def test_module():
import random
import AtomMath
import FileIO
import Structure
R = AtomMath.rmatrixu(numpy.array((0.0, 0.0, 1.0), float), math.pi / 2.0)
struct1 = FileIO.LoadStructure(fil="/home/jpaint/8rxn/8rxn.pdb")
struct2 = FileIO.LoadStructure(fil="/home/jpaint/8rxn/8rxn.pdb")
chn1 = struct1.get_chain("A")
chn2 = struct2.get_chain("A")
rc = lambda: 0.1 * (random.random() - 1.0)
for atm in chn2.iter_atoms():
atm.position = numpy.matrixmultiply(R, atm.position) + numpy.array(
(rc(), rc(), rc()), float)
alist = []
for atm1 in chn1.iter_atoms():
if atm1.name != "CA":
continue
atm2 = chn2.get_equivalent_atom(atm1)
if atm2 == None: continue
alist.append((atm1, atm2))
sup = SuperimposeAtoms(alist)
R = sup.R
Q = sup.Q
print Q
print R
so = sup.src_origin
do = sup.dst_origin
sup1 = Structure.Structure(structure_id="JMP1")
for atm in chn1.iter_atoms():
atm.position = numpy.matrixmultiply(R, atm.position - so)
sup1.add_atom(atm)
FileIO.SaveStructure(fil="super1.pdb", struct=sup1)
sup2 = Structure.Structure(structure_id="JMP2")
for atm in chn2.iter_atoms():
atm.position = atm.position - do
sup2.add_atom(atm)
FileIO.SaveStructure(fil="super2.pdb", struct=sup2)
def test_module():
import random
import AtomMath
import FileIO
import Structure
R = AtomMath.rmatrixu(numpy.array((0.0, 0.0, 1.0), float), math.pi/2.0)
struct1 = FileIO.LoadStructure(fil="/home/jpaint/8rxn/8rxn.pdb")
struct2 = FileIO.LoadStructure(fil="/home/jpaint/8rxn/8rxn.pdb")
chn1 = struct1.get_chain("A")
chn2 = struct2.get_chain("A")
rc = lambda: 0.1 * (random.random() - 1.0)
for atm in chn2.iter_atoms():
atm.position = numpy.matrixmultiply(R, atm.position) + numpy.array((rc(),rc(),rc()),float)
alist = []
for atm1 in chn1.iter_atoms():
if atm1.name != "CA":
continue
atm2 = chn2.get_equivalent_atom(atm1)
if atm2 == None: continue
alist.append((atm1, atm2))
sup = SuperimposeAtoms(alist)
R = sup.R
Q = sup.Q
print Q
print R
so = sup.src_origin
do = sup.dst_origin
sup1 = Structure.Structure(structure_id = "JMP1")
for atm in chn1.iter_atoms():
atm.position = numpy.matrixmultiply(R, atm.position - so)
sup1.add_atom(atm)
FileIO.SaveStructure(fil="super1.pdb", struct=sup1)
sup2 = Structure.Structure(structure_id = "JMP2")
for atm in chn2.iter_atoms():
atm.position = atm.position - do
sup2.add_atom(atm)
FileIO.SaveStructure(fil="super2.pdb", struct=sup2)
def glr_rotate_axis(self, deg, axis):
"""
"""
R = AtomMath.rmatrixu(axis, deg * Constants.DEG2RAD)
self.glr_mult_matrix_R(R)
def glr_rotate_axis(self, deg, axis):
"""
"""
R = AtomMath.rmatrixu(axis, deg * Constants.DEG2RAD)
self.glr_mult_matrix_R(R)
