def poly(seq_of_zeros):
"""
Find the coefficients of a polynomial with the given sequence of roots.
Returns the coefficients of the polynomial whose leading coefficient
is one for the given sequence of zeros (multiple roots must be included
in the sequence as many times as their multiplicity; see Examples).
A square matrix (or array, which will be treated as a matrix) can also
be given, in which case the coefficients of the characteristic polynomial
of the matrix are returned.
Parameters
----------
seq_of_zeros : array_like, shape (N,) or (N, N)
A sequence of polynomial roots, or a square array or matrix object.
Returns
-------
c : ndarray
1D array of polynomial coefficients from highest to lowest degree:
``c[0] * x**(N) + c[1] * x**(N-1) + ... + c[N-1] * x + c[N]``
where c[0] always equals 1.
Raises
------
ValueError
If input is the wrong shape (the input must be a 1-D or square
2-D array).
See Also
--------
polyval : Compute polynomial values.
roots : Return the roots of a polynomial.
polyfit : Least squares polynomial fit.
poly1d : A one-dimensional polynomial class.
Notes
-----
Specifying the roots of a polynomial still leaves one degree of
freedom, typically represented by an undetermined leading
coefficient. [1]_ In the case of this function, that coefficient -
the first one in the returned array - is always taken as one. (If
for some reason you have one other point, the only automatic way
presently to leverage that information is to use ``polyfit``.)
The characteristic polynomial, :math:`p_a(t)`, of an `n`-by-`n`
matrix **A** is given by
:math:`p_a(t) = \\mathrm{det}(t\\, \\mathbf{I} - \\mathbf{A})`,
where **I** is the `n`-by-`n` identity matrix. [2]_
References
----------
.. [1] M. Sullivan and M. Sullivan, III, "Algebra and Trignometry,
Enhanced With Graphing Utilities," Prentice-Hall, pg. 318, 1996.
.. [2] G. Strang, "Linear Algebra and Its Applications, 2nd Edition,"
Academic Press, pg. 182, 1980.
Examples
--------
Given a sequence of a polynomial's zeros:
>>> np.poly((0, 0, 0)) # Multiple root example
array([1, 0, 0, 0])
The line above represents z**3 + 0*z**2 + 0*z + 0.
>>> np.poly((-1./2, 0, 1./2))
array([ 1. , 0. , -0.25, 0. ])
The line above represents z**3 - z/4
>>> np.poly((np.random.random(1.)[0], 0, np.random.random(1.)[0]))
array([ 1. , -0.77086955, 0.08618131, 0. ]) #random
Given a square array object:
>>> P = np.array([[0, 1./3], [-1./2, 0]])
>>> np.poly(P)
array([ 1. , 0. , 0.16666667])
Or a square matrix object:
>>> np.poly(np.matrix(P))
array([ 1. , 0. , 0.16666667])
Note how in all cases the leading coefficient is always 1.
"""
seq_of_zeros = atleast_1d(seq_of_zeros)
sh = seq_of_zeros.shape
if len(sh) == 2 and sh[0] == sh[1] and sh[0] != 0:
seq_of_zeros = eigvals(seq_of_zeros)
elif len(sh) == 1:
dt = seq_of_zeros.dtype
# Let object arrays slip through, e.g. for arbitrary precision
if dt != object:
seq_of_zeros = seq_of_zeros.astype(mintypecode(dt.char))
else:
raise ValueError("input must be 1d or non-empty square 2d array.")
if len(seq_of_zeros) == 0:
return 1.0
dt = seq_of_zeros.dtype
a = ones((1,), dtype=dt)
for k in range(len(seq_of_zeros)):
a = NX.convolve(a, array([1, -seq_of_zeros[k]], dtype=dt),
mode='full')
if issubclass(a.dtype.type, NX.complexfloating):
# if complex roots are all complex conjugates, the roots are real.
roots = NX.asarray(seq_of_zeros, complex)
pos_roots = sort_complex(NX.compress(roots.imag > 0, roots))
neg_roots = NX.conjugate(sort_complex(
NX.compress(roots.imag < 0, roots)))
if (len(pos_roots) == len(neg_roots) and
NX.alltrue(neg_roots == pos_roots)):
a = a.real.copy()
return a
def poly(seq_of_zeros):
"""
Find the coefficients of a polynomial with the given sequence of roots.
Returns the coefficients of the polynomial whose leading coefficient
is one for the given sequence of zeros (multiple roots must be included
in the sequence as many times as their multiplicity; see Examples).
A square matrix (or array, which will be treated as a matrix) can also
be given, in which case the coefficients of the characteristic polynomial
of the matrix are returned.
Parameters
----------
seq_of_zeros : array_like, shape (N,) or (N, N)
A sequence of polynomial roots, or a square array or matrix object.
Returns
-------
c : ndarray
1D array of polynomial coefficients from highest to lowest degree:
``c[0] * x**(N) + c[1] * x**(N-1) + ... + c[N-1] * x + c[N]``
where c[0] always equals 1.
Raises
------
ValueError
If input is the wrong shape (the input must be a 1-D or square
2-D array).
See Also
--------
polyval : Evaluate a polynomial at a point.
roots : Return the roots of a polynomial.
polyfit : Least squares polynomial fit.
poly1d : A one-dimensional polynomial class.
Notes
-----
Specifying the roots of a polynomial still leaves one degree of
freedom, typically represented by an undetermined leading
coefficient. [1]_ In the case of this function, that coefficient -
the first one in the returned array - is always taken as one. (If
for some reason you have one other point, the only automatic way
presently to leverage that information is to use ``polyfit``.)
The characteristic polynomial, :math:`p_a(t)`, of an `n`-by-`n`
matrix **A** is given by
:math:`p_a(t) = \\mathrm{det}(t\\, \\mathbf{I} - \\mathbf{A})`,
where **I** is the `n`-by-`n` identity matrix. [2]_
References
----------
.. [1] M. Sullivan and M. Sullivan, III, "Algebra and Trignometry,
Enhanced With Graphing Utilities," Prentice-Hall, pg. 318, 1996.
.. [2] G. Strang, "Linear Algebra and Its Applications, 2nd Edition,"
Academic Press, pg. 182, 1980.
Examples
--------
Given a sequence of a polynomial's zeros:
>>> np.poly((0, 0, 0)) # Multiple root example
array([1, 0, 0, 0])
The line above represents z**3 + 0*z**2 + 0*z + 0.
>>> np.poly((-1./2, 0, 1./2))
array([ 1. , 0. , -0.25, 0. ])
The line above represents z**3 - z/4
>>> np.poly((np.random.random(1.)[0], 0, np.random.random(1.)[0]))
array([ 1. , -0.77086955, 0.08618131, 0. ]) #random
Given a square array object:
>>> P = np.array([[0, 1./3], [-1./2, 0]])
>>> np.poly(P)
array([ 1. , 0. , 0.16666667])
Or a square matrix object:
>>> np.poly(np.matrix(P))
array([ 1. , 0. , 0.16666667])
Note how in all cases the leading coefficient is always 1.
"""
seq_of_zeros = atleast_1d(seq_of_zeros)
sh = seq_of_zeros.shape
if len(sh) == 2 and sh[0] == sh[1] and sh[0] != 0:
seq_of_zeros = eigvals(seq_of_zeros)
elif len(sh) == 1:
dt = seq_of_zeros.dtype
# Let object arrays slip through, e.g. for arbitrary precision
if dt != object:
seq_of_zeros = seq_of_zeros.astype(mintypecode(dt.char))
else:
raise ValueError("input must be 1d or non-empty square 2d array.")
if len(seq_of_zeros) == 0:
return 1.0
dt = seq_of_zeros.dtype
a = ones((1, ), dtype=dt)
for k in range(len(seq_of_zeros)):
a = NX.convolve(a, array([1, -seq_of_zeros[k]], dtype=dt), mode='full')
if issubclass(a.dtype.type, NX.complexfloating):
# if complex roots are all complex conjugates, the roots are real.
roots = NX.asarray(seq_of_zeros, complex)
pos_roots = sort_complex(NX.compress(roots.imag > 0, roots))
neg_roots = NX.conjugate(
sort_complex(NX.compress(roots.imag < 0, roots)))
if (len(pos_roots) == len(neg_roots)
and NX.alltrue(neg_roots == pos_roots)):
a = a.real.copy()
return a
def test_matscalar(self):
b1 = matrix(ones((3,3),dtype=complex))
assert_equal(b1*1.0, b1)
def test_matscalar(self):
b1 = matrix(ones((3, 3), dtype=complex))
assert_equal(b1 * 1.0, b1)
def coarseMolSurface(molFrag,XYZd,isovalue=5.0,resolution=-0.4,padding=0.0, name='CoarseMolSurface',geom=None):
"""
Function adapted from the Vision network which compute a coarse molecular
surface in PMV
@type molFrag: MolKit.AtomSet
@param molFrag: the atoms selection
@type XYZd: array
@param XYZd: shape of the volume
@type isovalue: float
@param isovalue: isovalue for the isosurface computation
@type resolution: float
@param resolution: resolution of the final mesh
@type padding: float
@param padding: the padding
@type name: string
@param name: the name of the resultante geometry
@type geom: DejaVu.Geom
@param geom: update geom instead of creating a new one
@rtype: DejaVu.Geom
@return: the created or updated DejaVu.Geom
"""
import pdb
from MolKit.molecule import Atom
atoms = molFrag.findType(Atom)
coords = atoms.coords
radii = atoms.vdwRadius
from UTpackages.UTblur import blur
import numpy.core as Numeric
volarr, origin, span = blur.generateBlurmap(coords, radii, XYZd,resolution, padding = 0.0)
volarr.shape = (XYZd[0],XYZd[1],XYZd[2])
volarr = Numeric.ascontiguousarray(Numeric.transpose(volarr), 'f')
weights = Numeric.ones(len(radii), 'f')
h = {}
from Volume.Grid3D import Grid3DF
maskGrid = Grid3DF( volarr, origin, span , h)
h['amin'], h['amax'],h['amean'],h['arms']= maskGrid.stats()
from UTpackages.UTisocontour import isocontour
isocontour.setVerboseLevel(0)
data = maskGrid.data
origin = Numeric.array(maskGrid.origin).astype('f')
stepsize = Numeric.array(maskGrid.stepSize).astype('f')
if data.dtype.char!=Numeric.float32:
data = data.astype('f')#Numeric.Float32)
newgrid3D = Numeric.ascontiguousarray(Numeric.reshape( Numeric.transpose(data),
(1, 1)+tuple(data.shape) ), data.dtype.char)
ndata = isocontour.newDatasetRegFloat3D(newgrid3D, origin, stepsize)
isoc = isocontour.getContour3d(ndata, 0, 0, isovalue,
isocontour.NO_COLOR_VARIABLE)
vert = Numeric.zeros((isoc.nvert,3)).astype('f')
norm = Numeric.zeros((isoc.nvert,3)).astype('f')
col = Numeric.zeros((isoc.nvert)).astype('f')
tri = Numeric.zeros((isoc.ntri,3)).astype('i')
isocontour.getContour3dData(isoc, vert, norm, col, tri, 0)
if maskGrid.crystal:
vert = maskGrid.crystal.toCartesian(vert)
return (vert, tri)
# array()
# linspace()
# logspace()
# arange()
# zeros()
# ones()
"""
from numpy import *
arr = array(
[1, 2, 3, 4, 5.0]
) #implict conversion : means in the array one element is float so it will convert the entire array into float
print(arr.dtype)
print("\n example linspace()")
als = linspace(
0, 15, 25
) #linspace(start,stop,range)=> means in given range it will create mention range number of parts
print(als)
print("\n example of logspace()")
ls = logspace(1, 40, 5)
print(ls)
print("\n example of zeros()")
zs = zeros(5)
print(zs)
print("\n example of ones()")
os = ones(22)
print(os)
def coarseMolSurface(molFrag,
XYZd,
isovalue=5.0,
resolution=-0.4,
padding=0.0,
name='CoarseMolSurface',
geom=None):
"""
Function adapted from the Vision network which compute a coarse molecular
surface in PMV
@type molFrag: MolKit.AtomSet
@param molFrag: the atoms selection
@type XYZd: array
@param XYZd: shape of the volume
@type isovalue: float
@param isovalue: isovalue for the isosurface computation
@type resolution: float
@param resolution: resolution of the final mesh
@type padding: float
@param padding: the padding
@type name: string
@param name: the name of the resultante geometry
@type geom: DejaVu.Geom
@param geom: update geom instead of creating a new one
@rtype: DejaVu.Geom
@return: the created or updated DejaVu.Geom
"""
import pdb
from MolKit.molecule import Atom
atoms = molFrag.findType(Atom)
coords = atoms.coords
radii = atoms.vdwRadius
from UTpackages.UTblur import blur
import numpy.core as Numeric
volarr, origin, span = blur.generateBlurmap(coords,
radii,
XYZd,
resolution,
padding=0.0)
volarr.shape = (XYZd[0], XYZd[1], XYZd[2])
volarr = Numeric.ascontiguousarray(Numeric.transpose(volarr), 'f')
weights = Numeric.ones(len(radii), 'f')
h = {}
from Volume.Grid3D import Grid3DF
maskGrid = Grid3DF(volarr, origin, span, h)
h['amin'], h['amax'], h['amean'], h['arms'] = maskGrid.stats()
from UTpackages.UTisocontour import isocontour
isocontour.setVerboseLevel(0)
data = maskGrid.data
origin = Numeric.array(maskGrid.origin).astype('f')
stepsize = Numeric.array(maskGrid.stepSize).astype('f')
if data.dtype.char != Numeric.float32:
data = data.astype('f') #Numeric.Float32)
newgrid3D = Numeric.ascontiguousarray(
Numeric.reshape(Numeric.transpose(data), (1, 1) + tuple(data.shape)),
data.dtype.char)
ndata = isocontour.newDatasetRegFloat3D(newgrid3D, origin, stepsize)
isoc = isocontour.getContour3d(ndata, 0, 0, isovalue,
isocontour.NO_COLOR_VARIABLE)
vert = Numeric.zeros((isoc.nvert, 3)).astype('f')
norm = Numeric.zeros((isoc.nvert, 3)).astype('f')
col = Numeric.zeros((isoc.nvert)).astype('f')
tri = Numeric.zeros((isoc.ntri, 3)).astype('i')
isocontour.getContour3dData(isoc, vert, norm, col, tri, 0)
if maskGrid.crystal:
vert = maskGrid.crystal.toCartesian(vert)
return (vert, tri)