Public Member Functions
def	__init__ (self, target, model, chem_groups, chem_mapping, mapping, alns, opt_score=None)

def	target (self)

def	model (self)

def	chem_groups (self)

def	chem_mapping (self)

def	mapping (self)

def	alns (self)

def	opt_score (self)

def	GetFlatMapping (self, mdl_as_key=False)

def	JSONSummary (self)

Detailed Description

 Result object for the chain mapping functions in :class:`ChainMapper`

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

Definition at line 32 of file chain_mapping.py.

Constructor & Destructor Documentation

◆ init()

def __init__	(	self,
		target,
		model,
		chem_groups,
		chem_mapping,
		mapping,
		alns,
		opt_score = `None`
	)

Definition at line 38 of file chain_mapping.py.

Member Function Documentation

◆ alns()

def alns ( self )

 Alignments of mapped chains in :attr:`~target` and :attr:`~model`

Each alignment is accessible with ``alns[(t_chain,m_chain)]``. First
sequence is the sequence of :attr:`target` chain, second sequence the
one from :attr:`~model`. The respective :class:`ost.mol.EntityView` are
attached with :func:`ost.seq.ConstSequenceHandle.AttachView`.

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

Definition at line 99 of file chain_mapping.py.

◆ chem_groups()

def chem_groups ( self )

 Groups of chemically equivalent chains in :attr:`~target`

Same as :attr:`ChainMapper.chem_group`

:class:`list` of :class:`list` of :class:`str` (chain names)

Definition at line 68 of file chain_mapping.py.

◆ chem_mapping()

def chem_mapping ( self )

 Assigns chains in :attr:`~model` to :attr:`~chem_groups`.

:class:`list` of :class:`list` of :class:`str` (chain names)

Definition at line 78 of file chain_mapping.py.

◆ GetFlatMapping()

def GetFlatMapping	(	self,
		mdl_as_key = `False`
	)

 Returns flat mapping as :class:`dict` for all mapable chains

: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 124 of file chain_mapping.py.

◆ JSONSummary()

def JSONSummary ( self )

 Returns JSON serializable summary of results

Definition at line 143 of file chain_mapping.py.

◆ mapping()

def mapping ( self )

 Mapping of :attr:`~model` chains onto :attr:`~target`

Exact same shape as :attr:`~chem_groups` but containing the names of the
mapped chains in :attr:`~model`. May contain None for :attr:`~target`
chains that are not covered. No guarantee that all chains in
:attr:`~model` are mapped.

:class:`list` of :class:`list` of :class:`str` (chain names)

Definition at line 86 of file chain_mapping.py.

◆ model()

def model ( self )

 Model structure that gets mapped onto :attr:`~target`

Underwent same processing as :attr:`ChainMapper.target`, i.e.
only contains peptide/nucleotide chains of sufficient size.

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

Definition at line 57 of file chain_mapping.py.

◆ opt_score()

def opt_score ( self )

 Placeholder property without any guarantee of being set

Different scores get optimized in the various chain mapping algorithms.
Some of them may set their final optimal score in that property.
Consult the documentation of the respective chain mapping algorithm
for more information. Won't be in the return dict of
:func:`JSONSummary`.

Definition at line 113 of file chain_mapping.py.

◆ target()

def target ( self )

 Target/reference structure, i.e. :attr:`ChainMapper.target`

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

Definition at line 49 of file chain_mapping.py.

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

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

Public Member Functions