diff --git a/modules/bindings/pymod/export_tmalign.cc b/modules/bindings/pymod/export_tmalign.cc
index 060421d01230bb5a35e27f3a6b4ec3c09bd889b6..352e03e35dd66d482c282ea11a34469af7fa33be 100644
--- a/modules/bindings/pymod/export_tmalign.cc
+++ b/modules/bindings/pymod/export_tmalign.cc
@@ -40,9 +40,17 @@ ost::bindings::TMAlignResult WrapTMAlignView(const ost::mol::ChainView& chain1,
ost::bindings::MMAlignResult WrapMMAlignView(const ost::mol::EntityView& ent1,
const ost::mol::EntityView& ent2,
- bool fast) {
+ bool fast,
+ boost::python::dict& mapping) {
+ boost::python::list keys(mapping.keys());
+ boost::python::list values(mapping.values());
+ std::map<String, String> m_mapping;
+ for(uint i = 0; i < boost::python::len(keys); ++i) {
+ m_mapping[boost::python::extract<String>(keys[i])] =
+ boost::python::extract<String>(values[i]);
+ }
- return ost::bindings::WrappedMMAlign(ent1, ent2, fast);
+ return ost::bindings::WrappedMMAlign(ent1, ent2, fast, m_mapping);
}
void export_TMAlign() {
@@ -84,5 +92,6 @@ void export_TMAlign() {
arg("fast")=false));
def("WrappedMMAlign", &WrapMMAlignView, (arg("ent1"), arg("ent2"),
- arg("fast")=false));
+ arg("fast")=false,
+ arg("mapping")=boost::python::dict()));
}
diff --git a/modules/bindings/src/wrap_tmalign.cc b/modules/bindings/src/wrap_tmalign.cc
index 9be1639a4f601ffddcc4d41d8fa85c9cb9a04ba2..91544c06ce2973d026ea15a3eba932a1d3e556f9 100644
--- a/modules/bindings/src/wrap_tmalign.cc
+++ b/modules/bindings/src/wrap_tmalign.cc
@@ -428,9 +428,10 @@ MMAlignResult WrappedMMAlign(const std::vector<geom::Vec3List>& pos_one,
const ost::seq::SequenceList& seq2,
const std::vector<bool>& rna1,
const std::vector<bool>& rna2,
- bool fast) {
+ bool fast,
+ const std::map<int, int>& mapping) {
- std::map<int,int> chainmap;
+ std::map<int, int> chainmap(mapping);
// input checks
if(pos_one.empty() || pos_two.empty()) {
@@ -1081,7 +1082,8 @@ TMAlignResult WrappedTMAlign(const ost::mol::ChainView& chain1,
MMAlignResult WrappedMMAlign(const ost::mol::EntityView& ent1,
const ost::mol::EntityView& ent2,
- bool fast) {
+ bool fast,
+ const std::map<String, String>& mapping) {
ost::mol::ChainViewList chains1 = ent1.GetChainList();
int n1 = chains1.size();
std::vector<geom::Vec3List> pos1(n1);
@@ -1108,7 +1110,70 @@ MMAlignResult WrappedMMAlign(const ost::mol::EntityView& ent1,
s2.AddSequence(s);
}
- return WrappedMMAlign(pos1, pos2, s1, s2, rna1, rna2, fast);
+ std::map<int,int> int_mapping;
+ if(!mapping.empty()) {
+ // OpenStructure mapping is a dict with target chains as key and
+ // model chains as values. Target is ent2 and model is ent1.
+ // USalign needs the mapping the other way around,
+ // i.e. the chain idx of ent1 as key and chain idx of ent2 as value
+ std::set<int> mapped_trg_chains;
+ std::set<int> mapped_mdl_chains;
+ for(auto it = mapping.begin(); it != mapping.end(); ++it) {
+ String trg_cname = it->first;
+ String mdl_cname = it->second;
+ int trg_idx = -1;
+ int mdl_idx = -1;
+
+ for(int i = 0; i < n1; ++i) {
+ if(s1[i].GetName() == mdl_cname) {
+ mdl_idx = i;
+ break;
+ }
+ }
+
+ for(int i = 0; i < n2; ++i) {
+ if(s2[i].GetName() == trg_cname) {
+ trg_idx = i;
+ break;
+ }
+ }
+
+ if(mdl_idx == -1) {
+ std::stringstream ss;
+ ss << "Specified \""<<mdl_cname<<"\" as mdl chain name in custom ";
+ ss << "mapping. Mdl has no mappable chain with this name.";
+ throw ost::Error(ss.str());
+ }
+
+ if(mapped_mdl_chains.find(mdl_idx) != mapped_mdl_chains.end()) {
+ std::stringstream ss;
+ ss << "\""<<mdl_cname<<"\" appears more than once as mdl chain in ";
+ ss << "custom mapping";
+ throw ost::Error(ss.str());
+ }
+
+ if(trg_idx == -1) {
+ std::stringstream ss;
+ ss << "Specified \""<<trg_cname<<"\" as trg chain name in custom ";
+ ss << "mapping. Trg has no mappable chain with this name.";
+ throw ost::Error(ss.str());
+ }
+
+ if(mapped_trg_chains.find(trg_idx) != mapped_trg_chains.end()) {
+ std::stringstream ss;
+ ss << "\""<<trg_cname<<"\" appears more than once as trg chain in ";
+ ss << "custom mapping";
+ throw ost::Error(ss.str());
+ }
+
+ int_mapping[mdl_idx] = trg_idx;
+ mapped_trg_chains.insert(trg_idx);
+ mapped_mdl_chains.insert(mdl_idx);
+ }
+ }
+
+ return WrappedMMAlign(pos1, pos2, s1, s2, rna1, rna2, fast,
+ int_mapping);
}
}} //ns
diff --git a/modules/bindings/src/wrap_tmalign.hh b/modules/bindings/src/wrap_tmalign.hh
index 282209ca57597bef4e5d5a3f15fbbaafb3e2dd0a..bb96ff28c9a8498a84daf07408ce7ecc352ef19b 100644
--- a/modules/bindings/src/wrap_tmalign.hh
+++ b/modules/bindings/src/wrap_tmalign.hh
@@ -104,7 +104,9 @@ MMAlignResult WrappedMMAlign(const std::vector<geom::Vec3List>& pos_one,
const ost::seq::SequenceList& seq2,
const std::vector<bool>& rna1,
const std::vector<bool>& rna2,
- bool fast = false);
+ bool fast = false,
+ const std::map<int, int>& mapping =
+ std::map<int,int>());
TMAlignResult WrappedTMAlign(const ost::mol::ChainView& ent1,
const ost::mol::ChainView& ent2,
@@ -112,7 +114,9 @@ TMAlignResult WrappedTMAlign(const ost::mol::ChainView& ent1,
MMAlignResult WrappedMMAlign(const ost::mol::EntityView& ent1,
const ost::mol::EntityView& ent2,
- bool fast = false);
+ bool fast = false,
+ const std::map<String, String>& mapping =
+ std::map<String, String>());
}} //ns
#endif
diff --git a/modules/mol/alg/pymod/scoring.py b/modules/mol/alg/pymod/scoring.py
index 530a881bea6121795047225984484367a784d858..4cfcc614da4fa81dba62c2ba10343fe7beaa06c5 100644
--- a/modules/mol/alg/pymod/scoring.py
+++ b/modules/mol/alg/pymod/scoring.py
@@ -139,9 +139,7 @@ class Scorer:
:type n_max_naive: :class:`int`
:param oum: Override USalign Mapping. Inject mapping of :class:`Scorer`
object into USalign to compute TM-score. Experimental feature
- with limitations. Only works if external *usalign_exec* is
- provided that is reasonably new and contains the respective
- feature.
+ with limitations.
:type oum: :class:`bool`
"""
def __init__(self, model, target, resnum_alignments=False,
@@ -223,12 +221,6 @@ class Scorer:
raise RuntimeError(f"USalign exec ({usalign_exec}) "
f"is not executable")
- # this limitation can be removed as soon as custom chain mappings can
- # be injected in the OpenStructure internal USalign code
- if oum and (usalign_exec is None):
- raise RuntimeError("Must provide external USalign exec if oum "
- "enabled")
-
self.resnum_alignments = resnum_alignments
self.cad_score_exec = cad_score_exec
self.usalign_exec = usalign_exec
@@ -2103,7 +2095,14 @@ class Scorer:
def _compute_tmscore(self):
res = None
- if self.usalign_exec is not None:
+ if self.usalign_exec is None:
+ if self.oum:
+ flat_mapping = self.mapping.GetFlatMapping()
+ res = res = bindings.WrappedMMAlign(self.model, self.target,
+ mapping=flat_mapping)
+ else:
+ res = bindings.WrappedMMAlign(self.model, self.target)
+ else:
if self.oum:
flat_mapping = self.mapping.GetFlatMapping()
res = tmtools.USAlign(self.model, self.target,
@@ -2112,8 +2111,6 @@ class Scorer:
else:
res = tmtools.USAlign(self.model, self.target,
usalign = self.usalign_exec)
- else:
- res = bindings.WrappedMMAlign(self.model, self.target)
self._tm_score = res.tm_score
self._usalign_mapping = dict()