def set_top_level_directory(self):
"""
Sets top level working folder to contain all simulation steps.
"""
working_folder = os.path.abspath("{}_Pele".format(self.env.residue))
if not self.env.folder:
self.working_folder = (helpers.get_next_peledir(working_folder)
if not self.env.adaptive_restart else
helpers.get_next_peledir(working_folder))
else:
self.working_folder = os.path.abspath(self.env.folder)
def set_working_folder(self):
"""
Sets top level working folder named after the residue (unless the user specified 'working_folder' in YAML.
Folders for each mutation subset are enumerated automatically and placed within the top level directory.
"""
resname_folder = os.path.abspath("{}_Pele".format(self.env.residue))
if not self.env.folder:
self.working_folder = (helpers.get_next_peledir(resname_folder)
if not self.env.adaptive_restart else
helpers.get_latest_peledir(resname_folder))
else:
self.working_folder = os.path.abspath(self.env.folder)
def _set_params_global(self):
"""
Set parameters for global exploration. Users can choose their own working folder.
"""
self.original_dir = os.path.abspath(os.getcwd())
working_folder = os.path.abspath("{}_Pele".format(self.args.residue))
if not self.args.folder:
self.working_folder = (get_next_peledir(working_folder)
if not self.args.adaptive_restart else
get_latest_peledir(working_folder))
else:
self.working_folder = os.path.abspath(self.args.folder)
self.args.folder = os.path.join(self.working_folder,
"1_global_exploration")
self.args.full = True # needed for global exploration
def build_adaptive_variables(self, args):
"""
It builds the parameters for adaptive, according to the arguments
that are supplied, and returns the corresponding Parameters
instance.
Parameters
----------
args : a YamlParser object
The YamlParser object containing the input parameters chosen
by the user
Returns
-------
parameters : a Parameters object
The Parameters object containing the parameters for PELE
"""
import os
from pele_platform.features import adaptive
from pele_platform.Utilities.Helpers import helpers
# Define main PELE directory
main_dir = os.path.abspath("{}_Pele".format(args.residue))
# Set the PELE directory
# In case that folder is not set by the user, we will try to suggest
# the best candidate considering whether we want to restart a previous
# simulation or we want to run a new one from scratch.
if not args.folder:
# If the simulation is being restarted (after debug), adaptive_restarted (from last epoch)
# or if we're running only_analysis we need to retrieve the LAST pele_dir. Otherwise create a new one
# with a new index.
if args.restart or args.adaptive_restart or args.only_analysis:
pele_dir = helpers.get_latest_peledir(main_dir)
else:
pele_dir = helpers.get_next_peledir(main_dir)
# In case that the user has specified the output folder, we will
# use it, regardless it already exists.
else:
pele_dir = os.path.abspath(args.folder)
if (args.restart or args.adaptive_restart
or args.only_analysis) and not os.path.exists(pele_dir):
raise OSError(
f"Directory {pele_dir} was not found. Please ensure you set the correct path to the top level"
f" directory, e.g. 'LIG_Pele' using the 'working_folder' flag when restarting or analysing "
f"the simulation.")
# Retrieve the specific args for adaptive
specific_args = adaptive.retrieve_software_settings(args, pele_dir)
# Add pele_dir
specific_args['pele_dir'] = pele_dir
# Initialize Parameters object
self._parameters = Parameters(args, specific_args)
self._initialized = True
# Set software
self.parameters.software = "Adaptive"
return self.parameters
def run_ppi(parsed_yaml: dict) -> (pv.ParametersBuilder, pv.ParametersBuilder):
# Let user choose working folder
original_dir = os.path.abspath(os.getcwd())
working_folder = os.path.abspath("{}_Pele".format(parsed_yaml.residue))
if not parsed_yaml.folder:
working_folder = get_next_peledir(working_folder) if not parsed_yaml.adaptive_restart else get_latest_peledir(
working_folder)
else:
working_folder = os.path.abspath(parsed_yaml.folder)
# Set main folder
parsed_yaml.folder = os.path.join(working_folder, "1_interface_exploration")
# get arguments from input.yaml
n_waters = parsed_yaml.n_waters
parsed_yaml.n_waters = None
protein_file = parsed_yaml.system
chain = parsed_yaml.protein
ligand_pdb = parsed_yaml.ligand_pdb
# Parametrize hetero molecules before merging PDBs, if using peleffy. Otherwise they will go through Plop in
# Adaptive.simulation.
if parsed_yaml.use_peleffy:
templates, rotamers, to_skip = parametrize_hetero_ppi(parsed_yaml)
parsed_yaml.template = parsed_yaml.template.extend(templates) if parsed_yaml.template else templates
parsed_yaml.rotamers = parsed_yaml.rotamers.extend(rotamers) if parsed_yaml.rotamers else rotamers
parsed_yaml.skip_ligand_prep = parsed_yaml.skip_ligand_prep.extend(to_skip) if parsed_yaml.skip_ligand_prep else to_skip
# no waters in the first simulation
parsed_yaml.water_arg = None
parsed_yaml.use_peleffy = parsed_yaml.use_peleffy if parsed_yaml.use_peleffy is not None else False
# remove chains except for "protein" flag
protein_file = prepare_structure(protein_file, ligand_pdb, chain, True, peleffy=parsed_yaml.use_peleffy)
parsed_yaml.system = protein_file
# start simulation 1 - induced fit
parsed_yaml.induced_fit_long = True
simulation1 = si.run_adaptive(parsed_yaml)
simulation1_path = os.path.join(simulation1.pele_dir, simulation1.output)
# cluster best structures
if not parsed_yaml.debug:
with cd(simulation1_path):
cluster_best_structures("5", n_components=simulation1.n_components,
residue=simulation1.residue, topology=simulation1.topology,
directory=working_folder, logger=simulation1.logger)
# adjust original input.yaml
if not parsed_yaml.skip_refinement:
parsed_yaml.system = os.path.join(working_folder, "refinement_input/*.pdb")
parsed_yaml.folder = os.path.join(working_folder, "2_refinement_simulation")
parsed_yaml.induced_fit_long = None
parsed_yaml.ppi = None
parsed_yaml.poses = None
parsed_yaml.rescoring = True
del parsed_yaml.water_arg
# Set waters only if specified by user
if n_waters != 0:
parsed_yaml.waters = "all_waters"
parsed_yaml.n_waters = n_waters
else:
parsed_yaml.waters = None
parsed_yaml.n_waters = n_waters
parsed_yaml.adaptive_restart = False
if not parsed_yaml.test:
parsed_yaml.iterations = 1
parsed_yaml.steps = 100
parsed_yaml.box_center = simulation1.box_center
parsed_yaml.box_radius = 100 # We should have a look at how to set no box but at the moment super big
# start simulation 2 - minimisation
with cd(original_dir):
if not parsed_yaml.debug:
simulation2 = launch_simulation(parsed_yaml)
else:
simulation2 = None
else:
simulation2 = None
return simulation1, simulation2
def build_adaptive_variables(self, args):
"""
It builds the parameters for adaptive, according to the arguments
that are supplied, and returns the corresponding Parameters
instance.
Parameters
----------
args : a YamlParser object
The YamlParser object containing the input parameters chosen
by the user
Returns
-------
parameters : a Parameters object
The Parameters object containing the parameters for PELE
"""
import os
from pele_platform.constants import constants
from pele_platform.features import adaptive
from pele_platform.Utilities.Helpers import helpers
# Define main PELE directory
main_dir = os.path.abspath("{}_Pele".format(args.residue))
# Set the PELE directory
# In case that folder is not set by the user, we will try to suggest
# the best candidate considering whether we want to restart a previous
# simulation or we want to run a new one from scratch.
if not args.folder:
# Check if the simulation is being restarted or not
# TODO the restart flag is undocumented and counterintuitive
# since it apparently is doing the opposite of
# adaptive_restart
if args.restart in constants.FIRST_RESTART:
pele_dir = helpers.get_next_peledir(main_dir)
else:
pele_dir = helpers.get_latest_peledir(main_dir)
# Check if the adaptive simulation is being restarted or not
# Also check if we are only running the analysis
if args.adaptive_restart or args.only_analysis:
# Take the last folder name
pele_dir = helpers.get_latest_peledir(main_dir)
else:
# Get a new folder name
pele_dir = helpers.get_next_peledir(main_dir)
# In case that the user has specified the output folder, we will
# use it, regardless it already exists.
else:
pele_dir = os.path.abspath(args.folder)
# Retrieve the specific args for adaptive
specific_args = adaptive.retrieve_software_settings(args, pele_dir)
# Add pele_dir
specific_args['pele_dir'] = pele_dir
# Initialize Parameters object
self._parameters = Parameters(args, specific_args)
self._initialized = True
# Set software
self.parameters.software = "Adaptive"
return self.parameters