DynamiSpectra 1.0.4__py3-none-any.whl → 1.0.6__py3-none-any.whl

dynamispectra/SecondaryStructure.py

@@ -0,0 +1,201 @@
+import numpy as np
+import matplotlib.pyplot as plt
+from matplotlib.patches import Patch  # Para criar elementos de legenda personalizados
+import os
+
+# Mapeamento dos estados secundários para números
+state_mapping = {
+    'H': 1,  # Hélice-α
+    'E': 2,  # Folha-β
+    'C': 0,  # Loop/Coil
+    'T': 3,  # Turn
+    'S': 4,  # Bend
+    'G': 5,  # 3-Helix
+    '~': -1, # Sem estrutura definida
+    'B': -1, # Tratar como sem estrutura
+}
+
+# Nomes das estruturas secundárias
+state_names = {
+    0: 'Loop/Coil',
+    1: 'α-Helix',
+    2: 'β-Sheet',
+    3: 'Turn',
+    4: 'Bend',
+    5: '3-Helix',
+}
+
+def read_ss(file):
+    """
+    Reads secondary structure data from a .dat file.
+
+    Parameters:
+    -----------
+    file : str
+        Path to the .dat file.
+
+    Returns:
+    --------
+    ss_data : numpy.ndarray
+        Array of secondary structure data.
+    """
+    try:
+        print(f"Reading file: {file}")
+        
+        # Open the file and process line by line
+        ss_data = []
+        
+        with open(file, 'r') as f:
+            for line in f:
+                # Skip comment lines and empty lines
+                if line.startswith(('#', '@', ';')) or line.strip() == '':
+                    continue
+                
+                # Try to extract the secondary structure data
+                try:
+                    ss_line = [state_mapping.get(char, -1) for char in line.strip()]
+                    ss_data.append(ss_line)
+                except ValueError:
+                    # Skip lines that cannot be converted to numbers
+                    print(f"Error processing line: {line.strip()}")
+                    continue
+        
+        # Check if the data is valid
+        if len(ss_data) == 0:
+            raise ValueError(f"File {file} does not contain valid data.")
+        
+        # Convert lists to numpy arrays
+        ss_data = np.array(ss_data)
+        
+        return ss_data
+    
+    except Exception as e:
+        print(f"Error reading file {file}: {e}")
+        return None
+
+def calculate_probabilities(ss_data):
+    """
+    Calculates the probability of each secondary structure.
+
+    Parameters:
+    -----------
+    ss_data : numpy.ndarray
+        Array of secondary structure data.
+
+    Returns:
+    --------
+    probabilities : dict
+        Dictionary with probabilities for each secondary structure.
+    """
+    probabilities = {state: [] for state in state_names.values()}
+    total_frames = ss_data.shape[0]  # Total de frames
+
+    for estado, nome in state_names.items():
+        probabilities[nome] = np.sum(ss_data == estado, axis=1) / ss_data.shape[1]  # Probabilidade por frame
+
+    return probabilities
+
+def plot_ss_boxplot(probabilities_list, labels, colors, output_folder):
+    """
+    Generates a boxplot for secondary structure probabilities.
+
+    Parameters:
+    -----------
+    probabilities_list : list of dict
+        List of dictionaries with probabilities for each simulation.
+    labels : list of str
+        Labels for each simulation.
+    colors : list of str
+        Colors for each simulation.
+    output_folder : str
+        Output folder to save the plots.
+    """
+    # Preparar dados para o boxplot
+    x_labels = list(state_names.values())  # Estruturas secundárias
+    x = np.arange(len(x_labels))  # Posições no eixo X
+
+    # Criar figura para o boxplot
+    plt.figure(figsize=(7, 6))
+    plt.plot()
+
+    # Função para plotar boxplots
+    def plot_boxplot(data, positions, color, label):
+        box = plt.boxplot(data, positions=positions, widths=0.4, patch_artist=True, labels=[label] * len(positions), showfliers=False)  # Remover outliers
+        for boxplot in box['boxes']:
+            boxplot.set_facecolor(color)
+            boxplot.set_alpha(0.7)
+        for median in box['medians']:
+            median.set_color('black')
+        return box
+
+    # Plotar boxplots para cada simulação
+    for i, (probabilities, label, color) in enumerate(zip(probabilities_list, labels, colors)):
+        data = [probabilities[name] * 100 for name in x_labels]
+        plot_boxplot(data, x - 0.25 + i * 0.25, color, label)
+
+    # Configuração do gráfico
+    plt.xlabel('', fontsize=12)
+    plt.ylabel('Probability (%)', fontsize=12)  # Eixo y em percentual
+    plt.title('', fontsize=14, fontweight='bold')
+    plt.xticks(x, x_labels, rotation=45, fontsize=10)
+    plt.yticks(fontsize=10)
+    plt.grid(False)  # Remover a grade
+
+    # Cores e rótulos para a legenda
+    legend_elements = [
+        Patch(facecolor=color, edgecolor='black', linewidth=1.2, alpha=0.7, label=label)
+        for label, color in zip(labels, colors)
+    ]
+
+    # Posicionar a legenda
+    plt.legend(handles=legend_elements, frameon=False, fontsize=10, loc='upper right', edgecolor='black')  # Borda ao redor da legenda
+
+    # Ajustar layout para evitar cortes
+    plt.tight_layout()
+
+    # Salvar o gráfico em 300 dpi (PNG e TIFF)
+    os.makedirs(output_folder, exist_ok=True)  # Create the folder if it doesn't exist
+
+    # Salvar como PNG
+    plt.savefig(os.path.join(output_folder, 'secondary_structure_boxplot.png'), dpi=300, format='png', bbox_inches='tight')
+
+    # Salvar como TIFF
+    plt.savefig(os.path.join(output_folder, 'secondary_structure_boxplot.tiff'), dpi=300, format='tiff', bbox_inches='tight')
+
+    # Mostrar gráfico
+    plt.show()
+
+def ss_analysis(output_folder, *simulation_files_groups):
+    r"""
+    Main function to generate secondary structure analysis and plots.
+
+    Parameters:
+    -----------
+    output_folder : str
+        Output folder to save the plots.
+    \*simulation_files_groups : list of str
+        List of paths to .dat files for each simulation group.
+        You can pass 1, 2, or 3 groups.
+    """
+    # Helper function to process a group of files
+    def process_group(file_paths):
+        ss_data = []
+        for file in file_paths:
+            data = read_ss(file)
+            ss_data.append(data)
+        return ss_data
+    
+    # Process each group of files
+    probabilities_list = []
+    labels = []
+    colors = ['#333333', '#6A9EDA', '#54b36a']  # Cores para cada simulação
+
+    for i, group in enumerate(simulation_files_groups):
+        if group:  # Check if the list is not empty
+            ss_data = process_group(group)
+            probabilities = calculate_probabilities(ss_data[0])  # Assume only one file per group
+            probabilities_list.append(probabilities)
+            labels.append(f'Simulation {i + 1}')
+
+    # Generate plots
+    plot_ss_boxplot(probabilities_list, labels, colors[:len(probabilities_list)], output_folder)

dynamispectra/__init__.py

@@ -0,0 +1,21 @@
+# src/__init__.py
+from .Hbond import read_hbond, hbond_analysis
+from .RMSD import rmsd_analysis
+from .RMSF import read_rmsf, rmsf_analysis
+from .SASA import read_sasa, sasa_analysis
+from .Rg import read_rg, rg_analysis
+from .PCA import pca_analysis
+from .SecondaryStructure import (
+    read_ss,
+    calculate_probabilities,
+    plot_ss_boxplot,
+    ss_analysis,
+    state_mapping,
+    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', '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/main.py

@@ -0,0 +1,4 @@
+# src/dynamispectra/main.py
+
+def main():
+    print("DynamiSpectra is working!")

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-1.0.4.dist-info → dynamispectra-1.0.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: DynamiSpectra
-Version: 1.0.4
+Version: 1.0.6
 Summary: Scripts for Molecular dynamics analysis
 Home-page: https://github.com/Conradoou/DynamiSpectra
 Author: Iverson Conrado-Bezerra

dynamispectra-1.0.6.dist-info/RECORD

@@ -0,0 +1,18 @@
+dynamispectra/FractionSS.py,sha256=-4GiRsvTiwyn5rN17hNKfbmzfevnEOqOm1TxMl8gQOs,3647
+dynamispectra/Hbond.py,sha256=-Mb4g-tITqxEG1VbvYae4TgmTsIRyMis3NEm3Ey9Zu0,8658
+dynamispectra/PCA.py,sha256=nwQ7jEMvuhRAIvRRiGboQ8Cl0qrm15xSgHYCX0HlKiU,3482
+dynamispectra/RMSD.py,sha256=EUSv1Ql0f7P3VRhx6175NxjEn-2cIXx4lbVfeI88Gbk,8622
+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=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/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-1.0.4.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
 

dynamispectra-1.0.6.dist-info/top_level.txt

@@ -0,0 +1 @@
+dynamispectra

dynamispectra-1.0.4.dist-info/RECORD

@@ -1,5 +0,0 @@
-dynamispectra-1.0.4.dist-info/METADATA,sha256=XPOtwawaixbvV5DXlrinQ5uT6_ioStAXufmtQyIAXyI,3807
-dynamispectra-1.0.4.dist-info/WHEEL,sha256=pxyMxgL8-pra_rKaQ4drOZAegBVuX-G_4nRHjjgWbmo,91
-dynamispectra-1.0.4.dist-info/entry_points.txt,sha256=aaQocKWsZi_lJ7MZMsxHmc2DpQF4BSY0fwfE1s0CLxo,37
-dynamispectra-1.0.4.dist-info/top_level.txt,sha256=AbpHGcgLb-kRsJGnwFEktk7uzpZOCcBY74-YBdrKVGs,1
-dynamispectra-1.0.4.dist-info/RECORD,,

dynamispectra-1.0.4.dist-info/top_level.txt

@@ -1 +0,0 @@
-