OpenMMDL simulation functions

This page displays all the functions of OpenMMDL Simulation.

openmmdl_simulation.scripts.cleaning_procedures

cleanup(protein_name)

Cleans up the PDB Reporter Output File and MDTraj Files of the performed simulation.

Parameters:

protein_name (str) – Name of the protein PDB.

Returns:

None.

Return type:

None

create_directory_if_not_exists(directory_path)

Create a directory if it doesn’t exist, or overwrite it if already does.

Parameters:

directory_path (str) – Path of the directory that you want to create.

Returns:

None.

Return type:

None

copy_file(src, dest)

Copy a file to the destination path.

Parameters:

  • src (str) – Path of the file that needs to be copied.

  • dest (str) – Path of destination where the file needs to be copied to.

Returns:

None.

Return type:

None

organize_files(source, destination)

Organizes the files and moves them from the source to the destination directory.

Parameters:

  • source (str) – Path of the file that needs to be moved.

  • destination (str) – Path of destination where the file needs to be moved to.

Returns:

None.

Return type:

None

post_md_file_movement(protein_name: str, prmtop: str = None, inpcrd: str = None, ligands: List[str] = None)

Organizes and moves the files after the MD simulation to their respective directories.

Parameters:

  • protein_name (str) – Name of the protein PDB.

  • prmtop (Optional [str]) – Path to the AMBER topology file.

  • inpcrd (Optional [str]) – Path to the AMBER coordinate file.

  • ligands (Optional [List[str]]) – List of paths to the ligand files.

Returns:

None.

Return type:

None

openmmdl_simulation.scripts.forcefield_water

ff_selection(ff)

Selects the required XML forcefield file.

Parameters:

ff (str) – Input forcefield.

Returns:

Selected XML forcefield file.

Return type:

str

water_forcefield_selection(water, forcefield_selection)

Selects the required XML forcefield file.

Parameters:

  • water (str) – The chosen water model.

  • forcefield_selection (str) – The selected force field.

Returns:

The XML filename of the water forcefield.

Return type:

str

water_model_selection(water, forcefield_selection)

Selects the required water model forcefield XML file according to water selection and previous force field selection.

Parameters:

  • water (str) – Water model input.

  • forcefield_selection (str) – Input of selected forcefield XML file.

Returns:

Water model forcefield XML file.

Return type:

str

generate_forcefield(protein_ff, solvent_ff, add_membrane, rdkit_mol=None)

Generate an OpenMM Forcefield object and register a small molecule.

Parameters:

  • protein_ff (str) – Input of selected forcefield XML File.

  • solvent_ff (str) – Input of selected water model forcefield XML File.

  • add_membrane (bool) – Selection if the system should be built with a membrane.

  • rdkit_mol (rdkit.Chem.rdchem.Mol) – Small molecule to register in the force field.

Returns:

Forcefield with a registered small molecule.

Return type:

simtk.openmm.app.Forcefield

generate_transitional_forcefield(protein_ff, solvent_ff, add_membrane, rdkit_mol=None)

Generate an OpenMM transitional forcefield object with TIP3P water model for membrane building and register a small molecule.

Parameters:

  • protein_ff (str) – Name of the force field in XML format.

  • solvent_ff (str) – Name of the water model force field in XML format.

  • add_membrane (bool) – Selection if the system should be built with a membrane.

  • rdkit_mol (rdkit.Chem.rdchem.Mol) – Small molecule to register in the force field.

Returns:

A transitional forcefield with TIP3P water and a registered small molecule.

Return type:

simtk.openmm.app.Forcefield

openmmdl_simulation.scripts.post_md_conversions

mdtraj_conversion(pdb_file, mdtraj_output)

Recenter and apply periodic boundary conditions to the molecules in each frame of the trajectory, and save the centered trajectory and its first frame.

Parameters:

  • pdb_file (str) – Name of the PDB file. This PDB file stores the extracted frames from the MD trajectory.

  • mdtraj_output (str) – The selected format that will be used as an output of the topology and trajectory.

Returns:

None.

Return type:

None

MDanalysis_conversion(post_mdtraj_pdb_file, post_mdtraj_dcd_file, mda_output, output_selection, ligand_name=None, special_ligname=None)

Translate the trajectory so that all frames coincide with its center of geometry.

Parameters:

  • post_mdtraj_pdb_file (str) – Name of the post-MDtraj PDB file.

  • post_mdtraj_dcd_file (str) – Name of the post-MDtraj DCD File.

  • ligand_name (str) – Ligand name saved in the PDB file.

  • special_ligname (str) – Special residue name saved in the PDB file.

  • mda_output (str) – Selection of output formats.

  • output_selection (str) – Selection of topologies with specific atom selections that will be created.

Returns:

None.

Return type:

None