utilities

Utilities for the PDB2PQR software suite.

Code author: Todd Dolinsky

Code author: Yong Huang

Code author: Nathan Baker

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

pdb2pqr.utilities.analyze_connectivity(map_, key)[source]

Analyze the connectivity of a given map using the key value.

Parameters

  • map (dict) – map to analyze

  • key (str) – key value

Returns

list of connected values to the key

Return type

list

pdb2pqr.utilities.angle(coords1, coords2, coords3)[source]

Get the angle between three coordinates.

Parameters
Returns

angle between the atoms (in degrees)

Return type

float

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

pdb2pqr.utilities.dihedral(coords1, coords2, coords3, coords4)[source]

Calculate the dihedral angle from four atoms’ coordinates.

Parameters

  • coords1 ([float, float, float]) – one of four coordinates of form [x,y,z]

  • coords2 ([float, float, float]) – one of four coordinates of form [x,y,z]

  • coords3 ([float, float, float]) – one of four coordinates of form [x,y,z]

  • coords4 ([float, float, float]) – one of four coordinates of form [x,y,z]

Returns

the angle (in degrees)

Return type

float

pdb2pqr.utilities.distance(coords1, coords2)[source]

Calculate the distance between two coordinates.

Parameters
Returns

distance between the two coordinates

Return type

float

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

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

pdb2pqr.utilities.noninteger_charge(charge, error_tol=0.001) → str[source]

Test whether a charge is an integer.

Parameters

  • charge (float) – value to test

  • error_tol (float) – absolute error tolerance

Returns

string with descripton of problem or empty string if no problem

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

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 connected

Return type

list

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

pdb2pqr.utilities.subtract(coords1, coords2)[source]

Suntract one 3-dimensional point from another.

Parameters
Returns

list of coordinates equal to coords2 - coords1

Return type

numpy.ndarray