def PDBParser(open_file, structure_id=None, forgive=2):
"""Parse a PDB file and return a Structure object."""
file_ = open_file.readlines()
builder = StructureBuilder()
c_offset = get_coords_offset(file_)
t_offset = get_trailer_offset(file_)
raw_coords = file_[c_offset:t_offset]
raw_trailer = file_[t_offset:]
raw_header = file_[:c_offset]
parsed_header = parse_header(raw_header)
parsed_trailer = parse_trailer(raw_trailer)
structure_id = (structure_id or parsed_header.get('id'))
builder.initStructure(structure_id)
structure = parse_coords(builder, raw_coords, forgive)
# only X-ray structures will contain crystallographic data
if parsed_header.get('expdta') == 'X-RAY':
symetry_info = get_symmetry(raw_header)
parsed_header.update(symetry_info)
structure.header = parsed_header
structure.trailer = parsed_trailer
structure.raw_header = raw_header
structure.raw_trailer = raw_trailer
return structure
def PDBParser(open_file, structure_id=None, forgive=2):
"""Parse a PDB file and return a Structure object."""
file_ = open_file.readlines()
builder = StructureBuilder()
c_offset = get_coords_offset(file_)
t_offset = get_trailer_offset(file_)
raw_coords = file_[c_offset:t_offset]
raw_trailer = file_[t_offset:]
raw_header = file_[:c_offset]
parsed_header = parse_header(raw_header)
parsed_trailer = parse_trailer(raw_trailer)
structure_id = (structure_id or parsed_header.get('id'))
builder.initStructure(structure_id)
structure = parse_coords(builder, raw_coords, forgive)
# only X-ray structures will contain crystallographic data
if parsed_header.get('expdta') == 'X-RAY':
symetry_info = get_symmetry(raw_header)
parsed_header.update(symetry_info)
structure.header = parsed_header
structure.trailer = parsed_trailer
structure.raw_header = raw_header
structure.raw_trailer = raw_trailer
return structure
def test_parse_coords(self):
"""testing minimal structure building and coords parsing.
"""
builder = StructureBuilder()
builder.initStructure('JUNK')
atom = 'ATOM 10 CA PRO A 2 51.588 38.262 31.417 1.00 6.58 C \n'
hetatm = 'HETATM 1633 O HOH B 164 17.979 35.529 38.171 1.00 1.02 O \n'
lines = ['MODEL ', atom, hetatm]
z = parse_coords(builder, lines)
assert len(z[(0,)]) == 2
assert len(z[(0,)][('A',)]) == 1
assert len(z[(0,)][('B',)]) == 1
z.setTable()
atom1 = z.table['A'][('JUNK', 0, 'A', ('PRO', 2, ' '), ('CA', ' '))]
hetatm1 = z.table['A'][('JUNK', 0, 'B', ('H_HOH', 164, ' '), ('O', ' '))]
self.assertAlmostEqual([51.588 , 38.262 , 31.417][2], list(atom1.coords)[2])
self.assertAlmostEqual([17.979 , 35.529 , 38.171][2], list(hetatm1.coords)[2])
def test_parse_coords(self):
"""testing minimal structure building and coords parsing.
"""
builder = StructureBuilder()
builder.initStructure('JUNK')
atom = 'ATOM 10 CA PRO A 2 51.588 38.262 31.417 1.00 6.58 C \n'
hetatm = 'HETATM 1633 O HOH B 164 17.979 35.529 38.171 1.00 1.02 O \n'
lines = ['MODEL ', atom, hetatm]
z = parse_coords(builder, lines)
assert len(z[(0,)]) == 2
assert len(z[(0,)][('A',)]) == 1
assert len(z[(0,)][('B',)]) == 1
z.setTable()
atom1 = z.table['A'][('JUNK', 0, 'A', ('PRO', 2, ' '), ('CA', ' '))]
hetatm1 = z.table['A'][('JUNK', 0, 'B', ('H_HOH', 164, ' '), ('O', ' '))]
self.assertAlmostEqual([51.588 , 38.262 , 31.417][2], list(atom1.coords)[2])
self.assertAlmostEqual([17.979 , 35.529 , 38.171][2], list(hetatm1.coords)[2])
def test_parse_coords(self):
"""testing minimal structure building and coords parsing.
"""
builder = StructureBuilder()
builder.initStructure("JUNK")
atom = "ATOM 10 CA PRO A 2 51.588 38.262 31.417 1.00 6.58 C \n"
hetatm = "HETATM 1633 O HOH B 164 17.979 35.529 38.171 1.00 1.02 O \n"
lines = ["MODEL ", atom, hetatm]
z = parse_coords(builder, lines)
assert len(z[(0,)]) == 2
assert len(z[(0,)][("A",)]) == 1
assert len(z[(0,)][("B",)]) == 1
z.setTable()
atom1 = z.table["A"][("JUNK", 0, "A", ("PRO", 2, " "), ("CA", " "))]
hetatm1 = z.table["A"][("JUNK", 0, "B", ("H_HOH", 164, " "), ("O", " "))]
self.assertAlmostEqual([51.588, 38.262, 31.417][2], list(atom1.coords)[2])
self.assertAlmostEqual([17.979, 35.529, 38.171][2], list(hetatm1.coords)[2])