def test_module():
import Structure
a1 = Structure.Atom(x=0.0, y=-1.0, z=0.0)
a2 = Structure.Atom(x=0.0, y=0.0, z=0.0)
a3 = Structure.Atom(x=1.0, y=0.0, z=0.0)
a4 = Structure.Atom(x=1.0, y=1.0, z=-1.0)
print "a1:", a1.position
print "calc_angle:", calc_angle(a1, a2, a3)
print "calc_torsion_angle:", calc_torsion_angle(a1, a2, a3, a4)
def load_atom(self, atm_map):
"""Called repeatedly by the implementation of read_atoms to
load all the data for a single atom. The data is contained
in the atm_map argument, and is not well documented at this
point. Look at this function and you'll figure it out.
"""
## create atom object
atm = Structure.Atom(**atm_map)
## survey the atom and structure and determine if the atom requres
## being passed to the naming service
## absence of requred fields
if not atm.fragment_id or not atm.chain_id:
self.name_service_list.append(atm)
return atm
try:
self.struct.add_atom(atm, True)
except Structure.FragmentOverwrite:
ConsoleOutput.warning("FragmentOverwrite: %s" % (atm))
self.name_service_list.append(atm)
except Structure.AtomOverwrite, err:
ConsoleOutput.warning("AtomOverwrite: %s" % (err))
self.name_service_list.append(atm)
def test_module():
import Structure
a1 = Structure.Atom(x=0.0, y=-1.0, z=0.0)
a2 = Structure.Atom(x=0.0, y=0.0, z=0.0)
a3 = Structure.Atom(x=1.0, y=0.0, z=0.0)
#a4 = Structure.Atom(x=1.0, y=1.0, z=-1.0)
a4 = Structure.Atom(res_name='GLY', x=1.0, y=1.0, z=-1.0)
## Example taken from 1HMP.pdb
#ATOM 25 N VAL A 8 55.799 56.415 16.693 1.00 25.51 N
#ATOM 26 CA VAL A 8 55.049 57.431 15.929 1.00 20.42 C
#ATOM 27 C VAL A 8 55.655 57.849 14.605 1.00 21.66 C
#ATOM 28 O VAL A 8 56.846 58.112 14.504 1.00 31.38 O
#ATOM 29 CB VAL A 8 54.697 58.659 16.709 1.00 16.90 C
#ATOM 30 CG1 VAL A 8 54.131 59.664 15.699 1.00 19.06 C
#ATOM 31 CG2 VAL A 8 53.640 58.304 17.738 1.00 14.10 C
#ATOM 32 N ILE A 9 54.810 57.974 13.593 1.00 20.18 N
#ATOM 33 CA ILE A 9 55.221 58.358 12.242 1.00 16.49 C
#ATOM 34 C ILE A 9 54.461 59.575 11.722 1.00 28.07 C
#ATOM 35 O ILE A 9 53.439 59.455 11.009 1.00 31.82 O
#ATOM 36 CB ILE A 9 55.028 57.196 11.301 1.00 13.73 C
#ATOM 37 CG1 ILE A 9 55.941 56.045 11.712 1.00 20.33 C
#ATOM 38 CG2 ILE A 9 55.327 57.611 9.860 1.00 13.91 C
#ATOM 39 CD1 ILE A 9 55.871 54.892 10.733 1.00 21.80 C
#ATOM 40 N SER A 10 54.985 60.748 12.087 1.00 30.09 N
#
# PHI: C'-N-CA-C'
a1 = Structure.Atom(x=55.655, y=57.849, z=14.605, res_name='VAL')
a2 = Structure.Atom(x=54.810, y=57.974, z=13.593, res_name='ILE')
a3 = Structure.Atom(x=55.221, y=58.358, z=12.242, res_name='ILE')
a4 = Structure.Atom(x=54.461, y=59.575, z=11.722, res_name='ILE')
print "PHI: %.3f" % calc_torsion_angle(a1, a2, a3, a4)
# PSI: N-CA-C'-N
a1 = Structure.Atom(x=54.810, y=57.974, z=13.593, res_name='ILE')
a2 = Structure.Atom(x=55.221, y=58.358, z=12.242, res_name='ILE')
a3 = Structure.Atom(x=54.461, y=59.575, z=11.722, res_name='ILE')
a4 = Structure.Atom(x=54.985, y=60.748, z=12.087, res_name='SER')
print "PSI: %.3f" % calc_torsion_angle(a1, a2, a3, a4)
print "=" * 40
print "a1:", a1.position
print "calc_angle:", calc_angle(a1, a2, a3)
print "calc_torsion_angle:", calc_torsion_angle(a1, a2, a3, a4)
