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| | _PreprocessStructures (mdl, ref, mdl_ch1, mdl_ch2, ref_ch1, ref_ch2, ch1_aln=None, ch2_aln=None) |
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| | _GetContacts (ent, ch1, ch2, dist_thresh) |
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| | _ContactScores (mdl, ref, mdl_ch1, mdl_ch2, ref_ch1, ref_ch2, dist_thresh=5.0) |
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| | _RMSDScores (mdl, ref, mdl_ch1, mdl_ch2, ref_ch1, ref_ch2, dist_thresh=10.0, cb_mode=False) |
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| | _ScaleRMSD (rmsd, d) |
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| | _DockQ (fnat, lrmsd, irmsd, d1, d2) |
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| | DockQ (mdl, ref, mdl_ch1, mdl_ch2, ref_ch1, ref_ch2, ch1_aln=None, ch2_aln=None, contact_dist_thresh=5.0, interface_dist_thresh=10.0, interface_cb=False) |
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| _PreprocessStructures |
( |
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mdl, |
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ref, |
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mdl_ch1, |
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mdl_ch2, |
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ref_ch1, |
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ref_ch2, |
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ch1_aln = None, |
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ch2_aln = None |
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) |
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protected |
Preprocesses *mdl* and *ref*
Sets int properties to each residue in mdl_ch1, mdl_ch2 as well as
the respective reference chains.
dockq_mapped: 1 if a residues in mdl_ch1 is mapped to a residue in ref_ch1
and vice versa, 0 otherwise. Same is done for mdl_ch2 and
ref_ch2.
dockq_idx: If a pair of residue is mapped, the same index will be set
to both residues. The index is unique otherwise.
By default, mapping happens with residue numbers but you can enforce a
mapping with an alignment. In the example of ch1_aln, the first sequence
corresponds to the ATOMSEQ of ref_ch1 in ref and the second sequence to
the ATOMSEQ of mdl_ch1 in mdl.
Definition at line 5 of file dockq.py.
| DockQ |
( |
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mdl, |
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ref, |
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mdl_ch1, |
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mdl_ch2, |
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ref_ch1, |
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ref_ch2, |
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ch1_aln = None, |
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ch2_aln = None, |
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contact_dist_thresh = 5.0, |
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interface_dist_thresh = 10.0, |
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interface_cb = False |
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) |
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Computes DockQ for specified interface
DockQ is described in: Sankar Basu and Bjoern Wallner (2016), "DockQ: A
Quality Measure for Protein-Protein Docking Models", PLOS one
Residues are mapped based on residue numbers by default. If you provide
*ch1_aln* and *ch2_aln* you can enforce an arbitrary mapping.
:param mdl: Model structure
:type mdl: :class:`ost.mol.EntityView`/:class:`ost.mol.EntityHandle`
:param ref: Reference structure, i.e. native structure
:type ref: :class:`ost.mol.EntityView`/:class:`ost.mol.EntityHandle`
:param mdl_ch1: Specifies chain in model constituting first part of
interface
:type mdl_ch1: :class:`str`
:param mdl_ch2: Specifies chain in model constituting second part of
interface
:type mdl_ch2: :class:`str`
:param ref_ch1: ref equivalent of mdl_ch1
:type ref_ch1: :class:`str`
:param ref_ch2: ref equivalent of mdl_ch2
:type ref_ch2: :class:`str`
:param ch1_aln: Alignment with two sequences to map *ref_ch1* and *mdl_ch1*.
The first sequence must match the sequence in *ref_ch1* and
the second to *mdl_ch1*.
:type ch1_aln: :class:`ost.seq.AlignmentHandle`
:param ch2_aln: Alignment with two sequences to map *ref_ch2* and *mdl_ch2*.
The first sequence must match the sequence in *ref_ch2* and
the second to *mdl_ch2*.
:type ch2_aln: :class:`ost.seq.AlignmentHandle`
:param contact_dist_thresh: Residues with any atom within this threshold
are considered to be in contact. Affects contact
based scores fnat and fnonnat. CAPRI suggests
to lower the default of 5.0 to 4.0 for
protein-peptide interactions.
:type contact_dist_thresh: :class:`float`
:param interface_dist_thresh: Residues with any atom within this threshold
to another chain are considered interface
residues. Affects irmsd. CAPRI suggests to
lower the default of 10.0 to 8.0 in
combination with interface_cb=True for
protein-peptide interactions.
:type interface_dist_thresh: :class:`float`
:param interface_cb: Only use CB atoms (CA for GLY) to identify interface
residues for irmsd. CAPRI suggests to enable this
flag in combination with lowering
*interface_dist_thresh* to 8.0 for protein-peptide
interactions.
:type interface_cb: :class:`bool`
:returns: :class:`dict` with keys nnat, nmdl, fnat, fnonnat, irmsd, lrmsd,
DockQ which corresponds to the equivalent values in the original
DockQ implementation.
Definition at line 271 of file dockq.py.
