From 27485ce93f4efb5cdfe5f3802a689e06a1df47f4 Mon Sep 17 00:00:00 2001 From: Felix Simkovic Date: Tue, 26 Jun 2018 18:23:16 +0100 Subject: [PATCH] fixed some small bits --- ample/util/options_processor.py | 51 ++++++++++++++------------------- 1 file changed, 21 insertions(+), 30 deletions(-) diff --git a/ample/util/options_processor.py b/ample/util/options_processor.py index 04e4a4a9..acad7aa5 100644 --- a/ample/util/options_processor.py +++ b/ample/util/options_processor.py @@ -162,7 +162,7 @@ def process_modelling_options(optd): raise RuntimeError("Import cluster cannot find directory: {0}".format(optd['cluster_dir'])) if not glob.glob(os.path.join(optd['cluster_dir'], "*.pdb")): raise RuntimeError("Import cluster cannot find pdbs in directory: {0}".format(optd['cluster_dir'])) - logger.info("Importing pre-clustered models from directory: {0}\n".format(optd['cluster_dir'])) + logger.info("Importing pre-clustered models from directory: %d\n", optd['cluster_dir']) optd['cluster_method'] = 'import' optd['make_frags'] = False optd['make_models'] = False @@ -206,7 +206,7 @@ def process_modelling_options(optd): raise RuntimeError("Cannot import both models and ensembles/clusters!") # NMR Checks if optd['nmr_model_in']: - logger.info("Using nmr_model_in file: {0}".format(optd['nmr_model_in'])) + logger.info("Using nmr_model_in file: %s", optd['nmr_model_in']) if not os.path.isfile(optd['nmr_model_in']): msg = "nmr_model_in flag given, but cannot find file: {0}".format(optd['nmr_model_in']) exit_util.exit_error(msg) @@ -300,7 +300,7 @@ def process_modelling_options(optd): try: optd['scwrl_exe'] = ample_util.find_exe(optd['scwrl_exe']) except ample_util.FileNotFoundError as e: - logger.info("Cannot find Scwrl executable: {0}".format(optd['scwrl_exe'])) + logger.info("Cannot find Scwrl executable: %s", optd['scwrl_exe']) if optd['use_scwrl']: raise (e) if "subcluster_radius_thresholds" in optd and not optd["subcluster_radius_thresholds"]: @@ -373,15 +373,15 @@ def process_mr_options(optd): optd['shelxe_rebuild_arpwarp'] = True optd['shelxe_rebuild_buccaneer'] = True - # Model building programs if optd['refine_rebuild_arpwarp'] or optd['shelxe_rebuild_arpwarp']: - if not ('warpbin' in os.environ and os.path.isfile(os.path.join(os.environ['warpbin'], "auto_tracing.sh"))): - logger.warn('Cannot find arpwarp script! Disabling use of arpwarp.') - optd['refine_rebuild_arpwarp'] = False - optd['shelxe_rebuild_arpwarp'] = False - else: - logger.info('Using arpwarp script: %s', os.path.join(os.environ['warpbin'], "auto_tracing.sh")) - # Print out what is being done + auto_tracing_sh = os.path.join(os.environ['warpbin'], "auto_tracing.sh") + if 'warpbin' in os.environ and os.path.isfile(auto_tracing_sh): + logger.info('Using arpwarp script: %s', auto_tracing_sh) + else: + logger.warn('Cannot find arpwarp script! Disabling use of arpwarp.') + optd['refine_rebuild_arpwarp'] = False + optd['shelxe_rebuild_arpwarp'] = False + if optd['refine_rebuild_arpwarp'] or optd['shelxe_rebuild_arpwarp']: logger.info('Rebuilding in Bucaneer') else: @@ -438,7 +438,7 @@ def process_restart_options(optd): """ if not optd['restart_pkl']: return optd - logger.info('Restarting from existing pkl file: {0}'.format(optd['restart_pkl'])) + logger.info('Restarting from existing pkl file: %s', optd['restart_pkl']) # Go through and see what we need to do # Reset all variables for doing stuff - otherwise we will always restart from the earliest point @@ -452,9 +452,7 @@ def process_restart_options(optd): # job and we only set benchmark mode on seeing the native_pdb if optd['native_pdb']: if not os.path.isfile(optd['native_pdb']): - msg = "Cannot find native_pdb: {0}".format(optd['native_pdb']) - logger.critical(msg) - raise RuntimeError(msg) + raise RuntimeError("Cannot find native_pdb: {0}".format(optd['native_pdb'])) optd['benchmark_mode'] = True logger.info('Restart using benchmark mode') @@ -467,7 +465,7 @@ def process_restart_options(optd): if optd['do_mr']: if len(optd['mrbump_scripts']): - logger.info('Restarting from unfinished mrbump scripts: {0}'.format(optd['mrbump_scripts'])) + logger.info('Restarting from unfinished mrbump scripts: %s', optd['mrbump_scripts']) # Purge unfinished jobs for spath in optd['mrbump_scripts']: directory, script = os.path.split(spath) @@ -481,17 +479,16 @@ def process_restart_options(optd): shutil.rmtree(jobdir) elif 'ensembles' in optd and optd['ensembles'] and len(optd['ensembles']): # Rerun from ensembles - check for data/ensembles are ok? - logger.info('Restarting from existing ensembles: {0}'.format(optd['ensembles'])) + logger.info('Restarting from existing ensembles: %s', optd['ensembles']) elif 'models_dir' in optd and optd['models_dir'] and os.path.isdir(optd['models_dir']): - logger.info('Restarting from existing models: {0}'.format(optd['models_dir'])) - # Check the models + logger.info('Restarting from existing models: %s', optd['models_dir']) allsame = False if optd['homologs'] else True if not pdb_edit.check_pdb_directory(optd['models_dir'], sequence=None, single=True, allsame=allsame): - msg = "Error importing restart models: {0}".format(optd['models_dir']) - exit_util.exit_error(msg) + raise RuntimeError("Error importing restart models: {0}".format(optd['models_dir'])) + optd['make_ensembles'] = True elif optd['frags_3mers'] and optd['frags_9mers']: - logger.info('Restarting from existing fragments: {0}, {1}'.format(optd['frags_3mers'], optd['frags_9mers'])) + logger.info('Restarting from existing fragments: %s, %s', optd['frags_3mers'], optd['frags_9mers']) optd['make_models'] = True return optd @@ -527,16 +524,10 @@ def restart_amoptd(optd): """ if not optd['restart_pkl']: return optd - logger.info('Restarting from existing pkl file: {0}'.format(optd['restart_pkl'])) - # We use the old dictionary, but udpate it with any new values + logger.info('Restarting from existing pkl file: %s', optd['restart_pkl']) optd_old = ample_util.read_amoptd(optd['restart_pkl']) - - # Now update any variables that were given on the command-line for k in optd['cmdline_flags']: - logger.debug("Restart updating amopt variable: {0} : {1}".format(k, optd[k])) + logger.debug("Restart updating amopt variable: %s : %s", k, str(optd[k])) optd_old[k] = optd[k] - - # We can now replace the old dictionary with this new one optd = optd_old - return optd