def test_inData_outWrap(self):
cfr = CifFileReader(input='data')
cif_wrapper = cfr.read(self.TEST_CIF_FILE, output='cif_wrapper')
self.assertIsInstance(cif_wrapper["TEST_CIF"], CIFWrapper, "Failed to create CIFWrapper using lexical parser")
self.assertListEqual(list(cif_wrapper.keys()), ["TEST_CIF", "BLOCK_2"], "DataBlocks not read correctly")
self.assertEqual(cif_wrapper["BLOCK_2"]._extra.strange_value[0], "Three#Blind#Mice",
"All levels of CIF file not translated to dictionary correctly")
def test_inData_outDict(self):
cfr = CifFileReader(input='data')
cif_dictionary = cfr.read(self.TEST_CIF_FILE, output='cif_dictionary')
self.assertIsInstance(cif_dictionary, dict, "Failed to create python dictionary from cif file")
self.assertListEqual(list(cif_dictionary.keys()), ["TEST_CIF", "BLOCK_2"], "DataBlocks not read correctly")
self.assertEqual(cif_dictionary["BLOCK_2"]["_extra"]["strange_value"], "Three#Blind#Mice",
"All levels of CIF file not translated to dictionary correctly")
def test_inDict_outFile(self):
cfr = CifFileReader(input='dictionary')
cif_file = cfr.read(self.TEST_CIF_FILE, output='cif_file')
self.assertIsInstance(cif_file, CifFile, "Failed to create CifFile using lexical parser")
self.assertListEqual(cif_file.getDataBlockIds(), ["TEST_CIF", "BLOCK_2"], "DataBlocks not read correctly")
self.assertEqual(cif_file.getDataBlock("BLOCK_2").getCategory("_extra").getItem("strange_value").value,
"Three#Blind#Mice",
"All levels of CIF file not translated to dictionary correctly")
def read_ccd():
print('Reading components.cif ...')
sys.stdout.flush()
components = CifFileReader()
all_residues = components.read('components.cif')
print('Reading aa-variants-v1.cif ...')
amino_variants = components.read('aa-variants-v1.cif')
return itertools.chain(iter(all_residues.items()), iter(amino_variants.items()))
def read_ccd():
print 'Reading components.cif ...'
sys.stdout.flush()
components = CifFileReader()
all_residues = components.read('components.cif')
print 'Reading aa-variants-v1.cif ...'
amino_variants = components.read('aa-variants-v1.cif')
return itertools.chain(all_residues.iteritems(), amino_variants.iteritems())
def test_write_mmCIF_dictionary(self):
unit_test_file = "io_testcase_5.cif"
cfr = CifFileReader(input='dictionary')
cif_file = cfr.read(self.TEST_DIC_FILE, output='cif_file')
cfw = CifFileWriter(file_path=os.path.join(self.FILE_ROOT, unit_test_file))
cfw.write(cif_file)
test_file = cfr.read(os.path.join(self.FILE_ROOT, unit_test_file), output='cif_file')
test_value = test_file.getDataBlock('TEST')\
.getSaveFrame('some_interesting_category')\
.getCategory('category')\
.getItem('mandatory_code')\
.value
self.assertEquals(test_value, 'no', 'mmCIF dictionary file was not written correctly')
def test_ignoreCategories(self):
cfr = CifFileReader(input='data')
cif_file = cfr.read(self.TEST_CIF_FILE, output='cif_file', ignore=['_test_loop_2', '_valid_CIF'])
self.assertIsInstance(cif_file, CifFile, "Failed to create CifFile using algorithmic parser")
self.assertListEqual(cif_file.getDataBlockIds(), ["TEST_CIF", "BLOCK_2"], "DataBlocks not read correctly")
categories_A = cif_file.getDataBlock("TEST_CIF").getCategoryIds()
categories_A.sort()
self.assertEqual(categories_A,
['test_keyword', 'test_loop_1', 'valid_cif'],
"Categories were not ignored correctly")
categories_B = cif_file.getDataBlock("BLOCK_2").getCategoryIds()
categories_B.sort()
self.assertEqual(categories_B,
['equivalence_test', 'extra'],
"Categories were not ignored correctly")
def test_write_raw_dictionary_without_block_id(self):
unit_test_file = "io_testcase_4.cif"
# Test raw dictionary (WITHOUT datablock id)
cfw = CifFileWriter(file_path=os.path.join(self.FILE_ROOT, unit_test_file))
cfw.write(self.raw_dictionary['TEST_BLOCK_1'])
del cfw
cfr = CifFileReader(input='data')
test_file = cfr.read(os.path.join(self.FILE_ROOT, unit_test_file), output='cif_wrapper')
data_block_ids = test_file.keys()
data_block_ids.sort()
self.assertEqual(data_block_ids,
[unit_test_file,],
"Datablock(s) were not written correctly")
self.assertEqual(test_file[unit_test_file]._test_category_2.test_value_1,
['1', '2', '3', '4'],
"mmCIF data was not written correctly")
def test_write_ciffile_after_ciffile_dictionary_import(self):
# Test write CifFile initialized by dictionary
unit_test_file = "io_testcase_1.cif"
cfw = CifFileWriter()
cif_file = CifFile(os.path.join(self.FILE_ROOT, unit_test_file))
cif_file.import_mmcif_data_map(self.raw_dictionary)
cfw.write(cif_file)
cfr = CifFileReader(input='data')
test_file = cfr.read(os.path.join(self.FILE_ROOT, unit_test_file), output='cif_wrapper')
data_block_ids = test_file.keys()
data_block_ids.sort()
self.assertEqual(data_block_ids,
['TEST_BLOCK_1', 'TEST_BLOCK_2'],
"Datablock(s) were not written correctly")
self.assertEqual(test_file['TEST_BLOCK_1']._test_category_2.test_value_1,
['1', '2', '3', '4'],
"mmCIF data was not written correctly")
def test_write_ciffile_after_cifwrapper_dictionary_import(self):
# Test write CifFile initialized by CIFWrapper and dictionary import
unit_test_file = "io_testcase_2.cif"
cfw = CifFileWriter(file_path=os.path.join(self.FILE_ROOT, unit_test_file))
cif_obj = dict((k, CIFWrapper(v)) for k, v in self.raw_dictionary.items())
cif_wrapper = CIFWrapper({'TEST_BLOCK_1': self.raw_dictionary['TEST_BLOCK_1']})
cfw.write(cif_wrapper)
cif_wrapper = CIFWrapper({'TEST_BLOCK_2': self.raw_dictionary['TEST_BLOCK_2']})
cfw.write(cif_wrapper)
del cfw
cfr = CifFileReader(input='data')
test_file = cfr.read(os.path.join(self.FILE_ROOT, unit_test_file), output='cif_wrapper')
data_block_ids = test_file.keys()
data_block_ids.sort()
self.assertEqual(data_block_ids,
['TEST_BLOCK_1', 'TEST_BLOCK_2'],
"Datablock(s) were not written correctly")
self.assertEqual(test_file['TEST_BLOCK_1']._test_category_2.test_value_1,
['1', '2', '3', '4'],
"mmCIF data was not written correctly")
sys.path.insert(0, '..')
import utils
# to install mmCif: pip install git+git://github.com/glenveegee/PDBeCIF
from mmCif.mmcifIO import CifFileReader
ORDERS = dict(SING=1, DOUB=2, TRIP=3)
if __name__ == '__main__':
print 'This program regenerates the `residue_bonds` database using the "Chemical Component '
print 'Dictionary" and "Protonation Variants Dictionary" from http://www.wwpdb.org/data/ccd'
print 'These files are not included in the repository and must be downloaded manually.\n'
print 'Reading components.cif ...'
sys.stdout.flush()
components = CifFileReader()
all_residues = components.read('components.cif')
print 'Reading aa-variants-v1.cif ...'
amino_variants = components.read('aa-variants-v1.cif')
residues = []
db = utils.CompressedJsonDbm('residue_bonds', 'n')
for resname, data in itertools.chain(all_residues.iteritems(),
amino_variants.iteritems()):
if '_chem_comp_bond' not in data:
print '\nskipped %s (no bonds)' % resname
continue
