Public Member Functions
	__init__ (self, target, chem_groups, model, alns, contact_mode="aa", contact_d=5.0)

	cent1 (self)

	chem_groups (self)

	cent2 (self)

	alns (self)

	ScoreICS (self, mapping, check=True)

	ScoreICSInterface (self, trg_ch1, trg_ch2, mdl_ch1, mdl_ch2)

	ICSFromFlatMapping (self, flat_mapping)

	ScoreIPS (self, mapping, check=True)

	ScoreIPSInterface (self, trg_ch1, trg_ch2, mdl_ch1, mdl_ch2)

	IPSFromFlatMapping (self, flat_mapping)

Static Public Member Functions
	FromMappingResult (mapping_result, contact_mode="aa", contact_d=5.0)

Data Fields
	chem_groups

Protected Member Functions
	_MappedInterfaceScores (self, int1, int2)

	_InterfaceScores (self, int1, int2)

	_MappedSCScores (self, ref_ch, mdl_ch)

	_SCScores (self, ch1, ch2)

Protected Attributes
	_cent1

	_chem_groups

	_cent2

	_alns

	_mapped_cache_interface

	_mapped_cache_sc

Detailed Description

 Helper object to compute Contact scores

Tightly integrated into the mechanisms from the chain_mapping module.
The prefered way to derive an object of type :class:`ContactScorer` is
through the static constructor: :func:`~FromMappingResult`.

Usage is the same as for :class:`ost.mol.alg.QSScorer`

Definition at line 438 of file contact_score.py.

Constructor & Destructor Documentation

◆ init()

__init__	(	self,
		target,
		chem_groups,
		model,
		alns,
		contact_mode = `"aa"`,
		contact_d = `5.0`
	)

Definition at line 448 of file contact_score.py.

Member Function Documentation

◆ _InterfaceScores()

_InterfaceScores	(	self,
		int1,
		int2
	)

protected

Definition at line 812 of file contact_score.py.

◆ _MappedInterfaceScores()

_MappedInterfaceScores	(	self,
		int1,
		int2
	)

protected

Definition at line 800 of file contact_score.py.

◆ _MappedSCScores()

_MappedSCScores	(	self,
		ref_ch,
		mdl_ch
	)

protected

Definition at line 865 of file contact_score.py.

◆ _SCScores()

_SCScores	(	self,
		ch1,
		ch2
	)

protected

Definition at line 872 of file contact_score.py.

◆ alns()

alns ( self )

 Alignments between chains in :attr:`~cent1` and :attr:`~cent2`

Provided at object construction. Each alignment is accessible with
``alns[(t_chain,m_chain)]``. First sequence is the sequence of the
respective chain in :attr:`~cent1`, second sequence the one from
:attr:`~cent2`.

:type: :class:`dict` with key: :class:`tuple` of :class:`str`, value:
       :class:`ost.seq.AlignmentHandle`

Definition at line 532 of file contact_score.py.

◆ cent1()

cent1 ( self )

 Represents *target*

:type: :class:`ContactEntity`

Definition at line 506 of file contact_score.py.

◆ cent2()

cent2 ( self )

 Represents *model*

:type: :class:`ContactEntity`

Definition at line 524 of file contact_score.py.

◆ chem_groups()

chem_groups ( self )

 Groups of chemically equivalent chains in *target*

Provided at object construction

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

Definition at line 514 of file contact_score.py.

◆ FromMappingResult()

FromMappingResult	(	mapping_result,
		contact_mode = `"aa"`,
		contact_d = `5.0`
	)

static

 The preferred way to get a :class:`ContactScorer`

Static constructor that derives an object of type :class:`ContactScorer`
using a :class:`ost.mol.alg.chain_mapping.MappingResult`

:param mapping_result: Data source
:type mapping_result: :class:`ost.mol.alg.chain_mapping.MappingResult`

Definition at line 488 of file contact_score.py.

◆ ICSFromFlatMapping()

ICSFromFlatMapping	(	self,
		flat_mapping
	)

 Same as :func:`ScoreICS` but with flat mapping

:param flat_mapping: Dictionary with target chain names as keys and
                     the mapped model chain names as value
:type flat_mapping: :class:`dict` with :class:`str` as key and value
:returns: Result object of type :class:`ContactScorerResultICS`

Definition at line 634 of file contact_score.py.

◆ IPSFromFlatMapping()

IPSFromFlatMapping	(	self,
		flat_mapping
	)

 Same as :func:`ScoreIPS` but with flat mapping

:param flat_mapping: Dictionary with target chain names as keys and
                     the mapped model chain names as value
:type flat_mapping: :class:`dict` with :class:`str` as key and value
:returns: Result object of type :class:`ContactScorerResultIPS`

Definition at line 769 of file contact_score.py.

◆ ScoreICS()

ScoreICS	(	self,
		mapping,
		check = `True`
	)

 Computes ICS given chain mapping

Again, the preferred way is to get *mapping* is from an object
of type :class:`ost.mol.alg.chain_mapping.MappingResult`.

:param mapping: see 
                :attr:`ost.mol.alg.chain_mapping.MappingResult.mapping`
:type mapping: :class:`list` of :class:`list` of :class:`str`
:param check: Perform input checks, can be disabled for speed purposes
              if you know what you're doing.
:type check: :class:`bool`
:returns: Result object of type :class:`ContactScorerResultICS`

Definition at line 545 of file contact_score.py.

◆ ScoreICSInterface()

ScoreICSInterface	(	self,
		trg_ch1,
		trg_ch2,
		mdl_ch1,
		mdl_ch2
	)

 Computes ICS scores only considering one interface

This only works for interfaces that are computed in :func:`Score`, i.e.
interfaces for which the alignments are set up correctly.

:param trg_ch1: Name of first interface chain in target
:type trg_ch1: :class:`str`
:param trg_ch2: Name of second interface chain in target
:type trg_ch2: :class:`str`
:param mdl_ch1: Name of first interface chain in model
:type mdl_ch1: :class:`str`
:param mdl_ch2: Name of second interface chain in model
:type mdl_ch2: :class:`str`
:returns: Result object of type :class:`ContactScorerResultICS`
:raises: :class:`RuntimeError` if no aln for trg_ch1/mdl_ch1 or
         trg_ch2/mdl_ch2 is available.

Definition at line 582 of file contact_score.py.

◆ ScoreIPS()

ScoreIPS	(	self,
		mapping,
		check = `True`
	)

 Computes IPS given chain mapping

Again, the preferred way is to get *mapping* is from an object
of type :class:`ost.mol.alg.chain_mapping.MappingResult`.

:param mapping: see 
                :attr:`ost.mol.alg.chain_mapping.MappingResult.mapping`
:type mapping: :class:`list` of :class:`list` of :class:`str`
:param check: Perform input checks, can be disabled for speed purposes
              if you know what you're doing.
:type check: :class:`bool`
:returns: Result object of type :class:`ContactScorerResultIPS`

Definition at line 669 of file contact_score.py.

◆ ScoreIPSInterface()

ScoreIPSInterface	(	self,
		trg_ch1,
		trg_ch2,
		mdl_ch1,
		mdl_ch2
	)

 Computes IPS scores only considering one interface

This only works for interfaces that are computed in :func:`Score`, i.e.
interfaces for which the alignments are set up correctly.

:param trg_ch1: Name of first interface chain in target
:type trg_ch1: :class:`str`
:param trg_ch2: Name of second interface chain in target
:type trg_ch2: :class:`str`
:param mdl_ch1: Name of first interface chain in model
:type mdl_ch1: :class:`str`
:param mdl_ch2: Name of second interface chain in model
:type mdl_ch2: :class:`str`
:returns: Result object of type :class:`ContactScorerResultIPS`
:raises: :class:`RuntimeError` if no aln for trg_ch1/mdl_ch1 or
         trg_ch2/mdl_ch2 is available.

Definition at line 706 of file contact_score.py.

Field Documentation

◆ _alns

_alns

protected

Definition at line 464 of file contact_score.py.

◆ _cent1

_cent1

protected

Definition at line 450 of file contact_score.py.

◆ _cent2

_cent2

protected

Definition at line 462 of file contact_score.py.

◆ _chem_groups

_chem_groups

protected

Definition at line 461 of file contact_score.py.

◆ _mapped_cache_interface

_mapped_cache_interface

protected

Definition at line 477 of file contact_score.py.

◆ _mapped_cache_sc

_mapped_cache_sc

protected

Definition at line 485 of file contact_score.py.

◆ chem_groups

chem_groups

Definition at line 562 of file contact_score.py.

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

build-dev/stage/lib/python3.11/site-packages/ost/mol/alg/contact_score.py

Public Member Functions

Static Public Member Functions

Data Fields

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ __init__()

Member Function Documentation

◆ _InterfaceScores()

◆ _MappedInterfaceScores()

◆ _MappedSCScores()

◆ _SCScores()

◆ alns()

◆ cent1()

◆ cent2()

◆ chem_groups()

◆ FromMappingResult()

◆ ICSFromFlatMapping()

◆ IPSFromFlatMapping()

◆ ScoreICS()

◆ ScoreICSInterface()

◆ ScoreIPS()

◆ ScoreIPSInterface()

Field Documentation

◆ _alns

◆ _cent1

◆ _cent2

◆ _chem_groups

◆ _mapped_cache_interface

◆ _mapped_cache_sc

◆ chem_groups

◆ init()