import os
from typing import List, Optional
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import seaborn as sns
from qmmd.mdsim import config
sns.set(context="paper", font_scale=1.5)
[docs]
def plot_lig_dihedral(
md_path: str,
system_type: str = "noncov",
inhibitor_list: List[int] = config.inhibitor_list,
num_subplots: int = 6,
fig_type: str = "Hist",
save_path: Optional[str] = None,
show: bool = True,
) -> None:
"""
Plot ligand dihedral angle analysis from MD simulations.
Parameters
----------
md_path : str
Path to the MD data directory.
system_type : {"cov", "noncov"}, optional
Type of system.
inhibitor_list : List[int], optional
List of inhibitor IDs to plot.
num_subplots : int, optional
Number of subplots.
fig_type : {"Hist", "Line"}, optional
Type of plot.
save_path : str, optional
Path to save the plot.
show : bool, optional
Whether to show the plot.
"""
plots_width, plots_height = (
config.SIX_PLOTS_HORIZONTAL_WIDTH,
config.SIX_PLOTS_HORIZONTAL_HEIGHT,
)
num_row = int(num_subplots / 3)
fig, axes = plt.subplots(
nrows=num_row,
ncols=3,
sharex=True,
sharey=True,
figsize=(plots_width, plots_height),
)
if fig_type == "Line":
fig.subplots_adjust(
top=0.95, bottom=0.06, left=0.10, right=0.97, wspace=0.25, hspace=0.15
)
fig.text(0.5, 0.02, "Time (ns)", va="center", ha="center")
fig.text(
0.02,
0.5,
"Angle (\N{DEGREE SIGN})",
va="center",
ha="center",
rotation="vertical",
)
elif fig_type == "Hist":
fig.subplots_adjust(
top=0.98, bottom=0.08, left=0.09, right=0.98, wspace=0.25, hspace=0.15
)
fig.text(0.5, 0.02, "Angle (\N{DEGREE SIGN})", va="center", ha="center")
fig.text(0.02, 0.5, "Population", va="center", ha="center", rotation="vertical")
subplot_index = 0
for i, inhibitor in enumerate(inhibitor_list):
combined_df = pd.DataFrame(
list(np.arange(0.005, 100.005, 0.005)), columns=["Time (ns)"]
)
col_label = ["Time (ns)"]
label_list = []
for j in [1, 2]:
data_dir = os.path.join(
md_path,
str(inhibitor),
"MD",
system_type,
f"Rep{j}",
"analysis",
"dih",
)
for k in ["A", "B"]:
dat_file = f"{inhibitor}_dih{k}.dat"
dat_name = f"Rep{j} {inhibitor}{k}"
dat_path = os.path.join(data_dir, dat_file)
if os.path.exists(dat_path):
df = pd.read_csv(dat_path, index_col=0, sep=r"\s+")
df.reset_index(drop=True, inplace=True)
combined_df = pd.concat(
[combined_df, df], axis=1, ignore_index=True
)
label_list.append(dat_name)
if len(label_list) > 0:
combined_df.columns = col_label + label_list
subplot_index += 1
ax = plt.subplot(num_row, 3, subplot_index)
if fig_type == "Line":
combined_df.plot(
x="Time (ns)",
y=label_list,
kind="line",
ax=ax,
lw=0.3,
linestyle=":",
)
ax.xaxis.label.set_visible(False)
elif fig_type == "Hist":
combined_df.plot.kde(x="Time (ns)", y=label_list, bw_method=0.5, ax=ax)
ax.yaxis.label.set_visible(False)
ax.tick_params(
top=False,
bottom=True,
left=True,
right=False,
labelleft=True,
labelbottom=True,
)
leg = ax.legend(loc="upper right", fontsize="small")
plt.setp(leg.get_lines(), linewidth=4)
# Adding subplot labels (a, b, c...)
fig.text(0.089, 0.965, "(a)", va="center", ha="left")
fig.text(0.407, 0.965, "(b)", va="center", ha="left")
fig.text(0.725, 0.965, "(c)", va="center", ha="left")
fig.text(0.089, 0.483, "(d)", va="center", ha="left")
fig.text(0.407, 0.483, "(e)", va="center", ha="left")
fig.text(0.725, 0.483, "(f)", va="center", ha="left")
if save_path:
plt.savefig(save_path)
if show:
plt.show()
if __name__ == "__main__":
import argparse
parser = argparse.ArgumentParser(
description="Plot ligand dihedral angle analysis from MD simulations."
)
parser.add_argument("md_path", type=str, help="Path to the MD data directory.")
parser.add_argument(
"--system",
type=str,
default="noncov",
choices=["cov", "noncov"],
help="System type.",
)
parser.add_argument(
"--type", type=str, default="Hist", choices=["Hist", "Line"], help="Type of plot."
)
args = parser.parse_args()
plot_lig_dihedral(args.md_path, system_type=args.system, fig_type=args.type)