diff --git a/modules/mol/alg/pymod/chain_mapping.py b/modules/mol/alg/pymod/chain_mapping.py
index db28156de9cf09d06c2b839fa7767c2f3c24151f..29acb66541deedd75b02fa3d4bb07bb65555dda4 100644
--- a/modules/mol/alg/pymod/chain_mapping.py
+++ b/modules/mol/alg/pymod/chain_mapping.py
@@ -705,7 +705,8 @@ class ChainMapper:
def GetlDDTMapping(self, model, inclusion_radius=15.0,
thresholds=[0.5, 1.0, 2.0, 4.0], strategy="naive",
steep_opt_rate = None, full_n_mdl_chains = None,
- block_seed_size = 5, block_blocks_per_chem_group = 5):
+ block_seed_size = 5, block_blocks_per_chem_group = 5,
+ chem_mapping_result = None):
""" Identify chain mapping by optimizing lDDT score
Maps *model* chain sequences to :attr:`~chem_groups` and find mapping
@@ -771,6 +772,11 @@ class ChainMapper:
are extended in an initial search
for high scoring local solutions.
:type block_blocks_per_chem_group: :class:`int`
+ :param chem_mapping_result: Pro param. The result of
+ :func:`~GetChemMapping` where you provided
+ *model*. If set, *model* parameter is not
+ used.
+ :type chem_mapping_result: :class:`tuple`
:returns: A :class:`MappingResult`
"""
@@ -778,7 +784,10 @@ class ChainMapper:
if strategy not in strategies:
raise RuntimeError(f"Strategy must be in {strategies}")
- chem_mapping, chem_group_alns, mdl = self.GetChemMapping(model)
+ if chem_mapping_result is None:
+ chem_mapping, chem_group_alns, mdl = self.GetChemMapping(model)
+ else:
+ chem_mapping, chem_group_alns, mdl = chem_mapping_result
ref_mdl_alns = _GetRefMdlAlns(self.chem_groups,
self.chem_group_alignments,
@@ -836,7 +845,7 @@ class ChainMapper:
def GetQSScoreMapping(self, model, contact_d = 12.0, strategy = "naive",
full_n_mdl_chains = None, block_seed_size = 5,
block_blocks_per_chem_group = 5,
- steep_opt_rate = None):
+ steep_opt_rate = None, chem_mapping_result = None):
""" Identify chain mapping based on QSScore
Scoring is based on CA/C3' positions which are present in all chains of
@@ -874,6 +883,11 @@ class ChainMapper:
:type contact_d: :class:`float`
:param strategy: Strategy for sampling, must be in ["naive"]
:type strategy: :class:`str`
+ :param chem_mapping_result: Pro param. The result of
+ :func:`~GetChemMapping` where you provided
+ *model*. If set, *model* parameter is not
+ used.
+ :type chem_mapping_result: :class:`tuple`
:returns: A :class:`MappingResult`
"""
@@ -881,7 +895,10 @@ class ChainMapper:
if strategy not in strategies:
raise RuntimeError(f"strategy must be {strategies}")
- chem_mapping, chem_group_alns, mdl = self.GetChemMapping(model)
+ if chem_mapping_result is None:
+ chem_mapping, chem_group_alns, mdl = self.GetChemMapping(model)
+ else:
+ chem_mapping, chem_group_alns, mdl = chem_mapping_result
ref_mdl_alns = _GetRefMdlAlns(self.chem_groups,
self.chem_group_alignments,
chem_mapping,
@@ -934,7 +951,8 @@ class ChainMapper:
def GetRigidMapping(self, model, strategy = "greedy_single_gdtts",
single_chain_gdtts_thresh=0.4, subsampling=None,
- first_complete=False, iterative_superposition=False):
+ first_complete=False, iterative_superposition=False,
+ chem_mapping_result = None):
"""Identify chain mapping based on rigid superposition
Superposition and scoring is based on CA/C3' positions which are present
@@ -989,6 +1007,11 @@ class ChainMapper:
as oposed to
:func:`ost.mol.alg.SuperposeSVD`
:type iterative_superposition: :class:`bool`
+ :param chem_mapping_result: Pro param. The result of
+ :func:`~GetChemMapping` where you provided
+ *model*. If set, *model* parameter is not
+ used.
+ :type chem_mapping_result: :class:`tuple`
:returns: A :class:`MappingResult`
"""
@@ -997,7 +1020,10 @@ class ChainMapper:
if strategy not in strategies:
raise RuntimeError(f"strategy must be {strategies}")
- chem_mapping, chem_group_alns, mdl = self.GetChemMapping(model)
+ if chem_mapping_result is None:
+ chem_mapping, chem_group_alns, mdl = self.GetChemMapping(model)
+ else:
+ chem_mapping, chem_group_alns, mdl = chem_mapping_result
ref_mdl_alns = _GetRefMdlAlns(self.chem_groups,
self.chem_group_alignments,
chem_mapping,
@@ -1093,7 +1119,7 @@ class ChainMapper:
def GetRepr(self, substructure, model, topn=1, inclusion_radius=15.0,
thresholds=[0.5, 1.0, 2.0, 4.0], bb_only=False,
- only_interchain=False):
+ only_interchain=False, chem_mapping_result = None):
""" Identify *topn* representations of *substructure* in *model*
*substructure* defines a subset of :attr:`~target` for which one
@@ -1124,7 +1150,11 @@ class ChainMapper:
:param only_interchain: Only score interchain contacts in lDDT. Useful
if you want to identify interface patches.
:type only_interchain: :class:`bool`
-
+ :param chem_mapping_result: Pro param. The result of
+ :func:`~GetChemMapping` where you provided
+ *model*. If set, *model* parameter is not
+ used.
+ :type chem_mapping_result: :class:`tuple`
:returns: :class:`list` of :class:`ReprResult`
"""
@@ -1168,7 +1198,10 @@ class ChainMapper:
"a backbone atom named CA or C3\'")
# perform mapping and alignments on full structures
- chem_mapping, chem_group_alns, mdl = self.GetChemMapping(model)
+ if chem_mapping_result is None:
+ chem_mapping, chem_group_alns, mdl = self.GetChemMapping(model)
+ else:
+ chem_mapping, chem_group_alns, mdl = chem_mapping_result
ref_mdl_alns = _GetRefMdlAlns(self.chem_groups,
self.chem_group_alignments,
chem_mapping,
diff --git a/modules/mol/alg/pymod/scoring.py b/modules/mol/alg/pymod/scoring.py
index 6d5b345ec9bb012c6b262c43bb0b587ff096641d..b6635c24064d0908f80ea08bd2159639deada18f 100644
--- a/modules/mol/alg/pymod/scoring.py
+++ b/modules/mol/alg/pymod/scoring.py
@@ -109,10 +109,11 @@ class Scorer:
colored to True in
:class:`ost.mol.alg.MolckSettings` constructor.
:type molck_settings: :class:`ost.mol.alg.MolckSettings`
- :param naive_chain_mapping_thresh: Chain mappings for targets up to that
- number of chains will be fully enumerated
- to optimize for QS-score. Everything
- above is treated with a heuristic.
+ :param naive_chain_mapping_thresh: Chain mappings for targets/models up to
+ that number of chains will be fully
+ enumerated to optimize for QS-score.
+ Everything above is treated with a
+ heuristic.
:type naive_chain_mapping_thresh: :class:`int`
:param cad_score_exec: Explicit path to voronota-cadscore executable from
voronota installation from
@@ -356,15 +357,20 @@ class Scorer:
"""
if self._mapping is None:
n_trg_chains = len(self.chain_mapper.target.chains)
- if n_trg_chains <= self.naive_chain_mapping_thresh:
+ res = self.chain_mapper.GetChemMapping(self.model)
+ n_mdl_chains = len(res[2].chains)
+ thresh = self.naive_chain_mapping_thresh
+ if n_trg_chains <= thresh and n_mdl_chains <= thresh:
m = self.chain_mapper.GetQSScoreMapping(self.model,
- strategy="naive")
+ strategy="naive",
+ chem_mapping_result=res)
else:
m = self.chain_mapper.GetQSScoreMapping(self.model,
strategy="greedy_block",
steep_opt_rate=3,
block_seed_size=5,
- block_blocks_per_chem_group=6)
+ block_blocks_per_chem_group=6,
+ chem_mapping_result=res)
self._mapping = m
return self._mapping