From 58dfbf88a1254583bb1b621bb4a8c88bac35c54b Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Tue, 20 Sep 2022 08:53:47 +0200
Subject: [PATCH] chain mapping: Get one-to-one flat mapping out of mapping
result
---
modules/mol/alg/pymod/chain_mapping.py | 19 +++++++++++++++++++
modules/mol/alg/tests/test_chain_mapping.py | 13 +++++++++++++
2 files changed, 32 insertions(+)
diff --git a/modules/mol/alg/pymod/chain_mapping.py b/modules/mol/alg/pymod/chain_mapping.py
index 865e3b2ab..4b90652f2 100644
--- a/modules/mol/alg/pymod/chain_mapping.py
+++ b/modules/mol/alg/pymod/chain_mapping.py
@@ -89,6 +89,25 @@ class MappingResult:
"""
return self._alns
+ def GetFlatMapping(self, mdl_as_key=False):
+ """ Returns flat mapping as :class:`dict` for all mapable chains
+
+ :param mdl_as_key: Default is target chain name as key and model chain
+ name as value. This can be reversed with this flag.
+ :returns: :class:`dict` with :class:`str` as key/value that describe
+ one-to-one mapping
+ """
+ flat_mapping = dict()
+ for trg_chem_group, mdl_chem_group in zip(self.chem_groups,
+ self.mapping):
+ for a,b in zip(trg_chem_group, mdl_chem_group):
+ if a is not None and b is not None:
+ if mdl_as_key:
+ flat_mapping[b] = a
+ else:
+ flat_mapping[a] = b
+ return flat_mapping
+
def JSONSummary(self):
""" Returns JSON serializable summary of results
"""
diff --git a/modules/mol/alg/tests/test_chain_mapping.py b/modules/mol/alg/tests/test_chain_mapping.py
index d9a9362eb..0a663081c 100644
--- a/modules/mol/alg/tests/test_chain_mapping.py
+++ b/modules/mol/alg/tests/test_chain_mapping.py
@@ -284,6 +284,19 @@ class TestChainMapper(unittest.TestCase):
greedy_rigid_res = mapper.GetRigidMapping(mdl, strategy="greedy_iterative_rmsd")
self.assertEqual(greedy_rigid_res.mapping, [['X', 'Y'],[None],['Z']])
+ # test flat mapping functionality of MappingResult
+ flat_map = greedy_rigid_res.GetFlatMapping()
+ self.assertEqual(len(flat_map), 3)
+ self.assertEqual(flat_map[greedy_rigid_res.chem_groups[0][0]], 'X')
+ self.assertEqual(flat_map[greedy_rigid_res.chem_groups[0][1]], 'Y')
+ self.assertEqual(flat_map[greedy_rigid_res.chem_groups[2][0]], 'Z')
+ flat_map = greedy_rigid_res.GetFlatMapping(mdl_as_key=True)
+ self.assertEqual(len(flat_map), 3)
+ self.assertEqual(greedy_rigid_res.chem_groups[0][0], flat_map['X'])
+ self.assertEqual(greedy_rigid_res.chem_groups[0][1], flat_map['Y'])
+ self.assertEqual(greedy_rigid_res.chem_groups[2][0], flat_map['Z'])
+
+
if __name__ == "__main__":
from ost import testutils
if testutils.SetDefaultCompoundLib():
--
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