Package org.jmol.adapter.readers.cif
Class MSCifParser
java.lang.Object
org.jmol.adapter.readers.cif.MSRdr
org.jmol.adapter.readers.cif.MSCifParser
- All Implemented Interfaces:
MSInterface
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Field Summary
FieldsModifier and TypeFieldDescriptionprivate javajs.util.M3
private static final int
private static final int
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private static final int
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private static final int
private String
private static final int
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private static final int
private static final int
private static final int
private static final int
private static final int
private static final int
private static final int
private static final int
private static final int
private static final int
private static final int
private static final int
private static final int
private static final int
private static final int
private static final int
private static final int
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private static final int
private static final int
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private static final String[]
private static final int
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private static final int
(package private) static final String
private static final int
private static final int
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private static final int
private static final int
private static final int
private static final int
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private static final int
Fields inherited from class org.jmol.adapter.readers.cif.MSRdr
commensurateSection1, cr, htSubsystems, isCommensurate, modAverage, modAxes, modCoord, modDim
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprivate void
private int
fieldProperty
(CifReader cr, int i) private double
fixDouble
(double d) private javajs.util.Matrix
getSparseMatrix
(CifReader cr, String term, int i, int dim) private double
parseDouble
(String field) void
int
creates entries in htModulation with a key of the form: type_id_axis;atomLabel@model where type = W|F|D|O (wave vector, Fourier index, displacement, occupancy); id = 1|2|3|0|S (Fourier index, Crenel(0), sawtooth); axis (optional) = 0|x|y|z (0 indicates irrelevant -- occupancy); and ;atomLabel is only for D and O.private int
Methods inherited from class org.jmol.adapter.readers.cif.MSRdr
addLatticeVector, addModulation, addSubsystem, finalizeModulation, getAtomSymmetry, getMod, getModType, getModulationMap, getQCoefs, getSigma, getSymmetryFromCode, initialize, setMinMax0, setModDim, setModulation
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Field Details
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field
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FWV_ID
private static final int FWV_ID- See Also:
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WV_ID
private static final int WV_ID- See Also:
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WV_X
private static final int WV_X- See Also:
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WV_Y
private static final int WV_Y- See Also:
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WV_Z
private static final int WV_Z- See Also:
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FWV_X
private static final int FWV_X- See Also:
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FWV_Y
private static final int FWV_Y- See Also:
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FWV_Z
private static final int FWV_Z- See Also:
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FWV_Q_COEF
private static final int FWV_Q_COEF- See Also:
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JANA_FWV_Q1_COEF
private static final int JANA_FWV_Q1_COEF- See Also:
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JANA_FWV_Q2_COEF
private static final int JANA_FWV_Q2_COEF- See Also:
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JANA_FWV_Q3_COEF
private static final int JANA_FWV_Q3_COEF- See Also:
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FWV_DISP_LABEL
private static final int FWV_DISP_LABEL- See Also:
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FWV_DISP_AXIS
private static final int FWV_DISP_AXIS- See Also:
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FWV_DISP_SEQ_ID
private static final int FWV_DISP_SEQ_ID- See Also:
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FPARAM_DISP_COS
private static final int FPARAM_DISP_COS- See Also:
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FPARAM_DISP_SIN
private static final int FPARAM_DISP_SIN- See Also:
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FPARAM_DISP_MODULUS
private static final int FPARAM_DISP_MODULUS- See Also:
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FPARAM_DISP_PHASE
private static final int FPARAM_DISP_PHASE- See Also:
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DISP_SPEC_LABEL
private static final int DISP_SPEC_LABEL- See Also:
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DISP_SAW_AX
private static final int DISP_SAW_AX- See Also:
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DISP_SAW_AY
private static final int DISP_SAW_AY- See Also:
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DISP_SAW_AZ
private static final int DISP_SAW_AZ- See Also:
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DISP_SAW_C
private static final int DISP_SAW_C- See Also:
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DISP_SAW_W
private static final int DISP_SAW_W- See Also:
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FWV_OCC_LABEL
private static final int FWV_OCC_LABEL- See Also:
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FWV_OCC_SEQ_ID
private static final int FWV_OCC_SEQ_ID- See Also:
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FPARAM_OCC_COS
private static final int FPARAM_OCC_COS- See Also:
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FPARAM_OCC_SIN
private static final int FPARAM_OCC_SIN- See Also:
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FPARAM_OCC_MODULUS
private static final int FPARAM_OCC_MODULUS- See Also:
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FPARAM_OCC_PHASE
private static final int FPARAM_OCC_PHASE- See Also:
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OCC_SPECIAL_LABEL
private static final int OCC_SPECIAL_LABEL- See Also:
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OCC_CRENEL_C
private static final int OCC_CRENEL_C- See Also:
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OCC_CRENEL_W
private static final int OCC_CRENEL_W- See Also:
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FWV_U_LABEL
private static final int FWV_U_LABEL- See Also:
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FWV_U_TENS
private static final int FWV_U_TENS- See Also:
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FWV_U_SEQ_ID
private static final int FWV_U_SEQ_ID- See Also:
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FPARAM_U_COS
private static final int FPARAM_U_COS- See Also:
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FPARAM_U_SIN
private static final int FPARAM_U_SIN- See Also:
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FPARAM_U_MODULUS
private static final int FPARAM_U_MODULUS- See Also:
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FPARAM_U_PHASE
private static final int FPARAM_U_PHASE- See Also:
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FD_ID
private static final int FD_ID- See Also:
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FO_ID
private static final int FO_ID- See Also:
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FU_ID
private static final int FU_ID- See Also:
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FDPARAM_ID
private static final int FDPARAM_ID- See Also:
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FOPARAM_ID
private static final int FOPARAM_ID- See Also:
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FUPARAM_ID
private static final int FUPARAM_ID- See Also:
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JANA_OCC_ABS_LABEL
private static final int JANA_OCC_ABS_LABEL- See Also:
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JANA_OCC_ABS_O_0
private static final int JANA_OCC_ABS_O_0- See Also:
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FWV_SPIN_LABEL
private static final int FWV_SPIN_LABEL- See Also:
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FWV_SPIN_AXIS
private static final int FWV_SPIN_AXIS- See Also:
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FWV_SPIN_SEQ_ID
private static final int FWV_SPIN_SEQ_ID- See Also:
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FPARAM_SPIN_COS
private static final int FPARAM_SPIN_COS- See Also:
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FPARAM_SPIN_SIN
private static final int FPARAM_SPIN_SIN- See Also:
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FPARAM_SPIN_MODULUS
private static final int FPARAM_SPIN_MODULUS- See Also:
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FPARAM_SPIN_PHASE
private static final int FPARAM_SPIN_PHASE- See Also:
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SPIN_SPEC_LABEL
private static final int SPIN_SPEC_LABEL- See Also:
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SPIN_SAW_AX
private static final int SPIN_SAW_AX- See Also:
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SPIN_SAW_AY
private static final int SPIN_SAW_AY- See Also:
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SPIN_SAW_AZ
private static final int SPIN_SAW_AZ- See Also:
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SPIN_SAW_C
private static final int SPIN_SAW_C- See Also:
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SPIN_SAW_W
private static final int SPIN_SAW_W- See Also:
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LEG_DISP_LABEL
private static final int LEG_DISP_LABEL- See Also:
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LEG_DISP_AXIS
private static final int LEG_DISP_AXIS- See Also:
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LEG_DISP_ORDER
private static final int LEG_DISP_ORDER- See Also:
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LEG_DISP_COEF
private static final int LEG_DISP_COEF- See Also:
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LEG_U_LABEL
private static final int LEG_U_LABEL- See Also:
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LEG_U_TENS
private static final int LEG_U_TENS- See Also:
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LEG_U_ORDER
private static final int LEG_U_ORDER- See Also:
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LEG_U_COEF
private static final int LEG_U_COEF- See Also:
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LEG_OCC_LABEL
private static final int LEG_OCC_LABEL- See Also:
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LEG_OCC_ORDER
private static final int LEG_OCC_ORDER- See Also:
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LEG_OCC_COEF
private static final int LEG_OCC_COEF- See Also:
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DEPR_FD_COS
private static final int DEPR_FD_COS- See Also:
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DEPR_FD_SIN
private static final int DEPR_FD_SIN- See Also:
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DEPR_FO_COS
private static final int DEPR_FO_COS- See Also:
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DEPR_FO_SIN
private static final int DEPR_FO_SIN- See Also:
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DEPR_FU_COS
private static final int DEPR_FU_COS- See Also:
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DEPR_FU_SIN
private static final int DEPR_FU_SIN- See Also:
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modulationFields
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NONE
private static final int NONE- See Also:
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SEP
- See Also:
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comSSMat
private javajs.util.M3 comSSMat
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Constructor Details
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MSCifParser
public MSCifParser()
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Method Details
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processEntry
- Throws:
Exception
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processLoopBlock
creates entries in htModulation with a key of the form: type_id_axis;atomLabel@model where type = W|F|D|O (wave vector, Fourier index, displacement, occupancy); id = 1|2|3|0|S (Fourier index, Crenel(0), sawtooth); axis (optional) = 0|x|y|z (0 indicates irrelevant -- occupancy); and ;atomLabel is only for D and O.- Returns:
- 1:handled; -1: skip; 0: unrelated
- Throws:
Exception
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addMod
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processSubsystemLoopBlock
- Throws:
Exception
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getSparseMatrix
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parseDouble
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fixDouble
private double fixDouble(double d) -
fieldProperty
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