Python: module quatfit

quatfit (30 September 2003) | index /home/todd/release/pdb2pqr/quatfit.py

`Quatfit routines for PDB2PQR
This module is used to find the coordinates of a new
atom based on a reference set of
coordinates and a definition set of coordinates.
Original Code by David J. Heisterberg
The Ohio Supercomputer Center
1224 Kinnear Rd.
Columbus, OH 43212-1163
(614)292-6036
djh@osc.edu djh@ohstpy.bitnet ohstpy::djh
Translated to C from fitest.f program and interfaced with
Xmol program by Jan Labanowski, jkl@osc.edu jkl@ohstpy.bitnet
ohstpy::jkl
Adapted for PDB2PQR by Jens Erik Nielsen
UCSD/HHMI
Ported to Python by Todd Dolinsky (todd@ccb.wustl.edu)
Washington University in St. Louis`

Modules
`` |  |
math | string |  |

Functions
`` |  | 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)`

Data
`` |  | DIHEDRAL = 57.2958 SMALL = 9.9999999999999995e-08 __author__ = 'David Heisterberg, Jan Labanowski, Jens Erik Nielsen, Todd Dolinsky' __date__ = '30 September 2003' __file__ = './quatfit.pyc' __name__ = 'quatfit' e = 2.7182818284590451 pi = 3.1415926535897931

Author
`` |  | David Heisterberg, Jan Labanowski, Jens Erik Nielsen, Todd Dolinsky