Index

C

calculate_rotation_matrix() (in module pyvol.utilities) calculate_surface() (pyvol.spheres.Spheres method) check_dir() (in module pyvol.utilities) clean_logger() (in module pyvol.utilities) closest_vertex_normals() (in module pyvol.utilities) cluster_between_r() (in module pyvol.cluster)

cluster_improperly_grouped() (in module pyvol.cluster) cluster_within_r() (in module pyvol.cluster) configure_logger() (in module pyvol.utilities) construct_palette() (in module pyvol.pymol_utilities) coordinates_for_resid() (in module pyvol.utilities) copy() (pyvol.spheres.Spheres method)

D

display_pockets() (in module pyvol.pymol_interface)

display_pseudoatom_group() (in module pyvol.pymol_utilities) display_spheres_object() (in module pyvol.pymol_utilities)

E

extract_groups() (in module pyvol.cluster)

G

g() (pyvol.spheres.Spheres property)

H

hierarchically_cluster_spheres() (in module pyvol.cluster)

I

identify_closest_grouped() (in module pyvol.cluster)

identify_nonextraneous() (pyvol.spheres.Spheres method)

L

load_calculation() (in module pyvol.identify)

load_calculation_cmdline() (in module pyvol.pymol_interface)

M

merge_sphere_list() (in module pyvol.cluster) mesh_to_solid_CGO() (in module pyvol.pymol_utilities) mesh_to_wireframe_CGO() (in module pyvol.pymol_utilities) module pyvol.cluster pyvol.identify pyvol.pymol_interface pyvol.pymol_utilities pyvol.spheres pyvol.utilities

N

nearest() (pyvol.spheres.Spheres method)

nearest_coord_to_external() (pyvol.spheres.Spheres method)

P

pocket() (in module pyvol.identify) pocket_wrapper() (in module pyvol.identify) propagate_groups_to_external() (pyvol.spheres.Spheres method) pymol_pocket() (in module pyvol.pymol_interface) pymol_pocket_cmdline() (in module pyvol.pymol_interface) pyvol.cluster module pyvol.identify module

pyvol.pymol_interface module pyvol.pymol_utilities module pyvol.spheres module pyvol.utilities module

R

r() (pyvol.spheres.Spheres property) reassign_group() (in module pyvol.cluster) reassign_groups_to_closest() (in module pyvol.cluster) remove_duplicates() (pyvol.spheres.Spheres method) remove_groups() (pyvol.spheres.Spheres method)

remove_included_spheres() (in module pyvol.cluster) remove_interior() (in module pyvol.cluster) remove_overlap() (in module pyvol.cluster) remove_ungrouped() (pyvol.spheres.Spheres method) run_cmd() (in module pyvol.utilities)

S

sphere_multiprocessing() (in module pyvol.utilities) Spheres (class in pyvol.spheres)

subpockets() (in module pyvol.identify) surface_multiprocessing() (in module pyvol.utilities)

W

write() (pyvol.spheres.Spheres method)

write_cfg() (in module pyvol.identify) write_report() (in module pyvol.identify)

X

xyz() (pyvol.spheres.Spheres property)

xyzr() (pyvol.spheres.Spheres property) xyzrg() (pyvol.spheres.Spheres property)