relax_starting_structure Namespace Reference

Functions
def	main (args)

Variables
list	relax_commands
	parser = argparse.ArgumentParser(description="Relax an experimental structure in preparation for ddG predictions")
	type
	str
	default
	help
	action
	False
	args = parser.parse_args()
	int

Function Documentation

main()

def relax_starting_structure.main

(

args

)

References utility::options::OptionKeys::options.exit, join(), basic::database.open(), range, and str.

Variable Documentation

action

relax_starting_structure.action

args

relax_starting_structure.args = parser.parse_args()

default

relax_starting_structure.default

False

relax_starting_structure.False

help

relax_starting_structure.help

int

relax_starting_structure.int

parser

relax_starting_structure.parser = argparse.ArgumentParser(description="Relax an experimental structure in preparation for ddG predictions")

relax_commands

list relax_starting_structure.relax_commands

Initial value:

=  [
'minimize_with_cst -ignore_zero_occupancy false  -in:file:s ../../START_STRUCT_PREF.pdb  -score:weights SFXN  -ddg:out_pdb_prefix min1  -in:file:fullatom  -ddg::constraint_weight 1.0  -ddg::cst_dist_cutoff 15.0   -ddg::sc_min_only false',
 
'minimize_with_cst -ignore_zero_occupancy false  -in:file:s min1.START_STRUCT_PREF_0001.pdb  -score:weights SFXN  -ddg:out_pdb_prefix min2  -in:file:fullatom  -ddg::constraint_weight 0.8  -ddg::cst_dist_cutoff 15.0   -ddg::sc_min_only false',
 
'minimize_with_cst -ignore_zero_occupancy false  -in:file:s min2.min1_0001.pdb  -score:weights SFXN  -ddg:out_pdb_prefix min3  -in:file:fullatom  -ddg::constraint_weight 0.6  -ddg::cst_dist_cutoff 15.0   -ddg::sc_min_only false',
 
'minimize_with_cst -ignore_zero_occupancy false  -in:file:s min3.min2_0001.pdb  -score:weights SFXN  -ddg:out_pdb_prefix min4  -in:file:fullatom  -ddg::constraint_weight 0.4  -ddg::cst_dist_cutoff 15.0   -ddg::sc_min_only false',
 
'minimize_with_cst -ignore_zero_occupancy false  -in:file:s min4.min3_0001.pdb  -score:weights SFXN  -ddg:out_pdb_prefix min5  -in:file:fullatom  -ddg::constraint_weight 0.2  -ddg::cst_dist_cutoff 15.0   -ddg::sc_min_only false',
 
'minimize_with_cst -ignore_zero_occupancy false  -in:file:s min5.min4_0001.pdb  -score:weights SFXN  -ddg:out_pdb_prefix min6  -in:file:fullatom  -ddg::constraint_weight 0.1  -ddg::cst_dist_cutoff 15.0   -ddg::sc_min_only false',
 
'minimize_with_cst -ignore_zero_occupancy false  -in:file:s min6.min5_0001.pdb  -score:weights SFXN  -ddg:out_pdb_prefix min7  -in:file:fullatom  -ddg::constraint_weight 0.05  -ddg::cst_dist_cutoff 15.0   -ddg::sc_min_only false',
 
'minimize_with_cst -ignore_zero_occupancy false  -in:file:s min7.min6_0001.pdb  -score:weights SFXN  -ddg:out_pdb_prefix min8  -in:file:fullatom  -ddg::constraint_weight 0.0  -ddg::cst_dist_cutoff 15.0   -ddg::sc_min_only false',
 
'mutate_and_score_RNP -ignore_zero_occupancy false -s min8.min7_0001.pdb -score:weights SFXN -move_backbone true -move_protein_backbone true -out_prefix min_START_STRUCT_PREF_ -relax_cutoff_dist 200.0 -min_jumps true -protein_pack_reps 0 > relax_1.log',
 
'mutate_and_score_RNP -ignore_zero_occupancy false -s min_START_STRUCT_PREF_wildtype_bound.pdb -score:weights SFXN -move_backbone true -move_protein_backbone true -out_prefix min_again_START_STRUCT_PREF_ -relax_cutoff_dist 200.0 -min_jumps true -protein_pack_reps 0 > relax_2.log' 
]

str

relax_starting_structure.str

Referenced by main().

type

relax_starting_structure.type