Index

Symbols

--backend pocketvina-show command line option --batch-size pocketvina-dock command line option --box pocketvina-bench-gpu command line option pocketvina-dock command line option --center pocketvina-bench-gpu command line option --check pocketvina-setup-p2rank command line option --config pocketvina-bust command line option pocketvina-dock command line option --csv pocketvina-query command line option --database-path pocketvina-dock command line option --dir pocketvina-setup-p2rank command line option --energy-range pocketvina-dock command line option --engine-timeout pocketvina-bench-gpu command line option pocketvina-dock command line option --force pocketvina-dock command line option pocketvina-import-legacy command line option pocketvina-setup-p2rank command line option --format pocketvina-dock command line option pocketvina-export command line option --from pocketvina-setup-p2rank command line option --gpu pocketvina-bench-gpu command line option --gpus pocketvina-dock command line option --gzip-level pocketvina-dock command line option pocketvina-import-legacy command line option --json pocketvina-info command line option --ligand pocketvina-show command line option --ligand-prep pocketvina-bench-gpu command line option pocketvina-dock command line option --ligands pocketvina-bench-gpu command line option pocketvina-dock command line option --ligands-per-call pocketvina-dock command line option --mode pocketvina-show command line option --n-ligands pocketvina-bench-gpu command line option --no-posebusters pocketvina-dock command line option --num-modes pocketvina-dock command line option --out pocketvina-bench-gpu command line option pocketvina-dock command line option pocketvina-export command line option pocketvina-show command line option --overwrite pocketvina-bust command line option --p2rank-model pocketvina-bench-gpu command line option pocketvina-dock command line option --p2rank-threads pocketvina-dock command line option --pocket pocketvina-bench-gpu command line option pocketvina-show command line option

--pockets pocketvina-dock command line option --pockets-dir pocketvina-dock command line option --posebusters pocketvina-dock command line option --posebusters-workers pocketvina-dock command line option --procs pocketvina-bench-gpu command line option --procs-per-gpu pocketvina-dock command line option --protein pocketvina-bench-gpu command line option pocketvina-bust command line option pocketvina-export command line option pocketvina-query command line option pocketvina-show command line option --protein-list pocketvina-dock command line option --proteins pocketvina-dock command line option pocketvina-info command line option --quiet pocketvina command line option --results pocketvina-bust command line option pocketvina-export command line option pocketvina-import-legacy command line option pocketvina-info command line option pocketvina-query command line option pocketvina-show command line option --sample-interval pocketvina-bench-gpu command line option --seed pocketvina-bench-gpu command line option pocketvina-dock command line option --select pocketvina-bust command line option --smiles pocketvina-import-legacy command line option --split pocketvina-bench-gpu command line option --thread pocketvina-bench-gpu command line option pocketvina-dock command line option --timeouts pocketvina-bust command line option --tmp-dir pocketvina-bench-gpu command line option pocketvina-bust command line option pocketvina-dock command line option pocketvina-import-legacy command line option --top pocketvina-query command line option --top-k pocketvina-bust command line option --top-pockets pocketvina-dock command line option --verbose pocketvina command line option --version pocketvina command line option --vram-per-proc pocketvina-dock command line option --what pocketvina-export command line option --workers pocketvina-bust command line option -q pocketvina command line option -v pocketvina command line option

B

best_scores() (pocketvina.io.results.Results method) (pocketvina.main.PocketVinaGPU method)

bust() (pocketvina.selection.Selection method) bust_results() (in module pocketvina.bust)

C

check_java() (in module pocketvina.p2rank)

check_names() (in module pocketvina.bust) close() (pocketvina.io.results.Results method)

D

default_workers() (in module pocketvina.bust)

display() (pocketvina.viz.MolstarView method) duckdb() (pocketvina.io.results.Results method)

E

engine_path() (in module pocketvina.engine) ensure_p2rank() (in module pocketvina.p2rank)

execute_docking() (pocketvina.main.PocketVinaGPU method) export() (pocketvina.io.results.Results method) (pocketvina.selection.Selection method)

F

find_p2rank() (in module pocketvina.p2rank)

fitting_procs() (in module pocketvina.gpu)

G

GPU (class in pocketvina.gpu)

I

import_legacy() (in module pocketvina.io.importer)

index (pocketvina.gpu.GPU attribute)

J

JavaError

K

kernel_cache_dir() (in module pocketvina.engine)

L

ligand_idx() (pocketvina.io.results.Results method)

list_gpus() (in module pocketvina.gpu)

M

manifest() (pocketvina.io.results.Results method) memory_free_mib (pocketvina.gpu.GPU attribute) memory_total_mib (pocketvina.gpu.GPU attribute) module pocketvina.bust pocketvina.gpu pocketvina.io.results pocketvina.p2rank pocketvina.viz

MolstarView (class in pocketvina.viz)

N

name (pocketvina.gpu.GPU attribute) (pocketvina.selection.Selection property)

O

OUTPUT_DIR pocketvina-import-legacy command line option

P

p2rank_home() (in module pocketvina.p2rank) P2RankConfig (class in pocketvina.main) P2RankError P2RankProcessor (class in pocketvina.main) pairs() (pocketvina.io.results.Results method) plan_engine_slots() (in module pocketvina.pipeline) plan_slots() (in module pocketvina.gpu) PocketConfig (class in pocketvina.main) pocketvina command line option --quiet --verbose --version -q -v pocketvina-bench-gpu command line option --box --center --engine-timeout --gpu --ligand-prep --ligands --n-ligands --out --p2rank-model --pocket --procs --protein --sample-interval --seed --split --thread --tmp-dir pocketvina-bust command line option --config --overwrite --protein --results --select --timeouts --tmp-dir --top-k --workers pocketvina-dock command line option --batch-size --box --config --database-path --energy-range --engine-timeout --force --format --gpus --gzip-level --ligand-prep --ligands --ligands-per-call --no-posebusters --num-modes --out --p2rank-model --p2rank-threads --pockets --pockets-dir --posebusters --posebusters-workers --procs-per-gpu --protein-list --proteins --seed --thread --tmp-dir --top-pockets --vram-per-proc

pocketvina-export command line option --format --out --protein --results --what pocketvina-import-legacy command line option --force --gzip-level --results --smiles --tmp-dir OUTPUT_DIR pocketvina-info command line option --json --proteins --results pocketvina-query command line option --csv --protein --results --top SQL pocketvina-setup-p2rank command line option --check --dir --force --from pocketvina-show command line option --backend --ligand --mode --out --pocket --protein --results pocketvina.bust module pocketvina.gpu module pocketvina.io.results module pocketvina.p2rank module pocketvina.viz module PocketVinaConfig (class in pocketvina.main) PocketVinaGPU (class in pocketvina.main) pose_block() (pocketvina.io.results.Results method) pose_model() (pocketvina.io.results.Results method) posebusters() (pocketvina.io.results.Results method) posebusters_checks() (pocketvina.io.results.Results method) poses (pocketvina.selection.Selection property) process_file_list() (pocketvina.main.P2RankProcessor method) proteins() (pocketvina.io.results.Results method)

R

require_posebusters() (in module pocketvina.bust) resolve_tmp_dir() (in module pocketvina.engine)

Results (class in pocketvina.io.results) results() (pocketvina.main.PocketVinaGPU method) run_atlas() (in module pocketvina.pipeline)

S

save() (pocketvina.viz.MolstarView method) select() (pocketvina.io.results.Results method) (pocketvina.main.PocketVinaGPU method) select_gpus() (in module pocketvina.gpu) Selection (class in pocketvina.selection) show() (in module pocketvina.viz) (pocketvina.io.results.Results method) (pocketvina.main.PocketVinaGPU method) (pocketvina.selection.Selection method)

show_modes() (in module pocketvina.viz) SQL pocketvina-query command line option state_json() (pocketvina.viz.MolstarView method) structure() (pocketvina.io.results.Results method) structure_path() (pocketvina.io.results.Results method)

T

table() (in module pocketvina.viz) (pocketvina.io.results.Results method) to_combined_csv() (pocketvina.io.results.Results method)

to_html() (in module pocketvina.viz) (pocketvina.viz.MolstarView method) top_sdf() (pocketvina.io.results.Results method)

U

uuid (pocketvina.gpu.GPU attribute)