model_quality¶

Bindings for numeric::model_quality namespace

pyrosetta.rosetta.numeric.model_quality.BlankMatrixMult(A: pyrosetta.rosetta.ObjexxFCL.FArray2A_double_t, n: int, np: int, transposeA: int, B: pyrosetta.rosetta.ObjexxFCL.FArray2A_double_t, m: int, transposeB: int, AxB_out: pyrosetta.rosetta.ObjexxFCL.FArray2A_double_t) → None¶: C++: numeric::model_quality::BlankMatrixMult(class ObjexxFCL::FArray2A<double>, int, int, int, class ObjexxFCL::FArray2A<double>, int, int, class ObjexxFCL::FArray2A<double>) –> void

pyrosetta.rosetta.numeric.model_quality.MatrixMult(A: pyrosetta.rosetta.ObjexxFCL.FArray2A_double_t, n: int, np: int, transposeA: int, B: pyrosetta.rosetta.ObjexxFCL.FArray2A_double_t, m: int, transposeB: int, AxB_out: pyrosetta.rosetta.ObjexxFCL.FArray2A_double_t) → None¶: C++: numeric::model_quality::MatrixMult(class ObjexxFCL::FArray2A<double>, int, int, int, class ObjexxFCL::FArray2A<double>, int, int, class ObjexxFCL::FArray2A<double>) –> void

class pyrosetta.rosetta.numeric.model_quality.RmsData¶

Bases: SingletonBase_numeric_model_quality_RmsData_t

RmsData is a class intended to replace the global rms_obj namespace from rosetta++. Initial implementation is with a singleton design pattern to mimic a global namespace from rosetta++.

add_rms(self: pyrosetta.rosetta.numeric.model_quality.RmsData, i: int, xp: pyrosetta.rosetta.ObjexxFCL.FArray2A_double_t, xe: pyrosetta.rosetta.ObjexxFCL.FArray2A_double_t) → None¶

computes a 3x3 matrix of cross moments between the x,y,z components of the two input vectors.

the output is the running sum of these matricies

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C++: numeric::model_quality::RmsData::add_rms(int, class ObjexxFCL::FArray2A<double>, class ObjexxFCL::FArray2A<double>) –> void

clear_rms(self: pyrosetta.rosetta.numeric.model_quality.RmsData) → None¶

clear the data in this RmsData

C++: numeric::model_quality::RmsData::clear_rms() –> void

count(self: pyrosetta.rosetta.numeric.model_quality.RmsData) → int¶

returns the number of points in this RmsData

C++: numeric::model_quality::RmsData::count() –> int

static get_instance() → numeric::model_quality::RmsData¶: C++: utility::SingletonBase<numeric::model_quality::RmsData>::get_instance() –> class numeric::model_quality::RmsData *

xm(self: pyrosetta.rosetta.numeric.model_quality.RmsData) → pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t¶: C++: numeric::model_quality::RmsData::xm() –> class ObjexxFCL::FArray2D<double>

xre(self: pyrosetta.rosetta.numeric.model_quality.RmsData) → float¶: C++: numeric::model_quality::RmsData::xre() –> double

xrp(self: pyrosetta.rosetta.numeric.model_quality.RmsData) → float¶: C++: numeric::model_quality::RmsData::xrp() –> double

xse(self: pyrosetta.rosetta.numeric.model_quality.RmsData) → pyrosetta.rosetta.ObjexxFCL.FArray1D_double_t¶: C++: numeric::model_quality::RmsData::xse() –> class ObjexxFCL::FArray1D<double>

xsp(self: pyrosetta.rosetta.numeric.model_quality.RmsData) → pyrosetta.rosetta.ObjexxFCL.FArray1D_double_t¶: C++: numeric::model_quality::RmsData::xsp() –> class ObjexxFCL::FArray1D<double>

pyrosetta.rosetta.numeric.model_quality.calc_rms(p1_coords: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t, p2_coords: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t) → float¶: C++: numeric::model_quality::calc_rms(class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >, class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >) –> double

pyrosetta.rosetta.numeric.model_quality.calculate_dihedral_distance(dih1: float, dih2: float) → float¶

Calculate the dihedral angle distance from directional statistics.

Metric described in:

North B, Lehmann A, Dunbrack RL. A new clustering of antibody CDR loop conformations. J Mol Biol 2011; 406:228-256.

C++: numeric::model_quality::calculate_dihedral_distance(double, double) –> double

pyrosetta.rosetta.numeric.model_quality.det3(m: pyrosetta.rosetta.ObjexxFCL.FArray2A_double_t) → float¶

determinant of a 3x3 matrix

cute factoid: det of a 3x3 is the dot product of one row with the cross product of the other two. This explains why a right hand coordinate system has a positive determinant. cute huh?

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charlie strauss 2001

C++: numeric::model_quality::det3(class ObjexxFCL::FArray2A<double>) –> double

pyrosetta.rosetta.numeric.model_quality.erfcc(x: float) → float¶: C++: numeric::model_quality::erfcc(double) –> double

pyrosetta.rosetta.numeric.model_quality.findUU(*args, **kwargs)¶

Overloaded function.

findUU(XX: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t, YY: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t, WW: pyrosetta.rosetta.utility.vector1_double, Npoints: int, UU: pyrosetta.rosetta.numeric.xyzMatrix_double_t, sigma3: float) -> None

C++: numeric::model_quality::findUU(class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &, class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &, const class utility::vector1<double, class std::allocator<double> > &, int, class numeric::xyzMatrix<double> &, double &) –> void

findUU(XX: pyrosetta.rosetta.ObjexxFCL.FArray2_double_t, YY: pyrosetta.rosetta.ObjexxFCL.FArray2_double_t, WW: pyrosetta.rosetta.ObjexxFCL.FArray1_double_t, Npoints: int, UU: pyrosetta.rosetta.ObjexxFCL.FArray2_double_t, sigma3: float) -> None

C++: numeric::model_quality::findUU(class ObjexxFCL::FArray2<double> &, class ObjexxFCL::FArray2<double> &, const class ObjexxFCL::FArray1<double> &, int, class ObjexxFCL::FArray2<double> &, double &) –> void

pyrosetta.rosetta.numeric.model_quality.fixEigenvector(m_v: pyrosetta.rosetta.ObjexxFCL.FArray2A_double_t) → None¶: C++: numeric::model_quality::fixEigenvector(class ObjexxFCL::FArray2A<double>) –> void

pyrosetta.rosetta.numeric.model_quality.rms_fit(npoints: int, xx: pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t, yy: pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t, ww: pyrosetta.rosetta.ObjexxFCL.FArray1D_double_t, natsel: int, esq: float) → None¶: C++: numeric::model_quality::rms_fit(int, class ObjexxFCL::FArray2D<double>, class ObjexxFCL::FArray2D<double> &, class ObjexxFCL::FArray1D<double>, int, double &) –> void

pyrosetta.rosetta.numeric.model_quality.rms_wrapper(natoms: int, p1a: pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t, p2a: pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t) → float¶: C++: numeric::model_quality::rms_wrapper(int, class ObjexxFCL::FArray2D<double>, class ObjexxFCL::FArray2D<double>) –> double

pyrosetta.rosetta.numeric.model_quality.rms_wrapper_slow_and_correct(natoms: int, p1a: pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t, p2a: pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t) → float¶: C++: numeric::model_quality::rms_wrapper_slow_and_correct(int, class ObjexxFCL::FArray2D<double>, class ObjexxFCL::FArray2D<double>) –> double

pyrosetta.rosetta.numeric.model_quality.rmsfitca3(npoints: int, xx0: pyrosetta.rosetta.ObjexxFCL.FArray2A_double_t, xx: pyrosetta.rosetta.ObjexxFCL.FArray2A_double_t, yy0: pyrosetta.rosetta.ObjexxFCL.FArray2A_double_t, yy: pyrosetta.rosetta.ObjexxFCL.FArray2A_double_t, esq: float) → None¶

This function gets its alignment info via a namespace! Alignment (rotation matrix) and rms(esq) are computed on the basis of residues previously designated by calls to add_rms(). However, the rotation is applied to all Npoints of XX0,yy0 with the results returned in xx,yy.

most of this is double for good reasons. first there are some large differences of small numbers. second the rsymm_eignen() function can internally have numbers larger than the largest double number. (you could do some fancy foot work to rescale m_moment if you really had a problem with this.)

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NOTE: det is a double precision real NOTE: (xx,yy) can be same arrays as (xx_0,yy_0) if desired

C++: numeric::model_quality::rmsfitca3(int, class ObjexxFCL::FArray2A<double>, class ObjexxFCL::FArray2A<double>, class ObjexxFCL::FArray2A<double>, class ObjexxFCL::FArray2A<double>, double &) –> void