|
OpenStructure
|
Data Fields | |
| resnum_alignments | |
| cad_score_exec | |
| usalign_exec | |
| lddt_no_stereochecks | |
| n_max_naive | |
| oum | |
| min_pep_length | |
| min_nuc_length | |
| lddt_add_mdl_contacts | |
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.
:type custom_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 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`
Definition at line 92 of file scoring.py.
| def __init__ | ( | self, | |
| model, | |||
| target, | |||
resnum_alignments = False, |
|||
molck_settings = None, |
|||
cad_score_exec = None, |
|||
custom_mapping = None, |
|||
usalign_exec = None, |
|||
lddt_no_stereochecks = False, |
|||
n_max_naive = 40320, |
|||
oum = False, |
|||
min_pep_length = 6, |
|||
min_nuc_length = 4, |
|||
lddt_add_mdl_contacts = False |
|||
| ) |
Definition at line 179 of file scoring.py.
| def 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 410 of file scoring.py.
| def bb_lddt | ( | self | ) |
Backbone only global lDDT score in range [0.0, 1.0] Computed based on :attr:`~model` on 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 685 of file scoring.py.
| def bb_lddt_scorer | ( | self | ) |
Backbone only lDDT scorer for :attr:`~target` 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 622 of file scoring.py.
| def bb_local_lddt | ( | self | ) |
Backbone only per residue lDDT scores in range [0.0, 1.0] Computed based on :attr:`~model` on 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 699 of file scoring.py.
| def 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 1456 of file scoring.py.
| def chain_mapper | ( | self | ) |
Chain mapper object for given :attr:`target` :type: :class:`ost.mol.alg.chain_mapping.ChainMapper`
Definition at line 539 of file scoring.py.
| def 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 856 of file scoring.py.
| def contact_scorer | ( | self | ) |
Definition at line 648 of file scoring.py.
| def 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 840 of file scoring.py.
| def 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 1145 of file scoring.py.
| def 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 1169 of file scoring.py.
| def 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 1041 of file scoring.py.
| def dockq_scores | ( | self | ) |
DockQ scores for interfaces in :attr:`~dockq_interfaces` :class:`list` of :class:`float`
Definition at line 1061 of file scoring.py.
| def dockq_target_interfaces | ( | self | ) |
Interfaces in :attr:`target` that are relevant for DockQ
In principle a subset of :attr:`~contact_target_interfaces` that only
contains peptide sequences. Chain names are lexicographically sorted.
:type: :class:`list` of :class:`tuple` with 2 elements each:
(trg_ch1, trg_ch2)
Definition at line 1023 of file scoring.py.
| def dockq_wave | ( | self | ) |
Same as :attr:`dockq_ave`, weighted by native contacts :type: :class:`float`
Definition at line 1159 of file scoring.py.
| def 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 1182 of file scoring.py.
| def 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 1071 of file scoring.py.
| def 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 1103 of file scoring.py.
| def 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 1328 of file scoring.py.
| def 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 1346 of file scoring.py.
| def 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 1364 of file scoring.py.
| def 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 1383 of file scoring.py.
| def 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 1401 of file scoring.py.
| def gdtha | ( | self | ) |
avg GDT with thresholds: 4.0A, 2.0A, 1.0A and 0.5A :type: :class:`float`
Definition at line 1430 of file scoring.py.
| def gdtts | ( | self | ) |
avg GDT with thresholds: 8.0A, 4.0A, 2.0A and 1.0A :type: :class:`float`
Definition at line 1419 of file scoring.py.
| def 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 892 of file scoring.py.
| def ics_precision | ( | self | ) |
Fraction of model contacts that are also present in target :type: :class:`float`
Definition at line 872 of file scoring.py.
| def ics_recall | ( | self | ) |
Fraction of target contacts that are correctly reproduced in model :type: :class:`float`
Definition at line 882 of file scoring.py.
| def 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 969 of file scoring.py.
| def ips_precision | ( | self | ) |
Fraction of model interface residues that are also interface residues in target :type: :class:`float`
Definition at line 947 of file scoring.py.
| def ips_recall | ( | self | ) |
Fraction of target interface residues that are also interface residues in model :type: :class:`float`
Definition at line 958 of file scoring.py.
| def irmsd | ( | self | ) |
irmsd scores for interfaces in :attr:`~dockq_interfaces` irmsd: RMSD of interface (RMSD computed on N, CA, C, O atoms) which consists of each residue that has at least one heavy atom within 10A of other chain. :class:`list` of :class:`float`
Definition at line 1115 of file scoring.py.
| def 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 655 of file scoring.py.
| def lddt_scorer | ( | self | ) |
lDDT scorer for :attr:`~stereochecked_target` (default parameters) :type: :class:`ost.mol.alg.lddt.lDDTScorer`
Definition at line 609 of file scoring.py.
| def 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 1469 of file scoring.py.
| def 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 668 of file scoring.py.
| def lrmsd | ( | self | ) |
lrmsd scores for interfaces in :attr:`~dockq_interfaces` lrmsd: The interfaces are superposed based on the receptor (rigid min RMSD superposition) and RMSD for the ligand is reported. Superposition and RMSD are based on N, CA, C and O positions, receptor is the chain contributing to the interface with more residues in total. :class:`list` of :class:`float`
Definition at line 1129 of file scoring.py.
| def 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 1208 of file scoring.py.
| def 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 1194 of file scoring.py.
| def 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 553 of file scoring.py.
| def model | ( | self | ) |
Model with Molck cleanup :type: :class:`ost.mol.EntityHandle`
Definition at line 378 of file scoring.py.
| def model_bad_angles | ( | self | ) |
Model angles with unexpected stereochemistry
:type: :class:`list` of
:class:`ost.mol.alg.stereochemistry.AngleViolationInfo`
Definition at line 486 of file scoring.py.
| def model_bad_bonds | ( | self | ) |
Model bonds with unexpected stereochemistry
:type: :class:`list` of
:class:`ost.mol.alg.stereochemistry.BondViolationInfo`
Definition at line 475 of file scoring.py.
| def model_clashes | ( | self | ) |
Clashing model atoms :type: :class:`list` of :class:`ost.mol.alg.stereochemistry.ClashInfo`
Definition at line 465 of file scoring.py.
| def model_contacts | ( | self | ) |
Same for model
Definition at line 832 of file scoring.py.
| def 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 582 of file scoring.py.
| def model_orig | ( | self | ) |
The original model passed at object construction :type: :class:`ost.mol.EntityHandle`/:class:`ost.mol.EntityView`
Definition at line 386 of file scoring.py.
| def n_target_not_mapped | ( | self | ) |
Number of target residues which have no mapping to model :type: :class:`int`
Definition at line 1234 of file scoring.py.
| def 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 817 of file scoring.py.
| def nmdl | ( | self | ) |
N model contacts for interfaces in :attr:`~dockq_interfaces` :class:`list` of :class:`int`
Definition at line 1093 of file scoring.py.
| def nnat | ( | self | ) |
N native contacts for interfaces in :attr:`~dockq_interfaces` :class:`list` of :class:`int`
Definition at line 1083 of file scoring.py.
| def patch_dockq | ( | self | ) |
Same as :attr:`patch_qs` but for DockQ scores
Definition at line 1514 of file scoring.py.
| def 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 1482 of file scoring.py.
| def 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 435 of file scoring.py.
| def 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 932 of file scoring.py.
| def 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 905 of file scoring.py.
| def 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 919 of file scoring.py.
| def 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 1009 of file scoring.py.
| def 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 982 of file scoring.py.
| def 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 996 of file scoring.py.
| def 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 805 of file scoring.py.
| def per_interface_qs_global | ( | self | ) |
QS-score for each interface in :attr:`qs_interfaces` :type: :class:`list` of :class:`float`
Definition at line 795 of file scoring.py.
| def 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 727 of file scoring.py.
| def qs_global | ( | self | ) |
Global QS-score Computed based on :attr:`model` using :attr:`mapping` :type: :class:`float`
Definition at line 715 of file scoring.py.
| def 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 775 of file scoring.py.
| def 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 758 of file scoring.py.
| def 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 635 of file scoring.py.
| def 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 742 of file scoring.py.
| def 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 1275 of file scoring.py.
| def 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 1261 of file scoring.py.
| def 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 568 of file scoring.py.
| def rigid_n_target_not_mapped | ( | self | ) |
Number of target residues which have no rigid mapping to model :type: :class:`int`
Definition at line 1301 of file scoring.py.
| def rigid_transform | ( | self | ) |
Transform: :attr:`~rigid_mapped_model_pos` onto :attr:`~rigid_mapped_target_pos` Computed using Kabsch minimal rmsd algorithm :type: :class:`ost.geom.Mat4`
Definition at line 1311 of file scoring.py.
| def rigid_transformed_mapped_model_pos | ( | self | ) |
:attr:`~rigid_mapped_model_pos` with :attr:`~rigid_transform` applied :type: :class:`ost.geom.Vec3List`
Definition at line 1289 of file scoring.py.
| def rmsd | ( | self | ) |
RMSD Computed on :attr:`~rigid_transformed_mapped_model_pos` and :attr:`rigid_mapped_target_pos` :type: :class:`float`
Definition at line 1441 of file scoring.py.
| def 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 423 of file scoring.py.
| def 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 449 of file scoring.py.
| def stereochecked_target | ( | self | ) |
Same as :attr:`~stereochecked_model` for :attr:`~target` :type: :class:`ost.mol.EntityView`
Definition at line 497 of file scoring.py.
| def target | ( | self | ) |
Target with Molck cleanup :type: :class:`ost.mol.EntityHandle`
Definition at line 394 of file scoring.py.
| def target_bad_angles | ( | self | ) |
Target angles with unexpected stereochemistry
:type: :class:`list` of
:class:`ost.mol.alg.stereochemistry.AngleViolationInfo`
Definition at line 528 of file scoring.py.
| def target_bad_bonds | ( | self | ) |
Target bonds with unexpected stereochemistry
:type: :class:`list` of
:class:`ost.mol.alg.stereochemistry.BondViolationInfo`
Definition at line 517 of file scoring.py.
| def target_clashes | ( | self | ) |
Clashing target atoms :type: :class:`list` of :class:`ost.mol.alg.stereochemistry.ClashInfo`
Definition at line 507 of file scoring.py.
| def 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 597 of file scoring.py.
| def target_orig | ( | self | ) |
The original target passed at object construction :type: :class:`ost.mol.EntityHandle`/:class:`ost.mol.EntityView`
Definition at line 402 of file scoring.py.
| def 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 1522 of file scoring.py.
| def transform | ( | self | ) |
Transform: :attr:`~mapped_model_pos` onto :attr:`~mapped_target_pos` Computed using Kabsch minimal rmsd algorithm :type: :class:`ost.geom.Mat4`
Definition at line 1244 of file scoring.py.
| def transformed_mapped_model_pos | ( | self | ) |
:attr:`~mapped_model_pos` with :attr:`~transform` applied :type: :class:`ost.geom.Vec3List`
Definition at line 1222 of file scoring.py.
| def 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 1536 of file scoring.py.
| cad_score_exec |
Definition at line 265 of file scoring.py.
| lddt_add_mdl_contacts |
Definition at line 272 of file scoring.py.
| lddt_no_stereochecks |
Definition at line 267 of file scoring.py.
| min_nuc_length |
Definition at line 271 of file scoring.py.
| min_pep_length |
Definition at line 270 of file scoring.py.
| n_max_naive |
Definition at line 268 of file scoring.py.
| oum |
Definition at line 269 of file scoring.py.
| resnum_alignments |
Definition at line 264 of file scoring.py.
| usalign_exec |
Definition at line 266 of file scoring.py.
1.9.1