diff --git a/actions/ost-compare-structures b/actions/ost-compare-structures
index 86ab664e96a2d98a31ac4f4679cd486bec3f3288..30a14717c99e70b66e3332869a8e66ffcea9f8d1 100644
--- a/actions/ost-compare-structures
+++ b/actions/ost-compare-structures
@@ -251,6 +251,19 @@ def _ParseArgs():
action="store_true",
help=("Make alignment based on residue number instead of using\n"
"a global BLOSUM62-based alignment."))
+ parser.add_argument(
+ "--qs-max-mappings-extensive",
+ dest="qs_max_mappings_extensive",
+ type=int,
+ default=1000000,
+ help=("Maximal number of chain mappings to test for 'extensive'\n"
+ "chain mapping scheme which is used as a last resort if\n"
+ "other schemes failed. The extensive chain mapping search\n"
+ "must in the worst case check O(N!) possible mappings for\n"
+ "complexes with N chains. Two octamers without symmetry\n"
+ "would require 322560 mappings to be checked. To limit\n"
+ "computations, no scores are computed if we try more than\n"
+ "the maximal number of chain mappings."))
#
# lDDT options
#
@@ -683,13 +696,19 @@ def _Main():
qs_scorer = qsscoring.QSscorer(reference,
model,
opts.residue_number_alignment)
+ qs_scorer.max_mappings_extensive = opts.qs_max_mappings_extensive
if opts.chain_mapping is not None:
ost.LogInfo(
"Using custom chain mapping: %s" % str(
opts.chain_mapping))
qs_scorer.chain_mapping = opts.chain_mapping
else:
- qs_scorer.chain_mapping # just to initialize it
+ try:
+ qs_scorer.chain_mapping # just to initialize it
+ except qsscoring.QSscoreError as ex:
+ ost.LogError('Chain mapping failed:', str(ex))
+ ost.LogError('Skipping comparison')
+ continue
ost.LogInfo("-" * 80)
ost.LogInfo("Checking consistency between %s and %s" % (
model_name, reference_name))
diff --git a/modules/doc/actions.rst b/modules/doc/actions.rst
index 8c31b7d4108e670f8c6091059438f82e4a8bb5e9..20858ec9b306e5ef9bbd3025b80ad4c23cbe46d4 100644
--- a/modules/doc/actions.rst
+++ b/modules/doc/actions.rst
@@ -24,7 +24,9 @@ lDDT scores between two complexes from the command line with:
[-rs REFERENCE_SELECTION] [-ms MODEL_SELECTION]
[-ca] [-ft] [-cl COMPOUND_LIBRARY] [-qs]
[-c CHAIN_MAPPING [CHAIN_MAPPING ...]]
- [--qs-rmsd] [-rna] [-l] [-ir INCLUSION_RADIUS]
+ [--qs-rmsd] [-rna]
+ [--qs-max-mappings-extensive QS_MAX_MAPPINGS_EXTENSIVE]
+ [-l] [-ir INCLUSION_RADIUS]
[-ss SEQUENCE_SEPARATION] [-spr] [-ml]
[-rm REMOVE [REMOVE ...]] [-ce] [-mn] [-sc]
[-p PARAMETER_FILE] [-bt BOND_TOLERANCE]
diff --git a/modules/mol/alg/pymod/qsscoring.py b/modules/mol/alg/pymod/qsscoring.py
index 8339bf2fa966f29437d03331f1840adb8dd70df0..0e584fe7f988013687eb4fe1e31e1422f2a02d0b 100644
--- a/modules/mol/alg/pymod/qsscoring.py
+++ b/modules/mol/alg/pymod/qsscoring.py
@@ -143,6 +143,19 @@ class QSscorer:
:type: :class:`int`
+ .. attribute:: max_mappings_extensive
+
+ Maximal number of chain mappings to test for 'extensive'
+ :attr:`chain_mapping_scheme`. The extensive chain mapping search must in the
+ worst case check O(N^2) * O(N!) possible mappings for complexes with N
+ chains. Two octamers without symmetry would require 322560 mappings to be
+ checked. To limit computations, a :class:`QSscoreError` is thrown if we try
+ more than the maximal number of chain mappings.
+ The value must be set before the first use of :attr:`chain_mapping`.
+ By default it is set to 100000.
+
+ :type: :class:`int`
+
.. attribute:: res_num_alignment
Forces each alignment in :attr:`alignments` to be based on residue numbers
@@ -174,6 +187,7 @@ class QSscorer:
self.res_num_alignment = res_num_alignment
self.calpha_only = self.qs_ent_1.calpha_only or self.qs_ent_2.calpha_only
self.max_ca_per_chain_for_cm = 100
+ self.max_mappings_extensive = 100000
# init cached stuff
self._chem_mapping = None
self._ent_to_cm_1 = None
@@ -361,12 +375,13 @@ class QSscorer:
:type: :class:`dict` with key / value = :class:`str` (chain names, key
for :attr:`ent_to_cm_1`, value for :attr:`ent_to_cm_2`)
:raises: :class:`QSscoreError` if there are too many combinations to check
- to find a chain mapping.
+ to find a chain mapping (see :attr:`max_mappings_extensive`).
"""
if self._chain_mapping is None:
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)
+ self.symm_2, self.chem_mapping,
+ self.max_mappings_extensive)
LogInfo('Mapping found: %s' % str(self._chain_mapping))
return self._chain_mapping
@@ -1811,7 +1826,8 @@ def _FindSymmetry(qs_ent_1, qs_ent_2, ent_to_cm_1, ent_to_cm_2, chem_mapping):
return [], []
-def _GetChainMapping(ent_1, ent_2, symm_1, symm_2, chem_mapping):
+def _GetChainMapping(ent_1, ent_2, symm_1, symm_2, chem_mapping,
+ max_mappings_extensive):
"""
:return: Tuple with mapping from *ent_1* to *ent_2* (see
:attr:`QSscorer.chain_mapping`) and scheme used (see
@@ -1822,6 +1838,7 @@ def _GetChainMapping(ent_1, ent_2, symm_1, symm_2, chem_mapping):
:param symm_1: See :attr:`QSscorer.symm_1`
:param symm_2: See :attr:`QSscorer.symm_2`
:param chem_mapping: See :attr:`QSscorer.chem_mapping`
+ :param max_mappings_extensive: See :attr:`QSscorer.max_mappings_extensive`
"""
LogInfo('Symmetry-groups used in %s: %s' % (ent_1.GetName(), str(symm_1)))
LogInfo('Symmetry-groups used in %s: %s' % (ent_2.GetName(), str(symm_2)))
@@ -1861,8 +1878,8 @@ def _GetChainMapping(ent_1, ent_2, symm_1, symm_2, chem_mapping):
LogInfo('Inter Symmetry-group mappings to check: %s' \
% count['inter']['mappings'])
nr_mapp = count['intra']['mappings'] + count['inter']['mappings']
- # if nr_mapp > 100000: # 322560 is octamer vs octamer
- # raise QSscoreError('Too many possible mappings: %s' % nr_mapp)
+ if nr_mapp > max_mappings_extensive:
+ raise QSscoreError('Too many possible mappings: %s' % nr_mapp)
# to speed up the computations we cache chain views and RMSDs
cached_rmsd = _CachedRMSD(ent_1, ent_2)