Re: [Rdkit-discuss] [*External*] Re: Dragon fingerprints?

2020-11-10 Thread Guillaume GODIN via Rdkit-discuss 
Look at 3D descriptors in RDKit, I reproduced all of them and it’s part of the 
core of RDKit.

De : Michal Krompiec 
Date : mardi, 10 novembre 2020 à 23:32
À : RDKit Discuss , nils.wesk...@gmail.com 

Objet : [*External*] Re: [Rdkit-discuss] Dragon fingerprints?
Hi Nils,
Yes, of course, I meant descriptors, not fingerprints. Thanks for the link!
Best,
Michal

On Tue, Nov 10, 2020 at 10:30 PM Nils Weskamp 
mailto:nils.wesk...@gmail.com>> wrote:
Hello Michal,

you are probably referring to the Dragon Descriptors
(https://chm.kode-solutions.net/products_dragon.php, now called
alvaDesc)? That is a pretty comprehensive set of more than 5.000
descriptors and I would be surprised of someone had (re-)implemented all
of them.

The closest thing that I am aware of would be Mordred
(https://github.com/mordred-descriptor).

Hope this helps,
Nils

Am 10.11.2020 um 23:11 schrieb Michal Krompiec:
> Hello RDKitters,
> Are Dragon fingerprints (or something close) available in RDKit (or free
> codes that depend on RDKit)? I'm trying to reproduce results from one paper.
>
> Thanks,
> Michal Krompiec
> Merck KGaA
>
>
>
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Re: [Rdkit-discuss] Dragon fingerprints?

2020-11-10 Thread Michal Krompiec 
Hi Nils,
Yes, of course, I meant descriptors, not fingerprints. Thanks for the link!
Best,
Michal

On Tue, Nov 10, 2020 at 10:30 PM Nils Weskamp 
wrote:

> Hello Michal,
>
> you are probably referring to the Dragon Descriptors
> (https://chm.kode-solutions.net/products_dragon.php, now called
> alvaDesc)? That is a pretty comprehensive set of more than 5.000
> descriptors and I would be surprised of someone had (re-)implemented all
> of them.
>
> The closest thing that I am aware of would be Mordred
> (https://github.com/mordred-descriptor).
>
> Hope this helps,
> Nils
>
> Am 10.11.2020 um 23:11 schrieb Michal Krompiec:
> > Hello RDKitters,
> > Are Dragon fingerprints (or something close) available in RDKit (or free
> > codes that depend on RDKit)? I'm trying to reproduce results from one
> paper.
> >
> > Thanks,
> > Michal Krompiec
> > Merck KGaA
> >
> >
> >
> > ___
> > Rdkit-discuss mailing list
> > Rdkit-discuss@lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
> >
>
>
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Re: [Rdkit-discuss] Dragon fingerprints?

2020-11-10 Thread Nils Weskamp 

Hello Michal,

you are probably referring to the Dragon Descriptors 
(https://chm.kode-solutions.net/products_dragon.php, now called 
alvaDesc)? That is a pretty comprehensive set of more than 5.000 
descriptors and I would be surprised of someone had (re-)implemented all 
of them.


The closest thing that I am aware of would be Mordred 
(https://github.com/mordred-descriptor).


Hope this helps,
Nils

Am 10.11.2020 um 23:11 schrieb Michal Krompiec:

Hello RDKitters,
Are Dragon fingerprints (or something close) available in RDKit (or free 
codes that depend on RDKit)? I'm trying to reproduce results from one paper.


Thanks,
Michal Krompiec
Merck KGaA



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[Rdkit-discuss] Dragon fingerprints?

2020-11-10 Thread Michal Krompiec 
Hello RDKitters,
Are Dragon fingerprints (or something close) available in RDKit (or free
codes that depend on RDKit)? I'm trying to reproduce results from one paper.

Thanks,
Michal Krompiec
Merck KGaA
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Re: [Rdkit-discuss] Rdkit-discuss Digest, Vol 157, Issue 2

2020-11-10 Thread Joshua Meyers 
Also worth considering align-it

in this regard (also from silicos-it).
This focusses on the pharmacophoric features rather than the shape which
may be more sensible depending on the use case.
Seems pretty quick *shrug*.

J.



On Wed, 4 Nov 2020 at 19:12, Greg Landrum  wrote:

>
>
> On Wed, 4 Nov 2020 at 18:27, Mark Mackey  wrote:
>
>>  I did look at Shape-It way back when Silicos open-sourced it: as far as
>> I can remember the code looked clean enough but it was slow. Unfortunately
>> from the RDKit point of view it’s LGPL so can’t be used as the basis of an
>> RDKit shape algorithm.
>>
> Hans actually gave permission to relicense an RDKit shape-it port. There
> is a very old PR that made some progress on this but we never finished it
> since the performance was just no good. I can’t find that PR/fork at the
> moment, but if someone thinks that may be a starting point (I’m skeptical)
> I can look
>
>
>
>
>>
>> Regards,
>>
>> Mark
>>
>>
>>
>> *From:* Chris Swain 
>> *Sent:* 04 November 2020 15:56
>> *To:* rdkit-discuss@lists.sourceforge.net; Mark Mackey <
>> m...@cresset-group.com>
>> *Subject:* Re: 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-websiteu-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 
>> To: Lewis Martin , RDKit Discuss
>>   
>> Subject: Re: [Rdkit-discuss] GPU Implementation of shape-based 3D
>>   overlap on rdkit?
>> Message-ID:
>> <
>> dbbpr08mb4235128b45e0f546acfc5adb97...@dbbpr08mb4235.eurprd08.prod.outlook.com
>> >
>>
>> 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
>>

[Rdkit-discuss] How to change the atom label font size?

2020-11-10 Thread theozh 
Hi RDKiters,

for displaying structures in a PyQt QTableWidget, I was using

Draw.MolToQPixmap(mol,size=(300,300))

However, the atom labels are pretty misaligned, which is especially annoying in 
rings.
Furthermore, when using small image sizes the atom labels are too large 
relative to the rings.

Some time ago, Greg suggested to use MolToImage instead:

Draw.MolToImage(mol,size=(300,300))

The aligment looks better there, but for me the standard font size is too small 
relative to the rings.

How can I change the atom label font size in Draw.MolToImage()?

I was hoping for something simple, like Draw.MolToImage(mol, size=(300,300), 
atomLabelFontSize=16)

I couldn't find clear documentation about this.
The following link might be related:
https://www.rdkit.org/docs/source/rdkit.Chem.Draw.MolDrawing.html
but I don't know how to put it together.

I'm missing practial code examples.
Thank you for your help.
Theo.


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