Constraints

Constraints are locks that can prevent the molecule from violating certain conditions. These locks are useful in certain situations such as in energy minimization and simulaiton. The locks can be based on molecule confomration such as fixing two atoms at certain distance from each other or allowing a range of angle that a dihydral angle is permitted to be in.

import org.jme.constraint.*;
...
ConformationalConstraintFactory.constrainDistance(atom1, atom2, 1.4, 1.6);//locks the bond distance between 1.4 to 1.6 Å

Constraints can be combined with boolean operators such as not, and, or which are provided as methods in the Constraints interface.

Constraint constraint = bondConstraint.and(angleConstraint);