cg_openmm.utilities.random_builder

Functions

assign_position(positions, bond_length, ...)	Assign random position for a bead
assign_position_lattice_style(cgmodel, ...)	Assign random position for a particle
attempt_lattice_move(parent_coordinates, ...)	Given a set of cartesian coordinates this function positions a new particle a distance of 'bond_length' away in a random direction.
attempt_move(parent_coordinates, bond_length)	Given a set of cartesian coordinates, assign a new particle
collisions(distance_list, distance_cutoff)	Determine if there are any collisions between non-bonded particles, where a "collision" is defined as a distance shorter than 'distance_cutoff'.
distance(positions_1, positions_2)	Calculate the distance between two particles.
distance_matrix(positions)	Construct a matrix of the distances between an input array of particles.
distances(interaction_list, positions)	Calculate the distances between all non-bonded particles in a model, given a list of particle interactions and particle positions.
first_bead(positions)	Determine if the provided 'positions' contain any particles (are the coordinates non-zero).
get_move(trial_coordinates, move_direction, ...)	Used to build random structures.
get_random_positions(cgmodel[, ...])	Assign random positions for all beads in a coarse-grained polymer.
get_structure_from_library(cgmodel[, ...])	Given a coarse grained model class object, this function retrieves a set of positions for the model from the 'foldamers' ensemble library, in: 'foldamers/ensembles/${backbone_length}_${sidechain_length}_${sidechain_positions}' If this coarse grained model does not have an ensemble library, an error message will be returned and positions at random with 'random_positions()'.