calccontacts.contactProtein Class Reference

Public Member Functions
def	__init__
def	initializePDB
def	find_contacts
def	initContactProfile
def	convert_to_shell
def	outputMap
def	outputProfile

Public Attributes
	mode
	contactPDB
	contactMap

Detailed Description

The contactProtein class contains information about the protein's contacts
in two forms:
list of contacts
contact profile (contacts by residue)

Constructor & Destructor Documentation

def calccontacts.contactProtein.__init__	(		self,
			mode
	)

Member Function Documentation

def calccontacts.contactProtein.convert_to_shell

(

self

)

convert from contact profile format (list of residue contacts for each
residue) to shell format (list of atoms in the atomic shell of a given
residue)

References calccontacts.contactProtein.contactPDB, and calccontacts.makeShellProfile().

Referenced by calccontacts.contactProtein.initContactProfile().

def calccontacts.contactProtein.find_contacts	(		self,
			parserule
	)

References loadPDB.addIndices(), calccontacts.contactProtein.contactPDB, calccontacts.makeContactPDB(), calccontacts.parse_and_pair(), and loadPDB.popLigands().

def calccontacts.contactProtein.initContactProfile

(

self

)

References calccontacts.contactProtein.contactMap, calccontacts.contactProtein.contactPDB, calccontacts.contactProtein.convert_to_shell(), calccontacts.makeContactProfile(), and calccontacts.contactProtein.mode.

def calccontacts.contactProtein.initializePDB	(		self,
			PDBfile
	)

References calccontacts.contactProtein.contactPDB, and loadPDB.loadProt().

def calccontacts.contactProtein.outputMap	(		self,
			dest,
			PDBfile
	)

Output method to either print contacts or write them to a file
dest = 'print' outputs the contact map to the screen
dest = 'file' outputs the contact map to a file

References calccontacts.contactProtein.contactMap, and basic::database.open().

def calccontacts.contactProtein.outputProfile	(		self,
			dest,
			PDBfile
	)

Output method to print contact profile or write them to a file.
Number of contacts and hbonds for each residue
equivalent to find_interface.pl in interface mode
dest = 'print' sends the output to the screen
dest = 'file sends the output to a file (pdb.contactprofile)

References calccontacts.contactProtein.contactPDB, and basic::database.open().

Member Data Documentation

calccontacts.contactProtein.contactMap

Referenced by calccontacts.contactProtein.initContactProfile(), and calccontacts.contactProtein.outputMap().

calccontacts.contactProtein.contactPDB

Referenced by calccontacts.contactProtein.convert_to_shell(), calccontacts.contactProtein.find_contacts(), calccontacts.contactProtein.initContactProfile(), calccontacts.contactProtein.initializePDB(), and calccontacts.contactProtein.outputProfile().

calccontacts.contactProtein.mode

Referenced by calccontacts.contactProtein.initContactProfile().

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The documentation for this class was generated from the following file:

• src/python/bindings/app/surface_docking/post_processing/pdb_objects/calccontacts.py