hplattice.Monty¶

class hplattice.Monty.DistRestraint(contacts, kspring)[source]¶

A harmonic constraint based on squared distance \(D = d^2\), where \(D = \sum_{i,j} d^2_{ij}\) over all contacts.

Parameters:	contacts (list) – list of tuples, example `[(0, 4), (1, 6)]` kspring (float) – spring constant for restraint

D(chain)[source]¶

Compute the sum of squared-distances of a given chain.

Parameters:	chain (`hplattice.Chain.Chain`) – Compute the sum of squared-distances of this chain.
Returns:	the sum of squared-distances over the selected contacts.
Return type:	float

energy(chain)[source]¶

Compute the restraint energy of a given chain.

Parameters:	chain (`hplattice.Chain.Chain`) – Compute the restraint energy of this chain.
Returns:	energy of the distance restraint
Return type:	float

class hplattice.Monty.Monty(config, temp, chain)[source]¶

A collection of functions to perform Monte Carlo move-set operations on an HP chain.

Parameters:	config (`hplattice.Config.Config`) – configuration parameters for chain and simulation temp (float) – temperature (K) chain (`hplattice.Chain.Chain`) – do monte carlo on this chain

Returns:	\(k_b * T\)
Return type:	float

metropolis(replica)[source]¶

Judge the next conformation of the chain according to Metropolis criterion: \(e^{-\Delta E/kT}\).

Parameters:	replica (`hplattice.Replica.Replica`) – The replica containing the chain that should be judged.
Returns:	`True` if next conformation should be accepted.
Return type:	bool

move1(chain, vecindex=None, direction=None)[source]¶

Apply moveset MC1 (Dill and Chan, 1994, 1996) to the chain:

Parameters:	chain (`hplattice.Chain.Chain`) – apply move to this chain vecindex (int) – optional, vector to move. will be chosen randomly if no value is specified. direction (int) – optional, `1` for clockwise, `-1` for counterclockwise. will be chosen randomly if no value is specified.

move2(chain, vecindex=None, direction=None, moveseed=None)[source]¶

Apply moveset MC2 (Dill and Chan, 1994, 1996) to the chain:

Parameters:

chain (hplattice.Chain.Chain) – apply move to this chain
vecindex (int) – optional, vector to move. will be chosen randomly if no value is specified.
direction (int) – optional, 1 for clockwise, -1 for counterclockwise. will be chosen randomly if no value is specified.
moveseed (float) – optional, moveseed \(<1/3\) for three-bead flip; \(1/3<=\) moveseed \(<2/3\) for crankshaft; \(2/3<=\) moveseed for rigid rotation.

move3(chain, vecindex=None, direction=None)[source]¶

Apply rigid rotations to the chain:

Parameters:	chain (`hplattice.Chain.Chain`) – apply move to this chain vecindex (int) – optional, vector to move. will be chosen randomly if no value is specified. direction (int) – optional, `1` for clockwise, `-1` for counterclockwise. will be chosen randomly if no value is specified.