sharpdock 1.0.0__py3-none-any.whl → 2.0.0__py3-none-any.whl

sharpdock/__init__.py

@@ -1,2 +1,2 @@
-__version__ = "1.0.0"
+__version__ = "2.0.0"
 from .main import main

sharpdock/main.py

@@ -10,29 +10,29 @@ from tqdm import tqdm
 import sys
 
 # ===============================
-# HEADER 
+# HEADER
 # ===============================
 
 def print_header():
     header = r"""
-   ===========================================================
-   |                                                         |
-   |    _____ _                          _            _      |
-   |   / ____| |                        | |          | |     |
-   |  | (___ | |__   __ _ _ __ _ __   __| | ___   ___| | __  |
-   |   \___ \| '_ \ / _` | '__| '_ \ / _` |/ _ \ / __| |/ /  |
-   |   ____) | | | | (_| | |  | |_) | (_| | (_) | (__|   <   |
-   |  |_____/|_| |_|\__,_|_|  | .__/ \__,_|\___/ \___|_|\_\  |
-   |                          | |                            |
-   |                          |_|                            | 
-   |  [VERSION: 1.0.0]                                       |
-   |                                                         |
-   |  - An automated tool for focused molecular docking -    |
-   |                                                         |
-   |        GitHub: https://github.com/alpha-horizon/        |
-   |                                                         |
-   ===========================================================
-    """
+===========================================================
+|                                                         |
+|    _____ _                          _             _     |
+|   / ____| |                        | |           | |    |
+|  | (___ | |__   __ _ _ __ _ __   __| | ___   ___| | __  |
+|   \___ \| '_ \ / _` | '__| '_ \ / _` |/ _ \ / __| |/ /  |
+|   ____) | | | | (_| | |  | |_) | (_| | (_) | (__|   <   |
+|  |_____/|_| |_|\__,_|_|  | .__/ \__,_|\___/ \___|_|\_\  |
+|                          | |                            |
+|                          |_|                            |
+|  [VERSION: 2.0.0]                                       |
+|                                                         |
+|  - An automated tool for focused molecular docking -    |
+|                                                         |
+|        GitHub: https://github.com/alpha-horizon/        |
+|                                                         |
+===========================================================
+"""
     print(header)
 
 def compute_box(receptor_pdb, chain_res_map, padding):
@@ -40,19 +40,16 @@ def compute_box(receptor_pdb, chain_res_map, padding):
     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
+            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
+                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.")
+        print(f"\nError: No coordinates found for residues {chain_res_map}!\n")
         sys.exit(1)
 
     coords = np.array(coords)
@@ -60,7 +57,7 @@ def compute_box(receptor_pdb, chain_res_map, padding):
     size = coords.max(axis=0) - coords.min(axis=0) + padding
     return center, size
 
-def process_ligand(args_tuple):
+def process_ligand_task(args_tuple):
     """Worker function for parallel ligand preparation."""
     f, ligand_dir, pdbqt_dir = args_tuple
     base = os.path.splitext(f)[0]
@@ -73,91 +70,128 @@ def process_ligand(args_tuple):
         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)}"
+        return True
+    except Exception:
+        return False
 
 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]",
+        description="[SHARPDOCK: AN INTEGRATED PIPELINE FOR 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("-l", "--ligands", default="ligands", help="Folder with 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")
+    parser.add_argument("-n", "--top_hits", type=int, default=10, help="Number of top ligands to export")
     
     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)
+    # Paths Setup
+    RECEPTOR_PDB = args.receptor
+    LIGAND_DIR = args.ligands
+    OUTPUT_DIR = args.output
+    top_n_count = args.top_hits
+    padding = args.padding
+    
+    LIGAND_PDBQT_DIR = os.path.join(OUTPUT_DIR, "ligands_pdbqt")
+    RAW_OUTPUT = os.path.join(OUTPUT_DIR, "raw_output")
+    TOP_HITS_DIR = os.path.join(OUTPUT_DIR, "top_hits")
+    ALL_RESULTS_CSV = os.path.join(OUTPUT_DIR, "docking_results.csv")
+    AFFINITY_LOG = os.path.join(OUTPUT_DIR, "binding_affinities.log")
+    BOX_CONFIG = os.path.join(OUTPUT_DIR, "receptor.box.txt")
+    RECEPTOR_PDBQT = os.path.join(OUTPUT_DIR, "receptor.pdbqt")
+
+    os.makedirs(OUTPUT_DIR, exist_ok=True)
+    os.makedirs(LIGAND_PDBQT_DIR, exist_ok=True)
+    os.makedirs(RAW_OUTPUT, exist_ok=True)
+    os.makedirs(TOP_HITS_DIR, exist_ok=True)
 
     # Parse Chain/Residue Mapping
+    CHAIN_RES_MAP = {}
     try:
-        chain_res_map = {}
         for block in args.sites.split(";"):
+            block = block.strip()
+            if not block: continue
             ch, res = block.split(":")
-            chain_res_map[ch.strip()] = [int(r) for r in res.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'")
+        print("\nError: Sites format invalid. Use 'A:101 102; B:70'\n")
         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:
+    # STEP 1 — Compute Grid Box
+    print("# Grid box calculation.\n")
+    parser_pdb = PDBParser(QUIET=True)
+    # Corrected: Use RECEPTOR_PDB here because RECEPTOR_PDBQT is not created yet
+    structure = parser_pdb.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("Error: No coordinates found for specified residues!\n")
+        sys.exit(1)
+
+    coords = np.array(coords)
+    center = coords.mean(axis=0)
+    size = coords.max(axis=0) - coords.min(axis=0) + padding
+
+    with open(BOX_CONFIG, "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]
+    # STEP 2 — Prepare Receptor
+    print("# Receptor preparation.\n")
+    RECEPTOR_LOG = os.path.join(OUTPUT_DIR, "receptor_preparation.log")
+    rec_out_base = RECEPTOR_PDBQT.replace(".pdbqt", "")
+
+    with open(RECEPTOR_LOG, "w") as log_file:
+        subprocess.run(
+            [
+                "mk_prepare_receptor.py", "-i", RECEPTOR_PDB, "-o", rec_out_base,
+                "-p", "-v", "--box_center", f"{center[0]}", f"{center[1]}", f"{center[2]}",
+                "--box_size", f"{size[0]}", f"{size[1]}", f"{size[2]}",
+                "--default_altloc", "A", "--allow_bad_res", "-a"
+            ],
+            stdout=log_file, stderr=log_file
+        )
+
+    # STEP 3 — Prepare Ligands (Parallel)
+    ligand_files = [f for f in os.listdir(LIGAND_DIR) if f.endswith(".sdf")]
+    print(f"# Preparing {len(ligand_files)} ligands.\n")
+    
+    task_args = [(f, LIGAND_DIR, LIGAND_PDBQT_DIR) for f in ligand_files]
+
     with Pool(cpu_count()) as pool:
-        list(tqdm(pool.imap(process_ligand, prep_args), total=len(lig_files)))
+        list(tqdm(pool.imap_unordered(process_ligand_task, task_args), total=len(ligand_files), ascii=" ."))
 
-    # 4. Docking with Vina
-    print("[*] Starting Docking...")
+    # STEP 4 — Docking
+    print("\n# FOCUSED Molecular Docking started.\n")
     results = []
-    pdbqt_ligs = [f for f in os.listdir(pdbqt_lig_dir) if f.endswith(".pdbqt")]
+    pdbqt_ligands = [f for f in os.listdir(LIGAND_PDBQT_DIR) if f.endswith(".pdbqt")]
     
-    for lig_file in tqdm(pdbqt_ligs, desc="Docking progress"):
+    for lig_file in tqdm(pdbqt_ligands, desc="Autodock Vina - Molecular Docking Progress", ascii=" ."):
         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")
-        
+        out_path = os.path.join(RAW_OUTPUT, f"{base}_out.pdbqt")
         subprocess.run([
-            "vina", "--receptor", rec_pdbqt, "--ligand", lig_path,
-            "--config", config_path, "--exhaustiveness", str(args.exhaustiveness),
+            "vina", "--receptor", RECEPTOR_PDBQT, 
+            "--ligand", os.path.join(LIGAND_PDBQT_DIR, lig_file),
+            "--config", BOX_CONFIG, "--exhaustiveness", str(args.exhaustiveness),
             "--out", out_path
         ], capture_output=True)
 
@@ -165,18 +199,52 @@ def main():
             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])
+                        results.append([base, float(line.split()[3])])
                         break
 
-    # 5. Export Results
+    # Save and Sort Results
     results.sort(key=lambda x: x[1])
-    with open(os.path.join(args.output, "final_results.csv"), "w", newline="") as f:
+    
+    # Write CSV
+    with open(ALL_RESULTS_CSV, "w", newline="") as f:
         writer = csv.writer(f)
-        writer.writerow(["Ligand", "Affinity_kcal_mol"])
+        writer.writerow(["ligand", "binding_affinity (kcal/mol)"])
         writer.writerows(results)
 
-    print(f"\n[SUCCESS] Workflow completed. Results saved in: {args.output}")
+    # STEP 5 — Create Binding Affinities Log File
+    with open(AFFINITY_LOG, "w") as f:
+        # Header Section
+        f.write("-" * 80 + "\n")
+        f.write("=====[ <SHARPDOCK> - AN INTEGRATED PIPELINE FOR FOCUSED MOLECULAR DOCKING ]=====\n")
+        f.write("-" * 80 + "\n")
+        f.write(f"Receptor:      {args.receptor}\n")
+        f.write(f"Active Sites Selected:  {args.sites}\n")
+        f.write(f"Total Ligands: {len(results)}\n")
+        f.write("-" * 80 + "\n\n")
+        
+        # Table Header
+        f.write(f"{'Ligand Name':<45} | {'Affinity (kcal/mol)':<20}\n")
+        f.write("-" * 80 + "\n")
+        
+        # Data Rows
+        for name, affinity in results:
+            f.write(f"{name:<45} | {affinity:<20.2f}\n")
+            
+        # Footer
+        f.write("-" * 80 + "\n")
+        f.write("[ END OF REPORT ]\n")
+        f.write("-" * 80 + "\n")
+
+    # STEP 6 — Export Top Hits
+    print(f"\n# Exporting Top {top_n_count} hits to {TOP_HITS_DIR}")
+    
+    for i, (name, affinity) in enumerate(results[:top_n_count]):
+        source_file = os.path.join(RAW_OUTPUT, f"{name}_out.pdbqt")
+        dest_file = os.path.join(TOP_HITS_DIR, f"{name}.pdbqt")
+        if os.path.exists(source_file):
+            shutil.copy(source_file, dest_file)
+
+    print(f"\n===== |SHARPDOCK| < FOCUSED MOLECULAR DOCKING Completed! > Check for the Results in: {OUTPUT_DIR} =====\n")
 
 if __name__ == "__main__":
     main()

sharpdock-2.0.0.dist-info/METADATA

@@ -0,0 +1,105 @@
+Metadata-Version: 2.4
+Name: sharpdock
+Version: 2.0.0
+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 v2.0.0
+
+```text
+====================================================
+An Integrated Pipeline for Focused Molecular Docking
+====================================================
+```
+**SHARPDOCK** is a high-throughput, automated pipeline for focused molecular docking. It handles the ranking of ligands based on binding affinities by automating grid box generation, receptor/ligand preparation, and parallelized docking execution using AutoDock Vina.
+
+For more tools visit: https://github.com/alpha-horizon
+
+---
+## Features
+
+- Automated Grid Box Calculation: No more manual coordinate entry; define sites by chain and residue ID.
+
+- Parallel Ligand Preparation: Process large libraries of ligands in .sdf format.
+
+- Vina Integration: Seamlessly communicates with AutoDock Vina for industry-standard accuracy.
+
+- Formatted Reporting: Generates publication-ready CSVs and detailed log reports.
+
+- Top-Hit Extraction: Automatically isolates the most promising leads for downstream analysis.
+
+---
+## Input Requirements
+
+1. Receptor File (-r / --receptor)
+
+    Format: Standard .pdb file.
+    Note: It is recommended to remove water molecules, ions, and co-crystallized ligands from the PDB file before running the pipeline to prevent interference with the grid box calculation.
+
+2. Ligand Files (-l / --ligands)
+
+    Format: .sdf (Structure Data File).
+    Note: You can input ligands in 2D or 3D structure.
+
+3. Active Site Specification (-s / --sites)
+
+    The site string is the most critical input for Focused Docking. Use the following syntax:
+
+    Single Chain: "A:101 102 105"
+
+    Multiple Chains: "A:101 102; B:70 71"
+
+    Format: ChainID:ResidueID ResidueID; ChainID:ResidueID
+    
+---
+## 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 -r receptor.pdb -s "A:101 102; B:70" -l ./ligands -n 10
+
+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)|
+        -n	--top_hits	Number of top ligands to export	|10 (default)|
+        
+---  
+## Directory Structure
+
+- After execution, the output folder contains:
+
+- top_hits/: The best-scoring docked poses.
+
+- docking_results.csv: Comprehensive spreadsheet of all scores.
+
+- binding_affinities.log: A human-readable summary of the run parameters and results.
+
+- receptor.box.txt: The specific Vina configuration used for the grid.
+
+---
+## Contribution
+
+For more tools or to report issues, visit the official GitHub repository:
+
+GitHub: https://github.com/alpha-horizon
+
+---

sharpdock-2.0.0.dist-info/RECORD

@@ -0,0 +1,8 @@
+sharpdock/__init__.py,sha256=wI1PAOu7oSRWBxlVwLNFbsLA7lp8jv8C5-0K1rNbOWs,45
+sharpdock/main.py,sha256=j8-F7dw8mzuWEGKfLzT7W4jYIJKc-Sg3vu_JHk_wzY8,10008
+sharpdock-2.0.0.dist-info/licenses/LICENCE,sha256=g2i5njDeeyhislJ5tD5wlc3TLzukLmzxC7Z6sy5sLyk,1071
+sharpdock-2.0.0.dist-info/METADATA,sha256=8FZrz9Uwy4lDb78rEWJsen5MFvYv436dm7sBMhKc8xI,3308
+sharpdock-2.0.0.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+sharpdock-2.0.0.dist-info/entry_points.txt,sha256=X2nQpVbNCpGp442r5rnklFOChB7-txNhPtws30rhgr8,50
+sharpdock-2.0.0.dist-info/top_level.txt,sha256=pgak3KuZWSs6n1jG0120R_CMc9mt5qv4CSdPofGPSEo,10
+sharpdock-2.0.0.dist-info/RECORD,,

sharpdock-1.0.0.dist-info/METADATA

@@ -1,99 +0,0 @@
-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.dist-info/RECORD

@@ -1,8 +0,0 @@
-sharpdock/__init__.py,sha256=1xlnfAI0MBZmD--KdQ936I89GPE5Hqk1gIKYcsXrfxk,45
-sharpdock/main.py,sha256=bDMlJt9A-HHc6j5-nxKnP8DqKHHe9uEJEeNGNrb39b4,7350
-sharpdock-1.0.0.dist-info/licenses/LICENCE,sha256=g2i5njDeeyhislJ5tD5wlc3TLzukLmzxC7Z6sy5sLyk,1071
-sharpdock-1.0.0.dist-info/METADATA,sha256=vvUZ5d1Cp5cE4waD_COPspUazrpbf-UqC5SEYOMF4sg,2936
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