def test_pdbfix_KC1D_HUMAN_D0_4KB8_D():
set_loglevel('debug')
template_pdb_gz_filepath = get_installed_resource_filename(os.path.join('tests', 'resources', 'KC1D_HUMAN_D0_4KB8_D.pdb.gz'))
template_pdb_filepath = os.path.join(ensembler.core.default_project_dirnames.templates_structures_resolved, 'KC1D_HUMAN_D0_4KB8_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(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 = 'KC1D_HUMAN_D0_4KB8_D'
template.seq = 'LRVGNRYRLGRKIGSGSFGDIYLGTDIAAGEEVAIKLECVKTKHPQLHIESKIYKMMQGGVGIPTIRWCGAEGDYNVMVMELLGPSLEDLFNFCSRKFSLKTVLLLADQMISRIEYIHSKNFIHRDVKPDNFLMGLGKKGNLVYIIDFGLAKKYRDARTHQHIPYRENKNLTGTARYASINTHLGIEQSRRDDLESLGYVLMYFNLGSLPWQGLKAATKRQKYERISEKKMSTPIEVLCKGYPSEFATYLNFCRSLRFDDKPDYSYLRQLFRNLFHRQGFSYDYVFDWNMLKFGASRAADDAERERRDREERLRH'
missing_residues = pdbfix_template(template)
assert (0, 278) not in missing_residues
assert missing_residues == {
(0, 14): ['SER', 'GLY', 'SER', 'PHE', 'GLY'],
(0, 34): ['VAL', 'LYS', 'THR', 'LYS', 'HIS'],
(0, 147): ['ARG', 'THR', 'HIS'],
}
def test_loopmodel_KC1D_HUMAN_D0_4HNF_A():
with integrationtest_context(set_up_project_stage='templates_resolved'):
template = Mock()
template.id = 'KC1D_HUMAN_D0_4HNF_A'
template.seq = 'YRLGRKIGSGSFGDIYLGTDIAAGEEVAIKLECVKTKHPQLHIESKIYKMMQGGVGIPTIRWCGAEGDYNVMVMELLGPSLEDLFNFCSRKFSLKTVLLLADQMISRIEYIHSKNFIHRDVKPDNFLMGLGKKGNLVYIIDFGLAKKYRDARTHQHIPYRENKNLTGTARYASINTHLGIEQSRRDDLESLGYVLMYFNLGSLPWQGLKAATKRQKYERISEKKMSTPIEVLCKGYPSEFATYLNFCRSLRFDDKPDYSYLRQLFRNLF'
missing_residues = pdbfix_template(template)
loopmodel_template(template, missing_residues)
assert os.path.exists(os.path.join('templates', 'structures-modeled-loops', 'KC1D_HUMAN_D0_4HNF_A.pdb'))
def test_loopmodel_KC1D_HUMAN_D0_4HNF_A():
with integrationtest_context(set_up_project_stage='templates_resolved'):
template = Mock()
template.id = 'KC1D_HUMAN_D0_4HNF_A'
template.seq = 'YRLGRKIGSGSFGDIYLGTDIAAGEEVAIKLECVKTKHPQLHIESKIYKMMQGGVGIPTIRWCGAEGDYNVMVMELLGPSLEDLFNFCSRKFSLKTVLLLADQMISRIEYIHSKNFIHRDVKPDNFLMGLGKKGNLVYIIDFGLAKKYRDARTHQHIPYRENKNLTGTARYASINTHLGIEQSRRDDLESLGYVLMYFNLGSLPWQGLKAATKRQKYERISEKKMSTPIEVLCKGYPSEFATYLNFCRSLRFDDKPDYSYLRQLFRNLF'
missing_residues = pdbfix_template(template)
loopmodel_template(template, missing_residues)
assert os.path.exists(os.path.join('templates', 'structures-modeled-loops', 'KC1D_HUMAN_D0_4HNF_A.pdb'))
def test_loopmodel_KC1D_HUMAN_D0_3UZP_A():
"""
No missing residues
"""
with integrationtest_context(set_up_project_stage='templates_resolved'):
template = Mock()
template.id = 'KC1D_HUMAN_D0_3UZP_A'
template.seq = 'YRLGRKIGSGSFGDIYLGTDIAAGEEVAIKLECVKTKHPQLHIESKIYKMMQGGVGIPTIRWCGAEGDYNVMVMELLGPSLEDLFNFCSRKFSLKTVLLLADQMISRIEYIHSKNFIHRDVKPDNFLMGLGKKGNLVYIIDFGLAKKYRDARTHQHIPYRENKNLTGTARYASINTHLGIEQSRRDDLESLGYVLMYFNLGSLPWQGLKAATKRQKYERISEKKMSTPIEVLCKGYPSEFATYLNFCRSLRFDDKPDYSYLRQLFRNLF'
missing_residues = pdbfix_template(template)
loopmodel_template(template, missing_residues)
assert not os.path.exists(os.path.join(ensembler.core.default_project_dirnames.templates_structures_modeled_loops, 'KC1D_HUMAN_D0_3UZP_A.pdb'))
log = yaml.load(open(os.path.join(ensembler.core.default_project_dirnames.templates_structures_modeled_loops, 'KC1D_HUMAN_D0_3UZP_A-loopmodel-log.yaml')))
assert log['no_missing_residues'] == True
def test_loopmodel_KC1D_HUMAN_D0_3UZP_A():
"""
No missing residues
"""
with integrationtest_context(set_up_project_stage='templates_resolved'):
template = Mock()
template.id = 'KC1D_HUMAN_D0_3UZP_A'
template.seq = 'YRLGRKIGSGSFGDIYLGTDIAAGEEVAIKLECVKTKHPQLHIESKIYKMMQGGVGIPTIRWCGAEGDYNVMVMELLGPSLEDLFNFCSRKFSLKTVLLLADQMISRIEYIHSKNFIHRDVKPDNFLMGLGKKGNLVYIIDFGLAKKYRDARTHQHIPYRENKNLTGTARYASINTHLGIEQSRRDDLESLGYVLMYFNLGSLPWQGLKAATKRQKYERISEKKMSTPIEVLCKGYPSEFATYLNFCRSLRFDDKPDYSYLRQLFRNLF'
missing_residues = pdbfix_template(template)
loopmodel_template(template, missing_residues)
assert not os.path.exists(os.path.join(ensembler.core.default_project_dirnames.templates_structures_modeled_loops, 'KC1D_HUMAN_D0_3UZP_A.pdb'))
log = yaml.load(open(os.path.join(ensembler.core.default_project_dirnames.templates_structures_modeled_loops, 'KC1D_HUMAN_D0_3UZP_A-loopmodel-log.yaml')))
assert log['no_missing_residues'] == True
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 test_pdbfix_ABL1_HUMAN_D0_2E2B_B():
set_loglevel('debug')
template_pdb_gz_filepath = get_installed_resource_filename(os.path.join('tests', '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'],
}