meshi.symmetryComplex.proteinsGJ
Class FullModeller

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

All Implemented Interfaces:

KeyWords

public class FullModeller
extends BackboneCompleterAndMinimizer

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

FullModeller(java.lang.String pdbTemplate, java.lang.String sequence, CommandList commands, java.lang.String outputFileMask)

Method Summary

protected void	fullMinimization()
private MCM	getMCM(Protein model, TotalEnergy energy, CommandList commands, SimpleInflate inflate)

Methods inherited from class meshi.symmetryComplex.proteinsGJ.BackboneCompleterAndMinimizer

backboneMinimization, backboneMinimization

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

FullModeller

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

Throws:

java.io.IOException

Method Detail

fullMinimization

protected void fullMinimization()
                         throws java.io.IOException

Throws:

java.io.IOException

getMCM

private MCM getMCM(Protein model,
                   TotalEnergy energy,
                   CommandList commands,
                   SimpleInflate inflate)