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 molprobity_validation(targetid, ensembler_stage=None, loglevel=None):
set_loglevel(loglevel)
valid_model_ids = []
if mpistate.rank == 0:
if ensembler_stage is None:
ensembler_stage = get_most_advanced_ensembler_modeling_stage(
targetid)
valid_model_ids = get_valid_model_ids(ensembler_stage, targetid)
if ensembler_stage is None:
ensembler_stage = mpistate.comm.bcast(ensembler_stage, root=0)
valid_model_ids = mpistate.comm.bcast(valid_model_ids, root=0)
nvalid_model_ids = len(valid_model_ids)
model_structure_filename = model_filenames_by_ensembler_stage[
ensembler_stage]
models_target_dir = os.path.join(default_project_dirnames.models, targetid)
molprobity_results_filepath = os.path.join(
models_target_dir,
'validation_scores_sorted-molprobity-{}'.format(ensembler_stage))
molprobity_scores_sublist = []
for model_index in range(mpistate.rank, nvalid_model_ids, mpistate.size):
model_id = valid_model_ids[model_index]
logger.debug('MPI process {} working on model {}'.format(
mpistate.rank, model_id))
molprobity_score = run_molprobity_oneline_analysis_and_write_results(
targetid,
model_id,
ensembler_stage,
model_structure_filename=model_structure_filename,
models_target_dir=models_target_dir,
)
molprobity_scores_sublist.append((model_id, molprobity_score))
molprobity_scores_gathered_list = mpistate.comm.gather(
molprobity_scores_sublist, root=0)
if mpistate.rank == 0:
molprobity_scores_list_of_tuples = [
item for sublist in molprobity_scores_gathered_list
for item in sublist
]
molprobity_scores_sorted = sorted(molprobity_scores_list_of_tuples,
key=lambda x: x[1])
write_molprobity_scores_list(molprobity_scores_sorted,
molprobity_results_filepath)
def molprobity_validation(targetid, ensembler_stage=None, loglevel=None):
set_loglevel(loglevel)
valid_model_ids = []
if mpistate.rank == 0:
if ensembler_stage is None:
ensembler_stage = get_most_advanced_ensembler_modeling_stage(targetid)
valid_model_ids = get_valid_model_ids(ensembler_stage, targetid)
if ensembler_stage is None:
ensembler_stage = mpistate.comm.bcast(ensembler_stage, root=0)
valid_model_ids = mpistate.comm.bcast(valid_model_ids, root=0)
nvalid_model_ids = len(valid_model_ids)
model_structure_filename = model_filenames_by_ensembler_stage[ensembler_stage]
models_target_dir = os.path.join(default_project_dirnames.models, targetid)
molprobity_results_filepath = os.path.join(
models_target_dir, "validation_scores_sorted-molprobity-{}".format(ensembler_stage)
)
molprobity_scores_sublist = []
for model_index in range(mpistate.rank, nvalid_model_ids, mpistate.size):
model_id = valid_model_ids[model_index]
logger.debug("MPI process {} working on model {}".format(mpistate.rank, model_id))
molprobity_score = run_molprobity_oneline_analysis_and_write_results(
targetid,
model_id,
ensembler_stage,
model_structure_filename=model_structure_filename,
models_target_dir=models_target_dir,
)
molprobity_scores_sublist.append((model_id, molprobity_score))
molprobity_scores_gathered_list = mpistate.comm.gather(molprobity_scores_sublist, root=0)
if mpistate.rank == 0:
molprobity_scores_list_of_tuples = [item for sublist in molprobity_scores_gathered_list for item in sublist]
molprobity_scores_sorted = sorted(molprobity_scores_list_of_tuples, key=lambda x: x[1])
write_molprobity_scores_list(molprobity_scores_sorted, molprobity_results_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])
