Volume

PocketVolume(config=None)

The main class to run POVME.

Initialize POVME.

PARAMETER	DESCRIPTION
config	Pocket volume calculation configuration. TYPE: PocketVolumeConfig | None DEFAULT: None

config = config

gen_points(config)

run(path_pdb, output_prefix=None, chunk_size=10)

Start POVME

PARAMETER	DESCRIPTION
path_pdb	Path to PDB file. This will overwrite the configuration file. TYPE: str
output_prefix	Path to output directory including directories. TYPE: str | None DEFAULT: None

write_points(pts, output_prefix, config)

write_points_contig(regions_contig, output_prefix, config)

write_vol_dens(results, output_prefix, config)

write_vol_traj(results_vol, output_prefix, config)

TaskComputeVolumeFromPDBLines

Bases: RayTaskGeneral

process_item(item)

collect_pdb_frames_in_chunks(filename, chunk_size)

Read a multi-frame PDB and yield frames in chunks.

Each yielded chunk is a list of (frame_index, pdb_frame_string).

get_unique_rows(a)

Identifies unique points (rows) in an array of points.

PARAMETER	DESCRIPTION
a	A nx3 numpy.array representing 3D points.

RETURNS	DESCRIPTION
	A nx2 numpy.array containing the 3D points that are unique.