From 5c7e600e66fdc6e23470f24e6f5795a18204f329 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Fri, 5 May 2023 08:20:33 +0200
Subject: [PATCH] WrappedTMAlign bugfix: RNA needs custom secondary structure
assignment
---
modules/bindings/src/wrap_tmalign.cc | 13 +++++++++----
1 file changed, 9 insertions(+), 4 deletions(-)
diff --git a/modules/bindings/src/wrap_tmalign.cc b/modules/bindings/src/wrap_tmalign.cc
index 8c05e0228..18eb4ad88 100644
--- a/modules/bindings/src/wrap_tmalign.cc
+++ b/modules/bindings/src/wrap_tmalign.cc
@@ -72,8 +72,13 @@ TMAlignResult WrappedTMAlign(const geom::Vec3List& pos_one,
seqy[i] = seq2[i];
}
- make_sec(xa, xlen, secx);
- make_sec(ya, ylen, secy);
+ if(rna) {
+ make_sec(seqx, xa, xlen, secx, " C3'");
+ make_sec(seqy, ya, ylen, secy, " C3'");
+ } else {
+ make_sec(xa, xlen, secx);
+ make_sec(ya, ylen, secy);
+ }
// these variables are chosen such that running TMalign_main is the same as
// you would call the executable without any additional parameters
@@ -154,7 +159,7 @@ void ExtractChainInfo(const ost::mol::ChainView& chain, geom::Vec3List& pos,
if(rna_mode) {
std::stringstream ss;
ss << "Error in WrappedTMAlign: Chains cannot have peptide and RNA ";
- ss << "residues. Problematic chain: "<<chain.GetName();
+ ss << "residues in same chain. Problematic chain: "<<chain.GetName();
throw ost::Error(ss.str());
}
olcs.push_back(olc);
@@ -168,7 +173,7 @@ void ExtractChainInfo(const ost::mol::ChainView& chain, geom::Vec3List& pos,
if(rna_mode==false && !pos.empty()) {
std::stringstream ss;
ss << "Error in WrappedTMAlign: Chains cannot have peptide and RNA ";
- ss << "residues. Problematic chain: "<<chain.GetName();
+ ss << "residues in same chain. Problematic chain: "<<chain.GetName();
throw ost::Error(ss.str());
}
rna_mode = true;
--
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