meshi.energy
Class EnergyCreator

java.lang.Object
  meshi.energy.EnergyCreator

All Implemented Interfaces:

MeshiPotential, KeyWords

Direct Known Subclasses:

AtomicPairwisePMFSummaCreator, CompositePropensity2DCreator, CompositePropensityCreator, CooperativeAtomicPairwisePMFSummaCreator, CooperativePerAtomSummaCreator, CooperativePropensityCreator, CooperativeRamachandranCreator, CooperativeZPropensityCreator, CooperativeZRamachandranCreator, CooperativeZSummaCreator, CoulombElectrostaticCreator, CylinderCreator, EDMEnergyCreator, EVRot1BBCreator, ExcludedVolCreator, ExcludedVolCreator, ExcludedVolCreatorOLD, FiniteExcludedVolCreator, HbondsPunishHOCAngleCreator, HBondsPunishOHNAngleCreator, HydrogenBondsCreator, HydrogenBondsPairsCreator, LennardJonesCreator, LinearRgCreator, RamachandranCreator, RamachandranSidechainEnergyCreator, RgCreator, SideChainSolvateCreator, SimpleEnergyCreator, SimpleInflateCreator, SmoothRotamerLibraryEnergyCreator, SolvateCreatorHBforMinimization, SolvateCreatorLongHB, SolvateCreatorRegularHB, SolvateRot1Creator, SymmetryCreator, TemplateEnergyCreator, UnWarpEnergyCreator, WarpEnergyCreator

public abstract class EnergyCreator
extends java.lang.Object
implements MeshiPotential, KeyWords

Factory classes that generate energy terms. This is the carpet under which we hide all the boring details of what is needed for the creation of a given energy term. Each energy term requires a specific subclass. See meshi.energy.bond.BondCreator for a simple example.

Field Summary

protected Key	key The keyword for the energy term.
private static java.lang.String	parametersDirectory
protected AbstractEnergy	term
protected double	weight The weight of the energy term within the total energy function.
protected boolean	weightWasSet

Fields inherited from interface meshi.parameters.MeshiPotential

ACCESSIBLE, ALPHA_ANGLE_PARAMETERS, ALPHA_TORSION_PARAMETERS, ANGLE_PARAMETERS, ATOMIC_PAIRWISE_PMF_SUMMA_PARAMETERS, BOND_PARAMETERS, BURIED, COIL, COMPOSITE_PROPENSITY_2D_PARAMETERS, COMPOSITE_PROPENSITY_2D_WITH_PP_PARAMETERS, COMPOSITE_PROPENSITY_PARAMETERS, COMPOSITE_TORSIONS_PARAMETERS, CONTACTS_ENVIRONMENT_PARAMETERS, CONTACTS_PARAMETERS, COOPERATIVE_ATOMIC_PAIRWISE_PMF_SUMMA_PARAMETERS, COOPERATIVE_PROPENSITY_PARAMETERS, COOPERATIVE_RAMACHANDRAN_PARAMETERS, ELECTROSTATICS_PARAMETERS, EXCLUDED_VOL_PARAMETERS, FLAT_RAMACH_PARAMETERS, HELIX, HELIX_OR_COIL, HYDROGEN_BONDS_PAIRS_BETA_PARAMETERS, HYDROGEN_BONDS_PAIRS_HELIX_PARAMETERS, HYDROGEN_BONDS_PAIRS_PARAMETERS_SURFACE, LENNARD_JONES_PARAMETERS, LENNARD_JONES_PARAMETERS_BACKBONE, LENNARD_JONES_PARAMETERS_CA, LJ_ENVIRONMENT_PARAMETERS, LJ_ENVIRONMENT_PARAMETERS_BACKBONE, LJ_ENVIRONMENT_PARAMETERS_CA, ONE_ANGLE_PARAMETERS, OUT_OF_PLANE_PARAMETERS, PLANE_PARAMETERS, PROPENSITY_ANGLE_PARAMETERS, PROPENSITY_TORSION_PARAMETERS, SHEET, SHEET_OR_COIL, SOLVATE_LONG_HB_PARAMETERS, SOLVATE_MINIMIZE_HB_PARAMETERS, SOLVATE_NOHB_PARAMETERS, SOLVATE_PARAMETERS, SOLVATE_SC_PARAMETERS, TWO_ANGLES_PARAMETERS, TWO_TORSIONS_PARAMETERS

Fields inherited from interface meshi.util.KeyWords

AA_SEQUENCE, ACCESIBILITY_SEQUENCE, ALINMENT_FILE_PATH, ALL_CA, ALPHA_ANGLE_ENERGY, ALPHA_TORSION_ENERGY, ANGLE_ENERGY, ANGLE_X, ANGLE_Z, ATOMIC_PAIRWISE_PMF_SUMMA_ENERGY, BEAUTIFY_PROBLEMATIC_RANGE, BFGS, BOND_ENERGY, BUFFER_SIZE, CA_CLASH_DISTANCE, CA_LONG_DISTANCE, CA_MODEL, CA_SHORT_DISTANCE, CA_TETHER_ENERGY, CALPHA_HYDROGEN_BONDS, CALPHA_HYDROGEN_BONDS_PLANE, CASP_GROUP, CG, CHECK_INTERLOOP_DISTANCE, CLASH_DISTANCE, COMPOSITE_PROPENSITY_ENERGY, CONSENSUS_ENERGY, CONSTRICT, COOPERATIVE_ATOMIC_PAIRWISE_PMF_SUMMA_ENERGY, COOPERATIVE_ATOMIC_PAIRWISE_PMF_SUMMA_FILENAME, COOPERATIVE_PERATOM_SUMMA_ENERGY, COOPERATIVE_PERATOM_SUMMA_FILENAME, COOPERATIVE_PROPENSITY_ENERGY, COOPERATIVE_PROPENSITY_FILENAME, COOPERATIVE_RAMACHANDRAN_ENERGY, COOPERATIVE_RAMACHANDRAN_FILENAME, COOPERATIVE_Z_PROPENSITY_ENERGY, COOPERATIVE_Z_PROPENSITY_FILENAME, COOPERATIVE_Z_RAMACHANDRAN_ENERGY, COOPERATIVE_Z_RAMACHANDRAN_FILENAME, COOPERATIVE_Z_SUMMA_ENERGY, COOPERATIVE_Z_SUMMA_FILENAME, CORPUS_FILE_NAME, CSAonly_FILES_LOCATION_PATH, CUTOFF, CYLINDER_ENERGY, DICTIONARY_KEY, DIELECTRIC_CONSTANT, DISTANCE_CONSTRAINT_PCA, DISTANCE_CONSTRAINTS_ENERGY, DISTANCE_CONSTRAINTS_MASK, DISTANCE_FROM_CENTROID_ENERGY, DRESSER_FRAGMENTS, EDM_ENERGY, EDM_ENERGY_FILE_NAME, ELECTROSTATICS, END, EXCLUDED_VOL, FINAL_TEMPERATURE, FIX_C_TERMINAL, FIX_N_TERMINAL, FLAT_RAMACH_ENERGY, FREE_FINAL_MINIMIZATION, GRID_EDGE, HYDROGEN_BONDS, HYDROGEN_BONDS_ANGLES, HYDROGEN_BONDS_PAIRS, HYDROGEN_BONDS_PLANE, INFLATE_ENERGY, INITIAL_TEMPERATURE, INPUT_FILE, INTER_SEGMENT_FACTOR, INTER_SEGMENT_TOLERANCE, INTRA_SEGMENT_FACTOR, INTRA_SEGMENT_TOLERANCE, ITERATIONS_ALLATOM, ITERATIONS_BACKBONE, ITERATIONS_CA, KEY_KEY, KOEHL_FILE, LBFGS, LENNARD_JONES, LENNARD_JONES_CA, LINEAR_RG, LOOP1, LOOP2, LOOSEN_EDGE_LENGTH, MAX_ANGLE, MAX_CLASHES, MAX_DISTANCE, MAX_RUN_TIME, MAX_STEPS, MAX_WIDTH_OF_HAIRPIN, MCM, MCM_PERTURBATION, MESHILOG_KEY, METHOD, MIN_WIDTH_OF_HAIRPIN, MINIMIZATION_LOOP, MINIMIZE, MODE, MODEL, MODEL_DSSP, MODEL_NUMBER, N_ATOMS, N_TRIES, NON_FROZEN_BOND_DEPTH, NON_FROZEN_RADIUS, NONE, NUMBER, NUMBER_OF_CA_ITERATIONS, NUMBER_OF_CHAINS, NUMBER_OF_MODELS, NUMBER_OF_RUNS, OFF, ON, OPTIMIZER, OUT_OFPLANE_ENERGY, OUTPUT_FILE_NAME, OUTPUT_FILE_PATH, PARAMETERS_DIRECTORY, PDB_FILE, PLANE_ENERGY, PROPENSITY_TORSION_ENERGY, R_MAX, RAMACHANDRAN_SIDECHAIN_ENERGY, REFERENCE, RELAX, REPORT_EVERY, RESTART_EVERY, RMS_TARGET, ROTAMER_LIBRARY, SATURATION, SECONDARY_STRUCTURE, SEED, SEQUENCE, SHOTGUN_MODEL, SMOOTH_ROTAMER_LIBRARY_ENERGY, SOLVATE_ENERGY, SS_NAME, SS_SEQUENCE, STEEPEST_DECENT, STEPS, STRICT_CLASHES, STRUCTURE_NAMES, SUPERIMPOSE, SYMMETRY_ENERGY, TARGET_FILE_PATH, TARGET_NAME, TARGET_SEQUENCE, TEMPLATE_DISTANCE_CONSTRAINTS, TEMPLATE_DSSP, TEMPLATE_ENERGY, TEMPLATE_FILE_PATH, TEMPLATE_NAME, TEMPLATE_STRUCTURE, TEMPLATE_TARGET_ALIGNMENT, TETHER_ENERGY, TOLERANCE, TOPOLOGY_MAP, TWO_TORSIONS_ENERGY, UN_WARP_ENERGY, UNSATISFIED_CUTTOF, UP_TO_CUTOFF, USE_FAST_ARCCOS, VALUE_KEY, VOLUME_CONSTRAINT, WARP_ENERGY, WARP_STEP_SIZE, WARP_THRESHOLD, WEIGHT, WIDTH_OF_HAIRPIN

Constructor Summary

EnergyCreator(double weight)
Construct a somewhat degenerate creator object that cannot read commands from the commands list.

EnergyCreator(Key key)
Constructs an energy creator object.

EnergyCreator(Key key, CommandList commands)
Constructs an energy creator object.

Method Summary

abstract AbstractEnergy	createEnergyTerm(Protein protein, DistanceMatrix distanceMatrix, CommandList commands) Where each sub class gets the chance to show what it knows.
protected static void	getParametersDirectory(CommandList commands)
void	getWeight(CommandList commands) Get the weight of the energy term.
protected static java.lang.String	parametersDirectory(CommandList commands) Extract the path of the parameters directory from the commands list.
AbstractEnergy	term()
java.lang.String	toString()
double	weight() The weight of the energy term.
boolean	weightWasSet()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

weight

protected double weight

The weight of the energy term within the total energy function.

term

protected AbstractEnergy term

key

protected Key key

The keyword for the energy term. All commands relevant to this energy terms will sart with this word.

weightWasSet

protected boolean weightWasSet

parametersDirectory

private static java.lang.String parametersDirectory

Constructor Detail

EnergyCreator

public EnergyCreator(Key key)

Constructs an energy creator object. The key parameter will serve as a keyword that identify relevant commands in the commands list.

EnergyCreator

public EnergyCreator(Key key,
                     CommandList commands)

Constructs an energy creator object. The key parameter will serve as a keyword that identify relevant commands in the commands list.

EnergyCreator

public EnergyCreator(double weight)

Construct a somewhat degenerate creator object that cannot read commands from the commands list.

Method Detail

term

public AbstractEnergy term()

weight

public double weight()

The weight of the energy term.

parametersDirectory

protected static java.lang.String parametersDirectory(CommandList commands)

Extract the path of the parameters directory from the commands list.

getParametersDirectory

protected static void getParametersDirectory(CommandList commands)

createEnergyTerm

public abstract AbstractEnergy createEnergyTerm(Protein protein,
                                                DistanceMatrix distanceMatrix,
                                                CommandList commands)

Where each sub class gets the chance to show what it knows. Offers a standard interface to many energy functions that have different requirements.

getWeight

public void getWeight(CommandList commands)

Get the weight of the energy term.

weightWasSet

public boolean weightWasSet()

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object