From 7f66c1647991e83cef2f3d054e5011c4ad3b0b88 Mon Sep 17 00:00:00 2001
From: Marco Biasini <mvbiasini@gmail.com>
Date: Sun, 30 Dec 2012 09:49:55 +0100
Subject: [PATCH] Speeding up selections some more
This time, the speed improvement comes from eliminating excessive
calls of malloc/free caused by reallocation of the value stack for
the expression evaluation. Also, I've eliminated creating temporary
string copies wherever possible. The resulting Shark profile looks
much cleaner and is dominated by the actual evaluation rather than
mallocs/frees. Seems to improve speed by 10-20%.
---
modules/mol/base/src/query_state.cc | 36 +++++++++++++----------------
modules/mol/base/src/query_state.hh | 1 +
2 files changed, 17 insertions(+), 20 deletions(-)
diff --git a/modules/mol/base/src/query_state.cc b/modules/mol/base/src/query_state.cc
index c81d3b437..5f4ef1295 100644
--- a/modules/mol/base/src/query_state.cc
+++ b/modules/mol/base/src/query_state.cc
@@ -151,9 +151,8 @@ boost::logic::tribool QueryState::EvalChain(const ChainImplPtr& c) {
float float_value;
switch (ss.sel_id) {
case Prop::CNAME:
- value = c->GetName();
- s_[*i] = cmp_string(ss.comp_op,
- value,boost::get<StringOrRegexParam>(ss.param));
+ s_[*i] = cmp_string(ss.comp_op, c->GetName(),
+ boost::get<StringOrRegexParam>(ss.param));
continue;
default:
if (ss.sel_id>=Prop::CUSTOM) {
@@ -187,8 +186,7 @@ boost::logic::tribool QueryState::EvalResidue(const ResidueImplPtr& r) {
Real float_value;
switch (ss.sel_id) {
case Prop::RNAME:
- str_value = r->GetKey();
- s_[*i] = cmp_string(ss.comp_op,str_value,
+ s_[*i] = cmp_string(ss.comp_op,r->GetName(),
boost::get<StringOrRegexParam>(ss.param));
continue;
case Prop::RNUM:
@@ -234,7 +232,7 @@ boost::logic::tribool QueryState::EvalResidue(const ResidueImplPtr& r) {
}
s_[*i]=ss.comp_op==COP_EQ ? b : !b;
} else {
- str_value= String(1, (char)r->GetSecStructure());
+ str_value = String(1, (char)r->GetSecStructure());
s_[*i]=cmp_string(ss.comp_op,str_value,
boost::get<StringOrRegexParam>(ss.param));
}
@@ -265,19 +263,18 @@ boost::logic::tribool QueryState::EvalResidue(const ResidueImplPtr& r) {
boost::logic::tribool QueryState::EvalStack(Prop::Level level) {
const SelStack& stack = q_.sel_stacks_[(int)level];
SelStack::const_reverse_iterator i = stack.rbegin();
- std::vector<boost::logic::tribool> value_stack;
-
+ value_stack_.clear();
while (i!=stack.rend()) {
const SelItem& si = *i;
if (si.type==VALUE) {
- value_stack.push_back(s_[si.value]);
+ value_stack_.push_back(s_[si.value]);
++i;
continue;
} else {
- boost::logic::tribool lhs = value_stack.back();
- value_stack.pop_back();
- boost::logic::tribool rhs = value_stack.back();
- value_stack.pop_back();
+ boost::logic::tribool lhs = value_stack_.back();
+ value_stack_.pop_back();
+ boost::logic::tribool rhs = value_stack_.back();
+ value_stack_.pop_back();
LogicOP lop = (LogicOP)si.value;
boost::logic::tribool result;
switch(lop) {
@@ -288,12 +285,12 @@ boost::logic::tribool QueryState::EvalStack(Prop::Level level) {
result = lhs || rhs;
break;
}
- value_stack.push_back(result);
+ value_stack_.push_back(result);
++i;
}
}
- assert(value_stack.size()==1);
- return value_stack.back();
+ assert(value_stack_.size()==1);
+ return value_stack_.back();
}
namespace {
@@ -302,6 +299,7 @@ QueryImpl dummy_query_impl;
}
QueryState::QueryState()
: s_(), q_(dummy_query_impl) {
+ value_stack_.reserve(20);
}
boost::logic::tribool QueryState::EvalAtom(const AtomImplPtr& a) {
@@ -316,8 +314,7 @@ boost::logic::tribool QueryState::EvalAtom(const AtomImplPtr& a) {
int int_value;
switch (ss.sel_id) {
case Prop::ANAME:
- str_value = a->Name();
- s_[*i] = cmp_string(ss.comp_op,str_value,
+ s_[*i] = cmp_string(ss.comp_op,a->GetName(),
boost::get<StringOrRegexParam>(ss.param));
break;
case Prop::AINDEX:
@@ -345,8 +342,7 @@ boost::logic::tribool QueryState::EvalAtom(const AtomImplPtr& a) {
boost::get<float>(ss.param));
break;
case Prop::ELE:
- str_value = a->GetElement();
- s_[*i] = cmp_string(ss.comp_op,str_value,
+ s_[*i] = cmp_string(ss.comp_op,a->GetElement(),
boost::get<StringOrRegexParam>(ss.param));
break;
case Prop::ABFAC:
diff --git a/modules/mol/base/src/query_state.hh b/modules/mol/base/src/query_state.hh
index ad6feffd2..f2d8edfdd 100644
--- a/modules/mol/base/src/query_state.hh
+++ b/modules/mol/base/src/query_state.hh
@@ -82,6 +82,7 @@ private:
bool do_within(const geom::Vec3& pos, const impl::WithinParam& p,
impl::CompOP op);
std::vector<boost::logic::tribool> s_;
+ std::vector<boost::logic::tribool> value_stack_;
boost::shared_ptr<LazilyBoundData> r_;
const impl::QueryImpl& q_;
};
--
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