utilities (23 September 2003) | index /home/todd/release/pdb2pqr/utilities.py

`Utilities for PDB2PQR Suite
This module provides various utilities for the PDB2PQR suite to be
imported into other Python scripts.
Todd Dolinsky (todd@ccb.wustl.edu)
Washington University in St. Louis`

Modules
`` |  |
string |  |  |

Classes
`` |  | Matrix
class Matrix
`` | `Matrix class A class for handling matrices`
| Methods defined here: LU(self, b) `Solve the matrix Ax = b by LU decomposition: Given Ax = b and LU = A, Ax = (LU)x = L(Ux) = b Solve Ly = b, and then Ux = y. Parameters: b = 1 x N matrix, where N is the number of variables (Matrix) Returns: x = The solved N-element list (list)` __init__(self, lists) `Create a new matrix object. Parameters lists: A list of lists containing the matrix (list)` __str__(self) `Print the contents of the matrix Returns out: The printed matrix (string)` Data and non-method functions defined here: __doc__ = '\n Matrix class\n\n A class for handling matrices\n ' __module__ = 'utilities'

Functions
`` |  | acos(...) `acos(x) Return the arc cosine (measured in radians) of x.` add(coords1, coords2) `Add one 3-dimensional point to another Parameters coords1: coordinates of form [x,y,z] coords2: coordinates of form [x,y,z] Returns list: List of coordinates equal to coords2 + coords1 (list)` analyzeMap(map, value, list=[]) `Analyze a map of interactions to determine the overall connectivity. Parameters map : A dictionary of lists which contain the connections to the key (dictionary) value : The key value to analyze (variable) Returns list : A connectivity list of the map (list) Example Given map {1: [2], 4: [5], 7: [5,9], 9: [14]} list will return For 1: [1,2] For 4,5,7,9,14: [4,5,7,9,14] For all other X: [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.` cos(...) `cos(x) Return the cosine of x (measured in radians).` cosh(...) `cosh(x) Return the hyperbolic cosine of x.` cross(coords1, coords2) `Find the cross product of two 3-dimensional points Parameters coords1: coordinates of form [x,y,z] coords2: coordinates of form [x,y,z] Returns list: Cross product coords2 and coords1 (list)` distance(coords1, coords2) `Calculate the distance between two coordinates, as denoted by dist = sqrt((x2- x1)^2 + (y2 - y1)^2 + (z2 - z1)^2)) Parameters coords1: Coordinates of form [x,y,z] coords2: Coordinates of form [x,y,z] Returns dist: Distance between the two coordinates (float)` dot(coords1, coords2) `Find the dot product of two 3-dimensional points Parameters coords1: coordinates of form [x,y,z] coords2: coordinates of form [x,y,z] Returns value: Dot product coords2 and coords1 (float)` exp(...) `exp(x) Return e raised to the power of x.` fabs(...) `fabs(x) Return the absolute value of the float x.` 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.` getDihedral(coords1, coords2, coords3, coords4) `Calculate the angle using the four atoms Parameters coords1: First of four coordinates of form [x,y,z] coords2: Second of four coords3: Third of four coords4: Fourth of four Returns value: Size of the angle (float)` getFile(path) `Obtain a PDB file. First check the path given on the command line - if that file is not available, obtain the file from the PDB webserver at http://www.rcsb.org/pdb/ . Parameters path: Name of PDB file to obtain (string) Returns file: File object containing PDB file (file object)` hypot(...) `hypot(x,y) Return the Euclidean distance, sqrt(x*x + y*y).` 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.` normalize(coords) `Normalize a set of coordinates Parameters coords: coordinates of form [x,y,z] Returns list: normalized coordinates (list)` placeOxygen(CA, C, N) `Place an oxygen according to the planar atoms CA, C, and N using a trans-peptide geometry. Allows for a more accurate method of adding oxygen atoms. Parameters CA: The coordinates of the CA atom (list) C: The coordinates of the C atom (list) N: The coordinates of the peptide bonded N atom from the next residue (list) Returns location: The location of the residue (list)` pow(...) `pow(x,y) Return x**y (x to the power of y).` shortestPath(graph, start, end, path=[]) `Uses recursion to find the shortest path from one node to another in an unweighted graph. Adapted from http://www.python.org/doc/essays/graphs.html . Parameters: graph: A mapping of the graph to analyze, of the form {0: [1,2], 1:[3,4], ...} . Each key has a list of edges. start: The ID of the key to start the analysis from end: The ID of the key to end the analysis path: Optional argument used during the recursive step to keep the current path up to that point Returns: (variable): Returns a list of the shortest path (list) Returns None if start and end are not connected` 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.` subtract(coords1, coords2) `Subtract one 3-dimensional point from another Parameters coords1: coordinates of form [x,y,z] coords2: coordinates of form [x,y,z] Returns list: List of coordinates equal to coords1 - coords2 (list)` tan(...) `tan(x) Return the tangent of x (measured in radians).` tanh(...) `tanh(x) Return the hyperbolic tangent of x.`

Data
`` |  | DIHEDRAL = 57.2958 SMALL = 9.9999999999999995e-08 __author__ = 'Todd Dolinsky' __date__ = '23 September 2003' __file__ = './utilities.pyc' __name__ = 'utilities' e = 2.7182818284590451 pi = 3.1415926535897931

Author
`` |  | Todd Dolinsky