Class HeliumClusterMinimization

java.lang.Object
  meshi.util.MeshiProgram
      HeliumClusterMinimization

All Implemented Interfaces:

KeyWords

public class HeliumClusterMinimization
extends MeshiProgram
implements KeyWords

A program for the generation and energy minimization of a Helium atoms cluster.

Nested Class Summary

private static class

HeliumClusterMinimization.HeliumLennardJonesCreator

Field Summary

protected static AtomList	atomList List of atoms to optimize.
protected static DistanceMatrix	distanceMatrix of the atoms.
protected static TotalEnergy	energy function to minimize;
private static double	MIN_DISTANCE_SQR
protected static Minimizer	minimizer The optimization engine.
protected static int	nSteps Maximal number of minimization steps.
protected static java.lang.String	outputFile for the final coordinates.

Fields inherited from class meshi.util.MeshiProgram

commandLine, name

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

HeliumClusterMinimization()

Method Summary

private static AtomList	getAtomList(CommandList commands)
private static TotalEnergy	getEnergy(AtomList atomList, DistanceMatrix distanceMatrix, CommandList commands)
static Minimizer	getMinimizer(TotalEnergy energy, CommandList commands)
static MeshiWriter	getOutputFile(CommandList commands)
static void	main(java.lang.String[] args)
private static java.lang.String	usageString()

Methods inherited from class meshi.util.MeshiProgram

about, debug, get2ndString, getb, getB, getd, getD, getFlag, getFlagedArgument, geti, getI, getOrderedArgument, getS, getS, initRandom, initRandom, initRandom, printGlobalTable, randomNumberGenerator, seed, tableGet, tableIncludes, tableSet, toString, verbose

Methods inherited from class java.lang.Object

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

Field Detail

MIN_DISTANCE_SQR

private static final double MIN_DISTANCE_SQR

See Also:

Constant Field Values

atomList

protected static AtomList atomList

List of atoms to optimize.

outputFile

protected static java.lang.String outputFile

for the final coordinates.

distanceMatrix

protected static DistanceMatrix distanceMatrix

of the atoms.

minimizer

protected static Minimizer minimizer

The optimization engine.

nSteps

protected static int nSteps

Maximal number of minimization steps.

energy

protected static TotalEnergy energy

function to minimize;

Constructor Detail

HeliumClusterMinimization

public HeliumClusterMinimization()

Method Detail

main

public static void main(java.lang.String[] args)

usageString

private static java.lang.String usageString()

getAtomList

private static AtomList getAtomList(CommandList commands)

getEnergy

private static TotalEnergy getEnergy(AtomList atomList,
                                     DistanceMatrix distanceMatrix,
                                     CommandList commands)

getMinimizer

public static Minimizer getMinimizer(TotalEnergy energy,
                                     CommandList commands)

getOutputFile

public static MeshiWriter getOutputFile(CommandList commands)