schrodinger.application.desmond.stage.prepare.structure module

class schrodinger.application.desmond.stage.prepare.structure.BuildGeometry(*arg, **kwarg)

Bases: schrodinger.application.desmond.cmj.StageBase

NAME = 'build_geometry'
BG_CMD = '/scr/buildbot/savedbuilds/2024-2/NB/build-134/utilities/system_builder'
SOLVENT = {'DMSO': 'dmso.box.mae', 'METHANOL': 'methanol.box.mae', 'OCTANOL': 'octanol.box.mae', 'SPC': 'spc.box.mae', 'SPCE': 'spce.box.mae', 'SPCFW': 'spcfw.box.mae', 'TIP3P': 'tip3p.box.mae', 'TIP4P': 'tip4p.box.mae', 'TIP4P2005': 'tip4p2005.box.mae', 'TIP4PD': 'tip4pd.box.mae', 'TIP4PEW': 'tip4pew.box.mae', 'TIP5P': 'tip5p.box.mae', 'WATER': 'spc.box.mae'}
DEFAULT_ALCHEMICAL_EXCLUDE_DIST = 5
PARAM = <schrodinger.utils.sea.sea.Map object>
__init__(*arg, **kwarg)
crunch()
hook_captured_successful_job(job)
class schrodinger.application.desmond.stage.prepare.structure.ExtractStructures(*args, **kwargs)

Bases: schrodinger.application.desmond.cmj.StructureStageBase

This extracts one or more structures from an input mae file, adds some structure and atom properties, and passes the structures to the next stage.

NAME = 'extract_structures'
TAG = 'EXTRACT_STRUCTURES'
PARAM = <schrodinger.utils.sea.sea.Map object>
run(jobname: str, input_fname: str) → Optional[str]
Parameters

  • jobname – Jobname for this stage.

  • input_fname – Filename for the input structure.

Returns

Filename for the output structure or None if there was an error generating the output.

schrodinger.application.desmond.stage.prepare.structure.clear_user_restraints(st: schrodinger.structure._structure.Structure)

Clear structure and atom property user restraint values that may be present from previous simulations.

Parameters

sts – structure to clear the restraints from

class schrodinger.application.desmond.stage.prepare.structure.ExtractSoluteStructure(*args, **kwargs)

Bases: schrodinger.application.desmond.cmj.StructureStageBase

This extracts a solute structure from the output cms of an MD run, and clears the simulation box if present.

NAME = 'extract_solute_structure'
run(jobname: str, cms_fname: str) → Optional[str]
Parameters

  • jobname – Jobname for this stage.

  • input_fname – Filename for the input structure.

Returns

Filename for the output structure or None if there was an error generating the output.

class schrodinger.application.desmond.stage.prepare.structure.HashStructureTitle(*args, **kwargs)

Bases: schrodinger.application.desmond.cmj.StructureStageBase

This stores the structure title and corresponding hash id for one or more structures from an input mae file and passes it to the next stage.

NAME = 'hash_structure_title'
run(jobname: str, mae_fname: str) → Optional[str]
Parameters

  • jobname – Jobname for this stage.

  • input_fname – Filename for the input structure.

Returns

Filename for the output structure or None if there was an error generating the output.

class schrodinger.application.desmond.stage.prepare.structure.DisorderedSystemBuilder(*args, **kwargs)

Bases: schrodinger.application.desmond.cmj.StructureStageBase

This sets up and runs the disordered system builder, which takes in a ct and creates a disordered solid system for it.

NAME = 'disordered_system_builder'
N_MOLECULES = 64
PARAM = <schrodinger.utils.sea.sea.Map object>
run(jobname: str, mae_fname: str) → Optional[str]
Parameters

  • jobname – Jobname for this stage.

  • input_fname – Filename for the input structure.

Returns

Filename for the output structure or None if there was an error generating the output.

class schrodinger.application.desmond.stage.prepare.structure.ProteinMutationGenerator(should_pack=True)

Bases: schrodinger.application.desmond.cmj.StageBase

NAME = 'protein_mutation_generator'
PARAM = <schrodinger.utils.sea.sea.Map object>
crunch()

We will either read the mutations from a file or directly from the msj where mutations are defined as a list of space seperated strings

mutations = [“C:23->ALA” “C:23->SER”]

create_mutation_file(mutation_file)
class schrodinger.application.desmond.stage.prepare.structure.ReplicateStructure(*args, **kwargs)

Bases: schrodinger.application.desmond.cmj.StructureStageBase

This takes the output structure from the previous stage and replicates it, so it has the same number of molecules as the input mae_file. Then it copies the coordinates and structure properties from mae_file.

PARAM = <schrodinger.utils.sea.sea.Map object>
NAME = 'replicate_structure'
run(jobname: str, input_fname: str) → str
Parameters

  • jobname – Jobname for this stage.

  • input_fname – Filename for the input structure.

Returns

Filename for the output structure or None if there was an error generating the output.

class schrodinger.application.desmond.stage.prepare.structure.GroupWaters(*args, **kwargs)

Bases: schrodinger.application.desmond.cmj.StructureStageBase

Set the FEP_ABSOLUTE_ENERGY property on waters, optionally selecting only non-crystal waters

NAME = 'group_waters'
PARAM = <schrodinger.utils.sea.sea.Map object>
run(jobname, input_fname)
Parameters

  • jobname – Jobname for this stage.

  • input_fname – Filename for the input structure.

Returns

Filename for the output structure or None if there was an error generating the output.