From d05717af05b72fceca6cd87127db91727e28a1b5 Mon Sep 17 00:00:00 2001 From: Marti Municoy Date: Sat, 28 Nov 2020 00:59:23 +0100 Subject: [PATCH] Improve logger information --- peleffy/forcefield/selectors.py | 4 ++++ peleffy/main.py | 14 +++++++++++++- peleffy/solvent/solvent.py | 2 +- 3 files changed, 18 insertions(+), 2 deletions(-) diff --git a/peleffy/forcefield/selectors.py b/peleffy/forcefield/selectors.py index 776f9cb7..e5d5afc1 100644 --- a/peleffy/forcefield/selectors.py +++ b/peleffy/forcefield/selectors.py @@ -47,6 +47,10 @@ def get_by_name(self, forcefield_name): >>> openff = selector.get_by_name('openff_unconstrained-1.2.1.offxml') """ + from peleffy.utils import Logger + + log = Logger() + log.info(' - Loading \'{}\''.format(forcefield_name)) from .forcefield import (OpenForceField, OPLS2005ForceField) diff --git a/peleffy/main.py b/peleffy/main.py index 8306f6c6..7c80052a 100644 --- a/peleffy/main.py +++ b/peleffy/main.py @@ -162,11 +162,18 @@ def run_peleffy(pdb_file, rotamer_library.to_file(output_handler.get_rotamer_library_path()) # Parameterize molecule with the selected force field + log.info(' - Parameterizing molecule') parameters = forcefield.parameterize(molecule, charge_method=charge_method) # Generate the molecular topology topology = Topology(molecule, parameters) + log.info(' - Parameterization results:') + log.info(' - {} atoms'.format(len(topology.atoms))) + log.info(' - {} bonds'.format(len(topology.bonds))) + log.info(' - {} torsions'.format(len(topology.angles))) + log.info(' - {} propers'.format(len(topology.propers))) + log.info(' - {} impropers'.format(len(topology.impropers))) # Generate the impact template impact = Impact(topology) @@ -177,7 +184,12 @@ def run_peleffy(pdb_file, solvent = OBC2(topology) solvent.to_file(output_handler.get_solvent_template_path()) - log.info(' - All files were generated successfully') + log.info(' - All files were generated successfully:') + log.info(' - {}'.format(output_handler.get_rotamer_library_path())) + log.info(' - {}'.format(output_handler.get_impact_template_path())) + if with_solvent: + log.info(' - {}'.format(output_handler.get_solvent_template_path())) + log.info('-' * 60) diff --git a/peleffy/solvent/solvent.py b/peleffy/solvent/solvent.py index 156defb5..fe6c885b 100644 --- a/peleffy/solvent/solvent.py +++ b/peleffy/solvent/solvent.py @@ -113,7 +113,7 @@ def _initialize_from_topology(self): molecular Topology. """ logger = Logger() - logger.info(' - Loading solvent parameters') + logger.info(' - Generating solvent parameters') from peleffy.utils.toolkits import OpenForceFieldToolkitWrapper