def read_pdb(pdbin="undefined"):
log_string = "\n >> clipper_tools: io.molecules.read_pdb"
log_string += "\n pdbin: %s" % pdbin
xml_root = etree.Element('input_file')
xml_root.attrib['name'] = pdbin
xml_root.attrib['type'] = 'PDB'
if pdbin is not "undefined":
f = clipper.MMDBfile()
f.read_file(pdbin)
mmol = clipper.MiniMol()
f.import_minimol(mmol)
log_string += "\n << read_pdb has finished\n"
xml_root.attrib['ok'] = 'yes'
return log_string, xml_root, mmol
else:
log_string += "\n ERROR: No input PDB was supplied"
log_string += "\n << read_pdb has finished \n"
xml_root.attrib['ok'] = 'no'
return log_string, xml_root, None
def test_orth_frac(self, verbose=False):
'''
Test mateix methods of clipper-python bindings
'''
pdb_in_path = os.path.join(self.test_data_path, '1uoy.pdb')
assert os.path.exists(pdb_in_path)
# Set minimol
f = clipper.MMDBfile()
f.read_file(pdb_in_path)
mmol = clipper.MiniMol()
f.import_minimol(mmol)
atoms = mmol.atom_list()
cell = mmol.cell()
frac_matrix = cell.matrix_frac()
orth_matrix = cell.matrix_orth()
self.assertAlmostEqual(orth_matrix[0][0], 43.615, places=3)
self.assertAlmostEqual(orth_matrix[1][1], 58.436, places=3)
self.assertAlmostEqual(orth_matrix[2][2], 53.415, places=3)
self.assertAlmostEqual(frac_matrix[0][0], 0.02293, places=3)
self.assertAlmostEqual(frac_matrix[1][1], 0.01711, places=3)
self.assertAlmostEqual(frac_matrix[2][2], 0.01872, places=3)
for at in atoms:
c = at.coord_orth()
cnew = orth_matrix * (frac_matrix * c)
cdiff = cnew - c
xdiff,ydiff,zdiff = cdiff.x(), cdiff.y(), cdiff.z()
self.assertAlmostEqual(xdiff, 0.0, places=4)
self.assertAlmostEqual(ydiff, 0.0, places=4)
self.assertAlmostEqual(zdiff, 0.0, places=4)
new_cell = clipper.Cell(clipper.Cell_descr(cell.a()+.2,cell.b(),cell.c(),cell.alpha(),cell.beta(),cell.gamma()))
orth_matrix = new_cell.matrix_orth()
self.assertAlmostEqual(orth_matrix[0][0], 43.815, places=3)
self.assertAlmostEqual(orth_matrix[1][1], 58.436, places=3)
self.assertAlmostEqual(orth_matrix[2][2], 53.415, places=3)
for at in atoms:
c = at.coord_orth()
cnew = orth_matrix * (frac_matrix * c)
cdiff = cnew - c
xdiff,ydiff,zdiff = cdiff.x(), cdiff.y(), cdiff.z()
self.assertTrue(abs(xdiff)<0.2)
self.assertAlmostEqual(ydiff, 0.0, places=4)
self.assertAlmostEqual(zdiff, 0.0, places=4)
def write_pdb(pdbout="xyzout.pdb", molout=None):
log_string = "\n >> clipper_tools: io.molecules.write_pdb"
log_string += "\n pdbout: %s" % pdbout
xml_root = etree.Element('output_file')
xml_root.attrib['name'] = pdbout
xml_root.attrib['type'] = 'PDB'
if molout is None:
xml_root.attrib['ok'] = 'no'
log_string += "\n ERROR: No input MiniMol was supplied"
log_string += "\n << write_pdb has finished \n"
return log_string, xml_root
else:
mmdb = clipper.MMDBfile()
mmdb.export_minimol(molout)
mmdb.write_file(pdbout, 0)
log_string += "\n << write_pdb has finished \n"
xml_root.attrib['ok'] = 'yes'
return log_string, xml_root
import clipper
f = clipper.MMDBfile()
f.read_file("test.pdb")
mmol = clipper.MiniMol()
print mmol
f.import_minimol(mmol)
f.write_file("silly.pdb", 0)
f.write_file("silly.cif", clipper.MMDBManager.CIF)
print dir(f)
print dir(mmol)
atoms = mmol.atom_list()
print dir(atoms)
print atoms[0].coord_orth().x()
print len(atoms)
for i in range(len(atoms)):
print atoms[i]
for at in atoms:
c = at.coord_orth()
print c.x(), c.y(), c.z()
mod = mmol.model()
for poly in mod:
for mono in poly:
def test_minimol(self, verbose=False):
'''
Test minimol clipper-python bindings
'''
pdb_in_path = os.path.join(self.test_data_path, '1uoy.pdb')
assert os.path.exists(pdb_in_path)
# Set minimol
f = clipper.MMDBfile()
f.read_file(pdb_in_path)
mmol = clipper.MiniMol()
f.import_minimol(mmol)
# Test PDB/cif i/o
pdb_out_path = os.path.join(self.test_output, '1uoy_mm.pdb')
cif_out_path = os.path.join(self.test_output, '1uoy_mm.cif')
f.write_file(pdb_out_path, 0)
assert os.path.exists(pdb_out_path)
f.write_file(cif_out_path, clipper.MMDBManager.CIF)
assert os.path.exists(cif_out_path)
# What you get...
if verbose:
print(dir(f))
print(dir(mmol))
# Get atoms
atoms = mmol.atom_list()
if verbose:
print(dir(atoms))
print(atoms[0].coord_orth().x())
print(len(atoms))
# Loop through atoms
self.assertEqual(len(atoms), 581)
if verbose:
for i in range(len(atoms)):
print(atoms[i])
# Get atom coords
self.assertEqual(atoms[0].coord_orth().x(), -1.975)
if verbose:
for at in atoms:
c = at.coord_orth()
print(c.x(), c.y(), c.z())
# Loop through model, chain, residue, atom
mod = mmol.model()
for poly in mod:
for mono in poly:
for atom in mono:
if verbose:
print(atom.coord_orth().x(),
atom.coord_orth().y(),
atom.coord_orth().z())
# Access atom directly, set properties
self.assertEqual(mmol[0][0][0].occupancy(), 1.0)
mmol[0][0][0].set_occupancy(0.5)
print(mmol[0][0][0].occupancy())
self.assertEqual(mmol[0][0][0].occupancy(), 0.5)
mmol[0][0][0].set_u_iso(10.0)
print(mmol[0][0][0].u_iso())
self.assertEqual(mmol[0][0][0].u_iso(), 10.0)