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import utils
import os
import unittest
import io
TOPDIR = os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))
utils.set_search_paths(TOPDIR)
import modelcif.reader
import modelcif.dumper
class Tests(unittest.TestCase):
def test_model_with_assembly(self):
"""Test read of Model with Assembly followed by write"""
sin = io.StringIO("""
loop_
_entity.id
_entity.type
_entity.pdbx_description
_entity.pdbx_number_of_molecules
_entity.formula_weight
_entity.details
1 polymer Nup84 2 100.0 .
#
loop_
_entity_poly_seq.entity_id
_entity_poly_seq.num
_entity_poly_seq.mon_id
_entity_poly_seq.hetero
1 1 ALA .
1 2 CYS .
#
loop_
_struct_asym.id
_struct_asym.entity_id
_struct_asym.details
A 1 'Model subunit A'
#
loop_
_ma_struct_assembly.ordinal_id
_ma_struct_assembly.assembly_id
_ma_struct_assembly.entity_id
_ma_struct_assembly.asym_id
_ma_struct_assembly.seq_id_begin
_ma_struct_assembly.seq_id_end
1 1 1 A 1 2
#
loop_
_ma_model_list.ordinal_id
_ma_model_list.model_id
_ma_model_list.model_group_id
_ma_model_list.model_name
_ma_model_list.model_group_name
_ma_model_list.assembly_id
_ma_model_list.data_id
_ma_model_list.model_type
_ma_model_list.model_type_other_details
1 1 1 'Best scoring model' 'All models' 1 4 'Homology model' .
#
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_alt_id
_atom_site.label_comp_id
_atom_site.label_seq_id
_atom_site.auth_seq_id
_atom_site.pdbx_PDB_ins_code
_atom_site.label_asym_id
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.label_entity_id
_atom_site.auth_asym_id
_atom_site.B_iso_or_equiv
_atom_site.pdbx_PDB_model_num
ATOM 1 C CA . ALA 1 1 ? A 1.000 2.000 3.000 . 1 A . 1
""")
s, = modelcif.reader.read(sin)
sout = io.StringIO()
modelcif.dumper.write(sout, [s])
def test_model_without_assembly(self):
"""Test read of Model without Assembly followed by write"""
sin = io.StringIO("""
loop_
_entity.id
_entity.type
_entity.pdbx_description
_entity.pdbx_number_of_molecules
_entity.formula_weight
_entity.details
1 polymer Nup84 2 100.0 .
#
loop_
_entity_poly_seq.entity_id
_entity_poly_seq.num
_entity_poly_seq.mon_id
_entity_poly_seq.hetero
1 1 ALA .
1 2 CYS .
#
loop_
_struct_asym.id
_struct_asym.entity_id
_struct_asym.details
A 1 'Model subunit A'
#
loop_
_ma_model_list.ordinal_id
_ma_model_list.model_id
_ma_model_list.model_group_id
_ma_model_list.model_name
_ma_model_list.model_group_name
_ma_model_list.assembly_id
_ma_model_list.data_id
_ma_model_list.model_type
_ma_model_list.model_type_other_details
1 1 1 'Best scoring model' 'All models' . 4 'Homology model' .
#
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_alt_id
_atom_site.label_comp_id
_atom_site.label_seq_id
_atom_site.auth_seq_id
_atom_site.pdbx_PDB_ins_code
_atom_site.label_asym_id
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.label_entity_id
_atom_site.auth_asym_id
_atom_site.B_iso_or_equiv
_atom_site.pdbx_PDB_model_num
ATOM 1 C CA . ALA 1 1 ? A 1.000 2.000 3.000 . 1 A . 1
""")
s, = modelcif.reader.read(sin)
sout = io.StringIO()
modelcif.dumper.write(sout, [s])
if __name__ == '__main__':
unittest.main()
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