Index

A

add_protein_structure_from_scales() (in module vrprot.overview_util) alphafold_ver (vrprot.alphafold_db_parser.AlphafoldDBParser attribute)

AlphafoldDBParser (class in vrprot.alphafold_db_parser) argument_parser() (in module vrprot.argument_parser)

B

batch() (in module vrprot.batcher) (in module vrprot.util)

batch_size (vrprot.alphafold_db_parser.AlphafoldDBParser attribute)

C

call_ChimeraX_bundle() (in module vrprot.util) check_dirs() (vrprot.alphafold_db_parser.AlphafoldDBParser method) chimerax (vrprot.alphafold_db_parser.AlphafoldDBParser attribute) chimerax_process() (vrprot.alphafold_db_parser.AlphafoldDBParser method)

ChimeraXException clear_default_dirs() (vrprot.alphafold_db_parser.AlphafoldDBParser method) combine_fractions() (in module vrprot.util) convert_glb_to_ply() (in module vrprot.util) convert_glbs() (vrprot.alphafold_db_parser.AlphafoldDBParser method)

D

db (vrprot.alphafold_db_parser.AlphafoldDBParser attribute)

E

execute_fetch() (vrprot.alphafold_db_parser.AlphafoldDBParser method) execute_from_bulk() (vrprot.alphafold_db_parser.AlphafoldDBParser method)

execute_from_object() (vrprot.alphafold_db_parser.AlphafoldDBParser method) execute_local() (vrprot.alphafold_db_parser.AlphafoldDBParser method)

F

fetch_pdb() (in module vrprot.util) (vrprot.alphafold_db_parser.AlphafoldDBParser method) fetch_pdb_from_alphafold() (in module vrprot.util)

fetch_pdb_from_rcsb() (in module vrprot.util) fetch_pipeline() (vrprot.alphafold_db_parser.AlphafoldDBParser method) filter_already_processed() (vrprot.alphafold_db_parser.AlphafoldDBParser method)

G

gen_filennames() (in module vrprot.pointcloud2map_8bit) gen_maps() (vrprot.alphafold_db_parser.AlphafoldDBParser method)

get_filename() (vrprot.alphafold_db_parser.AlphafoldDBParser method) get_overview() (in module vrprot.overview_util) get_scale() (in module vrprot.overview_util)

I

img_size (vrprot.alphafold_db_parser.AlphafoldDBParser attribute) init_dirs() (vrprot.alphafold_db_parser.AlphafoldDBParser method)

init_overview() (in module vrprot.overview_util) init_structures_dict() (vrprot.alphafold_db_parser.AlphafoldDBParser method)

K

keep_temp (vrprot.alphafold_db_parser.AlphafoldDBParser attribute)

L

log (vrprot.alphafold_db_parser.AlphafoldDBParser attribute)

M

main() (in module vrprot.overview_util) module vrprot vrprot.alphafold_db_parser vrprot.argument_parser vrprot.batcher vrprot.exceptions vrprot.overview_util vrprot.pointcloud2map_8bit vrprot.sample_pointcloud vrprot.util

N

not_fetched (vrprot.alphafold_db_parser.AlphafoldDBParser attribute)

O

output_exists() (vrprot.alphafold_db_parser.AlphafoldDBParser method)

overview_file (vrprot.alphafold_db_parser.AlphafoldDBParser attribute) overwrite (vrprot.alphafold_db_parser.AlphafoldDBParser attribute)

P

pcd_to_png() (in module vrprot.pointcloud2map_8bit) pdb_pipeline() (vrprot.alphafold_db_parser.AlphafoldDBParser method)

processing (vrprot.alphafold_db_parser.AlphafoldDBParser attribute) proteins_from_dir() (vrprot.alphafold_db_parser.AlphafoldDBParser method) proteins_from_list() (vrprot.alphafold_db_parser.AlphafoldDBParser method)

R

read_overview() (in module vrprot.overview_util) remove_dirs() (in module vrprot.util)

run_batch() (in module vrprot.pointcloud2map_8bit) run_chimerax_coloring_script() (in module vrprot.util) run_for_batch() (in module vrprot.sample_pointcloud)

S

sample_pcd() (in module vrprot.sample_pointcloud) (vrprot.alphafold_db_parser.AlphafoldDBParser method) search_for_chimerax() (in module vrprot.util) set_alphafold_version() (vrprot.alphafold_db_parser.AlphafoldDBParser method) set_batch_size() (vrprot.alphafold_db_parser.AlphafoldDBParser method) set_chimerax() (vrprot.alphafold_db_parser.AlphafoldDBParser method) set_coloring_mode() (vrprot.alphafold_db_parser.AlphafoldDBParser method)

set_database() (vrprot.alphafold_db_parser.AlphafoldDBParser method) set_dirs() (vrprot.alphafold_db_parser.AlphafoldDBParser method) set_img_size() (vrprot.alphafold_db_parser.AlphafoldDBParser method) set_keep_tmp() (vrprot.alphafold_db_parser.AlphafoldDBParser method) set_version_from_filenames() (vrprot.alphafold_db_parser.AlphafoldDBParser method) StructureNotFoundError structures (vrprot.alphafold_db_parser.AlphafoldDBParser attribute)

U

update_existence() (vrprot.alphafold_db_parser.AlphafoldDBParser method)

update_output_dir() (vrprot.alphafold_db_parser.AlphafoldDBParser method)

V

vrprot module vrprot.alphafold_db_parser module vrprot.argument_parser module vrprot.batcher module vrprot.exceptions module

vrprot.overview_util module vrprot.pointcloud2map_8bit module vrprot.sample_pointcloud module vrprot.util module

W

WD (vrprot.alphafold_db_parser.AlphafoldDBParser attribute) write_overview() (in module vrprot.overview_util)

write_scale() (in module vrprot.overview_util) (vrprot.alphafold_db_parser.AlphafoldDBParser method)