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#
# Anna Dehof 2010-03-22
# get a system and add hydrogens
#
import sys
from BALL import *
#### for use in BALLView
system = getSystems()[0]
# print the number of atoms read from the file
print "read ", system.countAtoms(), " atoms."
# now we open a fragment database
print "reading fragment DB..."
fragment_db = FragmentDB("")
# and normalize the atom names, i.e. we convert different
# naming standards to the PDB naming scheme - just in case!
print "normalizing names..."
system.apply(fragment_db.normalize_names)
# now we add any missing hydrogens to the residues
# the data on the hydrogen positions stems from the
# fragment database. However the hydrogen positions
# created in this way are only good estimates
print "creating missing atoms..."
system.apply(fragment_db.add_hydrogens)
print "added ", fragment_db.add_hydrogens.getNumberOfInsertedAtoms(), " atoms"
# now we create the bonds between the atoms (PDB files hardly
# ever contain a complete set of CONECT records)
print "building bonds..."
system.apply(fragment_db.build_bonds)
# now we check whether the model we built is consistent
# The ResidueChecker checks for charges, bond lengths,
# and missing atoms
print "checking the built model..."
checker = ResidueChecker(fragment_db)
system.apply(checker)
# now we create an AMBER force field
print "setting up force field..."
FF= AmberFF()
# we then select all hydrogens (element(H))
# using a specialized processor (Selector)
system.deselect()
FF.setup(system)
selector = Selector("element(H)")
system.apply(selector)
#just for curiosity: check how many atoms we are going
# to optimize
print "optimizing ", FF.getNumberOfMovableAtoms(), " out of ", system.countAtoms(), " atoms"
# now we create a minimizer object that uses a conjugate
# gradient algorithm to optimize the atom positions
minimizer = ConjugateGradientMinimizer()
initial_energy = FF.updateEnergy()
print "initial energy: ", initial_energy , " kJ/mol"
# initialize the minimizer and perform (up to)
# 50 optimization steps
minimizer.setup(FF)
minimizer.setEnergyOutputFrequency(1)
minimizer.minimize(50)
# calculate the terminal energy and print it
terminal_energy = FF.getEnergy()
print "energy before/after minimization: ", initial_energy , "/", terminal_energy, " kJ/mol"
# done
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