From 2ac198854ea99ec977cf68be9bc83c29a9978a52 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Tue, 22 Aug 2017 11:08:50 +0200
Subject: [PATCH] don't assume the bb_list to have valid peptide bonds to
enforce consistency with DSSP
---
scoring/src/ss_agreement_env_listener.cc | 20 +++++++++++---------
1 file changed, 11 insertions(+), 9 deletions(-)
diff --git a/scoring/src/ss_agreement_env_listener.cc b/scoring/src/ss_agreement_env_listener.cc
index 19d885f4..7456098a 100644
--- a/scoring/src/ss_agreement_env_listener.cc
+++ b/scoring/src/ss_agreement_env_listener.cc
@@ -130,10 +130,9 @@ void SSAgreementEnvListener::ClearEnvironment(const BackboneScoreEnv& base_env,
env_data_[*i + 1].valid_h_pos = false;
}
- // we call FindOptimalDonors for the deleted residues.
- // the only thing that will happen:
- // according donor_for_one_ / donor_for_two_ gets set to -1
- FindOptimalDonors(*i);
+ // its no donor anymore
+ donor_for_one_[*i] = -1;
+ donor_for_two_[*i] = -1;
}
std::set<int> stuff_to_update;
@@ -155,7 +154,6 @@ void SSAgreementEnvListener::SetTemporaryInteractions(
temp_start_idx_ = start_idx;
temp_size_ = bb_list.size();
-
// lets first copy over all the data from the bb_list, as well as one before
// and one after
int idx = std::max(0, temp_start_idx_ - 1);
@@ -204,9 +202,13 @@ void SSAgreementEnvListener::SetTemporaryInteractions(
connected_to_next_[temp_start_idx_-1] = 0;
}
- // the bb_list is assumed to be connected
+ // connection of bb_list itself
for(int i = 0; i < temp_size_ - 1; ++i) {
- connected_to_next_[temp_start_idx_+1] = 1;
+ if(geom::Length2(bb_list.GetC(i) - bb_list.GetN(i+1)) <= 6.25) {
+ connected_to_next_[temp_start_idx_+i] = 1;
+ } else {
+ connected_to_next_[temp_start_idx_+i] = 0;
+ }
}
// lets see whether the last residue is connected
@@ -220,8 +222,8 @@ void SSAgreementEnvListener::SetTemporaryInteractions(
connected_to_next_[temp_start_idx_+temp_size_-1] = 0;
}
- // let's finally update the hydrogen positions of all bb_list residues
- // and the one residue after
+ // set h positions of all loop residues, as well as the one
+ // residue after (if present)
idx = temp_start_idx_;
end = temp_start_idx_ + temp_size_;
if(static_cast<uint>(end) < idx_handler_->GetNumResidues()) ++end;
--
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