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OpenStructure
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Public Member Functions | |
| def | __init__ (self, lDDT, substructure, ref_view, mdl_view) |
| def | lDDT (self) |
| def | substructure (self) |
| def | ref_view (self) |
| def | mdl_view (self) |
| def | ref_residues (self) |
| def | mdl_residues (self) |
| def | inconsistent_residues (self) |
| def | ref_bb_pos (self) |
| def | mdl_bb_pos (self) |
| def | ref_full_bb_pos (self) |
| def | mdl_full_bb_pos (self) |
| def | transform (self) |
| def | superposed_mdl_bb_pos (self) |
| def | bb_rmsd (self) |
| def | gdt_8 (self) |
| def | gdt_4 (self) |
| def | gdt_2 (self) |
| def | gdt_1 (self) |
| def | ost_query (self) |
| def | JSONSummary (self) |
| def | GetFlatChainMapping (self, mdl_as_key=False) |
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 160 of file chain_mapping.py.
| def __init__ | ( | self, | |
| lDDT, | |||
| substructure, | |||
| ref_view, | |||
| mdl_view | |||
| ) |
Definition at line 180 of file chain_mapping.py.
| def bb_rmsd | ( | self | ) |
RMSD between :attr:`ref_bb_pos` and :attr:`superposed_mdl_bb_pos` :type: :class:`float`
Definition at line 351 of file chain_mapping.py.
| def gdt_1 | ( | self | ) |
GDT with one single threshold: 1.0 :type: :class:`float`
Definition at line 391 of file chain_mapping.py.
| def gdt_2 | ( | self | ) |
GDT with one single threshold: 2.0 :type: :class:`float`
Definition at line 381 of file chain_mapping.py.
| def gdt_4 | ( | self | ) |
GDT with one single threshold: 4.0 :type: :class:`float`
Definition at line 371 of file chain_mapping.py.
| def gdt_8 | ( | self | ) |
GDT with one single threshold: 8.0 :type: :class:`float`
Definition at line 361 of file chain_mapping.py.
| def 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 445 of file chain_mapping.py.
| def 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 256 of file chain_mapping.py.
| def JSONSummary | ( | self | ) |
Returns JSON serializable summary of results
Definition at line 426 of file chain_mapping.py.
| def 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 204 of file chain_mapping.py.
| def 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 283 of file chain_mapping.py.
| def 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 308 of file chain_mapping.py.
| def mdl_residues | ( | self | ) |
The model residues :type: :class:`mol.ResidueViewList`
Definition at line 248 of file chain_mapping.py.
| def mdl_view | ( | self | ) |
The :attr:`ref_view` representation in the model :type: :class:`ost.mol.EntityView`
Definition at line 232 of file chain_mapping.py.
| def 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 401 of file chain_mapping.py.
| def 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 271 of file chain_mapping.py.
| def 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 295 of file chain_mapping.py.
| def ref_residues | ( | self | ) |
The reference residues :type: class:`mol.ResidueViewList`
Definition at line 240 of file chain_mapping.py.
| def ref_view | ( | self | ) |
View which contains the mapped subset of :attr:`substructure` :type: :class:`ost.mol.EntityView`
Definition at line 224 of file chain_mapping.py.
| def substructure | ( | self | ) |
The full substructure for which we searched for a representation :type: :class:`ost.mol.EntityView`
Definition at line 215 of file chain_mapping.py.
| def superposed_mdl_bb_pos | ( | self | ) |
:attr:`mdl_bb_pos` with :attr:`transform applied` :type: :class:`geom.Vec3List`
Definition at line 340 of file chain_mapping.py.
| def transform | ( | self | ) |
Transformation to superpose 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.geom.Mat4`
Definition at line 321 of file chain_mapping.py.
1.9.1