Representation of internal coordinate system, including methods to build it from cartesian coordinates, and to convert between coordinate systems.

class InternalCoordinateSet

Constructors

initialize(geometry, options = {})

Creates new instance of InternalCoordinateSet operating on specified Geometry. Possible options are:

:extra_redundant = distance - every pair of atoms within the distance is treated as a bond
:delocalized = true/false - use delocalized internal coordinates instead of redundant

Type conversion

to_vector_primitive

Vector of values of the primitive (redundant) internal coordinates

to_vector

Vector in the internal coordinates, either delocalized or redundant

Misc

prints the set of internal coordinates

fix_torsions_in_primitive_vector(v)

Value of torsions are adjusted to be in -pi...pi interval

fix_torsions_in_vector(v)

Fixes torsions in primitive coordinates. Nothing is done for delocalized coordinates.

no_of_nonredundant

Counts the degrees of freedom as number of nonzero eigenvalues of G matrix in the redundant coordinates

rotate_initial_geometry

Rotate the geometry so that translation/rotation degrees of freedom can be later eliminated easily.

Matrices

The matrices used are cached in instance variables. They depend only on current cartesian geometry, so the cache should be invalidated each time the geometry changes (by calling geometry_changed! method).

geometry_changed!

Invalidates matrices

b_matrix_primitive # => Matrix

Delocalized nonredundant coordinates

primitive_to_delocalized(q)

Transformations

do_step_cartesian_from_internal(sq)

k_matrix(gq) # => Matrix

grad_to_internal(gradient)

Converts cartesian gradient to projected gradient in internal coordinates

hessian_to_internal(hx)

hessian_from_primitive(hqp)

Search (private methods)

find_bonds(options = {:intermolecular => true, :h_bonds => false})

Identifies all covalent bonds and closest interfragment connections. Returns number of coordinates found.

find_inverse_intermolecular(options = {:hydrogens => true})

find_angles

Identifies all bond angles in the connectivity established by find_bonds. Returns number of coordinates found.

find_torsions

Identifies all torsions angles in the connectivity established by find_bonds. If none is found in sufficiently large molecule, looks for improper torsions. Returns number of coordinates found.

add_extra_redundant(distance)

add_extra_inverse(mindist, maxdist = 9.9e99)