From c32ba0f78e5e3a289b7cfc9f6d357fb74d7f185f Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Tue, 9 May 2023 11:53:08 +0200
Subject: [PATCH] Add "swapped" TMScore to TMAlignResult/MMAlignResult
That's the TMscore when using the other structure as reference
---
modules/bindings/doc/tmtools.rst | 2 ++
modules/bindings/pymod/export_tmalign.cc | 6 ++++--
modules/bindings/pymod/tmtools.py | 6 ++++--
modules/bindings/src/wrap_tmalign.cc | 7 ++++++-
modules/bindings/src/wrap_tmalign.hh | 16 +++++++++++-----
5 files changed, 27 insertions(+), 10 deletions(-)
diff --git a/modules/bindings/doc/tmtools.rst b/modules/bindings/doc/tmtools.rst
index f55cdb458..6d1307e7f 100644
--- a/modules/bindings/doc/tmtools.rst
+++ b/modules/bindings/doc/tmtools.rst
@@ -105,6 +105,7 @@ generated in order to call the executable.
:param rmsd: RMSD of the superposed residues
:param tm_score: TMScore of the superposed residues
+ :param tm_score_swapped: TMScore when reference is swapped
:param aligned_length: Number of superposed residues
:param transform: Transformation matrix to superpose first chain onto
reference
@@ -175,6 +176,7 @@ comparing full biounits:
:param rmsd: RMSD of the superposed residues
:param tm_score: TMScore of the superposed residues
+ :param tm_score_swapped: TMScore when reference is swapped
:param aligned_length: Number of superposed residues
:param transform: Transformation matrix to superpose mdl onto reference
:param alignments: Alignments of all mapped chains, with first sequence
diff --git a/modules/bindings/pymod/export_tmalign.cc b/modules/bindings/pymod/export_tmalign.cc
index 5d2e4a300..060421d01 100644
--- a/modules/bindings/pymod/export_tmalign.cc
+++ b/modules/bindings/pymod/export_tmalign.cc
@@ -46,10 +46,11 @@ ost::bindings::MMAlignResult WrapMMAlignView(const ost::mol::EntityView& ent1,
}
void export_TMAlign() {
- class_<ost::bindings::TMAlignResult>("TMAlignResult", init<Real, Real, int, const geom::Mat4&,
+ class_<ost::bindings::TMAlignResult>("TMAlignResult", init<Real, Real, Real, int, const geom::Mat4&,
const ost::seq::AlignmentHandle&>())
.add_property("rmsd", make_function(&ost::bindings::TMAlignResult::GetRMSD))
.add_property("tm_score", make_function(&ost::bindings::TMAlignResult::GetTMScore))
+ .add_property("tm_score_swapped", make_function(&ost::bindings::TMAlignResult::GetTMScoreSwapped))
.add_property("aligned_length", make_function(&ost::bindings::TMAlignResult::GetAlignedLength))
.add_property("transform", make_function(&ost::bindings::TMAlignResult::GetTransform,
return_value_policy<reference_existing_object>()))
@@ -57,12 +58,13 @@ void export_TMAlign() {
return_value_policy<reference_existing_object>()))
;
- class_<ost::bindings::MMAlignResult>("MMAlignResult", init<Real, Real, const geom::Mat4&, int,
+ class_<ost::bindings::MMAlignResult>("MMAlignResult", init<Real, Real, Real, int, const geom::Mat4&,
const ost::seq::AlignmentList&,
const std::vector<String>&,
const std::vector<String>&>())
.add_property("rmsd", make_function(&ost::bindings::MMAlignResult::GetRMSD))
.add_property("tm_score", make_function(&ost::bindings::MMAlignResult::GetTMScore))
+ .add_property("tm_score_swapped", make_function(&ost::bindings::MMAlignResult::GetTMScoreSwapped))
.add_property("transform", make_function(&ost::bindings::MMAlignResult::GetTransform,
return_value_policy<reference_existing_object>()))
.add_property("aligned_length", make_function(&ost::bindings::MMAlignResult::GetAlignedLength))
diff --git a/modules/bindings/pymod/tmtools.py b/modules/bindings/pymod/tmtools.py
index 94fc4ceed..d58691c04 100644
--- a/modules/bindings/pymod/tmtools.py
+++ b/modules/bindings/pymod/tmtools.py
@@ -55,7 +55,8 @@ def _CleanupFiles(dir_name):
def _ParseTmAlign(lines,lines_matrix):
info_line=lines[12].split(',')
aln_length=int(info_line[0].split('=')[1].strip())
- rmsd=float(info_line[1].split('=')[1].strip())
+ rmsd=float(info_line[1].split('=')[1].strip())
+ tm_score_swapped=float(lines[13].split('=')[1].split('(')[0].strip())
tm_score=float(lines[14].split('=')[1].split('(')[0].strip())
tf1=[float(i.strip()) for i in lines_matrix[2].split()]
tf2=[float(i.strip()) for i in lines_matrix[3].split()]
@@ -69,7 +70,8 @@ def _ParseTmAlign(lines,lines_matrix):
alignment = seq.CreateAlignment()
alignment.AddSequence(seq2)
alignment.AddSequence(seq1)
- return ost.bindings.TMAlignResult(rmsd, tm_score, aln_length, tf, alignment)
+ return ost.bindings.TMAlignResult(rmsd, tm_score, tm_score_swapped,
+ aln_length, tf, alignment)
def _RunTmAlign(tmalign, tmp_dir):
model1_filename=os.path.join(tmp_dir, 'model01.pdb')
diff --git a/modules/bindings/src/wrap_tmalign.cc b/modules/bindings/src/wrap_tmalign.cc
index 0084bac5b..78c372dba 100644
--- a/modules/bindings/src/wrap_tmalign.cc
+++ b/modules/bindings/src/wrap_tmalign.cc
@@ -160,6 +160,8 @@ MMAlignResult MMalign_final_hacked(
MMAlignResult res;
res.rmsd = rmsd0;
res.tm_score = TM1;
+ res.tm_score_swapped = TM2;
+ res.aligned_length = n_ali8;
res.transform = geom::Mat4(u0[0][0], u0[0][1], u0[0][2], t0[0],
u0[1][0], u0[1][1], u0[1][2], t0[1],
u0[2][0], u0[2][1], u0[2][2], t0[2],
@@ -405,6 +407,7 @@ TMAlignResult WrappedTMAlign(const geom::Vec3List& pos_one,
// collect results and return
TMAlignResult res;
res.tm_score = TM1;
+ res.tm_score_swapped = TM2;
res.rmsd = rmsd0;
res.aligned_length = n_ali8;
res.transform = geom::Mat4(u0[0][0], u0[0][1], u0[0][2], t0[0],
@@ -460,7 +463,9 @@ MMAlignResult WrappedMMAlign(const std::vector<geom::Vec3List>& pos_one,
ent1_mapped_chains.push_back(seq1[0].GetName());
ent2_mapped_chains.push_back(seq2[0].GetName());
return MMAlignResult(tm_result.rmsd, tm_result.tm_score,
- tm_result.transform, tm_result.aligned_length,
+ tm_result.tm_score_swapped,
+ tm_result.aligned_length,
+ tm_result.transform,
alns, ent1_mapped_chains,
ent2_mapped_chains);
}
diff --git a/modules/bindings/src/wrap_tmalign.hh b/modules/bindings/src/wrap_tmalign.hh
index 79bdc689b..282209ca5 100644
--- a/modules/bindings/src/wrap_tmalign.hh
+++ b/modules/bindings/src/wrap_tmalign.hh
@@ -31,9 +31,10 @@ struct TMAlignResult {
TMAlignResult() { }
- TMAlignResult(Real rm, Real tm, int aln_l, const geom::Mat4& t,
+ TMAlignResult(Real rm, Real tm, Real tm_swp, int aln_l, const geom::Mat4& t,
const ost::seq::AlignmentHandle& aln): rmsd(rm),
tm_score(tm),
+ tm_score_swapped(tm_swp),
aligned_length(aln_l),
transform(t),
alignment(aln) { }
@@ -41,11 +42,13 @@ struct TMAlignResult {
Real rmsd;
Real tm_score;
+ Real tm_score_swapped;
int aligned_length;
geom::Mat4 transform;
ost::seq::AlignmentHandle alignment;
Real GetTMScore() { return tm_score; }
+ Real GetTMScoreSwapped() { return tm_score_swapped; }
Real GetRMSD() { return rmsd; }
int GetAlignedLength() { return aligned_length; }
const geom::Mat4& GetTransform() { return transform; }
@@ -56,13 +59,14 @@ struct MMAlignResult {
MMAlignResult() { }
- MMAlignResult(Real rm, Real tm, const geom::Mat4& t,
- int al, const ost::seq::AlignmentList& alns,
+ MMAlignResult(Real rm, Real tm, Real tm_swp, int al, const geom::Mat4& t,
+ const ost::seq::AlignmentList& alns,
const std::vector<String>& e1c,
const std::vector<String>& e2c): rmsd(rm),
tm_score(tm),
- transform(t),
+ tm_score_swapped(tm_swp),
aligned_length(al),
+ transform(t),
alignments(alns),
ent1_mapped_chains(e1c),
ent2_mapped_chains(e2c) { }
@@ -70,13 +74,15 @@ struct MMAlignResult {
Real rmsd;
Real tm_score;
- geom::Mat4 transform;
+ Real tm_score_swapped;
int aligned_length;
+ geom::Mat4 transform;
ost::seq::AlignmentList alignments;
std::vector<String> ent1_mapped_chains;
std::vector<String> ent2_mapped_chains;
Real GetTMScore() { return tm_score; }
+ Real GetTMScoreSwapped() { return tm_score_swapped; }
Real GetRMSD() { return rmsd; }
int GetAlignedLength() { return aligned_length; }
const geom::Mat4& GetTransform() { return transform; }
--
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