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|
// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
#include <BALL/MOLMEC/AMBER/amberTorsion.h>
#include <BALL/MOLMEC/AMBER/amber.h>
#include <BALL/MOLMEC/COMMON/forceFieldComponent.h>
#include <BALL/MOLMEC/COMMON/forceField.h>
#include <BALL/KERNEL/atom.h>
#include <BALL/KERNEL/bond.h>
#include <algorithm>
using namespace std;
namespace BALL
{
// default constructor
AmberTorsion::AmberTorsion()
: ForceFieldComponent()
{
// set component name
setName("Amber Torsion");
}
// constructor
AmberTorsion::AmberTorsion(ForceField& force_field)
: ForceFieldComponent(force_field)
{
// set component name
setName( "Amber Torsion" );
}
// copy constructor
AmberTorsion::AmberTorsion(const AmberTorsion& component)
: ForceFieldComponent(component)
{
// assign the torsion array
torsion_ = component.torsion_;
}
// destructor
AmberTorsion::~AmberTorsion()
{
// clear the torsion array
torsion_.clear();
}
// setup the internal datastructures for the component
bool AmberTorsion::setup()
{
if (getForceField() == 0)
{
Log.error() << "AmberTorsion::setup: component not bound to force field" << endl;
return false;
}
// clear torsion array
torsion_.clear();
Options& options = getForceField()->options;
if (options.has(AMBER_TORSIONS_ENABLED))
{
if (!options.getBool(AMBER_TORSIONS_ENABLED))
{
setEnabled(false);
return true;
}
else
{
setEnabled(true);
}
}
// extract the torsion parameters from the parameter file
bool result;
AmberFF* amber_force_field = dynamic_cast<AmberFF*>(force_field_);
bool has_initialized_parameters = true;
if ((amber_force_field == 0) || !amber_force_field->hasInitializedParameters())
{
has_initialized_parameters = false;
}
if (!has_initialized_parameters)
{
result = torsion_parameters_.extractSection(getForceField()->getParameters(), "Torsions");
if (!result)
{
Log.error() << "AmberTorsion::setup: cannot find section Torsions" << endl;
return false;
}
}
// calculate the torsions
vector<Atom*>::const_iterator atom_it = getForceField()->getAtoms().begin();
Atom::BondIterator it1;
Atom::BondIterator it2;
Atom::BondIterator it3;
Atom* a1;
Atom* a2;
Atom* a3;
Atom* a4;
bool use_selection = getForceField()->getUseSelection();
// proper torsion will be added to the torsion vector
for (; atom_it != getForceField()->getAtoms().end(); ++atom_it)
{
for (it1 = (*atom_it)->beginBond(); +it1 ; ++ it1)
{
if (it1->getType() == Bond::TYPE__HYDROGEN) continue; // ignore H -bonds
if (*atom_it == it1->getFirstAtom())
{
// central atoms
a2 = *atom_it;
a3 = const_cast<Atom*>(it1->getSecondAtom());
for (it2 = (*atom_it)->beginBond(); +it2 ; ++it2)
{
if (it2->getType() == Bond::TYPE__HYDROGEN) continue; // ignore H -bonds
if (it2->getSecondAtom() != it1->getSecondAtom())
{
// determine the first atom
if (it2->getFirstAtom() == *atom_it)
{
a1 = const_cast<Atom*>(it2->getSecondAtom());
}
else
{
a1 = const_cast<Atom*>(it2->getFirstAtom());
}
for (it3 = const_cast<Atom*>(it1->getSecondAtom())->beginBond(); +it3 ; ++it3)
{
if (it3->getType() == Bond::TYPE__HYDROGEN) continue; // ignore H -bonds
if (it3->getFirstAtom() != a2 )
{
// determine the fourth atom a4
if (it3->getFirstAtom() == a3)
{
a4 = const_cast<Atom*>(it3->getSecondAtom());
}
else
{
a4 = const_cast<Atom*>(it3->getFirstAtom());
}
if (!use_selection || (use_selection
&& a1->isSelected()
&& a2->isSelected()
&& a3->isSelected()
&& a4->isSelected()))
{
// search torsion parameters for (a1,a2,a3,a4)
Atom::Type type_a1 = a1->getType();
Atom::Type type_a2 = a2->getType();
Atom::Type type_a3 = a3->getType();
Atom::Type type_a4 = a4->getType();
CosineTorsion::Values values;
CosineTorsion::SingleData tmp;
tmp.atom1 = a1;
tmp.atom2 = a2;
tmp.atom3 = a3;
tmp.atom4 = a4;
bool found = false;
if (torsion_parameters_.assignParameters(values, type_a1, type_a2, type_a3, type_a4))
{
found = true;
}
else if (torsion_parameters_.assignParameters(values, Atom::ANY_TYPE, type_a2, type_a3, Atom::ANY_TYPE))
{
found = true;
}
if (found)
{
for (unsigned char j = 0; j < values.n; j++)
{
tmp.values = values.values[j];
torsion_.push_back(tmp);
}
}
else
{
getForceField()->error() << "AmberTorsion::setup: cannot find torsion parameter for:"
<< force_field_->getParameters().getAtomTypes().getTypeName(type_a1) << "-"
<< force_field_->getParameters().getAtomTypes().getTypeName(type_a2) << "-"
<< force_field_->getParameters().getAtomTypes().getTypeName(type_a3) << "-"
<< force_field_->getParameters().getAtomTypes().getTypeName(type_a4)
<< " (atoms are: " << a1->getFullName() << "/" << a2->getFullName()
<< "/" << a3->getFullName() << "/" << a4->getFullName() << ")" << endl;
getForceField()->getUnassignedAtoms().insert(a1);
getForceField()->getUnassignedAtoms().insert(a2);
getForceField()->getUnassignedAtoms().insert(a3);
getForceField()->getUnassignedAtoms().insert(a4);
}
}
}
}
}
}
}
}
}
if (!has_initialized_parameters)
{
result = improper_parameters_.extractSection(getForceField()->getParameters(), "ImproperTorsions");
if (!result)
{
Log.error() << "AmberTorsion::setup: cannot find section ImproperTorsions" << endl;
return false;
}
}
// Improper torsions will be added to the torsion array
atom_it = getForceField()->getAtoms().begin();
// find all improper torsion atoms: their names are stored in
// the section ResidueImproperTorsions
if (!has_initialized_parameters)
{
result = impropers_.extractSection(getForceField()->getParameters(), "ResidueImproperTorsions");
if (!result)
{
Log.error() << "cannot find section ResidueImproperTorsions" << endl;
return false;
}
}
// check for each potential improper torsion atom (every atom having three bonds)
// whether it is contained in the list of impropers
for ( ; atom_it != getForceField()->getAtoms().end(); ++atom_it)
{
if ((*atom_it)->countBonds() == 3)
{
String res_name;
int terminal = 0;
Residue* res = (*atom_it)->getAncestor(RTTI::getDefault<Residue>());
if (res == 0)
{
if ((*atom_it)->getFragment() != 0)
{
res_name = (*atom_it)->getFragment()->getName();
res_name.trim();
}
}
else
{
res_name = res->getName();
res_name.trim();
String suffix = "-";
if (res->isNTerminal())
{
suffix = "-N";
}
if (res->isCTerminal())
{
suffix = "-C";
}
if (res->hasProperty(Residue::PROPERTY__HAS_SSBOND))
{
suffix += "S";
}
if (suffix != "-")
{
res_name += suffix;
}
}
String key;
if (res_name != "")
{
key = res_name + " " + (*atom_it)->getName();
switch (terminal)
{
case 1: key += " N"; break;
case 2: key += " C"; break;
default: key += " -";
}
}
if (impropers_.has(key))
{
for (it1 = (*atom_it)->beginBond(); +it1 ; ++ it1)
{
a3 = *atom_it;
a4 = it1->getPartner(*a3);
for (it2 = it1, ++it2; +it2 ; it2++)
{
a2 = it2->getPartner(**atom_it);
for (it3 = it2, ++it3; +it3 ; it3++)
{
a1 = it3->getPartner(**atom_it);
// test if (a1,a2,a3,a4) is improper torsion and search torsion parameters for (a1,a2,a3,a4)
CosineTorsion::SingleData tmp;
CosineTorsion::Values values;
tmp.atom1 = a1;
tmp.atom2 = a2;
tmp.atom3 = a3;
tmp.atom4 = a4;
// sort IJL according to the lexicographic order
// of their type name (AMBER!!)
if (a1->getTypeName() > a2->getTypeName()) swap(a1, a2);
if (a1->getTypeName() > a4->getTypeName()) swap(a1, a4);
if (a2->getTypeName() > a4->getTypeName()) swap(a2, a4);
if (!use_selection || (use_selection
&& a1->isSelected()
&& a2->isSelected()
&& a3->isSelected()
&& a4->isSelected()))
{
Atom::Type type_a1 = a1->getType();
Atom::Type type_a2 = a2->getType();
Atom::Type type_a3 = a3->getType();
Atom::Type type_a4 = a4->getType();
bool found = false;
if (improper_parameters_.hasParameters(type_a1, type_a2, type_a3, type_a4))
{
improper_parameters_.assignParameters(values, type_a1, type_a2, type_a3, type_a4);
found = true;
}
else if (improper_parameters_.hasParameters(Atom::ANY_TYPE, type_a2, type_a3, type_a4))
{
improper_parameters_.assignParameters(values, Atom::ANY_TYPE, type_a2, type_a3, type_a4);
found = true;
}
else if (improper_parameters_.hasParameters(Atom::ANY_TYPE, Atom::ANY_TYPE, type_a3, type_a4))
{
improper_parameters_.assignParameters(values, Atom::ANY_TYPE, Atom::ANY_TYPE, type_a3, type_a4);
found = true;
}
else if (improper_parameters_.hasParameters(Atom::ANY_TYPE, type_a2, type_a3, Atom::ANY_TYPE))
{
improper_parameters_.assignParameters(values, Atom::ANY_TYPE, type_a2, type_a3, Atom::ANY_TYPE);
found = true;
}
if (found)
{
for (Position j = 0; j < values.n; j++)
{
tmp.values = values.values[j];
torsion_.push_back(tmp);
}
}
}
}
}
}
}
}
}
return true;
}
// calculates the current energy of this component
double AmberTorsion::updateEnergy()
{
double cosphi;
Vector3 a21;
Vector3 a23;
Vector3 a34;
Vector3 cross2321;
Vector3 cross2334;
energy_ = 0;
vector<SingleAmberTorsion>::const_iterator it = torsion_.begin();
bool use_selection = getForceField()->getUseSelection();
for (; it != torsion_.end(); it++)
{
const Atom* atom1 = it->atom1;
const Atom* atom2 = it->atom2;
const Atom* atom3 = it->atom3;
const Atom* atom4 = it->atom4;
if (!use_selection || (use_selection &&
( atom1->isSelected() || atom2->isSelected()
|| atom3->isSelected() || atom4->isSelected())))
{
a21 = atom1->getPosition() - atom2->getPosition();
a23 = atom3->getPosition() - atom2->getPosition();
a34 = atom4->getPosition() - atom3->getPosition();
cross2321 = a23 % a21;
cross2334 = a23 % a34;
double length_cross2321 = cross2321.getLength();
double length_cross2334 = cross2334.getLength();
if (length_cross2321 != 0 && length_cross2334 != 0)
{
cross2321 /= length_cross2321;
cross2334 /= length_cross2334;
cosphi = cross2321 * cross2334;
if (cosphi > 1.0)
{
cosphi = 1.0;
}
if (cosphi < -1.0)
{
cosphi = -1.0;
}
energy_ += it->V * (1 + cos(it->f * acos(cosphi) - it->phase));
}
}
}
return energy_;
}
// calculates and adds its forces to the current forces of the force field
void AmberTorsion::updateForces()
{
double cosphi;
double dEdphi;
Vector3 ab; // vector from atom2 to atom1
Vector3 cb; // vector from atom2 to atom3
Vector3 dc; // vector from atom3 to atom4
bool use_selection = getForceField()->getUseSelection();
vector<SingleAmberTorsion>::iterator it = torsion_.begin();
for ( ; it != torsion_.end(); it++)
{
Atom* atom1 = it->atom1;
Atom* atom2 = it->atom2;
Atom* atom3 = it->atom3;
Atom* atom4 = it->atom4;
if (!use_selection || (use_selection &&
( atom1->isSelected() || atom2->isSelected()
|| atom3->isSelected() || atom4->isSelected())))
{
ab = atom1->getPosition() - atom2->getPosition();
double length_ab = ab.getLength();
Vector3 ba = atom2->getPosition() - atom1->getPosition();
cb = atom3->getPosition() - atom2->getPosition();
double length_cb = cb.getLength();
dc = atom4->getPosition() - atom3->getPosition();
double length_dc = dc.getLength();
if (length_ab != 0 && length_cb != 0 && length_dc != 0)
{
Vector3 t = ba % cb; // cross product of cb and ba
Vector3 u = cb % dc; // cross product of cb and dc
double length_t2 = t.getSquareLength();
double length_u2 = u.getSquareLength();
double length_t = sqrt(length_t2);
double length_u = sqrt(length_u2);
if (length_t != 0 && length_u != 0)
{
cosphi = (t * u) / (length_t * length_u);
if (cosphi > 1.0)
{
cosphi = 1.0;
}
if (cosphi < -1.0)
{
cosphi = -1.0;
}
// multiply with the barrier height and a factor
// for unit conversion: 1e13: kJ/(mol A) -> J/(mol m)
// AVOGADRO: J/mol -> J
dEdphi = (-it->V) * (1e13 / Constants::AVOGADRO) * it->f * sin(it->f * acos(cosphi) - it->phase);
double direction = (t % u) * cb;
if (direction > 0.0)
{
dEdphi = -dEdphi;
}
Vector3 ca = atom3->getPosition() - atom1->getPosition();
Vector3 db = atom4->getPosition() - atom2->getPosition();
Vector3 dEdt = (float)(dEdphi / (length_t2 * cb.getLength())) * (t % cb);
Vector3 dEdu = - (float)(dEdphi / (length_u2 * cb.getLength())) * (u % cb);
if (!use_selection)
{
atom1->getForce() += dEdt % cb;
atom2->getForce() += ca % dEdt + dEdu % dc;
atom3->getForce() += dEdt % ba + db % dEdu;
atom4->getForce() += dEdu % cb;
}
else
{
if (atom1->isSelected()) atom1->getForce() += dEdt % cb;
if (atom2->isSelected()) atom2->getForce() += ca % dEdt + dEdu % dc;
if (atom3->isSelected()) atom3->getForce() += dEdt % ba + db % dEdu;
if (atom4->isSelected()) atom4->getForce() += dEdu % cb;
}
}
}
}
}
}
} // namespace BALL
|
