Welcome to ligandparam’s documentation!

Indices and tables

Example Script

For detailed examples, please refer to the examples directory in the source code.

Here is a simple example of how to use the ligand_param module:

#!/usr/bin/env python

# Import the module
from ligandparam.recipes import FreeLigand

# Load the pdb as a instance of the FreeLigand class
parametrize_ligand = FreeLigand('thiophenol.pdb', netcharge=0,nproc=12,mem='60GB')

# Select the pre-initialized stages for Lazy Ligand
parametrize_ligand.setup()

# List the stages out to the user
parametrize_ligand.list_stages()

# Execute the stages in order.
parametrize_ligand.execute(dry_run=False)

The above script will load the pdb file thiophenol.pdb and initialize the stages for the ligand parameterization.

There are a number of different parametrization classes, including:

  • LazyLigand Which just does a single RESP calculation

  • FreeLigand: Which does a multiRESP calculation

  • BuildLigand: Which builds a ligand from a pdb file (and outputs a parm7/rst7 file in gas, aqueous, or a protein/rna target)

These classes are designed to be easily extensible, so you can add your own stages to the pipeline.

These stages are all subclasses of the Parameterization class, which is a subclass of the Driver class.

A key aspect of the code is that you can easily add your own stages to the pipeline, as mentioned above.

# Import the module
from ligandparam.recipes import FreeLigand

# Load the pdb as a instance of the FreeLigand class
parametrize_ligand = FreeLigand('thiophenol.pdb', netcharge=0,nproc=12,mem='60GB')

# Select the pre-initialized stages for Lazy Ligand
parametrize_ligand.setup()

# List the stages out to the user
parameterize_ligand.list_stages()

# Remove the Normalize stage
parametrize_ligand.remove_stage("Normalize1")

from ligandparam.stages import StageNormalizeCharge

# Add a new Normalize stage
parametrize_ligand.add_stage(StageNormalizeCharge("Normalize2", orig_mol2=test.base_name+".resp.mol2",
                  new_mol2=test.base_name+".resp.mol2"))

# Insert a new Normalize stage before Normalize2
parametrize_ligand.insert_stage(StageNormalizeCharge("Normalize3", orig_mol2=test.base_name+".resp.mol2",
                                                new_mol2=test.base_name+".resp.mol2"),"Normalize2")

parametrize_ligand.execute()