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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
#include <BALL/CONCEPT/classTest.h>
#include <BALLTestConfig.h>
#include <BALL/STRUCTURE/structureMapper.h>
#include <BALL/KERNEL/atom.h>
#include <BALL/KERNEL/fragment.h>
#include <BALL/KERNEL/system.h>
#include <BALL/MATHS/quaternion.h>
#include <BALL/FORMAT/PDBFile.h>
#include <vector>
START_TEST(StructureMapper)
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
using namespace BALL;
using std::vector;
StructureMapper* m;
CHECK(StructureMapper())
m = new StructureMapper();
TEST_NOT_EQUAL(m, 0)
RESULT
CHECK(~StructureMapper())
delete m;
RESULT
Fragment* frag1 = new Fragment;
Fragment* frag2 = new Fragment;
Matrix4x4 t;
CHECK(StructureMapper(AtomContainer& A, AtomContainer& B))
Atom* atom1 = new Atom;
Atom* atom2 = new Atom;
Atom* atom3 = new Atom;
Atom* atom4 = new Atom;
Atom* atom5 = new Atom;
Atom* atom6 = new Atom;
Atom* atom7 = new Atom;
Atom* atom8 = new Atom;
// create two fragments containing atoms
frag1->insert(*atom1);
frag1->insert(*atom2);
frag1->insert(*atom3);
frag1->insert(*atom4);
frag2->insert(*atom5);
frag2->insert(*atom6);
frag2->insert(*atom7);
frag2->insert(*atom8);
// set coordinates for all atoms
Vector3 v(0,0,0);
atom1->setPosition(v);
v.set(1,1,3);
atom2->setPosition(v);
v.set(2,5,3);
atom3->setPosition(v);
v.set(2,3,2);
atom4->setPosition(v);
Quaternion q(7,9,12,Constants::PI * 0.6);
q.normalize();
t = q.getRotationMatrix(t);
atom5->setPosition(t * atom1->getPosition());
atom6->setPosition(t * atom2->getPosition());
atom7->setPosition(t * atom3->getPosition());
atom8->setPosition(t * atom4->getPosition());
atom1->setName("A1");
atom2->setName("A2");
atom3->setName("A3");
atom4->setName("A4");
atom5->setName("A1");
atom6->setName("A2");
atom7->setName("A3");
atom8->setName("A4");
m = new StructureMapper(*frag1, *frag2);
TEST_NOT_EQUAL(m, 0)
RESULT
CHECK(bool mapFragments(const vector<Fragment*>& A, const vector<Fragment*>& B, Matrix4x4* transformation, double upper_bound = 8.0, double lower_bound = 2.5))
Matrix4x4 map_result;
vector<Fragment*> A;
vector<Fragment*> B;
A.push_back(frag1);
B.push_back(frag2);
TEST_EQUAL(m->mapFragments(A, B, &map_result), true)
TEST_REAL_EQUAL(map_result.m11, t.m11)
TEST_REAL_EQUAL(map_result.m12, t.m12)
TEST_REAL_EQUAL(map_result.m13, t.m13)
TEST_REAL_EQUAL(map_result.m14, t.m14)
TEST_REAL_EQUAL(map_result.m21, t.m21)
TEST_REAL_EQUAL(map_result.m22, t.m22)
TEST_REAL_EQUAL(map_result.m23, t.m23)
TEST_REAL_EQUAL(map_result.m24, t.m24)
TEST_REAL_EQUAL(map_result.m31, t.m31)
TEST_REAL_EQUAL(map_result.m32, t.m32)
TEST_REAL_EQUAL(map_result.m33, t.m33)
TEST_REAL_EQUAL(map_result.m34, t.m34)
TEST_REAL_EQUAL(map_result.m41, t.m41)
TEST_REAL_EQUAL(map_result.m42, t.m42)
TEST_REAL_EQUAL(map_result.m43, t.m43)
TEST_REAL_EQUAL(map_result.m44, t.m44)
RESULT
CHECK(static Matrix4x4 matchPoints(const Vector3& w1, const Vector3& w2, const Vector3& w3, const Vector3& v1, const Vector3& v2, const Vector3& v3))
PRECISION(1e-5)
Vector3 v1(2.0, 2.0, 2.0);
Vector3 v2(3.0, 2.0, 2.0);
Vector3 v3(2.0, 3.0, 2.0);
Vector3 w1(1.0, 1.0, 1.0);
Vector3 w2(2.0, 1.0, 1.0);
Vector3 w3(1.0, 2.0, 1.0);
Matrix4x4 T = StructureMapper::matchPoints(w1, w2, w3, v1, v2, v3);
STATUS("transformation:\n" << T)
TEST_REAL_EQUAL(T.m11, 1.0)
TEST_REAL_EQUAL(T.m12, 0.0)
TEST_REAL_EQUAL(T.m13, 0.0)
TEST_REAL_EQUAL(T.m14, 1.0)
TEST_REAL_EQUAL(T.m21, 0.0)
TEST_REAL_EQUAL(T.m22, 1.0)
TEST_REAL_EQUAL(T.m23, 0.0)
TEST_REAL_EQUAL(T.m24, 1.0)
TEST_REAL_EQUAL(T.m31, 0.0)
TEST_REAL_EQUAL(T.m32, 0.0)
TEST_REAL_EQUAL(T.m33, 1.0)
TEST_REAL_EQUAL(T.m34, 1.0)
TEST_REAL_EQUAL(T.m41, 0.0)
TEST_REAL_EQUAL(T.m42, 0.0)
TEST_REAL_EQUAL(T.m43, 0.0)
TEST_REAL_EQUAL(T.m44, 1.0)
TEST_REAL_EQUAL((T * w1 - v1).getSquareLength(), 0.0)
TEST_REAL_EQUAL((T * w2 - v2).getSquareLength(), 0.0)
TEST_REAL_EQUAL((T * w3 - v3).getSquareLength(), 0.0)
w1.set(5.0, 0.0, 0.0);
w2.set(5.0, 1.0, 0.0);
w3.set(5.0, 2.0, 1.0);
T = StructureMapper::matchPoints(w1, w2, w3, v1, v2, v3);
STATUS("transformation:\n" << T)
TEST_REAL_EQUAL(T.m11, 0.0)
TEST_REAL_EQUAL(T.m12, 1.0)
TEST_REAL_EQUAL(T.m13, 0.0)
TEST_REAL_EQUAL(T.m14, 2.0)
TEST_REAL_EQUAL(T.m21, 0.0)
TEST_REAL_EQUAL(T.m22, 0.0)
TEST_REAL_EQUAL(T.m23, 1.0)
TEST_REAL_EQUAL(T.m24, 2.0)
TEST_REAL_EQUAL(T.m31, 1.0)
TEST_REAL_EQUAL(T.m32, 0.0)
TEST_REAL_EQUAL(T.m33, 0.0)
TEST_REAL_EQUAL(T.m34, -3.0)
TEST_REAL_EQUAL(T.m41, 0.0)
TEST_REAL_EQUAL(T.m42, 0.0)
TEST_REAL_EQUAL(T.m43, 0.0)
TEST_REAL_EQUAL(T.m44, 1.0)
TEST_REAL_EQUAL((T * w1 - v1).getSquareLength(), 0.0)
TEST_REAL_EQUAL((T * w2 - v2).getSquareLength(), 0.0)
TEST_REAL_EQUAL((T * w3 - v3).getSquareLength(), 4.0)
// test co-linear case
w1.set(5.0, 0.0, 0.0);
w2.set(5.0, 1.0, 0.0);
w3.set(5.0, 2.0, 0.0);
T = StructureMapper::matchPoints(w1, w2, w3, v1, v2, v3);
STATUS("transformation:\n" << T)
TEST_REAL_EQUAL(T.m14, 2.0)
TEST_REAL_EQUAL(T.m24, -3.0)
TEST_REAL_EQUAL(T.m34, 2.0)
TEST_REAL_EQUAL(T.m44, 1.0)
TEST_REAL_EQUAL((T * w1 - v1).getSquareLength(), 0.0)
TEST_REAL_EQUAL((T * w2 - v2).getSquareLength(), 0.0)
// Test some weird pathological case found in 1BNA
// when using ReconstructFragmentProcessor
v1.set(17.221, 25.499, 18.629);
v2.set(18.217, 24.603, 18.897);
v3.set(19.526, 24.945, 18.571);
w1.set(22.167, 23.241, 33.694);
w2.set(21.100, 23.907, 33.243);
w3.set(20.022, 24.211, 34.147);
T = StructureMapper::matchPoints(w1, w2, w3, v1, v2, v3);
STATUS(T)
TEST_EQUAL(Maths::isNan(T(0,0)), false)
TEST_EQUAL(Maths::isNan(T(1,0)), false)
TEST_EQUAL(Maths::isNan(T(2,0)), false)
TEST_EQUAL(Maths::isNan(T(0,1)), false)
TEST_EQUAL(Maths::isNan(T(1,1)), false)
TEST_EQUAL(Maths::isNan(T(2,1)), false)
TEST_EQUAL(Maths::isNan(T(0,2)), false)
TEST_EQUAL(Maths::isNan(T(1,2)), false)
TEST_EQUAL(Maths::isNan(T(2,2)), false)
TEST_REAL_EQUAL(T(3,3), 1.0)
RESULT
CHECK(double calculateRMSD())
Fragment f1,f2;
Atom a1,a2,b1,b2;
a1.setName("a1");
a2.setName("a2");
b1.setName("b1");
b2.setName("b2");
a1.setPosition(Vector3(1,0,0));
b1.setPosition(Vector3(0,-1,0));
f1.insert(a1);
f1.insert(b1);
f2.insert(a2);
f2.insert(b2);
StructureMapper m(f1,f2);
TEST_REAL_EQUAL(m.calculateRMSD(), 1.0)
RESULT
CHECK((Matrix4x4 mapProteins(Protein& P1, Protein& P2, map<String, Size>& type_map, Size& no_matched_ca, double& rmsd, double upper_bound = 8.0, double lower_bound = 4.0, double tolerance = 0.6)))
// ???
RESULT
CHECK((Size mapResiduesByBackbone(const list<Residue*>& l1, const list<Residue*>& l2)))
// ???
RESULT
CHECK((StructureMapper::AtomBijection calculateFragmentBijection(const vector<Fragment*>& A, const vector<Fragment*>& B)))
// ???
RESULT
CHECK(bool calculateTransformation())
// ???
RESULT
CHECK((static Matrix4x4 matchBackboneAtoms(const Residue& r1, const Residue& r2)))
// ???
RESULT
CHECK((vector<vector<Fragment*>& searchPattern(vector<Fragment*>& pattern, AtomContainer& composite, double max_rmsd = 4.0, double max_center_tolerance = 2.0, double upper_bound = 8.0, double lower_bound = 4.0)))
// ???
RESULT
CHECK(const AtomBijection& getBijection() const)
// not much to be tested here...
StructureMapper sm;
TEST_EQUAL(sm.getBijection().size(), 0)
RESULT
CHECK(void calculateDefaultBijection())
{
AtomContainer ac1;
Residue* r1 = new Residue;
Residue* r2 = new Residue;
ac1.insert(*r1);
ac1.insert(*r2);
r1->setName("RES1");
r2->setName("RES2");
PDBAtom* a1 = new PDBAtom;
PDBAtom* a2 = new PDBAtom;
PDBAtom* a3 = new PDBAtom;
PDBAtom* a4 = new PDBAtom;
a1->setName("A1");
a2->setName("A2");
a3->setName("A3");
a4->setName("A4");
r1->insert(*a1);
r1->insert(*a2);
r2->insert(*a3);
r2->insert(*a4);
AtomContainer ac2;
Residue* r3 = new Residue;
Residue* r4 = new Residue;
ac2.insert(*r3);
ac2.insert(*r4);
r3->setName("RES1");
r4->setName("RES2");
PDBAtom* a5 = new PDBAtom;
PDBAtom* a6 = new PDBAtom;
PDBAtom* a7 = new PDBAtom;
PDBAtom* a8 = new PDBAtom;
a5->setName("A4");
a6->setName("A3");
a7->setName("A2");
a8->setName("A1");
r4->insert(*a6);
r4->insert(*a5);
r3->insert(*a8);
r3->insert(*a7);
StructureMapper sm(ac1, ac2);
sm.calculateDefaultBijection();
TEST_EQUAL(sm.getBijection().size(), 4)
ABORT_IF(sm.getBijection().size() != 4)
const AtomBijection& b = sm.getBijection();
TEST_EQUAL(b[0].first->getFullName(), b[0].second->getFullName())
TEST_NOT_EQUAL(b[0].first, b[0].second)
TEST_EQUAL(b[1].first->getFullName(), b[1].second->getFullName())
TEST_NOT_EQUAL(b[1].first, b[1].second)
TEST_EQUAL(b[2].first->getFullName(), b[2].second->getFullName())
TEST_NOT_EQUAL(b[2].first, b[2].second)
TEST_EQUAL(b[3].first->getFullName(), b[3].second->getFullName())
TEST_NOT_EQUAL(b[3].first, b[3].second)
}
{
AtomContainer ac1;
Residue* r1 = new Residue;
Residue* r2 = new Residue;
ac1.insert(*r1);
ac1.insert(*r2);
r1->setName("RES1");
r2->setName("RES2");
PDBAtom* a1 = new PDBAtom;
PDBAtom* a2 = new PDBAtom;
PDBAtom* a3 = new PDBAtom;
PDBAtom* a4 = new PDBAtom;
a1->setName("A1");
a2->setName("A2");
a3->setName("A3");
a4->setName("A4");
r1->insert(*a1);
r1->insert(*a2);
r2->insert(*a3);
r2->insert(*a4);
AtomContainer ac2;
Residue* r3 = new Residue;
Residue* r4 = new Residue;
ac2.insert(*r3);
ac2.insert(*r4);
r4->setName("RES1");
r3->setName("RES2");
PDBAtom* a5 = new PDBAtom;
PDBAtom* a6 = new PDBAtom;
PDBAtom* a7 = new PDBAtom;
PDBAtom* a8 = new PDBAtom;
a5->setName("A4");
a6->setName("A3");
a7->setName("A2");
a8->setName("A1");
r4->insert(*a6);
r4->insert(*a5);
r3->insert(*a8);
r3->insert(*a7);
StructureMapper sm(ac1, ac2);
sm.calculateDefaultBijection();
TEST_EQUAL(sm.getBijection().size(), 4)
ABORT_IF(sm.getBijection().size() != 4)
const AtomBijection& b = sm.getBijection();
TEST_EQUAL(b[0].first->getName(), b[0].second->getName())
TEST_NOT_EQUAL(b[0].first->getFullName(), b[0].second->getFullName())
TEST_NOT_EQUAL(b[0].first, b[0].second)
TEST_EQUAL(b[1].first->getName(), b[1].second->getName())
TEST_NOT_EQUAL(b[1].first->getFullName(), b[1].second->getFullName())
TEST_NOT_EQUAL(b[1].first, b[1].second)
TEST_EQUAL(b[2].first->getName(), b[2].second->getName())
TEST_NOT_EQUAL(b[2].first->getFullName(), b[2].second->getFullName())
TEST_NOT_EQUAL(b[2].first, b[2].second)
TEST_EQUAL(b[3].first->getName(), b[3].second->getName())
TEST_NOT_EQUAL(b[3].first->getFullName(), b[3].second->getFullName())
TEST_NOT_EQUAL(b[3].first, b[3].second)
}
// test for unnamed atoms -- they should be mapped by order only.
{
Molecule m1;
Atom* a1 = new Atom;
Atom* a2 = new Atom;
Atom* a3 = new Atom;
Atom* a4 = new Atom;
a1->setName("A1");
a2->setName("A2");
a3->setName("A3");
a4->setName("A4");
m1.insert(*a1);
m1.insert(*a2);
m1.insert(*a3);
m1.insert(*a4);
Molecule m2;
Atom* a5 = new Atom;
Atom* a6 = new Atom;
Atom* a7 = new Atom;
Atom* a8 = new Atom;
a5->setName("B1");
a6->setName("B2");
a7->setName("B3");
a8->setName("B4");
m2.insert(*a8);
m2.insert(*a7);
m2.insert(*a6);
m2.insert(*a5);
StructureMapper sm(m1, m2);
sm.calculateDefaultBijection();
TEST_EQUAL(sm.getBijection().size(), 4)
ABORT_IF(sm.getBijection().size() != 4)
const AtomBijection& b = sm.getBijection();
TEST_EQUAL(b[0].first->getName(), "A1")
TEST_EQUAL(b[0].second->getName(), "B4")
TEST_EQUAL(b[1].first->getName(), "A2")
TEST_EQUAL(b[1].second->getName(), "B3")
TEST_EQUAL(b[2].first->getName(), "A3")
TEST_EQUAL(b[2].second->getName(), "B2")
TEST_EQUAL(b[3].first->getName(), "A4")
TEST_EQUAL(b[3].second->getName(), "B1")
}
RESULT
CHECK((void set(AtomContainer& A, AtomContainer& B)))
// ???
RESULT
CHECK(RSMD for two bptis)
System s1, s2;
PDBFile pf(BALL_TEST_DATA_PATH(StructureMapper_test.pdb));
pf >> s1;
pf >> s2;
StructureMapper sm(s1, s2);
STATUS("Number of atoms in s1: " << s1.countAtoms())
STATUS("Number of atoms in s2: " << s2.countAtoms())
TEST_REAL_EQUAL(sm.calculateRMSD(), 0.0)
RESULT
delete frag1;
delete frag2;
delete m;
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
END_TEST
|
