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# Obtain the force field parameters for a given universe.
#
from MMTK import *
from MMTK.Proteins import Protein
from MMTK.ForceFields import Amber99ForceField
# Define system
universe = InfiniteUniverse(Amber99ForceField())
universe.protein = Protein('bala1')
# Get energy term parameters
parameters = universe.energyEvaluatorParameters()
documentation = {
"nonbonded":
"""
excluded_pairs and one_four_pairs: lists of pairs of atom indices
atom_subset: list of atom indices, or None for 'all atoms'
""",
"lennard_jones":
"""
type: array of atom type numbers
epsilon_sigma: 3D array. The first two indices are the atom type
numbers of the two atoms, the third index is 0
for epsilon and 1 for sigma
type_names: the atom type names from the force field (for documentation)
""",
"electrostatic":
"""
charge: array of partial charges
""",
"harmonic_distance_term":
"""
a list of tuples (atom_index1, atom_index2, length, force_constant)
""",
"harmonic_angle_term":
"""
a list of tuples (atom_index1, atom_index2, atom_index3, angle, force_constant)
""",
"cosine_dihedral_term":
"""
a list of tuples (atom_index1, atom_index2, atom_index3, atom_index4,
multiplicity, angle, force_constant)
""",
}
# Print the parameters in a readable format
for p_type in parameters:
p = parameters[p_type]
print p_type
print len(p_type)*'-'
print documentation[p_type]
if isinstance(p, list):
print "["
for data in p:
print " ", data, ","
print " ]"
elif isinstance(p, dict):
print "{"
for key, value in p.items():
s = repr(value)
if len(key) + len(s) < 75:
print " %s: %s," % (key, value)
else:
print " %s:" % key
print " %s," % value
print "}"
else:
print p
print
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