Utilities for REMD.
Copyright Schrodinger, LLC. All rights reserved.
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| is_water(site,
constraint) |
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| get_nonduplicated_atom(ct) |
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| get_num_wateratom(model,
selected_atom) |
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| get_num_nonwateratom(model,
selected_atom) |
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| get_num_constraint(model,
selected_atom) |
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| get_degrees_of_freedom(model,
selected_atom) |
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predict_temperature_ladder(temp,
exchange_probability,
model,
asl,
should_fix=True)
`temp' should be a two-tuple, specifying the temperature range. |
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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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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. |
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predict_with_temp_and_nreplica(temp,
n_replica,
model,
asl)
Given the temperature range and number of replicas, predicts the
exchange probability and returns the temperature ladder. |
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| split_ct(ct,
selected_atom) |
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| set_freezing_atommass(model,
mass_scale) |
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| freeze_atom(model,
asl,
frozen_atom_mass_threshold=1000000000.0) |
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| rescale_ff(ct,
atom_list,
scaling_factor) |
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| rescale_ff_solute_tempering(model,
out_fname,
asl,
scaling_factor) |
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| test_get_num_wateratom(model) |
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| test_get_num_nonwateratom(model) |
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| test_get_num_constraint(model) |
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| test_get_degrees_of_freedom(model) |
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| test_predict_temperature(model) |
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| test_predict_with_nreplica_and_exch(model) |
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| test_predict_with_temp_and_nreplica(model) |
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