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OpenStructure
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OpenStructure
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Public Member Functions | |
| def | __init__ |
| def | cent1 |
| def | chem_groups |
| def | cent2 |
| def | alns |
| def | ScoreICS |
| def | ScoreICSInterface |
| def | ICSFromFlatMapping |
| def | ScoreIPS |
| def | ScoreIPSInterface |
| def | IPSFromFlatMapping |
Static Public Member Functions | |
| def | FromMappingResult |
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 379 of file contact_score.py.
| def __init__ | ( | self, | |
| target, | |||
| chem_groups, | |||
| model, | |||
| alns, | |||
contact_mode = "aa", |
|||
contact_d = 5.0 |
|||
| ) |
Definition at line 390 of file contact_score.py.
| def 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 473 of file contact_score.py.
| def cent1 | ( | self | ) |
Represents *target* :type: :class:`ContactEntity`
Definition at line 447 of file contact_score.py.
| def cent2 | ( | self | ) |
Represents *model* :type: :class:`ContactEntity`
Definition at line 465 of file contact_score.py.
| def 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 455 of file contact_score.py.
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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 429 of file contact_score.py.
| def 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 575 of file contact_score.py.
| def 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 700 of file contact_score.py.
| def 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 486 of file contact_score.py.
| def 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 523 of file contact_score.py.
| def 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 610 of file contact_score.py.
| def 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 647 of file contact_score.py.
1.8.5