MappingResult Class Reference

Public Member Functions
	__init__ (self, target, model, chem_groups, chem_mapping, mdl_chains_without_chem_mapping, mapping, alns, opt_score=None)
	target (self)
	model (self)
	chem_groups (self)
	chem_mapping (self)
	mdl_chains_without_chem_mapping (self)
	mapping (self)
	alns (self)
	opt_score (self)
	GetFlatMapping (self, mdl_as_key=False)
	JSONSummary (self)

Data Fields
	chem_groups
	mapping

Protected Attributes
	_target
	_model
	_chem_groups
	_chem_mapping
	_mdl_chains_without_chem_mapping
	_mapping
	_alns
	_opt_score

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 33 of file chain_mapping.py.

Constructor & Destructor Documentation

__init__()

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

Definition at line 39 of file chain_mapping.py.

Member Function Documentation

alns()

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`.

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

Definition at line 111 of file chain_mapping.py.

chem_groups()

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 70 of file chain_mapping.py.

chem_mapping()

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 80 of file chain_mapping.py.

GetFlatMapping()

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 135 of file chain_mapping.py.

JSONSummary()

JSONSummary

(

self

)

 Returns JSON serializable summary of results

Definition at line 154 of file chain_mapping.py.

mapping()

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 98 of file chain_mapping.py.

mdl_chains_without_chem_mapping()

mdl_chains_without_chem_mapping

(

self

)

 Model chains that cannot be mapped to :attr:`chem_groups`

Depends on parameterization of :class:`ChainMapper`

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

Definition at line 88 of file chain_mapping.py.

model()

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 59 of file chain_mapping.py.

opt_score()

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 124 of file chain_mapping.py.

target()

target

(

self

)

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

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

Definition at line 51 of file chain_mapping.py.

Field Documentation

_alns

_alns

protected

Definition at line 47 of file chain_mapping.py.

_chem_groups

_chem_groups

protected

Definition at line 43 of file chain_mapping.py.

_chem_mapping

_chem_mapping

protected

Definition at line 44 of file chain_mapping.py.

_mapping

_mapping

protected

Definition at line 46 of file chain_mapping.py.

_mdl_chains_without_chem_mapping

_mdl_chains_without_chem_mapping

protected

Definition at line 45 of file chain_mapping.py.

_model

_model

protected

Definition at line 42 of file chain_mapping.py.

_opt_score

_opt_score

protected

Definition at line 48 of file chain_mapping.py.

_target

_target

protected

Definition at line 41 of file chain_mapping.py.

chem_groups

chem_groups

Definition at line 144 of file chain_mapping.py.

mapping

mapping

Definition at line 145 of file chain_mapping.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/chain_mapping.py