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OpenStructure
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Helper class to access the various scores available from ost.mol.alg
Deals with structure cleanup, chain mapping, interface identification etc.
Intermediate results are available as attributes.
:param model: Model structure - a deep copy is available as :attr:`~model`.
Additionally, :func:`ost.mol.alg.Molck` using *molck_settings*
is applied.
:type model: :class:`ost.mol.EntityHandle`/:class:`ost.mol.EntityView`
:param target: Target structure - a deep copy is available as :attr:`~target`.
Additionally, :func:`ost.mol.alg.Molck` using *molck_settings*
is applied.
:type target: :class:`ost.mol.EntityHandle`/:class:`ost.mol.EntityView`
:param resnum_alignments: Whether alignments between chemically equivalent
chains in *model* and *target* can be computed
based on residue numbers. This can be assumed in
benchmarking setups such as CAMEO/CASP.
:type resnum_alignments: :class:`bool`
:param molck_settings: Settings used for Molck on *model* and *target*, if
set to None, a default object is constructed by
setting everything except rm_zero_occ_atoms and
colored to True in
:class:`ost.mol.alg.MolckSettings` constructor.
:type molck_settings: :class:`ost.mol.alg.MolckSettings`
:param cad_score_exec: Explicit path to voronota-cadscore executable from
voronota installation from
https://github.com/kliment-olechnovic/voronota. If
not given, voronota-cadscore must be in PATH if any
of the CAD score related attributes is requested.
:type cad_score_exec: :class:`str`
:param custom_mapping: Provide custom chain mapping between *model* and
*target*. Dictionary with target chain names as key
and model chain names as value.
:attr:`~mapping` is constructed from this.
:type custom_mapping: :class:`dict`
:param custom_rigid_mapping: Provide custom chain mapping between *model*
and *target*. Dictionary with target chain
names as key and model chain names as value.
:attr:`~rigid_mapping` is constructed from
this.
:type custom_rigid_mapping: :class:`dict`
:param usalign_exec: Explicit path to USalign executable used to compute
TM-score. If not given, TM-score will be computed
with OpenStructure internal copy of USalign code.
:type usalign_exec: :class:`str`
:param lddt_no_stereochecks: Whether to compute LDDT without stereochemistry
checks
:type lddt_no_stereochecks: :class:`bool`
:param n_max_naive: Parameter for chain mapping. If the number of possible
mappings is <= *n_max_naive*, the full
mapping solution space is enumerated to find the
the optimum. A heuristic is used otherwise. The default
of 40320 corresponds to an octamer (8! = 40320).
A structure with stoichiometry A6B2 would be
6!*2! = 1440 etc.
:type n_max_naive: :class:`int`
:param oum: Override USalign Mapping. Inject rigid_mapping of
:class:`Scorer` object into USalign to compute TM-score.
Experimental feature with limitations.
:type oum: :class:`bool`
:param min_pep_length: Relevant parameter if short peptides are involved in
scoring. Minimum peptide length for a chain in the
target structure to be considered in chain mapping.
The chain mapping algorithm first performs an all vs.
all pairwise sequence alignment to identify \"equal\"
chains within the target structure. We go for simple
sequence identity there. Short sequences can be
problematic as they may produce high sequence identity
alignments by pure chance.
:type min_pep_length: :class:`int`
:param min_nuc_length: Relevant parameter if short nucleotides are involved
in scoring. Minimum nucleotide length for a chain in
the target structure to be considered in chain
mapping. The chain mapping algorithm first performs
an all vs. all pairwise sequence alignment to
identify \"equal\" chains within the target
structure. We go for simple sequence identity there.
Short sequences can be problematic as they may
produce high sequence identity alignments by pure
chance.
:type min_nuc_length: :class:`int`
:param lddt_add_mdl_contacts: LDDT specific flag. Only using contacts in
LDDT that are within a certain distance
threshold in the target does not penalize
for added model contacts. If set to True, this
flag will also consider target contacts
that are within the specified distance
threshold in the model but not necessarily in
the target. No contact will be added if the
respective atom pair is not resolved in the
target.
:type lddt_add_mdl_contacts: :class:`bool`
:param dockq_capri_peptide: Flag that changes two things in the way DockQ
and its underlying scores are computed which is
proposed by the CAPRI community when scoring
peptides (PMID: 31886916).
ONE: Two residues are considered in contact if
any of their atoms is within 5A. This is
relevant for fnat and fnonat scores. CAPRI
suggests to lower this threshold to 4A for
protein-peptide interactions.
TWO: irmsd is computed on interface residues. A
residue is defined as interface residue if any
of its atoms is within 10A of another chain.
CAPRI suggests to lower the default of 10A to
8A in combination with only considering CB atoms
for protein-peptide interactions.
This flag has no influence on patch_dockq
scores.
:type dockq_capri_peptide: :class:`bool`
:param lddt_symmetry_settings: Passed as *symmetry_settings* parameter to
LDDT scorer. Default: None
:type lddt_symmetry_settings: :class:`ost.mol.alg.lddt.SymmetrySettings`
:param lddt_inclusion_radius: LDDT inclusion radius.
:param pep_seqid_thr: Parameter that affects identification of identical
chains in target - see
:class:`ost.mol.alg.chain_mapping.ChainMapper`
:type pep_seqid_thr: :class:`float`
:param nuc_seqid_thr: Parameter that affects identification of identical
chains in target - see
:class:`ost.mol.alg.chain_mapping.ChainMapper`
:type nuc_seqid_thr: :class:`float`
:param mdl_map_pep_seqid_thr: Parameter that affects mapping of model chains
to target chains - see
:class:`ost.mol.alg.chain_mapping.ChainMapper`
:type mdl_map_pep_seqid_thr: :class:`float`
:param mdl_map_nuc_seqid_thr: Parameter that affects mapping of model chains
to target chains - see
:class:`ost.mol.alg.chain_mapping.ChainMapper`
:type mdl_map_nuc_seqid_thr: :class:`float`
:param seqres: Parameter that affects identification of identical chains in
target - see :class:`ost.mol.alg.chain_mapping.ChainMapper`
:type seqres: :class:`ost.seq.SequenceList`
:param trg_seqres_mapping: Parameter that affects identification of identical
chains in target - see
:class:`ost.mol.alg.chain_mapping.ChainMapper`
:type trg_seqres_mapping: :class:`dict`
Definition at line 135 of file scoring.py.
| __init__ | ( | self, | |
| model, | |||
| target, | |||
resnum_alignments = False, |
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molck_settings = None, |
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cad_score_exec = None, |
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custom_mapping = None, |
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custom_rigid_mapping = None, |
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usalign_exec = None, |
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lddt_no_stereochecks = False, |
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n_max_naive = 40320, |
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oum = False, |
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min_pep_length = 6, |
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min_nuc_length = 4, |
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lddt_add_mdl_contacts = False, |
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dockq_capri_peptide = False, |
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lddt_symmetry_settings = None, |
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lddt_inclusion_radius = 15.0, |
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pep_seqid_thr = 95., |
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nuc_seqid_thr = 95., |
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mdl_map_pep_seqid_thr = 0., |
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mdl_map_nuc_seqid_thr = 0., |
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seqres = None, |
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trg_seqres_mapping = None |
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| ) |
Definition at line 274 of file scoring.py.
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Definition at line 2123 of file scoring.py.
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Definition at line 2166 of file scoring.py.
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Definition at line 2438 of file scoring.py.
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Definition at line 2905 of file scoring.py.
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Definition at line 2695 of file scoring.py.
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Definition at line 2546 of file scoring.py.
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Definition at line 2605 of file scoring.py.
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Definition at line 2475 of file scoring.py.
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Definition at line 2637 of file scoring.py.
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Definition at line 2664 of file scoring.py.
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Definition at line 2222 of file scoring.py.
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Definition at line 3135 of file scoring.py.
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Definition at line 3117 of file scoring.py.
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Definition at line 2218 of file scoring.py.
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Definition at line 2531 of file scoring.py.
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Definition at line 2525 of file scoring.py.
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Definition at line 2169 of file scoring.py.
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Definition at line 3336 of file scoring.py.
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constructs a full blown MappingResult object from simple dict :param mapping: mapping with trg chains as key and mdl ch as values :type mapping: :class:`dict`
Definition at line 3240 of file scoring.py.
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Perform stereochemistry checks on model and target
Definition at line 2976 of file scoring.py.
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Definition at line 2789 of file scoring.py.
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Definition at line 2816 of file scoring.py.
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Definition at line 2847 of file scoring.py.
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Definition at line 2875 of file scoring.py.
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Select interface patches representative for specified residue
The patches for specified residue r in chain c are selected as follows:
* mdl_patch_one: All residues in c with CB (CA for GLY) positions within 8A
of r and within 12A of residues from any other chain.
* mdl_patch_two: Closest residue x to r in any other chain gets identified.
Patch is then constructed by selecting all residues from any other chain
within 8A of x and within 12A from any residue in c.
* trg_patch_one: Chain name and residue number based mapping from
mdl_patch_one
* trg_patch_two: Chain name and residue number based mapping from
mdl_patch_two
:param mdl_ch: Name of chain in *self.model* of residue of interest
:type mdl_ch: :class:`str`
:param mdl_rnum: Residue number of residue of interest
:type mdl_rnum: :class:`ost.mol.ResNum`
:returns: Tuple with 5 elements: 1) :class:`bool` flag whether all residues
in *mdl* patches are covered in *trg* 2) mtl_patch_one
3) mdl_patch_two 4) trg_patch_one 5) trg_patch_two
Definition at line 2998 of file scoring.py.
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Get interface residues
Thats all residues having a contact with at least one residue from another
chain (CB-CB distance <= 8A, CA in case of Glycine)
:param ent: Model for which to extract interface residues
:type ent: :class:`ost.mol.EntityView`
:returns: :class:`dict` with chain names as key and and :class:`list`
with residue numbers of the respective interface residues.
Definition at line 2956 of file scoring.py.
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Returns view with representative peptide atoms => CB, CA for GLY Ensures that each residue has exactly one atom with assertions :param ent: Entity for which you want the representative view :param ent: :class:`ost.mol.EntityHandle`/:class:`ost.mol.EntityView` :returns: :class:`ost.mol.EntityView` derived from ent
Definition at line 2942 of file scoring.py.
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Score interface residue patches with DockQ In detail: Construct two entities with two chains each. First chain consists of residues from <x>_patch_one and second chain consists of <x>_patch_two. The returned score is the QS-score between the two entities :param mdl_patch_one: Interface patch representing scored residue :type mdl_patch_one: :class:`ost.mol.EntityView` :param mdl_patch_two: Interface patch representing scored residue :type mdl_patch_two: :class:`ost.mol.EntityView` :param trg_patch_one: Interface patch representing scored residue :type trg_patch_one: :class:`ost.mol.EntityView` :param trg_patch_two: Interface patch representing scored residue :type trg_patch_two: :class:`ost.mol.EntityView` :returns: DockQ score
Definition at line 3192 of file scoring.py.
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Score interface residue patches with QS-score In detail: Construct two entities with two chains each. First chain consists of residues from <x>_patch_one and second chain consists of <x>_patch_two. The returned score is the QS-score between the two entities :param mdl_patch_one: Interface patch representing scored residue :type mdl_patch_one: :class:`ost.mol.EntityView` :param mdl_patch_two: Interface patch representing scored residue :type mdl_patch_two: :class:`ost.mol.EntityView` :param trg_patch_one: Interface patch representing scored residue :type trg_patch_one: :class:`ost.mol.EntityView` :param trg_patch_two: Interface patch representing scored residue :type trg_patch_two: :class:`ost.mol.EntityView` :returns: PatchQS score
Definition at line 3153 of file scoring.py.
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Constructs Entity with two chains named "A" and "B"" Blindly adds all residues from *patch_one* to chain A and residues from patch_two to chain B.
Definition at line 3218 of file scoring.py.
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Definition at line 3364 of file scoring.py.
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Definition at line 2572 of file scoring.py.
| aa_local_lddt | ( | self | ) |
Per atom LDDT scores in range [0.0, 1.0] Computed based on :attr:`~stereochecked_model` but scores for all atoms in :attr:`~model` are reported. If an atom has been removed by stereochemistry checks, the respective score is set to 0.0. If an atom is not covered by the target or is in a chain skipped by the chain mapping procedure (happens for super short chains), the respective score is set to None. In case of oligomers, :attr:`~mapping` is used. :type: :class:`dict`
Definition at line 922 of file scoring.py.
| aln | ( | self | ) |
Alignments of :attr:`~model`/:attr:`~target` chains Alignments for each pair of chains mapped in :attr:`~mapping`. First sequence is target sequence, second sequence the model sequence. :type: :class:`list` of :class:`ost.seq.AlignmentHandle`
Definition at line 596 of file scoring.py.
| bb_lddt | ( | self | ) |
Global LDDT score restricted to representative backbone atoms in range [0.0, 1.0] Computed based on :attr:`~model` on representative backbone atoms only. This is CA for peptides and C3' for nucleotides. No stereochecks are performed. In case of oligomers, :attr:`~mapping` is used. :type: :class:`float`
Definition at line 939 of file scoring.py.
| bb_lddt_scorer | ( | self | ) |
LDDT scorer for :attr:`~target`, restricted to representative backbone atoms No stereochecks applied for bb only LDDT which considers CA atoms for peptides and C3' atoms for nucleotides. :type: :class:`ost.mol.alg.lddt.lDDTScorer`
Definition at line 848 of file scoring.py.
| bb_local_lddt | ( | self | ) |
Per residue LDDT scores restricted to representative backbone atoms in range [0.0, 1.0] Computed based on :attr:`~model` on representative backbone atoms only. This is CA for peptides and C3' for nucleotides. No stereochecks are performed. If a residue is not covered by the target or is in a chain skipped by the chain mapping procedure (happens for super short chains), the respective score is set to None. In case of oligomers, :attr:`~mapping` is used. :type: :class:`dict`
Definition at line 954 of file scoring.py.
| cad_score | ( | self | ) |
The global CAD atom-atom (AA) score Computed based on :attr:`~model`. In case of oligomers, :attr:`~mapping` is used. :type: :class:`float`
Definition at line 2029 of file scoring.py.
| chain_mapper | ( | self | ) |
Chain mapper object for given :attr:`~target` :type: :class:`ost.mol.alg.chain_mapping.ChainMapper`
Definition at line 752 of file scoring.py.
| contact_model_interfaces | ( | self | ) |
Interfaces in :class:`model` which have at least one contact
Contact as defined in :attr:`~native_contacts`,
chain names are lexicographically sorted.
:type: :class:`list` of :class:`tuple` with 2 elements each
(mdl_ch1, mdl_ch2)
Definition at line 1139 of file scoring.py.
| contact_scorer | ( | self | ) |
Definition at line 877 of file scoring.py.
| contact_target_interfaces | ( | self | ) |
Interfaces in :class:`target` which have at least one contact
Contact as defined in :attr:`~native_contacts`,
chain names are lexicographically sorted.
:type: :class:`list` of :class:`tuple` with 2 elements each
(trg_ch1, trg_ch2)
Definition at line 1123 of file scoring.py.
| dockq_ave | ( | self | ) |
Average of DockQ scores in :attr:`~dockq_scores` In its original implementation, DockQ only operates on single interfaces. Thus the requirement to combine scores for higher order oligomers. :type: :class:`float`
Definition at line 1611 of file scoring.py.
| dockq_ave_full | ( | self | ) |
Same as :attr:`~dockq_ave` but penalizing for missing interfaces Interfaces that are not covered in model are added as 0.0 in average computation. :type: :class:`float`
Definition at line 1635 of file scoring.py.
| dockq_interfaces | ( | self | ) |
Interfaces in :attr:`~dockq_target_interfaces` that can be mapped
to model
Target chain names are lexicographically sorted
:type: :class:`list` of :class:`tuple` with 4 elements each:
(trg_ch1, trg_ch2, mdl_ch1, mdl_ch2)
Definition at line 1506 of file scoring.py.
| dockq_scores | ( | self | ) |
DockQ scores for interfaces in :attr:`~dockq_interfaces` :class:`list` of :class:`float`
Definition at line 1526 of file scoring.py.
| dockq_target_interfaces | ( | self | ) |
Interfaces in :attr:`~target` that are relevant for DockQ
All interfaces in :attr:`~target` with non-zero contacts that are
relevant for DockQ. Includes protein-protein, protein-nucleotide and
nucleotide-nucleotide interfaces. Chain names for each interface are
lexicographically sorted.
:type: :class:`list` of :class:`tuple` with 2 elements each:
(trg_ch1, trg_ch2)
Definition at line 1470 of file scoring.py.
| dockq_wave | ( | self | ) |
Same as :attr:`~dockq_ave`, weighted by native contacts :type: :class:`float`
Definition at line 1625 of file scoring.py.
| dockq_wave_full | ( | self | ) |
Same as :attr:`~dockq_ave_full`, but weighted Interfaces that are not covered in model are added as 0.0 in average computations and the respective weights are derived from number of contacts in respective target interface.
Definition at line 1648 of file scoring.py.
| fnat | ( | self | ) |
fnat scores for interfaces in :attr:`~dockq_interfaces` fnat: Fraction of native contacts that are also present in model :class:`list` of :class:`float`
Definition at line 1536 of file scoring.py.
| fnonnat | ( | self | ) |
fnonnat scores for interfaces in :attr:`~dockq_interfaces` fnat: Fraction of model contacts that are not present in target :class:`list` of :class:`float`
Definition at line 1568 of file scoring.py.
| gdt_05 | ( | self | ) |
Fraction CA (C3' for nucleotides) that can be superposed within 0.5A Uses :attr:`~rigid_mapped_model_pos` and :attr:`~rigid_mapped_target_pos`. Similar iterative algorithm as LGA tool :type: :class:`float`
Definition at line 1866 of file scoring.py.
| gdt_1 | ( | self | ) |
Fraction CA (C3' for nucleotides) that can be superposed within 1.0A Uses :attr:`~rigid_mapped_model_pos` and :attr:`~rigid_mapped_target_pos`. Similar iterative algorithm as LGA tool :type: :class:`float`
Definition at line 1891 of file scoring.py.
| gdt_2 | ( | self | ) |
Fraction CA (C3' for nucleotides) that can be superposed within 2.0A Uses :attr:`~rigid_mapped_model_pos` and :attr:`~rigid_mapped_target_pos`. Similar iterative algorithm as LGA tool :type: :class:`float`
Definition at line 1916 of file scoring.py.
| gdt_4 | ( | self | ) |
Fraction CA (C3' for nucleotides) that can be superposed within 4.0A Uses :attr:`~rigid_mapped_model_pos` and :attr:`~rigid_mapped_target_pos`. Similar iterative algorithm as LGA tool :type: :class:`float`
Definition at line 1942 of file scoring.py.
| gdt_8 | ( | self | ) |
Fraction CA (C3' for nucleotides) that can be superposed within 8.0A Similar iterative algorithm as LGA tool :type: :class:`float`
Definition at line 1967 of file scoring.py.
| gdtha | ( | self | ) |
avg GDT with thresholds: 4.0A, 2.0A, 1.0A and 0.5A :type: :class:`float`
Definition at line 2003 of file scoring.py.
| gdtts | ( | self | ) |
avg GDT with thresholds: 8.0A, 4.0A, 2.0A and 1.0A :type: :class:`float`
Definition at line 1992 of file scoring.py.
| ics | ( | self | ) |
ICS (Interface Contact Similarity) score Combination of :attr:`~ics_precision` and :attr:`~ics_recall` using the F1-measure :type: :class:`float`
Definition at line 1175 of file scoring.py.
| ics_precision | ( | self | ) |
Fraction of model contacts that are also present in target :type: :class:`float`
Definition at line 1155 of file scoring.py.
| ics_precision_trimmed | ( | self | ) |
Same as :attr:`~ics_precision` but with trimmed model Model is trimmed to residues which can me mapped to target in order to not penalize contacts in the model for which we have no experimental evidence. :type: :class:`float`
Definition at line 1278 of file scoring.py.
| ics_recall | ( | self | ) |
Fraction of target contacts that are correctly reproduced in model :type: :class:`float`
Definition at line 1165 of file scoring.py.
| ics_recall_trimmed | ( | self | ) |
Same as :attr:`~ics_recall` but with trimmed model Model is trimmed to residues which can me mapped to target in order to not penalize contacts in the model for which we have no experimental evidence. :type: :class:`float`
Definition at line 1292 of file scoring.py.
| ics_trimmed | ( | self | ) |
Same as :attr:`~ics` but with trimmed model Model is trimmed to residues which can me mapped to target in order to not penalize contacts in the model for which we have no experimental evidence. :type: :class:`float`
Definition at line 1264 of file scoring.py.
| ilddt | ( | self | ) |
Global interface LDDT score in range [0.0, 1.0] This is LDDT only based on inter-chain contacts. Value is None if no such contacts are present. For example if we're dealing with a monomer. Computed based on :attr:`~stereochecked_model` and :attr:`~mapping` for chain mapping. :type: :class:`float`
Definition at line 972 of file scoring.py.
| ips | ( | self | ) |
IPS (Interface Patch Similarity) score Jaccard coefficient of interface residues in target and their mapped counterparts in model :type: :class:`float`
Definition at line 1251 of file scoring.py.
| ips_precision | ( | self | ) |
Fraction of model interface residues that are also interface residues in target :type: :class:`float`
Definition at line 1229 of file scoring.py.
| ips_precision_trimmed | ( | self | ) |
Same as :attr:`~ips_precision` but with trimmed model Model is trimmed to residues which can me mapped to target in order to not penalize contacts in the model for which we have no experimental evidence. :type: :class:`float`
Definition at line 1361 of file scoring.py.
| ips_recall | ( | self | ) |
Fraction of target interface residues that are also interface residues in model :type: :class:`float`
Definition at line 1240 of file scoring.py.
| ips_recall_trimmed | ( | self | ) |
Same as :attr:`~ips_recall` but with trimmed model Model is trimmed to residues which can me mapped to target in order to not penalize contacts in the model for which we have no experimental evidence. :type: :class:`float`
Definition at line 1375 of file scoring.py.
| ips_trimmed | ( | self | ) |
Same as :attr:`~ips` but with trimmed model Model is trimmed to residues which can me mapped to target in order to not penalize contacts in the model for which we have no experimental evidence. :type: :class:`float`
Definition at line 1347 of file scoring.py.
| irmsd | ( | self | ) |
irmsd scores for interfaces in :attr:`~dockq_interfaces` irmsd: RMSD of interface (RMSD computed on backbone atoms) which consists of each residue that has at least one heavy atom within 10A of other chain. Backbone atoms for proteins: "CA","C","N","O", for nucleotides: "P", "OP1", "OP2", "O2'", "O3'", "O4'", "O5'", "C1'", "C2'", "C3'", "C4'", "C5'". :class:`list` of :class:`float`
Definition at line 1580 of file scoring.py.
| lddt | ( | self | ) |
Global LDDT score in range [0.0, 1.0] Computed based on :attr:`~stereochecked_model`. In case of oligomers, :attr:`~mapping` is used. :type: :class:`float`
Definition at line 892 of file scoring.py.
| lddt_scorer | ( | self | ) |
LDDT scorer for :attr:`~target`/:attr:`~stereochecked_target` Depending on :attr:`~lddt_no_stereocheck` and :attr:`~lddt_symmetry_settings`. :type: :class:`ost.mol.alg.lddt.lDDTScorer`
Definition at line 828 of file scoring.py.
| local_cad_score | ( | self | ) |
The per-residue CAD atom-atom (AA) scores Computed based on :attr:`~model`. In case of oligomers, :attr:`~mapping` is used. :type: :class:`dict`
Definition at line 2042 of file scoring.py.
| local_lddt | ( | self | ) |
Per residue LDDT scores in range [0.0, 1.0] Computed based on :attr:`~stereochecked_model` but scores for all residues in :attr:`~model` are reported. If a residue has been removed by stereochemistry checks, the respective score is set to 0.0. If a residue is not covered by the target or is in a chain skipped by the chain mapping procedure (happens for super short chains), the respective score is set to None. In case of oligomers, :attr:`~mapping` is used. :type: :class:`dict`
Definition at line 905 of file scoring.py.
| lrmsd | ( | self | ) |
lrmsd scores for interfaces in :attr:`~dockq_interfaces` lrmsd: The two chains involved in the interface are superposed based on the receptor (rigid min RMSD superposition) and the ligand RMSD is reported. Receptor is the chain with more residues. Superposition and RMSD is computed on same backbone atoms as :attr:`~irmsd`. :class:`list` of :class:`float`
Definition at line 1596 of file scoring.py.
| mapped_model_pos | ( | self | ) |
Mapped representative positions in model Thats CA positions for peptide residues and C3' positions for nucleotides. Has same length as :attr:`~mapped_target_pos` and mapping is based on :attr:`~mapping`. :type: :class:`ost.geom.Vec3List`
Definition at line 1688 of file scoring.py.
| mapped_model_pos_full_bb | ( | self | ) |
Mapped representative positions in model Thats the equivalent of :attr:`~mapped_model_pos` but containing more backbone atoms (N, CA, C for peptide residues and O5', C5', C4', C3', O3 for nucleotide residues). mapping is based on :attr:`~mapping`. :type: :class:`ost.geom.Vec3List`
Definition at line 1702 of file scoring.py.
| mapped_target_pos | ( | self | ) |
Mapped representative positions in target Thats CA positions for peptide residues and C3' positions for nucleotides. Has same length as :attr:`~mapped_model_pos` and mapping is based on :attr:`~mapping`. :type: :class:`ost.geom.Vec3List`
Definition at line 1660 of file scoring.py.
| mapped_target_pos_full_bb | ( | self | ) |
Mapped representative positions in target Thats the equivalent of :attr:`~mapped_target_pos` but containing more backbone atoms (N, CA, C for peptide residues and O5', C5', C4', C3', O3 for nucleotide residues). mapping is based on :attr:`~mapping`. :type: :class:`ost.geom.Vec3List`
Definition at line 1674 of file scoring.py.
| mapping | ( | self | ) |
Full chain mapping result for :attr:`~target`/:attr:`~model` Computed with :func:`ost.mol.alg.ChainMapper.GetMapping` :type: :class:`ost.mol.alg.chain_mapping.MappingResult`
Definition at line 772 of file scoring.py.
| model | ( | self | ) |
Model with Molck cleanup :type: :class:`ost.mol.EntityHandle`
Definition at line 538 of file scoring.py.
| model_bad_angles | ( | self | ) |
Model angles with unexpected stereochemistry
:type: :class:`list` of
:class:`ost.mol.alg.stereochemistry.AngleViolationInfo`
Definition at line 685 of file scoring.py.
| model_bad_bonds | ( | self | ) |
Model bonds with unexpected stereochemistry
:type: :class:`list` of
:class:`ost.mol.alg.stereochemistry.BondViolationInfo`
Definition at line 674 of file scoring.py.
| model_clashes | ( | self | ) |
Clashing model atoms :type: :class:`list` of :class:`ost.mol.alg.stereochemistry.ClashInfo`
Definition at line 664 of file scoring.py.
| model_contacts | ( | self | ) |
Same for :attr:`~model`
Definition at line 1107 of file scoring.py.
| model_interface_residues | ( | self | ) |
Interface residues in :attr:`~model`
Thats all residues having a contact with at least one residue from
another chain (CB-CB distance <= 8A, CA in case of Glycine)
:type: :class:`dict` with chain names as key and and :class:`list`
with residue numbers of the respective interface residues.
Definition at line 801 of file scoring.py.
| model_orig | ( | self | ) |
The original model passed at object construction :type: :class:`ost.mol.EntityHandle`/:class:`ost.mol.EntityView`
Definition at line 546 of file scoring.py.
| n_target_not_mapped | ( | self | ) |
Number of target residues which have no mapping to model :type: :class:`int`
Definition at line 1728 of file scoring.py.
| native_contacts | ( | self | ) |
Native contacts A contact is a pair or residues from distinct chains that have a minimal heavy atom distance < 5A. Contacts are specified as :class:`tuple` with two strings in format: <cname>.<rnum>.<ins_code> :type: :class:`list` of :class:`tuple`
Definition at line 1092 of file scoring.py.
| nmdl | ( | self | ) |
N model contacts for interfaces in :attr:`~dockq_interfaces` :class:`list` of :class:`int`
Definition at line 1558 of file scoring.py.
| nnat | ( | self | ) |
N native contacts for interfaces in :attr:`~dockq_interfaces` :class:`list` of :class:`int`
Definition at line 1548 of file scoring.py.
| patch_dockq | ( | self | ) |
Same as :attr:`~patch_qs` but for DockQ scores
Definition at line 2087 of file scoring.py.
| patch_qs | ( | self | ) |
Patch QS-scores for each residue in :attr:`~model_interface_residues`
Representative patches for each residue r in chain c are computed as
follows:
* mdl_patch_one: All residues in c with CB (CA for GLY) positions within
8A of r and within 12A of residues from any other chain.
* mdl_patch_two: Closest residue x to r in any other chain gets
identified. Patch is then constructed by selecting all residues from
any other chain within 8A of x and within 12A from any residue in c.
* trg_patch_one: Chain name and residue number based mapping from
mdl_patch_one
* trg_patch_two: Chain name and residue number based mapping from
mdl_patch_two
Results are stored in the same manner as
:attr:`~model_interface_residues`, with corresponding scores instead of
residue numbers. Scores for residues which are not
:class:`mol.ChemType.AMINOACIDS` are set to None. Additionally,
interface patches are derived from :attr:`~model`. If they contain
residues which are not covered by :attr:`~target`, the score is set to
None too.
:type: :class:`dict` with chain names as key and and :class:`list`
with scores of the respective interface residues.
Definition at line 2055 of file scoring.py.
| pepnuc_aln | ( | self | ) |
Alignments of :attr:`~model_orig`/:attr:`~target_orig` chains Selects for peptide and nucleotide residues before sequence extraction. Includes residues that would be removed by molck in structure preprocessing. :type: :class:`list` of :class:`ost.seq.AlignmentHandle`
Definition at line 621 of file scoring.py.
| pepnuc_model | ( | self | ) |
A selection of :attr:`~model_orig` Only contains peptide and nucleotide residues :type: :class:`ost.mol.EntityView`
Definition at line 554 of file scoring.py.
| pepnuc_target | ( | self | ) |
A selection of :attr:`~target_orig` Only contains peptide and nucleotide residues :type: :class:`ost.mol.EntityView`
Definition at line 583 of file scoring.py.
| per_interface_ics | ( | self | ) |
Per-interface ICS (Interface Contact Similarity) score :attr:`~ics` for each interface in :attr:`~contact_target_interfaces` :type: :class:`float`
Definition at line 1215 of file scoring.py.
| per_interface_ics_precision | ( | self | ) |
Per-interface ICS precision :attr:`~ics_precision` for each interface in :attr:`~contact_target_interfaces` :type: :class:`list` of :class:`float`
Definition at line 1188 of file scoring.py.
| per_interface_ics_precision_trimmed | ( | self | ) |
Same as :attr:`~per_interface_ics_precision` but with :attr:`~trimmed_model` :attr:`~ics_precision_trimmed` for each interface in :attr:`~contact_target_interfaces` :type: :class:`list` of :class:`float`
Definition at line 1306 of file scoring.py.
| per_interface_ics_recall | ( | self | ) |
Per-interface ICS recall :attr:`~ics_recall` for each interface in :attr:`~contact_target_interfaces` :type: :class:`list` of :class:`float`
Definition at line 1202 of file scoring.py.
| per_interface_ics_recall_trimmed | ( | self | ) |
Same as :attr:`~per_interface_ics_recall` but with :attr:`~trimmed_model` :attr:`~ics_recall_trimmed` for each interface in :attr:`~contact_target_interfaces` :type: :class:`list` of :class:`float`
Definition at line 1320 of file scoring.py.
| per_interface_ics_trimmed | ( | self | ) |
Same as :attr:`~per_interface_ics` but with :attr:`~trimmed_model` :attr:`~ics` for each interface in :attr:`~contact_target_interfaces` :type: :class:`float`
Definition at line 1333 of file scoring.py.
| per_interface_ips | ( | self | ) |
Per-interface IPS (Interface Patch Similarity) score :attr:`~ips` for each interface in :attr:`~contact_target_interfaces` :type: :class:`list` of :class:`float`
Definition at line 1415 of file scoring.py.
| per_interface_ips_precision | ( | self | ) |
Per-interface IPS precision :attr:`~ips_precision` for each interface in :attr:`~contact_target_interfaces` :type: :class:`list` of :class:`float`
Definition at line 1389 of file scoring.py.
| per_interface_ips_precision_trimmed | ( | self | ) |
Same as :attr:`~per_interface_ips_precision` but with :attr:`~trimmed_model` :attr:`~ips_precision_trimmed` for each interface in :attr:`~contact_target_interfaces` :type: :class:`list` of :class:`float`
Definition at line 1429 of file scoring.py.
| per_interface_ips_recall | ( | self | ) |
Per-interface IPS recall :attr:`~ips_recall` for each interface in :attr:`~contact_target_interfaces` :type: :class:`list` of :class:`float`
Definition at line 1402 of file scoring.py.
| per_interface_ips_recall_trimmed | ( | self | ) |
Same as :attr:`~per_interface_ips_recall` but with :attr:`~trimmed_model` :attr:`~ics_recall_trimmed` for each interface in :attr:`~contact_target_interfaces` :type: :class:`list` of :class:`float`
Definition at line 1443 of file scoring.py.
| per_interface_ips_trimmed | ( | self | ) |
Same as :attr:`~per_interface_ips` but with :attr:`~trimmed_model` :attr:`~ics` for each interface in :attr:`~contact_target_interfaces` :type: :class:`float`
Definition at line 1456 of file scoring.py.
| per_interface_qs_best | ( | self | ) |
QS-score for each interface in :attr:`~qs_interfaces` Only computed on aligned residues :type: :class:`list` of :class:`float`
Definition at line 1080 of file scoring.py.
| per_interface_qs_global | ( | self | ) |
QS-score for each interface in :attr:`~qs_interfaces` :type: :class:`list` of :class:`float`
Definition at line 1070 of file scoring.py.
| qs_best | ( | self | ) |
Global QS-score - only computed on aligned residues Computed based on :attr:`~model` using :attr:`~mapping`. The QS-score computation only considers contacts between residues with a mapping between target and model. As a result, the score won't be lowered in case of additional chains/residues in any of the structures. :type: :class:`float`
Definition at line 1002 of file scoring.py.
| qs_global | ( | self | ) |
Global QS-score Computed based on :attr:`~model` using :attr:`~mapping` :type: :class:`float`
Definition at line 990 of file scoring.py.
| qs_interfaces | ( | self | ) |
Interfaces in :attr:`~qs_target_interfaces` that can be mapped
to :attr:`~model`.
Target chain names are lexicographically sorted.
:type: :class:`list` of :class:`tuple` with 4 elements each:
(trg_ch1, trg_ch2, mdl_ch1, mdl_ch2)
Definition at line 1050 of file scoring.py.
| qs_model_interfaces | ( | self | ) |
Interfaces in :attr:`~model` with non-zero contribution to
:attr:`~qs_global`/:attr:`~qs_best`
Chain names are lexicographically sorted.
:type: :class:`list` of :class:`tuple` with 2 elements each:
(mdl_ch1, mdl_ch2)
Definition at line 1033 of file scoring.py.
| qs_scorer | ( | self | ) |
QS scorer constructed from :attr:`~mapping` The scorer object is constructed with default parameters and relates to :attr:`~model` and :attr:`~target` (no stereochecks). :type: :class:`ost.mol.alg.qsscore.QSScorer`
Definition at line 864 of file scoring.py.
| qs_target_interfaces | ( | self | ) |
Interfaces in :attr:`~target` with non-zero contribution to
:attr:`~qs_global`/:attr:`~qs_best`
Chain names are lexicographically sorted.
:type: :class:`list` of :class:`tuple` with 2 elements each:
(trg_ch1, trg_ch2)
Definition at line 1017 of file scoring.py.
| rigid_mapped_model_pos | ( | self | ) |
Mapped representative positions in model Thats CA positions for peptide residues and C3' positions for nucleotides. Has same length as :attr:`~mapped_target_pos` and mapping is based on :attr:`~rigid_mapping`. :type: :class:`ost.geom.Vec3List`
Definition at line 1791 of file scoring.py.
| rigid_mapped_model_pos_full_bb | ( | self | ) |
Mapped representative positions in model Thats the equivalent of :attr:`~rigid_mapped_model_pos` but containing more backbone atoms (N, CA, C for peptide residues and O5', C5', C4', C3', O3 for nucleotide residues). mapping is based on :attr:`~mapping`. :type: :class:`ost.geom.Vec3List`
Definition at line 1805 of file scoring.py.
| rigid_mapped_target_pos | ( | self | ) |
Mapped representative positions in target Thats CA positions for peptide residues and C3' positions for nucleotides. Has same length as :attr:`~rigid_mapped_model_pos` and mapping is based on :attr:`~rigid_mapping`. :type: :class:`ost.geom.Vec3List`
Definition at line 1763 of file scoring.py.
| rigid_mapped_target_pos_full_bb | ( | self | ) |
Mapped representative positions in target Thats the equivalent of :attr:`~rigid_mapped_target_pos` but containing more backbone atoms (N, CA, C for peptide residues and O5', C5', C4', C3', O3 for nucleotide residues). mapping is based on :attr:`~mapping`. :type: :class:`ost.geom.Vec3List`
Definition at line 1777 of file scoring.py.
| rigid_mapping | ( | self | ) |
Full chain mapping result for :attr:`~target`/:attr:`~model` Computed with :func:`ost.mol.alg.ChainMapper.GetRMSDMapping` :type: :class:`ost.mol.alg.chain_mapping.MappingResult`
Definition at line 787 of file scoring.py.
| rigid_n_target_not_mapped | ( | self | ) |
Number of target residues which have no rigid mapping to model :type: :class:`int`
Definition at line 1831 of file scoring.py.
| rigid_transform | ( | self | ) |
Transform: :attr:`~rigid_mapped_model_pos` onto :attr:`~rigid_mapped_target_pos` Computed using Kabsch minimal rmsd algorithm. If number of positions is too small (< 3), :attr:`~rigid_mapped_model_pos_full_bb` and :attr:`~rigid_mapped_target_pos_full_bb` are used. :type: :class:`ost.geom.Mat4`
Definition at line 1841 of file scoring.py.
| rigid_transformed_mapped_model_pos | ( | self | ) |
:attr:`~rigid_mapped_model_pos` with :attr:`~rigid_transform` applied :type: :class:`ost.geom.Vec3List`
Definition at line 1819 of file scoring.py.
| rmsd | ( | self | ) |
RMSD Computed on :attr:`~rigid_transformed_mapped_model_pos` and :attr:`~rigid_mapped_target_pos` :type: :class:`float`
Definition at line 2014 of file scoring.py.
| stereochecked_aln | ( | self | ) |
Stereochecked equivalent of :attr:`~aln` The alignments may differ, as stereochecks potentially remove residues :type: :class:`list` of :class:`ost.seq.AlignmentHandle`
Definition at line 609 of file scoring.py.
| stereochecked_model | ( | self | ) |
View of :attr:`~model` that has stereochemistry checks applied First, a selection for peptide/nucleotide residues is performed, secondly peptide sidechains with stereochemical irregularities are removed (full residue if backbone atoms are involved). Irregularities are clashes or bond lengths/angles more than 12 standard deviations from expected values. :type: :class:`ost.mol.EntityView`
Definition at line 648 of file scoring.py.
| stereochecked_target | ( | self | ) |
Same as :attr:`~stereochecked_model` for :attr:`~target` :type: :class:`ost.mol.EntityView`
Definition at line 696 of file scoring.py.
| target | ( | self | ) |
Target with Molck cleanup :type: :class:`ost.mol.EntityHandle`
Definition at line 567 of file scoring.py.
| target_bad_angles | ( | self | ) |
Target angles with unexpected stereochemistry
:type: :class:`list` of
:class:`ost.mol.alg.stereochemistry.AngleViolationInfo`
Definition at line 727 of file scoring.py.
| target_bad_bonds | ( | self | ) |
Target bonds with unexpected stereochemistry
:type: :class:`list` of
:class:`ost.mol.alg.stereochemistry.BondViolationInfo`
Definition at line 716 of file scoring.py.
| target_clashes | ( | self | ) |
Clashing target atoms :type: :class:`list` of :class:`ost.mol.alg.stereochemistry.ClashInfo`
Definition at line 706 of file scoring.py.
| target_interface_residues | ( | self | ) |
Same as :attr:`~model_interface_residues` for :attr:`~target`
:type: :class:`dict` with chain names as key and and :class:`list`
with residue numbers of the respective interface residues.
Definition at line 816 of file scoring.py.
| target_orig | ( | self | ) |
The original target passed at object construction :type: :class:`ost.mol.EntityHandle`/:class:`ost.mol.EntityView`
Definition at line 575 of file scoring.py.
| tm_score | ( | self | ) |
TM-score computed with USalign USalign executable can be specified with usalign_exec kwarg at Scorer construction, an OpenStructure internal copy of the USalign code is used otherwise. :type: :class:`float`
Definition at line 2095 of file scoring.py.
| transform | ( | self | ) |
Transform: :attr:`~mapped_model_pos` onto :attr:`~mapped_target_pos` Computed using Kabsch minimal rmsd algorithm. If number of positions is too small (< 3), :attr:`~mapped_model_pos_full_bb` and :attr:`~mapped_target_pos_full_bb` are used. :type: :class:`ost.geom.Mat4`
Definition at line 1738 of file scoring.py.
| transformed_mapped_model_pos | ( | self | ) |
:attr:`~mapped_model_pos` with :attr:`~transform` applied :type: :class:`ost.geom.Vec3List`
Definition at line 1716 of file scoring.py.
| trimmed_aln | ( | self | ) |
Alignments of :attr:`~trimmed_model`/:attr:`~target` chains Alignments for each pair of chains mapped in :attr:`~mapping`. First sequence is target sequence, second sequence the model sequence. :type: :class:`list` of :class:`ost.seq.AlignmentHandle`
Definition at line 635 of file scoring.py.
| trimmed_contact_scorer | ( | self | ) |
Definition at line 883 of file scoring.py.
| trimmed_model | ( | self | ) |
:attr:`~model` trimmed to target Removes residues that are not covered by :class:`target` given :attr:`~mapping`. In other words: no model residues without experimental evidence from :class:`target`. :type: :class:`ost.mol.EntityView`
Definition at line 738 of file scoring.py.
| trimmed_model_contacts | ( | self | ) |
Same for :attr:`~trimmed_model`
Definition at line 1115 of file scoring.py.
| usalign_mapping | ( | self | ) |
Mapping computed with USalign Dictionary with target chain names as key and model chain names as values. No guarantee that all chains are mapped. USalign executable can be specified with usalign_exec kwarg at Scorer construction, an OpenStructure internal copy of the USalign code is used otherwise. :type: :class:`dict`
Definition at line 2109 of file scoring.py.
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| cad_score_exec |
Definition at line 385 of file scoring.py.
| dockq_capri_peptide |
Definition at line 393 of file scoring.py.
| lddt_add_mdl_contacts |
Definition at line 392 of file scoring.py.
| lddt_inclusion_radius |
Definition at line 395 of file scoring.py.
| lddt_no_stereochecks |
Definition at line 387 of file scoring.py.
| lddt_symmetry_settings |
Definition at line 394 of file scoring.py.
| mapped_model_pos |
Definition at line 1723 of file scoring.py.
| mapped_model_pos_full_bb |
Definition at line 1749 of file scoring.py.
| mapped_target_pos |
Definition at line 1758 of file scoring.py.
| mapped_target_pos_full_bb |
Definition at line 1751 of file scoring.py.
| mdl_map_nuc_seqid_thr |
Definition at line 399 of file scoring.py.
| mdl_map_pep_seqid_thr |
Definition at line 398 of file scoring.py.
| min_nuc_length |
Definition at line 391 of file scoring.py.
| min_pep_length |
Definition at line 390 of file scoring.py.
| model |
Definition at line 782 of file scoring.py.
| n_max_naive |
Definition at line 388 of file scoring.py.
| nuc_seqid_thr |
Definition at line 397 of file scoring.py.
| oum |
Definition at line 389 of file scoring.py.
| pep_seqid_thr |
Definition at line 396 of file scoring.py.
| pepnuc_model |
Definition at line 2220 of file scoring.py.
| resnum_alignments |
Definition at line 384 of file scoring.py.
| rigid_mapped_model_pos |
Definition at line 1826 of file scoring.py.
| rigid_mapped_model_pos_full_bb |
Definition at line 1852 of file scoring.py.
| rigid_mapped_target_pos |
Definition at line 1861 of file scoring.py.
| rigid_mapped_target_pos_full_bb |
Definition at line 1854 of file scoring.py.
| rigid_transform |
Definition at line 1827 of file scoring.py.
| rigid_transformed_mapped_model_pos |
Definition at line 2025 of file scoring.py.
| seqres |
Definition at line 400 of file scoring.py.
| target |
Definition at line 824 of file scoring.py.
| transform |
Definition at line 1724 of file scoring.py.
| trg_seqres_mapping |
Definition at line 401 of file scoring.py.
| trimmed_aln |
Definition at line 888 of file scoring.py.
| trimmed_model |
Definition at line 887 of file scoring.py.
| usalign_exec |
Definition at line 386 of file scoring.py.
1.9.8