Class HomologyModeling

java.lang.Object
  HomologyModeling

All Implemented Interfaces:

KeyWords

public class HomologyModeling
extends java.lang.Object
implements KeyWords

Nested Class Summary

private static class	HomologyModeling.HomologyLogger
private static class	HomologyModeling.Loop
private static class	HomologyModeling.LoopAttribute
private static class	HomologyModeling.LoopComperator
static class	HomologyModeling.LoopMode
private static class	HomologyModeling.Three
private static class	HomologyModeling.TimeTerminator

Field Summary

static double	CA_CA_DISTANCE
private static double[][]	data
static EnergyCreator[]	energyCreatorsBondedTermsEVandRamachandran
static EnergyCreator[]	energyCreatorsBondedTermsOnly
static EnergyCreator[]	energyCreatorsBondedTermsPlusEV
static java.lang.String	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

HomologyModeling()

Method Summary

static void	addLoopQD(Protein model, HomologyModeling.Loop loop, CommandList commands, double clashDistance, int nTrys)
static void	addLoopsQuickAndDirty(Protein model, java.util.List<HomologyModeling.Loop> loops, CommandList commands, double clashDistance, int nTrys)
private static void	assignMissingAndHotSidechains(Protein model, CommandList commands)
private static void	completeResiduesWithRandomCoordinates(Protein model, ResidueAlignment alignment, CommandList commands) Adds random coordinates to residues that have some coordinates but miss a few (<3) other.
private static void	copyCoordinatesFromTemplate(Protein model, ResidueAlignment alignment, CommandList commands) When Done all the available information was extracted from the template.
private static void	correctRottenRamachandrans(Protein target, CommandList commands)
private static void	deletion(java.util.Iterator residues, java.util.List<HomologyModeling.Loop> tempList, HomologyModeling.Loop loop, HomologyModeling.Three three)
static EnergyCreator[]	energyCreatorsAll(CommandList commands)
static EnergyCreator[]	energyCreatorsAllTetherOriginalAtoms(CommandList commands, ResidueAlignment alignment)
private static void	finish(Protein model)
private static double	getDistanceGrade(Atom start, Atom end)
private static void	getLoops(Protein model, java.util.List<HomologyModeling.Loop> loops)
private static void	getLoopsBefore(java.util.Iterator residues, java.util.List<HomologyModeling.Loop> tempList, HomologyModeling.Three three)
private static void	initialModel(Protein model, ResidueAlignment alignment, java.util.List<HomologyModeling.Loop> loops, CommandList commands)
private static void	insertion(java.util.Iterator residues, java.util.List<HomologyModeling.Loop> tempList, HomologyModeling.Loop loop, HomologyModeling.Three three)
private static void	insertionEnd(java.util.Iterator residues, java.util.List<HomologyModeling.Loop> tempList, HomologyModeling.Loop loop, HomologyModeling.Three three)
static void	main(java.lang.String[] args)
private static boolean	majorMutation(ResidueType from, ResidueType to)
private static void	minimizationWithEV(Protein model, CommandList commands) Minimization of all sidechains accept the original ones.
static void	setCAsQD(Protein model, HomologyModeling.Loop loop, CommandList commands, double clashDistance, int nTrys)
static void	setHOsQD(Protein model, HomologyModeling.Loop loop, CommandList commands)
static void	setNCCBsQD(Protein model, HomologyModeling.Loop loop, CommandList commands)
private static void	step(java.util.Iterator residues, HomologyModeling.Three three)

Methods inherited from class java.lang.Object

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

Field Detail

NAME

public static final java.lang.String NAME

See Also:

Constant Field Values

CA_CA_DISTANCE

public static final double CA_CA_DISTANCE

See Also:

Constant Field Values

energyCreatorsBondedTermsOnly

public static final EnergyCreator[] energyCreatorsBondedTermsOnly

energyCreatorsBondedTermsPlusEV

public static final EnergyCreator[] energyCreatorsBondedTermsPlusEV

energyCreatorsBondedTermsEVandRamachandran

public static final EnergyCreator[] energyCreatorsBondedTermsEVandRamachandran

data

private static final double[][] data

Constructor Detail

HomologyModeling

public HomologyModeling()

Method Detail

main

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

Throws:

OptimizerException

initialModel

private static void initialModel(Protein model,
                                 ResidueAlignment alignment,
                                 java.util.List<HomologyModeling.Loop> loops,
                                 CommandList commands)

copyCoordinatesFromTemplate

private static void copyCoordinatesFromTemplate(Protein model,
                                                ResidueAlignment alignment,
                                                CommandList commands)

When Done all the available information was extracted from the template. The copied coordinates are: backbone coordinates and side-chain of minor mutations.

completeResiduesWithRandomCoordinates

private static void completeResiduesWithRandomCoordinates(Protein model,
                                                          ResidueAlignment alignment,
                                                          CommandList commands)

Adds random coordinates to residues that have some coordinates but miss a few (<3) other. Residues that were not mutated and have all the coordinates are marked as OriginalAtoms.

minimizationWithEV

private static void minimizationWithEV(Protein model,
                                       CommandList commands)

Minimization of all sidechains accept the original ones. Using excluded volium.

assignMissingAndHotSidechains

private static void assignMissingAndHotSidechains(Protein model,
                                                  CommandList commands)

finish

private static void finish(Protein model)

majorMutation

private static boolean majorMutation(ResidueType from,
                                     ResidueType to)

addLoopsQuickAndDirty

public static void addLoopsQuickAndDirty(Protein model,
                                         java.util.List<HomologyModeling.Loop> loops,
                                         CommandList commands,
                                         double clashDistance,
                                         int nTrys)

addLoopQD

public static void addLoopQD(Protein model,
                             HomologyModeling.Loop loop,
                             CommandList commands,
                             double clashDistance,
                             int nTrys)

setCAsQD

public static void setCAsQD(Protein model,
                            HomologyModeling.Loop loop,
                            CommandList commands,
                            double clashDistance,
                            int nTrys)

setNCCBsQD

public static void setNCCBsQD(Protein model,
                              HomologyModeling.Loop loop,
                              CommandList commands)

setHOsQD

public static void setHOsQD(Protein model,
                            HomologyModeling.Loop loop,
                            CommandList commands)

getDistanceGrade

private static double getDistanceGrade(Atom start,
                                       Atom end)

getLoops

private static void getLoops(Protein model,
                             java.util.List<HomologyModeling.Loop> loops)

getLoopsBefore

private static void getLoopsBefore(java.util.Iterator residues,
                                   java.util.List<HomologyModeling.Loop> tempList,
                                   HomologyModeling.Three three)

insertion

private static void insertion(java.util.Iterator residues,
                              java.util.List<HomologyModeling.Loop> tempList,
                              HomologyModeling.Loop loop,
                              HomologyModeling.Three three)

insertionEnd

private static void insertionEnd(java.util.Iterator residues,
                                 java.util.List<HomologyModeling.Loop> tempList,
                                 HomologyModeling.Loop loop,
                                 HomologyModeling.Three three)

deletion

private static void deletion(java.util.Iterator residues,
                             java.util.List<HomologyModeling.Loop> tempList,
                             HomologyModeling.Loop loop,
                             HomologyModeling.Three three)

step

private static void step(java.util.Iterator residues,
                         HomologyModeling.Three three)

correctRottenRamachandrans

private static void correctRottenRamachandrans(Protein target,
                                               CommandList commands)

energyCreatorsAll

public static EnergyCreator[] energyCreatorsAll(CommandList commands)

energyCreatorsAllTetherOriginalAtoms

public static EnergyCreator[] energyCreatorsAllTetherOriginalAtoms(CommandList commands,
                                                                   ResidueAlignment alignment)