Public Member Functions
	__init__ (self, lDDT, substructure, ref_view, mdl_view)

	lDDT (self)

	substructure (self)

	ref_view (self)

	mdl_view (self)

	ref_residues (self)

	mdl_residues (self)

	inconsistent_residues (self)

	ref_bb_pos (self)

	mdl_bb_pos (self)

	ref_full_bb_pos (self)

	mdl_full_bb_pos (self)

	superposition (self)

	transform (self)

	superposed_mdl_bb_pos (self)

	bb_rmsd (self)

	ost_query (self)

	JSONSummary (self)

	GetFlatChainMapping (self, mdl_as_key=False)

Data Fields
	ref_residues

	mdl_residues

	mdl_bb_pos

	ref_full_bb_pos

	ref_bb_pos

	transform

Protected Member Functions
	_GetFullBBPos (self, residues)

	_GetBBPos (self, residues)

	_GetInconsistentResidues (self, ref_residues, mdl_residues)

Protected Attributes
	_lDDT

	_substructure

	_ref_view

	_mdl_view

	_ref_bb_pos

	_mdl_bb_pos

	_ref_full_bb_pos

	_mdl_full_bb_pos

	_superposition

	_superposed_mdl_bb_pos

	_ost_query

	_flat_mapping

	_inconsistent_residues

Detailed Description

 Result object for :func:`ChainMapper.GetRepr`

Constructor is directly called within the function, no need to construct
such objects yourself.

:param lDDT: lDDT for this mapping. Depends on how you call
             :func:`ChainMapper.GetRepr` whether this is backbone only or
             full atom lDDT.
:type lDDT: :class:`float`
:param substructure: The full substructure for which we searched for a
                     representation
:type substructure: :class:`ost.mol.EntityView`
:param ref_view: View pointing to the same underlying entity as
                 *substructure* but only contains the stuff that is mapped
:type ref_view: :class:`mol.EntityView`
:param mdl_view: The matching counterpart in model
:type mdl_view: :class:`mol.EntityView`

Definition at line 171 of file chain_mapping.py.

Constructor & Destructor Documentation

◆ init()

__init__	(	self,
		lDDT,
		substructure,
		ref_view,
		mdl_view
	)

Definition at line 191 of file chain_mapping.py.

Member Function Documentation

◆ _GetBBPos()

_GetBBPos	(	self,
		residues
	)

protected

 Helper to extract single representative position for each residue

Definition at line 453 of file chain_mapping.py.

◆ _GetFullBBPos()

_GetFullBBPos	(	self,
		residues
	)

protected

 Helper to extract full backbone positions

Definition at line 431 of file chain_mapping.py.

◆ _GetInconsistentResidues()

_GetInconsistentResidues	(	self,
		ref_residues,
		mdl_residues
	)

protected

 Helper to extract a list of inconsistent residues.

Definition at line 467 of file chain_mapping.py.

◆ bb_rmsd()

bb_rmsd ( self )

 RMSD of the binding site backbone atoms after :attr:`superposition`

:type: :class:`float`

Definition at line 366 of file chain_mapping.py.

◆ GetFlatChainMapping()

GetFlatChainMapping	(	self,
		mdl_as_key = `False`
	)

 Returns flat mapping of all chains in the representation

:param mdl_as_key: Default is target chain name as key and model chain
                   name as value. This can be reversed with this flag.
:returns: :class:`dict` with :class:`str` as key/value that describe
          one-to-one mapping

Definition at line 415 of file chain_mapping.py.

◆ inconsistent_residues()

inconsistent_residues ( self )

 A list of mapped residue whose names do not match (eg. ALA in the
reference and LEU in the model).

The mismatches are reported as a tuple of :class:`~ost.mol.ResidueView`
(reference, model), or as an empty list if all the residue names match.

:type: :class:`list`

Definition at line 262 of file chain_mapping.py.

◆ JSONSummary()

JSONSummary ( self )

 Returns JSON serializable summary of results

Definition at line 400 of file chain_mapping.py.

◆ lDDT()

lDDT ( self )

 lDDT of representation result

Depends on how you call :func:`ChainMapper.GetRepr` whether this is
backbone only or full atom lDDT.

:type: :class:`float`

Definition at line 210 of file chain_mapping.py.

◆ mdl_bb_pos()

mdl_bb_pos ( self )

 Representative backbone positions for model residues.

Thats CA positions for peptides and C3' positions for Nucleotides.

:type: :class:`geom.Vec3List`

Definition at line 289 of file chain_mapping.py.

◆ mdl_full_bb_pos()

mdl_full_bb_pos ( self )

 Representative backbone positions for reference residues.

Thats N, CA and C positions for peptides and O5', C5', C4', C3', O3'
positions for Nucleotides.

:type: :class:`geom.Vec3List`

Definition at line 314 of file chain_mapping.py.

◆ mdl_residues()

mdl_residues ( self )

 The model residues

:type: :class:`mol.ResidueViewList`

Definition at line 254 of file chain_mapping.py.

◆ mdl_view()

mdl_view ( self )

 The :attr:`ref_view` representation in the model

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

Definition at line 238 of file chain_mapping.py.

◆ ost_query()

ost_query ( self )

 query for mdl residues in OpenStructure query language

Repr can be selected as ``full_mdl.Select(ost_query)``

Returns invalid query if residue numbers have insertion codes.

:type: :class:`str`

Definition at line 375 of file chain_mapping.py.

◆ ref_bb_pos()

ref_bb_pos ( self )

 Representative backbone positions for reference residues.

Thats CA positions for peptides and C3' positions for Nucleotides.

:type: :class:`geom.Vec3List`

Definition at line 277 of file chain_mapping.py.

◆ ref_full_bb_pos()

ref_full_bb_pos ( self )

 Representative backbone positions for reference residues.

Thats N, CA and C positions for peptides and O5', C5', C4', C3', O3'
positions for Nucleotides.

:type: :class:`geom.Vec3List`

Definition at line 301 of file chain_mapping.py.

◆ ref_residues()

ref_residues ( self )

 The reference residues

:type: class:`mol.ResidueViewList`

Definition at line 246 of file chain_mapping.py.

◆ ref_view()

ref_view ( self )

 View which contains the mapped subset of :attr:`substructure`

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

Definition at line 230 of file chain_mapping.py.

◆ substructure()

substructure ( self )

 The full substructure for which we searched for a
representation

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

Definition at line 221 of file chain_mapping.py.

◆ superposed_mdl_bb_pos()

superposed_mdl_bb_pos ( self )

 :attr:`mdl_bb_pos` with :attr:`transform applied`

:type: :class:`geom.Vec3List`

Definition at line 355 of file chain_mapping.py.

◆ superposition()

superposition ( self )

 Superposition of mdl residues onto ref residues

Superposition computed as minimal RMSD superposition on
:attr:`ref_bb_pos` and :attr:`mdl_bb_pos`. If number of positions is
smaller 3, the full_bb_pos equivalents are used instead.

:type: :class:`ost.mol.alg.SuperpositionResult`

Definition at line 328 of file chain_mapping.py.

◆ transform()

transform ( self )

 Transformation to superpose mdl residues onto ref residues

:type: :class:`ost.geom.Mat4`

Definition at line 347 of file chain_mapping.py.

Field Documentation

◆ _flat_mapping

_flat_mapping

protected

Definition at line 206 of file chain_mapping.py.

◆ _inconsistent_residues

_inconsistent_residues

protected

Definition at line 207 of file chain_mapping.py.

◆ _lDDT

_lDDT

protected

Definition at line 192 of file chain_mapping.py.

◆ _mdl_bb_pos

_mdl_bb_pos

protected

Definition at line 200 of file chain_mapping.py.

◆ _mdl_full_bb_pos

_mdl_full_bb_pos

protected

Definition at line 202 of file chain_mapping.py.

◆ _mdl_view

_mdl_view

protected

Definition at line 196 of file chain_mapping.py.

◆ _ost_query

_ost_query

protected

Definition at line 205 of file chain_mapping.py.

◆ _ref_bb_pos

_ref_bb_pos

protected

Definition at line 199 of file chain_mapping.py.

◆ _ref_full_bb_pos

_ref_full_bb_pos

protected

Definition at line 201 of file chain_mapping.py.

◆ _ref_view

_ref_view

protected

Definition at line 195 of file chain_mapping.py.

◆ _substructure

_substructure

protected

Definition at line 193 of file chain_mapping.py.

◆ _superposed_mdl_bb_pos

_superposed_mdl_bb_pos

protected

Definition at line 204 of file chain_mapping.py.

◆ _superposition

_superposition

protected

Definition at line 203 of file chain_mapping.py.

◆ mdl_bb_pos

mdl_bb_pos

Definition at line 338 of file chain_mapping.py.

◆ mdl_residues

mdl_residues

Definition at line 273 of file chain_mapping.py.

◆ ref_bb_pos

ref_bb_pos

Definition at line 343 of file chain_mapping.py.

◆ ref_full_bb_pos

ref_full_bb_pos

Definition at line 340 of file chain_mapping.py.

◆ ref_residues

ref_residues

Definition at line 273 of file chain_mapping.py.

◆ transform

transform

Definition at line 362 of file chain_mapping.py.

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

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

Public Member Functions

Data Fields

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ __init__()

Member Function Documentation

◆ _GetBBPos()

◆ _GetFullBBPos()

◆ _GetInconsistentResidues()

◆ bb_rmsd()

◆ GetFlatChainMapping()

◆ inconsistent_residues()

◆ JSONSummary()

◆ lDDT()

◆ mdl_bb_pos()

◆ mdl_full_bb_pos()

◆ mdl_residues()

◆ mdl_view()

◆ ost_query()

◆ ref_bb_pos()

◆ ref_full_bb_pos()

◆ ref_residues()

◆ ref_view()

◆ substructure()

◆ superposed_mdl_bb_pos()

◆ superposition()

◆ transform()

Field Documentation

◆ _flat_mapping

◆ _inconsistent_residues

◆ _lDDT

◆ _mdl_bb_pos

◆ _mdl_full_bb_pos

◆ _mdl_view

◆ _ost_query

◆ _ref_bb_pos

◆ _ref_full_bb_pos

◆ _ref_view

◆ _substructure

◆ _superposed_mdl_bb_pos

◆ _superposition

◆ mdl_bb_pos

◆ mdl_residues

◆ ref_bb_pos

◆ ref_full_bb_pos

◆ ref_residues

◆ transform

◆ init()