mol type conversion

[gabm...@gmail.com]

Hello,

i' m using oddt to generate some PLEC fingerprints for a library of binding site. My issue is related to the input file. I would like to give in input the pocket-ligand complexes ( in PDB format) and generate in an automated manner the ligand and protein Mol object. Using fixer.ExtractPocketAndLigand function (in the oddt.Toolkits.extras.rdkit module) I can obtaine two RWMol (a RDKIT object i think) object, but they are incompatible with the PLEC function. There is a function for convert a Mol type in another or at least a workaround for my issue?

Thanks in advice.

Best regards

Gabriele

[Maciek Wójcikowski]

Hi,

You should use RDKit molecule ROMol or RWMol as an argument for `oddt.toolkit.Molecule`. 

import oddt
# Make sure that RDKit is the default toolkit
oddt.toolkit = oddt.toolkits.rdk

 

mol = oddt.toolkit.Molecule(rdkit_mol)

Further use of `mol` in other ODDT functions should be seamless.

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[gabm...@gmail.com]

Hello,

Thank you for the help, it worked!

Il giorno martedì 30 aprile 2019 22:49:29 UTC+2, Maciek Wójcikowski ha scritto:

Hi,

You should use RDKit molecule ROMol or RWMol as an argument for `oddt.toolkit.Molecule`. 

import oddt
# Make sure that RDKit is the default toolkit
oddt.toolkit = oddt.toolkits.rdk

 

mol = oddt.toolkit.Molecule(rdkit_mol)

Further use of `mol` in other ODDT functions should be seamless.

wt., 30 kwi 2019, 16:05 użytkownik <gabm...@gmail.com> napisał:

Hello,

i' m using oddt to generate some PLEC fingerprints for a library of binding site. My issue is related to the input file. I would like to give in input the pocket-ligand complexes ( in PDB format) and generate in an automated manner the ligand and protein Mol object. Using fixer.ExtractPocketAndLigand function (in the oddt.Toolkits.extras.rdkit module) I can obtaine two RWMol (a RDKIT object i think) object, but they are incompatible with the PLEC function. There is a function for convert a Mol type in another or at least a workaround for my issue?

Thanks in advice.

Best regards

Gabriele

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