Class Beautify

java.lang.Object
  meshi.util.MeshiProgram
      Beautify

All Implemented Interfaces:

MeshiPotential, KeyWords

public class Beautify
extends MeshiProgram
implements MeshiPotential, KeyWords

Nested Class Summary

private static class

Beautify.BeautifyLogger

Field Summary

static AlphaAngleCreator	alphaAngleCreator
static AlphaTorsionCreator	alphaTorsionCreator
static AngleCreator	angleCreator
static BondCreator	bondCreator
static EnergyCreator[]	caEnergyCreators
static EnergyCreator[]	caEnergyCreators1
static CompositePropensityCreator	compositePropensityCreator
static ExcludedVolCreator	excludedVolCreator
static EnergyCreator[]	extendedCaEnergyCreators
private static double	extendedDistance
static double	FAR_AWAY
static int	FRAGMENT_LENGTH
static HbondsPunishHOCAngleCreator	hbondsPunishHOCAngleCreator
static HBondsPunishOHNAngleCreator	hBondsPunishOHNAngleCreator
static HydrogenBondsCreator	hydrogenBondsCreator
static HydrogenBondsPairsCreator	hydrogenBondsPairsCreator
static java.lang.String	NAME
static OutOfPlaneCreator	outOfPlaneCreator
static PlaneCreator	planeCreator
static RamachandranSidechainEnergyCreator	ramachandranSidechainEnergyCreator
static TetherCreator	tetherCreator
static WarpEnergyCreator	warpEnergyCreator

Fields inherited from class meshi.util.MeshiProgram

commandLine, name

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

Beautify()

Method Summary

static Protein	addLoops(ResidueSequence targetSequence, Protein shotgunModel, Beautify.BeautifyLogger log)
private static java.util.ArrayList<int[]>	attach(ResidueAlignment residueAlignment)
private static void	copyCoordinates(ResidueAlignment residueAlignment)
static Protein	createBackboneModel(Sequence targetSequence, Protein caModel, Protein shotgunModel, CommandList commands, Beautify.BeautifyLogger log)
private static java.lang.Object[]	createCaModel(Protein model, Protein shotgunModel, CommandList commands)
private static int	findProblematicShotgunResidues(Protein shotgunModel, CommandList commands)
private static int	findProblematicShotgunResidues(ResidueAlignment alignment)
static void	freezeReliableCAs(ResidueAlignment residueAlignment, Protein model)
static Protein	getBestCaModel(ResidueSequence targetSequence, Protein shotgunModel, CommandList commands, Beautify.BeautifyLogger log)
static Protein	getFinalModel(Protein backboneModel, CommandList commands, Protein shotgunModel, Beautify.BeautifyLogger log)
private static ResidueSequence	getResidueSequence(CommandList commands)
static double	getWarpThreshold(CommandList commands)
static boolean	isKnot(Protein model, CommandList commands)
static void	main(java.lang.String[] args)
private static TotalEnergy	mcm(Protein model, CommandList commands, Protein shotgunModel, Beautify.BeautifyLogger log)
private static boolean	problematic(Residue residue)
private static boolean	problematic(ResidueAlignment residueAlignment, int position)
static TotalEnergy	relax(Protein protein, CommandList commands, EnergyCreator[] energyCreators)
static TotalEnergy	relax(Protein model, CommandList commands, Protein shotgunModel, Beautify.BeautifyLogger log)
static TotalEnergy	relaxCaModel(Protein caModel, Protein shotgunModel, CommandList commands)
static void	test(Protein protein)
private static Protein	truncate(Protein target, Protein shotgunModel)
private static TotalEnergy	warp(Protein caModel, Protein shotgunModel, CommandList commands)

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

FRAGMENT_LENGTH

public static final int FRAGMENT_LENGTH

See Also:

Constant Field Values

FAR_AWAY

public static final double FAR_AWAY

See Also:

Constant Field Values

NAME

public static final java.lang.String NAME

See Also:

Constant Field Values

hydrogenBondsCreator

public static final HydrogenBondsCreator hydrogenBondsCreator

hydrogenBondsPairsCreator

public static final HydrogenBondsPairsCreator hydrogenBondsPairsCreator

hbondsPunishHOCAngleCreator

public static final HbondsPunishHOCAngleCreator hbondsPunishHOCAngleCreator

hBondsPunishOHNAngleCreator

public static final HBondsPunishOHNAngleCreator hBondsPunishOHNAngleCreator

warpEnergyCreator

public static final WarpEnergyCreator warpEnergyCreator

bondCreator

public static final BondCreator bondCreator

alphaAngleCreator

public static final AlphaAngleCreator alphaAngleCreator

alphaTorsionCreator

public static final AlphaTorsionCreator alphaTorsionCreator

excludedVolCreator

public static final ExcludedVolCreator excludedVolCreator

angleCreator

public static final AngleCreator angleCreator

planeCreator

public static final PlaneCreator planeCreator

outOfPlaneCreator

public static final OutOfPlaneCreator outOfPlaneCreator

tetherCreator

public static final TetherCreator tetherCreator

ramachandranSidechainEnergyCreator

public static final RamachandranSidechainEnergyCreator ramachandranSidechainEnergyCreator

compositePropensityCreator

public static final CompositePropensityCreator compositePropensityCreator

caEnergyCreators

public static final EnergyCreator[] caEnergyCreators

caEnergyCreators1

public static final EnergyCreator[] caEnergyCreators1

extendedCaEnergyCreators

public static final EnergyCreator[] extendedCaEnergyCreators

extendedDistance

private static double extendedDistance

Constructor Detail

Beautify

public Beautify()

Method Detail

main

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

Throws:

OptimizerException

getResidueSequence

private static ResidueSequence getResidueSequence(CommandList commands)

addLoops

public static Protein addLoops(ResidueSequence targetSequence,
                               Protein shotgunModel,
                               Beautify.BeautifyLogger log)

getBestCaModel

public static Protein getBestCaModel(ResidueSequence targetSequence,
                                     Protein shotgunModel,
                                     CommandList commands,
                                     Beautify.BeautifyLogger log)

createCaModel

private static java.lang.Object[] createCaModel(Protein model,
                                                Protein shotgunModel,
                                                CommandList commands)

test

public static void test(Protein protein)

relaxCaModel

public static TotalEnergy relaxCaModel(Protein caModel,
                                       Protein shotgunModel,
                                       CommandList commands)

truncate

private static Protein truncate(Protein target,
                                Protein shotgunModel)

warp

private static TotalEnergy warp(Protein caModel,
                                Protein shotgunModel,
                                CommandList commands)

problematic

private static boolean problematic(Residue residue)

problematic

private static boolean problematic(ResidueAlignment residueAlignment,
                                   int position)

attach

private static java.util.ArrayList<int[]> attach(ResidueAlignment residueAlignment)

findProblematicShotgunResidues

private static int findProblematicShotgunResidues(Protein shotgunModel,
                                                  CommandList commands)

findProblematicShotgunResidues

private static int findProblematicShotgunResidues(ResidueAlignment alignment)

copyCoordinates

private static void copyCoordinates(ResidueAlignment residueAlignment)

createBackboneModel

public static Protein createBackboneModel(Sequence targetSequence,
                                          Protein caModel,
                                          Protein shotgunModel,
                                          CommandList commands,
                                          Beautify.BeautifyLogger log)

getFinalModel

public static Protein getFinalModel(Protein backboneModel,
                                    CommandList commands,
                                    Protein shotgunModel,
                                    Beautify.BeautifyLogger log)

mcm

private static TotalEnergy mcm(Protein model,
                               CommandList commands,
                               Protein shotgunModel,
                               Beautify.BeautifyLogger log)

relax

public static TotalEnergy relax(Protein model,
                                CommandList commands,
                                Protein shotgunModel,
                                Beautify.BeautifyLogger log)

freezeReliableCAs

public static void freezeReliableCAs(ResidueAlignment residueAlignment,
                                     Protein model)

relax

public static TotalEnergy relax(Protein protein,
                                CommandList commands,
                                EnergyCreator[] energyCreators)

getWarpThreshold

public static double getWarpThreshold(CommandList commands)

isKnot

public static boolean isKnot(Protein model,
                             CommandList commands)