|
Calling Sequence
|
|
BondAngles(molecule, option)
BondAngles(molecule, i, j, k)
BondAngles(molecule, i, j, k, l)
BondAngles(molecule, [i,j,k])
BondAngles(molecule, [i,j,k,l])
BondAngles(molecule[i], molecule[j], molecule[k])
BondAngles(molecule[i], molecule[j], molecule[k], molecule[l])
|
|
Parameters
|
|
molecule
|
-
|
list of lists; each list has 4 elements, the string of an atom's symbol and atom's x, y, and z coordinates
|
i
|
-
|
integer; index denoting the i-th list of an atom and its coordinates in molecule
|
i,j,k
|
-
|
sequence of integers; the indices of the three atoms in the bond angle
|
i,j,k,l
|
-
|
sequence of integers; the indices of the four atoms in the dihedral bond angle
|
[i,j,k]
|
-
|
list of integers; the indices of the three atoms in the bond angle
|
[i,j,k,l]
|
-
|
list of integers; the indices of the four atoms in the dihedral bond angle
|
molecule[i]
|
-
|
list; list has 4 elements, the string of an atom's symbol and atom's x, y, and z coordinates
|
option
|
-
|
(optional) dihedral=true or false (default)
|
|
|
|
|
Description
|
|
•
|
The BondAngles(molecule, option) calling sequence returns all of the 3-atom bond angles in the molecule as a table.
|
•
|
The BondAngles(molecule, i, j, k) calling sequence returns the bond angle formed by the i, j, and k atoms in the molecule.
|
•
|
The BondAngles(molecule, i, j, k, l) calling sequence returns the dihedral bond angle formed by the i, j, k, and l atoms.
|
•
|
The BondAngles(molecule, [i,j,k]) calling sequence returns the bond angle formed by the i, j, and k atoms in the molecule.
|
•
|
The BondAngles(molecule, [i,j,k,l]) calling sequence returns the dihedral bond angle formed by the i, j, k, and l atoms.
|
•
|
The BondAngles(molecule[i], molecule[j], molecule[k]) calling sequence returns the bond angle.
|
•
|
The BondAngles(molecule[i], molecule[j], molecule[k], molecule[l[) calling sequence returns the dihedral bond angle.
|
•
|
If the optional keyword dihedral in BondAngles(molecule, option) is set to true, then all dihedral angles are also returned.
|
•
|
The bond angles are returned as floats in units of degrees.
|
|
|
Examples
|
|
>
|
|
Consider the molecule hydrogen peroxide
>
|
|
| (1) |
Compute all 3-atom bond angles
>
|
|
| (2) |
Compute all bond angles including the dihedral angle
>
|
|
| (3) |
Compute the bond angle formed by atoms 1, 2, and 3
>
|
|
or
>
|
|
Compute the dihedral angle formed by atoms 1, 2, 3, and 4
>
|
|
or
>
|
|
|
|
|
|