MISA_preprocessor Class Reference

Public Attributes
	ifile
	idir
	pdir
	run_intervor
	vdir
	run_vorlume
	verbose
	p
	misa_id2misa_chain_ids

Constructions
def	__init__ (self, ifile, idir, pdir, run_intervor, vdir, run_vorlume, verbose, p)
	Default constructor. More...
def	run (self)
	Handle the parsing from the ifile\, from the vorlume and from the intervor data Parse intervor output data if –no_intervor, otherwise intervor ouput data are (re)computed. More...

Load Files
def	parse_txt (self)
	Parse the ifile file_specs[('6yla', 'b')] = [('A', 'H', 'heavy', 'heavychain'), ('A', 'L', 'light', 'lightchain') ('spike', 'E', 'rbd', 'rbm')... More...
def	process_spec_file_line (self, pdbfile_match, line, file_specs, pdb_id2path, bound_pdb_complexes, unbound_pdb_complexes)
	Extract the spec data from a line of the ifile. More...

Internal Methods
def	run_intervor_calculation (self, file_specs, bound_pdb_complexes, pdb_id2path)
	Run intervor on all bound PDB files. More...
def	run_vorlume_calculation (self, misa_id2intervor_partners, pdb_id2path)
	Run vorlume on all PDB files. More...
def	extract_misa_chain_ids (self, file_specs)
	Create a map between the MISA ids and the associated MISA Chain ids. More...
def	adapt_windows (self, windows)
	If the provided windows are provided with the MISA id instead of the MISA chain id\, attribute the window to every chain composing the MISA id. More...
def	valid_vorlume_complexes (self, file_specs, bound_pdb_complexes, unbound_pdb_complexes)
	Select only the complete complexes for the vorlume computation. More...
def	parse_intervor_output (self, bound_pdb_complexes, pdb_id2path)
	Parse intervor output in the idir directory. More...

Constructor & Destructor Documentation

__init__()

def __init__	(		self,
			ifile,
			idir,
			pdir,
			run_intervor,
			vdir,
			run_vorlume,
			verbose,
			p
	)

Default constructor.

Member Function Documentation

adapt_windows()

def adapt_windows	(		self,
			windows
	)

If the provided windows are provided with the MISA id instead of the MISA chain id\, attribute the window to every chain composing the MISA id.

extract_misa_chain_ids()

def extract_misa_chain_ids	(		self,
			file_specs
	)

Create a map between the MISA ids and the associated MISA Chain ids.

parse_intervor_output()

def parse_intervor_output	(		self,
			bound_pdb_complexes,
			pdb_id2path
	)

Parse intervor output in the idir directory.

parse_txt()

def parse_txt

(

self

)

Parse the ifile file_specs[('6yla', 'b')] = [('A', 'H', 'heavy', 'heavychain'), ('A', 'L', 'light', 'lightchain') ('spike', 'E', 'rbd', 'rbm')...

], with bound_status = 'b' (for 'bound') if there is more than one different intervor_partner (here 'spike' and 'A' on the corresponding line of ifile, and bound_status = 'u' otherwise. bound_pdb_complexes['6yla'] = {'antibody': 'HL', 'rbd' : 'E'},{'antibody': 'BC', 'rbd' : 'A'}... unbound_pdb_complexes['xxxx'] = [{'antibody': EF},{'antibody': LM}...] pdb_id2path['6lzg'] = '../data/pdb-data/6lzg.pdb' windows['rbd_0'] = (410, 523)

process_spec_file_line()

def process_spec_file_line	(		self,
			pdbfile_match,
			line,
			file_specs,
			pdb_id2path,
			bound_pdb_complexes,
			unbound_pdb_complexes
	)

Extract the spec data from a line of the ifile.

run()

def run

(

self

)

Handle the parsing from the ifile\, from the vorlume and from the intervor data Parse intervor output data if –no_intervor, otherwise intervor ouput data are (re)computed.

run_intervor_calculation()

def run_intervor_calculation	(		self,
			file_specs,
			bound_pdb_complexes,
			pdb_id2path
	)

Run intervor on all bound PDB files.

run_vorlume_calculation()

def run_vorlume_calculation	(		self,
			misa_id2intervor_partners,
			pdb_id2path
	)

Run vorlume on all PDB files.

valid_vorlume_complexes()

def valid_vorlume_complexes	(		self,
			file_specs,
			bound_pdb_complexes,
			unbound_pdb_complexes
	)

Select only the complete complexes for the vorlume computation.

Member Data Documentation

idir

idir

ifile

ifile

misa_id2misa_chain_ids

misa_id2misa_chain_ids

p

p

pdir

pdir

run_intervor

run_intervor

run_vorlume

run_vorlume

vdir

vdir

verbose

verbose