vdw-surfgen 0.1__tar.gz

vdw_surfgen-0.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: vdw-surfgen
+Version: 0.1
+Summary: Generate van der Waals surface points from XYZ molecules
+Author: Stephen O. Ajagbe
+Requires-Python: >=3.7
+Requires-Dist: numpy
+Requires-Dist: matplotlib
+Dynamic: author
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary

vdw_surfgen-0.1/pyproject.toml

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+[build-system]
+requires = ["setuptools", "wheel"]
+build-backend = "setuptools.build_meta"

vdw_surfgen-0.1/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

vdw_surfgen-0.1/setup.py

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+from setuptools import setup, find_packages
+
+setup(
+    name="vdw-surfgen",
+    version="0.1",
+    packages=find_packages(),
+    install_requires=["numpy", "matplotlib"],
+    entry_points={
+        "console_scripts": [
+            "vsg=vdw_surfgen.cli:cli_entry",
+        ]
+    },
+    author="Stephen O. Ajagbe",
+    description="Generate van der Waals surface points from XYZ molecules",
+    python_requires=">=3.7",
+)

vdw_surfgen-0.1/vdw_surfgen/__init__.py

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+__version__ = "0.1"

vdw_surfgen-0.1/vdw_surfgen/cli.py

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+import argparse
+import numpy as np
+import os
+from pathlib import Path
+import matplotlib.pyplot as plt
+
+VDW_RADII = {  # shortened for brevity
+    'H': 1.20, 'C': 1.70, 'N': 1.55, 'O': 1.52, 'F': 1.47, 'P': 1.80, 'S': 1.80, 'Cl': 1.75,
+    'Br': 1.85, 'I': 1.98, 'He': 1.40, 'Ne': 1.54, 'Ar': 1.88, 'Kr': 2.02, 'Xe': 2.16,
+    'Li': 1.82, 'Na': 2.27, 'K': 2.75, 'Rb': 3.03, 'Cs': 3.43, 'Fr': 3.48, 'Be': 2.00,
+    'Mg': 1.73, 'Ca': 2.31, 'Sr': 2.49, 'Ba': 2.68, 'Ra': 2.83, 'B': 1.92, 'Al': 1.84,
+    'Si': 2.10, 'Ti': 2.15, 'Fe': 2.00, 'Zn': 2.10, 'Cu': 1.95, 'Mn': 2.05, 'Hg': 2.05,
+    'Pb': 2.02, 'U': 1.86
+}
+
+def read_xyz_file(filepath):
+    with open(filepath) as f:
+        lines = f.readlines()
+    natoms = int(lines[0])
+    atom_types = []
+    coords = []
+    for line in lines[2:2 + natoms]:
+        parts = line.split()
+        atom_types.append(parts[0])
+        coords.append([float(x) for x in parts[1:4]])
+    return atom_types, np.array(coords)
+
+
+def fibonacci_sphere(samples):
+    indices = np.arange(0, samples, dtype=float) + 0.5
+    phi = np.arccos(1 - 2 * indices / samples)
+    theta = np.pi * (1 + 5 ** 0.5) * indices
+    x = np.cos(theta) * np.sin(phi)
+    y = np.sin(theta) * np.sin(phi)
+    z = np.cos(phi)
+    return np.stack((x, y, z), axis=1)
+
+
+def generate_surface(coordinates, elements, scale_factor=1.0, density=1.0):
+    surface_points = []
+    for pos, elem in zip(coordinates, elements):
+        r = VDW_RADII.get(elem, 1.5) * scale_factor
+        area = 4 * np.pi * r ** 2
+        n_points = max(10, int(area * density))
+        directions = fibonacci_sphere(n_points)
+        points = pos + directions * r
+        surface_points.append(points)
+    return np.concatenate(surface_points, axis=0)
+
+
+def save_txt(filename, coords):
+    with open(filename, 'w') as f:
+        for p in coords:
+            f.write(f"{p[0]:.6f} {p[1]:.6f} {p[2]:.6f}\n")
+
+
+def save_xyz(filename, coords, atom='X'):
+    with open(filename, 'w') as f:
+        f.write(f"{len(coords)}\n")
+        f.write("VDW surface points\n")
+        for p in coords:
+            f.write(f"{atom} {p[0]:.6f} {p[1]:.6f} {p[2]:.6f}\n")
+
+
+def save_surface_figure(coords, original_coords, output_path):
+    fig = plt.figure(figsize=(8, 6))
+    ax = fig.add_subplot(projection='3d')
+    ax.scatter(coords[:, 0], coords[:, 1], coords[:, 2], s=1, alpha=0.5, label='VDW surface')
+    ax.scatter(original_coords[:, 0], original_coords[:, 1], original_coords[:, 2],
+               color='red', s=20, label='Atoms')
+    ax.set_xlabel('X')
+    ax.set_ylabel('Y')
+    ax.set_zlabel('Z')
+    ax.legend()
+    plt.tight_layout()
+    plt.savefig(output_path, dpi=300)
+    plt.close()
+
+
+def main():
+    parser = argparse.ArgumentParser(description="Generate VDW surface points from an XYZ file.")
+    parser.add_argument("xyz_file", help="Path to input XYZ file")
+    parser.add_argument("--scale", type=float, default=1.0, help="Scale factor for VDW radii (default: 1.0)")
+    parser.add_argument("--density", type=float, default=1.0, help="Point density per Ų (default: 1.0)")
+    parser.add_argument("--save_txt", action="store_true", help="Save surface points as TXT file")
+    parser.add_argument("--save_xyz", action="store_true", help="Save surface points as XYZ file")
+    parser.add_argument("--save_img", action="store_true", help="Save 3D surface plot image")
+
+    args = parser.parse_args()
+    xyz_file = args.xyz_file
+
+    if not os.path.isfile(xyz_file):
+        print(f"File not found: {xyz_file}")
+        return
+
+    name = Path(xyz_file).stem
+    elements, coords = read_xyz_file(xyz_file)
+    surface = generate_surface(coords, elements, scale_factor=args.scale, density=args.density)
+
+    if args.save_txt:
+        save_txt(f"{name}_vdw_surface.txt", surface)
+    if args.save_xyz:
+        save_xyz(f"{name}_vdw_surface.xyz", surface)
+    if args.save_img:
+        save_surface_figure(surface, coords, f"{name}_vdw_surface.png")
+
+    print(f"Generated {len(surface)} surface points.")
+    if args.save_txt or args.save_xyz or args.save_img:
+        print("Saved outputs:")
+        if args.save_txt:
+            print(f" - {name}_vdw_surface.txt")
+        if args.save_xyz:
+            print(f" - {name}_vdw_surface.xyz")
+        if args.save_img:
+            print(f" - {name}_vdw_surface.png")
+
+
+def cli_entry():
+    main()

vdw_surfgen-0.1/vdw_surfgen.egg-info/PKG-INFO

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+Metadata-Version: 2.4
+Name: vdw-surfgen
+Version: 0.1
+Summary: Generate van der Waals surface points from XYZ molecules
+Author: Stephen O. Ajagbe
+Requires-Python: >=3.7
+Requires-Dist: numpy
+Requires-Dist: matplotlib
+Dynamic: author
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary

vdw_surfgen-0.1/vdw_surfgen.egg-info/SOURCES.txt

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+pyproject.toml
+setup.py
+vdw_surfgen/__init__.py
+vdw_surfgen/cli.py
+vdw_surfgen.egg-info/PKG-INFO
+vdw_surfgen.egg-info/SOURCES.txt
+vdw_surfgen.egg-info/dependency_links.txt
+vdw_surfgen.egg-info/entry_points.txt
+vdw_surfgen.egg-info/requires.txt
+vdw_surfgen.egg-info/top_level.txt

vdw_surfgen-0.1/vdw_surfgen.egg-info/dependency_links.txt

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+

vdw_surfgen-0.1/vdw_surfgen.egg-info/entry_points.txt

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+[console_scripts]
+vsg = vdw_surfgen.cli:cli_entry

vdw_surfgen-0.1/vdw_surfgen.egg-info/requires.txt

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+numpy
+matplotlib

vdw_surfgen-0.1/vdw_surfgen.egg-info/top_level.txt

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+vdw_surfgen