Class CalculateEnergyFromStructuresListAverages

java.lang.Object
  meshi.util.MeshiProgram
      CalculateEnergyFromStructuresListAverages

All Implemented Interfaces:

KeyWords

public class CalculateEnergyFromStructuresListAverages
extends MeshiProgram
implements KeyWords

This program receives a list of structures, a list of energy terms, and a list of alpha values. The output of the program is the enregy calculated structures, the gaussian-calculated structures generated from the energy calculated structures and the energy ranks/values files for every pdbID in the given list of structures as well as one large file of energy ranks/values.

Note: the path of the structures will contain the calculated structures as well.

Since:

30-06-07

Nested Class Summary

private static class	CalculateEnergyFromStructuresListAverages.AveragesAndMaxs
private static class	CalculateEnergyFromStructuresListAverages.DistanceFromCatalyticAttribute
private static class	CalculateEnergyFromStructuresListAverages.GaussianAttribute
private static class	CalculateEnergyFromStructuresListAverages.GaussianAttributes

Field Summary

private static boolean

isFirstStructure

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

CalculateEnergyFromStructuresListAverages()

Method Summary

static void	addAtomAttributes(Protein protein)
static void	addTermToAtoms(Protein protein, AbstractEnergy term)
private static ResidueIdentifier[]	getCatalyticResPosFromCSAonlyFile(java.lang.String pdbId, java.lang.String path) This method reads the catalytic residue positions stated in a CSAonly file for the current protein.
private static java.lang.String	getCSAonlyFilesLocationPath(CommandList commands) This method reads the location path where the CSAonly files are found.
static double	getDistanceBetween2Residues(Residue R1, Residue R2) This method calculates the distance between two residues.
static void	getDistancesBetweenEveryResidueAndItsClosestFunctionalNeighbour(Protein protein, java.lang.String CSAonlyFileLocationPath)
static MeshiWriter	getOutputFile(CommandList commands)
static Protein	getProtein(java.lang.String name, CommandList commands)
static Protein	getProtein(java.lang.String name, java.util.List<java.lang.String> chainNames, CommandList commands)
static StringList	getStructureNames(CommandList commands)
static boolean	haveAllAtoms(Residue residue)
static void	main(java.lang.String[] args)
static void	printResidueFeatures(MeshiWriter writer, java.util.ArrayList<AbstractEnergy> energyTerms, Protein protein, java.lang.String CSAfileName)
static void	printResidueFeaturesHeader(MeshiWriter writer, java.util.ArrayList<AbstractEnergy> energyTerms)
private static void	processProtein(Protein protein, MeshiWriter output, CommandList commands, boolean flag)

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

isFirstStructure

private static boolean isFirstStructure

Constructor Detail

CalculateEnergyFromStructuresListAverages

public CalculateEnergyFromStructuresListAverages()

Method Detail

main

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

Throws:

java.io.IOException

processProtein

private static void processProtein(Protein protein,
                                   MeshiWriter output,
                                   CommandList commands,
                                   boolean flag)

addTermToAtoms

public static void addTermToAtoms(Protein protein,
                                  AbstractEnergy term)

printResidueFeaturesHeader

public static void printResidueFeaturesHeader(MeshiWriter writer,
                                              java.util.ArrayList<AbstractEnergy> energyTerms)

printResidueFeatures

public static void printResidueFeatures(MeshiWriter writer,
                                        java.util.ArrayList<AbstractEnergy> energyTerms,
                                        Protein protein,
                                        java.lang.String CSAfileName)

getProtein

public static Protein getProtein(java.lang.String name,
                                 CommandList commands)

getProtein

public static Protein getProtein(java.lang.String name,
                                 java.util.List<java.lang.String> chainNames,
                                 CommandList commands)

getStructureNames

public static StringList getStructureNames(CommandList commands)

getOutputFile

public static MeshiWriter getOutputFile(CommandList commands)

addAtomAttributes

public static void addAtomAttributes(Protein protein)

haveAllAtoms

public static boolean haveAllAtoms(Residue residue)

getDistancesBetweenEveryResidueAndItsClosestFunctionalNeighbour

public static void getDistancesBetweenEveryResidueAndItsClosestFunctionalNeighbour(Protein protein,
                                                                                   java.lang.String CSAonlyFileLocationPath)

getDistanceBetween2Residues

public static double getDistanceBetween2Residues(Residue R1,
                                                 Residue R2)

This method calculates the distance between two residues. The distance between two residues is defined as the minimal distance between any atom of R1 and any atom of R2.

Parameters:

R1 - - This is the Residue object for the first residue.

R2 - - This is the Residue object for the second residue.

Returns:

Returns a double value that represents the distance between R1 and R2.

getCSAonlyFilesLocationPath

private static java.lang.String getCSAonlyFilesLocationPath(CommandList commands)

This method reads the location path where the CSAonly files are found.

Parameters:

commands - - This is the commands list that contains the name of the text file that lists all of the CSAonly files for the program.

Returns:

Returns the location path where the CSAonly files are found.

getCatalyticResPosFromCSAonlyFile

private static ResidueIdentifier[] getCatalyticResPosFromCSAonlyFile(java.lang.String pdbId,
                                                                     java.lang.String path)

This method reads the catalytic residue positions stated in a CSAonly file for the current protein. The CSAonly file is a text file containing in each line the position of one cataytic residue.

Parameters:

pdbID - - This is the pdb id of the current protein.

path - - This is the location of the CSAonly file for the current protein.

Returns:

The method returns an int array of the positions of the catalytic residues.