Re: [Rdkit-discuss] Pandas to Excel

Hi Both, Many thanks for your rapid response, much appreciated. Cheers Chris ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

[Rdkit-discuss] Pandas to Excel

Hi, Is it possible to export from a Pandas data frame to Excel, inserting the structures as images in the excel sheet? Cheers Chris ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-

Re: [Rdkit-discuss] Aromatic atoms

Thanks Chris > On 5 Nov 2023, at 09:23, Wim Dehaen wrote: > > how about: > len(list(mol.GetAromaticAtoms())) > > best wishes > wim > > > On Sun, 5 Nov 2023, 08:41 Chris Swain via Rdkit-discuss, > <mailto:rdkit-discuss@lists.sourceforge.net>>

[Rdkit-discuss] Aromatic atoms

Hi, Perhaps I’m missing something obvious, but is there a way to calculate the number of aromatic atoms in a molecule? Cheers Chris ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-

Re: [Rdkit-discuss] CalcNumAtoms import error

gt; Hope this helps, > Ivan > > > On Thu, Jul 14, 2022 at 7:04 AM Chris Swain via Rdkit-discuss > <mailto:rdkit-discuss@lists.sourceforge.net>> wrote: > Hi, > > If I try > > from rdkit.Chem.rdMolDescriptors import CalcNumAtoms > > I get > > ca

[Rdkit-discuss] CalcNumAtoms import error

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 ___

[Rdkit-discuss] 2dpharmacophores

Hi Pavel, Thanks for this, I can confirm this workaround does make the error message disappear. Cheers, Chris > On 12 Aug 2021, at 14:56, rdkit-discuss-requ...@lists.sourceforge.net wrote: > > Hi Chris, > > Error reported a bin (0,2,0) which does not satisfy the triangle rule. I > cannot ch

[Rdkit-discuss] 2dpharmacophores

Hi, I’m trying to generate 2Dpharmacophore fingerprints as described here https://www.rdkit.org/docs/GettingStartedInPython.html#d-pharmacophore-fingerprints For the majority of molecules this works fine but

Re: [Rdkit-discuss] Rdkit-discuss Digest, Vol 157, Issue 2

Hi Mark, Have you ever looked at Optipharm for shape comparison? https://www.nature.com/articles/s41598-018-37908-6 Or Shape-it http://silicos-it.be.s3-website-eu-west-1.amazonaws.com/software/shape-it/1.0.1/shape-it.html Cheers Chris

Re: [Rdkit-discuss] Query about creating SMILES string of small chemical fragment

Hi, Are these not intended to be query strings so rather than SMILES they should be regarded as SMARTS? If so you can perhaps just use a text editor to do a find and replace using schema shown here https://www.daylight.com/dayhtml/doc/theory/theory.smarts.html

[Rdkit-discuss] Number of sp3 atoms

Hi, I’ve written a Jupyter notebook to calculate a variety of calculated properties of molecules (MWt, TPSA, HAC, HBD/A etc.) I’d like to include the number of sp3 atoms, is there an easy way to do this? Cheers, Chris ___ Rdkit-discuss mailing list

[Rdkit-discuss] Parallel conformation generation

Hi, I’ve been using the parallel conformation generation code ( https://buildmedia.readthedocs.org/media/pdf/rdkit/latest/rdkit.pdf page 95) in a number of projects including the open source antibiotics. https://opensourceantibiotics.github.io/murligase/CompChemTools/ConformationGenerationDocking

Re: [Rdkit-discuss] Interactive plots in Jupyter notebooks (Chris Swain)

<https://www.macinchem.org/reviews/fdamols/interaction.html> If anyone has other suggestions I’d be interested to hear about them. Cheers, Chris > > On 15 Jan 2020, at 10.30, Chris Swain via Rdkit-discuss > mailto:rdkit-discuss@lists.sourceforge.net>> > wrote: > > Hi, >

[Rdkit-discuss] Interactive plots in Jupyter notebooks

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/fi

Re: [Rdkit-discuss] Constructing a mol object from a PDB ligand (Dimitri Maziuk)

I had to do something similar on 40,000 PDB files ending up using PDB_tools https://pypi.org/project/pdb-tools/ Cheers, Chris ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-disc

Re: [Rdkit-discuss] Saving chains from PDB file

Hi, Thanks everyone for the suggestions. This list is wonderful! Someone suggested https://pypi.org/project/pdb-tools/ This seems to have worked fine (and quickly). Cheers, Chris ___ Rdkit-discuss mailing list

Re: [Rdkit-discuss] Saving chains from PDB file

e > rdmolops.GetMolFrags(asMols=True) which would avoid the bond/atom removal. > > Sorry for the poor formatting but this is what I could come up with IPython > on the iPhone :-( > > p. > > > On 5 Oct 2019, at 12:46, Chris Swain via Rdkit-discuss > > > &

[Rdkit-discuss] Saving chains from PDB file

Hi, I have a number of PDB files (foo.pdb.gz) and I want to separate each chain in each file out into a separate file. So if a file contains 4 chains it will generate 4 separate files. Can I do this using RDKit, if so how? Cheers Chris ___ Rdkit-di

Re: [Rdkit-discuss] Open-source business models and the RDKit (Greg Landrum)

This is an interesting discussion and suspect this does not only apply to open-source software developers, there are similar challenges for small independent software companies. On CICAG (http://www.rsccicag.org ) we have been discussing the possibility of organising a

[Rdkit-discuss] [Question] Ok to switch to conda-forge for RDKit builds?

OK with me, I’ve largely switched to condo/bioconda already. Chris > On 18 Oct 2018, at 13:14, rdkit-discuss-requ...@lists.sourceforge.net wrote: > > Message: 1 > Date: Thu, 18 Oct 2018 08:33:56 +0200 > From: Greg Landrum mailto:greg.land...@gmail.com>> > To: RDKit Discuss

Re: [Rdkit-discuss] Module SimilarityMaps

8 > <https://gist.github.com/greglandrum/3fab9a5de996d84e7b052966251074e8> > > -greg > > On Sat, Jun 9, 2018 at 7:23 PM Chris Swain <mailto:sw...@mac.com>> wrote: > Hi, > > I’m using Similarity Maps to map a property onto a molecule and then displa

[Rdkit-discuss] Module SimilarityMaps

Hi, I’m using Similarity Maps to map a property onto a molecule and then display as a contour map and export as an image. This all works fine but is it possible to annotate the image the the molecule ID (molID) Cheers, Chris

Re: [Rdkit-discuss] Non-redundant database of molecules (Wandr?)

Hi, I’d use a text based version of the structure InChiKey or canonical SMILES it then becomes a easy task to do the comparison in Python I wrote a script to do this in Vortex but it should be easy to modify. https://www.macinchem.org/reviews/vortex/tut28/scripting_vortex28.php

[Rdkit-discuss] . Re: using rdkit to read in chembl23 1.7 million compounds

I've not tried to read in ChEMBL but I have tried to process other large datasets e.g. ZINC. My impression was that problems arose with small heterocyclic systems, particularly if fused or containing multiple different heteroatoms. I did wonder if the different aromaticity models might be the i

Re: [Rdkit-discuss] Definition of HBA differs from pipeline pilot

, 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" > To: rdkit-discuss > Subject: [Rdkit-discuss] Definition of HBA differs from

Re: [Rdkit-discuss] Memory issue when storing more than 300K mol in a list

This sounds like the situation where a database might be a better option, tuned to store fingerprints in RAM? Chris Dr Chris Swain BA MA (Cantab) PhD CChem FRSC Macs in Chemistry sw...@mac.com http://www.macinchem.org > On 10 Jun 2017, at 13:10, rdkit-discuss-requ...@lists.sourceforge.

Re: [Rdkit-discuss] Clustering

f you want to specify the number of clusters, you can simply use K-means. >>>> High dimensionality of fingerprints might be a problem for memory >>>> consumption. In this case you can use PCA to reduce dimensions to something >>>> manageable. To avoid memo

[Rdkit-discuss] Clustering

Hi, I want to do clustering on around 4 million structures The Rdkit cookbook (http://www.rdkit.org/docs/Cookbook.html ) suggests "For large sets of molecules (more than 1000-2000), it’s most efficient to use the Butina clustering algorithm” However

Re: [Rdkit-discuss] delete a substructure

I use SMARTSviewer at Univ of Hamburg http://www.zbh.uni-hamburg.de/en/bioinformatics-server.html Chris > On 9 Mar 2017, at 17:21, rdkit-discuss-requ...@lists.sourceforge.net wrote: > > One last question I have is do you guys have co

Re: [Rdkit-discuss] aligning maximum common substructure of 2 molecule

Sorry if I’m a bit late to the discussion, this is the sort of thing I use Openbabel for http://openbabel.org/wiki/Obfit Align all the molecules in "testmv.sdf" on a single molecule of "testref.sdf" by superimposing them on its N-methylpiperidyl portion (and ou

Re: [Rdkit-discuss] RDKit Cookbook

yet, so the current calling > protocol should work for now. But we have been forewarned > > -P. > > On Wed, Jan 18, 2017 at 2:26 PM, Chris Swain <mailto:sw...@mac.com>> wrote: > Hi, > > I’ve been trying a few o the examples in > http://www.rdkit.o

[Rdkit-discuss] RDKit Cookbook

Hi, I’ve been trying a few o the examples in http://www.rdkit.org/docs/Cookbook.html and I’d like to use the Similarity Maps as shown below from rdkit.Chem.Draw import SimilarityMaps # helper function def getProba(fp, predictionFunction): return pre

Re: [Rdkit-discuss] drawing code take 3

At first glance this looks an interesting approach. Simulation-Based Algorithm for Two-Dimensional Chemical Structure Diagram Generation of Complex Molecules and Ligand–Protein Interactions DOI: http://dx.doi.org/10.1021/acs.jcim.6b00391 > On 27 Sep 2016, at 05:38, rdkit-discuss-requ...@lists.so

Re: [Rdkit-discuss] comparing two or more tables of molecules

Hi, I’ve done this sort of comparison many times I actually use a SVL script within Moe and there is an example here (http://www.cambridgemedchemconsulting.com/resources/hit_identification/fragment_collection_profiles.html

Re: [Rdkit-discuss] Pandas

Search and add similarity to resulting data frame > On 27 Nov 2016, at 07:55, Greg Landrum wrote: > > > You don't know if what could be done as a single line? > > -greg --

Re: [Rdkit-discuss] Pandas

:greg.land...@gmail.com>> wrote: > No worries. > This, and Anna's question about similarity searching and clustering > illustrate a great opportunity for a tutorial on fingerprints and similarity > searching. > > -greg > > > > > > On Wed, Nov 23,

Re: [Rdkit-discuss] Pandas

e the bulk similarity searching functionality for better > performance instead of the list comprehension? > > Best, > > Peter > > > On Wed, Nov 23, 2016 at 9:11 AM Greg Landrum <mailto:greg.land...@gmail.com>> wrote: > No worries. > This, and Anna's quest

Re: [Rdkit-discuss] Pandas

retty sure > Chris won't mind and the real Pandas experts may have a better answer than > me.] > > On Wed, Nov 23, 2016 at 9:51 AM, Chris Swain <mailto:sw...@mac.com>> wrote: > > I quite like storing molecules and associated data in a data frame and I’ve >

Re: [Rdkit-discuss] Atom Environments

om=amap[idx], canonical=True) > > You can then load the output into a DB for searching. You might be able to > tweak this to suit your purposes? > > best wishes > Richard > > -Original Message- > From: Chris Swain [mailto:sw...@mac.com] > Sent: 20 Novembe

[Rdkit-discuss] Atom Environments

Hi, I have a project where I would like to find similar atom environments to a specified atom in a selected molecule. For example Suppose I have this query molecule C1CNCC(C1)c1c1, and the selected atom is the nitrogen. I also have a file containing SMILES strings and ID for a list of re