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#include "obtest.h"
#include <openbabel/mol.h>
#include <openbabel/obconversion.h>
#include <openbabel/rotor.h>
#include <iostream>
#include <string>
#include <vector>
#include <algorithm>
using namespace std;
using namespace OpenBabel;
//! Comparison for doubles with a modulus: returns mod(a - b,m) < epsilon
bool IsNear_mod(const double &a, const double &b, const double &m, const double epsilon)
{
double arg=a-b;
while(arg<-m/2)
arg+=m;
while(arg>=m/2)
arg-=m;
return (fabs(arg) < epsilon);
}
void testOBRotorGetSet()
{
OBBond bond;
OBRotor rotor;
// SetBond/GetBond
rotor.SetBond(&bond);
OB_ASSERT(rotor.GetBond()->GetIdx() == bond.GetIdx());
// SetIdx/GetIdx
rotor.SetIdx(45);
OB_ASSERT(rotor.GetIdx() == 45);
// SetDihedralAtoms/GetDihedralAtoms
int ref_ptr[4] = {1, 2, 3, 4};
rotor.SetDihedralAtoms(ref_ptr);
rotor.GetDihedralAtoms(ref_ptr);
OB_ASSERT(ref_ptr[0] == 1);
OB_ASSERT(ref_ptr[1] == 2);
OB_ASSERT(ref_ptr[2] == 3);
OB_ASSERT(ref_ptr[3] == 4);
std::vector<int> ref_vector = rotor.GetDihedralAtoms();
OB_ASSERT(ref_vector[0] == 1);
OB_ASSERT(ref_vector[1] == 2);
OB_ASSERT(ref_vector[2] == 3);
OB_ASSERT(ref_vector[3] == 4);
rotor.SetDihedralAtoms(ref_vector);
ref_vector = rotor.GetDihedralAtoms();
OB_ASSERT(ref_vector[0] == 1);
OB_ASSERT(ref_vector[1] == 2);
OB_ASSERT(ref_vector[2] == 3);
OB_ASSERT(ref_vector[3] == 4);
// SetTorsionValues/GetTorsionValues/Size
std::vector<double> angles;
angles.push_back(0.0);
angles.push_back(3.1415);
rotor.SetTorsionValues(angles);
OB_ASSERT(rotor.GetTorsionValues().size() == 2);
OB_ASSERT(rotor.Size() == 2);
}
void testOBRotorSetToAngle()
{
// 1 2 3 4 5 6 7 8
// C-C-C-C-C-C-C-C
// 0 1 2 3 4 5 6
OBMolPtr mol = OBTestUtil::ReadFile("octane.cml");
OBBond *bond = mol->GetBond(3);
OBRotor rotor;
// set the bond to rotate
rotor.SetBond(bond);
// set the dihedral indexes (these start from 1)
int ref[4] = {3, 4, 5, 6};
rotor.SetDihedralAtoms(ref);
// find atoms to rotate
std::vector<int> atoms;
mol->FindChildren(atoms, 4, 5);
// convert to coordinate indexes (start from 0, multiplied by 3)
for (unsigned int i = 0; i < atoms.size(); ++i)
atoms[i] = (atoms[i] - 1) * 3;
rotor.SetRotAtoms(atoms);
OB_ASSERT(IsNear_mod(fabs(RAD_TO_DEG * rotor.CalcTorsion(mol->GetCoordinates())), 180.0, 360.0, 1.0));
// rotate
rotor.SetToAngle(mol->GetCoordinates(), 60.0 * DEG_TO_RAD);
OB_ASSERT(IsNear(RAD_TO_DEG * rotor.CalcTorsion(mol->GetCoordinates()), 60.0, 1.0));
}
void testOBRotorSetRotor()
{
// 1 2 3 4 5 6 7 8
// C-C-C-C-C-C-C-C
// 0 1 2 3 4 5 6
OBMolPtr mol = OBTestUtil::ReadFile("octane.cml");
OBBond *bond = mol->GetBond(3);
OBRotor rotor;
// set the bond to rotate
rotor.SetBond(bond);
// set the dihedral indexes (these start from 1)
int ref[4] = {3, 4, 5, 6};
rotor.SetDihedralAtoms(ref);
// find atoms to rotate
std::vector<int> atoms;
mol->FindChildren(atoms, 4, 5);
// convert to coordinate indexes (start from 0, multiplied by 3)
for (unsigned int i = 0; i < atoms.size(); ++i)
atoms[i] = (atoms[i] - 1) * 3;
rotor.SetRotAtoms(atoms);
OB_ASSERT(IsNear_mod(fabs(RAD_TO_DEG * rotor.CalcTorsion(mol->GetCoordinates())), 180.0, 360.0, 1.0));
rotor.SetToAngle(mol->GetCoordinates(), 60.0 * DEG_TO_RAD);
// set torsion values
std::vector<double> angles;
angles.push_back(0.0);
angles.push_back(3.1415);
rotor.SetTorsionValues(angles);
// rotate to 0.0 radians
rotor.SetRotor(mol->GetCoordinates(), 0);
OB_ASSERT(IsNear(RAD_TO_DEG * rotor.CalcTorsion(mol->GetCoordinates()), 0.0, 1.0));
// rotate to 3.1415 radians
rotor.SetRotor(mol->GetCoordinates(), 1);
OB_ASSERT(IsNear_mod(RAD_TO_DEG * rotor.CalcTorsion(mol->GetCoordinates()), 180.0, 360.0, 1.0));
// rotate to 0.0 radians
rotor.SetRotor(mol->GetCoordinates(), 0, 1);
OB_ASSERT(IsNear(RAD_TO_DEG * rotor.CalcTorsion(mol->GetCoordinates()), 0.0, 1.0));
}
void testOBRotorListFixedBonds()
{
// 1 2 3 4 5 6 7 8
// C-C-C-C-C-C-C-C
// 0 1 2 3 4 5 6
OBMolPtr mol = OBTestUtil::ReadFile("octane.cml");
// test with no bonds fixed
OBRotorList rlist1;
rlist1.Setup(*mol);
OB_ASSERT(rlist1.Size() == 5);
// test with bond 3 fixed
OBBitVec fixedBonds;
fixedBonds.SetBitOn(3);
rlist1.SetFixedBonds(fixedBonds);
rlist1.Setup(*mol);
OB_ASSERT(rlist1.Size() == 4);
// test with bond 1, 3, 5 fixed
fixedBonds.SetBitOn(1);
fixedBonds.SetBitOn(5);
rlist1.SetFixedBonds(fixedBonds);
rlist1.Setup(*mol);
OB_ASSERT(rlist1.Size() == 2);
// test with bond 1, 2, 3, 5 fixed
fixedBonds.SetBitOn(2);
rlist1.SetFixedBonds(fixedBonds);
rlist1.Setup(*mol);
OB_ASSERT(rlist1.Size() == 1);
}
int rotortest(int argc, char* argv[])
{
int defaultchoice = 1;
int choice = defaultchoice;
if (argc > 1) {
if(sscanf(argv[1], "%d", &choice) != 1) {
printf("Couldn't parse that input as a number\n");
return -1;
}
}
// Define location of file formats for testing
#ifdef FORMATDIR
char env[BUFF_SIZE];
snprintf(env, BUFF_SIZE, "BABEL_LIBDIR=%s", FORMATDIR);
putenv(env);
#endif
switch(choice) {
// OBRotor
case 1:
testOBRotorGetSet();
break;
case 2:
testOBRotorSetToAngle();
break;
case 3:
testOBRotorSetRotor();
break;
// OBRotorList
case 4:
testOBRotorListFixedBonds();
break;
default:
cout << "Test number " << choice << " does not exist!\n";
return -1;
}
return 0;
}
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