model_quality

Bindings for numeric::model_quality namespace

pyrosetta.rosetta.numeric.model_quality.BlankMatrixMult(A: ObjexxFCL::FArray2A<double>, n: int, np: int, transposeA: int, B: ObjexxFCL::FArray2A<double>, m: int, transposeB: int, AxB_out: ObjexxFCL::FArray2A<double>) → 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: ObjexxFCL::FArray2A<double>, n: int, np: int, transposeA: int, B: ObjexxFCL::FArray2A<double>, m: int, transposeB: int, AxB_out: ObjexxFCL::FArray2A<double>) → 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: pyrosetta.rosetta.utility.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++.

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__

Initialize self. See help(type(self)) for accurate signature.

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

add_rms(self: pyrosetta.rosetta.numeric.model_quality.RmsData, i: int, xp: ObjexxFCL::FArray2A<double>, xe: ObjexxFCL::FArray2A<double>) → 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

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) → ObjexxFCL::FArray2D<double>

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) → ObjexxFCL::FArray1D<double>

C++: numeric::model_quality::RmsData::xse() –> class ObjexxFCL::FArray1D<double>

xsp(self: pyrosetta.rosetta.numeric.model_quality.RmsData) → ObjexxFCL::FArray1D<double>

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.det3(m: ObjexxFCL::FArray2A<double>) → 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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_read

_write

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.

1. 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

2. findUU(XX: pyrosetta.rosetta.ObjexxFCL.FArray2_double_t, YY: pyrosetta.rosetta.ObjexxFCL.FArray2_double_t, WW: ObjexxFCL::FArray1<double>, 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: ObjexxFCL::FArray2A<double>) → None

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

pyrosetta.rosetta.numeric.model_quality.rms_fit(npoints: int, xx: ObjexxFCL::FArray2D<double>, yy: ObjexxFCL::FArray2D<double>, ww: ObjexxFCL::FArray1D<double>, 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: ObjexxFCL::FArray2D<double>, p2a: ObjexxFCL::FArray2D<double>) → 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: ObjexxFCL::FArray2D<double>, p2a: ObjexxFCL::FArray2D<double>) → 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: ObjexxFCL::FArray2A<double>, xx: ObjexxFCL::FArray2A<double>, yy0: ObjexxFCL::FArray2A<double>, yy: ObjexxFCL::FArray2A<double>, 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