schrodinger.application.desmond.stage.app.absolute_binding.restraint module¶
- schrodinger.application.desmond.stage.app.absolute_binding.restraint.prepare_ligand_restraints(st: schrodinger.structure._structure.Structure, ligand_asl: str, force_constants: List[float], sigmas: List[float], schedule_name: str) str¶
Given a structure, return the dihedral restraint parameters encoded as a string. This adds restraints with fixed sigma to any six membered rings present in the ligand.
- Parameters
st – Simulation structure on which the restraints will be applied.
ligand_asl – ASL to identify the ligand.
force_constants – Force constants for the restraint at the lambda endpoints.
sigmas – Sigma values for the restraint at the lambda endpoints.
schedule_name – Name of the schedule associated with the restraint.
- Returns
The restraints encoded as a string.
- schrodinger.application.desmond.stage.app.absolute_binding.restraint.prepare_adaptive_ligand_restraints(msys_model: msys.System, cms_model: schrodinger.application.desmond.cms.Cms, trj: List[traj.TrajFrame], ligand_asl: str, force_constants: List[float], schedule_name: str) str¶
Given a cms model and corresponding trajectory, return the dihedral restraint parameters encoded as a string.
This adds restraints with adaptive width to all rotatable ligand torsions. This excludes torsions that are part of a ring. Adaptive width means the sigma values are calculated from the dihedral values for each rotatable torsion over the MD simulation that was run.
- Parameters
msys_model – Msys model used for trajectory analysis.
cms_model – Cms model read in with
traj_util.read_cms_and_traj.trj – Trajectory read in with
traj_util.read_cms_and_traj.ligand_asl – ASL to identify the ligand.
force_constants – Force constants for the restraint at the lambda endpoints.
schedule_name – Name of the schedule associated with the restraint.
- Returns
The restraints encoded as a string.
- schrodinger.application.desmond.stage.app.absolute_binding.restraint.use_representative_frame(msys_model: msys.System, cms_model: schrodinger.application.desmond.cms.Cms, trj: List[traj.TrajFrame], ligand_asl: str)¶
Given a cms model and corresponding trajectory, update the
cms_modelwith the representative frame coordinates. This is calculated based on the ligand torsions.- Parameters
msys_model – Msys model used for trajectory analysis.
cms_model – Cms model read in with
traj_util.read_cms_and_traj. The coordinates are updated in place with those from the representative frame.trj – Trajectory read in with
traj_util.read_cms_and_traj.ligand_asl – ASL to identify the ligand.
- schrodinger.application.desmond.stage.app.absolute_binding.restraint.overwrite_hotatoms(graph: graph.Graph, has_ligand_restraint: bool)¶
Overwrite the hot atoms settings on the graph in accordance with the graphs ligand restraints