Examples with OpenMM_System_addConstraint simtk.openmm.OpenMMLibrary.OpenMM_System_addConstraint used on opensource projects

Example 1 with OpenMM_System_addConstraint

use of simtk.openmm.OpenMMLibrary.OpenMM_System_addConstraint in project ffx by mjschnie.

the class ForceFieldEnergyOpenMM method setUpHydrogenConstraints.

public void setUpHydrogenConstraints(PointerByReference system) {
    int i;
    int iAtom1;
    int iAtom2;
    // Atom[] atoms = molecularAssembly.getAtomArray();
    Bond[] bonds = super.getBonds();
    logger.info(String.format(" Setting up Hydrogen constraints"));
    if (bonds == null || bonds.length < 1) {
        return;
    }
    int nBonds = bonds.length;
    Atom atom1;
    Atom atom2;
    Atom parentAtom;
    Bond bondForBondLength;
    BondType bondType;
    for (i = 0; i < nBonds; i++) {
        Bond bond = bonds[i];
        atom1 = bond.getAtom(0);
        atom2 = bond.getAtom(1);
        if (atom1.isHydrogen()) {
            parentAtom = atom1.getBonds().get(0).get1_2(atom1);
            bondForBondLength = atom1.getBonds().get(0);
            bondType = bondForBondLength.bondType;
            iAtom1 = atom1.getXyzIndex() - 1;
            iAtom2 = parentAtom.getXyzIndex() - 1;
            OpenMM_System_addConstraint(system, iAtom1, iAtom2, bondForBondLength.bondType.distance * OpenMM_NmPerAngstrom);
        } else if (atom2.isHydrogen()) {
            parentAtom = atom2.getBonds().get(0).get1_2(atom2);
            bondForBondLength = atom2.getBonds().get(0);
            bondType = bondForBondLength.bondType;
            iAtom1 = atom2.getXyzIndex() - 1;
            iAtom2 = parentAtom.getXyzIndex() - 1;
            OpenMM_System_addConstraint(system, iAtom1, iAtom2, bondForBondLength.bondType.distance * OpenMM_NmPerAngstrom);
        }
    }
}