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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
#include <BALL/DOCKING/COMMON/conformationSet.h>
#include <BALL/KERNEL/atomContainer.h>
#include <BALL/FORMAT/DCDFile.h>
#include <BALL/MOLMEC/COMMON/snapShotManager.h>
#include <BALL/MOLMEC/COMMON/forceField.h>
#include <stdlib.h>
#include <iostream>
using namespace std;
namespace BALL
{
ConformationSet::ConformationSet(const ConformationSet& cs)
: snapshot_order_(cs.snapshot_order_),
system_(cs.system_),
structures_(cs.structures_),
parent_(cs.parent_)
{
}
ConformationSet::ConformationSet(const System& system)
: system_(system),
parent_(NULL)
{
}
void ConformationSet::setup(const System& system)
{
system_ = system;
parent_ = NULL;
}
void ConformationSet::add(const float score, const System& conformation)
{
SnapShot sn;
sn.takeSnapShot(conformation);
structures_.push_back(sn);
Conformation c(snapshot_order_.size(), score);
snapshot_order_.push_back(c);
}
const System& ConformationSet::getSystem() const
{
return system_;
}
System& ConformationSet::getSystem()
{
return system_;
}
const std::vector < ConformationSet::Conformation > & ConformationSet::getScoring() const
{
return snapshot_order_;
}
void ConformationSet::setScoring(std::vector < Conformation > & score)
{
snapshot_order_ = score;
}
void ConformationSet::resetScoring()
{
snapshot_order_.resize(structures_.size());
for (Size i = 0; i < snapshot_order_.size(); i++)
{
snapshot_order_[i].first = i;
snapshot_order_[i].second = 0.0;
}
}
const std::vector < SnapShot > & ConformationSet::getUnscoredConformations() const
{
return structures_;
}
const SnapShot& ConformationSet::operator [] (const Index pos) const
{
return structures_[snapshot_order_[pos].first];
}
bool ConformationSet::writeDCDFile(const String& filename, const Size num)
{
try
{
ForceField ff(system_);
DCDFile dcd(filename, std::ios::out);
SnapShotManager ssm(&system_, &ff, &dcd);
Size min = ((num < snapshot_order_.size()) && (num != 0)) ? num : snapshot_order_.size();
for (Size i = 0; i < min; i++)
{
structures_[snapshot_order_[i].first].applySnapShot(system_);
ssm.takeSnapShot();
}
ssm.flushToDisk();
dcd.close();
}
catch(...)
{
return false;
}
return true;
}
bool ConformationSet::readDCDFile(const String& filename)
{
try
{
SnapShot snapshot;
vector<SnapShot> structures;
DCDFile file(filename, ios::in | ios::binary);
for (Size i = 0; i < file.getNumberOfSnapShots(); ++i)
{
file.read(snapshot);
structures.push_back(snapshot);
}
structures_ = structures;
}
catch(...)
{
return false;
}
return true;
}
Size ConformationSet::size() const
{
return snapshot_order_.size();
}
}
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