Utilities

Jupyter Notebook is available at : Utilities¶

In [ ]:

import sys 
import os
sys.path.insert(0, os.path.abspath('..')) 

from docksuitex.utils import (
    fetch_pdb, fetch_sdf, 
    convert, get_supported_formats,
    parse_vina_log, parse_ad4_dlg, 
    view_molecule, view_grid_box, view_docked_poses
)

import sys import os sys.path.insert(0, os.path.abspath('..')) from docksuitex.utils import ( fetch_pdb, fetch_sdf, convert, get_supported_formats, parse_vina_log, parse_ad4_dlg, view_molecule, view_grid_box, view_docked_poses )

1. Molecule Fetching¶

DockSuiteX can download structures by ID from RCSB PDB, PubChem, and ChEMBL. It supports both single-molecule and batch downloads.

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# Batch download proteins (PDB)
protein_files = fetch_pdb(pdbid=["1M17", "1HVR"], save_to="data/proteins")

# Batch download ligands from different sources (PubChem CID and ChEMBL ID)
ligand_files = fetch_sdf(molecule_id=["2244", "CHEMBL25"], save_to="data/ligands")

print(f"Proteins: {protein_files}")
print(f"Ligands: {ligand_files}")

# Batch download proteins (PDB) protein_files = fetch_pdb(pdbid=["1M17", "1HVR"], save_to="data/proteins") # Batch download ligands from different sources (PubChem CID and ChEMBL ID) ligand_files = fetch_sdf(molecule_id=["2244", "CHEMBL25"], save_to="data/ligands") print(f"Proteins: {protein_files}") print(f"Ligands: {ligand_files}")

2. Format Conversion (Open Babel)¶

The convert utility is a powerful wrapper for Open Babel, supporting single files, lists, or entire directories.

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# 1. Convert a single file (e.g., SDF to PDB)
pdb_file = convert(input="data/ligands/2244.sdf", output_format="pdb")

# 2. Convert an entire directory of SDFs to PDBQT for docking
pdbqt_files = convert(input="data/ligands", output_format="pdbqt", output_dir="data/pdbqt_ligands")

# 3. Split a multi-model PDB into individual residue/model files
models = convert(input="multi_model.pdb", output_format="pdb", split=True)

# 4. Check what formats are supported locally
formats = get_supported_formats()
print(f"Supported formats: {len(formats)}")
print(f"Example: {formats['sdf']}")

# 1. Convert a single file (e.g., SDF to PDB) pdb_file = convert(input="data/ligands/2244.sdf", output_format="pdb") # 2. Convert an entire directory of SDFs to PDBQT for docking pdbqt_files = convert(input="data/ligands", output_format="pdbqt", output_dir="data/pdbqt_ligands") # 3. Split a multi-model PDB into individual residue/model files models = convert(input="multi_model.pdb", output_format="pdb", split=True) # 4. Check what formats are supported locally formats = get_supported_formats() print(f"Supported formats: {len(formats)}") print(f"Example: {formats['sdf']}")

3. Advanced Visualization¶

Grid Box Visualization¶

Visualize the docking search space overlayed on your receptor.

In [ ]:

# View 1M17 with a custom 20x20x20 grid box
view_grid_box(
    protein_file="data/proteins/1M17.pdb", 
    grid_center=(25.0, 1.5, 53.0), 
    grid_size=(20, 20, 20)
)

# View 1M17 with a custom 20x20x20 grid box view_grid_box( protein_file="data/proteins/1M17.pdb", grid_center=(25.0, 1.5, 53.0), grid_size=(20, 20, 20) )

Interactive Pose Browser¶

Step through docking poses with full animation controls.

In [ ]:

# This requires a docking output file (pdbqt)
view_docked_poses(protein_file="receptor.pdb", ligand_file="output.pdbqt")

# This requires a docking output file (pdbqt) view_docked_poses(protein_file="receptor.pdb", ligand_file="output.pdbqt")

4. Log Parsing¶

Analyze logs from both AutoDock Vina and AutoDock4.

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# Parse Vina result summary
df_vina = parse_vina_log("vina_log.txt")

# Parse AutoDock4 DLG clusters
df_ad4 = parse_ad4_dlg("dock.dlg")

# Parse Vina result summary df_vina = parse_vina_log("vina_log.txt") # Parse AutoDock4 DLG clusters df_ad4 = parse_ad4_dlg("dock.dlg")