DynamiSpectra 1.0.5__py3-none-any.whl → 1.0.6__py3-none-any.whl

dynamispectra/__init__.py

@@ -14,6 +14,8 @@ from .SecondaryStructure import (
     state_names
 )
 from .FractionSS import fractions_ss_analysis
+from .saltbridge import saltbridge_analysis
+from .ligand_density import ligand_density_analysis
 
 
-__all__ = ['read_hbond', 'hbond_analysis', 'read_rmsd', 'rmsd_analysis', 'read_rmsf', 'rmsf_analysis', 'read_sasa', 'sasa_analysis', 'read_rg', 'rg_analysis', 'pca_analysis', 'read_ss', 'calculate_probabilities', 'plot_ss_boxplot', 'ss_analysis', 'state_mapping', 'state_names', 'fractions_ss_analysis']
+__all__ = ['read_hbond', 'hbond_analysis', 'read_rmsd', 'rmsd_analysis', 'read_rmsf', 'rmsf_analysis', 'read_sasa', 'sasa_analysis', 'read_rg', 'rg_analysis', 'pca_analysis', 'read_ss', 'calculate_probabilities', 'plot_ss_boxplot', 'ss_analysis', 'state_mapping', 'state_names', 'fractions_ss_analysis', 'saltbridge_analysis', 'ligand_density_analysis']

dynamispectra/ligand_density.py

@@ -0,0 +1,55 @@
+import numpy as np
+import matplotlib.pyplot as plt
+import os
+
+def read_xpm(file_path):
+    with open(file_path, 'r') as f:
+        lines = f.readlines()
+
+    lines = [l.strip() for l in lines if l.strip().startswith('"')]
+    header_line = lines[0].strip().strip('",')
+    width, height, ncolors, chars_per_pixel = map(int, header_line.split())
+
+    color_map = {}
+    for i in range(1, ncolors + 1):
+        line = lines[i].strip().strip('",')
+        symbol = line[:chars_per_pixel]
+        color_map[symbol] = i - 1
+
+    matrix = []
+    for line in lines[ncolors + 1:]:
+        line = line.strip().strip('",')
+        row = [color_map[line[i:i+chars_per_pixel]] for i in range(0, len(line), chars_per_pixel)]
+        matrix.append(row)
+
+    return np.array(matrix)
+
+def plot_density(matrix, cmap='inferno', xlabel='X', ylabel='Y', title='', 
+                 colorbar_label='Relative density', save_path=None):
+    """
+    Plots the density matrix and optionally saves it as .png and .tiff in 300 dpi.
+    """
+    plt.figure()
+    plt.imshow(matrix, cmap=cmap, origin='lower', aspect='auto')
+    plt.colorbar(label=colorbar_label)
+    plt.xlabel(xlabel)
+    plt.ylabel(ylabel)
+    plt.title(title)
+    plt.tight_layout()
+
+    if save_path:
+        base, _ = os.path.splitext(save_path)
+        plt.savefig(f"{base}.png", dpi=300)
+        plt.savefig(f"{base}.tiff", dpi=300)
+        print(f"Gráficos salvos como {base}.png e {base}.tiff")
+
+    plt.show()
+
+def ligand_density_analysis(xpm_file_path, plot=True, save_path=None):
+    """
+    Reads an XPM file, plots the ligand density, and optionally saves the figure.
+    """
+    matrix = read_xpm(xpm_file_path)
+    if plot:
+        plot_density(matrix, save_path=save_path)
+    return matrix

dynamispectra/saltbridge.py

@@ -0,0 +1,171 @@
+import numpy as np
+import matplotlib.pyplot as plt
+from scipy.stats import gaussian_kde
+import os
+
+def read_saltbridge(file):
+    """
+    Reads salt-bridge distance data from a .xvg file.
+
+    Parameters:
+    -----------
+    file : str
+        Path to the .xvg file.
+
+    Returns:
+    --------
+    times : numpy.ndarray
+        Time values from simulation.
+    distances : numpy.ndarray
+        Salt-bridge distances.
+    """
+    try:
+        print(f"Reading file: {file}")
+        times, distances = [], []
+
+        with open(file, 'r') as f:
+            for line in f:
+                if line.startswith(('#', '@', ';')) or line.strip() == '':
+                    continue
+                try:
+                    values = line.split()
+                    if len(values) >= 2:
+                        time, distance = map(float, values[:2])
+                        times.append(time / 1000.0)  # Convert ps to ns
+                        distances.append(distance)
+                except ValueError:
+                    print(f"Error processing line: {line.strip()}")
+                    continue
+
+        if len(times) == 0 or len(distances) == 0:
+            raise ValueError(f"File {file} does not contain valid data.")
+
+        return np.array(times), np.array(distances)
+
+    except Exception as e:
+        print(f"Error reading file {file}: {e}")
+        return None, None
+
+def check_simulation_times(*time_arrays):
+    for i in range(1, len(time_arrays)):
+        if not np.allclose(time_arrays[0], time_arrays[i]):
+            raise ValueError(f"Simulation times do not match between file 1 and file {i+1}")
+
+def plot_saltbridge(time1, mean1, std1,
+                    time2, mean2, std2,
+                    time3, mean3, std3,
+                    output_folder):
+    """
+    Generates the salt-bridge distance plot with mean and standard deviation.
+    """
+    plt.figure(figsize=(7, 6))
+
+    if time1 is not None:
+        plt.plot(time1, mean1, label='Simulation 1', color='#333333', linewidth=2)
+        plt.fill_between(time1, mean1 - std1, mean1 + std1, color='#333333', alpha=0.2)
+
+    if time2 is not None:
+        plt.plot(time2, mean2, label='Simulation 2', color='#6A9EDA', linewidth=2)
+        plt.fill_between(time2, mean2 - std2, mean2 + std2, color='#6A9EDA', alpha=0.2)
+
+    if time3 is not None:
+        plt.plot(time3, mean3, label='Simulation 3', color='#54b36a', linewidth=2)
+        plt.fill_between(time3, mean3 - std3, mean3 + std3, color='#54b36a', alpha=0.2)
+
+    plt.xlabel('Time (ns)', fontsize=12)
+    plt.ylabel('Salt-Bridge Distance (nm)', fontsize=12)
+    plt.legend(frameon=False, loc='upper right', fontsize=10)
+    plt.tick_params(axis='both', which='major', labelsize=10)
+    plt.grid(False)
+
+    # Ajuste do limite do eixo x para o último tempo dos dados
+    max_time = max(
+        max(time1) if time1 is not None else 0,
+        max(time2) if time2 is not None else 0,
+        max(time3) if time3 is not None else 0,
+    )
+    plt.xlim(0, max_time)
+
+    plt.tight_layout()
+
+    os.makedirs(output_folder, exist_ok=True)
+    plt.savefig(os.path.join(output_folder, 'saltbridge_plot.tiff'), format='tiff', dpi=300)
+    plt.savefig(os.path.join(output_folder, 'saltbridge_plot.png'), format='png', dpi=300)
+    plt.show()
+
+def plot_density(mean1, mean2, mean3, output_folder):
+    """
+    Generates the density plot for salt-bridge mean values.
+    """
+    plt.figure(figsize=(6, 6))
+
+    if mean1 is not None:
+        kde1 = gaussian_kde(mean1)
+        x_vals = np.linspace(0, max(mean1), 1000)
+        plt.fill_between(x_vals, kde1(x_vals), color='#333333', alpha=0.5, label='Simulation 1')
+
+    if mean2 is not None:
+        kde2 = gaussian_kde(mean2)
+        x_vals = np.linspace(0, max(mean2), 1000)
+        plt.fill_between(x_vals, kde2(x_vals), color='#6A9EDA', alpha=0.5, label='Simulation 2')
+
+    if mean3 is not None:
+        kde3 = gaussian_kde(mean3)
+        x_vals = np.linspace(0, max(mean3), 1000)
+        plt.fill_between(x_vals, kde3(x_vals), color='#54b36a', alpha=0.5, label='Simulation 3')
+
+    plt.xlabel('Salt-Bridge Distance (nm)', fontsize=12)
+    plt.ylabel('Density', fontsize=12)
+    plt.legend(frameon=False, loc='upper right', fontsize=10)
+    plt.tick_params(axis='both', which='major', labelsize=10)
+    plt.grid(False)
+    plt.tight_layout()
+
+    plt.savefig(os.path.join(output_folder, 'saltbridge_density.tiff'), format='tiff', dpi=300)
+    plt.savefig(os.path.join(output_folder, 'saltbridge_density.png'), format='png', dpi=300)
+    plt.show()
+
+def saltbridge_analysis(output_folder, *simulation_files_groups):
+    """
+    Main function to generate salt-bridge analysis and plots.
+
+    Parameters:
+    -----------
+    output_folder : str
+        Output folder to save plots.
+    *simulation_files_groups : list of str
+        List of .xvg files for each simulation group.
+    """
+    def process_group(file_paths):
+        times, distances = [], []
+        for file in file_paths:
+            time, dist = read_saltbridge(file)
+            times.append(time)
+            distances.append(dist)
+        check_simulation_times(*times)
+        mean_dist = np.mean(distances, axis=0)
+        std_dist = np.std(distances, axis=0)
+        return times[0], mean_dist, std_dist
+
+    results = []
+    for group in simulation_files_groups:
+        if group:
+            time, mean, std = process_group(group)
+            results.append((time, mean, std))
+
+    if len(results) == 1:
+        plot_saltbridge(results[0][0], results[0][1], results[0][2],
+                        None, None, None, None, None, None, output_folder)
+        plot_density(results[0][1], None, None, output_folder)
+    elif len(results) == 2:
+        plot_saltbridge(results[0][0], results[0][1], results[0][2],
+                        results[1][0], results[1][1], results[1][2],
+                        None, None, None, output_folder)
+        plot_density(results[0][1], results[1][1], None, output_folder)
+    elif len(results) == 3:
+        plot_saltbridge(results[0][0], results[0][1], results[0][2],
+                        results[1][0], results[1][1], results[1][2],
+                        results[2][0], results[2][1], results[2][2], output_folder)
+        plot_density(results[0][1], results[1][1], results[2][1], output_folder)
+    else:
+        raise ValueError("You must provide at least one group of simulation files.")

{dynamispectra-1.0.5.dist-info → dynamispectra-1.0.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: DynamiSpectra
-Version: 1.0.5
+Version: 1.0.6
 Summary: Scripts for Molecular dynamics analysis
 Home-page: https://github.com/Conradoou/DynamiSpectra
 Author: Iverson Conrado-Bezerra

{dynamispectra-1.0.5.dist-info → dynamispectra-1.0.6.dist-info}/RECORD

@@ -6,11 +6,13 @@ dynamispectra/RMSF.py,sha256=M2b-KfvogfFbLUtv6PgZB4_nxWBeg9XbBpY0HjNQ9fw,8545
 dynamispectra/Rg.py,sha256=4F_vjdgcRG9LNqNCig1kdaUpMIRZrtQppYwL2OpJFYk,8557
 dynamispectra/SASA.py,sha256=o6_hcsmeY9yjAKUgsd0RpMikwC9VhoKAmQ1JLtPuXos,8661
 dynamispectra/SecondaryStructure.py,sha256=7jiYnqRgDaiR-16Zk40aCyv060y-1R__m44AVkhvm9g,6764
-dynamispectra/__init__.py,sha256=r13WozJ-uCGqA2QH84LzO-wzsv3HiMoVpZoIBydrPWk,771
+dynamispectra/__init__.py,sha256=iIXzlsDvnIF4DFUSxotB10EHWA5aQtZZQYr4tEyLIi0,919
 dynamispectra/cly.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+dynamispectra/ligand_density.py,sha256=oNAnVkbeLKhG88Q6JEzCYsbyCkm78wj7-hBnjQJDzpU,1802
 dynamispectra/main.py,sha256=YhivGFXZb1qwRCPUNmST5LeejqTyHmthMhzJs9uebJY,84
-dynamispectra-1.0.5.dist-info/METADATA,sha256=PvTAdyQx1tNbIMq5F0RREWuIoC7BMkg4nddVF6-KNQ8,3807
-dynamispectra-1.0.5.dist-info/WHEEL,sha256=pxyMxgL8-pra_rKaQ4drOZAegBVuX-G_4nRHjjgWbmo,91
-dynamispectra-1.0.5.dist-info/entry_points.txt,sha256=aaQocKWsZi_lJ7MZMsxHmc2DpQF4BSY0fwfE1s0CLxo,37
-dynamispectra-1.0.5.dist-info/top_level.txt,sha256=MDRYQBL4n7V0YVNSoOO_yf7iv_Kz3JGoVUEHiq_zT6U,14
-dynamispectra-1.0.5.dist-info/RECORD,,
+dynamispectra/saltbridge.py,sha256=lN16ArvXU_sngvNvpUkGSh7enANNMbVz41TD8-OT2lM,6553
+dynamispectra-1.0.6.dist-info/METADATA,sha256=-6HEb3F7PmP8q9PkNaw_ZSTpqM8ElbwwNINnv9IXyl0,3807
+dynamispectra-1.0.6.dist-info/WHEEL,sha256=Nw36Djuh_5VDukK0H78QzOX-_FQEo6V37m3nkm96gtU,91
+dynamispectra-1.0.6.dist-info/entry_points.txt,sha256=aaQocKWsZi_lJ7MZMsxHmc2DpQF4BSY0fwfE1s0CLxo,37
+dynamispectra-1.0.6.dist-info/top_level.txt,sha256=MDRYQBL4n7V0YVNSoOO_yf7iv_Kz3JGoVUEHiq_zT6U,14
+dynamispectra-1.0.6.dist-info/RECORD,,

{dynamispectra-1.0.5.dist-info → dynamispectra-1.0.6.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (79.0.0)
+Generator: setuptools (80.7.1)
 Root-Is-Purelib: true
 Tag: py3-none-any