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harryswift01 merged 5 commits into from
Mar 17, 2025
Merged

Introduction of a YAML configuration file for CodeEntropy: #65

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19bd557
Introduction of a YAML configuration file for CodeEntropy:
harryswift01 Mar 14, 2025
3bc5250
Addition of 'force_partitioning' and 'waterEntropy' arguments
harryswift01 Mar 14, 2025
88c0bc0
Refactor YAML Configuration for CodeEntropy:
harryswift01 Mar 17, 2025
531b58a
Removal of .coveragerc file and included PyYAML as a dependency in th…
harryswift01 Mar 17, 2025
ad0af42
Updated version of PyYAML
harryswift01 Mar 17, 2025
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358 changes: 154 additions & 204 deletions CodeEntropy/main_mcc.py
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Original file line number Diff line number Diff line change
@@ -1,234 +1,184 @@
import argparse
import math
import os

import MDAnalysis as mda

# import numpy as np
import pandas as pd
import yaml

from CodeEntropy import EntropyFunctions as EF
from CodeEntropy import LevelFunctions as LF
from CodeEntropy import MDAUniverseHelper as MDAHelper

# from datetime import datetime

arg_map = {
"top_traj_file": {
"type": str,
"nargs": "+",
"help": "Path to Structure/topology file followed by Trajectory file(s)",
"default": [],
},
"selection_string": {
"type": str,
"help": "Selection string for CodeEntropy",
"default": "all",
},
"start": {
"type": int,
"help": "Start analysing the trajectory from this frame index",
"default": 0,
},
"end": {
"type": int,
"help": "Stop analysing the trajectory at this frame index",
"default": -1,
},
"step": {
"type": int,
"help": "Interval between two consecutive frames to be read index",
"default": 1,
},
"bin_width": {
"type": int,
"help": "Bin width in degrees for making the histogram",
"default": 30,
},
"tempra": {
"type": float,
"help": "Temperature for entropy calculation (K)",
"default": 298.0,
},
"verbose": {
"type": bool,
"help": "True/False flag for noisy or quiet output",
"default": False,
},
"thread": {"type": int, "help": "How many multiprocess to use", "default": 1},
"outfile": {
"type": str,
"help": "Name of the file where the output will be written",
"default": "outfile.out",
},
"resfile": {
"type": str,
"help": "Name of the file where the residue entropy output will be written",
"default": "res_outfile.out",
},
"mout": {
"type": str,
"help": "Name of the file where certain matrices will be written",
"default": None,
},
"force_partitioning": {"type": float, "help": "Force partitioning", "default": 0.5},
"waterEntropy": {"type": bool, "help": "Calculate water entropy", "default": False},
}


def load_config(file_path):
"""Load YAML configuration file."""
if not os.path.exists(file_path):
raise FileNotFoundError(f"Configuration file '{file_path}' not found.")

with open(file_path, "r") as file:
config = yaml.safe_load(file)

# If YAML content is empty, return an empty dictionary
if config is None:
config = {}

return config


def setup_argparse():
"""Setup argument parsing dynamically based on arg_map."""
parser = argparse.ArgumentParser(
description="CodeEntropy: Entropy calculation with MCC method."
)

for arg, properties in arg_map.items():
kwargs = {key: properties[key] for key in properties if key != "help"}
parser.add_argument(f"--{arg}", **kwargs, help=properties.get("help"))

return parser


def merge_configs(args, run_config):
"""Merge CLI arguments with YAML configuration."""
if run_config is None:
run_config = {}

if not isinstance(run_config, dict):
raise TypeError("run_config must be a dictionary or None.")

# Step 1: Merge YAML configuration into args
for key, value in run_config.items():
if getattr(args, key, None) is None:
setattr(args, key, value)

# Step 2: Set default values for any missing arguments from `arg_map`
for key, params in arg_map.items():
if getattr(args, key, None) is None:
setattr(args, key, params.get("default"))

# Step 3: Override with CLI values if provided
for key in arg_map.keys():
cli_value = getattr(args, key, None)
if cli_value is not None:
run_config[key] = cli_value

return args


def main():
"""
Main function for calculating the entropy of a system using the multiscale cell
correlation method.
"""

try:
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@jimboid jimboid Mar 14, 2025

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Nice structure to handle errors in an informative way

parser = argparse.ArgumentParser(
description="""
CodeEntropy-POSEIDON is a tool to compute entropy using the
multiscale-cell-correlation (MCC) theory and force/torque covariance
methods with the ablity to compute solvent entropy.
Version:
0.3.1;

Authors:
Arghya Chakravorty (arghya90),
Jas Kalayan (jkalayan),
Donald Chang,
Sarah Fegan
Ioana Papa;

Output:
*.csv = results from different calculateion,
*.pkl - Pickled reduced universe for further analysis,
*.out - detailed output such as matrix and spectra"""
)

parser.add_argument(
"-f",
"--top_traj_file",
required=True,
dest="filePath",
action="store",
nargs="+",
help="Path to Structure/topology file (AMBER PRMTOP, GROMACS TPR which "
"contains topology and dihedral information) followed by Trajectory "
"file(s) (AMBER NETCDF or GROMACS TRR) you will need to output the "
"coordinates and forces to the same file. Required.",
)
parser.add_argument(
"-l",
"--selectString",
action="store",
dest="selection_string",
type=str,
default="all",
help="Selection string for CodeEntropy such as protein or resid, refer to "
"MDAnalysis.select_atoms for more information.",
)
parser.add_argument(
"-b",
"--begin",
action="store",
dest="start",
help="Start analysing the trajectory from this frame index. Defaults to 0",
default=0,
type=int,
)
parser.add_argument(
"-e",
"--end",
action="store",
dest="end",
help="Stop analysing the trajectory at this frame index. Defaults to -1 "
"(end of trajectory file)",
default=-1,
type=int,
)
parser.add_argument(
"-d",
"--step",
action="store",
dest="step",
help="interval between two consecutive frames to be read index. "
"Defaults to 1",
default=1,
type=int,
)
parser.add_argument(
"-n",
"--bin_width",
action="store",
dest="bin_width",
default=30,
type=int,
help="Bin width in degrees for making the histogram of the dihedral angles "
"for the conformational entropy. Default: 30",
)
parser.add_argument(
"-k",
"--tempra",
action="store",
dest="temp",
help="Temperature for entropy calculation (K). Default to 298.0 K",
default=298.0,
type=float,
)
parser.add_argument(
"-v",
"--verbose",
action="store",
dest="verbose",
default=False,
type=bool,
help="True/False flag for noisy or quiet output. Default: False",
)
parser.add_argument(
"-t",
"--thread",
action="store",
dest="thread",
help="How many multiprocess to use. Default 1 for single core execution.",
default=1,
type=int,
)
parser.add_argument(
"-o",
"--out",
action="store",
dest="outfile",
default="outfile.out",
help="Name of the file where the output will be written. "
"Default: outfile.out",
)
parser.add_argument(
"-r",
"--resout",
action="store",
dest="resfile",
default="res_outfile.out",
help="Name of the file where the residue entropy output will be written. "
"Default: res_outfile.out",
)
parser.add_argument(
"-m",
"--mout",
action="store",
dest="moutfile",
default=None,
help="Name of the file where certain matrices will be written "
"(default: None).",
)

parser.add_argument(
"-c",
"--cutShell",
action="store",
dest="cutShell",
default=None,
type=float,
help="include cutoff shell analysis, add cutoff distance in angstrom "
"Default None will ust the RAD Algorithm",
)
parser.add_argument(
"-p",
"--pureAtomNum",
action="store",
dest="puteAtomNum",
default=1,
type=int,
help="Reference molecule resid for system of pure liquid. " "Default to 1",
)
parser.add_argument(
"-x",
"--excludedResnames",
dest="excludedResnames",
action="store",
nargs="+",
default=None,
help="exclude a list of molecule names from nearest non-like analysis. "
"Default: None. Multiples are gathered into list.",
)
parser.add_argument(
"-w",
"--water",
dest="waterResnames",
action="store",
default="WAT",
nargs="+",
help="resname for water molecules. "
"Default: WAT. Multiples are gathered into list.",
)
parser.add_argument(
"-s",
"--solvent",
dest="solventResnames",
action="store",
nargs="+",
default=None,
help="include resname of solvent molecules (case-sensitive) "
"Default: None. Multiples are gathered into list.",
)
parser.add_argument(
"--solContact",
action="store_true",
dest="doSolContact",
default=False,
help="Do solute contact calculation",
)
config = load_config("config.yaml")

if config is None:
raise ValueError(
"No configuration file found, and no CLI arguments were provided."
)

parser = setup_argparse()
args, unknown = parser.parse_known_args()

# Process each run in the YAML configuration
for run_name, run_config in config.items():
if isinstance(run_config, dict):
# Merging CLI arguments with YAML configuration
args = merge_configs(args, run_config)

# Ensure necessary arguments are provided
if not getattr(args, "top_traj_file"):
raise ValueError(
"The 'top_traj_file' argument is required but not provided."
)
if not getattr(args, "selection_string"):
raise ValueError(
"The 'selection_string' argument is required but not provided."
)

args = parser.parse_args()
except argparse.ArgumentError:
print("Command line arguments are ill-defined, please check the arguments")
# REPLACE INPUTS
print(f"Printing all input for {run_name}")
for arg in vars(args):
print(f" {arg}: {getattr(args, arg) or ''}")
else:
print(f"Run configuration for {run_name} is not a dictionary.")
except ValueError as e:
print(e)
raise

# REPLACE INPUTS
print("printing all input")
for arg in vars(args):
print(" {} {}".format(arg, getattr(args, arg) or ""))

# startTime = datetime.now()

# Get topology and trajectory file names and make universe
tprfile = args.filePath[0]
trrfile = args.filePath[1:]
tprfile = args.top_traj_file[0]
trrfile = args.top_traj_file[1:]
u = mda.Universe(tprfile, trrfile)

# Define bin_width for histogram from inputs
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