Re: [Rdkit-discuss] Pandas to Excel

[Chris Swain via Rdkit-discuss]

Hi Both,

Many thanks for your rapid response, much appreciated.

Cheers

Chris


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[Rdkit-discuss] Pandas to Excel

[Chris Swain via Rdkit-discuss]

Hi,

Is it possible to export from a Pandas data frame to Excel, inserting the 
structures as images in the excel sheet?

Cheers

Chris

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Re: [Rdkit-discuss] Aromatic atoms

[Chris Swain via Rdkit-discuss]

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>> wrote:
>> Hi,
>> 
>> Perhaps I’m missing something obvious, but is there a way to calculate the 
>> number of aromatic atoms in a molecule?
>> 
>> Cheers
>> 
>> Chris
>> 
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[Rdkit-discuss] Aromatic atoms

[Chris Swain via Rdkit-discuss]

Hi,

Perhaps I’m missing something obvious, but is there a way to calculate the 
number of aromatic atoms in a molecule?

Cheers

Chris

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Re: [Rdkit-discuss] CalcNumAtoms import error

[Chris Swain via Rdkit-discuss]

Hi Ivan and Axel,

Thanks upgrading to the last version works,

Cheers

Chris

> On 14 Jul 2022, at 13:37, Ivan Tubert-Brohman 
>  wrote:
> 
> Hi Chris,
> 
> Please try a more recent version of RDKit. I believe this function was added 
> in the 2021.09 release.
> 
> 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
> 
> 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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[Rdkit-discuss] CalcNumAtoms import error

[Chris Swain via Rdkit-discuss]

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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[Rdkit-discuss] 2dpharmacophores

[Chris Swain via Rdkit-discuss]

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 for a few I get this error, 
any idea what the issue is?

Chris

qmol = 
Chem.MolFromSmiles('COc1ccc(C(C)C)cc1CN[C@H]1C2CCN(CC2)[C@H]1C(c1c1)c1c1')
fpquery = Generate.Gen2DFingerprint(qmol,sigFactory)
fpquery

---
ValueErrorTraceback (most recent call last)
~/miniconda3/lib/python3.7/site-packages/rdkit/Chem/Pharm2D/SigFactory.py in 
GetBitIdx(self, featIndices, dists, sortIndices)
248 print('\tbins:', repr(self._bins), type(self._bins))
--> 249 bin_ = self._findBinIdx(dists, self._bins, 
self._scaffolds[len(dists)])
250 except ValueError:

~/miniconda3/lib/python3.7/site-packages/rdkit/Chem/Pharm2D/SigFactory.py in 
_findBinIdx(self, dists, bins, scaffolds)
167 whichBins[i] = where
--> 168 res = scaffolds.index(tuple(whichBins))
169 if _verbose:

ValueError: (0, 2, 0) is not in list

During handling of the above exception, another exception occurred:

IndexErrorTraceback (most recent call last)
 in 
  1 qmol = 
Chem.MolFromSmiles('COc1ccc(C(C)C)cc1CN[C@H]1C2CCN(CC2)[C@H]1C(c1c1)c1c1')
> 2 fpquery = Generate.Gen2DFingerprint(qmol,sigFactory)
  3 fpquery

~/miniconda3/lib/python3.7/site-packages/rdkit/Chem/Pharm2D/Generate.py in 
Gen2DFingerprint(mol, sigFactory, perms, dMat, bitInfo)
160 for match in matchesToMap:
161   if sigFactory.shortestPathsOnly:
--> 162 idx = _ShortestPathsMatch(match, perm, sig, dMat, sigFactory)
163 if idx is not None and bitInfo is not None:
164   l = bitInfo.get(idx, [])

~/miniconda3/lib/python3.7/site-packages/rdkit/Chem/Pharm2D/Generate.py in 
_ShortestPathsMatch(match, featureSet, sig, dMat, sigFactory)
 71 dist[i] = d
 72 
---> 73   idx = sigFactory.GetBitIdx(featureSet, dist, sortIndices=False)
 74   if _verbose:
 75 print('\t', dist, minD, maxD, idx)

~/miniconda3/lib/python3.7/site-packages/rdkit/Chem/Pharm2D/SigFactory.py in 
GetBitIdx(self, featIndices, dists, sortIndices)
252 fams = [fams[x] for x in featIndices]
253 raise IndexError('distance bin not found: feats: %s; 
dists=%s; bins=%s; scaffolds: %s' %
--> 254  (fams, dists, self._bins, self._scaffolds))
255 
256 return startIdx + offset + bin_

IndexError: distance bin not found: feats: ['Acceptor', 'Aromatic', 
'Hydrophobe']; dists=[1, 5, 1]; bins=[(0, 2), (2, 5), (5, 8)]; scaffolds: [0, 
[(0,), (1,), (2,)], 0, [(0, 0, 0), (0, 0, 1), (0, 1, 0), (0, 1, 1), (0, 1, 2), 
(0, 2, 1), (0, 2, 2), (1, 0, 0), (1, 0, 1), (1, 0, 2), (1, 1, 0), (1, 1, 1), 
(1, 1, 2), (1, 2, 0), (1, 2, 1), (1, 2, 2), (2, 0, 1), (2, 0, 2), (2, 1, 0), 
(2, 1, 1), (2, 1, 2), (2, 2, 0), (2, 2, 1), (2, 2, 2)], 0]

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

[Chris Swain via Rdkit-discuss]

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



> On 4 Nov 2020, at 14:28, rdkit-discuss-requ...@lists.sourceforge.net wrote:
> 
> From: Mark Mackey mailto:m...@cresset-group.com>>
> To: Lewis Martin  >, RDKit Discuss
>>
> Subject: Re: [Rdkit-discuss] GPU Implementation of shape-based 3D
>   overlap on rdkit?
> Message-ID:
>   
>   
> >
>   
> Content-Type: text/plain; charset="utf-8"
> 
> Hi Lewis,
> 
> The standard shape alignment algorithm that everyone uses is from Grant & 
> Pickup 1996 
> (https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291096-987X%2819961115%2917%3A14%3C1653%3A%3AAID-JCC7%3E3.0.CO%3B2-K
>  
> ).
> 
> It?s a Taylor-series-like expansion using spherical Gaussians as stand-ins 
> for hard spheres - you take the atomic volumes, subtract off the pairwise 
> overlaps, add back in the three-way overlaps, subtract off the four-way 
> overlaps, and so on. I did a fair few tests some years back and you really 
> need to go to 6 terms to get decent accuracy. However, all of the commercial 
> algorithms (ROCS, Phase Shape, etc) seem to truncate at 2, so go figure. OTOH 
> the ?high throughput? versions all seem to be operated with ludicrously low 
> number of conformations so the error in incomplete coverage of conformer 
> space dwarfs the 5% noise that you get from truncating at 2 terms rather than 
> 6.
> 
> If you want something slightly more accurate at the same computational cost, 
> look at WEGA (https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.23603 
>  and references 
> therein) which heuristically corrects for some flaws in the truncated 
> Grant calculations.
> 
> If you want a fast GPU-accelerated version, then forget about actually 
> applying the algorithm directly[*]. Instead, to compare a reference molecule 
> A to a database molecule B, precompute a grid over A containing the pairwise 
> overlap value of an atom at each point in the grid with A. You can then 
> compute the shape overlap for a given orientation of B by a simple 3D texture 
> lookup rather than faffing around trying to compute exponential functions.. 
> This is simplified by assuming that all atoms have the same atomic radius and 
> neglecting hydrogens (we?re going for speed over accuracy here, remember?) 
> You can get a similar lookup texture for gradients, I think. One thing GPUs 
> are really good at is texture lookups and interpolation. They?re less good at 
> evaluating exponential functions. Your GPU algorithm is then a massively 
> parallel CG or NR optimiser with the objective function computing shape 
> overlap values for as many molecules as you can cram into GPU memory all in 
> parallel.
> 
> [*] gWEGA (I believe) is a GPU-accelerated version of the standard WEGA 
> algorithm and based on the published timings is an order of magnitude or more 
> slower than fastROCS
> 
> Having said all of that, our GPU-accelerated shape similarity function just 
> brute forces through the overlap series to sixth order, as (a) my happy place 
> is on the accuracy side of the speed/accuracy tradeoff, and (b) our 
> electrostatic similarity calculations are sufficiently complex that making 
> the shape function faster wouldn?t be that much of a net win. As a result, 
> take all of the above with a grain of salt ?.
> 
> Regards,
> Mark
> 
> --
> Mark Mackey
> Chief Scientific Officer
> Cresset
> New Cambridge House, Bassingbourn Road, Litlington, Cambridgeshire, SG8 0SS, 
> UK
> tel: +44 (0)1223 858890mobile: +44 (0)7595 099165fax: +44 (0)1223 
> 853667
> email: m...@cresset-group.com 
>  >web: www.cresset-group.com 
>  >skype: mark_cresset

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

[Chris Swain via Rdkit-discuss]

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 


Cheers,

Chris

> 
> Message: 1
> Date: Mon, 22 Jun 2020 17:09:36 +0200
> From: Goutam Mukherjee 
> To: rdkit-discuss 
> Subject: [Rdkit-discuss] Query about creating SMILES string of small
>   chemical fragment
> Message-ID:
>   
> Content-Type: text/plain; charset="utf-8"
> 
> Dear Members,
> 
> I want to generate a list of SMILES strings of these following chemical
> fragments (pseudo SMILES notation):
> 
> [R]N([R])C(=S)N([R])C([R])=O  
> [R]N([R])C(=O)C([R])=O
> [R]SS[R]  
> [R]N([R])N([R])C([R])=O   
> [R]P(O)(O)=O  
> [R]C([Nar])=O 
> [R]N([R])C(=O)N([R])C([R])=O  
> [R]C=O
> [R][N+]([R])([R])[R]  
> [R]N([R])C(=S)N([R])[R]   
> [R]N1CC(=O)N([R])C1=O 
> [R]N([R])S(=O)(=O)N([R])[R]   
> [R]S([R])=O   
> [R]S([Nar])(=O)=O 
> [R]OP(O)(O)=O 
> [R]SCN([R])C([R])=O   
> [R]N([R])C(=S)N([R])N=C   
> [R]N([R])CN([R])C([R])=O  
> O=[Nar]
> 
> Where R is a substitution that may be carbon or hydrogen and ar is aromatic 
> one.
> 
> A detail of such moieties can be found in the following links:
> https://static-content.springer.com/esm/art%3A10.1186%2Fs13321-017-0225-z/MediaObjects/13321_2017_225_MOESM1_ESM.txt.
> 
> Could anyone please help me how to convert these pseudo-SMILES to a
> SMILES notation.
> 
> 
> Thanks and Best Regards,
> 
> Goutam
> -- next part --
> An HTML attachment was scrubbed...
> 

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[Rdkit-discuss] Number of sp3 atoms

[Chris Swain via Rdkit-discuss]

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

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

[Chris Swain via Rdkit-discuss]

Hi,

Thanks for all the suggestions, both on and off list, it is clear that this is 
of considerable interest. Several people have asked me to post details.

I’ve tried to summarise my findings, bear in mind this is a work in progress! 
(There is also a download link to the notebook and the datafile)

https://www.macinchem.org/reviews/fdamols/interactiveplots.php 
<https://www.macinchem.org/reviews/fdamols/interactiveplots.php>

I’ve also put up a Jupyter notebook with examples of the different options 
here, 

https://www.macinchem.org/reviews/fdamols/interaction.html 
<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,
> 
> 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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> Subject: Digest Footer
> 
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> End of Rdkit-discuss Digest, Vol 147, Issue 16
> **

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[Rdkit-discuss] Interactive plots in Jupyter notebooks

[Chris Swain via Rdkit-discuss]

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] Constructing a mol object from a PDB ligand (Dimitri Maziuk)

[Chris Swain via Rdkit-discuss]

I had to do something similar on 40,000 PDB files ending up using PDB_tools

https://pypi.org/project/pdb-tools/

Cheers,

Chris




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

[Chris Swain via Rdkit-discuss]

Thanks

Chris

> On 5 Oct 2019, at 16:34, Maciek Wójcikowski  wrote:
> 
> Paolo and Chris,
> 
> There actually is Rdkit function to do this very task: SplitMolByPDBChainId
> http://rdkit.org/docs/source/rdkit.Chem.rdmolops.html#rdkit.Chem.rdmolops.SplitMolByPDBChainId
>  
> <http://rdkit.org/docs/source/rdkit.Chem.rdmolops.html#rdkit.Chem.rdmolops.SplitMolByPDBChainId>
> 
> 
> sob., 5 paź 2019, 14:42 użytkownik Paolo Tosco  <mailto:paolo.tosco.m...@gmail.com>> napisał:
> Hi Chris,
> 
> The following, though quite inefficient, will work:
> 
> from rdkit import Chem
> mol = Chem.MolFromPDBFile("1CX2.pdb")
> chains = {a.GetPDBResidueInfo().GetChainId() for a in mol.GetAtoms()}
> chain_mols = {c: Chem.RWMol(mol) for c in chains}
> for c, m in chain_mols.items():
> bonds_to_remove = [(b.GetBeginAtomIdx(), b.GetEndAtomIdx()) for b in 
> m.GetBonds() if b.GetBeginAtom().GetPDBResidueInfo().GetChainId() != c or 
> b.GetEndAtom().GetPDBResidueInfo().GetChainId() != c]
> atoms_to_remove = [a.GetIdx() for a in m.GetAtoms() if 
> a.GetPDBResidueInfo().GetChainId() != c]
> [m.RemoveBond(*b) for b in bonds_to_remove]
> [m.RemoveAtom(a) for a in sorted(atoms_to_remove, reverse=True)]
> Chem.MolToPDBFile(m, "{0:s}.pdb".format(c))
> 
> Individual chains are saved to .
> 
> As chains will be separate fragments, a more efficient way would to use 
> 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 
> >  > <mailto:rdkit-discuss@lists.sourceforge.net>> wrote:
> > 
> > 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
> > 
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Re: [Rdkit-discuss] Open-source business models and the RDKit (Greg Landrum)

[Chris Swain via Rdkit-discuss]

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 (probably one day) meeting around 
the topic of open data/software/publishing and sustainability.

Most people I’ve spoken to think it is a very important topic, but they are not 
sure if there is an audience.

I’d appreciate any feedback/suggestions etc.

Chris


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

[Chris Swain via Rdkit-discuss]

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  >,  RDKit
>   Developers List  >
> Subject: [Rdkit-discuss] [Question] Ok to switch to conda-forge for
>   RDKit builds?
> Message-ID:
>>
> Content-Type: text/plain; charset="utf-8"
> 
> Dear all,
> 
> TL;DR: Now that RDKit builds are available on conda-forge, I would like to
> stop doing builds on the rdkit conda channel. I'm looking for feedback
> about that here.
> 
> Thanks to the persistence of Peter St John and Matt Swain, the RDKit is now
> available on conda-forge:
> https://anaconda.org/conda-forge/rdkit/files 
> 
> If you take a look, you'll find builds for Mac, Linux, and Windows together
> with multiple versions of Python. The build/deployment steps are all
> automated. It's really cool!
> 
> Given that these packages now exist, I don't see much value in continuing
> to also host standard RDKit builds in the rdkit conda channel. So I would
> propose that we switch to using conda-forge as the primary channel for
> doing RDKit builds/distributions. Having the automated process available
> would save me a lot of time and remove the chance for me to make a mistake
> while doing the builds.[1]
> If we go this way, I will update the documentation to point to conda-forge
> and will only do the occasional nightly or beta build in the rdkit conda
> channel.
> 
> Does anyone have any objections to this or see any problems that it might
> cause?
> 
> Many thanks to Matt and Peter for making the conda-forge builds happen!
> 
> -greg
> [1] As fun as these are, I think I can live without them. ;-)

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