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)

Definition at line 544 of file calccontacts.py.

Constructor & Destructor Documentation

def calccontacts.contactProtein.__init__	(	self,
		mode
	)

Definition at line 551 of file calccontacts.py.

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)

Definition at line 583 of file calccontacts.py.

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

Referenced by calccontacts.contactProtein.initContactProfile().

def calccontacts.contactProtein.find_contacts	(	self,
		parserule
	)

Definition at line 559 of file calccontacts.py.

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

def calccontacts.contactProtein.initContactProfile ( self )

Definition at line 577 of file calccontacts.py.

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

def calccontacts.contactProtein.initializePDB	(	self,
		PDBfile
	)

Definition at line 556 of file calccontacts.py.

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

Definition at line 591 of file calccontacts.py.

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)

Definition at line 621 of file calccontacts.py.

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