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

Internal Methods
	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.
	remove_chain_from_MISA (self, chain_name)
	Remove one chain by its name from the MISA.
	create_one_istring (self, chain_name)
	Compute what character to display at each position of each Istring.
	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)
	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.
	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.
	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.
	create_all_istring (self)
	Handle the call to the Istring constructor for each chain.
	record_interfaces (self)
	Record the interface of every chain in a text file.
	process (self)
	Main function which processes the MISA.

Detailed Description

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

Constructor & Destructor Documentation

◆ init()

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

Default constructor.

Member Function Documentation

◆ add_chain()

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

Update the header and the Interface Oneside.

◆ apply_windows() [1/2]

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]

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()

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()

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()

create_all_istring ( self )

Handle the call to the Istring constructor for each chain.

◆ create_one_istring()

create_one_istring	(		self,
			chain_name )

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

◆ initialize_header()

initialize_header	(	self,
		MISA_id,
		prefix,
		windows )

The header contains all the metadata of the chains.

◆ map_windows_no_MSA()

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()

process ( self )

Main function which processes the MISA.

◆ record_interfaces()

record_interfaces ( self )

Record the interface of every chain in a text file.

◆ remove_chain_from_MISA()

remove_chain_from_MISA	(		self,
			chain_name )

Remove one chain by its name from the MISA.

◆ update_extreme_indexes()

update_extreme_indexes	(	self,
		min_id,
		max_id )

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

◆ update_header()

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

Add the metadata of the chain to the header.

Constructions

Internal Methods