relax_starting_structure Namespace Reference

Functions
def	main

Variables
list	relax_commands
tuple	parser = argparse.ArgumentParser(description="Relax an experimental structure in preparation for ddG predictions")
tuple	args = parser.parse_args()

Function Documentation

def relax_starting_structure.main

(

args

)

References utility::options::OptionKeys::options.exit, ObjexxFCL.len(), basic::database.open(), and basic::options::OptionKeys::relax::range.range.

Variable Documentation

tuple relax_starting_structure.args = parser.parse_args()

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

list relax_starting_structure.relax_commands

Initial value:

= [
'minimize_with_cst -ignore_zero_occupancy false  -in:file:l ../input_lists/input_1.txt  -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 -restore_talaris_behavior',

'minimize_with_cst -ignore_zero_occupancy false  -in:file:l ../input_lists/input_2.txt  -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 -restore_talaris_behavior',

'minimize_with_cst -ignore_zero_occupancy false  -in:file:l ../input_lists/input_3.txt  -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 -restore_talaris_behavior',

'minimize_with_cst -ignore_zero_occupancy false  -in:file:l ../input_lists/input_4.txt  -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 -restore_talaris_behavior',

'minimize_with_cst -ignore_zero_occupancy false  -in:file:l ../input_lists/input_5.txt  -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 -restore_talaris_behavior',

'minimize_with_cst -ignore_zero_occupancy false  -in:file:l ../input_lists/input_6.txt  -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 -restore_talaris_behavior',

'minimize_with_cst -ignore_zero_occupancy false  -in:file:l ../input_lists/input_7.txt  -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 -restore_talaris_behavior',

'minimize_with_cst -ignore_zero_occupancy false  -in:file:l ../input_lists/input_8.txt  -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 -restore_talaris_behavior',

'rnp_ddg -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 -restore_talaris_behavior > relax_1.log',

'rnp_ddg -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 -restore_talaris_behavior > relax_2.log' 
]