meshi.util
Class Scmod

java.lang.Object
  meshi.util.MeshiProgram
      meshi.util.Scmod

All Implemented Interfaces:

MeshiPotential, KeyWords

public final class Scmod
extends MeshiProgram
implements KeyWords, MeshiPotential

eThis class perform conccurent sidechain modeling as describe in Kalisman and Keasar (2006). There are two modes of operations. One as a stand alone application that prints the new pdb coordinates. Run as follow: java -Xmx300m SCMOD The second mode is to give an instance of Protein to the static method "scmod". This mode is usful if ones wish to do sidechain modeling as part of a larger application. The coordinates of the Protein instance are changed. Important points: ----------------- 1) The number of iterations can be 0-Inf. If it is 0 all rotamers are put into their most probable back bone dependent rotamer. If it is 1, the sidecahin are modeled only by their excluded volume clashes and the BBDEP rotamer probability. If it is 2 or more, also solvation and HB energy terms are included. 2) In the second mode, residues in the protein that have their CA atoms frozen are not modeled. The stand alone application models all the residues. 3) In the second mode, the protein instance must contain ALL the atom including hydrogens. 4) This class uses the package "meshi.energy.sideChainModelingSolvate" which is a truncated form of the package "meshi.energy.solvate", that is suitable for this application ONLY.

Field Summary

private static double	excludedVolumeWeight
private static double[]	i1w1
private static double[]	i1w2
private static double[]	i1w3
private static double[]	i1w4
private static double[]	i1w5
private static double[]	i1w6
private static double[]	i2w1
private static double[]	i2w2
private static double[]	i2w3
private static double[]	i2w4
private static double[]	i2w5
private static double[]	i2w6
private static DunbrackLib	lib The implemented interfaces defines the names of atom and residue types.
private static double	safeRadius
private static int[]	seder
private static double[]	w1
private static double[]	w2
private static double[]	w3
private static double[]	w4
private static double[]	w5
private static double[]	w6

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

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

Constructor Summary

Scmod()

Method Summary

protected static double[]	calcVariousEnergies(int resnum, double prob, int stage, Protein protein, TotalEnergy energy, DistanceMatrix distanceMatrix, SideChainSolvateEnergy energyTerm, ExcludedVolParametersList parametersList)
static void	scmod(CommandList commands, Protein protein, int maxIter)
static void	scmod(CommandList commands, Protein protein, int maxIter, double excludedVolumeWeight)
static void	scmod(CommandList commands, Protein protein, int maxIter, double excludedVolumeWeight, TotalEnergy totalEnergy)

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

lib

private static DunbrackLib lib

The implemented interfaces defines the names of atom and residue types.

excludedVolumeWeight

private static double excludedVolumeWeight

safeRadius

private static double safeRadius

seder

private static int[] seder

w1

private static double[] w1

w2

private static double[] w2

w3

private static double[] w3

w4

private static double[] w4

w5

private static double[] w5

w6

private static double[] w6

i2w1

private static double[] i2w1

i2w2

private static double[] i2w2

i2w3

private static double[] i2w3

i2w4

private static double[] i2w4

i2w5

private static double[] i2w5

i2w6

private static double[] i2w6

i1w1

private static double[] i1w1

i1w2

private static double[] i1w2

i1w3

private static double[] i1w3

i1w4

private static double[] i1w4

i1w5

private static double[] i1w5

i1w6

private static double[] i1w6

Constructor Detail

Scmod

public Scmod()

Method Detail

scmod

public static void scmod(CommandList commands,
                         Protein protein,
                         int maxIter)

scmod

public static void scmod(CommandList commands,
                         Protein protein,
                         int maxIter,
                         double excludedVolumeWeight)

scmod

public static void scmod(CommandList commands,
                         Protein protein,
                         int maxIter,
                         double excludedVolumeWeight,
                         TotalEnergy totalEnergy)

calcVariousEnergies

protected static double[] calcVariousEnergies(int resnum,
                                              double prob,
                                              int stage,
                                              Protein protein,
                                              TotalEnergy energy,
                                              DistanceMatrix distanceMatrix,
                                              SideChainSolvateEnergy energyTerm,
                                              ExcludedVolParametersList parametersList)