schrodinger.application.desmond.packages.energygroup module¶
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exception
schrodinger.application.desmond.packages.energygroup.
EnergyGroupError
¶ Bases:
Exception
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__init__
¶ Initialize self. See help(type(self)) for accurate signature.
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args
¶
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with_traceback
()¶ Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.
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class
schrodinger.application.desmond.packages.energygroup.
EnergyGroupBase
¶ Bases:
object
Its subclasses work with
EnergyFacade
to perform energy group calculations.The subclass instance should have the following public attributes: -
key
: immutable and iterable. It is used as the key to retrievecalculation result from cache inEnergyFacade
kwargs
:dict
. It is the keyword arguments forget_energies
.
Its roles include: - store and validate the parameters - retrieve result from the cache in
EnergyFacade
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getResult
(result)¶ Retrieve and format the result from the cache in
EnergyFacade
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__init__
¶ Initialize self. See help(type(self)) for accurate signature.
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class
schrodinger.application.desmond.packages.energygroup.
MoleculeEnergy
(cms_model, molecule_number, type, type2)¶ Bases:
schrodinger.application.desmond.packages.energygroup.EnergyGroupBase
Analyzer for energy group calculation with single molecule selection. The pre-defined energy groups are (see COMPONENT_LIST)
- Selected molecule
- All atoms - group 1, 3, 4, 5
- Solute atoms - group 1
- Membrane atoms - group 1
- Solvent atoms - group 1
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TYPE_MAP
= {'Angle': 'angle', 'Bond': 'stretch', 'Coulomb': 'elec', 'Torsion': 'dihedral', 'Total': 'Total', 'vdW': 'vdw'}¶
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COMPONENT_LIST
= ['Self', 'Other', 'Solute', 'Membrane', 'Solvent']¶
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__init__
(cms_model, molecule_number, type, type2)¶ Parameters: - molecule_number (
int
) – index of the molecule - type (
str
) – pre-defined energy type, see TYPE_MAP - type2 (
str
) – pre-defined atom group, see COMPONENT_LIST
- molecule_number (
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class
schrodinger.application.desmond.packages.energygroup.
InteractionEnergy
(cms_model, asl1, asl2)¶ Bases:
schrodinger.application.desmond.packages.energygroup.EnergyGroupBase
Analyzer for interaction energy group calculation.
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__init__
(cms_model, asl1, asl2)¶ Parameters: - asl1 (
str
) – atom selection for group 1 - asl2 (
str
) – atom selection for group 2
- asl1 (
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class
schrodinger.application.desmond.packages.energygroup.
Bulk
(cms_model, type)¶ Bases:
schrodinger.application.desmond.packages.energygroup.EnergyGroupBase
Analyzer for material science energy group calculation
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MAX_GROUPS
= 870¶
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OPTIONS
= {'COHES_E', 'DENSITY', 'HEAT_VAP', 'INTRA_E', 'PRESSURE_TENSOR', 'SOL_PARAM', 'SPECIFIC_HEAT', 'TOTAL_E', 'VOLUME'}¶
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__init__
(cms_model, type)¶ Initialize self. See help(type(self)) for accurate signature.
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getResult
(result)¶ Retrieve and format the result from the cache in
EnergyFacade
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getCfgParams
(cfg_file)¶ Parameters: cfg_file – path to the simulation configuration file
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parseEnergies
(tmp_dir, num_groups)¶ Parse the vrun output.engp file for total molecular interaction energies, and other requested quantities. See for example https://opengrok.schrodinger.com/xref/desmond-gpu-src/test/data/bulktest/gpu https://opengrok.schrodinger.com/xref/desmond-gpu-src/test/data/bulktest/cpu
Return type: dict
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class
schrodinger.application.desmond.packages.energygroup.
SliceParams
(first, interval, last)¶ Bases:
tuple
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__contains__
¶ Return key in self.
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__init__
¶ Initialize self. See help(type(self)) for accurate signature.
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__len__
¶ Return len(self).
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count
(value) → integer -- return number of occurrences of value¶
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first
¶ Alias for field number 0
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index
(value[, start[, stop]]) → integer -- return first index of value.¶ Raises ValueError if the value is not present.
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interval
¶ Alias for field number 1
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last
¶ Alias for field number 2
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class
schrodinger.application.desmond.packages.energygroup.
EnergyComponent
¶ Bases:
object
Class for storing different energy components
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add
(term, val)¶
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elec
¶
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vdw
¶
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__init__
¶ Initialize self. See help(type(self)) for accurate signature.
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schrodinger.application.desmond.packages.energygroup.
temp_dir
()¶
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schrodinger.application.desmond.packages.energygroup.
get_energies
(sim_cfg, tr_path, cms_model, slicing, groups, max_groups=870, parse=<function _parse_energies>)¶ Calculate energies between groups of atoms specified by ASL selections, list of list of AIDs, or molecule number. Note there should be no overlap between any pair of the atom groups.
Parameters: parse (callable) – parser for the energy-group output data file Return type: (c{list} of c{float}s, c{list} of EnergyComponent
)Returns: simulation times, and various energies for each frame See
EnergyFacade
for other arguments
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class
schrodinger.application.desmond.packages.energygroup.
EnergyFacade
(sim_cfg, tr_path, cms_model, slicing)¶ Bases:
object
A helper class to manage energy group calculations. Different energy group calculations have different input/output formats. All these details are hidden by using this class and the subclasses of
EnergyGroupBase
.To get full control over the energy group calculation, call
get_energies
directly.-
__init__
(sim_cfg, tr_path, cms_model, slicing)¶ Parameters: - sim_cfg (
str
orNone
) – Path to Desmond simulaiton configuration. - tr_path (
str
) – Path to trajectory folder
- sim_cfg (
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get
(ene)¶
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