Class ZMatrix

Create a ZMatrix instance

Parameters:

• struct (schrodinger.structure.Structure) - The structure this zmatrix is for

Overrides: object.__init__

Bump all atom indexes for this z-matrix

Parameters:

• bump (int) - The amount to modify each index

Free all the internal coordinates for a single atom

Parameters:

• index (int) - The atom index (1-based) of the atom to free

Free all the bond internal coordinate for a single atom

Parameters:

• index (int) - The atom index (1-based) of the atom to free

Free all the angle internal coordinate for a single atom

Parameters:

• index (int) - The atom index (1-based) of the atom to free

Free all the angle internal coordinate for a single atom

Parameters:

• index (int) - The atom index (1-based) of the atom to free

Find an angle between atom_a, atom_b and some other atom that is smaller than linear

Parameters:

• struct (schrodinger.structure.Structure) - The struct to use
• atom_a (int) - The 1-indexed index of atom A for the A-B-C angle
• atom_b (int) - The 1-indexed index of atom B for the A-B-C angle
• do_not_use (set) - An set of atom indexes that should not be used for the C atom for the A-B-C angle
• index_less_than (int) - Only look for indexes less than this number
• linear (float) - The threshold where any angle greater than this is considered linear

Returns: int, float or None, None

The index of an atom that forms an angle with atom_a and atom_b that is less than linear degrees, and the angle it forms. None, None is returned if none of the indexes in choose_from gave a non-linear angle.

Combine the atom lists from this (parent) z-matrix and another (child) z-matrix. This involves not just combining the lists, but also defining the following new internal coordinates:

child_atom_1: bond, angle, dihedral child_atom_2: angle, dihedral child_atom_3: dihedral

All new internal coordinates will reference an atom from the parent structure. These six new internal coordinates fully specify the parent-child orientation.

Parameters:

• child_zmat (ZMatrix) - The child z-matrix to merge with this one
• struct (schrodinger.structure.Structure) - The structure that results from merging these two z-matrices. This is needed to compute the new bonds, angles and dihedrals.
• glue_index (int) - The index of the atom in the parent structure that should be bonded to the first atom of the child structure. This index should be 1-based (i.e. structure.atom indexed, not list indexed)