QSEntity Class Reference

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

Data Fields
	chain_names
	contact_d

Protected Attributes
	_view
	_contact_d
	_chain_names
	_interacting_chains
	_sequence
	_pos
	_pair_dist
	_min_pos
	_max_pos

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__()

__init__	(		self,
			ent,
			contact_d = 12.0
	)

Definition at line 20 of file qsscore.py.

Member Function Documentation

chain_names()

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()

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()

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()

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()

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()

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()

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()

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()

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()

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()

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.

Field Documentation

_chain_names

_chain_names

protected

Definition at line 27 of file qsscore.py.

_contact_d

_contact_d

protected

Definition at line 24 of file qsscore.py.

_interacting_chains

_interacting_chains

protected

Definition at line 28 of file qsscore.py.

_max_pos

_max_pos

protected

Definition at line 35 of file qsscore.py.

_min_pos

_min_pos

protected

Definition at line 34 of file qsscore.py.

_pair_dist

_pair_dist

protected

Definition at line 31 of file qsscore.py.

_pos

_pos

protected

Definition at line 30 of file qsscore.py.

_sequence

_sequence

protected

Definition at line 29 of file qsscore.py.

_view

_view

protected

Definition at line 23 of file qsscore.py.

chain_names

chain_names

Definition at line 78 of file qsscore.py.

contact_d

contact_d

Definition at line 80 of file qsscore.py.

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

• build-dev/stage/lib64/python3.11/site-packages/ost/mol/alg/qsscore.py