system = System()
system.add(qmff)
system.add(intraff)
system.add(intraclj)
system.add(solute)
print(system.energy())
chg_constraint = QMChargeConstraint(solute)
chg_constraint.setChargeCalculator( AM1BCC() )
system.add(chg_constraint)
print(system.constraintsSatisfied())
print(system.energy())
print(system.constraintsSatisfied())
mol = system[ MGIdx(0) ][ mol.number() ].molecule()
print(mol.property("charge").array())
water = PDB().read("test/io/water.pdb")
tip4p = water[ MolIdx(0) ].molecule()
tip4p = protoms.parameterise(tip4p, ProtoMS.SOLVENT)
chgs = tip4p.property("charge")
mol = mol.edit().rename("SB2").commit()
mol = protoms.parameterise(mol, ProtoMS.SOLUTE)
perturbations = mol.property("perturbations")
print(perturbations)
print(perturbations.requiredSymbols())
print(perturbations.requiredProperties())
lam = perturbations.symbols().Lambda()
system = System()
solute = MoleculeGroup("solute", mol)
system.add(solute)
system.setConstant(lam, 0.0)
system.add( PerturbationConstraint(solute) )
print(system.constraintsSatisfied())
for i in range(0,101,10):
system.setConstant(lam, 0.01 * i)
PDB().write(system.molecules(), "test_%003d.pdb" % i)
