meshi.symmetryComplex.proteinsGJ
Class BackboneCompleterAndMinimizer

java.lang.Object
  meshi.symmetryComplex.proteinsGJ.GJModeller
      meshi.symmetryComplex.proteinsGJ.BackboneCompleterAndMinimizer

All Implemented Interfaces:

KeyWords

Direct Known Subclasses:

BackboneMCM, FullModeller

public class BackboneCompleterAndMinimizer
extends GJModeller

Nested Class Summary

Nested classes/interfaces inherited from class meshi.symmetryComplex.proteinsGJ.GJModeller

GJModeller.HBRangesAndGoodResiduesFilter, GJModeller.HBRangesFilter

Field Summary

Fields inherited from class meshi.symmetryComplex.proteinsGJ.GJModeller

alignment, caHelicesProtein, commands, creator, DISTANCE_AS_NEIGHBOUR_CHAINS, energy, gj, innerBarrelFilter, numberOfChains, outerBarrelFilter, outputFileMask, sequence, stage, startTime, topology

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

BackboneCompleterAndMinimizer(java.lang.String sequence, CommandList commands, java.lang.String outputFileMask)

BackboneCompleterAndMinimizer(java.lang.String tmCasPdbLocation, java.lang.String sequence, CommandList commands, java.lang.String outputFileMask, java.lang.Boolean generateAllData)

Method Summary

protected void	backboneMinimization()
protected void	backboneMinimization(java.lang.String templatefileName)

Methods inherited from class meshi.symmetryComplex.proteinsGJ.GJModeller

backboneRelax, caRelax, creator, generateData, generateFiles, generateLoopData, getChainLetters, makeActualSymmetryComplex, restoreAll, setGJ, timeStamp, toContinue

Methods inherited from class java.lang.Object

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

Constructor Detail

BackboneCompleterAndMinimizer

public BackboneCompleterAndMinimizer(java.lang.String sequence,
                                     CommandList commands,
                                     java.lang.String outputFileMask)
                              throws java.io.IOException

Throws:

java.io.IOException

BackboneCompleterAndMinimizer

public BackboneCompleterAndMinimizer(java.lang.String tmCasPdbLocation,
                                     java.lang.String sequence,
                                     CommandList commands,
                                     java.lang.String outputFileMask,
                                     java.lang.Boolean generateAllData)
                              throws java.io.IOException

Throws:

java.io.IOException

Method Detail

backboneMinimization

protected void backboneMinimization()
                             throws java.io.IOException

Throws:

java.io.IOException

backboneMinimization

protected void backboneMinimization(java.lang.String templatefileName)
                             throws java.io.IOException

Throws:

java.io.IOException