implicit_solvent_ddm.restraint_helper

Helper functions used to construct conformational and orientational restraints.

Functions

compute_dihedral_angle(atom1, atom2, atom3, ...)	Function is one of two options to calculate dihedral angles
create_atom_neighbor_array(atom_coordinates)	Efficiently find all atom pairs within a given cutoff using cKDTree.
distance_calculator(point_a, point_b)	Function calcualtes the distance between two points
distance_filter(distance)	Returns a boolean whether the atoms pairs are within 6 angstroms
find_angle(point_a, point_b, point_c)	Function calculates the angle created by two lines connectin 3 points, where point_b is the vertex.
norm_distance(point_a, point_b, point_c)	Compute normal distance between 3 atom positions
refactor_find_heavy_bonds(parmed_traj_bonds)	Find heavy atoms that are covalently bonded to another heavy atom (i.e. NOT hydrogens) Iterate through list of parmed Atom descriptions and return a list of boolean expression whether the atom has more than one heavy atom bounded to it. parmed_traj_bonds: list[parmed.topologyobjects.Atom] AtomList instances.
screen_for_distance_restraints(num_atoms, ...)	This function combs a molecule object (num_atoms) to find the atom closest to the coordinates at (com).
shortest_distance_between_molecules(...)	Finds the shortest distance between host and guest atoms.