mchammer

MCHammer package.

Classes

Atom	Atom.
Bond	Bond between two atoms.
Collapser	Moves rigid-subunits toward center of mass of molecule.
MCStepResult	Results of a step.
Molecule	Molecule to optimize.
Optimizer	Optimize target bonds using MC algorithm.
Result	Result of optimization.
StepResult	Results of a step.

Functions

get_atom_distance	Return the distance between two atoms.
get_bond_vector	Get vector from atom1 to atom2 in bond.
get_radius	Get the radius of an element.
rotate_molecule_by_angle	Rotate a molecule by an angle about an axis and origin.
rotation_matrix_arbitrary_axis	Returns a rotation matrix of angle radians about axis.
test_move	Test an MC move based on boltzmann energy.
translate_atoms_along_vector	Translate atoms with given ids along a vector.
translate_molecule_along_vector	Translate a whole molecule along a vector.