[Rdkit-discuss] Is it possible to compute pi and sigma partial charges with rdkit?

[Francois BERENGER]

Hello,

Is it possible to decompose partial charges with rdkit?

I am afraid that Gasteiger-Marsili (PEOE) is mostly about sigma bonds, 
but I might be wrong.


Regards,
F.

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Re: [Rdkit-discuss] position restraints on all atoms

[Greg Landrum]

Hi Katrina,

welcome to the RDKit community!

On Mon, Jul 24, 2017 at 10:45 PM, Katrina Lexa  wrote:

>
> I'm relatively new to RDKit, so I apologize for what may be a silly
> question. I'd like to generate a set of local minimum conformations around
> my input conformation, using a set of defined flat bottom potentials (0.2,
> 0.6, 1.0, and 1.4), in order to better compare my bound conformation with
> its unrestrained minimum.
>

> Ultimately, I'd like to write a script that reads in one input 3D
> conformation and prints out the energy and rmsd (and structure) of those
> local minimums as well as the lowest energy unrestrained conformation.
>
> There are plenty of examples of conformer generation scripts for RDKit,
> but I'm struggling with the constraints piece. I see the MMFFFixedAtoms &
> MMFFPositionConstraints code, but based on the code it's not obvious to me
> whether it's possible to implement either as a constraint on all atoms in
> my input molecule. Is there a way or is there another route I should be
> taking?
>

Apologies for asking what may be an obvious clarification question, but
what are you planning on constraining? It sounds like you want to attach
"springs" (well, flat bottom potentials) between the atoms in your
generated conformations and the corresponding atoms in a reference
conformation and calculate the energy of that system. Is that right?

If so, you can do this by generating a force field for the molecule with
your generated conformations, adding fixed points corresponding to your
reference conformation, and then adding distance contraints with the
appropriate min (I guess 0) and max values and reasonable force constants.
Subtracting the energy of the generated conformation from the energy of
this full system gives you the energy contributed by the constraints.

I can provide a bit of sample code showing how to do this, but I want to be
sure that this is actually what you're asking for.

-greg
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Re: [Rdkit-discuss] position restraints on all atoms

[Francois BERENGER]

On 07/25/2017 05:45 AM, Katrina Lexa wrote:

Hi All,

I'm relatively new to RDKit, so I apologize for what may be a silly 
question. I'd like to generate a set of local minimum conformations 
around my input conformation, using a set of defined flat bottom 
potentials (0.2, 0.6, 1.0, and 1.4), in order to better compare my bound 
conformation with its unrestrained minimum.


Ultimately, I'd like to write a script that reads in one input 3D 
conformation and prints out the energy and rmsd (and structure) of those 
local minimums as well as the lowest energy unrestrained conformation.


There are plenty of examples of conformer generation scripts for RDKit, 
but I'm struggling with the constraints piece. I see the MMFFFixedAtoms 
& MMFFPositionConstraints code, but based on the code it's not obvious 
to me whether it's possible to implement either as a constraint on all 
atoms in my input molecule. Is there a way or is there another route I 
should be taking?


Maybe this can give you some inspiration:

"3D diverse conformers generation using rdkit"
https://github.com/UnixJunkie/smi2sdf3d


Thanks for the help,

Katrina


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Re: [Rdkit-discuss] Need help with B SVG

[Greg Landrum]

Hi Andreas,

That's a really good question, but I'm afraid that there's not good answer
for it: the new drawing code does not currently have an option to support
either black and white rendering or using custom colors for the elements.

I just created the github item for B rendering here:
https://github.com/rdkit/rdkit/issues/1510

It should be an easy one to get into the next release.

In the meantime, someone who is better with regular expressions than me can
probably suggest a pattern to replace the specified drawing colors in the
SVG with #00 without changing the background color to black as well.
That's a hack, but possibly better than nothing.

-greg


On Tue, Jul 25, 2017 at 2:27 PM, Andreas Schulz  wrote:

> Hi ,
> there was a disscussion about how to draw molecules in black and white in
> 2015
> Today I search for a solution to create black & white SVG with something
> like
>
> drawer.DrawMolecule(mol, options=???)
>
> Are there any hints where I could find an example, please?
>
> Thanks
> Andreas
>
> PS: Sorry, first mail today was html 
>
>
> 
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[Rdkit-discuss] Need help with B SVG

[Andreas Schulz]

Hi ,
there was a disscussion about how to draw molecules in black and white in 
2015
Today I search for a solution to create black & white SVG with something like
 
drawer.DrawMolecule(mol, options=???)
 
Are there any hints where I could find an example, please?
 
Thanks
Andreas

PS: Sorry, first mail today was html 
 

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[Rdkit-discuss] Need help with B SVG

[Andreas Schulz]

Hi ,

there was a disscussion about how to draw molecules in black and white in 2015

Today I search for a solution to create black & white SVG with something like

 

drawer.DrawMolecule(mol, options=???)

 

Are there any hints where I could find an example, please?

 

Thanks

Andreas

 

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[Rdkit-discuss] position restraints on all atoms

[Katrina Lexa]

Hi All,

I'm relatively new to RDKit, so I apologize for what may be a silly
question. I'd like to generate a set of local minimum conformations around
my input conformation, using a set of defined flat bottom potentials (0.2,
0.6, 1.0, and 1.4), in order to better compare my bound conformation with
its unrestrained minimum.

Ultimately, I'd like to write a script that reads in one input 3D
conformation and prints out the energy and rmsd (and structure) of those
local minimums as well as the lowest energy unrestrained conformation.

There are plenty of examples of conformer generation scripts for RDKit, but
I'm struggling with the constraints piece. I see the MMFFFixedAtoms &
MMFFPositionConstraints code, but based on the code it's not obvious to me
whether it's possible to implement either as a constraint on all atoms in
my input molecule. Is there a way or is there another route I should be
taking?

Thanks for the help,

Katrina
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