sharpdock 1.0.0__tar.gz

sharpdock-1.0.0/LICENCE

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+MIT License
+
+Copyright (c) 2026 alpha-horizon
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+

sharpdock-1.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: sharpdock
+Version: 1.0.0
+Summary: Automated focused molecular docking pipeline for Autodock Vina
+Author: alpha-horizon
+Requires-Python: >=3.7
+Description-Content-Type: text/markdown
+License-File: LICENCE
+Requires-Dist: numpy
+Requires-Dist: biopython
+Requires-Dist: tqdm
+Dynamic: license-file
+
+# SHARPDOCK v1.0.0
+
+```text
+====================================================
+An Integrated Pipeline for Focused Molecular Docking
+====================================================
+```
+**SHARPDOCK** is a tool, designed for Automated Focused Molecular Docking. It handles the calculating grid box coordinates based on specific amino acid residues to parallelizing ligand preparation and executing AutoDock Vina.
+
+For more tools visit: https://github.com/alpha-horizon
+
+---
+## Features
+
+- Grid Calculation: Automatically centers and sizes the docking box based on a user-provided list of active site residues.
+
+- Parallel Processing: Prepare multiple ligands simultaneously, Can handle ligands in 2D/3D format.
+
+- Summary: Outputs a sorted CSV of binding affinities and organized docking poses.
+
+---
+## Input Requirements
+1. Receptor (-r)
+
+    Format: .pdb
+
+    NOTE: Ensure the protein structure is clean (remove non-essential waters or ions).
+
+2. Ligands (-l)
+
+    Format: .sdf (2D/3D)
+
+    NOTE: Place all ligand files in a single directory.
+
+3. Active Site Specification (-s)
+
+    Use the following format:
+
+    "ChainID:ResidueID ResidueID; ChainID:ResidueID"
+
+    Example: "A:101 102 105; B:45" (This focuses the docking on residues 101, 102, and 105 of Chain A, and residue 45 of Chain B).
+    
+---
+## pip Installation
+
+To install SHARPDOCK, you can use the command mentioned below.
+
+        pip install sharpdock
+        
+---
+## Command Line Usage
+
+This tool supports full argument-based execution for automation and pipelines:
+
+        sharpdock --receptor receptor.pdb --sites "A:101 102; B:70" --ligands ./my_ligands --output results
+
+Options:
+
+        -r	--receptor       Path to receptor PDB file	
+        -s	--sites	         Active site residues (e.g., 'A:10 11; B:50')	
+        -l	--ligands	     Folder containing ligand .sdf files |ligands (default)|
+        -o	--output	     Output directory name |sharpdock_results (default)|
+        -p	--padding	     Grid box padding in Angstroms (Å) |5.0 (default)|
+        -e	--exhaustiveness Vina search exhaustiveness |32 (default)|
+        
+---  
+## Directory Structure
+
+SHARPDOCK organizes your results automatically:
+
+- final_results.csv: A ranked list of ligands and their best binding affinities (kcal/mol).
+
+- docking_outputs/: Contains the .pdbqt files of the docked poses.
+
+- ligands_pdbqt/: The prepared and optimized ligand files.
+
+- box_config.txt: The exact grid coordinates used for the Vina run.
+
+---
+## Contribution
+
+For more tools or to report issues, visit the official GitHub repository:
+
+GitHub: https://github.com/alpha-horizon
+
+---

sharpdock-1.0.0/README.md

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+# SHARPDOCK v1.0.0
+
+```text
+====================================================
+An Integrated Pipeline for Focused Molecular Docking
+====================================================
+```
+**SHARPDOCK** is a tool, designed for Automated Focused Molecular Docking. It handles the calculating grid box coordinates based on specific amino acid residues to parallelizing ligand preparation and executing AutoDock Vina.
+
+For more tools visit: https://github.com/alpha-horizon
+
+---
+## Features
+
+- Grid Calculation: Automatically centers and sizes the docking box based on a user-provided list of active site residues.
+
+- Parallel Processing: Prepare multiple ligands simultaneously, Can handle ligands in 2D/3D format.
+
+- Summary: Outputs a sorted CSV of binding affinities and organized docking poses.
+
+---
+## Input Requirements
+1. Receptor (-r)
+
+    Format: .pdb
+
+    NOTE: Ensure the protein structure is clean (remove non-essential waters or ions).
+
+2. Ligands (-l)
+
+    Format: .sdf (2D/3D)
+
+    NOTE: Place all ligand files in a single directory.
+
+3. Active Site Specification (-s)
+
+    Use the following format:
+
+    "ChainID:ResidueID ResidueID; ChainID:ResidueID"
+
+    Example: "A:101 102 105; B:45" (This focuses the docking on residues 101, 102, and 105 of Chain A, and residue 45 of Chain B).
+    
+---
+## pip Installation
+
+To install SHARPDOCK, you can use the command mentioned below.
+
+        pip install sharpdock
+        
+---
+## Command Line Usage
+
+This tool supports full argument-based execution for automation and pipelines:
+
+        sharpdock --receptor receptor.pdb --sites "A:101 102; B:70" --ligands ./my_ligands --output results
+
+Options:
+
+        -r	--receptor       Path to receptor PDB file	
+        -s	--sites	         Active site residues (e.g., 'A:10 11; B:50')	
+        -l	--ligands	     Folder containing ligand .sdf files |ligands (default)|
+        -o	--output	     Output directory name |sharpdock_results (default)|
+        -p	--padding	     Grid box padding in Angstroms (Å) |5.0 (default)|
+        -e	--exhaustiveness Vina search exhaustiveness |32 (default)|
+        
+---  
+## Directory Structure
+
+SHARPDOCK organizes your results automatically:
+
+- final_results.csv: A ranked list of ligands and their best binding affinities (kcal/mol).
+
+- docking_outputs/: Contains the .pdbqt files of the docked poses.
+
+- ligands_pdbqt/: The prepared and optimized ligand files.
+
+- box_config.txt: The exact grid coordinates used for the Vina run.
+
+---
+## Contribution
+
+For more tools or to report issues, visit the official GitHub repository:
+
+GitHub: https://github.com/alpha-horizon
+
+---

sharpdock-1.0.0/pyproject.toml

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+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "sharpdock"
+version = "1.0.0"
+authors = [{name="alpha-horizon"}]
+description = "Automated focused molecular docking pipeline for Autodock Vina"
+readme = "README.md"
+requires-python = ">=3.7"
+dependencies = [
+    "numpy",
+    "biopython",
+    "tqdm"
+]
+
+[project.scripts]
+sharpdock = "sharpdock.main:main"

sharpdock-1.0.0/setup.cfg

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

sharpdock-1.0.0/sharpdock/__init__.py

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+__version__ = "1.0.0"
+from .main import main

sharpdock-1.0.0/sharpdock/main.py

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+import os
+import subprocess
+import shutil
+import csv
+import argparse
+import numpy as np
+from Bio.PDB import PDBParser
+from multiprocessing import Pool, cpu_count
+from tqdm import tqdm
+import sys
+
+# ===============================
+# HEADER 
+# ===============================
+
+def print_header():
+    header = r"""
+   ===========================================================
+   |                                                         |
+   |    _____ _                          _            _      |
+   |   / ____| |                        | |          | |     |
+   |  | (___ | |__   __ _ _ __ _ __   __| | ___   ___| | __  |
+   |   \___ \| '_ \ / _` | '__| '_ \ / _` |/ _ \ / __| |/ /  |
+   |   ____) | | | | (_| | |  | |_) | (_| | (_) | (__|   <   |
+   |  |_____/|_| |_|\__,_|_|  | .__/ \__,_|\___/ \___|_|\_\  |
+   |                          | |                            |
+   |                          |_|                            | 
+   |  [VERSION: 1.0.0]                                       |
+   |                                                         |
+   |  - An automated tool for focused molecular docking -    |
+   |                                                         |
+   |        GitHub: https://github.com/alpha-horizon/        |
+   |                                                         |
+   ===========================================================
+    """
+    print(header)
+
+def compute_box(receptor_pdb, chain_res_map, padding):
+    """Calculates the center and size of the grid box based on active site residues."""
+    parser = PDBParser(QUIET=True)
+    structure = parser.get_structure("rec", receptor_pdb)
+    coords = []
+    
+    for model in structure:
+        for chain in model:
+            if chain.id not in chain_res_map:
+                continue
+            for res in chain:
+                if res.id[1] not in chain_res_map[chain.id]:
+                    continue
+                for atom in res:
+                    coords.append(atom.get_coord())
+
+    if not coords:
+        print(f"Error: No residues found for {chain_res_map}. Check your PDB file.")
+        sys.exit(1)
+
+    coords = np.array(coords)
+    center = coords.mean(axis=0)
+    size = coords.max(axis=0) - coords.min(axis=0) + padding
+    return center, size
+
+def process_ligand(args_tuple):
+    """Worker function for parallel ligand preparation."""
+    f, ligand_dir, pdbqt_dir = args_tuple
+    base = os.path.splitext(f)[0]
+    sdf_input = os.path.join(ligand_dir, f)
+    sdf_h = os.path.join(ligand_dir, f"{base}_H.sdf")
+    pdbqt_out = os.path.join(pdbqt_dir, f"{base}.pdbqt")
+
+    try:
+        # Scrub/Optimize Ligand
+        subprocess.run(["scrub.py", sdf_input, "-o", sdf_h], capture_output=True, check=True)
+        # Convert to PDBQT
+        subprocess.run(["mk_prepare_ligand.py", "-i", sdf_h, "-o", pdbqt_out], capture_output=True, check=True)
+        
+        if os.path.exists(sdf_h):
+            os.remove(sdf_h)
+        return f"{base}: Success"
+    except Exception as e:
+        return f"{base}: Failed - {str(e)}"
+
+def main():
+    # 1. Call the header first
+    print_header()
+
+    # Create a formatter that allows more room for long argument names
+    formatter = lambda prog: argparse.HelpFormatter(prog, max_help_position=40)
+
+    parser = argparse.ArgumentParser(
+        description="[SharpDock: Automated Focused Molecular Docking]",
+        formatter_class=formatter
+    )
+    
+    # Add Version Flag
+    parser.add_argument("-v", "--version", action="version", version="sharpdock 1.0.0") 
+    
+    # Arguments with improved help descriptions for better alignment
+    parser.add_argument("-r", "--receptor", required=True, help="Path to receptor PDB file")
+    parser.add_argument("-s", "--sites", required=True, help="Active sites (e.g., 'A:101 102; B:70')")
+    parser.add_argument("-l", "--ligands", default="ligands", help="Folder containing ligands in .sdf format")
+    parser.add_argument("-o", "--output", default="sharpdock_results", help="Directory for output files")
+    parser.add_argument("-p", "--padding", type=float, default=5.0, help="Grid box padding in Å")
+    parser.add_argument("-e", "--exhaustiveness", type=int, default=32, help="Vina search exhaustiveness")
+    
+    args = parser.parse_args()
+
+    # Create Directories
+    os.makedirs(args.output, exist_ok=True)
+    pdbqt_lig_dir = os.path.join(args.output, "ligands_pdbqt")
+    raw_out_dir = os.path.join(args.output, "docking_outputs")
+    os.makedirs(pdbqt_lig_dir, exist_ok=True)
+    os.makedirs(raw_out_dir, exist_ok=True)
+
+    # Parse Chain/Residue Mapping
+    try:
+        chain_res_map = {}
+        for block in args.sites.split(";"):
+            ch, res = block.split(":")
+            chain_res_map[ch.strip()] = [int(r) for r in res.split()]
+    except Exception:
+        print("Error: Sites format invalid. Use 'A:101 102; B:70'")
+        sys.exit(1)
+
+    # 1. Compute Box
+    center, size = compute_box(args.receptor, chain_res_map, args.padding)
+    config_path = os.path.join(args.output, "box_config.txt")
+    with open(config_path, "w") as f:
+        f.write(f"center_x = {center[0]:.3f}\ncenter_y = {center[1]:.3f}\ncenter_z = {center[2]:.3f}\n")
+        f.write(f"size_x = {size[0]:.3f}\nsize_y = {size[1]:.3f}\nsize_z = {size[2]:.3f}\n")
+
+    # 2. Prepare Receptor
+    rec_pdbqt = os.path.join(args.output, "receptor.pdbqt")
+    print(f"[*] Preparing {args.receptor}...")
+    subprocess.run([
+        "mk_prepare_receptor.py", "-i", args.receptor, "-o", rec_pdbqt,
+        "--box_center", f"{center[0]}", f"{center[1]}", f"{center[2]}",
+        "--box_size", f"{size[0]}", f"{size[1]}", f"{size[2]}"
+    ], check=True)
+
+    # 3. Parallel Ligand Preparation
+    lig_files = [f for f in os.listdir(args.ligands) if f.endswith(".sdf")]
+    print(f"[*] Preparing {len(lig_files)} ligands...")
+    prep_args = [(f, args.ligands, pdbqt_lig_dir) for f in lig_files]
+    with Pool(cpu_count()) as pool:
+        list(tqdm(pool.imap(process_ligand, prep_args), total=len(lig_files)))
+
+    # 4. Docking with Vina
+    print("[*] Starting Docking...")
+    results = []
+    pdbqt_ligs = [f for f in os.listdir(pdbqt_lig_dir) if f.endswith(".pdbqt")]
+    
+    for lig_file in tqdm(pdbqt_ligs, desc="Docking progress"):
+        base = os.path.splitext(lig_file)[0]
+        lig_path = os.path.join(pdbqt_lig_dir, lig_file)
+        out_path = os.path.join(raw_out_dir, f"{base}_out.pdbqt")
+        
+        subprocess.run([
+            "vina", "--receptor", rec_pdbqt, "--ligand", lig_path,
+            "--config", config_path, "--exhaustiveness", str(args.exhaustiveness),
+            "--out", out_path
+        ], capture_output=True)
+
+        if os.path.exists(out_path):
+            with open(out_path) as f:
+                for line in f:
+                    if "REMARK VINA RESULT:" in line:
+                        affinity = float(line.split()[3])
+                        results.append([base, affinity])
+                        break
+
+    # 5. Export Results
+    results.sort(key=lambda x: x[1])
+    with open(os.path.join(args.output, "final_results.csv"), "w", newline="") as f:
+        writer = csv.writer(f)
+        writer.writerow(["Ligand", "Affinity_kcal_mol"])
+        writer.writerows(results)
+
+    print(f"\n[SUCCESS] Workflow completed. Results saved in: {args.output}")
+
+if __name__ == "__main__":
+    main()

sharpdock-1.0.0/sharpdock.egg-info/PKG-INFO

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+Metadata-Version: 2.4
+Name: sharpdock
+Version: 1.0.0
+Summary: Automated focused molecular docking pipeline for Autodock Vina
+Author: alpha-horizon
+Requires-Python: >=3.7
+Description-Content-Type: text/markdown
+License-File: LICENCE
+Requires-Dist: numpy
+Requires-Dist: biopython
+Requires-Dist: tqdm
+Dynamic: license-file
+
+# SHARPDOCK v1.0.0
+
+```text
+====================================================
+An Integrated Pipeline for Focused Molecular Docking
+====================================================
+```
+**SHARPDOCK** is a tool, designed for Automated Focused Molecular Docking. It handles the calculating grid box coordinates based on specific amino acid residues to parallelizing ligand preparation and executing AutoDock Vina.
+
+For more tools visit: https://github.com/alpha-horizon
+
+---
+## Features
+
+- Grid Calculation: Automatically centers and sizes the docking box based on a user-provided list of active site residues.
+
+- Parallel Processing: Prepare multiple ligands simultaneously, Can handle ligands in 2D/3D format.
+
+- Summary: Outputs a sorted CSV of binding affinities and organized docking poses.
+
+---
+## Input Requirements
+1. Receptor (-r)
+
+    Format: .pdb
+
+    NOTE: Ensure the protein structure is clean (remove non-essential waters or ions).
+
+2. Ligands (-l)
+
+    Format: .sdf (2D/3D)
+
+    NOTE: Place all ligand files in a single directory.
+
+3. Active Site Specification (-s)
+
+    Use the following format:
+
+    "ChainID:ResidueID ResidueID; ChainID:ResidueID"
+
+    Example: "A:101 102 105; B:45" (This focuses the docking on residues 101, 102, and 105 of Chain A, and residue 45 of Chain B).
+    
+---
+## pip Installation
+
+To install SHARPDOCK, you can use the command mentioned below.
+
+        pip install sharpdock
+        
+---
+## Command Line Usage
+
+This tool supports full argument-based execution for automation and pipelines:
+
+        sharpdock --receptor receptor.pdb --sites "A:101 102; B:70" --ligands ./my_ligands --output results
+
+Options:
+
+        -r	--receptor       Path to receptor PDB file	
+        -s	--sites	         Active site residues (e.g., 'A:10 11; B:50')	
+        -l	--ligands	     Folder containing ligand .sdf files |ligands (default)|
+        -o	--output	     Output directory name |sharpdock_results (default)|
+        -p	--padding	     Grid box padding in Angstroms (Å) |5.0 (default)|
+        -e	--exhaustiveness Vina search exhaustiveness |32 (default)|
+        
+---  
+## Directory Structure
+
+SHARPDOCK organizes your results automatically:
+
+- final_results.csv: A ranked list of ligands and their best binding affinities (kcal/mol).
+
+- docking_outputs/: Contains the .pdbqt files of the docked poses.
+
+- ligands_pdbqt/: The prepared and optimized ligand files.
+
+- box_config.txt: The exact grid coordinates used for the Vina run.
+
+---
+## Contribution
+
+For more tools or to report issues, visit the official GitHub repository:
+
+GitHub: https://github.com/alpha-horizon
+
+---

sharpdock-1.0.0/sharpdock.egg-info/SOURCES.txt

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+LICENCE
+README.md
+pyproject.toml
+sharpdock/__init__.py
+sharpdock/main.py
+sharpdock.egg-info/PKG-INFO
+sharpdock.egg-info/SOURCES.txt
+sharpdock.egg-info/dependency_links.txt
+sharpdock.egg-info/entry_points.txt
+sharpdock.egg-info/requires.txt
+sharpdock.egg-info/top_level.txt

sharpdock-1.0.0/sharpdock.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

sharpdock-1.0.0/sharpdock.egg-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+sharpdock = sharpdock.main:main

sharpdock-1.0.0/sharpdock.egg-info/requires.txt

@@ -0,0 +1,3 @@
+numpy
+biopython
+tqdm

sharpdock-1.0.0/sharpdock.egg-info/top_level.txt

@@ -0,0 +1 @@
+sharpdock