Python: module src.utilities

src.utilities (28 February 2006) | index /Users/baker/coding/manifold/pdb2pqr/trunk/pdb2pqr/src/utilities.py

`Utilities for PDB2PQR Suite
This module provides various utilities for the PDB2PQR suite to be
imported into other Python scripts.
----------------------------
PDB2PQR -- An automated pipeline for the setup, execution, and analysis of
Poisson-Boltzmann electrostatics calculations
Nathan A. Baker (baker@biochem.wustl.edu)
Todd Dolinsky (todd@ccb.wustl.edu)
Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology
Washington University in St. Louis
Jens Nielsen (Jens.Nielsen@ucd.ie)
University College Dublin
Additional contributing authors listed in documentation and supporting
package licenses.
Copyright (c) 2003-2007. Washington University in St. Louis.
All Rights Reserved.
This file is part of PDB2PQR.
PDB2PQR is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
PDB2PQR is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with PDB2PQR; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
----------------------------`

Modules
`` |  |
math | os | string | sys

Functions
`` |  | 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)` analyzeConnectivity(map, key) `Analyze the connectivity of a given map using the key value. Parameters map: The map to analyze (dict) key: The key value (variable) Returns list: A list of connected values to the key (list)` 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)` factorial(n) `Returns the factorial of the given number n` getAngle(coords1, coords2, coords3) `Get the angle between three coordinates Parameters coords1: The first coordinate set (atom) coords2: The second (vertex) coordinate set (atom) coords3: The third coordinate set (atom) Returns angle: The angle between the atoms (float)` getDatFile(name) `Grab a data file. If the file cannot be found in the given directory, try the current system path. Parameters name: The name of the file to get (string) Returns path: The path to the file (string)` 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)` getFFfile(name) `Grab the forcefield file. May or may not residue in the dat/ directory.` getNamesFile(name) `Grab the *.names file that contains the XML mapping. Parameters name: The name of the forcefield (string) Returns path: The path to the file (string)` getPDBFile(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)` normalize(coords) `Normalize a set of coordinates Parameters coords: coordinates of form [x,y,z] Returns list: normalized coordinates (list)` 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` sortDictByValue(dict) `Sort a dictionary by its values Parameters dict: The dictionary to sort (dict) Returns items: The dictionary sorted by value (list)` 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)`

Data
`` |  | DIHEDRAL = 57.2958 SMALL = 9.9999999999999995e-08 __author__ = 'Todd Dolinsky' __date__ = '28 February 2006'

Author
`` |  | Todd Dolinsky