Class ZAtom

Create a ZAtom object

Parameters:

• jagin (schrodinger.application.jaguar.input.JaguarInput) - The JaguarInput object the Z-matrix is for
• index (int) - The atom index (1-based) that this ZAtom is for

Overrides: object.__init__

Constrain the given coord so it can't be optimized

Parameters:

• coord (int) - 0 (bond), 1 (angle) or 2 (dihedral)

Allow the given coord to be optimized

Parameters:

• coord (int) - 0 (bond), 1 (angle) or 2 (dihedral)

Modify all the indexes (both for self and any referenced atoms) by a constant number. Used when this z-matrix is being added to another, and now atom 1 is actually atom 20...

Parameters:

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

Get the line that defines the atoms for the bond, angle and dihedral and also the coordinate names. i.e. C11 H1 r11 C2 a11 C7 d11

Returns: str

The string defining the z-matrix coordinates for this atom. Includes the trailing return character

        Get a series of lines that defines each coordinate.
        i.e.:
        r11 = 1.452
a11 = 102.4
d11 = 180.


        @rtype: str
        @return: The string defining the z-matrix coordinate values for this
        atom.  Includes the trailing return character at the end of the block.
        

Get the name of an atom with the given element and index

Parameters:

• element (str) - The atomic symbol of the atom
• index (int) - The index of the atom

Returns: str

The name of the atom, such as "C12"

Get the name of a coordinate for this atom, such as r11 or d7

Parameters:

• coord (int) - 0 (bond), 1 (angle) or 2 (dihedral)

Returns: str

The name of the coordinate, such as "r12"

Add an internal coordinate for this atom referenced to a target atom. Note that coordinates must be added in the order bond, angle, dihedral.

Parameters:

• index (int) - The atom index of the target atom (such as the atom the bond extends to)
• element (str) - The element of the target atom
• value (float) - The value of this coordinate

Change the definition of an existing internal coordinate. If index and element are passed in the target atom for the coordinate will be changed.

Parameters:

• coord (int) - 0 (bond), 1 (angle) or 2 (dihedral)
• value (float) - The value of this coordinate
• index (int) - The atom index of the target atom (such as the atom the bond extends to), 1-based. Both index and element must be supplied for them to be used.
• element (str) - The element of the target atom. Both index and element must be supplied for them to be used.