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Functions | Variables
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)

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:
1 = [
2 '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',
3 
4 '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',
5 
6 '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',
7 
8 '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',
9 
10 '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',
11 
12 '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',
13 
14 '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',
15 
16 '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',
17 
18 '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',
19 
20 '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'
21 ]