utilities
¶
Utilities for the PDB2PQR software suite.
Code author: Todd Dolinsky
Code author: Yong Huang
Code author: Nathan Baker
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pdb2pqr.utilities.
add
(coords1, coords2)[source]¶ Add one 3-dimensional point to another.
Parameters: Returns: list of coordinates equal to coords2 + coords1
Return type: numpy.ndarray
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pdb2pqr.utilities.
analyze_connectivity
(map_, key)[source]¶ Analyze the connectivity of a given map using the key value.
Parameters: Returns: list of connected values to the key
Return type:
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pdb2pqr.utilities.
angle
(coords1, coords2, coords3)[source]¶ Get the angle between three coordinates.
Parameters: Returns: angle between the atoms (in degrees)
Return type:
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pdb2pqr.utilities.
cross
(coords1, coords2)[source]¶ Find the cross-product of one 3-dimensional point with another.
Parameters: Returns: list of coordinates equal to coords2 cross coords1
Return type: numpy.ndarray
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pdb2pqr.utilities.
dihedral
(coords1, coords2, coords3, coords4)[source]¶ Calculate the dihedral angle from four atoms’ coordinates.
Parameters: Returns: the angle (in degrees)
Return type:
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pdb2pqr.utilities.
distance
(coords1, coords2)[source]¶ Calculate the distance between two coordinates.
Parameters: Returns: distance between the two coordinates
Return type:
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pdb2pqr.utilities.
dot
(coords1, coords2)[source]¶ Find the dot-product of one 3-dimensional point with another.
Parameters: Returns: list of coordinates equal to the inner product of coords2 with coords1
Return type: numpy.ndarray
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pdb2pqr.utilities.
factorial
(num)[source]¶ Returns the factorial of the given number.
Parameters: num (int) – number for which to compute factorial Returns: factorial of number Return type: int
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pdb2pqr.utilities.
normalize
(coords)[source]¶ Normalize a set of coordinates to unit vector.
Parameters: coords ([float, float, float]) – coordinates of form [x,y,z] Returns: normalized coordinates Return type: numpy.ndarray
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pdb2pqr.utilities.
shortest_path
(graph, start, end, path=[])[source]¶ Find the shortest path between two nodes.
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 (dict) – a mapping of the graph to analyze, of the form {0: [1,2], 1:[3,4], …} . Each key has a list of edges.
- start (str) – the ID of the key to start the analysis from
- end (str) – the ID of the key to end the analysis
- path (list) – optional argument used during the recursive step to keep the current path up to that point
Returns: list of the shortest path or
None
if start and end are not connectedReturn type:
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pdb2pqr.utilities.
sort_dict_by_value
(inputdict)[source]¶ Sort a dictionary by its values.
Parameters: inputdict (dict) – the dictionary to sort Returns: list of keys sorted by value Return type: list