FishingLure
Name | Parameter Description | Parameter Type | Parameter Default | Parameter Range |
---|---|---|---|---|
atom-type | Atom type to be consider in the evaluation: BB,SC,ALL | string | BB | 0-2 |
biassed | Use biassed or non biassed forcefield | bool | false | |
command | string | |||
config | Set a configuration file | path | ||
database-name | Set the mySQL database name | string | PepXDB | |
database-pass | Set the mySQL password | string | modelx | |
database-port | Set the mySQL database port | int | 3306 | |
database-server | Set the mySQL server | string | localhost | |
database-user | Set the mySQL username | string | modelx | |
excluded | File with excluded pdb from queries | path | ||
help | Show help screen | |||
max-threads | Set the maximum number of threads | int | 1 | |
output-dir | Set output directory | path | ||
output-file | Get Pdb file without dna | path | noDna.pdb | |
pdb | Set a PDB file | path | ||
pdb-dir | Set PDB directory | path | ||
renumber | Renumber the pdb | bool | false |
>modelx --command=FishingLure --pdb=FishingLure.pdb --fisher-mol=A --exclude-hook=B --hooks-length=6 --max-threads=12 --pep-mismatches=6 --contact-th=3 --cbeta-angles=10 --dubiety=0.5 --sections=37 --fit-threshold=1 --fit-level=1 --database-name=FishXDB --database-server=localhost --database-user=modelx --database-pass=modelx
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