schrodinger.application.desmond.stage.app.absolute_binding.restraint module¶
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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.
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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.
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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_model
with 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.
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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