Index

Symbols

--address command line option --alphafold-3d-beacon command line option --blast-expect command line option, [1] --blast-gap-extend command line option, [1] --blast-gap-open command line option, [1] --blast-matrix command line option, [1] --blast-no-filter command line option, [1] --blast-no-gapped command line option, [1] --blast-report-limit command line option, [1] --blast-word-size command line option, [1] --clash-distance-cutoff command line option, [1] --config command line option, [1], [2], [3], [4] --context command line option --custom-dir command line option --db-dbname command line option, [1] --db-dir command line option, [1], [2] --db-host command line option, [1] --db-link-template command line option --db-password command line option, [1] --db-port command line option, [1] --db-user command line option, [1]

--help command line option, [1], [2], [3], [4] --ligands command line option, [1] --max-ligand-to-backbone-distance command line option, [1] --metadata-name-pattern command line option, [1] --min-alignment-length command line option, [1] --min-hsp-identity command line option, [1] --min-separation-distance command line option, [1] --no-daemon,-F command line option --pae-file command line option --pdb-dir command line option, [1], [2], [3] --pdb-fasta command line option, [1], [2] --pdb-name-pattern command line option, [1] --port command line option --quiet command line option, [1], [2], [3], [4] --structure-name-pattern command line option, [1] --threads command line option, [1], [2] --user command line option --verbose command line option, [1], [2], [3], [4] --version command line option, [1], [2], [3], [4] --yasara command line option -t command line option, [1], [2], [3]

A

address command line option

alphafold-3d-beacon command line option

B

blast-expect command line option blast-gap-extend command line option blast-gap-open command line option blast-matrix command line option

blast-no-filter command line option blast-no-gapped command line option blast-report-limit command line option blast-word-size command line option

C

clash-distance-cutoff command line option command line option --address --alphafold-3d-beacon --blast-expect, [1] --blast-gap-extend, [1] --blast-gap-open, [1] --blast-matrix, [1] --blast-no-filter, [1] --blast-no-gapped, [1] --blast-report-limit, [1] --blast-word-size, [1] --clash-distance-cutoff, [1] --config, [1], [2], [3], [4] --context --custom-dir --db-dbname, [1] --db-dir, [1], [2] --db-host, [1] --db-link-template --db-password, [1] --db-port, [1] --db-user, [1] --help, [1], [2], [3], [4] --ligands, [1] --max-ligand-to-backbone-distance, [1] --metadata-name-pattern, [1] --min-alignment-length, [1] --min-hsp-identity, [1] --min-separation-distance, [1] --no-daemon,-F --pae-file --pdb-dir, [1], [2], [3] --pdb-fasta, [1], [2] --pdb-name-pattern, [1] --port --quiet, [1], [2], [3], [4] --structure-name-pattern, [1] --threads, [1], [2] --user --verbose, [1], [2], [3], [4] --version, [1], [2], [3], [4] --yasara -t, [1], [2], [3] address alphafold-3d-beacon blast-expect blast-gap-extend blast-gap-open blast-matrix blast-no-filter blast-no-gapped blast-report-limit blast-word-size clash-distance-cutoff context custom-dir db-dbname db-dir db-host db-link-template db-password db-port db-user ligands max-ligand-to-backbone-distance metadata-name-pattern min-alignment-length min-hsp-identity min-separation-distance pdb-dir pdb-fasta pdb-name-pattern port structure-name-pattern threads user yasara

context command line option custom-dir command line option

D

db-dbname command line option db-dir command line option db-host command line option db-link-template command line option

db-password command line option db-port command line option db-user command line option

L

ligands command line option

M

max-ligand-to-backbone-distance command line option metadata-name-pattern command line option min-alignment-length command line option

min-hsp-identity command line option min-separation-distance command line option

P

pdb-dir command line option pdb-fasta command line option

pdb-name-pattern command line option port command line option

S

structure-name-pattern command line option

T

threads command line option

U

user command line option

Y

yasara command line option