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- acos(...)
- acos(x)
Return the arc cosine (measured in radians) of x.
- asin(...)
- asin(x)
Return the arc sine (measured in radians) of x.
- atan(...)
- atan(x)
Return the arc tangent (measured in radians) of x.
- atan2(...)
- atan2(y, x)
Return the arc tangent (measured in radians) of y/x.
Unlike atan(y/x), the signs of both x and y are considered.
- ceil(...)
- ceil(x)
Return the ceiling of x as a float.
This is the smallest integral value >= x.
- center(numpoints, refcoords)
- Center a molecule using equally weighted points
Parameters
numpoints: Number of points
refcoords: List of reference coordinates, with each set
a list of form [x,y,z] (list)
Returns
refcenter: Center of the set of points (list)
relcoords: Moved refcoords relative to refcenter (list)
- cos(...)
- cos(x)
Return the cosine of x (measured in radians).
- cosh(...)
- cosh(x)
Return the hyperbolic cosine of x.
- exp(...)
- exp(x)
Return e raised to the power of x.
- fabs(...)
- fabs(x)
Return the absolute value of the float x.
- findCoordinates(numpoints, refcoords, defcoords, defatomcoords)
- Driver for the quaternion file. Provide the coordinates as inputs
and obtain the coordinates for the new atom as output.
Parameters
numpoints: The number of points in each list (int)
refcoords: The reference coordinates, a list of lists of form
[x,y,z] (list)
defcoords: The definition coordinates, a list of lists of form
[x,y,z] (list)
defatomcoords: The definition coordinates for the atom to be
placed in the reference frame (list)
Returns
newcoords: The coordinates of the new atom in the
reference frame (list)
- floor(...)
- floor(x)
Return the floor of x as a float.
This is the largest integral value <= x.
- fmod(...)
- fmod(x,y)
Return fmod(x, y), according to platform C. x % y may differ.
- frexp(...)
- frexp(x)
Return the mantissa and exponent of x, as pair (m, e).
m is a float and e is an int, such that x = m * 2.**e.
If x is 0, m and e are both 0. Else 0.5 <= abs(m) < 1.0.
- hypot(...)
- hypot(x,y)
Return the Euclidean distance, sqrt(x*x + y*y).
- jacobi(a, nrot)
- Jacobi diagonalizer with sorted output, only good for 4x4 matrices
Parameters
a: Matrix to diagonalize (4x4 list)
nrot: Maximum number of sweeps
Returns
d: Eigenvalues
v: Eigenvectors
- ldexp(...)
- ldexp(x, i) -> x * (2**i)
- log(...)
- log(x) -> the natural logarithm (base e) of x.
- log10(...)
- log10(x) -> the base 10 logarithm of x.
- modf(...)
- modf(x)
Return the fractional and integer parts of x. Both results carry the sign
of x. The integer part is returned as a real.
- pow(...)
- pow(x,y)
Return x**y (x to the power of y).
- q2mat(q)
- Generate a left rotation matrix from a normalized quaternion
Parameters
q: The normalized quaternion (list)
Returns
u: The rotation matrix (2-dimensional list)
- qchichange(initcoords, refcoords, angle)
- Change the chiangle of the reference coordinate using the
initcoords and the given angle
Parameters
initcoords: Coordinates based on the point and basis atoms
(one dimensional list)
difchi : The angle to use (float)
refcoords : The atoms to analyze (list of many coordinates)
Returns
newcoords : The new coordinates of the atoms (list of many coords)
- qfit(numpoints, refcoords, defcoords)
- Method for getting new atom coordinates from sets of reference
and definition coordinates.
Parameters
numpoints: The number of points in each list (int)
refcoords: List of reference coordinates, with each set
a list of form [x,y,z] (list)
defcoords: List of definition coordinates, with each set
a list of form [x,y,z] (list)
- qtransform(numpoints, defcoords, refcenter, fitcenter, rotation)
- Transform the set of defcoords using the reference center, the fit
center, and a rotation matrix.
Parameters
numpoints: The number of points in each list (int)
defcoords: Definition coordinates (list)
refcenter: The reference center (list)
defcenter: The definition center (list)
rotation: The rotation matrix (list)
Returns
newcoords: The coordinates of the new point (list)
- qtrfit(numpoints, defcoords, refcoords, nrot)
- Find the quaternion, q, [and left rotation matrix, u] that minimizes
| qTXq - Y | ^ 2 [|uX - Y| ^ 2]
This is equivalent to maximizing Re (qTXTqY)
The left rotation matrix, u, is obtained from q by
u = qT1q
Parameters
numpoints: The number of points in each list (int)
defcoords: List of definition coordinates, with each set
a list of form [x,y,z] (list)
refcoords: List of fitted coordinates, with each set
a list of form [x,y,z] (list)
nrot : The maximum number of jacobi sweeps
Returns
q : The best-fit quaternion
u : The best-fit left rotation matrix
- rotmol(numpoints, x, u)
- Rotate a molecule
Parameters
numpoints: The number of points in the list (int)
x: The input coordinates (list)
u: The left rotation matrix (list)
Returns
out: The rotated coordinates out=u * x (list)
- sin(...)
- sin(x)
Return the sine of x (measured in radians).
- sinh(...)
- sinh(x)
Return the hyperbolic sine of x.
- sqrt(...)
- sqrt(x)
Return the square root of x.
- tan(...)
- tan(x)
Return the tangent of x (measured in radians).
- tanh(...)
- tanh(x)
Return the hyperbolic tangent of x.
- translate(numpoints, refcoords, center, mode)
- Translate a molecule using equally weighted points
Parameters
numpoints: Number of points
refcoords: List of reference coordinates, with each set
a list of form [x,y,z] (list)
center: Center of the system(list)
mode: If 1, center will be subtracted from refcoords
If 2, center will be added to refcoords
Returns
relcoords: Moved refcoords relative to refcenter (list)
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