schrodinger.application.desmond.remd module¶
Utilities for REMD.
Copyright Schrodinger, LLC. All rights reserved.
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schrodinger.application.desmond.remd.
is_water
(site, constraint)¶
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schrodinger.application.desmond.remd.
get_nonduplicated_atom
(ct)¶
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schrodinger.application.desmond.remd.
get_num_wateratom
(model, selected_atom)¶
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schrodinger.application.desmond.remd.
get_num_nonwateratom
(model, selected_atom)¶
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schrodinger.application.desmond.remd.
get_num_constraint
(model, selected_atom)¶
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schrodinger.application.desmond.remd.
get_degrees_of_freedom
(model, selected_atom)¶
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schrodinger.application.desmond.remd.
get_rest_params
(model, asl)¶ Returns parameters that are required for temperature ladder prediction
Return the tuple with the following values: degrees of freedom, number of selected waters, number of selected non-waters, number of constraints. :rtype tuple(int, int, int, int)
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schrodinger.application.desmond.remd.
predict_temperature_ladder
(temperature, exchange_probability, model, asl, should_fix=True, floaty=False)¶ Parameters: - temperature (tuple(float, float)) – a tuple (t0, t1) temperature range in Kelvin
- should_fix (bool) –
???
- floaty (bool) –
???
Returns: returns a tuple with two lists. First list is a temperature profile, second list is probability profile.
Return type: tuple(list of floats, list of floats)
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schrodinger.application.desmond.remd.
get_prob_from_temp_ladder
(temp_ladder: List[float], model: schrodinger.application.desmond.cms.Cms, asl: str) → List[float]¶ Return the probability given the temperature ladder
temp_ladder
and the corresponding cmsmodel
and aslasl
for the hot atoms.
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schrodinger.application.desmond.remd.
predict_with_temp_and_exch
(temp, exchange_probability, model, asl)¶ Given temperature range and exchange_probability, predicts the number of replica and returns the temperature ladder.
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schrodinger.application.desmond.remd.
predict_with_nreplica_and_exch
(n_replica, exchange_probability, base_temp, model, asl)¶ Given the base temperature, number of replicas, and exchange_probability, predicts the top temperature and returns the temperature ladder. :type n_replica: int :type exchange_probability: float :type base_temp: float :type model:
schrodinger.application.desmond.cms.Cms
:type asl: strReturns: a list of temperatures in Kelvin (length n_replica) and exchange a list of corresponding exchange probabilities (length n_replica-1) Return type: (list of floats, list of floats)
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schrodinger.application.desmond.remd.
predict_with_temp_and_nreplica
(temperature, n_replica, model, asl)¶ Given the temperature range and number of replicas, predicts the exchange probability and returns the temperature ladder. :param temperature: a tuple of (min, max) temperatures, in Kelvin :type temperature: tuple(float, float) :type exchange_probability: float :type base_temp: float :type model:
schrodinger.application.desmond.cms.Cms
:type asl: strReturns: a list of temperatures (length n_replica) and exchange a list of corresponding exchange probabilities (length n_replica-1) Return type: (list of floats, list of floats)
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schrodinger.application.desmond.remd.
split_ct
(ct, selected_atom)¶
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schrodinger.application.desmond.remd.
set_freezing_atommass
(model, mass_scale)¶
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schrodinger.application.desmond.remd.
freeze_atom
(model, asl, frozen_atom_mass_threshold=1000000000.0)¶
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schrodinger.application.desmond.remd.
write_ff_solute_tempering
(model, out_fname, asl, scaling_factor, should_scale_torsion=True)¶ write cms.Cms to a file with scaled force field terms
Parameters: - model (cms.Cms) – input cms.Cms
- out_fname (str) – output file name
- asl (str) – ASL expression to define rest atoms
- scaling_factor (float) – T_ref/T_hot
- should_scale_torsion (Boolean) – whether to scale dihedral terms
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schrodinger.application.desmond.remd.
rescale_ff_solute_tempering
(model, asl, scaling_factor, should_scale_torsion=True)¶ return cms.Cms with scaled force field terms
Parameters: - model (cms.Cms) – input cms.Cms
- asl (str) – ASL expression to define rest atoms
- scaling_factor (float) – T_ref/T_hot
- should_scale_torsion (Boolean) – whether to scale dihedral terms
Return type: Returns: rescaled cms.Cms
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schrodinger.application.desmond.remd.
rescale_ff
(ct, rest_atoms, scaling_factor, should_scale_torsion=True)¶ scales force field terms for rest atoms
Parameters: - ct (ffiostructure.FFIOStructure) – input/output structure handle
- rest_atoms (list of int) – sequence of atom indices in rest region
- scaling_factor (float) – T_ref/T_hot
- should_scale_torsion (Boolean) – whether to scale dihedral terms