schrodinger.application.matsci.montecarlo module

Classes related to Monte Carlo simulations

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.application.matsci.montecarlo.ClashChecker(basename='cell', backend=None, logger=None, color=None, vdw_scale=1.0)

Bases: schrodinger.application.matsci.amorphous.BuilderWithClashDetection

A builder used just for checking for clashes during Monte Carlo simulations

checkForRings(struct)

Check for rings in struct and cache them

Parameters:struct (schrodinger.structure.Structure) – The structure to check for rings
findRings(struct)

Return the cache of found rings - struct is not used because the structure may change coordinates but never bonding during an MC run. It is kept for API compatibility with the parent class.

Parameters:struct – unused
Return type:list
Returns:The list of found rings
class schrodinger.application.matsci.montecarlo.Metropolizer(scaffold, cell=None, weight_rotate=0.5, weight_translate=0.5, translate_mu=0.25, translate_sigma=1.0, max_rotate=360.0, temperatures=[300.0], iterations=10000, clash_penalty=50.0, minimize_interval=None, forcefield=14, vdw_scale=1.0, gravity=True, gravity_weight=4.0, logger=None, cleanup=True)

Bases: object

A class that runs a Monte Carlo simulation using the Metropolis algorithm

ROTATE = 0
TRANSLATE = 1
findFirstDisorderedMolecule()

Find the first molecule number that isn’t part of the scaffold

Return type:int
Returns:The first non-scaffold molecule number
getClashPenalty(candidate)

Get the energy penalty due to clashes

Parameters:candidate (schrodinger.structure.Structure) – The structure to check for clashes
Return type:float
Returns:The penalty based on the number of clashes
getClosestApproach(coords)

Get the closest approach between the given set of coordinates and the scaffold molecule or gravity center if no scaffold.

Parameters:coords (numpy.array) – The XYZ coordinates to check for close approach to the scaffold - such as from the getXYZ()
Return type:float
Returns:The closest approach between coords and the scaffold, or the gravity center if no scaffold was used.
getEnergy(candidate, target=None)

Compute the total energy of the system

Parameters:
Return type:

(float, float, float, float)
Returns:

The total energy, forcefield energy, gravitational energy and clash energy (total energy is the sum of the last three)
getGravityEnergy(target)

Evaluate the gravitational energy of the given target. The energy is simply the difference of the original distance between the target and the gravitational source and the new distance between them.

Parameters:target (MonteCarloMolecule) – A molecule that has been randomly moved
Return type:float
Returns:The gravitational energy of the target’s new position
getNumClashes(struct)

Get the number of clashes for the proposed structure

Parameters:struct (schrodinger.structure.Structure) – The structure to check for clashes
Return type:int
Returns:The total number of clashes found
getTargetMolecule(candidate, first, last)

Select the molecule to move this iteration

Parameters:
  • candidate (schrodinger.structure.Structure) – The entire cell containing all molecules
  • first (int) – The first valid molecule number to pick
  • last (int) – The last valid molecule number to pick
Return type:

MonteCarloMolecule
Returns:

The MCM object for the chosen molecule
isAccepted(old_energy, new_energy)

Use the Metropolis equation to determine if the move is accepted

Parameters:
  • old_energy (float) – The previous energy
  • new_energy (float) – The new energy
Return type:

bool
Returns:

Whether the move is accepted or not
log(msg, level=20)

Add a message to the log file

Parameters:
  • msg (str) – The message to add
  • level (int) – A logging priority level of the message
performMovement(target)

Move the molecule randomly

Parameters:target (MonteCarloMolecule) – The MCM object to move
Return type:int
Returns:A class constant indicating whether the move was ROTATE or TRANSLATE
setupGravity()

Pre-compute data for the gravity term

simulate()

Run the Monte Carlo simulated annealing

class schrodinger.application.matsci.montecarlo.MonteCarloMolecule(cell, molnum, box)

Bases: object

Class for treatment of a moving molecule during a Monte Carlo iteration

getCoordinates()

Get the xyz coordinate for this molecule

Return type:numpy.array
Returns:The xyz coordinates of this molecule
randomlyRotate(max_degrees)

Randomly rotate the molecule by no more than the given number of degrees

Parameters:max_degrees (float) – The largest rotation allowed
randomlyTranslate(mu_sigma)

Randomly translate the molecule. The distribution of translation distances is given by a lognormal distribution.

Parameters:mu_sigma ((float, float)) – (mu, sigma). mu gives the mean value of the lognormal distribution the translation is taken from. sigma gives the standard deviation of the distribution
updateCoordinates()

Update the coordinates of this molecule within the entire cell