meshi.applications.corpus
Class Corpus

java.lang.Object
  meshi.applications.corpus.Corpus

All Implemented Interfaces:

CompositeTorsionsDefinitions, MeshiPotential, KeyWords

public class Corpus
extends java.lang.Object
implements CompositeTorsionsDefinitions, MeshiPotential, KeyWords

A class that hold the 20-type-mutation energy data of one or several proteins. This class can be loaded from disk or created from a PDB file of a protein. Another way to create this class is by merging two instances into a larger corpus.

Field Summary

static double[][]	blosum62
protected double[][][]	coors
protected double[][][]	energies
protected java.lang.String[]	energyNames
protected java.lang.String[]	excludedProteinsFromUngapped
protected double[][]	forAlign1
protected double[][]	forAlign2
protected int	Nenergies
protected int	Nres
protected double[]	prePro
protected java.lang.String[]	proteinNames
protected int[]	protInd
protected boolean[]	resHasAllEne
protected int[]	resNum
protected int[]	resType
protected double[][]	torsions
protected int[]	ungapped

Fields inherited from interface meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions

ALL, CHI_1, CHI_2, CHI_3, CHI_4, COIL, HELIX, NUM_SIDECHAIN_TORSIONS, OMG, OMNI, PHI, POLYNOMIAL_CHI_1, POLYNOMIAL_CHI_1_CHI_2, POLYNOMIAL_CHI_1_CHI_2_TORSIONS, POLYNOMIAL_CHI_1_CHI_3, POLYNOMIAL_CHI_1_CHI_3_TORSIONS, POLYNOMIAL_CHI_1_CHI_4, POLYNOMIAL_CHI_1_CHI_4_TORSIONS, POLYNOMIAL_CHI_1_TORSIONS, POLYNOMIAL_PHI_PSI, POLYNOMIAL_PHI_PSI_CHI_1, POLYNOMIAL_PHI_PSI_CHI_1_TORSIONS, POLYNOMIAL_PHI_PSI_TORSIONS, PREPRO, PSI, SHEET, TOTAL_TORSION_ANGLES, UNIDENTIFIED_TORSION_TYPE

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

Corpus(java.lang.String exsitingCorpusFile)
Reading a corpus from file.

Corpus(java.lang.String PDBfile, CommandList commands, EnergyCreator[] energyCreators)

Method Summary

void	buildUngappedArray(int fragL)
void	buildUngappedArray(int fragL, java.lang.String[] excludeProteins) Building the ungapped array for fragments of length fragL.
void	buildUngappedArraynoPG(int fragL)
double	calcRmsBetweenStruct(int ind1, int ind2, int fragL, int manner, int overlap) This method gives the rms between two fragments in the corpus (starting in ind1 and ind2).
private void	calculateSolRot1(java.lang.String PDBfile, CommandList commands)
private static void	extractCoordinatesOfRes(Residue res, double[][] co)
void	findDisDist(int len) Find the distributaion of distances between ends.
int	findInUngapped(java.lang.String proteinName, int residueNumber)
void	findPhiPsiRelations(int howMany) Find the relation between Delta{phi,psi} and RMS
void	GeneralThreadingExperiment(int fragL, int Ninstances, java.lang.String header, int RMSind1, int RMSind2) This is a method for general ungapped threading.
private static boolean	haveAllBackboneAtoms(Residue res)
void	merge(Corpus corpus)
void	setExcludedProteinsFromUngapped(java.lang.String[] list)
private void	specialMutate(Protein aux, int mutateThis, int mutateTo, double[][] pp, DunbrackLib lib)
void	threadingExperiment_withPP(int fragL, double Wprop, double Wsolv)
void	threadingExperiment(int fragL)
void	threadingExperimentnoPG(int fragL)
void	writeToDisk(java.lang.String fileName) This overload writes the entire corpus to disk.
private void	writeToDisk(java.lang.String fileName, boolean[] toWrite) Writing all the residues in the corpus that are marked as TRUE in the 'toWrite' input array (its length must be as the corpus's).
void	writeToDisk(java.lang.String fileName, int indAr, int fragL) This overload writes to disk a subset of the corpus, all the residues that have of the previous method, that writes to disk only residues from the fragments whos indices are given in the input array.

Methods inherited from class java.lang.Object

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

Field Detail

proteinNames

protected java.lang.String[] proteinNames

energyNames

protected java.lang.String[] energyNames

Nenergies

protected int Nenergies

Nres

protected int Nres

protInd

protected int[] protInd

resNum

protected int[] resNum

resType

protected int[] resType

prePro

protected double[] prePro

energies

protected double[][][] energies

coors

protected double[][][] coors

torsions

protected double[][] torsions

resHasAllEne

protected boolean[] resHasAllEne

ungapped

protected int[] ungapped

excludedProteinsFromUngapped

protected java.lang.String[] excludedProteinsFromUngapped

forAlign1

protected double[][] forAlign1

forAlign2

protected double[][] forAlign2

blosum62

public static final double[][] blosum62

Constructor Detail

Corpus

public Corpus(java.lang.String PDBfile,
              CommandList commands,
              EnergyCreator[] energyCreators)

Corpus

public Corpus(java.lang.String exsitingCorpusFile)

Reading a corpus from file. See the file format in the method 'writeToDisk'

Method Detail

writeToDisk

private void writeToDisk(java.lang.String fileName,
                         boolean[] toWrite)

Writing all the residues in the corpus that are marked as TRUE in the 'toWrite' input array (its length must be as the corpus's). The format is: ... ... > ... ... ... > > ... ... ... > .... > ... ... ... >

writeToDisk

public void writeToDisk(java.lang.String fileName)

This overload writes the entire corpus to disk. Residues that do not have all the energies are not written.

writeToDisk

public void writeToDisk(java.lang.String fileName,
                        int indAr,
                        int fragL)

This overload writes to disk a subset of the corpus, all the residues that have of the previous method, that writes to disk only residues from the fragments whos indices are given in the input array. This is useful to create more compact libraries from a big one. The format is as for the other method.

merge

public void merge(Corpus corpus)

buildUngappedArray

public void buildUngappedArray(int fragL)

buildUngappedArray

public void buildUngappedArray(int fragL,
                               java.lang.String[] excludeProteins)

Building the ungapped array for fragments of length fragL. Fragments from the proteins in the provided list are excluded.

threadingExperiment

public void threadingExperiment(int fragL)

threadingExperiment_withPP

public void threadingExperiment_withPP(int fragL,
                                       double Wprop,
                                       double Wsolv)

GeneralThreadingExperiment

public void GeneralThreadingExperiment(int fragL,
                                       int Ninstances,
                                       java.lang.String header,
                                       int RMSind1,
                                       int RMSind2)

This is a method for general ungapped threading. You give it the frag length 'fragL', and the number of instances you want 'Ninstances'. It will randomly pick 'Ninstances' random fragments and thread the sequence of the first into all the others. Than print:

<1>

<2>

<3> ...

The RMS is calculated between two indices (inclusive) in the FRAG reference frame.

haveAllBackboneAtoms

private static boolean haveAllBackboneAtoms(Residue res)

extractCoordinatesOfRes

private static void extractCoordinatesOfRes(Residue res,
                                            double[][] co)

calculateSolRot1

private void calculateSolRot1(java.lang.String PDBfile,
                              CommandList commands)

specialMutate

private void specialMutate(Protein aux,
                           int mutateThis,
                           int mutateTo,
                           double[][] pp,
                           DunbrackLib lib)

findInUngapped

public int findInUngapped(java.lang.String proteinName,
                          int residueNumber)

calcRmsBetweenStruct

public double calcRmsBetweenStruct(int ind1,
                                   int ind2,
                                   int fragL,
                                   int manner,
                                   int overlap)

This method gives the rms between two fragments in the corpus (starting in ind1 and ind2). fragL is the fragment length. The fragments are superimposed according to an overlap region who's size is a parameter. The type of the overlap region are given by manner: -1 - overlap of the N-terminus 0 - two overlap regions in both termini (each of length overlap) 1 - overlap of the C-terminus You can force the overlap of the entire fragments by giving (overlap=fragL) and (manner=1)

buildUngappedArraynoPG

public void buildUngappedArraynoPG(int fragL)

threadingExperimentnoPG

public void threadingExperimentnoPG(int fragL)

findDisDist

public void findDisDist(int len)

Find the distributaion of distances between ends.

findPhiPsiRelations

public void findPhiPsiRelations(int howMany)

Find the relation between Delta{phi,psi} and RMS

setExcludedProteinsFromUngapped

public void setExcludedProteinsFromUngapped(java.lang.String[] list)