def test_pdbfix_templates():
template1_pdb_gz_filepath = get_installed_resource_filename(os.path.join('resources', 'KC1D_HUMAN_D0_4KB8_D.pdb.gz'))
template1_pdb_filepath = os.path.join(ensembler.core.default_project_dirnames.templates_structures_resolved, 'KC1D_HUMAN_D0_4KB8_D.pdb')
template2_pdb_gz_filepath = get_installed_resource_filename(os.path.join('resources', 'KC1D_HUMAN_D0_3UYS_D.pdb.gz'))
template2_pdb_filepath = os.path.join(ensembler.core.default_project_dirnames.templates_structures_resolved, 'KC1D_HUMAN_D0_3UYS_D.pdb')
with ensembler.utils.enter_temp_dir():
ensembler.utils.create_dir(ensembler.core.default_project_dirnames.templates_structures_resolved)
ensembler.utils.create_dir(ensembler.core.default_project_dirnames.templates_structures_modeled_loops)
with gzip.open(template1_pdb_gz_filepath) as template1_pdb_gz_file:
with open(template1_pdb_filepath, 'w') as template1_pdb_file:
contents = template1_pdb_gz_file.read()
if type(contents) == bytes:
contents = contents.decode('utf-8')
template1_pdb_file.write(contents)
with gzip.open(template2_pdb_gz_filepath) as template2_pdb_gz_file:
with open(template2_pdb_filepath, 'w') as template2_pdb_file:
contents = template2_pdb_gz_file.read()
if type(contents) == bytes:
contents = contents.decode('utf-8')
template2_pdb_file.write(contents)
template1 = Mock()
template1.id = 'KC1D_HUMAN_D0_4KB8_D'
template1.seq = 'LRVGNRYRLGRKIGSGSFGDIYLGTDIAAGEEVAIKLECVKTKHPQLHIESKIYKMMQGGVGIPTIRWCGAEGDYNVMVMELLGPSLEDLFNFCSRKFSLKTVLLLADQMISRIEYIHSKNFIHRDVKPDNFLMGLGKKGNLVYIIDFGLAKKYRDARTHQHIPYRENKNLTGTARYASINTHLGIEQSRRDDLESLGYVLMYFNLGSLPWQGLKAATKRQKYERISEKKMSTPIEVLCKGYPSEFATYLNFCRSLRFDDKPDYSYLRQLFRNLFHRQGFSYDYVFDWNMLKFGASRAADDAERERRDREERLRH'
template2 = Mock()
template2.id = 'KC1D_HUMAN_D0_3UYS_D'
template2.seq = 'MELRVGNRYRLGRKIGSGSFGDIYLGTDIAAGEEVAIKLECVKTKHPQLHIESKIYKMMQGGVGIPTIRWCGAEGDYNVMVMELLGPSLEDLFNFCSRKFSLKTVLLLADQMISRIEYIHSKNFIHRDVKPDNFLMGLGKKGNLVYIIDFGLAKKYRDARTHQHIPYRENKNLTGTARYASINTHLGIEQSRRDDLESLGYVLMYFNLGSLPWQGLKAATKRQKYERISEKKMSTPIEVLCKGYPSEFATYLNFCRSLRFDDKPDYSYLRQLFRNLFHRQGFSYDYVFDWNMLK'
templates = [template1, template2]
missing_residues_list = pdbfix_templates(templates)
def _copy_modeling_files(self, target_level_files=None, template_level_files=None):
for target in self.targets_list:
for filename in target_level_files:
shutil.copy(
get_installed_resource_filename(os.path.join('example_project', default_project_dirnames.models, target, filename)),
os.path.join(self.project_dir, default_project_dirnames.models, target)
)
for template in self.templates_list:
for filename in template_level_files:
shutil.copy(
get_installed_resource_filename(os.path.join('example_project', default_project_dirnames.models, target, template, filename)),
os.path.join(self.project_dir, default_project_dirnames.models, target, template)
)
def test_align_command():
ref_resources_dirpath = get_installed_resource_filename('example_project')
with integrationtest_context(set_up_project_stage='templates_modeled_loops'):
targets = ['KC1D_HUMAN_D0', 'EGFR_HUMAN_D0']
templates = ['KC1D_HUMAN_D0_4KB8_D', 'KC1D_HUMAN_D0_4HNF_A']
args = {
'--targets': ','.join(targets),
'--targetsfile': False,
'--templates': ','.join(templates),
'--templatesfile': False,
'--verbose': False,
}
ensembler.cli_commands.align.dispatch(args)
for target in targets:
naln_files = 0
for dir, subdirs, files in os.walk(os.path.join(ensembler.core.default_project_dirnames.models, target)):
for file in files:
if file == 'alignment.pir':
naln_files += 1
assert naln_files == len(templates)
for target in targets:
seqid_filepath = os.path.join(ensembler.core.default_project_dirnames.models, target, 'sequence-identities.txt')
ref_seqid_filepath = os.path.join(ref_resources_dirpath, seqid_filepath)
with open(seqid_filepath) as seqid_file:
seqid_file_text = seqid_file.read()
with open(ref_seqid_filepath) as ref_seqid_file:
ref_seqid_file_text = ref_seqid_file.read()
print(seqid_file_text)
print(ref_seqid_file_text)
assert seqid_file_text == ref_seqid_file_text
def templates_modeled_loops(self):
self.templates_resolved()
distutils.dir_util.copy_tree(
get_installed_resource_filename(
os.path.join('example_project', default_project_dirnames.templates_structures_modeled_loops)
),
os.path.join(self.project_dir, default_project_dirnames.templates_structures_modeled_loops)
)
def test_extract_residues_by_resnum_from_4CFE():
# 4CFE contains a 'TPO' residue
pdb_input_filepath = get_installed_resource_filename(os.path.join('resources', '4CFE.pdb.gz'))
template = Mock()
template.chainid= 'A'
template.resolved_pdbresnums = [str(x) for x in range(16, 269)]
ofile = StringIO()
ensembler.pdb.extract_residues_by_resnum(ofile, pdb_input_filepath, template)
ofile.close()
def test_extract_residues_by_resnum_from_3HLL():
# 3HLL contains resnums '56A' and '93B'
pdb_input_filepath = get_installed_resource_filename(os.path.join('resources', '3HLL.pdb.gz'))
template = Mock()
template.chainid = 'A'
template.resolved_pdbresnums = [str(x) for x in range(24, 172) + range(183, 309)]
template.resolved_pdbresnums[template.resolved_pdbresnums.index('56')] = '56A'
template.resolved_pdbresnums[template.resolved_pdbresnums.index('93')] = '93B'
ofile = StringIO()
ensembler.pdb.extract_residues_by_resnum(ofile, pdb_input_filepath, template)
ofile.close()
def test_extract_residues_by_resnum_output():
pdb_input_filepath = get_installed_resource_filename(os.path.join('resources', '3HLL.pdb.gz'))
template = Mock()
template.chainid = 'A'
template.resolved_pdbresnums = [str(x) for x in range(24, 172) + range(183, 309)]
template.resolved_pdbresnums[template.resolved_pdbresnums.index('56')] = '56A'
template.resolved_pdbresnums[template.resolved_pdbresnums.index('93')] = '93B'
ofile = StringIO()
ensembler.pdb.extract_residues_by_resnum(ofile, pdb_input_filepath, template)
ofile_text = ofile.getvalue()
first_line = ofile_text[0: ofile_text.index('\n')]
assert first_line == 'ATOM 175 N TYR A 24 50.812 43.410 19.390 1.00 38.55 N '
ofile.close()
def test_build_model():
template_filepath = get_installed_resource_filename(os.path.join('resources', 'mock_template.pdb'))
aln_filepath = get_installed_resource_filename(os.path.join('resources', 'mock_template-alignment.pir'))
with enter_temp_dir():
target = Mock()
template = Mock()
target_setup_data = Mock()
target.id = 'mock_target'
target.seq = 'YILGDTLGVGGKVKVGKH'
template.id = 'mock_template'
template.seq = 'YQNLSPVGSGGSVCAAFD'
target_setup_data.target_starttime = datetime.datetime.utcnow()
target_setup_data.models_target_dir = os.path.join(ensembler.core.default_project_dirnames.models, target.id)
os.mkdir(ensembler.core.default_project_dirnames.models)
model_dir = os.path.join(ensembler.core.default_project_dirnames.models, 'mock_target', 'mock_template')
os.makedirs(model_dir)
os.mkdir(ensembler.core.default_project_dirnames.templates)
os.mkdir(ensembler.core.default_project_dirnames.templates_structures_resolved)
shutil.copy(template_filepath, ensembler.core.default_project_dirnames.templates_structures_resolved)
shutil.copy(aln_filepath, os.path.join(model_dir, 'alignment.pir'))
ensembler.modeling.build_model(target, template, target_setup_data=target_setup_data)
# Example model.pdb.gz contents (not testing this as it may be dependent
# upon Modeller version as well as modelling stochasticity):
#
# ..EXPDTA THEORETICAL MODEL, MODELLER 9.12 2014/08/26 13:15:44
# REMARK 6 MODELLER OBJECTIVE FUNCTION: 326.6798
# REMARK 6 MODELLER BEST TEMPLATE % SEQ ID: 27.778
# ATOM 1 N TYR 1 48.812 50.583 13.949 1.00110.28 N
# ATOM 2 CA TYR 1 49.070 50.334 15.387 1.00110.28 C
model_filepath = os.path.join(target_setup_data.models_target_dir, template.id, 'model.pdb.gz')
assert os.path.exists(model_filepath)
assert os.path.getsize(model_filepath) > 0
def templates_resolved(self):
self.targets()
shutil.copy(
get_installed_resource_filename(
os.path.join('example_project', default_project_dirnames.templates, 'meta0.yaml')
),
os.path.join(self.project_dir, default_project_dirnames.templates))
shutil.copy(
get_installed_resource_filename(
os.path.join('example_project', default_project_dirnames.templates, 'templates-resolved-seq.fa')
),
os.path.join(self.project_dir, default_project_dirnames.templates))
shutil.copy(
get_installed_resource_filename(
os.path.join('example_project', default_project_dirnames.templates, 'templates-full-seq.fa')
),
os.path.join(self.project_dir, default_project_dirnames.templates)
)
distutils.dir_util.copy_tree(
get_installed_resource_filename(
os.path.join('example_project', default_project_dirnames.templates_structures_resolved)
),
os.path.join(self.project_dir, default_project_dirnames.templates_structures_resolved)
)
def test_pdbfix_ABL1_HUMAN_D0_2E2B_B():
template_pdb_gz_filepath = get_installed_resource_filename(os.path.join('resources', 'ABL1_HUMAN_D0_2E2B_B.pdb.gz'))
template_pdb_filepath = os.path.join(ensembler.core.default_project_dirnames.templates_structures_resolved, 'ABL1_HUMAN_D0_2E2B_B.pdb')
with ensembler.utils.enter_temp_dir():
ensembler.utils.create_dir(ensembler.core.default_project_dirnames.templates_structures_resolved)
ensembler.utils.create_dir(ensembler.core.default_project_dirnames.templates_structures_modeled_loops)
with gzip.open(template_pdb_gz_filepath) as template_pdb_gz_file:
with open(template_pdb_filepath, 'w') as template_pdb_file:
contents = template_pdb_gz_file.read()
if type(contents) == bytes:
contents = contents.decode('utf-8')
template_pdb_file.write(contents)
template = Mock()
template.id = 'ABL1_HUMAN_D0_2E2B_B'
template.seq = 'ITMKHKLGGGQYGEVYEGVWKKYSLTVAVKTLKEDTMEVEEFLKEAAVMKEIKHPNLVQLLGVCTREPPFYIITEFMTYGNLLDYLRECNRQEVNAVVLLYMATQISSAMEYLEKKNFIHRDLAARNCLVGENHLVKVADFGLSRLMTGDTYTAHAGAKFPIKWTAPESLAYNKFSIKSDVWAFGVLLWEIATYGMSPYPGIDLSQVYELLEKDYRMERPEGCPEKVYELMRACWQWNPSDRPSFAEIHQAFETMFQESSISDEVEKELGKQ'
missing_residues = pdbfix_template(template)
assert (0, 271) not in missing_residues
assert missing_residues == {
(0, 32): ['LYS', 'GLU', 'ASP', 'THR', 'MET'],
(0, 139): ['ARG', 'LEU', 'MET', 'THR', 'GLY', 'ASP'],
}
def targets(self):
self.init()
distutils.dir_util.copy_tree(
get_installed_resource_filename(os.path.join('example_project', default_project_dirnames.targets)),
os.path.join(self.project_dir, default_project_dirnames.targets)
)
def init(self):
ensembler.initproject.InitProject(self.project_dir)
shutil.copy(get_installed_resource_filename(os.path.join('example_project', 'meta0.yaml')), self.project_dir)