moleculekit.smallmol.smallmolcdp module

class moleculekit.smallmol.smallmolcdp.SmallMolCDP(filename)

Bases: object

property atomtype

property bonds

property bondtype

property charge

property coords

property element

property formalcharge

generateConformers(num_confs=1, timeout=3600, min_rmsd=0.5, e_window=20.0)

Generate conformers for the molecule.

Parameters:

• num_confs (int) – Number of conformers to generate. If set to 1 it will generate the lowest energy conformer.

• timeout (int) – Maximum allowed molecule processing time in seconds.

• min_rmsd (float) – Output conformer RMSD threshold.

• e_window (float) – Output conformer energy window.

property ligname

property name

property numAtoms

property numFrames

toMolecule()

Return a moleculekit.molecule.Molecule

Returns:

mol – The moleculekit Molecule object

Return type:

moleculekit.molecule.Molecule

view(*args, **kwargs)