Re: [Rdkit-discuss] MMFF94 scoring of a protein-ligand complex

2023-01-30 Thread Paolo Tosco 
Hi Francois,

there is no inherent limitation to small molecules n the RDKit MMFF94
implementation - you may assess the energy of systems of any size,
including protein ligand complexes, provided that all atom types in your
complex are defined in MMFF94.

Cheers,
p.


On Mon, Jan 30, 2023 at 2:38 AM Francois Berenger  wrote:

> Dear list,
>
> Is it possible with the MMFF94 implementation in RDKit
> to score a protein-ligand complex?
>
>  From what I understand currently, the implementation only
> allows to work with a single isolated small molecule for
> energy calculation and conformer optimization.
>
> If there are some examples out there to process a protein-ligand
> complex, that would be really nice.
>
> Regards,
> F.
>
>
> ___
> 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] SMARTS: "NOT Hydrogen" wildcard?

2023-01-30 Thread Dan Nealschneider 
Thomas -
Check out https://www.rdkit.org/docs/RDKit_Book.html#smarts-reference. It's
always hard to make a SMARTS expression that works for both implicit
hydrogen and explicit hydrogen ROMols. I think that you probably want:

[#6d1]


Which will match any carbon with non-hydrogen degree one, including
terminal methyls, and also =C and ≡C. If you also want the neighbor:

[!#0][#6d1]


If you want terminal methyls only:

[!#0][#6H3]


Good luck!

dan nealschneider | senior staff developer

*he/him/his*

[image: Schrödinger, Inc.] 


On Mon, Jan 30, 2023 at 8:48 AM Greg Landrum  wrote:

> Hi Thomas,
>
> * in SMARTS just means "any atom".
> [!H], for historical reasons, means "and atom without a single Hydrogen"
> (i.e. it matches CH2 and CH3, but not CH)
> You want [!#0], that is "not hydrogen"
>
> -greg
>
>
> On Mon, Jan 30, 2023 at 5:40 PM Thomas  wrote:
>
>> I thought that the wildcard * would match any atom except hydrogen, but
>> that's true unless hydrogens are explicit in the molecule
>>
>> I have some patterns in the form of SMILES with wildcards and implicit
>> hydrogens. For example C* means "terminal carbons" only.
>> (" * "  stands for any atom except hydrogen)
>>
>> I want to transform this SMILES in SMARTS, if I just write:
>>
>> smarts = rdkit.MolFromSmarts('*C')
>>
>> the smarts I get matches any C with AT LEAST one non-hydrogen bond (not
>> EXACTLY one).
>>
>> If I add explicit hydrogens to the smarts (and to the molecules to be
>> tested)
>>
>> smartsH = rdkit.AddHs(smarts)
>> rdkit.MolToSmiles(smartsH)
>> '*C([H])([H])[H]'
>>
>> I get this pattern where the wildcard matches ANY atom including hydrogen
>> (it matches with the single carbon atom).
>>
>> Basically I am trying to get the SMARTS *C[H3] starting from the
>> respective SMILES *C. Is there a way?
>>
>> I've already tried to replace the * with a [!H] (NOT hydrogen) with no
>> luck.
>> Thanks to anyone :)
>> Thomas
>> ___
>> 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 mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] SMARTS: "NOT Hydrogen" wildcard?

2023-01-30 Thread Greg Landrum 
Hi Thomas,

* in SMARTS just means "any atom".
[!H], for historical reasons, means "and atom without a single Hydrogen"
(i.e. it matches CH2 and CH3, but not CH)
You want [!#0], that is "not hydrogen"

-greg


On Mon, Jan 30, 2023 at 5:40 PM Thomas  wrote:

> I thought that the wildcard * would match any atom except hydrogen, but
> that's true unless hydrogens are explicit in the molecule
>
> I have some patterns in the form of SMILES with wildcards and implicit
> hydrogens. For example C* means "terminal carbons" only.
> (" * "  stands for any atom except hydrogen)
>
> I want to transform this SMILES in SMARTS, if I just write:
>
> smarts = rdkit.MolFromSmarts('*C')
>
> the smarts I get matches any C with AT LEAST one non-hydrogen bond (not
> EXACTLY one).
>
> If I add explicit hydrogens to the smarts (and to the molecules to be
> tested)
>
> smartsH = rdkit.AddHs(smarts)
> rdkit.MolToSmiles(smartsH)
> '*C([H])([H])[H]'
>
> I get this pattern where the wildcard matches ANY atom including hydrogen
> (it matches with the single carbon atom).
>
> Basically I am trying to get the SMARTS *C[H3] starting from the
> respective SMILES *C. Is there a way?
>
> I've already tried to replace the * with a [!H] (NOT hydrogen) with no
> luck.
> Thanks to anyone :)
> Thomas
> ___
> 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] SMARTS: "NOT Hydrogen" wildcard?

2023-01-30 Thread Thomas 
I thought that the wildcard * would match any atom except hydrogen, but
that's true unless hydrogens are explicit in the molecule

I have some patterns in the form of SMILES with wildcards and implicit
hydrogens. For example C* means "terminal carbons" only.
(" * "  stands for any atom except hydrogen)

I want to transform this SMILES in SMARTS, if I just write:

smarts = rdkit.MolFromSmarts('*C')

the smarts I get matches any C with AT LEAST one non-hydrogen bond (not
EXACTLY one).

If I add explicit hydrogens to the smarts (and to the molecules to be
tested)

smartsH = rdkit.AddHs(smarts)
rdkit.MolToSmiles(smartsH)
'*C([H])([H])[H]'

I get this pattern where the wildcard matches ANY atom including hydrogen
(it matches with the single carbon atom).

Basically I am trying to get the SMARTS *C[H3] starting from the respective
SMILES *C. Is there a way?

I've already tried to replace the * with a [!H] (NOT hydrogen) with no luck.
Thanks to anyone :)
Thomas
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss