Index

A | B | C | D | E | F | G | I | L | M | N | P | R | S | T | U

A

AcceptanceCounter (class in meld.remd.adaptor)
adapt() (meld.remd.adaptor.EqualAcceptanceAdaptor method)
adapt_now (meld.remd.adaptor.AdaptationPolicy.AdaptationRequired attribute)
AdaptationPolicy (class in meld.remd.adaptor)
AdaptationPolicy.AdaptationRequired (class in meld.remd.adaptor)
add_disulfide() (meld.system.protein.ProteinBase method)
AlwaysActiveCollection (class in meld.system.restraints)

B

backup() (meld.vault.DataStore method)
broadcast_alphas_to_slaves() (meld.comm.MPICommunicator method)
broadcast_states_for_energy_calc_to_slaves() (meld.comm.MPICommunicator method)
broadcast_states_to_slaves() (meld.comm.MPICommunicator method)

C

close() (meld.vault.DataStore method)
CMAPResidue (class in meld.system.openmm_runner.cmap)
compute_exchanges() (meld.remd.ladder.NearestNeighborLadder method)
ConfinementRestraint (class in meld.system.restraints)
ConstantScaler (class in meld.system.restraints)

D

DataStore (class in meld.vault)
DistanceRestraint (class in meld.system.restraints)

E

end (meld.parse.SecondaryRun attribute)
EqualAcceptanceAdaptor (class in meld.remd.adaptor)
exchange_states_for_energy_calc() (meld.comm.MPICommunicator method)

F

FakeSystemRunner (class in meld.system.runner)
from_master() (meld.remd.slave_runner.SlaveReplicaExchangeRunner class method)

G

gather_energies_from_slaves() (meld.comm.MPICommunicator method)
gather_states_from_slaves() (meld.comm.MPICommunicator method)
get_constructor_for_key() (meld.system.restraints.RestraintRegistry class method)
(meld.system.restraints.ScalerRegistry class method)
get_secondary_structure_restraints() (in module meld.parse)
get_sequence_from_AA1() (in module meld.parse)
get_sequence_from_AA3() (in module meld.parse)

I

in_temp_dir() (in module meld.util)
index_C (meld.system.openmm_runner.cmap.CMAPResidue attribute)
index_CA (meld.system.openmm_runner.cmap.CMAPResidue attribute)
index_N (meld.system.openmm_runner.cmap.CMAPResidue attribute)
initialize() (meld.comm.MPICommunicator method)
(meld.vault.DataStore method)
is_master() (meld.comm.MPICommunicator method)
iterate_permutation_vectors() (meld.vault.DataStore method)
iterate_positions() (meld.vault.DataStore method)

L

LinearScaler (class in meld.system.restraints)
load_acceptance_probabilities() (meld.vault.DataStore method)
load_all_acceptance_probabilities() (meld.vault.DataStore method)
load_all_alphas() (meld.vault.DataStore method)
load_all_energies() (meld.vault.DataStore method)
load_all_permutation_vectors() (meld.vault.DataStore method)
load_all_positions() (meld.vault.DataStore method)
load_all_velocities() (meld.vault.DataStore method)
load_alphas() (meld.vault.DataStore method)
load_communicator() (meld.vault.DataStore method)
load_data_store() (meld.vault.DataStore class method)
load_energies() (meld.vault.DataStore method)
load_permutation_vector() (meld.vault.DataStore method)
load_positions() (meld.vault.DataStore method)
load_positions_random_access() (meld.vault.DataStore method)
load_remd_runner() (meld.vault.DataStore method)
load_states() (meld.vault.DataStore method)
load_velocities() (meld.vault.DataStore method)

M

MasterReplicaExchangeRunner (class in meld.remd.master_runner)
meld.comm (module)
meld.parse (module)
meld.pdb_writer (module)
meld.remd.adaptor (module)
meld.remd.ladder (module)
meld.remd.master_runner (module)
meld.remd.multiplex_runner (module)
meld.remd.reseed (module)
meld.remd.slave_runner (module)
meld.system.builder (module)
meld.system.openmm_runner.cmap (module)
meld.system.openmm_runner.runner (module)
meld.system.openmm_runner.softcore (module)
meld.system.protein (module)
meld.system.restraints (module)
meld.system.runner (module)
meld.system.state (module)
meld.system.system (module)
meld.util (module)
meld.vault (module)
MPICommunicator (class in meld.comm)
MultiplexReplicaExchangeRunner (class in meld.remd.multiplex_runner)

N

NearestNeighborLadder (class in meld.remd.ladder)
NonLinearScaler (class in meld.system.restraints)
NonSelectableRestraint (class in meld.system.restraints)
NullReseeder (class in meld.remd.reseed)

P

ProteinBase (class in meld.system.protein)
ProteinMoleculeFromPdbFile (class in meld.system.protein)
ProteinMoleculeFromSequence (class in meld.system.protein)

R

RdcRestraint (class in meld.system.restraints)
receive_alpha_from_master() (meld.comm.MPICommunicator method)
receive_state_from_master() (meld.comm.MPICommunicator method)
receive_states_for_energy_calc_from_master() (meld.comm.MPICommunicator method)
res_name (meld.system.openmm_runner.cmap.CMAPResidue attribute)
res_num (meld.system.openmm_runner.cmap.CMAPResidue attribute)
reseed() (meld.remd.reseed.Reseeder method)
Reseeder (class in meld.remd.reseed)
reset() (meld.remd.adaptor.EqualAcceptanceAdaptor method)
reset_now (meld.remd.adaptor.AdaptationPolicy.AdaptationRequired attribute)
Restraint (class in meld.system.restraints)
RestraintManager (class in meld.system.restraints)
RestraintRegistry (class in meld.system.restraints)
run() (meld.remd.master_runner.MasterReplicaExchangeRunner method)
(meld.remd.multiplex_runner.MultiplexReplicaExchangeRunner method)
(meld.remd.slave_runner.SlaveReplicaExchangeRunner method)

S

save_acceptance_probabilities() (meld.vault.DataStore method)
save_alphas() (meld.vault.DataStore method)
save_communicator() (meld.vault.DataStore method)
save_data_store() (meld.vault.DataStore method)
save_energies() (meld.vault.DataStore method)
save_permutation_vector() (meld.vault.DataStore method)
save_positions() (meld.vault.DataStore method)
save_remd_runner() (meld.vault.DataStore method)
save_states() (meld.vault.DataStore method)
save_velocities() (meld.vault.DataStore method)
Scaler (class in meld.system.restraints)
ScalerRegistry (class in meld.system.restraints)
SecondaryRun (class in meld.parse)
SelectableRestraint (class in meld.system.restraints)
SelectivelyActiveCollection (class in meld.system.restraints)
send_energies_to_master() (meld.comm.MPICommunicator method)
send_state_to_master() (meld.comm.MPICommunicator method)
set_rotation() (meld.system.protein.ProteinBase method)
set_translation() (meld.system.protein.ProteinBase method)
should_adapt() (meld.remd.adaptor.AdaptationPolicy method)
SlaveReplicaExchangeRunner (class in meld.remd.slave_runner)
start (meld.parse.SecondaryRun attribute)
SystemState (class in meld.system.state)

T

to_slave() (meld.remd.master_runner.MasterReplicaExchangeRunner method)
TorsionRestraint (class in meld.system.restraints)

U

update() (meld.remd.adaptor.EqualAcceptanceAdaptor method)