From 0f7868c5e904a420df0d3cfb7be45f7f5ac96966 Mon Sep 17 00:00:00 2001
From: Gerardo Tauriello <gerardo.tauriello@unibas.ch>
Date: Wed, 18 Jul 2018 14:43:33 +0200
Subject: [PATCH] Added chain_mapping_scheme to qsscoring and
compare-structures.
---
actions/ost-compare-structures | 1 +
modules/doc/actions.rst | 3 +-
modules/mol/alg/pymod/qsscoring.py | 45 ++++++++++++++++++++++++++----
3 files changed, 42 insertions(+), 7 deletions(-)
diff --git a/actions/ost-compare-structures b/actions/ost-compare-structures
index 3b6b9107b..b4a192631 100644
--- a/actions/ost-compare-structures
+++ b/actions/ost-compare-structures
@@ -697,6 +697,7 @@ def _Main():
reference_results["info"]["residue_names_consistent"] = is_cons
reference_results["info"]["mapping"] = {
"chain_mapping": qs_scorer.chain_mapping,
+ "chain_mapping_scheme": qs_scorer.chain_mapping_scheme,
"alignments": _GetAlignmentsAsFasta(qs_scorer.alignments)}
skip_score = False
if opts.consistency_checks:
diff --git a/modules/doc/actions.rst b/modules/doc/actions.rst
index 779a95ea4..81813ef34 100644
--- a/modules/doc/actions.rst
+++ b/modules/doc/actions.rst
@@ -251,7 +251,8 @@ In the example above the output file looks as follows:
"chain_mapping": {
"A": "B",
"B": "A"
- },
+ },
+ "chain_mapping_scheme": "strict",
"alignments": [
">reference:A\n-PGLFLTLEGLDGSGKTTQARRLAAFLEAQGRPVLLTREPGGGLPEVRSL---QELSPEAEYLLFSADRAEHVRKVILPGLAAGKVVISDRYLDSSLAYQGYGRGLPLPWLREVAREATRGLKPRLTFLLDLPPEAALRRVR-------LGLEFFRRVREGYLALARAEPGRFVVLDATLPEEEIARAIQAHLRPLLP\n>model:B\nMPGLFLTLEGLDGSGKTTQARRLAAFLEAQGRPVLLTREPGGGLPEVRSLLLTQELSPEAEYLLFSADRAEHVRKVILPGLAAGKVVISDRYLDSSLAYQGYGRGLPLPWLREVAREATRGLKPRLTFLLDLPPEAALRRVRRPDRLEGLGLEFFRRVREGYLALARAEPGRFVVLDATLPEEEIARAIQAHLRPLLP",
">reference:B\n-PGLFLTLEGLDGSGKTTQARRLAAFLEAQGRPVLLTREPGGGLPEVRSLLLTQELSPEAEYLLFSADRAEHVRKVILPGLAAGKVVISDRYLDSSLAYQGYGRGLPLPWLREVAREATRGLKPRLTFLLDLPPEAALRRVRRPDRLEGLGLEFFRRVREGYLALARAEPGRFVVLDATLPEEEIARAIQAHLRPLLP\n>model:A\nMPGLFLTLEGLDGSGKTTQARRLAAFLEAQGRPVLLTREPGGGLPEVRSLLLTQELSPEAEYLLFSADRAEHVRKVILPGLAAGKVVISDRYLDSSLAYQGYGRGLPLPWLREVAREATRGLKPRLTFLLDLPPEAALRRVRRPDRLEGLGLEFFRRVREGYLALARAEPGRFVVLDATLPEEEIARAIQAHLRPLLP"
diff --git a/modules/mol/alg/pymod/qsscoring.py b/modules/mol/alg/pymod/qsscoring.py
index dbe8c1dba..b67746f6f 100644
--- a/modules/mol/alg/pymod/qsscoring.py
+++ b/modules/mol/alg/pymod/qsscoring.py
@@ -181,6 +181,7 @@ class QSscorer:
self._symm_1 = None
self._symm_2 = None
self._chain_mapping = None
+ self._chain_mapping_scheme = None
self._alignments = None
self._mapped_residues = None
self._global_score = None
@@ -364,12 +365,42 @@ class QSscorer:
to find a chain mapping.
"""
if self._chain_mapping is None:
- self._chain_mapping = _GetChainMapping(self.ent_to_cm_1, self.ent_to_cm_2,
- self.symm_1, self.symm_2,
- self.chem_mapping)
+ self._chain_mapping, self._chain_mapping_scheme = \
+ _GetChainMapping(self.ent_to_cm_1, self.ent_to_cm_2, self.symm_1,
+ self.symm_2, self.chem_mapping)
LogInfo('Mapping found: %s' % str(self._chain_mapping))
return self._chain_mapping
+ @property
+ def chain_mapping_scheme(self):
+ """Mapping scheme used to get :attr:`chain_mapping`.
+
+ Possible values:
+
+ - 'strict': 80% overlap needed within 4 Angstrom (overlap based mapping).
+ - 'tolerant': 40% overlap needed within 6 Angstrom (overlap based mapping).
+ - 'permissive': 20% overlap needed within 8 Angstrom (overlap based
+ mapping). It's best if you check mapping manually!
+ - 'extensive': Extensive search used for mapping detection (fallback). This
+ approach has known limitations and may be removed in future versions.
+ Mapping should be checked manually!
+ - 'user': :attr:`chain_mapping` was set by user before first use of this
+ attribute.
+
+ :getter: Computed with :attr:`chain_mapping` on first use (cached)
+ :type: :class:`str`
+ :raises: :class:`QSscoreError` if there are too many combinations to check
+ to find a chain mapping.
+ """
+ if self._chain_mapping_scheme is None:
+ # default: user provided
+ self._chain_mapping_scheme = 'user'
+ # get chain mapping and make sure internal variable is set
+ # -> will not compute and only update _chain_mapping if user provided
+ # -> will compute and overwrite _chain_mapping_scheme else
+ self._chain_mapping = self.chain_mapping
+ return self._chain_mapping_scheme
+
@property
def alignments(self):
"""List of successful sequence alignments using :attr:`chain_mapping`.
@@ -1782,7 +1813,9 @@ def _FindSymmetry(qs_ent_1, qs_ent_2, ent_to_cm_1, ent_to_cm_2, chem_mapping):
def _GetChainMapping(ent_1, ent_2, symm_1, symm_2, chem_mapping):
"""
- :return: Mapping from *ent_1* to *ent_2* (see :attr:`QSscorer.chain_mapping`)
+ :return: Tuple with mapping from *ent_1* to *ent_2* (see
+ :attr:`QSscorer.chain_mapping`) and scheme used (see
+ :attr:`QSscorer.chain_mapping_scheme`)
:param ent_1: See :attr:`QSscorer.ent_to_cm_1`
:param ent_2: See :attr:`QSscorer.ent_to_cm_2`
@@ -1808,7 +1841,7 @@ def _GetChainMapping(ent_1, ent_2, symm_1, symm_2, chem_mapping):
if scheme == 'permissive':
LogWarning('Permissive thresholds used for overlap based mapping ' + \
'detection: check mapping manually: %s' % mapping)
- return mapping
+ return mapping, scheme
# NOTE that what follows below is sub-optimal:
# - if the two structures don't fit at all, we may map chains rather randomly
@@ -1908,7 +1941,7 @@ def _GetChainMapping(ent_1, ent_2, symm_1, symm_2, chem_mapping):
LogWarning('Extensive search used for mapping detection (fallback). This ' + \
'approach has known limitations. Check mapping manually: %s' \
% mapping)
- return mapping
+ return mapping, 'extensive'
def _GetSymmetrySubgroups(qs_ent, ent, chem_groups):
--
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