From 6ee43e37263f285c6593d966560e8600dfa360db Mon Sep 17 00:00:00 2001
From: Marco Biasini <mvbiasini@gmail.com>
Date: Tue, 5 Mar 2013 20:15:48 +0100
Subject: [PATCH] speed up intersection at expense of memory
---
modules/mol/base/src/chain_view.cc | 20 ++++++++++++++++----
1 file changed, 16 insertions(+), 4 deletions(-)
diff --git a/modules/mol/base/src/chain_view.cc b/modules/mol/base/src/chain_view.cc
index b8fc1b55b..8f8d2c0e1 100644
--- a/modules/mol/base/src/chain_view.cc
+++ b/modules/mol/base/src/chain_view.cc
@@ -72,6 +72,17 @@ public:
}
EntityViewDataWeakPtr entity;
ResidueViewList residues;
+ std::map<unsigned long, ResidueView> handle_to_view;
+
+ ResidueView ViewForHandle(const ResidueHandle& r)
+ {
+ std::map<unsigned long, ResidueView>::iterator i=handle_to_view.find(r.GetHashCode());
+ if (i!=handle_to_view.end()) {
+ return i->second;
+ }
+ return ResidueView();
+ }
+
bool in_sequence;
};
@@ -184,10 +195,7 @@ ResidueView ChainView::FindResidue(const ResidueHandle& residue) const {
ResidueView ChainView::ViewForHandle(const ResidueHandle& handle) const {
this->CheckValidity();
- const ResidueViewList& l=data_->residues;
- ResidueViewList::const_iterator i;
- i=std::find_if(l.begin(), l.end(), bind(&ResidueView::GetHandle, _1)==handle);
- return i==data_->residues.end() ? ResidueView() : *i;
+ return data_->ViewForHandle(handle);
}
@@ -209,6 +217,7 @@ ResidueView ChainView::AddResidue(const ResidueHandle& residue_handle,
data_->in_sequence=false;
}
data_->residues.push_back(rv);
+ data_->handle_to_view[rv.GetHandle().GetHashCode()] = rv;
if (flags & ViewAddFlag::INCLUDE_ATOMS) {
const impl::AtomImplList& l=residue_handle.Impl()->GetAtomList();
for (impl::AtomImplList::const_iterator i=l.begin(); i!=l.end(); ++i) {
@@ -267,6 +276,7 @@ void ChainView::RemoveResidue(ResidueView view) {
}
}
data_->residues.erase(to_del);
+ data_->handle_to_view.erase(view.GetHandle().GetHashCode());
}
ResidueView ChainView::AddResidue(const ResidueView& residue_view,
@@ -287,6 +297,7 @@ ResidueView ChainView::AddResidue(const ResidueView& residue_view,
data_->in_sequence=false;
}
data_->residues.push_back(rv);
+ data_->handle_to_view[rv.GetHandle().GetHashCode()] = rv;
if (flags & ViewAddFlag::INCLUDE_ATOMS) {
AtomViewList::const_iterator i=residue_view.GetAtomList().begin();
for (; i!=residue_view.GetAtomList().end(); ++i) {
@@ -301,6 +312,7 @@ void ChainView::RemoveResidues() {
std::for_each(data_->residues.begin(), data_->residues.end(),
bind(&ResidueView::RemoveAtoms, _1));
data_->residues.clear();
+ data_->handle_to_view.clear();
}
--
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