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// Molecular Mechanics: Fresno force field, buried polar component
// ----------------------------------------------------
// $Maintainer: Marcel Schumann $
// $Authors: Slick-development Team, Marcel Schumann $
// ----------------------------------------------------
#include <BALL/SCORING/COMPONENTS/buriedPolar.h>
#include <BALL/SCORING/COMPONENTS/fresnoTypes.h>
#include <BALL/KERNEL/PTE.h>
#include <BALL/SYSTEM/timer.h>
using namespace std;
using namespace BALL;
const char* BuriedPolar::Option::BP_R1_OFFSET = "bp_r1_offset";
const char* BuriedPolar::Option::BP_R2_OFFSET = "bp_r2_offset";
const char* BuriedPolar::Option::VERBOSITY = "verbosity";
const float BuriedPolar::Default::BP_R1_OFFSET = 0.5;
const float BuriedPolar::Default::BP_R2_OFFSET = 3.0;
const Size BuriedPolar::Default::VERBOSITY = 0;
BuriedPolar::BuriedPolar(ScoringFunction& sf)
: ScoringComponent(sf),
possible_buried_polar_interactions_(),
r1_offset_(0.0),
r2_offset_(0.0)
{
setName("BuriedPolar");
type_name_ = "BP";
receptor_fresno_types_ = 0;
ligand_fresno_types_ = 0;
gridable_ = false;
}
BuriedPolar::BuriedPolar(const BuriedPolar& bp)
: ScoringComponent(bp),
possible_buried_polar_interactions_(bp.possible_buried_polar_interactions_),
r1_offset_(bp.r1_offset_),
r2_offset_(bp.r2_offset_)
{
setName("BuriedPolar");
type_name_ = "BP";
receptor_fresno_types_ = 0;
ligand_fresno_types_ = 0;
gridable_ = false;
}
BuriedPolar::~BuriedPolar()
{
}
void BuriedPolar::clear()
{
possible_buried_polar_interactions_.clear();
}
bool BuriedPolar::setup()
{
ScoringFunction* sf = getScoringFunction();
if (sf == 0)
{
Log.error() << "BuriedPolar::setup(): "
<< "component not bound to force field." << endl;
return false;
}
// clear the vector of buried polar interactions
possible_buried_polar_interactions_.clear();
Options options = getScoringFunction()->getOptions();
r1_offset_
= options.setDefaultReal(BuriedPolar::Option::BP_R1_OFFSET,
BuriedPolar::Default::BP_R1_OFFSET);
r2_offset_
= options.setDefaultReal(BuriedPolar::Option::BP_R2_OFFSET,
BuriedPolar::Default::BP_R2_OFFSET);
verbosity_
= options.setDefaultInteger(BuriedPolar::Option::VERBOSITY,
BuriedPolar::Default::VERBOSITY);
delete receptor_fresno_types_;
receptor_fresno_types_ = new FresnoTypes(getScoringFunction()->getReceptor());
setupLigand();
if (verbosity_ > 2)
{
Log.info() << "BuriedPolar setup statistics:" << endl;
Log.info() << "Found " << possible_buried_polar_interactions_.size()
<< " possible buried polar interactions" << endl << endl;
}
return true;
}
void BuriedPolar::setupLigand()
{
delete ligand_fresno_types_;
ligand_fresno_types_ = new FresnoTypes(getScoringFunction()->getLigand());
}
Size BuriedPolar::getType(Atom* atom)
{
HashMap<const Atom*, Size>::const_iterator it = receptor_fresno_types_->getTypeMap()->find(atom);
if (it != receptor_fresno_types_->getTypeMap()->end())
{
return it->second;
}
it = ligand_fresno_types_->getTypeMap()->find(atom);
if (it != ligand_fresno_types_->getTypeMap()->end())
{
return it->second;
}
return FresnoTypes::UNKNOWN;
}
bool BuriedPolar::isBackboneAtom(const Atom* atom)
{
return atom->getName() == "O" || atom->getName() == "N"
|| atom->getName() == "H" || atom->getName() == "C";
}
void BuriedPolar::update(const vector<std::pair<Atom*, Atom*> >& pair_vector)
{
possible_buried_polar_interactions_.clear();
for (vector < std::pair < Atom*, Atom* > > ::const_iterator it = pair_vector.begin(); it != pair_vector.end(); it++)
{
int type_A = getType(it->first);
if (type_A == FresnoTypes::UNKNOWN) continue;
int type_B = getType(it->second);
if (type_B == FresnoTypes::UNKNOWN || isBackboneAtom(it->second)) continue;
if ( (((type_B == FresnoTypes::POLAR)
|| (type_B == FresnoTypes::HBOND_ACCEPTOR)
|| (type_B == FresnoTypes::HBOND_DONOR)
|| (type_B == FresnoTypes::HBOND_ACCEPTOR_DONOR)
|| (type_B == FresnoTypes::HBOND_HYDROGEN))
&& (type_A == FresnoTypes::LIPOPHILIC))
/*|| ((type_B == FresnoTypes::LIPOPHILIC)
&& ((type_A == FresnoTypes::POLAR)
|| (type_A == FresnoTypes::HBOND_ACCEPTOR)
|| (type_A == FresnoTypes::HBOND_DONOR)
|| (type_A == FresnoTypes::HBOND_ACCEPTOR_DONOR)
|| (type_A == FresnoTypes::HBOND_HYDROGEN)))*/ )
{
possible_buried_polar_interactions_.push_back(*it);
if (verbosity_ >= 10)
{
Log.info() << "found possible buried polar int.: "
<< it->first->getFullName() << "..." << it->second->getFullName()
<< " (length: "
<< (it->first->getPosition() - it->second->getPosition()).getLength()
<< " A) "
<< endl;
}
}
}
}
double BuriedPolar::updateScore()
{
score_ = 0.0;
float val = 0.0;
float distance;
float R1;
float R2;
Atom* atom1;
Atom* atom2;
AtomPairVector::const_iterator it;
for (it = possible_buried_polar_interactions_.begin(); it != possible_buried_polar_interactions_.end(); ++it)
{
atom1 = it->first;
atom2 = it->second;
R1 = atom1->getElement().getVanDerWaalsRadius()+atom2->getElement().getVanDerWaalsRadius()-1;
R2 = R1 + 1.5;
distance = (atom1->getPosition() - atom2->getPosition()).getLength();
// if the distance is too large, the product of g1 and g2 is zero, so
// we can skip the rest
if (distance <= R2)
{
// we could possibly speed up the next step by using the fact that the
// difference between R1 and R2 is constant
val = base_function_->calculate(distance, R1, R2);
if (scoring_function_->storeInteractionsEnabled())
{
double scaled_atom_score = val;
scaled_atom_score = scaleScore(scaled_atom_score);
atom1->addInteraction(atom2, "pol", scaled_atom_score);
atom2->addInteraction(atom1, "pol", scaled_atom_score);
}
score_ += val;
if (verbosity_ >= 1)
{
Log.info() << "BP: " << val << " "
<< atom1->getFullName() << " "
<< endl;
if (atom1->getResidue() != 0)
{
Log.info() << "[" << atom1->getResidue()->getID() << "]";
}
Log.info() << "..." << atom2->getFullName() << " "
<< endl;
if (atom2->getResidue() != 0)
{
Log.info() << "[" << atom2->getResidue()->getID() << "]";
}
Log.info() << " (d " << distance << ", R1 " << R1
<< ", R2 " << R2 << ")" << endl;
}
}
}
if (verbosity_ > 0)
{
Log.info() << "BP: energy is " << score_ << endl;
}
return score_;
}
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