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- 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)
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