Skip to content

Builder API

The PRISMBuilder module provides automated protein-ligand system construction for GROMACS simulations.

PRISMBuilder

Main class for building protein-ligand MD systems.

from prism import PRISMBuilder

builder = PRISMBuilder(
    protein_path="protein.pdb",
    ligand_path="ligand.mol2",
    output_dir="my_system",
    ligand_forcefield="gaff",
    config_path=None,
    forcefield="amber99sb",
    water_model="tip3p"
)

Parameters

  • protein_path (str): Path to protein PDB file
  • ligand_path (str): Path to ligand MOL2/SDF file
  • output_dir (str): Output directory
  • ligand_forcefield (str): Ligand force field (gaff, gaff2, openff, opls, etc.)
  • config_path (str, optional): YAML configuration file
  • forcefield (str, optional): Protein force field
  • water_model (str, optional): Water model (tip3p, tip4p, spce)

Methods

run()

Build complete MD system.

builder.run()

generate_ligand_forcefield()

Generate ligand force field parameters.

lig_ff_dir = builder.generate_ligand_forcefield()

Returns: Path to ligand force field directory

clean_protein()

Clean and prepare protein structure.

cleaned = builder.clean_protein(
    ion_mode='smart',
    distance_cutoff=5.0,
    keep_crystal_water=False
)

Parameters: - ion_mode (str): 'smart', 'keep_all', or 'remove_all' - distance_cutoff (float): Distance in Å for metal ion filtering - keep_crystal_water (bool): Keep crystallographic water

Returns: Path to cleaned protein file

build_model()

Build GROMACS topology and coordinate files.

model_dir = builder.build_model(protein_file)

generate_mdp_files()

Generate MD parameter files.

builder.generate_mdp_files()

generate_localrun_script()

Create automation script for running MD.

script_path = builder.generate_localrun_script()

PRISMSystem

High-level system interface.

import prism

system = prism.system(
    "protein.pdb",
    "ligand.mol2",
    output_dir="output",
    ligand_forcefield="gaff",
    **kwargs
)

Methods

build()

Build complete system.

output_path = system.build()

Returns: Path to output directory

info()

Display system information.

system.info()

get_output_files()

Get dictionary of all output file paths.

files = system.get_output_files()
print(files['system_gro'])
print(files['system_top'])

Returns: dict with file paths

Examples

Basic Usage

from prism import PRISMBuilder

builder = PRISMBuilder(
    "protein.pdb",
    "ligand.mol2",
    "output"
)
builder.run()

Step-by-Step

builder = PRISMBuilder("protein.pdb", "ligand.mol2", "output")

# Step 1: Ligand parameters
lig_ff = builder.generate_ligand_forcefield()

# Step 2: Clean protein
clean_prot = builder.clean_protein()

# Step 3: Build model
model = builder.build_model(clean_prot)

# Step 4: Generate MDPs
builder.generate_mdp_files()

# Step 5: Create run script
builder.generate_localrun_script()

Custom Configuration

builder = PRISMBuilder(
    "protein.pdb",
    "ligand.mol2",
    "output",
    config_path="custom_config.yaml"
)
builder.run()