# Path: ensembler/core.py
# class MPIState:
# class DummyMPIState:
# class DummyMPIComm:
# class literal_str(str): pass
# class LogFile:
# class ManualOverrides:
# class TargetManualOverrides:
# class TemplateManualOverrides:
# class RefinementManualOverrides:
# class ProjectMetadata:
#     def __init__(self):
#     def __init__(self):
#     def Barrier(self):
#     def bcast(self, obj, root=0):
#     def gather(self, obj, root=0):
# def change_style(style, representer):
#     def new_representer(dumper, data):
# def get_utcnow_formatted():
# def strf_timedelta(delta_t):
# def check_project_toplevel_dir(raise_exception=True):
#     def __init__(self, log_filepath):
#     def log(self, new_log_data={}):
#     def __init__(self, manual_overrides_filepath=None):
#     def __init__(self, manual_overrides_yaml):
#     def __init__(self, manual_overrides_yaml):
#     def __init__(self, manual_overrides_yaml):
# def gen_metadata_filename(ensembler_stage, metadata_file_index):
#     def __init__(self, project_stage='init', target_id=None, project_toplevel_dir='.'):
#     def add_all_prev_metadata(self, project_stage):
#     def add_prev_metadata(self, project_stage):
#     def determine_latest_metadata_filepath(self, project_stage):
#     def metadata_dir_mapper(self, project_stage, target_id=None):
#     def metadata_file_basename_mapper(self, project_stage):
#     def determine_latest_metadata_file_index(self, project_stage):
#     def gen_metadata_filepath_from_dir_index_and_file_basename(self, dirpath, file_basename, index):
#     def add_data(self, data, project_stage=None):
#     def add_iteration_number_to_metadata(self, iter_number):
#     def write(self):
# def encode_url_query(uniprot_query):
#     def replace_all(text, replace_dict):
# def xpath_match_regex_case_sensitive(context, attrib_values, regex_str):
# def xpath_match_regex_case_insensitive(context, attrib_values, regex_str):
# def sequnwrap(sequence):
# def seqwrap(sequence, add_star=False):
# def construct_fasta_str(id, seq):
# def get_targets():
# def get_templates_resolved_seq():
# def get_templates_full_seq():
# def get_targets_and_templates():
# def find_loopmodel_executable():
# def check_ensembler_modeling_stage_first_model_file_exists(ensembler_stage, targetid):
# def check_ensembler_modeling_stage_metadata_exists(ensembler_stage, targetid):
# def check_ensembler_modeling_stage_complete(ensembler_stage, targetid):
# def get_most_advanced_ensembler_modeling_stage(targetid):
# def get_valid_model_ids(ensembler_stage, targetid):
# def select_templates_by_seqid_cutoff(targetid, seqid_cutoff=None):
# def select_templates_by_validation_score(targetid,
#                                          validation_score_cutoff=None,
#                                          validation_score_percentile=None
#                                          ):


import os
import datetime
import traceback
import gzip
import sys
import subprocess
import yaml
import warnings
import socket
import numpy as np
import Bio
import ensembler
import ensembler.version
import simtk.unit as unit
import simtk.openmm as openmm
import simtk.openmm.app as app
import simtk.openmm.version
        import time
        import time
    import os.path
        import gzip
from yaml.scanner import ScannerError
from collections import deque
from copy import deepcopy
from ensembler.core import mpistate, logger, ManualOverrides
                'model_seqid_cutoff': model_seqid_cutoff,
                'write_trajectory': write_trajectory,
                'include_disulfide_bonds': include_disulfide_bonds,
                'custom_residue_variants': custom_residue_variants,
                'ff': ff,
                'implicit_water_model': implicit_water_model,
                'sim_length': str(sim_length),
                'timestep': str(timestep),
                'temperature': str(temperature),
                'collision_rate': str(collision_rate),
                'cutoff': str(cutoff),
                'nsteps_per_iteration': nsteps_per_iteration,
                'ph': ph,
                'nsuccessful_refinements': nsuccessful_refinements,
                'python_version': sys.version.split('|')[0].strip(),
                'python_full_version': ensembler.core.literal_str(sys.version),
                'ensembler_version': ensembler.version.short_version,
                'ensembler_commit': ensembler.version.git_revision,
                'biopython_version': Bio.__version__,
                'openmm_version': simtk.openmm.version.short_version,
                'openmm_commit': simtk.openmm.version.git_revision,
            }

            project_metadata.add_data(metadata)
            project_metadata.write()

        mpistate.comm.Barrier()

    mpistate.comm.Barrier()
    if mpistate.rank == 0:

# Path: ensembler/core.py
# class MPIState:
# class DummyMPIState:
# class DummyMPIComm:
# class literal_str(str): pass
# class LogFile:
# class ManualOverrides:
# class TargetManualOverrides:
# class TemplateManualOverrides:
# class RefinementManualOverrides:
# class ProjectMetadata:
#     def __init__(self):
#     def __init__(self):
#     def Barrier(self):
#     def bcast(self, obj, root=0):
#     def gather(self, obj, root=0):
# def change_style(style, representer):
#     def new_representer(dumper, data):
# def get_utcnow_formatted():
# def strf_timedelta(delta_t):
# def check_project_toplevel_dir(raise_exception=True):
#     def __init__(self, log_filepath):
#     def log(self, new_log_data={}):
#     def __init__(self, manual_overrides_filepath=None):
#     def __init__(self, manual_overrides_yaml):
#     def __init__(self, manual_overrides_yaml):
#     def __init__(self, manual_overrides_yaml):
# def gen_metadata_filename(ensembler_stage, metadata_file_index):
#     def __init__(self, project_stage='init', target_id=None, project_toplevel_dir='.'):
#     def add_all_prev_metadata(self, project_stage):
#     def add_prev_metadata(self, project_stage):
#     def determine_latest_metadata_filepath(self, project_stage):
#     def metadata_dir_mapper(self, project_stage, target_id=None):
#     def metadata_file_basename_mapper(self, project_stage):
#     def determine_latest_metadata_file_index(self, project_stage):
#     def gen_metadata_filepath_from_dir_index_and_file_basename(self, dirpath, file_basename, index):
#     def add_data(self, data, project_stage=None):
#     def add_iteration_number_to_metadata(self, iter_number):
#     def write(self):
# def encode_url_query(uniprot_query):
#     def replace_all(text, replace_dict):
# def xpath_match_regex_case_sensitive(context, attrib_values, regex_str):
# def xpath_match_regex_case_insensitive(context, attrib_values, regex_str):
# def sequnwrap(sequence):
# def seqwrap(sequence, add_star=False):
# def construct_fasta_str(id, seq):
# def get_targets():
# def get_templates_resolved_seq():
# def get_templates_full_seq():
# def get_targets_and_templates():
# def find_loopmodel_executable():
# def check_ensembler_modeling_stage_first_model_file_exists(ensembler_stage, targetid):
# def check_ensembler_modeling_stage_metadata_exists(ensembler_stage, targetid):
# def check_ensembler_modeling_stage_complete(ensembler_stage, targetid):
# def get_most_advanced_ensembler_modeling_stage(targetid):
# def get_valid_model_ids(ensembler_stage, targetid):
# def select_templates_by_seqid_cutoff(targetid, seqid_cutoff=None):
# def select_templates_by_validation_score(targetid,
#                                          validation_score_cutoff=None,
#                                          validation_score_percentile=None
#                                          ):


# Path: ensembler/refinement.py
import os
import datetime
import traceback
import gzip
import sys
import subprocess
import yaml
import warnings
import socket
import numpy as np
import Bio
import ensembler
import ensembler.version
import simtk.unit as unit
import simtk.openmm as openmm
import simtk.openmm.app as app
import simtk.openmm.version
        import time
        import time
    import os.path
        import gzip
from yaml.scanner import ScannerError
from collections import deque
from copy import deepcopy
from ensembler.core import mpistate, logger, ManualOverrides

                'model_seqid_cutoff': model_seqid_cutoff,
                'write_trajectory': write_trajectory,
                'include_disulfide_bonds': include_disulfide_bonds,
                'custom_residue_variants': custom_residue_variants,
                'ff': ff,
                'implicit_water_model': implicit_water_model,
                'sim_length': str(sim_length),
                'timestep': str(timestep),
                'temperature': str(temperature),
                'collision_rate': str(collision_rate),
                'cutoff': str(cutoff),
                'nsteps_per_iteration': nsteps_per_iteration,
                'ph': ph,
                'nsuccessful_refinements': nsuccessful_refinements,
                'python_version': sys.version.split('|')[0].strip(),
                'python_full_version': ensembler.core.literal_str(sys.version),
                'ensembler_version': ensembler.version.short_version,
                'ensembler_commit': ensembler.version.git_revision,
                'biopython_version': Bio.__version__,
                'openmm_version': simtk.openmm.version.short_version,
                'openmm_commit': simtk.openmm.version.git_revision,
            }

            project_metadata.add_data(metadata)
            project_metadata.write()

        mpistate.comm.Barrier()

    mpistate.comm.Barrier()
    if mpistate.rank == 0:

        logger.info('Done.')