From 0a51546658790740e70842c71b523f3b3b3d1f4f Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Wed, 14 Sep 2022 11:11:39 +0200
Subject: [PATCH] chain mapping: Add substructure attribute to ReprResult
object
---
modules/mol/alg/pymod/chain_mapping.py | 25 ++++++++++++++++++++-----
1 file changed, 20 insertions(+), 5 deletions(-)
diff --git a/modules/mol/alg/pymod/chain_mapping.py b/modules/mol/alg/pymod/chain_mapping.py
index 7cd711b1f..865e3b2ab 100644
--- a/modules/mol/alg/pymod/chain_mapping.py
+++ b/modules/mol/alg/pymod/chain_mapping.py
@@ -116,13 +116,18 @@ class ReprResult:
:func:`ChainMapper.GetRepr` whether this is backbone only or
full atom lDDT.
:type lDDT: :class:`float`
- :param ref_view: The reference substructure
+ :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`
"""
- def __init__(self, lDDT, ref_view, mdl_view):
+ def __init__(self, lDDT, substructure, ref_view, mdl_view):
self._lDDT = lDDT
+ self._substructure = substructure
assert(len(ref_view.residues) == len(mdl_view.residues))
self._ref_view = ref_view
self._mdl_view = mdl_view
@@ -150,9 +155,18 @@ class ReprResult:
"""
return self._lDDT
+ @property
+ def substructure(self):
+ """ The full substructure for which we searched for a
+ representation
+
+ :type: :class:`ost.mol.EntityView`
+ """
+ return self._substructure
+
@property
def ref_view(self):
- """ View representing the reference substructure
+ """ View which contains the mapped subset of :attr:`substructure`
:type: :class:`ost.mol.EntityView`
"""
@@ -160,7 +174,7 @@ class ReprResult:
@property
def mdl_view(self):
- """ View representing the matching counterpart in model
+ """ The :attr:`ref_view` represention in the model
:type: :class:`ost.mol.EntityView`
"""
@@ -1185,7 +1199,8 @@ class ChainMapper:
mol.ViewAddFlag.INCLUDE_ALL)
mdl_view.AddResidue(col.GetResidue(1),
mol.ViewAddFlag.INCLUDE_ALL)
- results.append(ReprResult(scored_mapping[0], ref_view, mdl_view))
+ results.append(ReprResult(scored_mapping[0], substructure,
+ ref_view, mdl_view))
return results
def GetNMappings(self, model):
--
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