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

Constructor

def __init__ (self, fname)
 init More...
 

Loading MCI Specification

def __read_vertextypes_from_file__ (self, fhandle)
 Read vertex labels from input file assuming that the labels are given between a 'BEGIN-TYPES' tag and a 'END-TYPES' tag. More...
 
def __read_oligomers_from_file__ (self, fhandle)
 Read oligomers from input file assuming that the sets are given between a 'BEGIN-OLIGOMERS' tag and a 'END-OLIGOMERS' tag. More...
 
def __read_annotated_contacts_from_file__ (self, fhandle, unweighted)
 Read annotated contacts given in the input spec file Labels: F (Forbidden), E (Enforced), P (Possible, default) Weights: a floating point number in the interval [0,1], default: 1 Annotated contact havel both label (default, P) and weight (default, 0.5) More...
 
def read_MCI_spec_from_input_file (self, unweighted)
 read_MCI_spec_from_input_file More...
 

Accessors / Modifiers

def get_vertices (self)
 get_vertices More...
 
def get_oligomers (self)
 Returns oligomers, which is object of the class MCI_oligomers. More...
 
def get_pool_of_contacts_explored (self)
 Returns the set of pool of contacts from which algorithm chooses the contacts. More...
 
def get_annotated_contacts (self)
 Returns annotated contacts, which is object of the class MCI_set_of_contacts. More...
 
def set_annotated_contact (self, contact)
 Set contact label or weight if contact is already present then update weight and/or label else add the contact. More...
 
def update_vertices (self, vertices)
 update_vertices More...
 
def update_oligomers (self, key, oligomer)
 update_oligomers More...
 

Detailed Description

A class to specify the input of a connectivity inference problem.

This class specifies the input of a connectivity inference problem, as a set of vertices and oligomers. The oligomers are object instance of the class MCI_oligomers. xfc: make the labels and weights available from this class

Constructor & Destructor Documentation

◆ __init__()

def __init__ (   self,
  fname 
)

init

Member Function Documentation

◆ __read_annotated_contacts_from_file__()

def __read_annotated_contacts_from_file__ (   self,
  fhandle,
  unweighted 
)

Read annotated contacts given in the input spec file Labels: F (Forbidden), E (Enforced), P (Possible, default) Weights: a floating point number in the interval [0,1], default: 1 Annotated contact havel both label (default, P) and weight (default, 0.5)

◆ __read_oligomers_from_file__()

def __read_oligomers_from_file__ (   self,
  fhandle 
)

Read oligomers from input file assuming that the sets are given between a 'BEGIN-OLIGOMERS' tag and a 'END-OLIGOMERS' tag.

Example: BEGIN-OLIGOMERS Csn1 Csn2 Csn3 Csn4 Csn6 Csn7 Csn8 Csn1 Csn3 Csn4 Csn5 Csn6 Csn7 Csn8 ... Csn4 Csn6 Csn7 Csn3 Csn8 END-OLIGOMERS

◆ __read_vertextypes_from_file__()

def __read_vertextypes_from_file__ (   self,
  fhandle 
)

Read vertex labels from input file assuming that the labels are given between a 'BEGIN-TYPES' tag and a 'END-TYPES' tag.

Example: BEGIN-TYPES Csn1 Csn2 Csn3 Csn4 Csn5 Csn6 Csn7 Csn8 END-TYPES

◆ get_annotated_contacts()

def get_annotated_contacts (   self)

Returns annotated contacts, which is object of the class MCI_set_of_contacts.

◆ get_oligomers()

def get_oligomers (   self)

Returns oligomers, which is object of the class MCI_oligomers.

◆ get_pool_of_contacts_explored()

def get_pool_of_contacts_explored (   self)

Returns the set of pool of contacts from which algorithm chooses the contacts.

◆ get_vertices()

def get_vertices (   self)

get_vertices

◆ read_MCI_spec_from_input_file()

def read_MCI_spec_from_input_file (   self,
  unweighted 
)

read_MCI_spec_from_input_file

◆ set_annotated_contact()

def set_annotated_contact (   self,
  contact 
)

Set contact label or weight if contact is already present then update weight and/or label else add the contact.

◆ update_oligomers()

def update_oligomers (   self,
  key,
  oligomer 
)

update_oligomers

◆ update_vertices()

def update_vertices (   self,
  vertices 
)

update_vertices