Residue_mapping Class Reference

Constructions
	__init__ (self, verbose, pdb_id2path, adir)
	Default constructor.

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

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__()

__init__	(		self,
			verbose,
			pdb_id2path,
			adir )

Default constructor.

Member Function Documentation

call_to_clustalo()

call_to_clustalo	(		self,
			MISA_id )

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

compute_mapping()

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()

compute_MSA	(		self,
			MISA_id,
			chains_to_map )

Compute the MSA using Clustal Omega.

create_FASTA()

create_FASTA	(		self,
			MISA_id,
			chains_to_map )

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

get_dic_sequence()

get_dic_sequence	(		self,
			pdbfile,
			chain_name )

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

process_id()

process_id	(		self,
			chain_name )

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