peppr.ContactMeasurement#

class peppr.ContactMeasurement(receptor: AtomArray, ligand: AtomArray, cutoff: float, ph: float = 7.4)[source]#

This class allows measurements of receptor-ligand contacts of specific types (e.g. hydrogen bonds) by using SMARTS patterns.

The actual measurement is performed by calling find_contacts_by_pattern().

Parameters:
receptor, ligandAtomArray

The receptor and ligand to measure contacts between. They must only contain heavy atoms, hydrogen atoms are treated implicitly.

cutofffloat

The cutoff distance to use for determining the receptor binding site. This means a receptor atom is only taken into consideration, if it is part of a residue where at least one atom is within the cutoff distance to at least one ligand atom.

phfloat, optional

The pH of the environment. By default a physiological pH value is used [1].

References

__init__(receptor: AtomArray, ligand: AtomArray, cutoff: float, ph: float = 7.4)#

Methods

__init__(receptor, ligand, cutoff[, ph])

find_contacts_by_pattern(receptor_pattern, ...)

Find contacts between the receptor and ligand atoms that fulfill the given SMARTS patterns.

find_pi_cation_interactions([...])

Find π-cation interactions between aromatic rings and cations across the binding interface.

find_salt_bridges([threshold, use_resonance])

Find salt bridges between the receptor and ligand atoms.

find_stacking_interactions([threshold, ...])

Find π-stacking interactions between aromatic rings across the binding interface.