Ligand Modeler
- class LigandModelerProject(client)
Bases:
BaseProjectA class for creating and manipulating ligand reader & modeler projects.
- Parameters:
client (APIClient)
- change_dihedral(file_name, atom_index_1, atom_index_2, angle, visual_protein=False)
Rotate ligand dihedral around a selected atom-atom axis.
- Parameters:
file_name (str) – Target ligand file name.
atom_index_1 (int) – First atom index of rotation axis.
atom_index_2 (int) – Second atom index of rotation axis.
angle (int) – Rotation angle (0-360).
visual_protein (bool, optional) – Whether to overlay reference protein. Defaults to False.
- Returns:
Modified ligand payload for gen_ligand_ff.
- Return type:
dict
Example
modified_ligand = lrmbuilder.change_dihedral(‘1a.sdf’, 30, 8, 180)
- check_atom_index(file_name, visual_protein=False)
Visualize atom indices of a ligand structure for dihedral editing.
- Parameters:
file_name (str) – Target ligand file name in self.files_data.
visual_protein (bool, optional) – Whether to overlay reference protein. Defaults to False.
- Returns:
None
- create_project(title, ff, sdf_paths, pdbreader_project_id=None, native_ligand=None, complete_ring_match=False, stric_match=True, handle_chirality=True)
Create a new ligand modeler project.
- Parameters:
title (str) – The title of the new project.
ff (str) – Project force field type.
sdf_paths (list) – List of SDF file paths to be uploaded.
pdbreader_project_id (str, optional) – The ID of the associated PDBreader project. Defaults to None.
native_ligand (str, optional) – Native ligand name in the PDB Reader project. Defaults to None.
complete_ring_match (bool, optional) – Ring matching option for alignment. Defaults to False.
stric_match (bool, optional) – Strict coordinate matching option. Defaults to True.
handle_chirality (bool, optional) – Whether to preserve chirality during matching. Defaults to True.
- Returns:
True if project creation was successful, False otherwise.
- Return type:
bool
- download_project(filename='lrm.tar.gz')
Download the entire project as a compressed file.
- Parameters:
filename (str) – Name of the file to save the project as. Defaults to ‘lrm.tar.gz’.
- Returns:
None
- gen_ligand_ff(ligand_ff, modified_ligands=None)
Generate ligand force-field data for selected ligands.
- Parameters:
ligand_ff (list[LigandForceField]) – Ligand FF options to generate.
modified_ligands (list) – Optional modified ligand payloads.
- Returns:
True if generation task succeeded, False otherwise.
- Return type:
bool
Example
lrmbuilder.gen_ligand_ff([LigandForceField.OPENFF_FAST])
- get_native_ligands(pdbreader_project_id)
Retrieve native ligand information from a PDB Reader project.
- Parameters:
pdbreader_project_id (str) – PDB Reader project ID.
- Returns:
Native ligand metadata list.
- Return type:
list[dict]