meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma
Class AtomicPairwisePMFSummaParameters

java.lang.Object
  meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSummaParameters

All Implemented Interfaces:

MeshiPotential, KeyWords

public class AtomicPairwisePMFSummaParameters
extends java.lang.Object
implements KeyWords, MeshiPotential

Parameters for the atomic pairwise PMF. Class includes polynomial splines for all atom-atom PMFs.

Field Summary

private java.lang.String[]	atomNames
private static java.lang.String[]	atomNamesTranslationsMESHI
private static java.lang.String[]	atomNamesTranslationsSumma
private double[]	bins
private CoefficientsMatrixForAtomPairSpline[][]	coefs
private static java.lang.String	LABEL_ATOM_NAMES_BEGIN
private static java.lang.String	LABEL_ATOM_NAMES_END
private static java.lang.String	LABEL_BINS_BEGIN
private static java.lang.String	LABEL_BINS_END
private static java.lang.String	LABEL_PMF_BEGIN
private static java.lang.String	LABEL_PMF_END
private static int[]	MESHI2SUMMA
private static boolean	parametersLoaded

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

AtomicPairwisePMFSummaParameters(CommandList commands)
Load parameters list from file.

Method Summary

private void	loadingParametersFailed(java.lang.String line) Throws exception.
private static java.lang.String	meshiAtomTypeToSummaAtomName(AtomType atomType) Translates MESHI atom type to Summa atom name.
CoefficientsMatrixForAtomPairSpline	splineForAtomPair(AtomType atom1Type, AtomType atom2Type) Retrieve spline for atom pair.
CoefficientsMatrixForAtomPairSpline	splineForAtomPair(int atom1TypeOrdinal, int atom2TypeOrdinal)
private int	summaAtomNameToParametersAtomIndex(java.lang.String name) Translates Summa atom name to parameters file atom index.

Methods inherited from class java.lang.Object

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

Field Detail

LABEL_BINS_BEGIN

private static final java.lang.String LABEL_BINS_BEGIN

See Also:

Constant Field Values

LABEL_BINS_END

private static final java.lang.String LABEL_BINS_END

See Also:

Constant Field Values

LABEL_ATOM_NAMES_BEGIN

private static final java.lang.String LABEL_ATOM_NAMES_BEGIN

See Also:

Constant Field Values

LABEL_ATOM_NAMES_END

private static final java.lang.String LABEL_ATOM_NAMES_END

See Also:

Constant Field Values

LABEL_PMF_BEGIN

private static final java.lang.String LABEL_PMF_BEGIN

See Also:

Constant Field Values

LABEL_PMF_END

private static final java.lang.String LABEL_PMF_END

See Also:

Constant Field Values

MESHI2SUMMA

private static final int[] MESHI2SUMMA

parametersLoaded

private static boolean parametersLoaded

bins

private double[] bins

atomNames

private java.lang.String[] atomNames

coefs

private CoefficientsMatrixForAtomPairSpline[][] coefs

atomNamesTranslationsMESHI

private static java.lang.String[] atomNamesTranslationsMESHI

atomNamesTranslationsSumma

private static java.lang.String[] atomNamesTranslationsSumma

Constructor Detail

AtomicPairwisePMFSummaParameters

public AtomicPairwisePMFSummaParameters(CommandList commands)

Load parameters list from file.

Method Detail

loadingParametersFailed

private void loadingParametersFailed(java.lang.String line)

Throws exception. Called when loading the file failed.

splineForAtomPair

public CoefficientsMatrixForAtomPairSpline splineForAtomPair(AtomType atom1Type,
                                                             AtomType atom2Type)

Retrieve spline for atom pair. Return null if not found.

splineForAtomPair

public CoefficientsMatrixForAtomPairSpline splineForAtomPair(int atom1TypeOrdinal,
                                                             int atom2TypeOrdinal)

meshiAtomTypeToSummaAtomName

private static java.lang.String meshiAtomTypeToSummaAtomName(AtomType atomType)

Translates MESHI atom type to Summa atom name. Return null if not found.

summaAtomNameToParametersAtomIndex

private int summaAtomNameToParametersAtomIndex(java.lang.String name)

Translates Summa atom name to parameters file atom index. Return -1 if not found.