyway (suboptimal config?). Or maybe the dataset
was too small to actually benefit. Same data, same query is much faster in
PostgreSQL + RDKit + Full-text index and easier to use. (Yes, PostgreSQL
supports full-text search similar to elastic. if one doesn't need very
advanced features or has a lot of data, for sure worth a look)

Any "real solution" must also do the subgraph matching inside elastic
itself which means writing a plugin / extension for elasticsearch. This was
simply too involved for me to even try. (If that is of interest, you should
probably also look at the very recent licensing changes to elasticsearch).

The presentation Joshua mentioned is actually only about similarity search
which naturally is easier to implement and fast.

Having said that, there is a commercial solution available from PerkinElmer
in their Signals Data factory offering. Of course this has nothing to do
with RDKit but it does hint that it's possible to do this if you have the
time, budget and skills/knowledge.

Another  commercial "fast substructure search" option would be nextmoves
Arthor but that has nothing to do with elasticsearch. Question is if you
want elasticsearch due to the speed or due to the combination with text
search. I would probably avoid it if the text search part is not important.

Just using RDKit default functionality is actually pretty fast (see on
Gregs blog), well it does run in memory. Nowadays a machine with lots of
RAM doesn't cost all that much so I could see that scaling to 10-20 million
structures easily.

hope that helps you a bit to come to a conclusion on what to do.

Best Regards,

Joos


-- Forwarded message --
> From: Naomi Jacobs 
> To: rdkit-discuss@lists.sourceforge.net
> Cc: Alan Pierce , Larry Taylor 
> Bcc:
> Date: Wed, 20 Jan 2021 22:27:32 -0800
> Subject: [Rdkit-discuss] RDKit ElasticSearch Plugin
> Hi all,
>
> We're looking for information about whether anyone has built an
> ElasticSearch plugin using RDKit to support chemical search. I didn't see
> anything open-source online, but was thinking some folks may have heard
> about internal efforts and would be willing to share any code and/or chat
> about it. Thanks!
>
> Cheers,
> Naomi
>
> --
> *Naomi Jacobs*
> Software Engineer | benchling.com
> (415) 590-2798
>
>
>
> -- Forwarded message --
> From: Greg Landrum 
> To: Naomi Jacobs 
> Cc: RDKit Discuss , Larry Taylor <
> la...@benchling.com>
> Bcc:
> Date: Thu, 21 Jan 2021 08:54:08 +0100
> Subject: Re: [Rdkit-discuss] RDKit ElasticSearch Plugin
> Hi Naomi,
>
> I'm not personally aware of any ElasticSearch work, but there is a
> prototype for a lucene plugin which could, I believe, be used as the basis
> for an ElasticSearch plugin:
> https://github.com/rdkit/org.rdkit.lucene
>
> It's (obviously) been a while since anyone did anything with that code and
> it may no longer work, but the more recent (and still functional)
> RDKit-neo4j integration (https://github.com/rdkit/neo4j-rdkit) can
> provide some patterns for how the RDKit java integration can be used in
> this type of context.
>
> I hope this helps, and would be interested to hear if you end up doing
> anything with the RDKit and ElasticSearch.
> -greg
>
>
>
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Re: [Rdkit-discuss] MolsToGridImage with varying number of mols per row

[Joos Kiener]

Hi Greg,

thanks that works great.

After trying it out I have another suggestion. With above current
implementation the empty cells in the grid will be transparent (alpha=0)
and hence depending on how the image is used or saved (png vs jpeg) will
not look very nice. Therefore I suggest to either set the default alpha
channel to 255 (white) and/or make it an argument for the user to set.

Best Regards,

Joos

2016-02-16 10:45 GMT+01:00 Greg Landrum <greg.land...@gmail.com>:

> Hi Joos,
>
>
> On Tue, Feb 16, 2016 at 7:34 AM, Joos Kiener <joos.kie...@gmail.com>
> wrote:
>
>>
>> I'm trying to draw a grid using Draw.MolsToGridImage. However I have
>> different number of molecules per row. If I use "None" for columns where no
>> molecules should be an exception is thrown (c++ signature does not match,
>> mol vs NoneType).
>>
>> Is there any easy why to to this? Or do I need to roll my own function?
>>
>
> Nice idea, and pretty easy to do. It's a small change to
> $RDBASE/rdkit/Chem/Draw/__init__.py to ignore None :
>
> glandrum@Otter:/scratch/RDKit_git/rdkit/Chem/Draw$ git diff -w
> diff --git a/rdkit/Chem/Draw/__init__.py b/rdkit/Chem/Draw/__init__.py
> index 08df30a..f7742f3 100644
> --- a/rdkit/Chem/Draw/__init__.py
> +++ b/rdkit/Chem/Draw/__init__.py
> @@ -315,8 +315,10 @@ def
> MolsToGridImage(mols,molsPerRow=3,subImgSize=(200,200),legends=None,
>  highlights=None
>  if highlightAtomLists and highlightAtomLists[i]:
>highlights=highlightAtomLists[i]
> -
>  
> res.paste(MolToImage(mol,subImgSize,legend=legends[i],highlightAtoms=highlights,
> - **kwargs),(col*subImgSize[0],row*subImgSize[1]))
> +if mol is not None:
> +  img =
> MolToImage(mol,subImgSize,legend=legends[i],highlightAtoms=highlights,
> +   **kwargs)
> +  res.paste(img,(col*subImgSize[0],row*subImgSize[1]))
>return res
>
>  def ReactionToImage(rxn, subImgSize=(200,200),**kwargs):
>
> We'll get this checked in on github in the next day or so.
>
> -greg
>
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[Rdkit-discuss] MolsToGridImage with varying number of mols per row

[Joos Kiener]

Hi all,

I'm trying to draw a grid using Draw.MolsToGridImage. However I have
different number of molecules per row. If I use "None" for columns where no
molecules should be an exception is thrown (c++ signature does not match,
mol vs NoneType).

Is there any easy why to to this? Or do I need to roll my own function?

Best Regards,

Joos
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Re: [Rdkit-discuss] Fingerprints and explicit Hydrogens

[Joos Kiener]

Hi Greg,

thanks for your prompt reply.

What added to my confusion was the comparing of AtomPair fingerprints in 2D
and 3D eg:

http://nbviewer.jupyter.org/github/greglandrum/rdkit_blog/blob/master/notebooks/Atom%20Pair%20Fingerprints.ipynb

So if I understand you correctly here you need the Hs in 2D because you
have them present in 3D?
And if you use AtomPair FP in 2D only, you do not need hydrogens?

Best Regards,

Joos

2016-01-20 14:19 GMT+01:00 Greg Landrum <greg.land...@gmail.com>:

> Hi Joos,
>
> As long as you are sure to be consistent, it is certainly ok to generate
> fingerprints for molecules with Hs still attached, but it's very easy to
> make a mistake.
>
> The default behavior of the RDKit is to remove Hs. This is what I would
> recommend before doing things like generating fingerprints or descriptors.
>
>
> -greg
>
>
> On Wed, Jan 20, 2016 at 7:06 AM, Joos Kiener <joos.kie...@gmail.com>
> wrote:
>
>> Hi all,
>>
>> I've been looking at different Fingerprints within the RDKit when I
>> realized, that it matters  for many of them whether Hydrogens are
>> explicitly present or not. This probably was obvious and clear for many of
>> you but I wasn't aware of that.
>>
>> To visualize what I mean please see below notebook:
>>
>>
>> http://nbviewer.jupyter.org/github/kienerj/notebooks/blob/master/Fingerprint%20Similarity%20-%20with%20and%20without%20hydrogens.ipynb
>>
>> Now my questions are:
>>
>> Should I always add hydrogens before generating fingerprints or should I
>> remove them?
>>
>> How is this handled in KNIME nodes? Do I need to perform the according
>> action (add/remove H) before generating the fingerprint? Or is this done
>> correctly already internally of the node?
>>
>> Thank you for your help.
>>
>> Best Regards,
>>
>> Joos
>>
>>
>> --
>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
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>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>>
>
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[Rdkit-discuss] Molecule losing properties

[Joos Kiener]

Hi all,

I have a strange issue. I'm trying to display pairs of molecules (the pair
has a certain similarity threshold) and show a property for both molecules.
This is in IPyhton Notebook.

The weird thing is the first molecule of the pair loses all properties:

toShow=[]

lbls=[]

for idx in pairs:

did=dindices[idx]

mol1=und[did[0]] # und = list of molecules loaded from sd-file

mol2=und[did[1]]

toShow.append(mol1)

toShow.append(mol2)

lbls.append('Active: %.2f'%mol1.GetProp('Activ'))

lbls.append('Active: %.2f'%mol2.GetProp('Activ'))

Draw.MolsToGridImage(toShow,molsPerRow=2,legends=lbls)

---KeyError
 Traceback (most recent call
last) in ()  7
toShow.append(mol1)  8 toShow.append(mol2)> 9
lbls.append('Active: %.2f'%mol1.GetProp('Activ')) 10
lbls.append('Active: %.2f'%mol2.GetProp('Activ')) 11
Draw.MolsToGridImage(toShow,molsPerRow=2,legends=lbls)
KeyError: 'Activ'

If I change the code (remove the label) and print all properties of
mol1, the are displayed correctly.

toShow=[]
lbls=[]
for idx in pairs:
did=dindices[idx]
mol1=und[did[0]]
mol2=und[did[1]]
toShow.append(mol1)
toShow.append(mol2)
for prop in mol1.GetPropNames():
print prop + ": "  + mol1.GetProp(prop)
#lbls.append('Active: %.2f'%mol1.GetProp('Activ'))
#lbls.append('Active: %.2f'%mol2.GetProp('Activ'))
Draw.MolsToGridImage(toShow,molsPerRow=2)

This shows all the properties of mol1 plus draws the grid. No error.

However directly accessing the property by name fails with key error:

toShow=[]

lbls=[]

for idx in pairs:

did=dindices[idx]

mol1=und[did[0]]

mol2=und[did[1]]

toShow.append(mol1)

toShow.append(mol2)

print mol1.GetProp('Activ')

#lbls.append('Active: %.2f'%mol1.GetProp('Activ'))

#lbls.append('Active: %.2f'%mol2.GetProp('Activ'))

Draw.MolsToGridImage(toShow,molsPerRow=2)

---KeyError
 Traceback (most recent call
last) in ()  7
toShow.append(mol1)  8 toShow.append(mol2)> 9 print
mol1.GetProp('Activ') 10 #lbls.append('Active:
%.2f'%mol1.GetProp('Activ')) 11 #lbls.append('Active:
%.2f'%mol2.GetProp('Activ'))
KeyError: 'Activ'


This all works fine for mol2:

toShow=[]

lbls=[]

for idx in pairs:

did=dindices[idx]

mol1=und[did[0]]

mol2=und[did[1]]

toShow.append(mol1)

toShow.append(mol2)

print mol2.GetProp('Activ')

#lbls.append('Active: %.2f'%mol1.GetProp('Activ'))

#lbls.append('Active: %.2f'%mol2.GetProp('Activ'))

Draw.MolsToGridImage(toShow,molsPerRow=2)

2.5
7.7
10.93
2.0434
190.0
25.0
...

What is going on here??? How can I resolve this?

Best Regards,

Joos
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[Rdkit-discuss] Fingerprints and explicit Hydrogens

[Joos Kiener]

Hi all,

I've been looking at different Fingerprints within the RDKit when I
realized, that it matters  for many of them whether Hydrogens are
explicitly present or not. This probably was obvious and clear for many of
you but I wasn't aware of that.

To visualize what I mean please see below notebook:

http://nbviewer.jupyter.org/github/kienerj/notebooks/blob/master/Fingerprint%20Similarity%20-%20with%20and%20without%20hydrogens.ipynb

Now my questions are:

Should I always add hydrogens before generating fingerprints or should I
remove them?

How is this handled in KNIME nodes? Do I need to perform the according
action (add/remove H) before generating the fingerprint? Or is this done
correctly already internally of the node?

Thank you for your help.

Best Regards,

Joos
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[Rdkit-discuss] rdkit 2015.09.2 in Anaconda still version 2015.03.1

[Joos Kiener]

Hi all,

I wanted to try put the new conformer generation code using anaconda
install and ipython notebook.

Therefore I update the installation with following command:

*conda update -c https://conda.anaconda.org/rdkit
<https://conda.anaconda.org/rdkit> rdkit*

This updated several other dependencies. I I now run the command again it
says:






*C:\Anaconda>conda update -c https://conda.anaconda.org/rdkit
<https://conda.anaconda.org/rdkit> rdkitFetching package metadata: ..#
All requested packages already installed.# packages in environment at
C:\Anaconda:#rdkit 2015.09.2   np110py27_0
rdkit*

However when I try to run the new code according to

http://sourceforge.net/p/rdkit/mailman/message/34650697/

eg:

AllChem.EmbedMultipleConfs(mol, useExpTorsionAnglePrefs=True,
useBasicKnowledge=True)



I get an ArgumentError:

ArgumentError: Python argument types in
rdkit.Chem.rdDistGeom.EmbedMultipleConfs(Mol)
did not match C++ signature:

And the C++ signature does not contain these 2 new flags.

Also running

from rdkit import rdBase
rdBase.rdkitVersion

returns

'2015.03.1'

My conclusion is that the package on conda is in fact still the old version?
Note: this is for windows 32-bit.

Or am I missing something?


Best Regards,

Joos Kiener
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Re: [Rdkit-discuss] Count carbon atoms

[Joos Kiener]

Hi Greg,

thanks for your reply.

Can confirm it's way faster than other 2 options. For my use case it's fast
enough.

Best Regards,

Joos

2015-10-14 6:55 GMT+02:00 Greg Landrum <greg.land...@gmail.com>:

>
>
> On Wed, Oct 7, 2015 at 11:12 AM, Joos Kiener <joos.kie...@gmail.com>
> wrote:
>
>> Hi all,
>>
>> is there an easy way I'm missing to get the number of C-Atoms in a
>> molecule?
>>
>> Currently I iterate all atoms and check if it's symbol is C. Doesn't seem
>> very efficient.
>>
>
> There's an, obviously under-documented, simple (and fast) way to do this:
>
> from rdkit.Chem import rdqueries
> q = rdqueries.AtomNumEqualsQueryAtom(6)
> len(mol.GetAtomsMatchingQuery(q))
>
> This is, based on the testing I just did, significantly faster than either
> the substructure-based or GetAtoms() based approaches. I'm not sure how
> generally useful it is, but this could be made even faster by adding a
> Mol.CountAtomsMatchingQuery() function to the C++ interface.
>
> You can find a bit of explanation, as well as a list of the types of
> QueryAtom functions available, by searching for QueryAtom here:
> https://github.com/rdkit/UGM_2014/blob/master/Notebooks/Whats_new.ipynb
>
> Best,
> -greg
>
>
>
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[Rdkit-discuss] Count carbon atoms

[Joos Kiener]

Hi all,

is there an easy way I'm missing to get the number of C-Atoms in a molecule?

Currently I iterate all atoms and check if it's symbol is C. Doesn't seem
very efficient.

Best Regards,

Joos Kiener
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