Source code for schrodinger.application.desmond.packages.msys.posre

def apply(mol, atoms, fcx, fcy, fcz, replace=False):
    ''' add position restraints to atoms '''

    table = mol.addTableFromSchema('posre_harm')
    index = {}
    if replace:
        for t in table.terms:
            t.remove()
    else:
        for t in table.terms:
            index[t.atoms[0]] = t

    param = table.params.addParam()
    param['fcx'] = fcx
    param['fcy'] = fcy
    param['fcz'] = fcz

    for a in atoms:
        t = index.get(a)
        if t is None:
            t = table.addTerm([a])
        t.param = param
        t['x0'] = a.x
        t['y0'] = a.y
        t['z0'] = a.z

    return table.nterms