Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
Label_selector Class Reference

Public Member Functions

def __init__ (self, cradle_utils_label_selection_options)
 
def build_state_map (self)
 
def run (self)
 

Public Attributes

 m_options
 

Static Public Attributes

string path1 = './lrmsd_matrices/'
 Step 1 : write rmsd distance matrix per subdomain per state in a folder. More...
 
 state_map
 
 writer_1_options = Cradle_utils_label_selection_options(self.m_options.m_idir, self.m_options.m_pdbfiles, self.m_options.m_pdb_info, self.m_options.m_state_map_file, self.m_options.m_spec_files)
 
 writer_1 = Write_Matrix_per_label(writer_1_options, self.state_map, path1)
 
string path2 = './lrmsd_stat/'
 Step 2 : write lrmsd statistics (lrmsd average, median, std, min and max) intra- and inter-state. More...
 
 writer_2 = Stat_per_label(path1, path2)
 
 writer_3_options = Cradle_utils_label_selection_options(self.m_options.m_idir, self.m_options.m_pdbfiles, self.m_options.m_pdb_info, self.m_options.m_state_map_file, self.m_options.m_spec_files)
 Step 3 : compute mean displacement per subdomain from bfactor. More...
 
 writer_3 = Get_Mean_Displacement(writer_3_options, path2)
 
 selector_1 = Subdomain_Selector_1(path2)
 Step 4 : write summary table comparing mean displacement to lrmsd per subdomain intra and inter-state. More...
 

Detailed Description

Selection of subdomains which are dynamic, see paper The selection of dynamic subdomains hinges on 4 steps 1) Compute RMSDcomb for specifed subdomains 2) write statistics of RMSDcomb per subdomain intra- and inter-states 3) compute mean displacement per subdomain 4) Write table comparing mean displacement to lrmsd per subdomain intra- and inter-states.

Constructor & Destructor Documentation

◆ __init__()

def __init__ (   self,
  cradle_utils_label_selection_options 
)

Member Function Documentation

◆ build_state_map()

def build_state_map (   self)

◆ run()

def run (   self)

Member Data Documentation

◆ m_options

m_options

◆ path1

string path1 = './lrmsd_matrices/'
static

Step 1 : write rmsd distance matrix per subdomain per state in a folder.

◆ path2

string path2 = './lrmsd_stat/'
static

Step 2 : write lrmsd statistics (lrmsd average, median, std, min and max) intra- and inter-state.

◆ selector_1

selector_1 = Subdomain_Selector_1(path2)
static

Step 4 : write summary table comparing mean displacement to lrmsd per subdomain intra and inter-state.

◆ state_map

state_map
static

◆ writer_1

writer_1 = Write_Matrix_per_label(writer_1_options, self.state_map, path1)
static

◆ writer_1_options

writer_1_options = Cradle_utils_label_selection_options(self.m_options.m_idir, self.m_options.m_pdbfiles, self.m_options.m_pdb_info, self.m_options.m_state_map_file, self.m_options.m_spec_files)
static

◆ writer_2

writer_2 = Stat_per_label(path1, path2)
static

◆ writer_3

◆ writer_3_options

writer_3_options = Cradle_utils_label_selection_options(self.m_options.m_idir, self.m_options.m_pdbfiles, self.m_options.m_pdb_info, self.m_options.m_state_map_file, self.m_options.m_spec_files)
static

Step 3 : compute mean displacement per subdomain from bfactor.