tmquick 1.0.0__py3-none-any.whl

tmq/__init__.py

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+__version__ = "1.0"
+from .core.traj2pdb import traj2pdb
+from .core.pdb2csv import pdb2csv  
+from .core.trajmap import trajmap
+from .core.csv2shift import shift
+from .core.shift2graph import shift2graph
+from .core.hotspot import detect_shifts
+from .core.hotspot import create_submatrices
+from .core.hotspot import plot_shift_regions
+from .core.hotspot import slice_shifts
+from .core.hotspot import plot_slice_regions
+from .core.hotspot import plot_hotspot_regions
+from .core.diff2graph import diff_map
+from .core.average_trajmap import avg_trajmap

tmq/cli.py

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+"""Main CLI launcher
+"""
+
+import argparse
+import time
+from .commands.traj2pdb_cli import traj2pdb_cli
+from .commands.pdb2csv_cli import pdb2csv_cli  
+from .commands.trajmap_cli import trajmap_cli
+from .commands.csv2shift_cli import shift_cli
+from .commands.shift2graph_cli import shift2graph_cli
+from .commands.hotspot_cli import detect_shift_cli
+from .commands.hotspot_cli import create_submatrices_cli
+from .commands.hotspot_cli import slice_shifts_cli
+from .commands.hotspot_cli import run_hotspot_cli
+from .commands.diff2graph_cli import diff_map_cli
+from .commands.average_trajmap_cli import avg_trajmap_cli
+from colorama import init, Fore, Style
+init(convert=False)
+
+
+"""Time counter"""
+def print_final_message(total):
+    print(
+        Fore.GREEN +
+        "\nTrajMapQuick analysis complete. \n" +
+        Fore.CYAN +
+        "\nAll tasks completed successfully.\n"+
+        Style.RESET_ALL
+    )
+    print(f"Total computation time: {total:.2f} seconds \n" +
+        Fore.MAGENTA +
+        "\nThank you for using TrajMapQuick 1.0 — ResLaR Labs, Afe Babalola University, Ado-Ekiti Nigeria.\n" +
+        Style.RESET_ALL)
+    
+
+"""Display logo"""
+def main():
+    start_time = time.perf_counter()
+    init()
+    print(Fore.GREEN + r"""
+
+     _______         _ __  __              ____  
+    |__   __|       (_)  \/  |            / __ \ 
+        | |_ __ __ _ _| \  / | __ _ _ __ | |  | |
+        | | '__/ _` | | |\/| |/ _` | '_ \| |  | |
+        | | | | (_| | | |  | | (_| | |_) | |__| |
+        |_|_|  \__,_| |_|  |_|\__,_| .__/ \___\_\
+                   _/ |            | |           
+                  |__/             |_|           
+          
+
+          """ + Style.RESET_ALL)
+    print("========== Welcome to TrajMapQuick 1.0 ==========")
+    print("")
+    print("Authors : " + Fore.BLUE + "Wande M. Oluyemi, Adeniyi T. Adewumi, Shadrach C. Eze & Stephen C. Nnemolisa @ ResLaR Labs, Afe Babalola University, Ado-Ekiti Nigeria" + Style.RESET_ALL)
+    print("")
+    print("")
+
+    parser = argparse.ArgumentParser(
+        prog="tmq",
+        add_help=False,
+        formatter_class=argparse.RawTextHelpFormatter,
+        description="""
+    A command-line toolkit for MD trajectory map analysis:
+    • matrix extraction
+    • shift computation
+    • visualization
+
+    Built on the original work of Kožić & Bertoša, 2024,
+    Trajectory maps: molecular dynamics visualization and analysis,
+    https://doi.org/10.1093/nargab/lqad114
+
+    TrajMapQuick is faster, improves batch processing, and allows
+    automatic shift detection from trajectory maps.
+    """
+    )
+    
+    parser.add_argument(
+    "-h", "--help",
+    action="help",
+    help="Show usage information")
+
+    subparsers = parser.add_subparsers(
+        title="Available subcommands",
+        dest="command",
+        metavar=""
+    )
+
+    """SHIFT SUBCOMMAND"""
+    shift_parser = subparsers.add_parser(
+        "shift",
+        help="Extract matrices, compute residue-residue shifts and make plots: For more, use tmq shift --help",
+        description=(
+            "Converts your trajectory into pdb multimodel form and then to a CSV file, "
+            "extracts a distance matrix from the CSV file and computes "
+            "a shift value between a residue range over a specified frame.\n\n"
+            "Example:\n"
+            "  tmq shift --traj traj.pdb --top top.parmtop --str 1 --resr 1-300 --resrs 110-125 --cent backbone --plot --out shift_output\n\n"
+            "This will compute the shift of the backbone atoms, for residues 110-125, across the trajectory of a protein with residues 1-300, and will generate plots automatically."),
+        formatter_class=argparse.RawTextHelpFormatter
+    )
+
+    shift_parser.add_argument("-tr", "--traj", required=True,
+                              help="Input trajectory, accepts pdb, nc, xtc xtr")
+    shift_parser.add_argument("-to", "--top", required=True,
+                              help="Topology file, accepts parmtop, pdb, gro")
+    shift_parser.add_argument("-st", "--str", type=int, default=1,
+                              help="Stride of the trajectory, (default: 1)")
+    shift_parser.add_argument("-rr", "--resr", type=str, required=True,
+                              help="Residue range of your protein in the form start-end (e.g., 1-300")
+    shift_parser.add_argument("-rs", "--resrs", type=str, required=True,
+                              help="Residue range for shift calculation, in the form start-end (e.g., 110-125")
+    shift_parser.add_argument("-ce", "--cent", type=str, default="backbone", required=True,
+                              help="Centre of calculations, either the backbone " \
+                              "atoms or the ca atoms, (default: backbone)")
+    shift_parser.add_argument("-ma", "--max", type=int, default=5, required=False,
+                              help="Max shift value for color scaling, (default: 5)")
+    shift_parser.add_argument("-o", "--out", type=str, required=True,
+                              help="Basename for all outputs")
+    
+
+    """HOTSPOT SUBCOMMAND"""
+    dehot_parser = subparsers.add_parser(
+        "hotspot",
+        help="Detect hotspots in residue shifts and create plots: For more, use tmq hotspot --help",
+        description=(
+            "Detect hotspots in residue shifts and creates publication-ready plot with trajectory map"
+            "and hotspot regions annotated, and also generates shift graphs for detected hotspot regions.\n\n"
+            "Example:\n"
+            "  tmq hotspot --traj traj.pdb --top top.parmtop --str 1 --resr 1-300 --cent backbone --out hotspot_output\n\n"
+        ),
+        formatter_class=argparse.RawTextHelpFormatter
+    )
+
+    dehot_parser.add_argument("-tr", "--traj", required=True,
+                              help="Input trajectory, accepts Pdb, nc, xtc xtr")
+    dehot_parser.add_argument("-to", "--top", required=True,
+                              help="Topology file, accepts .parmtop, pdb, gro")
+    dehot_parser.add_argument("-st", "--str", type=int, default=1,
+                              help="Stride of the trajectory, (default: 1)")
+    dehot_parser.add_argument("-rr", "--resr", type=str, required=True,
+                              help="Residue range of your protein in the form start-end (e.g., 1-300")
+    dehot_parser.add_argument("-ce", "--cent", type=str, default="backbone", required=True,
+                              help="Centre of calculations, either the backbone " \
+                              "atoms or the ca atoms, (default: backbone)")
+    dehot_parser.add_argument("-win", "--window", type=int, default=5, required=False,
+                            help="Rolling window size for smoothing, (default: 5) (Not Required)")
+    dehot_parser.add_argument("-md", "--mindist", type=int, default=3, required=False,
+                               help="Minimum distance between peaks, (default: 3) (Not Required)")
+    dehot_parser.add_argument("-hs", "--hot", type=int, default=10, required=False,
+                          help="Number of top peaks to extract, (default: 10) (Not Required)")
+    dehot_parser.add_argument("-ma", "--max", type=int, default=5, required=False,
+                              help="Max shift value for color scaling, (default: 5) (Not Required)")
+    dehot_parser.add_argument("-o", "--out", type=str, required=True,
+                              help="Basename for outputs")
+    
+
+    """DIFFERENCE SUBCOMMAND"""
+    dehot_parser = subparsers.add_parser(
+        "diff",
+        help="Computes difference between two matrices and creates the difference map: For more, use tmq diff --help",
+        description=(
+            "Computes difference between two matrices and creates publication-ready plot with difference map.\n\n"
+            "The input matrices must be supplied by the names of the output of previous 'Shift' runs.\n\n"
+            "A subsequent downstream processing after 'Shift' runs; thus, matrices must have equal lengths.\n\n"
+            "Example:\n"
+            "  tmq diff --mat1 apo --mat2 holo --resr 1-300 --max 8 --out my_diff\n\n"
+        ),
+        formatter_class=argparse.RawTextHelpFormatter
+    )
+
+    dehot_parser.add_argument("-m1", "--mat1", required=True,
+                              help="First matrix, accepts only the name without extension")
+    dehot_parser.add_argument("-m2", "--mat2", required=True,
+                              help="Second matrix, accepts only the name without extension")
+    dehot_parser.add_argument("-rr", "--resr", type=str, required=True,
+                              help="Residue range of your protein in the form start-end (e.g., 1-300")
+    dehot_parser.add_argument("-ma", "--max", type=int, default=5, required=True,
+                              help="Max shift value for color scaling, (default: 5)")
+    dehot_parser.add_argument("-o", "--out", type=str, required=True,
+                              help="Basename for outputs")
+
+
+
+    """DIFFERENCE SUBCOMMAND"""
+    dehot_parser = subparsers.add_parser(
+        "average",
+        help="Computes average of n matrices and creates the average map: For more, use tmq average --help",
+        description=(
+            "Computes average of n matrices and creates publication-ready plot with average map. \n\n"
+            "The input matrices must be supplied by the names of the output of previous 'Shift' runs as comma separated values.\n\n"
+            "A subsequent downstream processing after 'Shift' runs; thus, matrices must have equal lengths.\n\n"
+            "Example:\n"
+            "  tmq average --mat apo,holo,bound --resr 1-300 --max 8 --out my_avg\n\n"
+        ),
+        formatter_class=argparse.RawTextHelpFormatter
+    )
+
+    dehot_parser.add_argument("-m", "--mat", required=True, type=str,
+                              help="Comma-separated list of matrix names, accepts only the name without extension")
+    dehot_parser.add_argument("-rr", "--resr", type=str, required=True,
+                              help="Residue range of your protein in the form start-end (e.g., 1-300")
+    dehot_parser.add_argument("-ma", "--max", type=int, default=5, required=True,
+                              help="Max shift value for color scaling, (default: 5)")
+    dehot_parser.add_argument("-o", "--out", type=str, required=True,
+                              help="Basename for outputs")
+
+
+    print("")
+    args = parser.parse_args()
+
+    if args.command == "shift":
+        traj2pdb_cli(args)
+        pdb2csv_cli(args)
+        shift_cli(args)
+        trajmap_cli(args)
+        shift2graph_cli(args)
+        end_time = time.perf_counter()
+        total = end_time - start_time    
+        print_final_message(total)
+    elif args.command == "hotspot":
+        traj2pdb_cli(args)
+        pdb2csv_cli(args)
+        trajmap_cli(args)
+        detect_shift_cli(args)
+        create_submatrices_cli(args)
+        run_hotspot_cli(args)  
+        slice_shifts_cli(args)
+        run_hotspot_cli(args)
+        end_time = time.perf_counter()
+        total = end_time - start_time    
+        print_final_message(total)
+
+    elif args.command == "diff":
+        diff_map_cli(args)
+        end_time = time.perf_counter()
+        total = end_time - start_time    
+        print_final_message(total)
+
+    elif args.command == "average":
+        avg_trajmap_cli(args)
+        end_time = time.perf_counter()
+        total = end_time - start_time    
+        print_final_message(total)        
+        
+    else:
+        parser.print_help()
+        print("")
+        print("Cite this as: " + Fore.BLUE + "SHEDOOMTC. (2026). TrajMapQuick: Towards Fast Trajectory Map Analysis and Visualization (v1.0). Zenodo. https://doi.org/10.5281/zenodo.20681061" + Style.RESET_ALL)
+        print("")

tmq/commands/__init__.py

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+__version__ = "1.0"
+

tmq/commands/average_trajmap_cli.py

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+"""Parse input matrices, compute their element-wise average, 
+and save an averaged trajectory map PNG.
+"""
+
+import time
+from ..core.average_trajmap import avg_trajmap
+import matplotlib
+matplotlib.use("Agg")
+import matplotlib.pyplot as plt
+from ..utils.utils import ensure_csv_extension, ensure_png_extension, parse_range, load_matrix_4_diff_map, csv2matrix
+
+
+def avg_trajmap_cli(args):
+    start_time = time.perf_counter()
+    print("")
+    print("Plotting Average map...")
+
+    """split the matrix argument to get list of matrices
+    """
+    matrix_names = args.mat.split(",")
+    prefix = "_pdb2csv_"
+    matrices = [csv2matrix(ensure_csv_extension(name + prefix)) for name in matrix_names]
+
+    residue_start, residue_end = parse_range(args.resr)
+
+    """pass the matrices to the core function
+    """
+    fig = avg_trajmap(residue_start, residue_end, args.max, *matrices)
+
+    prefix1 = "_average_map_"
+    savename = ensure_png_extension(args.out + prefix1)
+    fig.savefig(savename, dpi=800, bbox_inches='tight')
+    print(f"Difference map saved to {savename}")
+    plt.close(fig)
+    total = time.perf_counter() - start_time
+    print(f"Time taken to plot Difference map: {total:.2f} seconds")

tmq/commands/csv2shift_cli.py

@@ -0,0 +1,27 @@
+"""Load a distance matrix, compute residue-range shifts across frames, and write a shift CSV.
+"""
+
+import time
+from ..core.csv2shift import shift
+from ..utils.utils import csv2matrix, ensure_csv_extension, parse_range
+
+
+def shift_cli(args):
+    start_time = time.perf_counter()
+    print("")
+    prefix = "_pdb2csv_"
+    file = ensure_csv_extension(args.out + prefix)
+    matrix = csv2matrix(file)
+    residue_start, residue_end = parse_range(args.resrs)
+    n_frames = matrix.shape[1]
+    print(f"Calculating shift for residues {residue_start} to {residue_end} "
+          f"across frames 0 to {n_frames - 1}...")
+
+    shifta = shift(matrix, residue_start, residue_end)
+
+    prefix2 = "_shift_"
+    savename = ensure_csv_extension(args.out + prefix2)
+    shifta.to_csv(savename, index=False)
+    print(f"Shift saved to {savename}")
+    total = time.perf_counter() - start_time
+    print(f"Time taken to calculate shift: {total:.2f} seconds")

tmq/commands/diff2graph_cli.py

@@ -0,0 +1,35 @@
+"""Load two matrices, render their difference heatmap (A−B), and save the figure PNG.
+"""
+
+import time
+from ..core.diff2graph import diff_map
+import matplotlib
+matplotlib.use("Agg")
+import matplotlib.pyplot as plt
+from ..utils.utils import ensure_csv_extension, ensure_png_extension, parse_range, load_matrix_4_diff_map
+
+
+
+def diff_map_cli(args):
+    start_time = time.perf_counter()
+    print("")
+    print("Plotting Difference map...")
+
+    prefix = "_pdb2csv_"
+    file1 = ensure_csv_extension(args.mat1 + prefix)
+    file2 = ensure_csv_extension(args.mat2 + prefix)
+
+    A = load_matrix_4_diff_map(file1)
+    B = load_matrix_4_diff_map(file2)
+
+    residue_start, residue_end = parse_range(args.resr)
+
+    fig = diff_map(A, B, args.max, residue_start, residue_end)
+
+    prefix1 = "_diff_map_"
+    savename = ensure_png_extension(args.out + prefix1)
+    fig.savefig(savename, dpi=800, bbox_inches='tight')
+    print(f"Difference map saved to {savename}")
+    plt.close(fig)
+    total = time.perf_counter() - start_time
+    print(f"Time taken to plot Difference map: {total:.2f} seconds")

tmq/commands/hotspot_cli.py

@@ -0,0 +1,89 @@
+"""Run hotspot detection and save a summary hotspot-region plot PNG.
+"""
+
+import time
+import matplotlib
+matplotlib.use("Agg")
+import matplotlib.pyplot as plt
+from matplotlib.ticker import MultipleLocator
+from ..core.hotspot import create_submatrices, detect_shifts, plot_hotspot_regions, plot_shift_regions, plot_slice_regions, slice_shifts
+from ..utils.utils import csv2matrix, ensure_csv_extension, ensure_png_extension, parse_range, shift_to_dataframe
+
+
+def detect_shift_cli(args):
+    print("")
+    print("Detecting shift regions...")
+    prefix = "_pdb2csv_"
+    file = ensure_csv_extension(args.out + prefix)
+    matrix = csv2matrix(file)
+    mean_shift, smooth, regions = detect_shifts(
+        matrix=matrix,
+        window=args.window,
+        mindist=args.mindist,
+        hotspot=args.hot,)
+    return mean_shift, smooth, regions
+
+
+def create_submatrices_cli(args):
+    print("")
+    print("Extracting region submatrices...")
+    prefix = "_pdb2csv_"
+    file = ensure_csv_extension(args.out + prefix)
+    matrix = csv2matrix(file)
+    prefix1 = "_matrix_"
+    savematrix = ensure_csv_extension(args.out + prefix1)
+    matrix.to_csv(savematrix, index=False)
+
+    """Call backend"""
+    submatrices, regions, mean_shift, smooth = create_submatrices(
+        matrix=matrix,
+        window=args.window,
+        mindist=args.mindist,
+        hotspot=args.hot)
+    return submatrices
+
+
+def slice_shifts_cli(args):
+    start_time = time.perf_counter()
+    print("")
+    print("Searching for hotspot regions and plotting individual shift graphs...")
+    prefix = "_pdb2csv_"
+    file = ensure_csv_extension(args.out + prefix)
+    matrix = csv2matrix(file)
+
+    """Backend: detect"""
+    results = slice_shifts(
+        matrix=matrix,
+        window=args.window,
+        mindist=args.mindist,
+        hotspot=args.hot)
+    
+    for start, end, shift_data in results:
+        fig = plot_slice_regions(shift_data, start, end)
+        savename = f"{args.out}_shift_{start}_{end}.png"
+        fig.savefig(savename, dpi=800, bbox_inches='tight')
+        plt.close(fig)
+        print(f"Hotspot region shift graph saved to {savename}")
+    total = time.perf_counter() - start_time
+    print(f"Time taken to search for hotspot regions: {total:.2f} seconds")
+
+
+"""Hotspot region detection and plotting
+"""
+def run_hotspot_cli(args):
+    start_time = time.perf_counter()
+    print("")
+    print("Detecting hotspot regions based on mean shift and plotting...")
+    mean_shift, smooth, regions = detect_shift_cli(args)
+
+    fig = plot_hotspot_regions(
+        mean_shift,
+        smooth,
+        regions,
+        title="Residue Shift Hotspots")
+    savename = f"{args.out}_shift_hotspots.png"
+    fig.savefig(savename, dpi=800, bbox_inches='tight')
+    plt.close(fig)
+    print(f"Hotspot region plot saved to {savename}")
+    total = time.perf_counter() - start_time
+    print(f"Time taken to detect hotspot regions: {total:.2f} seconds")

tmq/commands/pdb2csv_cli.py

@@ -0,0 +1,29 @@
+"""Convert a multi-model PDB (produced from trajectories) into a residue×frame distance CSV.
+"""
+
+import time
+from ..utils.utils import parse_range, ensure_csv_extension
+from ..core.pdb2csv import pdb2csv 
+
+
+def pdb2csv_cli(args):
+    start_time = time.perf_counter()
+    prefix = "_pdb2csv_"
+    prefix2 = "_traj2pdb_"
+    savename = ensure_csv_extension(args.out + prefix)
+    pdb_file = args.out + prefix2 + ".pdb"
+    start, end = parse_range(args.resr)
+    mode = args.cent
+    print("")
+    print("Converting PDB to CSV distance matrix...")
+
+    matrix= pdb2csv(
+        pdb_file=pdb_file,
+        residue_start=start,
+        residue_end=end,
+        mode=mode)
+
+    matrix.to_csv(savename)
+    print(f"Distance matrix saved to {savename}")
+    total = time.perf_counter() - start_time
+    print(f"Time taken to convert PDB to CSV: {total:.2f} seconds")

tmq/commands/shift2graph_cli.py

@@ -0,0 +1,29 @@
+"""Load a shift CSV, plot the time-series with rolling-average, and save a PNG graph.
+"""
+
+import time
+import matplotlib
+matplotlib.use("Agg")
+import matplotlib.pyplot as plt
+from ..core.shift2graph import shift2graph
+from ..utils.utils import ensure_csv_extension, ensure_png_extension, shift_to_dataframe
+
+
+def shift2graph_cli(args):
+    start_time = time.perf_counter()
+    print("")
+    print("Plotting shift graph...")
+    prefix = "_shift_"
+    file = ensure_csv_extension(args.out + prefix)
+    prefix1 = "_shift_graph_"
+    savename = ensure_png_extension(args.out + prefix1)
+    df = shift_to_dataframe(file)
+
+    fig = shift2graph(df, args.resrs)
+
+    fig.savefig(savename, dpi=800, bbox_inches='tight')
+    print(f"Shift graph saved to {savename}")
+    plt.close(fig)
+    total = time.perf_counter() - start_time
+    print(f"Time taken to plot shift graph: {total:.2f} seconds")
+

tmq/commands/traj2pdb_cli.py

@@ -0,0 +1,21 @@
+"""Load a residue×frame matrix, render a trajectory heatmap, and save the PNG figure.
+"""
+
+import time
+from ..core.traj2pdb import traj2pdb
+from ..utils.utils import ensure_pdb_extension
+
+
+def traj2pdb_cli(args):
+    start_time = time.perf_counter()
+    prefix = "_traj2pdb_"
+    savename = ensure_pdb_extension(args.out + prefix)
+    print("Loading trajectory...")
+    traj = traj2pdb(args.top, args.traj, args.str)
+    print("Selecting backbone...")
+    print("Aligning...")
+    print("Saving trajectory to", savename)
+    traj.save_pdb(savename)
+    end_time = time.perf_counter()
+    total = end_time - start_time       
+    print(f"Time taken to convert trajectory to PDB: {total:.2f} seconds")

tmq/commands/trajmap_cli.py

@@ -0,0 +1,29 @@
+"""Load a residue×frame matrix, render a trajectory heatmap, and save the PNG figure.
+"""
+
+import time
+import matplotlib
+matplotlib.use("Agg")
+import matplotlib.pyplot as plt
+from ..core.trajmap import trajmap
+from ..utils.utils import csv2matrix, ensure_csv_extension, ensure_png_extension, parse_range
+
+
+def trajmap_cli(args):
+    start_time = time.perf_counter()
+    print("")
+    print("Plotting trajectory map...")
+    prefix = "_pdb2csv_"
+    file = ensure_csv_extension(args.out + prefix)
+    matrix = csv2matrix(file)
+    residue_start, residue_end = parse_range(args.resr)
+    prefix1 = "_trajmap_"
+    savename = ensure_png_extension(args.out + prefix1)
+
+    fig = trajmap(matrix, residue_start, residue_end, args.max)
+
+    fig.savefig(savename, dpi=800, bbox_inches='tight')
+    print(f"Trajectory map saved to {savename}")
+    plt.close(fig)
+    total = time.perf_counter() - start_time
+    print(f"Time taken to plot trajectory map: {total:.2f} seconds")

tmq/core/__init__.py

@@ -0,0 +1,2 @@
+__version__ = "1.0"
+ 

tmq/core/average_trajmap.py

@@ -0,0 +1,35 @@
+""" Compute an element-wise average of input matrices 
+and render a trajectory map figure
+
+"""
+
+import pandas as pd
+import numpy as np
+import matplotlib
+matplotlib.use("Agg")
+from ..core.trajmap import trajmap
+
+
+
+def avg_trajmap(residue_start, residue_end, vmax, *matrices):
+    """
+    Take the element-wise average of two or more matrices.
+    All matrices must have the same shape.
+    """
+    
+    mats = [np.asarray(m) for m in matrices]
+    print("Loaded shapes:", [m.shape for m in mats])
+
+    shapes = {m.shape for m in mats}
+    if len(shapes) != 1:
+        raise ValueError(f"All matrices must have the same shape, got: {shapes}")
+    
+
+    avg_array = np.nanmean(mats, axis=0)
+    avg_array = np.nan_to_num(avg_array, nan=0.0)
+
+    matrix = pd.DataFrame(avg_array)
+
+
+    fig = trajmap(matrix, residue_start, residue_end, vmax)
+    return fig

tmq/core/csv2shift.py

@@ -0,0 +1,17 @@
+""" This computes shift in Armstrongs for 
+a given loop region of the protein
+
+"""
+
+import numpy as np
+import pandas as pd
+from ..utils.utils import matrix2shift
+
+
+def shift(matrix, residue_start, residue_end):
+    n_frames = matrix.shape[1]
+    start_frame = 0
+    end_frame = n_frames - 1
+    params = [residue_start, residue_end, start_frame, end_frame]
+    shift = matrix2shift(matrix, params)
+    return shift