schrodinger.application.matsci.geometry module

Utilities for geometry manipulation or property calculation

Copyright Schrodinger, LLC. All rights reserved.

Perform a BFS to find a deterministic backbone-respecting path.

Parameters:

  • sub_graph ('networkx.classes.graph.Graph') – The graph to find path in structure

  • start (int) – First atom index

  • end (int) – Index of last atom

  • backbone_indices (set) – Index of all marked backbone atoms

Return type:

list or None

Returns:

List of atom indices in the valid path or None

schrodinger.application.matsci.geometry.find_marked_backbone_path(struct, sub_graph)

Find the shortest path based on atoms marked as backbone.

Parameters:

  • struct (schrodinger.structure.Structure) – The structure to find backbone path in.

  • sub_graph ('networkx.classes.graph.Graph') – The graph to find path in structure

Return type:

list or None

Returns:

list of nodes in the path in the graph. The selected path must contain the marked backbone atoms.

schrodinger.application.matsci.geometry.get_backbone_atoms(struct, exclude_hydrogen=True, max_fix=True)

Return dictionary of backbone atoms for each molecule in the structure.

Parameters:

  • struct (Structure) – The structure to find backbone atoms in.

  • exclude_hydrogen (bool) – If true hydrogen will be excluded in creation of graph and searching for backbone atoms. This results in much faster calculation.

  • max_fix (bool) – Whether to fix internal degeneracy when maximum number of path checks are reached

Return dict:

A dictionary mapping molecule number to a list of backbone atom indices. If there are less than two atoms in the molecule the associated value will be an empty list.

schrodinger.application.matsci.geometry.get_ordered_polymer_backbone(struct, backbone_path, remove_side_chain)

Backbone of a polymer chain should follow H–TH–TH–T format, where backbone starts with head and ends with tail.

Parameters:

  • struct (Structure) – The structure to find backbone atoms in.

  • backbone_path (list) – list of atom indexes in the backbone

  • remove_side_chain (bool) – If true it will remove the side chain atoms from the backbone in the start and end.

Return list:

list of atom indexes in the backbone such that first atom is always a head.

schrodinger.application.matsci.geometry.get_ordered_backbone_atoms(struct)

Return dictionary of backbone atoms for each molecule in the structure.

Parameters:

struct (Structure) – The structure to find backbone atoms in.

Return dict(list):

the key of the dictionary is molecule number and the value is the list of backbone atoms

schrodinger.application.matsci.geometry.radius_of_gyration(struct, molecule_coms=False)

Calculate radius of gyration for a structure

Parameters:

  • struct (Structure) – The structure to calculate RG for

  • molecule_coms (bool) – Whether to use center of mass of each molecule in the structure for calculating Rg

Return type:

float

Returns:

The radius of gyration

schrodinger.application.matsci.geometry.fit_structure_to_ellipsoid(struct)

Fit the structure to an ellipsoid and return the ellipsoid semi-axes and principal moments of inertia

The method is taken from https://pubs.acs.org/doi/abs/10.1021/jp047138e and uses the following equations to calculate the semi-axes values: I1 = M/5 * (a**2 + b**2) I2 = M/5 * (a**2 + c**2) I3 = M/5 * (b**2 + c**2) Also see https://en.wikipedia.org/wiki/Ellipsoid#Dynamical_properties

Parameters:

struct (Structure) – The structure to fit to an ellipsoid

Return type:

tuple of (float, float, float, [float, float, float])

Returns:

Tuple of semi-axes values in Angstroms and principal moments of inertia in u * A**2

schrodinger.application.matsci.geometry.fit_points_to_circle(x_vals, y_vals, center_x=None)

Fit 2D points to a circle

Parameters:

  • x_vals (numpy.array) – Array containing point x values

  • y_vals (numpy.array) – Array containing point y values

  • center_x (float) – If provided, this will be the x value of the circle center

Return type:

tuple(float, float, float)

Returns:

Center x value, center y value, and radius

schrodinger.application.matsci.geometry.get_center(st, atom_ids=None)

Get the structure’s center of mass, limited to the given atom_ids. Return None if atom_ids is empty or None

Parameters:

  • st (Structure) – Structure

  • atom_ids (list(int)) – Atom ids for which center of mass has to be calculated

Returns:

centroid given as 3-element array [x, y, z]

Return type:

numpy.array(float) or None