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

Hi Francois, The only partial charge implementations currently available in the RDKit are the Gasteiger-Marsilli charges and the charges associated with MMFF. Neither offers a way to decompose the charged into sigma/pi contributions. Best, -greg On Wed, Jul 26, 2017 at 6:58 AM, Francois BERENGE

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

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. -- Check out the vibrant tech community on one o

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

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

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

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

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

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&W rendering here: https:/

[Rdkit-discuss] Need help with B&W SVG

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, fi

[Rdkit-discuss] Need help with B&W SVG

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   --

[Rdkit-discuss] position restraints on all atoms

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 wit