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

Public Attributes

 verbose
 
 pdb_id2path
 
 adir
 
 old2new
 
 new2old
 
 new_resids
 

Constructions

def __init__ (self, verbose, pdb_id2path, adir)
 Default constructor. More...
 

Basic Statistics

Compute mapping from the old index to the new index

def get_dic_sequence (self, pdbfile, chain_name)
 Return the original numbering of a chain according to the PDB file. More...
 
def process_id (self, chain_name)
 Extract the tag\, the pdbid and the chain from the complete chain name. More...
 
def compute_mapping (self, MISA_id)
 Compute the mapping between the original index of each chain and its new index according to the MSA. More...
 
def compute_MSA (self, MISA_id, chains_to_map)
 Compute the MSA using Clustal Omega. More...
 
def create_FASTA (self, MISA_id, chains_to_map)
 Create a FASTA file from the sequence of each chain to align. More...
 
def call_to_clustalo (self, MISA_id)
 Call Clustal Omega on the FASTA files from all the chains from the MISA id. More...
 

Detailed Description

Realign homologous chains with a different numbering. Compute or read the MSA and compute reindexing of the chains after realignment.

Constructor & Destructor Documentation

◆ __init__()

def __init__ (   self,
  verbose,
  pdb_id2path,
  adir 
)

Default constructor.

Member Function Documentation

◆ call_to_clustalo()

def call_to_clustalo (   self,
  MISA_id 
)

Call Clustal Omega on the FASTA files from all the chains from the MISA id.

◆ compute_mapping()

def compute_mapping (   self,
  MISA_id 
)

Compute the mapping between the original index of each chain and its new index according to the MSA.

◆ compute_MSA()

def compute_MSA (   self,
  MISA_id,
  chains_to_map 
)

Compute the MSA using Clustal Omega.

◆ create_FASTA()

def create_FASTA (   self,
  MISA_id,
  chains_to_map 
)

Create a FASTA file from the sequence of each chain to align.

◆ get_dic_sequence()

def get_dic_sequence (   self,
  pdbfile,
  chain_name 
)

Return the original numbering of a chain according to the PDB file.

◆ process_id()

def process_id (   self,
  chain_name 
)

Extract the tag\, the pdbid and the chain from the complete chain name.

Member Data Documentation

◆ adir

adir

◆ new2old

new2old

◆ new_resids

new_resids

◆ old2new

old2new

◆ pdb_id2path

pdb_id2path

◆ verbose

verbose