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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
#include<BALL/NMR/randomCoilShiftProcessor.h>
#include<BALL/FORMAT/parameterSection.h>
namespace BALL
{
const char* RandomCoilShiftProcessor::PROPERTY__RANDOM_COIL_SHIFT = "RandomCoilShift";
RandomCoilShiftProcessor::RandomCoilShiftProcessor()
{
system_ = NULL;
}
RandomCoilShiftProcessor::RandomCoilShiftProcessor(const RandomCoilShiftProcessor& processor)
: ShiftModule(processor),
shift_map_(processor.shift_map_)
{
system_ = NULL;
}
RandomCoilShiftProcessor::~RandomCoilShiftProcessor()
{
}
void RandomCoilShiftProcessor::init()
{
// We assume the worst case.
valid_ = false;
system_ = NULL;
// Make sure we have correct parameters.
if (parameters_ == 0)
{
return;
}
// Extract the data from the correct section.
ParameterSection parameter_section;
parameter_section.extractSection(*parameters_, "RandomCoilShifts");
// Make sure the section contains the required columns.
if (!parameter_section.hasVariable("shift"))
{
return;
}
// Extract the random coil shifts from the parameter section.
Position shift_column = parameter_section.getColumnIndex("shift");
for (Position i = 0; i < parameter_section.getNumberOfKeys(); i++)
{
shift_map_.insert(parameter_section.getKey(i),
parameter_section.getValue(i, shift_column).toFloat());
}
// Initialization complete - mark the module as valid.
valid_ = true;
return;
}
Processor::Result RandomCoilShiftProcessor::operator () (Composite& composite)
{
// We are just interested in atoms.
Atom* atom_ptr = dynamic_cast<Atom*>(&composite);
if (atom_ptr == 0)
{
return Processor::CONTINUE;
}
// Try to get the system.
if (!system_ && (RTTI::isKindOf<System>(&atom_ptr->getRoot())))
{
system_ = dynamic_cast<System*>(&(atom_ptr->getRoot()));
}
// Get the atoms full name.
String full_name = atom_ptr->getFullName();
full_name.substitute(":", " ");
if (!shift_map_.has(full_name))
{
full_name = atom_ptr->getFullName(Atom::NO_VARIANT_EXTENSIONS);
full_name.substitute(":", " ");
if (!shift_map_.has(full_name))
{
full_name = "* " + atom_ptr->getName();
if (!shift_map_.has(full_name))
{
full_name = "";
}
}
}
if (full_name != "")
{
// Retrieve the random coil shift from the hash map.
const float& delta_RC = shift_map_[full_name];
// Add the random coil shift to the total shift value.
float delta = atom_ptr->getProperty(ShiftModule::PROPERTY__SHIFT).getFloat();
delta += delta_RC;
atom_ptr->setProperty(ShiftModule::PROPERTY__SHIFT, delta);
// Store the random coil shift as the random coil shift property.
atom_ptr->setProperty(RandomCoilShiftProcessor::PROPERTY__RANDOM_COIL_SHIFT, delta_RC);
}
return Processor::CONTINUE;
}
void RandomCoilShiftProcessor::postprocessing_()
{
if (system_)
{
// Add for all CA 0.2 times the values of HA ramdon coil shift contribution.
for (BALL::ResidueIterator r_it = system_->beginResidue();
r_it != system_->endResidue();
++r_it)
{
Atom* CA = 0;
Atom* HA = 0;
for (BALL::AtomIterator at_it = r_it->beginAtom(); +at_it; ++at_it)
{
if (at_it->getName() == "CA")
CA = &(*at_it);
if (at_it->getName() == "HA")
HA = &(*at_it);
}
if (CA && HA)
{
float total = CA->getProperty(ShiftModule::PROPERTY__SHIFT).getFloat();
float ca_shift = CA->getProperty(BALL::RandomCoilShiftProcessor::PROPERTY__RANDOM_COIL_SHIFT).getFloat();
float ha_shift = HA->getProperty(BALL::RandomCoilShiftProcessor::PROPERTY__RANDOM_COIL_SHIFT).getFloat();
CA->setProperty(BALL::RandomCoilShiftProcessor::PROPERTY__RANDOM_COIL_SHIFT, ca_shift + 0.2*ha_shift);
CA->setProperty(ShiftModule::PROPERTY__SHIFT, total+ 0.2*ha_shift );
}
}
}
else
{
Log.error() << "Error in RandomCoilShiftProcessor: no system found for postprocessing. ("
<< __FILE__ << " " << __LINE__ << ")" << std::endl;
}
}
}//namespace BALL
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