From 155c80dfe65c28d419c1795ad6bfa9f86cd871f3 Mon Sep 17 00:00:00 2001
From: stefan <stefan@5a81b35b-ba03-0410-adc8-b2c5c5119f08>
Date: Tue, 2 Mar 2010 12:59:22 +0000
Subject: [PATCH] -Optimized mol::Difference()
-Fixed ViewOp Test
git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@1753 5a81b35b-ba03-0410-adc8-b2c5c5119f08
---
modules/mol/base/src/view_op.cc | 54 +++++++++++++++++---------
modules/mol/base/tests/test_view_op.cc | 6 +--
2 files changed, 39 insertions(+), 21 deletions(-)
diff --git a/modules/mol/base/src/view_op.cc b/modules/mol/base/src/view_op.cc
index c59ea852a..2999c1274 100644
--- a/modules/mol/base/src/view_op.cc
+++ b/modules/mol/base/src/view_op.cc
@@ -108,42 +108,60 @@ mol::EntityView Difference(const mol::EntityView& ev1,
Profile diff_time("mol::Difference");
if (ev1.GetHandle()!=ev2.GetHandle()) {
throw IntegrityError(combining_not_allowed);
- }
- mol::EntityView diff=ev1.Copy();
- mol::ChainViewList::const_iterator c_it=ev2.GetChainList().begin();
- for ( ; c_it!=ev2.GetChainList().end(); ++c_it) {
+ }
+ mol::EntityView diff=ev1.CreateEmptyView();
+ mol::ChainViewList::const_iterator c_it=ev1.GetChainList().begin();
+ for ( ; c_it!=ev1.GetChainList().end(); ++c_it) {
mol::ChainView cv=*c_it;
- mol::ChainView cv2=diff.FindChain(cv.GetHandle());
+ mol::ChainView cv2=ev2.FindChain(cv.GetHandle());
if (!cv2) {
- continue;
+ diff.AddChain(cv,mol::ViewAddFlag::INCLUDE_ALL);
} else {
+ bool chain_added = false;
mol::ResidueViewList::const_iterator r_it=cv.GetResidueList().begin();
for (; r_it!=cv.GetResidueList().end(); ++r_it) {
mol::ResidueView rv=*r_it;
mol::ResidueView rv2=cv2.FindResidue(rv.GetHandle());
if (!rv2) {
- continue;
+ if(!chain_added){
+ diff.AddChain(cv);
+ chain_added = true;
+ }
+ diff.AddResidue(rv,mol::ViewAddFlag::INCLUDE_ALL);
} else {
+ bool residue_added = false;
mol::AtomViewList::const_iterator a_it=rv.GetAtomList().begin();
for (; a_it!=rv.GetAtomList().end(); ++a_it) {
- if (mol::AtomView av=rv2.FindAtom((*a_it).GetHandle())) {
- rv2.RemoveAtom(av);
+ if (!rv2.FindAtom((*a_it).GetHandle())) {
+ if(!residue_added){
+ diff.AddResidue(rv);
+ residue_added = true;
+ }
+ diff.AddAtom((*a_it).GetHandle(),mol::ViewAddFlag::INCLUDE_ALL);
}
}
- if (rv2.GetAtomList().empty()) {
- cv2.RemoveResidue(rv2);
- }
}
}
- if (cv2.GetResidueList().empty()) {
- diff.RemoveChain(cv2);
- }
}
}
- BondHandleList bonds=ev2.GetBondList();
- for (BondHandleList::const_iterator i=bonds.begin(),
+
+ BondSet bond_set;
+ // prepare for bond insertion
+ BondHandleList bonds=ev1.GetBondList();
+ for (BondHandleList::const_iterator i=bonds.begin(),
e=bonds.end(); i!=e; ++i) {
- diff.RemoveBond(*i);
+ bond_set.insert(*i);
+ }
+
+ BondHandleList bond_ev2 = ev2.GetBondList();
+ for (BondHandleList::const_iterator i=bond_ev2.begin(),
+ e=bond_ev2.end(); i!=e; ++i) {
+ bond_set.erase(*i);
+ }
+
+ for (BondSet::const_iterator i=bond_set.begin(),
+ e=bond_set.end(); i!=e; ++i) {
+ diff.AddBond(*i);
}
return diff;
}
diff --git a/modules/mol/base/tests/test_view_op.cc b/modules/mol/base/tests/test_view_op.cc
index eccefc02b..6af7d87f3 100644
--- a/modules/mol/base/tests/test_view_op.cc
+++ b/modules/mol/base/tests/test_view_op.cc
@@ -65,13 +65,13 @@ BOOST_AUTO_TEST_SUITE( mol_base )
BOOST_AUTO_TEST_CASE(test_difference)
{
- std::cout << "TEST DIFFERENCE!" << std::endl;
+
EntityHandle ent=mk_test_ent();
EntityView full=ent.CreateFullView();
EntityView v1=ent.Select("aname=A,B,C");
EntityView diff_view=mol::Difference(full, v1);
- BOOST_CHECK_EQUAL(diff_view.GetBondCount(), 4);
+ BOOST_CHECK_EQUAL(diff_view.GetBondCount(), 5);
BOOST_CHECK_EQUAL(diff_view.GetAtomCount(), 5);
BOOST_CHECK_EQUAL(diff_view.GetResidueCount(), 3);
BOOST_CHECK_EQUAL(diff_view.GetChainCount(), 2);
@@ -103,7 +103,7 @@ BOOST_AUTO_TEST_CASE(test_difference)
BOOST_CHECK(!find_bond(ent.FindAtom("A", mol::ResNum(1), "B"),
ent.FindAtom("A", mol::ResNum(2), "C"),
bonds));
- BOOST_CHECK(!find_bond(ent.FindAtom("A", mol::ResNum(2), "C"),
+ BOOST_CHECK(find_bond(ent.FindAtom("A", mol::ResNum(2), "C"),
ent.FindAtom("A", mol::ResNum(2), "D"),
bonds));
BOOST_CHECK(find_bond(ent.FindAtom("B", mol::ResNum(1), "E"),
--
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