def test_command_gather_targets_from_uniprot():
with integrationtest_context(set_up_project_stage='init'):
ref_fasta = """\
>EGFR_HUMAN_D0
FKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDN
PHVCRLLGICLTSTVQLITQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDR
RLVHRDLAARNVLVKTPQHVKITDFGLAKLLGAEEKEYHAEGGKVPIKWMALESILHRIY
THQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMVKCW
MIDADSRPKFRELIIEFSKMARDPQRYL
>KC1D_HUMAN_D0
YRLGRKIGSGSFGDIYLGTDIAAGEEVAIKLECVKTKHPQLHIESKIYKMMQGGVGIPTI
RWCGAEGDYNVMVMELLGPSLEDLFNFCSRKFSLKTVLLLADQMISRIEYIHSKNFIHRD
VKPDNFLMGLGKKGNLVYIIDFGLAKKYRDARTHQHIPYRENKNLTGTARYASINTHLGI
EQSRRDDLESLGYVLMYFNLGSLPWQGLKAATKRQKYERISEKKMSTPIEVLCKGYPSEF
ATYLNFCRSLRFDDKPDYSYLRQLFRNLF
"""
args = {
'--gather_from': 'uniprot',
'--query': 'mnemonic:EGFR_HUMAN OR mnemonic:KC1D_HUMAN',
'--dbapi_uri': False,
'--uniprot_domain_regex': '^Protein kinase',
'--verbose': False,
'--help': False,
}
ensembler.cli_commands.gather_targets.dispatch(args)
test_fasta = open(
os.path.join(ensembler.core.default_project_dirnames.targets,
'targets.fa')).read()
assert test_fasta == ref_fasta
def test_align_command():
ref_resources_dirpath = get_installed_resource_filename(os.path.join('tests', '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 test_command_gather_targets_from_uniprot():
with integrationtest_context(set_up_project_stage='init'):
ref_fasta = """\
>EGFR_HUMAN_D0
FKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDN
PHVCRLLGICLTSTVQLITQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDR
RLVHRDLAARNVLVKTPQHVKITDFGLAKLLGAEEKEYHAEGGKVPIKWMALESILHRIY
THQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMVKCW
MIDADSRPKFRELIIEFSKMARDPQRYL
>KC1D_HUMAN_D0
YRLGRKIGSGSFGDIYLGTDIAAGEEVAIKLECVKTKHPQLHIESKIYKMMQGGVGIPTI
RWCGAEGDYNVMVMELLGPSLEDLFNFCSRKFSLKTVLLLADQMISRIEYIHSKNFIHRD
VKPDNFLMGLGKKGNLVYIIDFGLAKKYRDARTHQHIPYRENKNLTGTARYASINTHLGI
EQSRRDDLESLGYVLMYFNLGSLPWQGLKAATKRQKYERISEKKMSTPIEVLCKGYPSEF
ATYLNFCRSLRFDDKPDYSYLRQLFRNLF
"""
args = {
'--gather_from': 'uniprot',
'--query': 'mnemonic:EGFR_HUMAN OR mnemonic:KC1D_HUMAN',
'--dbapi_uri': False,
'--uniprot_domain_regex': '^Protein kinase',
'--verbose': False,
'--help': False,
}
ensembler.cli_commands.gather_targets.dispatch(args)
test_fasta = open(os.path.join(ensembler.core.default_project_dirnames.targets, 'targets.fa')).read()
assert test_fasta == ref_fasta
def test_refine_explicit_md_short():
with integrationtest_context(set_up_project_stage='solvated'):
targetid = 'EGFR_HUMAN_D0'
templateid = 'KC1D_HUMAN_D0_4KB8_D'
refine_explicit_md(
process_only_these_targets=[targetid],
process_only_these_templates=[templateid],
sim_length=2.0*unit.femtosecond,
nsteps_per_iteration=1,
verbose=True
)
explicit_metadata_filepath = os.path.join(
default_project_dirnames.models, targetid, 'refine_explicit_md-meta0.yaml'
)
explicit_model_filepath = os.path.join(
default_project_dirnames.models, targetid, templateid, 'explicit-refined.pdb.gz'
)
explicit_energies_filepath = os.path.join(
default_project_dirnames.models, targetid, templateid, 'explicit-energies.txt'
)
explicit_log_filepath = os.path.join(
default_project_dirnames.models, targetid, templateid, 'explicit-log.yaml'
)
assert all(map(
os.path.exists,
[explicit_model_filepath, explicit_energies_filepath, explicit_log_filepath]
))
with open(explicit_log_filepath) as explicit_log_file:
explicit_log = yaml.load(explicit_log_file)
assert explicit_log.get('finished') is True
assert explicit_log.get('successful') is True
explicit_model_traj = mdtraj.load_pdb(explicit_model_filepath)
def test_refine_explicit_md_short():
with integrationtest_context(set_up_project_stage='solvated'):
targetid = 'EGFR_HUMAN_D0'
templateid = 'KC1D_HUMAN_D0_4KB8_D'
refine_explicit_md(process_only_these_targets=[targetid],
process_only_these_templates=[templateid],
sim_length=2.0 * unit.femtosecond,
nsteps_per_iteration=1,
verbose=True)
explicit_metadata_filepath = os.path.join(
default_project_dirnames.models, targetid,
'refine_explicit_md-meta0.yaml')
explicit_model_filepath = os.path.join(default_project_dirnames.models,
targetid, templateid,
'explicit-refined.pdb.gz')
explicit_energies_filepath = os.path.join(
default_project_dirnames.models, targetid, templateid,
'explicit-energies.txt')
explicit_log_filepath = os.path.join(default_project_dirnames.models,
targetid, templateid,
'explicit-log.yaml')
assert all(
map(os.path.exists, [
explicit_model_filepath, explicit_energies_filepath,
explicit_log_filepath
]))
with open(explicit_log_filepath) as explicit_log_file:
explicit_log = yaml.load(explicit_log_file)
assert explicit_log.get('finished') is True
assert explicit_log.get('successful') is True
explicit_model_traj = mdtraj.load_pdb(explicit_model_filepath)
def test_get_valid_model_filepaths():
targetid = 'EGFR_HUMAN_D0'
templateids = ['KC1D_HUMAN_D0_4KB8_D', 'KC1D_HUMAN_D0_4HNF_A']
with integrationtest_context('refined_implicit'):
valid_model_filenames = get_valid_model_ids('refine_implicit_md',
targetid)
assert all([fpath in templateids for fpath in valid_model_filenames])
def test_build_models_command():
with integrationtest_context(set_up_project_stage='aligned'):
args = {
'--targets':
'EGFR_HUMAN_D0',
'--targetsfile':
None,
'--model_seqid_cutoff':
None,
'--templates':
','.join(['KC1D_HUMAN_D0_4KB8_D', 'KC1D_HUMAN_D0_4HNF_A']),
'--templatesfile':
None,
'--write_modeller_restraints_file':
None,
'--verbose':
False,
'--help':
False,
}
ensembler.cli_commands.build_models.dispatch(args)
assert os.path.exists(
os.path.join(ensembler.core.default_project_dirnames.models,
'EGFR_HUMAN_D0', 'KC1D_HUMAN_D0_4KB8_D', 'model.pdb'))
assert os.path.exists(
os.path.join(ensembler.core.default_project_dirnames.models,
'EGFR_HUMAN_D0', 'KC1D_HUMAN_D0_4HNF_A', 'model.pdb'))
assert not os.path.exists(
os.path.join(ensembler.core.default_project_dirnames.models,
'EGFR_HUMAN_D0', 'KC1D_HUMAN_D0_4KB8_D',
'restraints.rsr.gz'))
assert not os.path.exists(
os.path.join(ensembler.core.default_project_dirnames.models,
'EGFR_HUMAN_D0', 'KC1D_HUMAN_D0_4HNF_A',
'restraints.rsr.gz'))
def test_gather_templates_from_pdb():
ref_templates_resolved_seq = """\
>KC1D_HUMAN_D0_4KB8_A
YRLGRKIGSGSFGDIYLGTDIAAGEEVAIKLECVKTKHPQLHIESKIYKMMQGGVGIPTI
RWCGAEGDYNVMVMELLGPSLEDLFNFCSRKFSLKTVLLLADQMISRIEYIHSKNFIHRD
VKPDNFLMGLGKKGNLVYIIDFGLAKKYGTARYASINTHLGIEQSRRDDLESLGYVLMYF
NLGSLPWQGLKERISEKKMSTPIEVLCKGYPSEFATYLNFCRSLRFDDKPDYSYLRQLFR
NLF
>KC1D_HUMAN_D0_4KB8_D
YRLGRKIGDIYLGTDIAAGEEVAIKLECPQLHIESKIYKMMQGGVGIPTIRWCGAEGDYN
VMVMELLGPSLEDLFNFCSRKFSLKTVLLLADQMISRIEYIHSKNFIHRDVKPDNFLMGL
GKKGNLVYIIDFGLAKKYRDAQHIPYRENKNLTGTARYASINTHLGIEQSRRDDLESLGY
VLMYFNLGSLPWQGLKAATKRQKYERISEKKMSTPIEVLCKGYPSEFATYLNFCRSLRFD
DKPDYSYLRQLFRNLF
"""
with integrationtest_context(set_up_project_stage='targets'):
pdbids = ['4KB8']
chainids = {'4KB8': ['A', 'D']}
uniprot_domain_regex = '^Protein kinase'
ensembler.initproject.gather_templates_from_pdb(pdbids,
uniprot_domain_regex,
chainids=chainids)
assert open(
os.path.join(ensembler.core.default_project_dirnames.templates,
'templates-resolved-seq.fa')).read(
) == ref_templates_resolved_seq
def test_get_structure_files_for_single_pdbchain():
with integrationtest_context(set_up_project_stage='targets'):
ensembler.initproject.get_structure_files_for_single_pdbchain('1OPL')
assert os.path.exists(os.path.join(
ensembler.core.default_project_dirnames.structures_pdb, '1OPL.pdb.gz'
))
assert os.path.exists(os.path.join(
ensembler.core.default_project_dirnames.structures_sifts, '1OPL.xml.gz'
))
def test_cluster_models_command():
with integrationtest_context(set_up_project_stage='modeled'):
args = {
'--targetsfile': False,
'--targets': False,
'--cutoff': False,
'--verbose': False,
'--help': False,
}
ensembler.cli_commands.cluster.dispatch(args)
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_cluster_models_command():
with integrationtest_context(set_up_project_stage='modeled'):
args = {
'--targetsfile': False,
'--targets': False,
'--cutoff': False,
'--verbose': False,
'--help': False,
}
ensembler.cli_commands.cluster.dispatch(args)
def test_refine_implicit_md_short():
with integrationtest_context(set_up_project_stage='clustered'):
targetid = 'EGFR_HUMAN_D0'
templateid = 'KC1D_HUMAN_D0_4KB8_D'
#targetid = 'MYB_HUMAN_D0'
#templateid = 'MYB_MOUSE_D0_1GUU'
refine_implicit_md(process_only_these_targets=[targetid],
process_only_these_templates=[templateid],
sim_length=2.0 * unit.femtosecond,
nsteps_per_iteration=1,
minimization_steps=1,
loglevel='debug')
implicit_metadata_filepath = os.path.join(
default_project_dirnames.models, targetid,
'refine_implicit_md-meta0.yaml')
implicit_model_filepath = os.path.join(default_project_dirnames.models,
targetid, templateid,
'implicit-refined.pdb.gz')
implicit_energies_filepath = os.path.join(
default_project_dirnames.models, targetid, templateid,
'implicit-energies.txt')
implicit_log_filepath = os.path.join(default_project_dirnames.models,
targetid, templateid,
'implicit-log.yaml')
assert os.path.exists(implicit_model_filepath
), "%s does not exist" % implicit_model_filepath
assert os.path.exists(
implicit_energies_filepath
), "%s does not exist" % implicit_energies_filepath
assert os.path.exists(
implicit_log_filepath), "%s does not exist" % implicit_log_filepath
with open(implicit_log_filepath) as implicit_log_file:
implicit_log = yaml.load(implicit_log_file)
assert implicit_log.get('finished') is True
assert implicit_log.get('successful') is True
assert implicit_log.get('ph') == 8.0
assert os.path.exists(implicit_metadata_filepath)
with open(implicit_metadata_filepath) as implicit_metadata_file:
implicit_metadata = yaml.load(implicit_metadata_file)
assert implicit_metadata.get('refine_implicit_md').get(
'custom_residue_variants'
) == {
'EGFR_HUMAN_D0': {
49: 'ASH'
}
#assert implicit_metadata.get('refine_implicit_md').get('custom_residue_variants') == {
# 'MYB_HUMAN_D0': {47: 'ASH'}
}
implicit_model_traj = mdtraj.load_pdb(implicit_model_filepath)
resis = [resi for resi in implicit_model_traj.top.residues]
resi49 = resis[49]
resi49_atom_strings = [str(atom) for atom in resi49.atoms]
assert 'ASP50-HD2' in resi49_atom_strings
def test_get_structure_files_for_single_pdbchain():
with integrationtest_context(set_up_project_stage='targets'):
ensembler.initproject.get_structure_files_for_single_pdbchain('1OPL')
assert os.path.exists(
os.path.join(
ensembler.core.default_project_dirnames.structures_pdb,
'1OPL.pdb.gz'))
assert os.path.exists(
os.path.join(
ensembler.core.default_project_dirnames.structures_sifts,
'1OPL.xml.gz'))
def test_get_structure_files_bad_structure_dir():
with integrationtest_context(set_up_project_stage='targets'):
pdbchains = [{'pdbid': '1OPL'}]
ensembler.initproject.get_structure_files(pdbchains,
structure_dirs=['BlAh1'])
assert os.path.exists(
os.path.join(
ensembler.core.default_project_dirnames.structures_pdb,
'1OPL.pdb.gz'))
assert os.path.exists(
os.path.join(
ensembler.core.default_project_dirnames.structures_sifts,
'1OPL.xml.gz'))
def test_get_structure_files_bad_structure_dir():
with integrationtest_context(set_up_project_stage='targets'):
pdbchains = [
{
'pdbid': '1OPL'
}
]
ensembler.initproject.get_structure_files(pdbchains, structure_dirs=['BlAh1'])
assert os.path.exists(os.path.join(
ensembler.core.default_project_dirnames.structures_pdb, '1OPL.pdb.gz'
))
assert os.path.exists(os.path.join(
ensembler.core.default_project_dirnames.structures_sifts, '1OPL.xml.gz'
))
def test_package_for_fah():
with integrationtest_context(set_up_project_stage='refined_explicit'):
package_for_fah(process_only_these_targets=['EGFR_HUMAN_D0'],
process_only_these_templates=[
'KC1D_HUMAN_D0_4HNF_A', 'KC1D_HUMAN_D0_4KB8_D'
])
packaged_project_base_path = os.path.join(
default_project_dirnames.packaged_models, 'fah-projects',
'EGFR_HUMAN_D0')
assert os.path.exists(packaged_project_base_path)
assert os.path.exists(os.path.join(packaged_project_base_path, 'RUN0'))
assert os.path.exists(os.path.join(packaged_project_base_path, 'RUN1'))
target_filenames = [
'system.xml',
'integrator.xml',
]
for target_filename in target_filenames:
assert os.path.exists(
os.path.join(packaged_project_base_path, target_filename))
run_filenames = [
'template.txt',
'system.pdb',
'protein.pdb',
'sequence-identity.txt',
'state0.xml',
]
for run_id in range(2):
for run_filename in run_filenames:
assert os.path.exists(
os.path.join(packaged_project_base_path,
'RUN{}'.format(run_id), run_filename))
# test whether kinetic energy in new state file is reasonable
test_state_filepath = os.path.join(packaged_project_base_path, 'RUN0',
'state0.xml')
with open(test_state_filepath) as test_state_file:
test_state = mm.XmlSerializer.deserialize(test_state_file.read())
ref_state_filepath = get_installed_resource_filename(
os.path.join('tests', 'example_project', 'models', 'EGFR_HUMAN_D0',
'KC1D_HUMAN_D0_4HNF_A', 'explicit-state.xml.gz'))
with gzip.open(ref_state_filepath) as ref_state_file:
ref_state = mm.XmlSerializer.deserialize(ref_state_file.read())
test_state_kinetic_energy = test_state.getKineticEnergy()
ref_state_kinetic_energy = ref_state.getKineticEnergy()
assert abs(test_state_kinetic_energy -
ref_state_kinetic_energy) < ref_state_kinetic_energy
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_build_models_command():
with integrationtest_context(set_up_project_stage='aligned'):
args = {
'--targets': 'EGFR_HUMAN_D0',
'--targetsfile': None,
'--model_seqid_cutoff': None,
'--templates': ','.join(['KC1D_HUMAN_D0_4KB8_D', 'KC1D_HUMAN_D0_4HNF_A']),
'--templatesfile': None,
'--write_modeller_restraints_file': None,
'--verbose': False,
'--help': False,
}
ensembler.cli_commands.build_models.dispatch(args)
assert os.path.exists(os.path.join(ensembler.core.default_project_dirnames.models, 'EGFR_HUMAN_D0', 'KC1D_HUMAN_D0_4KB8_D', 'model.pdb'))
assert os.path.exists(os.path.join(ensembler.core.default_project_dirnames.models, 'EGFR_HUMAN_D0', 'KC1D_HUMAN_D0_4HNF_A', 'model.pdb'))
assert not os.path.exists(os.path.join(ensembler.core.default_project_dirnames.models, 'EGFR_HUMAN_D0', 'KC1D_HUMAN_D0_4KB8_D', 'restraints.rsr.gz'))
assert not os.path.exists(os.path.join(ensembler.core.default_project_dirnames.models, 'EGFR_HUMAN_D0', 'KC1D_HUMAN_D0_4HNF_A', 'restraints.rsr.gz'))
def test_refine_implicit_md_short():
with integrationtest_context(set_up_project_stage='clustered'):
targetid = 'EGFR_HUMAN_D0'
templateid = 'KC1D_HUMAN_D0_4KB8_D'
refine_implicit_md(
process_only_these_targets=[targetid],
process_only_these_templates=[templateid],
sim_length=2.0*unit.femtosecond,
nsteps_per_iteration=1,
minimization_steps=1,
loglevel='debug'
)
implicit_metadata_filepath = os.path.join(
default_project_dirnames.models, targetid, 'refine_implicit_md-meta0.yaml'
)
implicit_model_filepath = os.path.join(
default_project_dirnames.models, targetid, templateid, 'implicit-refined.pdb.gz'
)
implicit_energies_filepath = os.path.join(
default_project_dirnames.models, targetid, templateid, 'implicit-energies.txt'
)
implicit_log_filepath = os.path.join(
default_project_dirnames.models, targetid, templateid, 'implicit-log.yaml'
)
assert all(map(
os.path.exists,
[implicit_model_filepath, implicit_energies_filepath, implicit_log_filepath]
))
with open(implicit_log_filepath) as implicit_log_file:
implicit_log = yaml.load(implicit_log_file)
assert implicit_log.get('finished') is True
assert implicit_log.get('successful') is True
assert implicit_log.get('ph') == 8.0
assert os.path.exists(implicit_metadata_filepath)
with open(implicit_metadata_filepath) as implicit_metadata_file:
implicit_metadata = yaml.load(implicit_metadata_file)
assert implicit_metadata.get('refine_implicit_md').get('custom_residue_variants') == {
'EGFR_HUMAN_D0': {49: 'ASH'}
}
implicit_model_traj = mdtraj.load_pdb(implicit_model_filepath)
resis = [resi for resi in implicit_model_traj.top.residues]
resi49 = resis[49]
resi49_atom_strings = [str(atom) for atom in resi49.atoms]
assert 'ASP50-HD2' in resi49_atom_strings
def test_molprobity_validation():
target_id = "EGFR_HUMAN_D0"
template_ids = ["KC1D_HUMAN_D0_4KB8_D", "KC1D_HUMAN_D0_4HNF_A"]
with integrationtest_context("refined_explicit"):
molprobity_validation(target_id)
for template_id in template_ids:
results_filepath = os.path.join(
default_project_dirnames.models, target_id, template_id, "molprobity-refine_explicit_md.yaml"
)
assert os.path.exists(results_filepath)
with open(results_filepath) as results_file:
results_dict = yaml.load(results_file)
assert results_dict.get("pct_badbonds") == ref_pct_badbonds[template_id]
target_results_filepath = os.path.join(
default_project_dirnames.models, target_id, "validation_scores_sorted-molprobity-refine_explicit_md"
)
with open(target_results_filepath) as target_results_file:
target_results = target_results_file.read().splitlines()
assert target_results[0] == "KC1D_HUMAN_D0_4KB8_D 3.828"
assert target_results[1] == "KC1D_HUMAN_D0_4HNF_A 4.035"
def test_gather_templates_from_pdb():
ref_templates_resolved_seq = """\
>KC1D_HUMAN_D0_4KB8_A
YRLGRKIGSGSFGDIYLGTDIAAGEEVAIKLECVKTKHPQLHIESKIYKMMQGGVGIPTI
RWCGAEGDYNVMVMELLGPSLEDLFNFCSRKFSLKTVLLLADQMISRIEYIHSKNFIHRD
VKPDNFLMGLGKKGNLVYIIDFGLAKKYGTARYASINTHLGIEQSRRDDLESLGYVLMYF
NLGSLPWQGLKERISEKKMSTPIEVLCKGYPSEFATYLNFCRSLRFDDKPDYSYLRQLFR
NLF
>KC1D_HUMAN_D0_4KB8_D
YRLGRKIGDIYLGTDIAAGEEVAIKLECPQLHIESKIYKMMQGGVGIPTIRWCGAEGDYN
VMVMELLGPSLEDLFNFCSRKFSLKTVLLLADQMISRIEYIHSKNFIHRDVKPDNFLMGL
GKKGNLVYIIDFGLAKKYRDAQHIPYRENKNLTGTARYASINTHLGIEQSRRDDLESLGY
VLMYFNLGSLPWQGLKAATKRQKYERISEKKMSTPIEVLCKGYPSEFATYLNFCRSLRFD
DKPDYSYLRQLFRNLF
"""
with integrationtest_context(set_up_project_stage='targets'):
pdbids = ['4KB8']
chainids = {'4KB8': ['A', 'D']}
uniprot_domain_regex = '^Protein kinase'
ensembler.initproject.gather_templates_from_pdb(pdbids, uniprot_domain_regex, chainids=chainids)
assert open(os.path.join(ensembler.core.default_project_dirnames.templates, 'templates-resolved-seq.fa')).read() == ref_templates_resolved_seq
def test_align_command():
ref_resources_dirpath = get_installed_resource_filename(
os.path.join('tests', '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 test_molprobity_validation():
target_id = 'EGFR_HUMAN_D0'
template_ids = ['KC1D_HUMAN_D0_4KB8_D', 'KC1D_HUMAN_D0_4HNF_A']
with integrationtest_context('refined_explicit'):
molprobity_validation(target_id)
for template_id in template_ids:
results_filepath = os.path.join(
default_project_dirnames.models, target_id, template_id,
'molprobity-refine_explicit_md.yaml')
assert os.path.exists(results_filepath)
with open(results_filepath) as results_file:
results_dict = yaml.load(results_file)
assert results_dict.get(
'pct_badbonds') == ref_pct_badbonds[template_id]
target_results_filepath = os.path.join(
default_project_dirnames.models, target_id,
'validation_scores_sorted-molprobity-refine_explicit_md')
with open(target_results_filepath) as target_results_file:
target_results = target_results_file.read().splitlines()
assert target_results[0] == 'KC1D_HUMAN_D0_4KB8_D 3.828'
assert target_results[1] == 'KC1D_HUMAN_D0_4HNF_A 4.035'
def test_cluster_models():
with integrationtest_context(set_up_project_stage='modeled'):
ensembler.modeling.cluster_models()
def test_cluster_models():
with integrationtest_context(set_up_project_stage='modeled'):
ensembler.modeling.cluster_models()
def test_package_for_fah():
with integrationtest_context(set_up_project_stage='refined_explicit'):
package_for_fah(
process_only_these_targets=['EGFR_HUMAN_D0'],
process_only_these_templates=[
'KC1D_HUMAN_D0_4HNF_A',
'KC1D_HUMAN_D0_4KB8_D'
]
)
packaged_project_base_path = os.path.join(
default_project_dirnames.packaged_models,
'fah-projects',
'EGFR_HUMAN_D0'
)
assert os.path.exists(packaged_project_base_path)
assert os.path.exists(os.path.join(
packaged_project_base_path,
'RUN0'
))
assert os.path.exists(os.path.join(
packaged_project_base_path,
'RUN1'
))
target_filenames = [
'system.xml',
'integrator.xml',
]
for target_filename in target_filenames:
assert os.path.exists(os.path.join(
packaged_project_base_path,
target_filename
))
run_filenames = [
'template.txt',
'system.pdb',
'protein.pdb',
'sequence-identity.txt',
'state0.xml',
]
for run_id in range(2):
for run_filename in run_filenames:
assert os.path.exists(os.path.join(
packaged_project_base_path,
'RUN{}'.format(run_id),
run_filename
))
# test whether kinetic energy in new state file is reasonable
test_state_filepath = os.path.join(packaged_project_base_path, 'RUN0', 'state0.xml')
with open(test_state_filepath) as test_state_file:
test_state = mm.XmlSerializer.deserialize(test_state_file.read())
ref_state_filepath = get_installed_resource_filename(os.path.join(
'tests', 'example_project', 'models',
'EGFR_HUMAN_D0', 'KC1D_HUMAN_D0_4HNF_A', 'explicit-state.xml.gz'
))
with gzip.open(ref_state_filepath) as ref_state_file:
ref_state = mm.XmlSerializer.deserialize(ref_state_file.read())
test_state_kinetic_energy = test_state.getKineticEnergy()
ref_state_kinetic_energy = ref_state.getKineticEnergy()
assert abs(
test_state_kinetic_energy - ref_state_kinetic_energy
) < ref_state_kinetic_energy
def test_mktraj_implicit_start():
with integrationtest_context(set_up_project_stage="refined_explicit"):
MkTrajImplicitStart(targetid="EGFR_HUMAN_D0", loglevel="debug")
def test_loopmodel_logs():
with integrationtest_context(set_up_project_stage='templates_modeled_loops'):
loopmodel_logs = LoopmodelLogs()
loopmodel_logs.add_missing_resis_data()
def test_get_valid_model_filepaths():
targetid = 'EGFR_HUMAN_D0'
templateids = ['KC1D_HUMAN_D0_4KB8_D', 'KC1D_HUMAN_D0_4HNF_A']
with integrationtest_context('refined_implicit'):
valid_model_filenames = get_valid_model_ids('refine_implicit_md', targetid)
assert all([fpath in templateids for fpath in valid_model_filenames])
def test_mktraj_implicit_start():
with integrationtest_context(set_up_project_stage='refined_explicit'):
MkTrajImplicitStart(targetid='EGFR_HUMAN_D0', loglevel='debug')
def test_loopmodel_logs():
with integrationtest_context(
set_up_project_stage='templates_modeled_loops'):
loopmodel_logs = LoopmodelLogs()
loopmodel_logs.add_missing_resis_data()
