molecular_simulations.build.build_interface module

class molecular_simulations.build.build_interface.InterfaceBuilder(path, pdb, interfaces, target, binder, padding=10.0, protein=True, rna=False, dna=False, polarizable=False)

Bases: ExplicitSolvent

For a given target/binder pair, build systems for driving binding to each of the supplied interfaces using DeepDriveMD. Includes writing out the required yaml files for running DeepDrive.

Parameters:

path (Path | str)
pdb (str)
interfaces (dict[str, Any])
target (Path | str)
binder (Path | str)
padding (float)
protein (bool)
rna (bool)
dna (bool)
polarizable (bool)

build_all(): Iterates through each interface site for a given target and builds the corresponding system for the supplied miniprotein binder.

merge_proteins(binder)

Merges the target and binder AtomGroups and writes out a unified PDB at self.pdb so as to leverage the existing pipeline for building explicit solvent systems.

Return type:: None
Parameters:: binder (AtomGroup)

parse_interface(site='site0')

Returns the relevant data for the current interface site.

Return type:: dict[str, Any]
Parameters:: site (str)

place_binder(vector, com)

Move binder nearby to the interface as defined by vector. Returns an MDAnalysis AtomGroup for the binder.

Return type:

None

Parameters:

vector (ndarray)
com (ndarray)

write_cvae_yaml(input_shape)

Writes the CVAE options yaml for a DeepDriveMD simulation.

Return type:: None
Parameters:: input_shape (list[int])

write_ddmd_yaml(contact_selection, distance_selection)

Writes the simulation options yaml for a DeepDriveMD simulation.

Return type:

None

Parameters:

contact_selection (str)
distance_selection (str)