// Descr: evident
TEST(GeometryTest, GetBond)
{
vector<Bond> bonds;
Bond bond1 = Bond(1, 2, 3.0, false);
Bond bond2 = Bond(3, 4, 3.0, false);
Bond bond3 = Bond(2, 3, 3.0, false);
bonds.push_back(bond1);
EXPECT_EQ( 1, bonds[0].atom1);
bonds.push_back(bond2);
bonds.push_back(bond3);
Bond testBond1 = getBond(bonds, 1, 2);
Bond testBond2 = getBond(bonds, 3, 4);
Bond testBond3 = getBond(bonds, 2, 3);
Bond testBond4 = getBond(bonds, 1, 4);
EXPECT_EQ( bond1.atom1, testBond1.atom1);
EXPECT_EQ( -1 , testBond4.atom1);
EXPECT_TRUE( bond1.atom1 == testBond1.atom1 && bond1.atom2 == testBond1.atom2 && bond1.distance == testBond1.distance );
EXPECT_TRUE( bond2.atom1 == testBond2.atom1 && bond2.atom2 == testBond2.atom2 && bond2.distance == testBond2.distance );
EXPECT_TRUE( bond3.atom1 == testBond3.atom1 && bond3.atom2 == testBond3.atom2 && bond3.distance == testBond3.distance );
EXPECT_TRUE( testBond4.atom1 == -1 && testBond4.atom2 == -1 && testBond4.distance == -1.0 );
}
void testGetBond()
{
cout <<"Testing GetBond"<<endl;
vector<Bond> bonds;
Bond bond1 = createBond(1, 2, 3.0, false);
Bond bond2 = createBond(3, 4, 3.0, false);
Bond bond3 = createBond(2, 3, 3.0, false);
bonds.push_back(bond1);
bonds.push_back(bond2);
bonds.push_back(bond3);
Bond testBond1 = getBond(bonds, 1, 2);
Bond testBond2 = getBond(bonds, 3, 4);
Bond testBond3 = getBond(bonds, 2, 3);
Bond testBond4 = getBond(bonds, 1, 4);
assert(bond1.atom1 == testBond1.atom1 && bond1.atom2 == testBond1.atom2 && bond1.distance == testBond1.distance);
assert(bond2.atom1 == testBond2.atom1 && bond2.atom2 == testBond2.atom2 && bond2.distance == testBond2.distance);
assert(bond3.atom1 == testBond3.atom1 && bond3.atom2 == testBond3.atom2 && bond3.distance == testBond3.distance);
assert(testBond4.atom1 == -1 && testBond4.atom2 == -1 && testBond4.distance == -1.0);
cout <<"Testing GetBond Completed\n"<<endl;
}
// Sets the phosphate-sugar bond type differently based on the bond
// direction. This allows the phosphate to be closer to one sugar
// than the other, based on the strand direction.
static void
pam5_phosphate_sugar_match(struct patternMatch *match)
{
struct part *p = match->p;
struct atom *aPl = p->atoms[match->atomIndices[0]];
struct atom *aSs = p->atoms[match->atomIndices[1]];
struct bond *b = getBond(p, aPl, aSs);
BAIL();
struct stretch *s = getStretch(p, aPl, aSs);
BAIL();
int reverse;
pam5_requires_gromacs(match->p);
BAIL();
init_stack_match();
BAIL();
switch (b->direction) {
case 'F':
reverse = (b->a1 == aSs);
break;
case 'R':
reverse = (b->a1 == aPl);
break;
default:
ERROR2("pam5_phosphate_sugar_match: bond between ids %d and %d has no direction", aPl->atomID, aSs->atomID);
p->parseError(p->stream);
return;
}
s->stretchType = reverse ? stretch_5_Ss_Pl_3 : stretch_5_Pl_Ss_3 ;
trace_setStretchType(match, s);
//printMatch(match);
}
// Creates the Gv-Pl interaction, which replaces the Gv-Ss-Pl bend
// term. Only do this on the 5' side.
static void
pam5_groove_phosphate_match(struct patternMatch *match)
{
struct part *p = match->p;
struct atom *aGv = p->atoms[match->atomIndices[0]];
struct atom *aSs = p->atoms[match->atomIndices[1]];
struct atom *aPl = p->atoms[match->atomIndices[2]];
struct bond *b = getBond(p, aPl, aSs);
BAIL();
struct bond *bond;
struct bend *bend;
int reverse;
char order;
pam5_requires_gromacs(p);
BAIL();
switch (b->direction) {
case 'F':
reverse = (b->a1 == aSs);
break;
case 'R':
reverse = (b->a1 == aPl);
break;
default:
ERROR2("pam5_phosphate_sugar_match: bond between ids %d and %d has no direction", aPl->atomID, aSs->atomID);
p->parseError(p->stream);
return;
}
if (reverse) {
order = '2';
} else {
order = '1';
bend = getBend(p, aGv, aSs, aPl);
bend->bendType = bend_Gv_Ss_Pl_5;
}
bond = makeBond(p, aPl, aGv, order);
queueBond(p, bond);
trace_makeBond(match, bond);
//printMatch(match);
}
