Re: [Rdkit-discuss] how to set the stereochemistry of a molecule
Hello Alfredo, The tag "CHI_TETRAHEDRAL_CW" means clockwise and CCW means anti-clockwise (I have no idea why it is coded CCW rather than ACW, but whatever ;) ). These chiral tags are related but not corresponding to the absolute chirality (R/S) defined in organic chemistry. Look at the SMILES you provided and you will find that both of the chiral carbons are [C@@H]. According to the theory of Smiles in DayLight (https://www.daylight.com/dayhtml/doc/theory/theory.smiles.html 3.3.3) > The symbol "@" indicates that the following neighbors are listed > anticlockwise (it is a "visual mnemonic" in that the symbol looks like an > anticlockwise spiral around a central circle). "@@" indicates that the > neighbors are listed clockwise (you guessed it, anti-anti-clockwise). Then you may have realized that the tags "CHI_TETRAHEDRAL_CW" are corresponding to your SMILES but not the real chirality. I suggest you read the chapter 3.3.3 to understand the meaning of "chiral tag", then you will understand why they are not the absolute chirality. Absolute chirality depends on the chiral tag as well as the CIPRanks of the neighbor atoms. That is why the chirality of the two carbons are different while their chiral tags are the same. I am not sure if Lukas had the same question? Best regards, Hongbin Yang 杨弘宾, Ph.D. Research: Toxicophore and Chemoinformatics On 10/29/2019 21:14，Alfredo Quevedo wrote： Good morning, I am trying to manually set/change the stereochemistry of a chiral center of a molecule, and I cant understand how to set the CHI_TETRAHEDRAL_CW/CHI_TETRAHEDRAL_CCW tag on a certain atom. So far my script does the following: - from rdkit import Chem from rdkit.Chem import AllChem molecule='C[C@@H](C(=O)COc1c(F)c(F)cc(F)c1F)n1cc([C@@H](NCc2ccc3c(c2)OCO3)c2ncc[nH]2)nn1' molecule_smiles=Chem.MolFromSmiles(molecule) chiralty=Chem.FindMolChiralCenters(molecule_smiles) centers=len(chiralty) for i in range(centers): current_center=chiralty[i][1] print(current_center) center_to_change=chiralty[i][0] print(center_to_change) for a in molecule_smiles.GetAtoms(): print(a.GetChiralTag()) executing the above mentioned script I can see that the molecule has 2 chiral centers, the first one on index 1, which is S, and the second one, with index 19, which is R. Both chiral tags are set to: CHI_TETRAHEDRAL_CW. now, I want to manually change the configuration of index 19 to S, so I want to change its tag to CHI_TETRAHEDRAL_CCW. Which would be the command to set this tag and how is the index indicated? thanks in advance for the help, kind regards Alfredo ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] 2019.09.1 RDKit Release
Hi Greg, Great to know the release! But the docs for Python API does not work in my browser. It is empty for every page such as http://rdkit.org/docs/source/rdkit.Chem.AllChem.html Am I the only one? Best, Hongbin Yang 杨弘宾, Ph.D. Research: Toxicophore and Chemoinformatics On 10/25/2019 15:20，Greg Landrum wrote： Dear all, I'm pleased to announce that the next version of the RDKit - 2019.09 - is released. The release notes are below. The release files are on the github release page: https://github.com/rdkit/rdkit/releases/tag/Release_2019_09_1 Binaries have been uploaded to anaconda.org (https://anaconda.org/rdkit). The available conda binaries for this release are: Linux 64bit: python 3.6, 3.7 Mac OS 64bit: python 3.6, 3.7 Windows 64bit: python 3.6, 3.7 Conda builds of the PostgreSQL cartridge are also available: Linux 64bit: postgresql 9.6, 10, 11 Mac OS 64bit: postgresql 9.6, 10, 11 I believe that conda-forge will also switch to the new version in the near future. The online version of the documentation at rdkit.org (http://rdkit.org/docs/index.html) has been updated. Some things that will be finished over the next couple of days: - The conda build scripts will be updated to reflect the new version - The homebrew script Thanks to everyone who submitted code, bug reports, and suggestions for this release! Please let me know if you find any problems with the release or have suggestions for the next one, which is scheduled for March/April 2020. Best Regards, -greg # Release_2019.09.1 (Changes relative to Release_2019.03.1) ## Important - The atomic van der Waals radii used by the RDKit were corrected/updated in #2154. This leads to different results when generating conformations, molecular volumes, and molecular shapes. ## Backwards incompatible changes - See the note about atomic van der Waals radii above. - As part of the enhancements to the MolDraw2D class, we changed the type of DrawColour from a tuple to be an actual struct. We also added a 4th element to capture alpha values. This should have no affect on Python code (the alpha value is optional when providing color tuples), but will require changes to C++ and Java/C# code that is using DrawColour. - When reading Mol blocks, atoms with the symbol "R" are now converted into queries that match any atom when doing a substructure search (analogous to "*" in SMARTS). The previous behavior was to only match other dummy atoms - When loading SDF files using PandasTools.LoadSDF(), we now default to producing isomeric smiles in pandas tables. To reproduce the original behavior, use isomericSmiles=False in the call to the function. - The SMARTS generated by the RDKit no longer contains redundant wildcard queries. This means the SMARTS strings generated by this release will generally be different from that in previous releases, although the results produced by the queries should not change. - The RGroupDecomposition code now removes Hs from output R groups by default. To restore the old behavior create an RGroupDecompositionParameters object and set removeHydrogensPostMatch to false. - The default values for some of the new fingerprint generators have been changed so that they more closely resemble the original fingerprinting code. In particular most fingerprinters no longer do count simulation by default and the RDKit fingerprint now sets two bits per feature by default. - The SMARTS generated for MCS results using the ringMatchesRingOnly or completeRingsOnly options now includes ring-membership queries. ## Highlights: - The substructure matching code is now about 30% faster. This also improves the speed of reaction matching and the FMCS code. (#2500) - A minimal JavaScript wrapper has been added as part of the core release. (#2444) - It's now possible to get information about why molecule sanitization failed. (#2587) - A flexible new molecular hashing scheme has been added. (#2636) ## Acknowledgements: Patricia Bento, Francois Berenger, Jason Biggs, David Cosgrove, Andrew Dalke, Thomas Duigou, Eloy Felix, Guillaume Godin, Lester Hedges, Anne Hersey, Christoph Hillisch, Christopher Ing, Jan Holst Jensen, Gareth Jones, Eisuke Kawashima, Brian Kelley, Alan Kerstjens, Karl Leswing, Pat Lorton, John Mayfield, Mike Mazanetz, Dan Nealschneider, Noel O'Boyle, Stephen Roughley, Roger Sayle, Ricardo Rodriguez Schmidt, Paula Schmiel, Peter St. John, Marvin Steijaert, Matt Swain, Amol Thakkar Paolo Tosco, Yi-Shu Tu, Ricardo Vianello, Marc Wittke, '7FeiW', 'c56pony', 'sirbiscuit' ## Bug Fixes: - MCS returning partial rings with completeRingsOnly=True (github issue #945 from greglandrum) - Alternating canonical SMILES for fused ring with N (github issue #1028 from greglandrum) - Atom index out of range error (github issue #1868 from A-Thakkar) - Incorrect cis/trans stereo symbol for conjugated ring (github issue #2023 from baoilleach) - Hardcoded
Re: [Rdkit-discuss] parsing reactions for reactants, agents, products
Hi Benjamin,
The magic code uses a feature of python named "list comprehension".
https://www.pythonforbeginners.com/basics/list-comprehensions-in-python
It does not read the rxn string directly, but splits the string first. Since
the reaction string should be `reactants smiles>agents smiles>product smiles`,
we can get these SMILES strings by "rxn_string.split('>')".
Then for each part, we can use splitter "." to get single molecules. So
finally, [mols.split('.') for mols in rxn_string.split('>')] becomes
[[reactant1, reactant2, ..], [agent1, agent2, ..], [product1, product2, ...]].
But they are all SMILES strings.
mols_from_smiles_list is defined here:
https://github.com/connorcoley/ASKCOS/blob/master/makeit/utilities/io/draw.py#L16
It just reads the smiles strings in a list into a molecule list. The only API
is uses is "Chem.MolFromSmiles".
The magic code can be translated into:
reactants_smiles, agents_smiles, product_smiles= mols in rxn_string.split('>')
package_results = []
for mols in reactants_smiles, agents_smiles, product_smiles:
x = mols.split('.')
y = mols_from_smiles_list(x) # x is a list of SMILES, and y is a list of
molecule objects
package_results.append(y)
reactants, agents, products = package_results
The code now is not cool enough.
I have no idea with the second question. May I ask where the parameters
threshold_unmapped_reactant_atoms and move_unmmapped_reactants_to_agents are
defined?
Best,
Hongbin Yang 杨弘宾, Ph.D.
Research: Toxicophore and Chemoinformatics
On 10/22/2019 13:08，Benjamin Datko wrote：
Hello all,
While reading the source code for ASKCOS
(https://github.com/connorcoley/ASKCOS/blob/master/makeit/utilities/io/draw.py)
I noticed this code snippet (line 216 on the GitHub):
reactants, agents, products = [mols_from_smiles_list(x) for x in
[mols.split('.') for mols in rxn_string.split('>')]]
When the above code is applied on a SMILES reaction string, the result unpacks
the reactants, agents, and products mol objects into the respected variables,
with pretty good accuracy. The function 'mols_from_smiles' essentially just
applies Chem.MolFromSmiles over a list of smiles.
I think this code snippet is really cool but I cannot find any documentation on
how this is working. Searching this mailing list I came across the thread
(https://sourceforge.net/p/rdkit/mailman/message/36316849/) where this
operation of labeling reactants, agents, and products seems to be determined by
the threshold_unmapped_reactant_atoms explained in the quoted text from the
message (linked above)
Here's what's going on: By default the cartridge code does an extra step after
reading a reaction from SMILES/SMARTS: it looks at all the reactants and moves
any that don't have a sufficient fraction of mapped atoms to the agents. We do
this by default because the reactions that we found "in the wild" often have
agents, solvents, etc. mixed in with the reactants. The key parameter used
there is threshold_unmapped_reactant_atoms, which defaults to 0.2.
The only further reading I can find is from Greg's paper
(https://pubs.acs.org/doi/10.1021/ci5006614). I have two main questions:
1. Where in the code is this atom mapping being applied? I cannot tell when
this method is being applied or where the meta data is being saved. Applying
the code snippet above to a SMILES reaction string results in a list of
rdkit.Chem.rdchem.Mol objects. I cannot seem to find any static method or
attributes specifying if it's a reactant, agent, or product when inspecting a
mol object using help in a python terminal.
2. How can I change the value of the variables
threshold_unmapped_reactant_atoms and move_unmmapped_reactants_to_agents? I am
using rdkit version 2019.03.4 in an Anaconda environment. I want to experiment
changing the mapping threshold.
Very Respectfully,
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Re: [Rdkit-discuss] Compatibility with pylint in vscode
Dear Paolo, Thank you. The configuration can solve the problem. But after I add it to python->linting->Pylint Args, more (numerous) errors/warnings rush out, which are correct but unwanted. I guess that the configuration of "Use Minimal Checkers" is disabled though it is still be checked. (I don't know why) Finally, I decide to uncheck "Whether to lint python files using pylint" :) Best, Hongbin Yang 杨弘宾, Ph.D. Research: Toxicophore and Chemoinformatics On 10/12/2019 14:35，Paolo Tosco wrote： Hi Hongbin, Try configuring extension-pkg-whitelist=rdkit Then pylint should recognise RDKit methods. Cheers, p. On 12 Oct 2019, at 08:12, Hongbin Yang wrote: Dear RDKit users, Does any one use vscode with pylint support? In my IDE, it hints me that "Module 'rdkit.Chem' has no 'MolFromSmiles' member." where there is a red wavy line under the code "Chem". The environment of conda/python is correctly configured and the scripts can run. I know that it may be caused by the fact that some modules and functions in RDKit are just wrappers of C++, so pylint may not have recognized these modules or functions. But the red wavy line is really offending. Is there any suggestions in addition to disabling pylint? Best regards, Hongbin Yang 杨弘宾, Ph.D. Research: Toxicophore and Chemoinformatics ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Compatibility with pylint in vscode
Dear RDKit users, Does any one use vscode with pylint support? In my IDE, it hints me that "Module 'rdkit.Chem' has no 'MolFromSmiles' member." where there is a red wavy line under the code "Chem". The environment of conda/python is correctly configured and the scripts can run. I know that it may be caused by the fact that some modules and functions in RDKit are just wrappers of C++, so pylint may not have recognized these modules or functions. But the red wavy line is really offending. Is there any suggestions in addition to disabling pylint? Best regards, Hongbin Yang 杨弘宾, Ph.D. Research: Toxicophore and Chemoinformatics ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Boc Deprotection
Hi Sean,
You are right that using [#7:H] could be incorrect.
How about using explicit hydrogen and then “remove" it?
reaction = AllChem.ReactionFromSmarts('[#7:1]C(=O)OC(C)(C)C>>[#7:1][H]')
reactants_1 =
[Chem.MolFromSmiles('CC(C)(C)OC(=O)NC1(C(=O)O)CCN(C(=O)OCC2c3c3-c3c32)CC1')]
display(Draw._moltoimg(product, (450, 150), [], legend='mol_1'))
products = reaction.RunReactants(reactants_1)
product = products[0][0]
product = AllChem.RemoveHs(product)
display(Draw._moltoimg(product, (450, 150), [], legend='mol_1 deprotected'))
product.UpdatePropertyCache()
display(Draw._moltoimg(product, (450, 150), [], legend='mol_1 updated'))
Then you will get the correct products in both aromatic and aliphatic cases.
Best,
Hongbin Yang 杨弘宾, Ph.D.
Research: Toxicophore and Chemoinformatics
On 10/4/2019 05:04，Sean Stromberg wrote：
Thanks Hongbin,
The problem is that there are two cases aliphatic and aromatic. If I add the
explicit hydrogen like you suggest then the aliphatic case has the incorrect
number of hydrogens. My question is how to contain the generality of the
chemistry in the reaction smarts. Is that possible with the reaction smarts
syntax, or should I just define two reactions, do a substructure search and
apply the appropriate reaction for every building block I want to deprotect?
Thanks again,
Sean
From: Hongbin Yang
Sent: Wednesday, October 2, 2019 10:09 PM
To: Sean Stromberg
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re:[Rdkit-discuss] Boc Deprotection
Hi Sean,
The problem in this case is that in a non-kekulized SMILES, an aromatic
nitrogen atom binding with a hydrogen should be symbolised as “[nH]”. The “H”
is compulsory.
So you can change your reaction into "[#7:1]C(=O)OC(C)(C)C>>[#7H:1]"
Best,
Hongbin Yang 杨弘宾, Ph.D.
Research: Toxicophore and Chemoinformatics
On 10/3/2019 04:53，Sean Stromberg wrote：
Dear Rdkit Community,
I’m trying to learn reaction smarts with rdkit and would appreciate some
clarification. I’m doing Boc deprotection on a large set of building blocks and
the way I’ve defined my reaction, the number of hydrogens added after the
deprotection is always wrong. I normally can call UpdatePropertyCache() to fix
this, but when it’s an indole that is being deprotected when I call
UpdatePropertyCache() it raises:
ValueError: Sanitization error: Can't kekulize mol. Unkekulized atoms: 0 1 2 3
4 5 7 8 10
I know how to add hydrogens explicitly in the reaction smarts but not with
reference to the nitrogen’s original bonds. Can I add explicit hydrogens
conditionally? What is the best way to obtain results from the two reactant
cases in my example code?
from rdkit import Chem
from rdkit.Chem import AllChem
reaction = AllChem.ReactionFromSmarts('[#7:1]C(=O)OC(C)(C)C>>[#7:1]')
reactants_1 =
[Chem.MolFromSmiles('CC(C)(C)OC(=O)NC1(C(=O)O)CCN(C(=O)OCC2c3c3-c3c32)CC1')]
display(Draw.MolToImage(reactants_1[0], legend='mol_1'))
products = reaction.RunReactants(reactants_1)
product = products[0][0]
display(Draw.MolToImage(product, legend='mol_1 deprotected'))
product.UpdatePropertyCache()
display(Draw.MolToImage(product, legend='mol_1 deprotected and updated'))
reactants_2 =
[Chem.MolFromSmiles('CC(C)(C)OC(=O)n1cc(C[C@@H](NC(=O)OCC2c3c3-c3c32)C(=O)O)c2c21')]
display(Draw.MolToImage(reactants_2[0], legend='mol_2'))
products = reaction.RunReactants(reactants_2)
product = products[0][0]
display(Draw.MolToImage(product, legend='mol_2 deprotected'))
product.UpdatePropertyCache()
display(Draw.MolToImage(product, legend='mol_2 deprotected and updated'))
Thanks for any clarification you can provide!
Sincerely,
Sean Stromberg
P.S. Does anyone know why I get so many products when I run these reactions?
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Re: [Rdkit-discuss] Boc Deprotection
Hi Sean,
The problem in this case is that in a non-kekulized SMILES, an aromatic
nitrogen atom binding with a hydrogen should be symbolised as “[nH]”. The “H”
is compulsory.
So you can change your reaction into "[#7:1]C(=O)OC(C)(C)C>>[#7H:1]"
Best,
Hongbin Yang 杨弘宾, Ph.D.
Research: Toxicophore and Chemoinformatics
On 10/3/2019 04:53，Sean Stromberg wrote：
Dear Rdkit Community,
I’m trying to learn reaction smarts with rdkit and would appreciate some
clarification. I’m doing Boc deprotection on a large set of building blocks and
the way I’ve defined my reaction, the number of hydrogens added after the
deprotection is always wrong. I normally can call UpdatePropertyCache() to fix
this, but when it’s an indole that is being deprotected when I call
UpdatePropertyCache() it raises:
ValueError: Sanitization error: Can't kekulize mol. Unkekulized atoms: 0 1 2 3
4 5 7 8 10
I know how to add hydrogens explicitly in the reaction smarts but not with
reference to the nitrogen’s original bonds. Can I add explicit hydrogens
conditionally? What is the best way to obtain results from the two reactant
cases in my example code?
from rdkit import Chem
from rdkit.Chem import AllChem
reaction = AllChem.ReactionFromSmarts('[#7:1]C(=O)OC(C)(C)C>>[#7:1]')
reactants_1 =
[Chem.MolFromSmiles('CC(C)(C)OC(=O)NC1(C(=O)O)CCN(C(=O)OCC2c3c3-c3c32)CC1')]
display(Draw.MolToImage(reactants_1[0], legend='mol_1'))
products = reaction.RunReactants(reactants_1)
product = products[0][0]
display(Draw.MolToImage(product, legend='mol_1 deprotected'))
product.UpdatePropertyCache()
display(Draw.MolToImage(product, legend='mol_1 deprotected and updated'))
reactants_2 =
[Chem.MolFromSmiles('CC(C)(C)OC(=O)n1cc(C[C@@H](NC(=O)OCC2c3c3-c3c32)C(=O)O)c2c21')]
display(Draw.MolToImage(reactants_2[0], legend='mol_2'))
products = reaction.RunReactants(reactants_2)
product = products[0][0]
display(Draw.MolToImage(product, legend='mol_2 deprotected'))
product.UpdatePropertyCache()
display(Draw.MolToImage(product, legend='mol_2 deprotected and updated'))
Thanks for any clarification you can provide!
Sincerely,
Sean Stromberg
P.S. Does anyone know why I get so many products when I run these reactions?
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[Rdkit-discuss] 答复: Non Round-trippable Molecule
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
发送时间: 2019年9月3日 16:45
收件人: RDKit Discuss
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] 答复: Generating R-group representation
Hi Tim, Greg posted a gist on how to generate R-group matrices shortly before. https://sourceforge.net/p/rdkit/mailman/message/36744886/ Does it help? Hongbin Yang 发件人: Tim Dudgeon 发送时间: 2019年8月26日 21:08 收件人: rdkit-discuss@lists.sourceforge.net 主题: [Rdkit-discuss] Generating R-group representation I have a set of molecules that share a common scaffold and differ by substitution at a small number of sites (typically one or two). I'd like to generate a generic R-group molecule that summarises the molecules (e.g. showing the scaffold with the sites of substitution as R1, R2 etc.). Finding the MCS of such a set of molecules with RDKit seems straight forward, but the output of that is a SMARTS expression for the MCS. Does anyone have any examples (or hints) of using this to generate a R-group representation? Tim ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] SAR matrices
Hi Greg,
Very nice demo!
I’d like to ask whether we can set the size of the “elements” in a molecular
graph rather than the figure size?
It is easy to set the width and height when drawing a compound. But when we set
two compounds as the same size, e.g. 200*150, they may be actually in different
size from the view of a chemist, because in their mind the size of an element
(such as a ring, a bond or the font size of an atom symbol) should be the same.
So can we make the size of a molecular graph dynamic and keep their element
size the same, which means a complex molecule should have a higher size than a
simple one.
In this example mentioned by Ken, the TOC in
https://pubs.acs.org/doi/full/10.1021/ci300206e, the size of the substitutes
might be 100*100 or 100*120, and the scaffolds are about 300*150.
I am not sure if it is suitable to ask under this thread, but I think you
should consider this to “draw” such R-group tables.
Best,
Hongbin Yang 杨弘宾, Ph.D.
Research: Toxicophore and Chemoinformatics
Pharmaceutical Science, School of Pharmacy
East China University of Science and Technology
On 08/20/2019 17:36，Greg Landrum wrote：
I actually had a bit of inspiration while waiting for a connecting flight and
think I will have a little demo of this ready in a day or so.
-greg
On Tue, 20 Aug 2019 at 03:29, Greg Landrum wrote:
This is a great problem, but it's certainly not a trivial one.
It's a bit of a triviality, but here's at least a demo of how to draw the R
groups with the dummies as "attachment points":
https://gist.github.com/greglandrum/f7e310045542ab71447351a8043bbf3f
-greg
On Sun, Aug 18, 2019 at 2:43 PM ken wrote:
Hello,
I am trying to build a 2-D R-group grid (or table, or spreadsheet), where the
row headers contain R1 values and the column headers contain R2 values (or vice
versa). Compounds that have given R1 and R2 groups would be represented on the
table as a filled cell that intersects those R1 and R2. For example, the input
could be an SD file containing the following three compounds:
The desired output grid from the sd file would look something like this ("Y"
can be replaced with cell formatting or some other indicator):
The closest thing to this that I have been able to find is the "SAR Matrix"
(https://f1000research.com/articles/3-113/v2), but the code that was used to
generate the matrices does not appear to be available. Does anyone happen to
have such code or know how I can generate it? I imagine the first step would be
to perform an R-group decomposition, but I'm not sure what to do from there.
I started to see if I could build the program from scratch, but then I thought
that someone must've done this before and I shouldn't needlessly reinvent it.
I've been (re)learning Python for the past year or so and I think I have a
pretty good handle on the language, but I wouldn't mind putting said learning
to the test on a "real" project, so if anyone has a solution that outputs
something that even vaguely resembles the desired grid/matrix, maybe I can
modify it to fit my needs.
At some point, I would need the grid to be editable in Word, but I'll cross
that bridge when I get to it...
Thank you in advance for your help,
Ken
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Re: [Rdkit-discuss] SAR matrices
Hi Ken,
I am afraid that you may have underestimated the amount of your demand. At
least it includes R group decomposition (and it seems that only two substitutes
are considered in your example), drawing molecules, and rendering the “table”.
You can use RDKit to decompose the compounds. For example, use maximum common
substructure to setup the scaffold, followed by identification of the
connecting points by comparing the the compounds and the scaffold.
As for drawing molecules, I think RDKit cannot draw the substituent group (I’m
not sure) like what ChemDraw does.
If you just want to analyse the compounds by R-group decomposition, I believe
some kinds of commercial software such as Schrodinger and StarDrap are pretty
good.
And as for the example in the paper by Gupta-Ostermann et al. I guess that
they drew the figures via ChemDraw and Powerpoint rather than scripts.
Best regards,
Hongbin Yang 杨弘宾, Ph.D.
Research: Toxicophore and Chemoinformatics
On 08/18/2019 20:23，ken wrote：
Hello,
I am trying to build a 2-D R-group grid (or table, or spreadsheet), where the
row headers contain R1 values and the column headers contain R2 values (or vice
versa). Compounds that have given R1 and R2 groups would be represented on the
table as a filled cell that intersects those R1 and R2. For example, the input
could be an SD file containing the following three compounds:
The desired output grid from the sd file would look something like this ("Y"
can be replaced with cell formatting or some other indicator):
The closest thing to this that I have been able to find is the "SAR Matrix"
(https://f1000research.com/articles/3-113/v2), but the code that was used to
generate the matrices does not appear to be available. Does anyone happen to
have such code or know how I can generate it? I imagine the first step would be
to perform an R-group decomposition, but I'm not sure what to do from there.
I started to see if I could build the program from scratch, but then I thought
that someone must've done this before and I shouldn't needlessly reinvent it.
I've been (re)learning Python for the past year or so and I think I have a
pretty good handle on the language, but I wouldn't mind putting said learning
to the test on a "real" project, so if anyone has a solution that outputs
something that even vaguely resembles the desired grid/matrix, maybe I can
modify it to fit my needs.
At some point, I would need the grid to be editable in Word, but I'll cross
that bridge when I get to it...
Thank you in advance for your help,
Ken
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[Rdkit-discuss] RDKit cannot sanitize metal atom like platinum
Dear all, I encountered a problem when reading the molecule “Oxaliplatin”. In DrugBank, the SMILES of Oxaliplatin is `[H][N]1([H])[C@@H]2[C@H]2[N]([H])([H])[Pt]11OC(=O)C(=O)O1`. If you use Chem.MolFromSmiles without denying sanitisation, it will return an error, "Explicit valence for atom # 0 N, 4, is greater than permitted”. In this molecule, the nitrogens have four bonds, one of which is coordination bond. It seems that SMILES cannot present this bond type. My question is how to read it? Sanitisation is necessary to e.g. calculate fingerprint so skipping sanitisation is not a good idea. One alternative is to use ionisation. For example, the SMILES of Oxaliplatin in PubChem is `C1CC[C@H]([C@@H](C1)[NH-])[NH-].C(=O)(C(=O)[O-])[O-].[Pt+4]`. It transfers the covalent bonds into ionic bonds, which I think is not good enough, but it’s OK. If this is the only solution, my question is how to transfer the “incorrect” SMILES in DrugBank into the “correct” one in PubChem within RDKit. PS, I though it should be a common issue but I could not find anything similar in GitHub Issue and Mailing list history. (Maybe it is because we are always discarding organometallic compounds ?) Best regards, Hongbin Yang 杨弘宾, Ph.D. Research: Toxicophore and Chemoinformatics Pharmaceutical Science, School of Pharmacy East China University of Science and Technology ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Definition of HBA differs from pipeline pilot
Hi, Chris,
? ? Thank you very much for the suggestion. But I tend to tell my fellows to
use?Lipinski' HBA in PP :).
? ? (BTW,?http://www.macinchem.org?is pretty good. I like the website and
thanks for the "advertisement")
Cheers,
Hongbin Yang?
?From:?Chris SwainDate:?2017-06-21?14:08To:?rdkit-discussSubject:?Re:
[Rdkit-discuss] Definition of HBA differs from pipeline pilotHi,
Many applications have multiple definitions of HBA/D from simple heteroatom
counts to sophisticated SMARTS definitions, as long as they are documented and
referenced I’d vote for keeping all definitions. It certainly helps if you want
to go back and try to repeat published work.?
Cheers,
Chris
Dr Chris Swain BA MA (Cantab) PhD?CChem FRSC
Macs in Chemistry
sw...@mac.com
http://www.macinchem.org
Message: 2
Date: Tue, 20 Jun 2017 23:52:48 +0800
From: "Hongbin Yang" <yanyangh...@163.com>
To: rdkit-discuss <rdkit-discuss@lists.sourceforge.net>
Subject: [Rdkit-discuss] Definition of HBA differs from pipeline pilot
Message-ID: <2017062023524801328...@163.com>
Content-Type: text/plain; charset="gb2312"
Hi, Rdkiters,
? ?The definition of HBA in rdkit is (by Lipinski) :
32 ?HAcceptorSmarts = Chem.MolFromSmarts('[$([O,S;H1;v2]-[!$(*=[O,N,P,S])]),' +
33
??'$([O,S;H0;v2]),$([O,S;-]),$([N;v3;!$(N-*=!@[O,N,P,S])]),'
+
34 ??'$([nH0,o,s;+0])]')
? ? But in pipeline pilot (3.5), there are two HBA definitions, one of which is
Lipinsk's. I guess the other is the "first edition", which is defined as:22 ?#
HAcceptor ?'[$([!#6;+0]);!$([F,Cl,Br,I]);
23 ?# !$([o,s,nX3]);!$([Nv5,Pv5,Sv4,Sv6])]'
? ?Does it mean that we should use the newest edition of HBA and?get rid of the
default definition in pipeline pilot. These may change the?datasets filtered by
rules such RO5.
(I am not sure whether the HBA defined in PP is the same as defined in Line
22-23. I made a test.?Abacavir have 7 (current edition) and 6 (old)
respectively. And in PP, it also returned these two results).
reference:?http://www.rdkit.org/docs/api/rdkit.Chem.Lipinski-pysrc.html#NumHAcceptors?
Hongbin Yang ???
Research: Toxicophore and Chemoinformatics
Pharmaceutical Science, School of Pharmacy
East China University of Science and Technology?
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Re: [Rdkit-discuss] Reverse scale of svg coordinates to atom coordinates
Hi, Esben Jannik Bjerrum,
I have studied how to do it, though it may not be the best way. In
`rdMolDraw` there are `getAtomCoords` and `getDrawCoords` in C++ APIs
http://www.rdkit.org/docs/cppapi/classRDKit_1_1MolDraw2D.html#abd327050dfa838543103d1f2c5f28f23
But these APIs are not wrapped for python. So you may have to add the
wrapper into the source and compile it manually.
Here are some codes I made in older version:### in
`rdkit/Code/GraphMol/MolDraw2D/Wrap` ###namespace RDKit {Point2D
getDrawCoordsViaId(MolDraw2D , int at_num) {
return self.getDrawCoords(at_num);
}
Point2D getAtomCoordsViaId(MolDraw2D , int at_num) {
return self.getAtomCoords(at_num);
}
}...BOOST_PYTHON_MODULE(rdMolDraw2D)
{...python::class_<RDKit::MolDraw2D,boost::noncopyable>("MolDraw2D",docString.c_str(),python::no_init)
.def ...) .def("getDrawCoords", RDKit::getDrawCoordsViaId, "a")
.def("getAtomCoords", RDKit::getAtomCoordsViaId,"b")
;...
(I don't know why I added "a" and "b" and they may not necessary. I am not good
at C++ and boost-python) BTW, I wonder is it possible to open these APIs
officially ?
Hongbin Yang
From: Esben Jannik Bjerrum via Rdkit-discussDate: 2017-06-21 22:38To:
rdkit-discuss@lists.sourceforge.netSubject: [Rdkit-discuss] Reverse scale of
svg coordinates to atom coordinates
Hi RDkitters,
I'm experimenting a bit with an application with some user interactivity. I
get the
SVG coordinates from the Mol SVG drawing from the user interaction and
need to get back to the atom coordinates with the goal of identifying
the atom nearest the selected coordinates (or is there a smarter way to
achieve that goal?).
Is this possible from Python currently?
I see that there is a MolDraw2D::getAtomCoords function in the cpp code for
MolDraw2D, but I can't see it from the Python side, and there don't seem to be
a way to get the scaling from the MolDraw2DSVG object.
As
I understand it, the coordinates from the molecule are offset and
scaled (and flipped for y) to fit the drawing canvas of the specified
size. To get back to the original atom coordinates I must somehow
reverse the transformation. Here's some script snippets illustrating
what I try to achieve.
#Get som SVG depiction of a mol
mol = Chem.MolFromSmiles('')
mc = Chem.Mol(mol.ToBinary())
rdDepictor.Compute2DCoords(mc)
drawer = rdMolDraw2D.MolDraw2DSVG(300,300)
drawer.DrawMolecule(mc)
drawer.FinishDrawing()
svg = drawer.GetDrawingText().replace('svg:','')
##Visualization and User interaction code here gives SVG coordinates
#
svg_x = 271.0svg_y = 237.0
#Is there a function to scale back the coordinates? alternatively get the
scaling and the offset from drawer and handle it manually
atomcoords = drawer.getAtomCoords((svg_x, svg_y))
#But this function doesn't exist:-(
#...#Continue working with the rdkit mol
I would welcome some hints or suggestions.
Esben Jannik Bjerrum
cand.pharm, Ph.D
/Sent from my Ubuntu Touch Phone
Phone +45 2823 8009
http://dk.linkedin.com/in/esbenbjerrum
http://www.wildcardconsulting.dk
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[Rdkit-discuss] Definition of HBA differs from pipeline pilot
Hi, Rdkiters,
? ?The definition of HBA in rdkit is (by Lipinski) :
32 HAcceptorSmarts = Chem.MolFromSmarts('[$([O,S;H1;v2]-[!$(*=[O,N,P,S])]),' +
33
'$([O,S;H0;v2]),$([O,S;-]),$([N;v3;!$(N-*=!@[O,N,P,S])]),' +
34 '$([nH0,o,s;+0])]')
? ? But in pipeline pilot (3.5), there are two HBA definitions, one of which is
Lipinsk's. I guess the other is the "first edition", which is defined as:22 #
HAcceptor '[$([!#6;+0]);!$([F,Cl,Br,I]);
23 # !$([o,s,nX3]);!$([Nv5,Pv5,Sv4,Sv6])]'
? ?Does it mean that we should use the newest edition of HBA and?get rid of the
default definition in pipeline pilot. These may change the?datasets filtered by
rules such RO5.
(I am not sure whether the HBA defined in PP is the same as defined in Line
22-23. I made a test.?Abacavir have 7 (current edition) and 6 (old)
respectively. And in PP, it also returned these two results).
reference:?http://www.rdkit.org/docs/api/rdkit.Chem.Lipinski-pysrc.html#NumHAcceptors?
Hongbin Yang 杨弘宾
Research: Toxicophore and Chemoinformatics
Pharmaceutical Science, School of Pharmacy
East China University of Science and Technology?
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[Rdkit-discuss] Which package should be used to improve the drawing quality in win64
Hi, all,? ??? ? By default, rdkit uses pillow to render images when using rdkit.Chem.DrawMolecule. But the quality is not good enough, like this:? ??If memory does not fail me, pycairo can solve this problem. But unfortunately, I cannot find (a good) win64 pycairo in any channel in anaconda. In rdkit document, aggdraw (?http://effbot.org/downloads/#aggdraw?) is suggested to install. But I think it's too old, not to speak of the support?for?win64-python27. (So is it necessary to update the document?)? ??? ? So I wonder which package I should install to improve the drawing quality? (rdMolDraw is good, but its not as easy to use as DrawMolecule). Hongbin Yang? -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Another Can't kekulize mol observation
Hi Markus,“c1ccc(cc1)-c1nnc(n1)-c1c1” is different from
"c1ccc(cc1)-c1nncn1-c1c1", so you cannot remove the parentheses.
The error "Can't kekulize mol." is caused by the triazole in your molecule.
"c1nncn1" tells that the molecule is aromatic, but it do not tell where the H
is.
For example, "C1=NN=CN1" is "4H-1,2,4-triazole" and "C1=NC=NN1" is
1H-1,2,4-triazole. They are different in Kekulize but both of them can
represented by "c1nncn1"
There's two solutions I suggest:1. use
`Chem.MolFromSmiles('c1ccc(cc1)-c1nnc(n1)-c1c1',False)` (reference:
http://www.rdkit.org/docs/api/rdkit.Chem.rdmolfiles-module.html#MolFromSmiles)
2. Manually Kekulize it:
`Chem.MolFromSmiles('c1ccc(cc1)-C1=NN=C(N1)-c1c1')` . This indicate the H
is on the 4'N.
Hongbin Yang
From: Markus MetzDate: 2017-04-27 09:30To: RDKit DiscussSubject:
[Rdkit-discuss] Another Can't kekulize mol observationHello all:
I obtained this smiles string:c1ccc(cc1)-c1nnc(n1)-c1c1by removing atoms
from the n1 in parentheses.
Using:mol = Chem.MolFromSmiles("c1ccc(cc1)-c1nnc(n1)-c1c1")throws an error:
Can't kekulize mol.
Using mol = Chem.MolFromSmiles("c1ccc(cc1)-c1nncn1-c1c1")
works fine.
Is there any workaround?Any input is highly appreciated.
Cheers,Markus
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Re: [Rdkit-discuss] Cannot import rdBase after installed rdkit by source in a non-administrator linux cluster
Hi, Greg, Thanks for your suggestion. However, I cannot install it correctly by "original conda" as suggested in document. > `conda create -c rdkit -n hbyang-rdkit-env rdkit`> The same error occured >just like what I installed from >source:/home/hbyang/.conda/envs/hbyang-rdkit-env/lib/python2.7/site-packages/rdkit/../../../libboost_serialization.so.1.56.0: > undefined symbol: >_ZN5boost13serialization6detail17singleton_wrapperINS_7archive6detail12extra_detail3mapINS3_15binary_oarchive14m_is_de Fortunately, I solved the problem referring to the previous mail-list https://sourceforge.net/p/rdkit/mailman/message/35103418/ > the linux packages that are available from the rdkit channel on anaconda.org are based on centos6> rdkit packages compatible with the rhel5 distribution could be available from the bioconda channel So I added the channel via `conda config --add channels bioconda` , installed rdkit by `conda install rdkit` and it worked. I found that it requires boost 1.57.0-4 and thus I guess that 1.56.0 is not well compatible with rhel5. The cost is that I can not use the lastest version, but it's ok. Hongbin Yang 杨弘宾 From: Greg LandrumDate: 2017-03-29 14:01To: 杨弘宾CC: rdkit-discussSubject: Re: [Rdkit-discuss] Cannot import rdBase after installed rdkit by source in a non-administrator linux clusterA first thing that's important to know and that may make all of this easier:You can install the rdkit using conda even if you don't have write access to the directory where anaconda python is installed.If you follow the directions in the documentation and create an environment to use the RDKit in you should be able to install your own packages without any problems. Environments are (normally) created in a subdir of your home directory, where you will (hopefully) have write access. If you cannot do that or, for some other reason, want to install the RDKit from source, I will try and provide more help on that. -greg On Tue, Mar 28, 2017 at 5:56 PM, 杨弘宾 <yanyangh...@163.com> wrote: Hi, rdkiters, Have you tried install rdkit from source? It's ok when I installed rdkit by conda in my PC. But when I tried installing it in a server in which I am only a user who cannot use "sudo" and the "python" is in a read-only directory. Here is my cmake command:`~applic/cmake/bin/cmake -D PYTHON_LIBRARY=/home/yccai/Programs/Anaconda/lib/python2.7/config/libpython2.7.a -D PYTHON_INCLUDE_DIR=/home/yccai/Programs/Anaconda/include/python2.7 -D PYTHON_EXECUTABLE=/home/yccai/Programs/Anaconda/bin/python -D BOOST_ROOT=/home/yccai/Programs/Anaconda -D Boost_NO_SYSTEM_PATHS=ON ..` And output: -- The C compiler identification is GNU 4.1.2 -- The CXX compiler identification is GNU 4.1.2 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check if the system is big endian -- Searching 16 bit integer -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of unsigned short -- Check size of unsigned short - done -- Using unsigned short -- Check if the system is big endian - little endian -- Found PythonInterp: /home/yccai/Programs/Anaconda/bin/python (found version "2.7.12") -- Found PythonLibs: /home/yccai/Programs/Anaconda/lib/python2.7/config/libpython2.7.a (found version "2.7.12") -- Boost version: 1.56.0 -- Found the following Boost libraries: -- python -- Could NOT find Eigen3 (missing: EIGEN3_INCLUDE_DIR EIGEN3_VERSION_OK) (Required is at least version "2.91.0") Eigen3 not found, disabling the Descriptors3D build. -- Looking for include file pthread.h -- Looking for include file pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - not found -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Boost version: 1.56.0 -- Found the following Boost libraries: -- thread -- system -- Boost version: 1.56.0 -- Found the following Boost libraries: -- serialization == Using strict rotor definition == Updating Filters.cpp from pains file == Done updating pains files -- Boost version: 1.56.0 -- Found the following Boost libraries: -- regex -- Configuring done -- Generating done -- Build files have been written to: /home/hbyang/applic/rdkit-Release_2016_09_4/build There was no error in `make` and `make install`. B
Re: [Rdkit-discuss] Cannot import rdBase after installed rdkit by source in a non-administrator linux cluster
Hi, Andrew, I did set the LD_LIBRARY_PATH and added the $conda/lib in it. Today, I tried installing a new boost (1.60.0) myself with the following commands:```./bootstrap.sh ./b2 install ``` Interestingly, I colud not `make` successfully this time, with the several errors such as :```/home/hbyang/.local/lib/libboost_thread.so: undefined reference to `std::__cxx11::basic_string<char, std::char_traits, std::allocator >::_M_create(unsigned long&, unsigned long)@GLIBCXX_3.4.21' /home/hbyang/.local/lib/libboost_thread.so: undefined reference to `std::__cxx11::basic_string<char, std::char_traits, std::allocator >::_M_append(char const*, unsigned long)@GLIBCXX_3.4.21' ``` Then I tried install by conda with `conda create -c rdkit -n hbyang-rdkit-env rdkit` The same error occured just like what I installed from source:/home/hbyang/.conda/envs/hbyang-rdkit-env/lib/python2.7/site-packages/rdkit/../../../libboost_serialization.so.1.56.0: undefined symbol: _ZN5boost13serialization6detail17singleton_wrapperINS_7archive6detail12extra_detail3mapINS3_15binary_oarchive14m_is_destroyedE By the way, I found a similar problem reported at the end of the issue [#762](https://github.com/rdkit/rdkit/issues/762 ) user-agent conda/4.3.4 requests/2.12.4 CPython/2.7.12 Linux/2.6.18-308.el5 CentOS/5.8 glibc/2.5 Hongbin Yang 杨弘宾 Research: Toxicophore and Chemoinformatics Pharmaceutical Science, School of Pharmacy East China University of Science and Technology From: Andrew DalkeDate: 2017-03-29 03:35To: CC: rdkit-discussSubject: Re: [Rdkit-discuss] Cannot import rdBase after installed rdkit by source in a non-administrator linux clusterOn Mar 28, 2017, at 17:56, 杨弘宾 <yanyangh...@163.com> wrote: > Have you tried install rdkit from source? It's ok when I installed rdkit >by conda in my PC. But when I tried installing it in a server in which I am >only a user who cannot use "sudo" and the "python" is in a read-only directory. Yes I have, and I find it rather difficult. (My system has Python 2.7 and Python 3.5, for several versions of RDKit, so I can do regression testing across multiple environments.) I use Python virtual environments which helps, in that I effectively can control a Python installation, but also adds its own layer of complexity. > But when I used: > `from rdkit import rdBase` > error happened: > ImportError: > /home/yccai/Programs/Anaconda/bin/../lib/libboost_serialization.so.1.56.0: > undefined symbol: > _ZN5boost13serialization6detail17singleton_wrapperINS_7archive6detail12extra_detail3mapINS3_15binary_oarchive14m_is_destroyedE I think you are missing an LD_LIBRARY_PATH entry to point to your Boost libraries. Andrew da...@dalkescientific.com -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
