meshi.util
Class Utils

java.lang.Object
  meshi.util.Utils

All Implemented Interfaces:

MeshiPotential, KeyWords

public class Utils
extends java.lang.Object
implements MeshiPotential, KeyWords

Where we store useful static methods that do not make sense anywhere else.

Nested Class Summary

private static class	Utils.DefaultExceptionHandler
private static class	Utils.DoNothingExceptionHandler

Field Summary

static ExceptionHandler	defaultExceptionHandler
static ExceptionHandler	doNothing

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

Utils()

Method Summary

static boolean	addAtoms(Protein model, CommandList commands)
static boolean	addAtoms(Protein model, CommandList commands, int maxNumberOfRandomCoordinatesPerResidue)
static void	addHydrogens(Protein protein, CommandList commands)
static ResidueAlignment	alignProteinsByAlignmentFile(CommandList commands, Key key, Chain chain0, Chain chain1)
static void	assignBackboneCoordinates(AtomList modelAtoms, AtomList tempAtoms)
static void	AssignDSSP(Protein protein, CommandList commands, Key key)
static void	AssignDSSP(Protein protein, java.lang.String dsspFileName)
static void	assignRandomCaCoordinates(Chain chain)
static boolean	assignRandomCoordinates(Residue residue, CommandList commands, int maxMissingAtoms)
static void	assignSecondaryStructure(Chain chain, CommandList commands, Key key)
static void	assignSecondaryStructure(Protein protein, CommandList commands, Key key)
static void	assignSecondaryStructure(Protein protein, SequenceAlignment targetSecondaryStructure)
static void	colorByEnergy(AtomList atomList)
static AtomList	duplicateInAnewMolecularSystem(AtomList atomList)
static boolean	equals(java.lang.Object obj1, java.lang.Object obj2) Static version of equals.
static java.util.ArrayList	filter(java.util.ArrayList list, Filter filter, java.util.ArrayList out)
static DistanceList	filter(DistanceList list, Filter filter, DistanceList out)
static AngleParametersList	getAngleParameters(CommandList commands)
static BondParametersList	getBondParameters(CommandList commands)
static int	getClashes(Atom atom, java.util.List<Atom> neighbors, double clashDistance)
static Atom	getCovalentNeighbor(Atom atom)
private static Atom	getCovalentNeighborUp(Atom atom) May be used only by getCovalentNeighbor(Atom atom)
static DistanceMatrix	getDistanceMatrix(AtomList atomList, CommandList commands) A standard method to build distance matrices.
static java.lang.String[]	getEnergyTermsNames(TotalEnergy totalEnergy)
static double[]	getEnergyValues(TotalEnergy totalEnergy)
static ResidueList	getFragment(Protein protein, int start, int end)
static LBFGS	getLBFGS(TotalEnergy energy, CommandList commands)
static LBFGS	getLBFGS(TotalEnergy energy, CommandList commands, Key key)
static java.util.List<Atom>	getNeighbors(Atom atom, Protein protein, double clashDistance)
static AtomList	getNeighbors(ResidueList residueList, Protein protein, double clashDistance)
static ResidueAlignment	getOriginalAtomsAlignment(ResidueAlignment alignment, OriginalAtoms originalAtoms, int row) Gets a residue alignment as a parameters and returns a new alignment that includes only residues with original atoms.
static MeshiWriter	getOutputFile(CommandList commands)
static Protein	getProtein(CommandList commands, Key key1, Key key2, ResidueCreator creator, ExceptionHandler exceptionHandler) Reads a protein structure from the file pointed at by the command list.
static Protein	getProtein(CommandList commands, Key key, ResidueCreator creator, ExceptionHandler exceptionHandler) Creates a Protein object in a new MolecularSystem.
static Protein	getProtein(CommandList commands, java.lang.String fileName, ResidueCreator creator, ExceptionHandler exceptionHandler)
static java.lang.String	getProteinNameFromPdbFileName(java.lang.String fullFileName) Reads a protein structure from the file pointed at by the command list.
static Protein	getReferenceProtein(CommandList commands)
static ResidueSequence	getResidueSequence(CommandList commands, Key key)
static int[]	getSeqOfProt(Protein prot, int fromRes, int toRes)
static StringList	getStructureNames(CommandList commands)
static void	hideAllBut(AtomList atomList)
static CommandList	init(java.lang.String[] args, int numberOfParameters, int seed, java.lang.String errorMessage)
static CommandList	init(java.lang.String[] args, int numberOfParameters, java.lang.String errorMessage)
static CommandList	init(java.lang.String[] args, java.lang.String name) A standard method to create the commands list.
static void	moveHydrogensCloseToHeavy(AtomList atoms, double radius)
static MeshiWriter	newPdbWriter(CommandList commands, Key pathKey, Key nameKey, int runNumber) Opens a file for writing (warped by MeshiWriter object) with a name and location specified by the commands and a ...pdb suffix.
static int	numberOfAtomsWithCoordinates(Protein protein)
static int	numberOfNonDummyResidues(Protein protein)
static TotalEnergy	oldRelax(AtomList atoms, Protein protein, EnergyCreator[] energyCreators, CommandList commands)
static TotalEnergy	oldRelax(AtomList atoms, Protein protein, EnergyCreator[] energyCreators, CommandList commands, Key key)
static void	print(java.util.ArrayList list, int rawLength, java.lang.String format) Print the list elements in raws.
static void	print(java.lang.Iterable list)
static void	printCaspFormat(ModelData modelData, CommandList commands, int modelNum)
static double	radius(MolecularSystem molecularSystem)
static TotalEnergy	relax(AtomList atoms, Protein protein, EnergyCreator[] energyCreators, CommandList commands)
static TotalEnergy	relax(AtomList atoms, Protein protein, EnergyCreator[] energyCreators, CommandList commands, Key key)
static void	RmsGdtEnergy(MeshiWriter output, ResidueAlignment modelRefeenceAlignment, TotalEnergy totalEnergy, java.lang.String tag, int refLength)
static void	RmsGdtEnergy(java.lang.Object output, Protein model, Protein reference, TotalEnergy totalEnergy, java.lang.String tag)
static void	RmsGdtEnergy(java.lang.Object output, ResidueSequence model, ResidueSequence reference, TotalEnergy totalEnergy, java.lang.String tag)
static void	RmsGdtEnergy(StringList output, ResidueAlignment modelRefeenceAlignment, TotalEnergy totalEnergy, java.lang.String tag, int refLength)
static void	testMolecularSystemIntegrity(MolecularSystem ms, java.lang.String comment)
static void	testNonBondedList(DistanceList nonBondedList)
static double	toDouble(java.lang.String s) Converts a string to a double.
static int	toInt(java.lang.String s) Converts a string to an int.
static boolean	weirdAtom(Atom atom)

Methods inherited from class java.lang.Object

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

Field Detail

defaultExceptionHandler

public static final ExceptionHandler defaultExceptionHandler

doNothing

public static final ExceptionHandler doNothing

Constructor Detail

Utils

public Utils()

Method Detail

init

public static CommandList init(java.lang.String[] args,
                               java.lang.String name)

A standard method to create the commands list.

init

public static CommandList init(java.lang.String[] args,
                               int numberOfParameters,
                               java.lang.String errorMessage)

init

public static CommandList init(java.lang.String[] args,
                               int numberOfParameters,
                               int seed,
                               java.lang.String errorMessage)

getOriginalAtomsAlignment

public static ResidueAlignment getOriginalAtomsAlignment(ResidueAlignment alignment,
                                                         OriginalAtoms originalAtoms,
                                                         int row)

Gets a residue alignment as a parameters and returns a new alignment that includes only residues with original atoms.

assignSecondaryStructure

public static void assignSecondaryStructure(Protein protein,
                                            CommandList commands,
                                            Key key)

assignSecondaryStructure

public static void assignSecondaryStructure(Chain chain,
                                            CommandList commands,
                                            Key key)

assignSecondaryStructure

public static void assignSecondaryStructure(Protein protein,
                                            SequenceAlignment targetSecondaryStructure)

alignProteinsByAlignmentFile

public static ResidueAlignment alignProteinsByAlignmentFile(CommandList commands,
                                                            Key key,
                                                            Chain chain0,
                                                            Chain chain1)

getDistanceMatrix

public static DistanceMatrix getDistanceMatrix(AtomList atomList,
                                               CommandList commands)

A standard method to build distance matrices.

getEnergyValues

public static double[] getEnergyValues(TotalEnergy totalEnergy)

getEnergyTermsNames

public static java.lang.String[] getEnergyTermsNames(TotalEnergy totalEnergy)

relax

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

oldRelax

public static TotalEnergy oldRelax(AtomList atoms,
                                   Protein protein,
                                   EnergyCreator[] energyCreators,
                                   CommandList commands)

oldRelax

public static TotalEnergy oldRelax(AtomList atoms,
                                   Protein protein,
                                   EnergyCreator[] energyCreators,
                                   CommandList commands,
                                   Key key)

relax

public static TotalEnergy relax(AtomList atoms,
                                Protein protein,
                                EnergyCreator[] energyCreators,
                                CommandList commands,
                                Key key)

getStructureNames

public static StringList getStructureNames(CommandList commands)

getOutputFile

public static MeshiWriter getOutputFile(CommandList commands)

newPdbWriter

public static MeshiWriter newPdbWriter(CommandList commands,
                                       Key pathKey,
                                       Key nameKey,
                                       int runNumber)

Opens a file for writing (warped by MeshiWriter object) with a name and location specified by the commands and a ...pdb suffix.

RmsGdtEnergy

public static void RmsGdtEnergy(java.lang.Object output,
                                ResidueSequence model,
                                ResidueSequence reference,
                                TotalEnergy totalEnergy,
                                java.lang.String tag)

RmsGdtEnergy

public static void RmsGdtEnergy(java.lang.Object output,
                                Protein model,
                                Protein reference,
                                TotalEnergy totalEnergy,
                                java.lang.String tag)

RmsGdtEnergy

public static void RmsGdtEnergy(MeshiWriter output,
                                ResidueAlignment modelRefeenceAlignment,
                                TotalEnergy totalEnergy,
                                java.lang.String tag,
                                int refLength)

RmsGdtEnergy

public static void RmsGdtEnergy(StringList output,
                                ResidueAlignment modelRefeenceAlignment,
                                TotalEnergy totalEnergy,
                                java.lang.String tag,
                                int refLength)

equals

public static boolean equals(java.lang.Object obj1,
                             java.lang.Object obj2)

Static version of equals. Useful when the compared objects may be null. This is NOT the right place for highly sofisticate algorithms.

toInt

public static int toInt(java.lang.String s)

Converts a string to an int.

toDouble

public static double toDouble(java.lang.String s)

Converts a string to a double.

getSeqOfProt

public static int[] getSeqOfProt(Protein prot,
                                 int fromRes,
                                 int toRes)

radius

public static double radius(MolecularSystem molecularSystem)

testMolecularSystemIntegrity

public static void testMolecularSystemIntegrity(MolecularSystem ms,
                                                java.lang.String comment)

hideAllBut

public static void hideAllBut(AtomList atomList)

getLBFGS

public static LBFGS getLBFGS(TotalEnergy energy,
                             CommandList commands)

getLBFGS

public static LBFGS getLBFGS(TotalEnergy energy,
                             CommandList commands,
                             Key key)

addAtoms

public static boolean addAtoms(Protein model,
                               CommandList commands)

addAtoms

public static boolean addAtoms(Protein model,
                               CommandList commands,
                               int maxNumberOfRandomCoordinatesPerResidue)

printCaspFormat

public static void printCaspFormat(ModelData modelData,
                                   CommandList commands,
                                   int modelNum)

numberOfNonDummyResidues

public static int numberOfNonDummyResidues(Protein protein)

numberOfAtomsWithCoordinates

public static int numberOfAtomsWithCoordinates(Protein protein)

getProteinNameFromPdbFileName

public static java.lang.String getProteinNameFromPdbFileName(java.lang.String fullFileName)

Reads a protein structure from the file pointed at by the command list.

getFragment

public static ResidueList getFragment(Protein protein,
                                      int start,
                                      int end)

addHydrogens

public static void addHydrogens(Protein protein,
                                CommandList commands)

getProtein

public static Protein getProtein(CommandList commands,
                                 Key key,
                                 ResidueCreator creator,
                                 ExceptionHandler exceptionHandler)

Creates a Protein object in a new MolecularSystem.

getProtein

public static Protein getProtein(CommandList commands,
                                 java.lang.String fileName,
                                 ResidueCreator creator,
                                 ExceptionHandler exceptionHandler)

getProtein

public static Protein getProtein(CommandList commands,
                                 Key key1,
                                 Key key2,
                                 ResidueCreator creator,
                                 ExceptionHandler exceptionHandler)

Reads a protein structure from the file pointed at by the command list. The protein is created in a new MolecularSystem.

getReferenceProtein

public static Protein getReferenceProtein(CommandList commands)

assignRandomCaCoordinates

public static void assignRandomCaCoordinates(Chain chain)

assignRandomCoordinates

public static boolean assignRandomCoordinates(Residue residue,
                                              CommandList commands,
                                              int maxMissingAtoms)

getCovalentNeighbor

public static Atom getCovalentNeighbor(Atom atom)

getCovalentNeighborUp

private static Atom getCovalentNeighborUp(Atom atom)

May be used only by getCovalentNeighbor(Atom atom)

colorByEnergy

public static void colorByEnergy(AtomList atomList)

assignBackboneCoordinates

public static void assignBackboneCoordinates(AtomList modelAtoms,
                                             AtomList tempAtoms)

AssignDSSP

public static void AssignDSSP(Protein protein,
                              CommandList commands,
                              Key key)

AssignDSSP

public static void AssignDSSP(Protein protein,
                              java.lang.String dsspFileName)

getNeighbors

public static AtomList getNeighbors(ResidueList residueList,
                                    Protein protein,
                                    double clashDistance)

weirdAtom

public static boolean weirdAtom(Atom atom)

getNeighbors

public static java.util.List<Atom> getNeighbors(Atom atom,
                                                Protein protein,
                                                double clashDistance)

getClashes

public static int getClashes(Atom atom,
                             java.util.List<Atom> neighbors,
                             double clashDistance)

getResidueSequence

public static ResidueSequence getResidueSequence(CommandList commands,
                                                 Key key)

print

public static void print(java.lang.Iterable list)

print

public static void print(java.util.ArrayList list,
                         int rawLength,
                         java.lang.String format)

Print the list elements in raws. The number of elements in a raw is determined by the parameter

filter

public static java.util.ArrayList filter(java.util.ArrayList list,
                                         Filter filter,
                                         java.util.ArrayList out)

filter

public static DistanceList filter(DistanceList list,
                                  Filter filter,
                                  DistanceList out)

testNonBondedList

public static void testNonBondedList(DistanceList nonBondedList)

duplicateInAnewMolecularSystem

public static AtomList duplicateInAnewMolecularSystem(AtomList atomList)

moveHydrogensCloseToHeavy

public static void moveHydrogensCloseToHeavy(AtomList atoms,
                                             double radius)

getBondParameters

public static BondParametersList getBondParameters(CommandList commands)

getAngleParameters

public static AngleParametersList getAngleParameters(CommandList commands)