PPhiPsiDistribution Class Reference

#include <PPhiPsiDistribution.h>

List of all members.

---

Detailed Description

The PPhiPsiDistribution class is for sampling backbone conformations according to a certain distribution. Currenlty, the seed sampling methods can take in only 1 distribution (for all amino acids) or 20 distributions (one for each amino acid, such as a Ramachandran distribution). In the later case, the name of the distribution must be 3-letter amino acid name in all capital letters. In the previous case, name doesn't matter, and set to "anything" by default.

Public Member Functions
	PPhiPsiDistribution ()
	PPhiPsiDistribution (const vector< vector< double > > &v, const string &name="anything")
void	print (ostream &out) const
double	getProbPhiPsi (double phi, double psi) const
vector< double >	getPhiDistribution (double psiValue) const
vector< double >	getPsiDistribution (double phiValue) const
vector< double >	getPhiDistribution () const
vector< double >	getPsiDistribution () const
bool	isEmpty () const
int	numPhiIntervals () const
int	numPsiIntervals () const
Static Public Member Functions
static map< string, PPhiPsiDistribution >	generateRamachandran ()

---

Constructor & Destructor Documentation

PPhiPsiDistribution::PPhiPsiDistribution

(

)

[inline]

PPhiPsiDistribution::PPhiPsiDistribution	(	const vector< vector< double > > &	v,
		const string &	name = "anything"
	)

Construct a PPhiPsiDistribution object by providing the distribution v and a corresponding name. In v, the 1st dimension is about Phi and the 2nd dimension is about Psi i.e., v[i][j] is the probability of taking the Phi in the ith interval and Psi in the jth interval. Important: 1. All inner vectors must have the same size. 2. All entries should sum up to 1. 3. v[i][0] to v[i][n-1] store the probability of Psi in 360/n degree intervals from -180 to +179. v[0][j] to v[n-1][j] store the probability of Phi in 360/n degree intervals from -180 to +179. For example: vector<double> row1, row2; row1.push_back(0.1); row1.push_back(0.2); row1.push_back(0.3); row2.push_back(0.2); row2.push_back(0.1); row2.push_back(0.1); vector< vector<double> > phipsi; phipsi.push_back(row1); phipsi.push_back(row2); This means: the phi angle has two intervals: [-180,0) and [0,+179], and psi angle has three intervals: [-180,-60), [-60,+60) and [+60,179]. The probabilty of a residue taking phi angle in [-180,0) and psi angle in [+60,+179] is 0.3.

---

Member Function Documentation

void PPhiPsiDistribution::print

(

ostream &

out

)

const

double PPhiPsiDistribution::getProbPhiPsi	(	double	phi,
		double	psi
	)			const

vector< double > PPhiPsiDistribution::getPhiDistribution

(

double

psiValue

)

const

vector< double > PPhiPsiDistribution::getPsiDistribution

(

double

phiValue

)

const

vector<double> PPhiPsiDistribution::getPhiDistribution

(

)

const [inline]

vector<double> PPhiPsiDistribution::getPsiDistribution

(

)

const [inline]

bool PPhiPsiDistribution::isEmpty

(

)

const [inline]

int PPhiPsiDistribution::numPhiIntervals

(

)

const [inline]

Returns the number of phi intervals in this distribution.

int PPhiPsiDistribution::numPsiIntervals

(

)

const [inline]

Returns the number of psi intervals in this distribution.

map< string, PPhiPsiDistribution > PPhiPsiDistribution::generateRamachandran

(

)

[static]

---

The documentation for this class was generated from the following files:

• src/core/PPhiPsiDistribution.h
• src/core/PPhiPsiDistribution.cc

---