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

Main class which compute and store the MISA. More...

Public Attributes

 chain_instances
 
 interface_oneside
 
 interface_string
 
 interface_pool
 
 need_MSA
 
 residue_mapping
 
 odir
 
 verbose
 
 coloring_value
 
 header
 

Constructions

def __init__ (self, MISA_id, prefix, verbose, pdir, odir, adir, need_MSA, pdb_id2path, windows=None)
 Default constructor. More...
 
def initialize_header (self, MISA_id, prefix, windows)
 The header contains all the metadata of the chains. More...
 
def add_chain (self, spec, bound_status, pdbid, pdbfile)
 Update the header and the Interface Oneside. More...
 
def update_header (self, bound_status, pdbid, spec, pdbfile)
 Add the metadata of the chain to the header. More...
 
def update_extreme_indexes (self, min_id, max_id)
 Record the extreme resids at the interface among all the chains of the MISA. More...
 

Internal Methods

def apply_windows (self)
 Compute the extreme indexes which are the minimum from the minimum index of each chain and the maximum of the maximum index of each chain. More...
 
def remove_chain_from_MISA (self, chain_name)
 Remove one chain by its name from the MISA. More...
 
def create_one_istring (self, chain_name)
 Compute what character to display at each position of each Istring. More...
 
def compute_mapping_no_MSA (self)
 In the absence of an MSA\, trivial alignment is applied so that the same operating pipeline can be applied in both cases (with and without MSA) More...
 
def compute_mapping_MSA (self)
 Computes the mapping for each chain between the index of its residues in the MSA and the index in the PDB file. More...
 
def map_windows_no_MSA (self)
 For sequences that do not require a MSA\, we map the windows to the new numbering and thus taking into account the insertion codes. More...
 
def apply_windows (self)
 Filter the residues to be displayed\, to only keep the residues included in a windows or if no windows was provided\, those included in the extreme indexes of the interface. More...
 
def create_all_istring (self)
 Handle the call to the Istring constructor for each chain. More...
 
def record_interfaces (self)
 Record the interface of every chain in a text file. More...
 
def process (self)
 Main function which processes the MISA. More...
 

Detailed Description

Main class which compute and store the MISA.

Collection of Chain Instances, Interface Strings, Interface Pool and Interface Oneside. Main class which compute and store the MISA.

Constructor & Destructor Documentation

◆ __init__()

def __init__ (   self,
  MISA_id,
  prefix,
  verbose,
  pdir,
  odir,
  adir,
  need_MSA,
  pdb_id2path,
  windows = None 
)

Default constructor.

Member Function Documentation

◆ add_chain()

def add_chain (   self,
  spec,
  bound_status,
  pdbid,
  pdbfile 
)

Update the header and the Interface Oneside.

◆ apply_windows() [1/2]

def apply_windows (   self)

Compute the extreme indexes which are the minimum from the minimum index of each chain and the maximum of the maximum index of each chain.

◆ apply_windows() [2/2]

def apply_windows (   self)

Filter the residues to be displayed\, to only keep the residues included in a windows or if no windows was provided\, those included in the extreme indexes of the interface.

◆ compute_mapping_MSA()

def compute_mapping_MSA (   self)

Computes the mapping for each chain between the index of its residues in the MSA and the index in the PDB file.

◆ compute_mapping_no_MSA()

def compute_mapping_no_MSA (   self)

In the absence of an MSA\, trivial alignment is applied so that the same operating pipeline can be applied in both cases (with and without MSA)

◆ create_all_istring()

def create_all_istring (   self)

Handle the call to the Istring constructor for each chain.

◆ create_one_istring()

def create_one_istring (   self,
  chain_name 
)

Compute what character to display at each position of each Istring.

◆ initialize_header()

def initialize_header (   self,
  MISA_id,
  prefix,
  windows 
)

The header contains all the metadata of the chains.

◆ map_windows_no_MSA()

def map_windows_no_MSA (   self)

For sequences that do not require a MSA\, we map the windows to the new numbering and thus taking into account the insertion codes.

◆ process()

def process (   self)

Main function which processes the MISA.

◆ record_interfaces()

def record_interfaces (   self)

Record the interface of every chain in a text file.

◆ remove_chain_from_MISA()

def remove_chain_from_MISA (   self,
  chain_name 
)

Remove one chain by its name from the MISA.

◆ update_extreme_indexes()

def update_extreme_indexes (   self,
  min_id,
  max_id 
)

Record the extreme resids at the interface among all the chains of the MISA.

◆ update_header()

def update_header (   self,
  bound_status,
  pdbid,
  spec,
  pdbfile 
)

Add the metadata of the chain to the header.

Member Data Documentation

◆ chain_instances

chain_instances

◆ coloring_value

coloring_value

◆ header

header

◆ interface_oneside

interface_oneside

◆ interface_pool

interface_pool

◆ interface_string

interface_string

◆ need_MSA

need_MSA

◆ odir

odir

◆ residue_mapping

residue_mapping

◆ verbose

verbose