bool SLICKEnergy::setup()
{
setName("SLICKEnergy");
options_.set(NonpolarSolvation::Option::NONPOLAR_METHOD, NonpolarSolvation::CALCULATION__PCM);
options_.setInteger(PolarSolvation::Option::POLAR_METHOD, PolarSolvation::CALCULATION__FULL_CYCLE_FOCUSED);
options_.setInteger(VanDerWaalsSlick::Option::VDW_METHOD, VanDerWaalsSlick::CALCULATION__SOFTENED_LJ_POTENTIAL_LOG);
options_.setReal(VanDerWaalsSlick::Option::VDW_SOFTENING_LIMIT, 5.0f);
float CONST = options_.setDefaultReal(SLICKEnergy::Option::CONST, SLICKEnergy::Default::CONST);
setIntercept(CONST);
// register all components of the force field
registerComponents_();
// check whether we know which molecule is the protein and which is the
// ligand in this complex. In case we don't know, we have to guess.
// This can be wrong if we got two PDB files which will both be tagged
// as protein.
if ((getReceptor() == 0) || (getLigand() == 0))
{
Log.error() << "I don't know what the protein and the ligand is."
<< std::endl;
return false;
}
return true ;
}
bool SLICKScore::setup()
{
setName("SLICKScore");
// Set VDW to use a cut repulsive potential with a limit of 5 kJ/mol per interaction
options_.setInteger(VanDerWaalsSlick::Option::VDW_METHOD, VanDerWaalsSlick::CALCULATION__SOFTENED_LJ_POTENTIAL_LOG);
options_.setReal(VanDerWaalsSlick::Option::VDW_SOFTENING_LIMIT, 5.0f);
// Use simple (and fast) Coulomb interactions for the scoring
options_.setInteger(PolarSolvation::Option::POLAR_METHOD, PolarSolvation::CALCULATION__COULOMB);
// Now extract options_ from options table and set the coefficients of
// the components accordingly.
float CONST = options_.setDefaultReal(SLICKScore::Option::CONST, SLICKScore::Default::CONST);
setIntercept(CONST);
// register all components of the force field
registerComponents_();
// check whether we know which molecule is the protein and which is the
// ligand in this complex. In case we don't know, we have to guess.
// This can be wrong if we got two PDB files which will both be tagged
// as protein.
if ((getReceptor() == 0) || (getLigand() == 0))
{
Log.error() << "I don't know what the protein and the ligand is."
<< std::endl;
return false;
}
return true;
}
void VolumeModel::init(const ModelInfo::Params & params) {
AbstractModelWithPoints::init(params);
VolumeInfo::PhysicalSize physicalSize = params["physicalSize"].value<VolumeInfo::PhysicalSize>();
VolumeInfo::Size size = params["size"].value<VolumeInfo::Size>();
VolumeInfo::Scaling scaling = params["scaling"].value<VolumeInfo::Scaling>();
scale(scaling);
setSlope(params["slope"].value<VolumeInfo::Slope>());
setIntercept(params["intercept"].value<VolumeInfo::Intercept>());
setWindowCenter(params["windowCenter"].value<VolumeInfo::WindowCenter>());
setWindowWidth(params["windowWidth"].value<VolumeInfo::WindowWidth>());
setHuRange(params["huRange"].value<VolumeInfo::HuRange>());
setValueRange(params["valueRange"].value<VolumeInfo::ValueRange>());
ModelInfo::VerticesVTPtr vertices = new ModelInfo::VerticesVT;
ModelInfo::IndicesPtr indices = new ModelInfo::Indices;
GLfloat scalingFactor = (GLfloat) scene()->scalingFactor();
GLfloat zCurrent = - physicalSize.z() * scaling.z() / scalingFactor / 2.0f;
GLfloat step = - (zCurrent * 2.0f) / size.z();
GLfloat stepTexture = 1.0f / size.z();
GLfloat zCurrentTexture = 0.0f;
GLfloat w = physicalSize.x() / 2.0f * scaling.x() / scalingFactor;
GLfloat h = physicalSize.y() / 2.0f * scaling.y() / scalingFactor;
for (int i = 0; i != (int) size.z(); ++ i) {
vertices->push_back(ModelInfo::VertexVT(- w, - h, zCurrent, 0.0f, 1.0f, zCurrentTexture));
vertices->push_back(ModelInfo::VertexVT(- w, h, zCurrent, 0.0f, 0.0f, zCurrentTexture));
vertices->push_back(ModelInfo::VertexVT(w, h, zCurrent, 1.0f, 0.0f, zCurrentTexture));
vertices->push_back(ModelInfo::VertexVT(w, - h, zCurrent, 1.0f, 1.0f, zCurrentTexture));
indices->push_back(4 * i);
indices->push_back(4 * i + 2);
indices->push_back(4 * i + 1);
indices->push_back(4 * i);
indices->push_back(4 * i + 3);
indices->push_back(4 * i + 2);
zCurrent += step;
zCurrentTexture += stepTexture;
};
ModelInfo::BuffersVT buffers;
buffers.vertices = ModelInfo::VerticesVTPointer(vertices);
buffers.indices = ModelInfo::IndicesPointer(indices);
fillBuffers<ModelInfo::BuffersVT>(buffers);
}
Maths::Regression::Linear::Linear(double m_b_arg, double m_a_arg, double m_coeff_arg)
{
//! Returns the slope of the regression line
setSlope(m_b_arg);
//! Returns the intercept on the Y axis of the regression line
setIntercept(m_a_arg);
//! Returns the linear regression coefficient
setCoefficient(m_coeff_arg);
}