Public Member Functions
def	__init__ (self, ent, contact_d=5.0, contact_mode="aa")

def	view (self)

def	contact_mode (self)

def	contact_d (self)

def	chain_names (self)

def	interacting_chains (self)

def	contacts (self)

def	hr_contacts (self)

def	interface_residues (self)

def	hr_interface_residues (self)

def	GetChain (self, chain_name)

def	GetSequence (self, chain_name)

Data Fields
	contact_mode

Detailed Description

 Helper object for Contact-score computation

Definition at line 9 of file contact_score.py.

Constructor & Destructor Documentation

◆ init()

def __init__	(	self,
		ent,
		contact_d = `5.0`,
		contact_mode = `"aa"`
	)

Definition at line 12 of file contact_score.py.

Member Function Documentation

◆ chain_names()

def chain_names ( self )

 Chain names in :attr:`~view`

Names are sorted

:type: :class:`list` of :class:`str`

Definition at line 96 of file contact_score.py.

◆ contact_d()

def contact_d ( self )

 Pairwise distance of residues to be considered as contacts

Given at :class:`ContactScorer` construction

:type: :class:`float`

Definition at line 86 of file contact_score.py.

◆ contact_mode()

def contact_mode ( self )

 The contact mode

Can either be "aa", meaning that all atoms are considered to identify
contacts, or "repr" which only considers distances between
representative atoms. For peptides thats CB (CA for GLY), for
nucleotides thats C3'.

:type: :class:`str`

Definition at line 73 of file contact_score.py.

◆ contacts()

def contacts ( self )

 Interchain contacts

Organized as :class:`dict` with key (cname1, cname2) and values being
a set of tuples with the respective residue indices. 
cname1 < cname2 evaluates to True.

Definition at line 118 of file contact_score.py.

◆ GetChain()

def GetChain	(	self,
		chain_name
	)

 Get chain by name

:param chain_name: Chain in :attr:`~view`
:type chain_name: :class:`str`

Definition at line 165 of file contact_score.py.

◆ GetSequence()

def GetSequence	(	self,
		chain_name
	)

 Get sequence of chain

Returns sequence of specified chain as raw :class:`str`

:param chain_name: Chain in :attr:`~view`
:type chain_name: :class:`str`

Definition at line 176 of file contact_score.py.

◆ hr_contacts()

def hr_contacts ( self )

 Human readable interchain contacts

Human readable version of :attr:`~contacts`. Simple list with tuples
containing two strings specifying the residues in contact. Format:
<cname>.<rnum>.<ins_code>

Definition at line 130 of file contact_score.py.

◆ hr_interface_residues()

def hr_interface_residues ( self )

 Human readable interface residues

Human readable version of :attr:`interface_residues`. :class:`list` of
strings specifying the interface residues in format:
<cname>.<rnum>.<ins_code>

Definition at line 154 of file contact_score.py.

◆ interacting_chains()

def interacting_chains ( self )

 Pairs of chains in :attr:`~view` with at least one contact

:type: :class:`list` of :class:`tuples`

Definition at line 108 of file contact_score.py.

◆ interface_residues()

def interface_residues ( self )

 Interface residues

Residues in each chain that are in contact with any other chain.
Organized as :class:`dict` with key cname and values the respective
residue indices in a :class:`set`.

Definition at line 142 of file contact_score.py.

◆ view()

def view ( self )

 The structure depending on *contact_mode*

Full view in case of "aa", view that only contains representative
atoms in case of "repr".

:type: :class:`ost.mol.EntityView`

Definition at line 62 of file contact_score.py.

Field Documentation

◆ contact_mode

contact_mode

Definition at line 44 of file contact_score.py.

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

build-dev-doc/stage/lib64/python3.9/site-packages/ost/mol/alg/contact_score.py

Public Member Functions

Data Fields