QSEntity Class Reference

Public Member Functions
def	__init__ (self, ent, contact_d=12.0)
def	view (self)
def	contact_d (self)
def	chain_names (self)
def	interacting_chains (self)
def	GetChain (self, chain_name)
def	GetSequence (self, chain_name)
def	GetPos (self, chain_name)
def	PairDist (self, chain_name_one, chain_name_two)
def	GetMinPos (self, chain_name)
def	GetMaxPos (self, chain_name)
def	PotentialInteraction (self, chain_name_one, chain_name_two)

Detailed Description

 Helper object for QS-score computation

Holds structural information and getters for interacting chains, i.e.
interfaces. Peptide residues are represented by their CB position
(CA for GLY) and nucleotides by C3'.

:param ent: Structure for QS score computation
:type ent: :class:`ost.mol.EntityView`/:class:`ost.mol.EntityHandle`
:param contact_d: Pairwise distance of residues to be considered as contacts
:type contact_d: :class:`float`

Definition at line 8 of file qsscore.py.

Constructor & Destructor Documentation

__init__()

def __init__	(		self,
			ent,
			contact_d = 12.0
	)

Definition at line 20 of file qsscore.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 59 of file qsscore.py.

contact_d()

def contact_d

(

self

)

 Pairwise distance of residues to be considered as contacts

Given at :class:`QSEntity` construction

:type: :class:`float`

Definition at line 49 of file qsscore.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 84 of file qsscore.py.

GetMaxPos()

def GetMaxPos	(		self,
			chain_name
	)

 Get max x,y,z cooridnates for given chain

Based on positions that are extracted with GetPos

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

Definition at line 154 of file qsscore.py.

GetMinPos()

def GetMinPos	(		self,
			chain_name
	)

 Get min x,y,z cooridnates for given chain

Based on positions that are extracted with GetPos

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

Definition at line 142 of file qsscore.py.

GetPos()

def GetPos	(		self,
			chain_name
	)

 Get representative positions of chain

That's CB positions for peptide residues (CA for GLY) and C3' for
nucleotides. Returns positions as a numpy array of shape
(n_residues, 3).

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

Definition at line 109 of file qsscore.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 95 of file qsscore.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 71 of file qsscore.py.

PairDist()

def PairDist	(		self,
			chain_name_one,
			chain_name_two
	)

 Get pairwise distances between two chains

Returns distances as numpy array of shape (a, b).
Where a is the number of residues of the chain that comes BEFORE the
other in :attr:`~chain_names` 

Definition at line 127 of file qsscore.py.

PotentialInteraction()

def PotentialInteraction	(		self,
			chain_name_one,
			chain_name_two
	)

 Returns True if chains potentially interact

Based on crude collision detection. There is no guarantee
that they actually interact if True is returned. However,
if False is returned, they don't interact for sure.

:param chain_name_one: Chain in :attr:`~view`
:type chain_name_one: class:`str`
:param chain_name_two: Chain in :attr:`~view`
:type chain_name_two: class:`str`

Definition at line 166 of file qsscore.py.

view()

def view

(

self

)

 Processed structure

View that only contains representative atoms. That's CB for peptide
residues (CA for GLY) and C3' for nucleotides.

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

Definition at line 38 of file qsscore.py.

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

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