meshi.util
Interface KeyWords

All Known Implementing Classes:

AbInitio, AlignmentTools, AlphaAngleCreator, AlphaTorsionCreator, AngleCreator, AtomicPairwisePMFSummaCreator, AtomicPairwisePMFSummaParameters, BackboneCompleterAndMinimizer, BackboneMCM, Beautify, BondCreator, BoundariesMap, CalcGDT, CalculateEnergyFromStructuresListAverages, ChooseTemplate, ColorByEnergy, Command, CommandList, CompositePropensity2DCreator, CompositePropensityCreator, CooperativeAtomicPairwisePMFSummaCreator, CooperativeAtomicPairwisePMFSummaParameters, CooperativePerAtomSummaCreator, CooperativePerAtomSummaParameters, CooperativePropensityCreator, CooperativePropensityParameters, CooperativeRamachandranCreator, CooperativeRamachandranParameters, CooperativeZParameters, CooperativeZPropensityCreator, CooperativeZPropensityParameters, CooperativeZRamachandranCreator, CooperativeZRamachandranParameters, CooperativeZSummaCreator, CoordinatesAssigner, Corpus, CoulombElectrostaticCreator, CylinderCreator, DresserFullFrag, DunbrackLib, EDMEnergyCreator, EnergyCreator, EnergyStatistics, EnergyStatisticsForAtom, EVRot1BBCreator, ExcludedVolCreator, ExcludedVolCreator, ExcludedVolCreatorOLD, FastaList, FiniteExcludedVolCreator, FullModeller, GJModeller, HbondsPunishHOCAngleCreator, HBondsPunishOHNAngleCreator, HeliumClusterMinimization, HeliumClusterMinimization.HeliumLennardJonesCreator, HomologyModeling, HydrogenBondsCreator, HydrogenBondsPairsCreator, HydrogenTest, InitialEvaluation, LennardJonesCreator, LennardJonesCreatorCa, LinearRgCreator, LocalFragmentLib, Loop, MinimizeProtein, ModelRanker, Optimize, OutOfPlaneCreator, Perturbation, PlaneCreator, RamachandranCreator, RamachandranSidechainEnergyCreator, Refine, RgCreator, Rms, RoisFirstMeshiProgram, RotamericTools, Scmod, SCMOD, SelectForCASP, SequenceList, SideChainSolvateCreator, SimpleEnergyCreator, SimpleInflateCreator, SimplestMinimizeProtein, SmoothRotamerLibraryEnergyCreator, SolvateCreatorHBforMinimization, SolvateCreatorLongHB, SolvateCreatorRegularHB, SolvateRot1Creator, SymmetricComplexCompleter, SymmetryCreator, TemplateEnergyCreator, TestElectrostatics, TetherCreator, Topology, UnWarpEnergyCreator, Utils, WarpEnergyCreator

public interface KeyWords

Field Summary

static Key	AA_SEQUENCE
static Key	ACCESIBILITY_SEQUENCE
static Key	ALINMENT_FILE_PATH
static Key	ALL_CA
static Key	ALPHA_ANGLE_ENERGY
static Key	ALPHA_TORSION_ENERGY
static Key	ANGLE_ENERGY
static Key	ANGLE_X
static Key	ANGLE_Z
static Key	ATOMIC_PAIRWISE_PMF_SUMMA_ENERGY
static Key	BEAUTIFY_PROBLEMATIC_RANGE
static Key	BFGS
static Key	BOND_ENERGY
static Key	BUFFER_SIZE
static Key	CA_CLASH_DISTANCE
static Key	CA_LONG_DISTANCE
static Key	CA_MODEL
static Key	CA_SHORT_DISTANCE
static Key	CA_TETHER_ENERGY
static Key	CALPHA_HYDROGEN_BONDS
static Key	CALPHA_HYDROGEN_BONDS_PLANE
static Key	CASP_GROUP
static Key	CG
static Key	CHECK_INTERLOOP_DISTANCE
static Key	CLASH_DISTANCE
static Key	COMPOSITE_PROPENSITY_ENERGY
static Key	CONSENSUS_ENERGY
static Key	CONSTRICT
static Key	COOPERATIVE_ATOMIC_PAIRWISE_PMF_SUMMA_ENERGY
static Key	COOPERATIVE_ATOMIC_PAIRWISE_PMF_SUMMA_FILENAME
static Key	COOPERATIVE_PERATOM_SUMMA_ENERGY
static Key	COOPERATIVE_PERATOM_SUMMA_FILENAME
static Key	COOPERATIVE_PROPENSITY_ENERGY
static Key	COOPERATIVE_PROPENSITY_FILENAME
static Key	COOPERATIVE_RAMACHANDRAN_ENERGY
static Key	COOPERATIVE_RAMACHANDRAN_FILENAME
static Key	COOPERATIVE_Z_PROPENSITY_ENERGY
static Key	COOPERATIVE_Z_PROPENSITY_FILENAME
static Key	COOPERATIVE_Z_RAMACHANDRAN_ENERGY
static Key	COOPERATIVE_Z_RAMACHANDRAN_FILENAME
static Key	COOPERATIVE_Z_SUMMA_ENERGY
static Key	COOPERATIVE_Z_SUMMA_FILENAME
static Key	CORPUS_FILE_NAME
static Key	CSAonly_FILES_LOCATION_PATH
static Key	CUTOFF
static Key	CYLINDER_ENERGY
static Key	DICTIONARY_KEY
static Key	DIELECTRIC_CONSTANT
static Key	DISTANCE_CONSTRAINT_PCA
static Key	DISTANCE_CONSTRAINTS_ENERGY
static Key	DISTANCE_CONSTRAINTS_MASK
static Key	DISTANCE_FROM_CENTROID_ENERGY
static Key	DRESSER_FRAGMENTS
static Key	EDM_ENERGY
static Key	EDM_ENERGY_FILE_NAME
static Key	ELECTROSTATICS
static Key	END
static Key	EXCLUDED_VOL
static Key	FINAL_TEMPERATURE
static Key	FIX_C_TERMINAL
static Key	FIX_N_TERMINAL
static Key	FLAT_RAMACH_ENERGY
static Key	FREE_FINAL_MINIMIZATION
static Key	GRID_EDGE
static Key	HYDROGEN_BONDS
static Key	HYDROGEN_BONDS_ANGLES
static Key	HYDROGEN_BONDS_PAIRS
static Key	HYDROGEN_BONDS_PLANE
static Key	INFLATE_ENERGY
static Key	INITIAL_TEMPERATURE
static Key	INPUT_FILE
static Key	INTER_SEGMENT_FACTOR
static Key	INTER_SEGMENT_TOLERANCE
static Key	INTRA_SEGMENT_FACTOR
static Key	INTRA_SEGMENT_TOLERANCE
static Key	ITERATIONS_ALLATOM
static Key	ITERATIONS_BACKBONE
static Key	ITERATIONS_CA
static Key	KEY_KEY
static Key	KOEHL_FILE
static Key	LBFGS
static Key	LENNARD_JONES
static Key	LENNARD_JONES_CA
static Key	LINEAR_RG
static Key	LOOP1
static Key	LOOP2
static Key	LOOSEN_EDGE_LENGTH
static Key	MAX_ANGLE
static Key	MAX_CLASHES
static Key	MAX_DISTANCE
static Key	MAX_RUN_TIME
static Key	MAX_STEPS
static Key	MAX_WIDTH_OF_HAIRPIN
static Key	MCM
static Key	MCM_PERTURBATION
static Key	MESHILOG_KEY
static Key	METHOD
static Key	MIN_WIDTH_OF_HAIRPIN
static Key	MINIMIZATION_LOOP
static Key	MINIMIZE
static Key	MODE
static Key	MODEL
static Key	MODEL_DSSP
static Key	MODEL_NUMBER
static Key	N_ATOMS
static Key	N_TRIES
static Key	NON_FROZEN_BOND_DEPTH
static Key	NON_FROZEN_RADIUS
static Key	NONE
static Key	NUMBER
static Key	NUMBER_OF_CA_ITERATIONS
static Key	NUMBER_OF_CHAINS
static Key	NUMBER_OF_MODELS
static Key	NUMBER_OF_RUNS
static Key	OFF
static Key	ON
static Key	OPTIMIZER
static Key	OUT_OFPLANE_ENERGY
static Key	OUTPUT_FILE_NAME
static Key	OUTPUT_FILE_PATH
static Key	PARAMETERS_DIRECTORY
static Key	PDB_FILE
static Key	PLANE_ENERGY
static Key	PROPENSITY_TORSION_ENERGY
static Key	R_MAX
static Key	RAMACHANDRAN_SIDECHAIN_ENERGY
static Key	REFERENCE
static Key	RELAX
static Key	REPORT_EVERY
static Key	RESTART_EVERY
static Key	RMS_TARGET
static Key	ROTAMER_LIBRARY
static Key	SATURATION
static Key	SECONDARY_STRUCTURE
static Key	SEED
static Key	SEQUENCE
static Key	SHOTGUN_MODEL
static Key	SMOOTH_ROTAMER_LIBRARY_ENERGY
static Key	SOLVATE_ENERGY
static Key	SS_NAME
static Key	SS_SEQUENCE
static Key	STEEPEST_DECENT
static Key	STEPS
static Key	STRICT_CLASHES
static Key	STRUCTURE_NAMES
static Key	SUPERIMPOSE
static Key	SYMMETRY_ENERGY
static Key	TARGET_FILE_PATH
static Key	TARGET_NAME
static Key	TARGET_SEQUENCE
static Key	TEMPLATE_DISTANCE_CONSTRAINTS
static Key	TEMPLATE_DSSP
static Key	TEMPLATE_ENERGY
static Key	TEMPLATE_FILE_PATH
static Key	TEMPLATE_NAME
static Key	TEMPLATE_STRUCTURE
static Key	TEMPLATE_TARGET_ALIGNMENT
static Key	TETHER_ENERGY
static Key	TOLERANCE
static Key	TOPOLOGY_MAP
static Key	TWO_TORSIONS_ENERGY
static Key	UN_WARP_ENERGY
static Key	UNSATISFIED_CUTTOF
static Key	UP_TO_CUTOFF
static Key	USE_FAST_ARCCOS
static Key	VALUE_KEY
static Key	VOLUME_CONSTRAINT
static Key	WARP_ENERGY
static Key	WARP_STEP_SIZE
static Key	WARP_THRESHOLD
static Key	WEIGHT
static Key	WIDTH_OF_HAIRPIN

Field Detail

SEQUENCE

static final Key SEQUENCE

SECONDARY_STRUCTURE

static final Key SECONDARY_STRUCTURE

MODEL_NUMBER

static final Key MODEL_NUMBER

CLASH_DISTANCE

static final Key CLASH_DISTANCE

MAX_CLASHES

static final Key MAX_CLASHES

N_TRIES

static final Key N_TRIES

OPTIMIZER

static final Key OPTIMIZER

MINIMIZE

static final Key MINIMIZE

RELAX

static final Key RELAX

TOLERANCE

static final Key TOLERANCE

MAX_STEPS

static final Key MAX_STEPS

REPORT_EVERY

static final Key REPORT_EVERY

RESTART_EVERY

static final Key RESTART_EVERY

STEEPEST_DECENT

static final Key STEEPEST_DECENT

BFGS

static final Key BFGS

LBFGS

static final Key LBFGS

CG

static final Key CG

STRUCTURE_NAMES

static final Key STRUCTURE_NAMES

CSAonly_FILES_LOCATION_PATH

static final Key CSAonly_FILES_LOCATION_PATH

DISTANCE_FROM_CENTROID_ENERGY

static final Key DISTANCE_FROM_CENTROID_ENERGY

PARAMETERS_DIRECTORY

static final Key PARAMETERS_DIRECTORY

LENNARD_JONES_CA

static final Key LENNARD_JONES_CA

LENNARD_JONES

static final Key LENNARD_JONES

ANGLE_ENERGY

static final Key ANGLE_ENERGY

BOND_ENERGY

static final Key BOND_ENERGY

CONSENSUS_ENERGY

static final Key CONSENSUS_ENERGY

PLANE_ENERGY

static final Key PLANE_ENERGY

OUT_OFPLANE_ENERGY

static final Key OUT_OFPLANE_ENERGY

TEMPLATE_DISTANCE_CONSTRAINTS

static final Key TEMPLATE_DISTANCE_CONSTRAINTS

DISTANCE_CONSTRAINTS_ENERGY

static final Key DISTANCE_CONSTRAINTS_ENERGY

INFLATE_ENERGY

static final Key INFLATE_ENERGY

VOLUME_CONSTRAINT

static final Key VOLUME_CONSTRAINT

HYDROGEN_BONDS

static final Key HYDROGEN_BONDS

HYDROGEN_BONDS_PAIRS

static final Key HYDROGEN_BONDS_PAIRS

MAX_DISTANCE

static final Key MAX_DISTANCE

MAX_ANGLE

static final Key MAX_ANGLE

TWO_TORSIONS_ENERGY

static final Key TWO_TORSIONS_ENERGY

FLAT_RAMACH_ENERGY

static final Key FLAT_RAMACH_ENERGY

PROPENSITY_TORSION_ENERGY

static final Key PROPENSITY_TORSION_ENERGY

ALPHA_ANGLE_ENERGY

static final Key ALPHA_ANGLE_ENERGY

ALPHA_TORSION_ENERGY

static final Key ALPHA_TORSION_ENERGY

SOLVATE_ENERGY

static final Key SOLVATE_ENERGY

EXCLUDED_VOL

static final Key EXCLUDED_VOL

ELECTROSTATICS

static final Key ELECTROSTATICS

DIELECTRIC_CONSTANT

static final Key DIELECTRIC_CONSTANT

TETHER_ENERGY

static final Key TETHER_ENERGY

CA_TETHER_ENERGY

static final Key CA_TETHER_ENERGY

CALPHA_HYDROGEN_BONDS

static final Key CALPHA_HYDROGEN_BONDS

CALPHA_HYDROGEN_BONDS_PLANE

static final Key CALPHA_HYDROGEN_BONDS_PLANE

HYDROGEN_BONDS_ANGLES

static final Key HYDROGEN_BONDS_ANGLES

HYDROGEN_BONDS_PLANE

static final Key HYDROGEN_BONDS_PLANE

DISTANCE_CONSTRAINT_PCA

static final Key DISTANCE_CONSTRAINT_PCA

WARP_ENERGY

static final Key WARP_ENERGY

UN_WARP_ENERGY

static final Key UN_WARP_ENERGY

LINEAR_RG

static final Key LINEAR_RG

SMOOTH_ROTAMER_LIBRARY_ENERGY

static final Key SMOOTH_ROTAMER_LIBRARY_ENERGY

RAMACHANDRAN_SIDECHAIN_ENERGY

static final Key RAMACHANDRAN_SIDECHAIN_ENERGY

COOPERATIVE_RAMACHANDRAN_ENERGY

static final Key COOPERATIVE_RAMACHANDRAN_ENERGY

COOPERATIVE_RAMACHANDRAN_FILENAME

static final Key COOPERATIVE_RAMACHANDRAN_FILENAME

COOPERATIVE_Z_RAMACHANDRAN_ENERGY

static final Key COOPERATIVE_Z_RAMACHANDRAN_ENERGY

COOPERATIVE_Z_RAMACHANDRAN_FILENAME

static final Key COOPERATIVE_Z_RAMACHANDRAN_FILENAME

COMPOSITE_PROPENSITY_ENERGY

static final Key COMPOSITE_PROPENSITY_ENERGY

COOPERATIVE_PROPENSITY_ENERGY

static final Key COOPERATIVE_PROPENSITY_ENERGY

COOPERATIVE_PROPENSITY_FILENAME

static final Key COOPERATIVE_PROPENSITY_FILENAME

COOPERATIVE_Z_PROPENSITY_ENERGY

static final Key COOPERATIVE_Z_PROPENSITY_ENERGY

COOPERATIVE_Z_PROPENSITY_FILENAME

static final Key COOPERATIVE_Z_PROPENSITY_FILENAME

TEMPLATE_ENERGY

static final Key TEMPLATE_ENERGY

ATOMIC_PAIRWISE_PMF_SUMMA_ENERGY

static final Key ATOMIC_PAIRWISE_PMF_SUMMA_ENERGY

COOPERATIVE_ATOMIC_PAIRWISE_PMF_SUMMA_ENERGY

static final Key COOPERATIVE_ATOMIC_PAIRWISE_PMF_SUMMA_ENERGY

COOPERATIVE_ATOMIC_PAIRWISE_PMF_SUMMA_FILENAME

static final Key COOPERATIVE_ATOMIC_PAIRWISE_PMF_SUMMA_FILENAME

COOPERATIVE_PERATOM_SUMMA_FILENAME

static final Key COOPERATIVE_PERATOM_SUMMA_FILENAME

COOPERATIVE_PERATOM_SUMMA_ENERGY

static final Key COOPERATIVE_PERATOM_SUMMA_ENERGY

COOPERATIVE_Z_SUMMA_FILENAME

static final Key COOPERATIVE_Z_SUMMA_FILENAME

COOPERATIVE_Z_SUMMA_ENERGY

static final Key COOPERATIVE_Z_SUMMA_ENERGY

RMS_TARGET

static final Key RMS_TARGET

INTRA_SEGMENT_FACTOR

static final Key INTRA_SEGMENT_FACTOR

INTRA_SEGMENT_TOLERANCE

static final Key INTRA_SEGMENT_TOLERANCE

INTER_SEGMENT_FACTOR

static final Key INTER_SEGMENT_FACTOR

INTER_SEGMENT_TOLERANCE

static final Key INTER_SEGMENT_TOLERANCE

SATURATION

static final Key SATURATION

UNSATISFIED_CUTTOF

static final Key UNSATISFIED_CUTTOF

UP_TO_CUTOFF

static final Key UP_TO_CUTOFF

DISTANCE_CONSTRAINTS_MASK

static final Key DISTANCE_CONSTRAINTS_MASK

SUPERIMPOSE

static final Key SUPERIMPOSE

REFERENCE

static final Key REFERENCE

MODE

static final Key MODE

ALL_CA

static final Key ALL_CA

MINIMIZATION_LOOP

static final Key MINIMIZATION_LOOP

ITERATIONS_CA

static final Key ITERATIONS_CA

ITERATIONS_BACKBONE

static final Key ITERATIONS_BACKBONE

ITERATIONS_ALLATOM

static final Key ITERATIONS_ALLATOM

MCM

static final Key MCM

INITIAL_TEMPERATURE

static final Key INITIAL_TEMPERATURE

FINAL_TEMPERATURE

static final Key FINAL_TEMPERATURE

MCM_PERTURBATION

static final Key MCM_PERTURBATION

TARGET_NAME

static final Key TARGET_NAME

TEMPLATE_NAME

static final Key TEMPLATE_NAME

TARGET_FILE_PATH

static final Key TARGET_FILE_PATH

ALINMENT_FILE_PATH

static final Key ALINMENT_FILE_PATH

TEMPLATE_FILE_PATH

static final Key TEMPLATE_FILE_PATH

TEMPLATE_STRUCTURE

static final Key TEMPLATE_STRUCTURE

TEMPLATE_DSSP

static final Key TEMPLATE_DSSP

TEMPLATE_TARGET_ALIGNMENT

static final Key TEMPLATE_TARGET_ALIGNMENT

OUTPUT_FILE_PATH

static final Key OUTPUT_FILE_PATH

OUTPUT_FILE_NAME

static final Key OUTPUT_FILE_NAME

SS_NAME

static final Key SS_NAME

LOOSEN_EDGE_LENGTH

static final Key LOOSEN_EDGE_LENGTH

NON_FROZEN_BOND_DEPTH

static final Key NON_FROZEN_BOND_DEPTH

NON_FROZEN_RADIUS

static final Key NON_FROZEN_RADIUS

NUMBER_OF_MODELS

static final Key NUMBER_OF_MODELS

TARGET_SEQUENCE

static final Key TARGET_SEQUENCE

MAX_RUN_TIME

static final Key MAX_RUN_TIME

METHOD

static final Key METHOD

CASP_GROUP

static final Key CASP_GROUP

SHOTGUN_MODEL

static final Key SHOTGUN_MODEL

CA_MODEL

static final Key CA_MODEL

NUMBER_OF_CA_ITERATIONS

static final Key NUMBER_OF_CA_ITERATIONS

WARP_THRESHOLD

static final Key WARP_THRESHOLD

WARP_STEP_SIZE

static final Key WARP_STEP_SIZE

FREE_FINAL_MINIMIZATION

static final Key FREE_FINAL_MINIMIZATION

NUMBER_OF_RUNS

static final Key NUMBER_OF_RUNS

CA_CLASH_DISTANCE

static final Key CA_CLASH_DISTANCE

CA_SHORT_DISTANCE

static final Key CA_SHORT_DISTANCE

CA_LONG_DISTANCE

static final Key CA_LONG_DISTANCE

BEAUTIFY_PROBLEMATIC_RANGE

static final Key BEAUTIFY_PROBLEMATIC_RANGE

MODEL

static final Key MODEL

MODEL_DSSP

static final Key MODEL_DSSP

DICTIONARY_KEY

static final Key DICTIONARY_KEY

MESHILOG_KEY

static final Key MESHILOG_KEY

KEY_KEY

static final Key KEY_KEY

VALUE_KEY

static final Key VALUE_KEY

AA_SEQUENCE

static final Key AA_SEQUENCE

SS_SEQUENCE

static final Key SS_SEQUENCE

ACCESIBILITY_SEQUENCE

static final Key ACCESIBILITY_SEQUENCE

N_ATOMS

static final Key N_ATOMS

R_MAX

static final Key R_MAX

BUFFER_SIZE

static final Key BUFFER_SIZE

GRID_EDGE

static final Key GRID_EDGE

PDB_FILE

static final Key PDB_FILE

KOEHL_FILE

static final Key KOEHL_FILE

ON

static final Key ON

OFF

static final Key OFF

END

static final Key END

WEIGHT

static final Key WEIGHT

INPUT_FILE

static final Key INPUT_FILE

CUTOFF

static final Key CUTOFF

NONE

static final Key NONE

USE_FAST_ARCCOS

static final Key USE_FAST_ARCCOS

DRESSER_FRAGMENTS

static final Key DRESSER_FRAGMENTS

ROTAMER_LIBRARY

static final Key ROTAMER_LIBRARY

FIX_N_TERMINAL

static final Key FIX_N_TERMINAL

FIX_C_TERMINAL

static final Key FIX_C_TERMINAL

SEED

static final Key SEED

CORPUS_FILE_NAME

static final Key CORPUS_FILE_NAME

SYMMETRY_ENERGY

static final Key SYMMETRY_ENERGY

CYLINDER_ENERGY

static final Key CYLINDER_ENERGY

EDM_ENERGY

static final Key EDM_ENERGY

EDM_ENERGY_FILE_NAME

static final Key EDM_ENERGY_FILE_NAME

TOPOLOGY_MAP

static final Key TOPOLOGY_MAP

NUMBER_OF_CHAINS

static final Key NUMBER_OF_CHAINS

NUMBER

static final Key NUMBER

LOOP1

static final Key LOOP1

LOOP2

static final Key LOOP2

ANGLE_X

static final Key ANGLE_X

ANGLE_Z

static final Key ANGLE_Z

WIDTH_OF_HAIRPIN

static final Key WIDTH_OF_HAIRPIN

MIN_WIDTH_OF_HAIRPIN

static final Key MIN_WIDTH_OF_HAIRPIN

MAX_WIDTH_OF_HAIRPIN

static final Key MAX_WIDTH_OF_HAIRPIN

STEPS

static final Key STEPS

CONSTRICT

static final Key CONSTRICT

STRICT_CLASHES

static final Key STRICT_CLASHES

CHECK_INTERLOOP_DISTANCE

static final Key CHECK_INTERLOOP_DISTANCE