Package org.jmol.adapter.readers.cif
Class MSCifParser
- java.lang.Object
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- org.jmol.adapter.readers.cif.MSRdr
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- org.jmol.adapter.readers.cif.MSCifParser
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- All Implemented Interfaces:
MSInterface
public class MSCifParser extends MSRdr
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Field Summary
Fields Modifier and Type Field Description private javajs.util.M3
comSSMat
private static int
DEPR_FD_COS
private static int
DEPR_FD_SIN
private static int
DEPR_FO_COS
private static int
DEPR_FO_SIN
private static int
DEPR_FU_COS
private static int
DEPR_FU_SIN
private static int
DISP_SAW_AX
private static int
DISP_SAW_AY
private static int
DISP_SAW_AZ
private static int
DISP_SAW_C
private static int
DISP_SAW_W
private static int
DISP_SPEC_LABEL
private static int
FD_ID
private static int
FDP_ID
private java.lang.String
field
private static int
FO_ID
private static int
FOP_ID
private static int
FU_ID
private static int
FUP_ID
private static int
FWV_DISP_AXIS
private static int
FWV_DISP_COS
private static int
FWV_DISP_LABEL
private static int
FWV_DISP_MODULUS
private static int
FWV_DISP_PHASE
private static int
FWV_DISP_SEQ_ID
private static int
FWV_DISP_SIN
private static int
FWV_ID
private static int
FWV_OCC_COS
private static int
FWV_OCC_LABEL
private static int
FWV_OCC_MODULUS
private static int
FWV_OCC_PHASE
private static int
FWV_OCC_SEQ_ID
private static int
FWV_OCC_SIN
private static int
FWV_Q_COEF
private static int
FWV_SPIN_AXIS
private static int
FWV_SPIN_COS
private static int
FWV_SPIN_LABEL
private static int
FWV_SPIN_MODULUS
private static int
FWV_SPIN_PHASE
private static int
FWV_SPIN_SEQ_ID
private static int
FWV_SPIN_SIN
private static int
FWV_U_COS
private static int
FWV_U_LABEL
private static int
FWV_U_MODULUS
private static int
FWV_U_PHASE
private static int
FWV_U_SEQ_ID
private static int
FWV_U_SIN
private static int
FWV_U_TENS
private static int
FWV_X
private static int
FWV_Y
private static int
FWV_Z
private static int
JANA_FWV_Q1_COEF
private static int
JANA_FWV_Q2_COEF
private static int
JANA_FWV_Q3_COEF
private static int
JANA_OCC_ABS_LABEL
private static int
JANA_OCC_ABS_O_0
private static int
LEG_DISP_AXIS
private static int
LEG_DISP_COEF
private static int
LEG_DISP_LABEL
private static int
LEG_DISP_ORDER
private static int
LEG_OCC_COEF
private static int
LEG_OCC_LABEL
private static int
LEG_OCC_ORDER
private static int
LEG_U_COEF
private static int
LEG_U_LABEL
private static int
LEG_U_ORDER
private static int
LEG_U_TENS
private static java.lang.String[]
modulationFields
private static int
NONE
private static int
OCC_CRENEL_C
private static int
OCC_CRENEL_W
private static int
OCC_SPECIAL_LABEL
private static int
SPIN_SAW_AX
private static int
SPIN_SAW_AY
private static int
SPIN_SAW_AZ
private static int
SPIN_SAW_C
private static int
SPIN_SAW_W
private static int
SPIN_SPEC_LABEL
private static int
WV_ID
private static int
WV_X
private static int
WV_Y
private static int
WV_Z
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Fields inherited from class org.jmol.adapter.readers.cif.MSRdr
commensurateSection1, cr, htSubsystems, isCommensurate, modAverage, modAxes, modDim
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Constructor Summary
Constructors Constructor Description MSCifParser()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description private void
addMod(java.lang.String id, java.lang.String fid, double[] params)
private int
fieldProperty(CifReader cr, int i)
private javajs.util.Matrix
getSparseMatrix(CifReader cr, java.lang.String term, int i, int dim)
void
processEntry()
int
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.private int
processSubsystemLoopBlock()
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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 Detail
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field
private java.lang.String field
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FWV_ID
private static final int FWV_ID
- See Also:
- Constant Field Values
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WV_ID
private static final int WV_ID
- See Also:
- Constant Field Values
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WV_X
private static final int WV_X
- See Also:
- Constant Field Values
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WV_Y
private static final int WV_Y
- See Also:
- Constant Field Values
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WV_Z
private static final int WV_Z
- See Also:
- Constant Field Values
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FWV_X
private static final int FWV_X
- See Also:
- Constant Field Values
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FWV_Y
private static final int FWV_Y
- See Also:
- Constant Field Values
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FWV_Z
private static final int FWV_Z
- See Also:
- Constant Field Values
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FWV_Q_COEF
private static final int FWV_Q_COEF
- See Also:
- Constant Field Values
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JANA_FWV_Q1_COEF
private static final int JANA_FWV_Q1_COEF
- See Also:
- Constant Field Values
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JANA_FWV_Q2_COEF
private static final int JANA_FWV_Q2_COEF
- See Also:
- Constant Field Values
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JANA_FWV_Q3_COEF
private static final int JANA_FWV_Q3_COEF
- See Also:
- Constant Field Values
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FWV_DISP_LABEL
private static final int FWV_DISP_LABEL
- See Also:
- Constant Field Values
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FWV_DISP_AXIS
private static final int FWV_DISP_AXIS
- See Also:
- Constant Field Values
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FWV_DISP_SEQ_ID
private static final int FWV_DISP_SEQ_ID
- See Also:
- Constant Field Values
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FWV_DISP_COS
private static final int FWV_DISP_COS
- See Also:
- Constant Field Values
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FWV_DISP_SIN
private static final int FWV_DISP_SIN
- See Also:
- Constant Field Values
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FWV_DISP_MODULUS
private static final int FWV_DISP_MODULUS
- See Also:
- Constant Field Values
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FWV_DISP_PHASE
private static final int FWV_DISP_PHASE
- See Also:
- Constant Field Values
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DISP_SPEC_LABEL
private static final int DISP_SPEC_LABEL
- See Also:
- Constant Field Values
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DISP_SAW_AX
private static final int DISP_SAW_AX
- See Also:
- Constant Field Values
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DISP_SAW_AY
private static final int DISP_SAW_AY
- See Also:
- Constant Field Values
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DISP_SAW_AZ
private static final int DISP_SAW_AZ
- See Also:
- Constant Field Values
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DISP_SAW_C
private static final int DISP_SAW_C
- See Also:
- Constant Field Values
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DISP_SAW_W
private static final int DISP_SAW_W
- See Also:
- Constant Field Values
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FWV_OCC_LABEL
private static final int FWV_OCC_LABEL
- See Also:
- Constant Field Values
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FWV_OCC_SEQ_ID
private static final int FWV_OCC_SEQ_ID
- See Also:
- Constant Field Values
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FWV_OCC_COS
private static final int FWV_OCC_COS
- See Also:
- Constant Field Values
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FWV_OCC_SIN
private static final int FWV_OCC_SIN
- See Also:
- Constant Field Values
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FWV_OCC_MODULUS
private static final int FWV_OCC_MODULUS
- See Also:
- Constant Field Values
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FWV_OCC_PHASE
private static final int FWV_OCC_PHASE
- See Also:
- Constant Field Values
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OCC_SPECIAL_LABEL
private static final int OCC_SPECIAL_LABEL
- See Also:
- Constant Field Values
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OCC_CRENEL_C
private static final int OCC_CRENEL_C
- See Also:
- Constant Field Values
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OCC_CRENEL_W
private static final int OCC_CRENEL_W
- See Also:
- Constant Field Values
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FWV_U_LABEL
private static final int FWV_U_LABEL
- See Also:
- Constant Field Values
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FWV_U_TENS
private static final int FWV_U_TENS
- See Also:
- Constant Field Values
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FWV_U_SEQ_ID
private static final int FWV_U_SEQ_ID
- See Also:
- Constant Field Values
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FWV_U_COS
private static final int FWV_U_COS
- See Also:
- Constant Field Values
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FWV_U_SIN
private static final int FWV_U_SIN
- See Also:
- Constant Field Values
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FWV_U_MODULUS
private static final int FWV_U_MODULUS
- See Also:
- Constant Field Values
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FWV_U_PHASE
private static final int FWV_U_PHASE
- See Also:
- Constant Field Values
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FD_ID
private static final int FD_ID
- See Also:
- Constant Field Values
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FO_ID
private static final int FO_ID
- See Also:
- Constant Field Values
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FU_ID
private static final int FU_ID
- See Also:
- Constant Field Values
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FDP_ID
private static final int FDP_ID
- See Also:
- Constant Field Values
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FOP_ID
private static final int FOP_ID
- See Also:
- Constant Field Values
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FUP_ID
private static final int FUP_ID
- See Also:
- Constant Field Values
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JANA_OCC_ABS_LABEL
private static final int JANA_OCC_ABS_LABEL
- See Also:
- Constant Field Values
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JANA_OCC_ABS_O_0
private static final int JANA_OCC_ABS_O_0
- See Also:
- Constant Field Values
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FWV_SPIN_LABEL
private static final int FWV_SPIN_LABEL
- See Also:
- Constant Field Values
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FWV_SPIN_AXIS
private static final int FWV_SPIN_AXIS
- See Also:
- Constant Field Values
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FWV_SPIN_SEQ_ID
private static final int FWV_SPIN_SEQ_ID
- See Also:
- Constant Field Values
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FWV_SPIN_COS
private static final int FWV_SPIN_COS
- See Also:
- Constant Field Values
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FWV_SPIN_SIN
private static final int FWV_SPIN_SIN
- See Also:
- Constant Field Values
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FWV_SPIN_MODULUS
private static final int FWV_SPIN_MODULUS
- See Also:
- Constant Field Values
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FWV_SPIN_PHASE
private static final int FWV_SPIN_PHASE
- See Also:
- Constant Field Values
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SPIN_SPEC_LABEL
private static final int SPIN_SPEC_LABEL
- See Also:
- Constant Field Values
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SPIN_SAW_AX
private static final int SPIN_SAW_AX
- See Also:
- Constant Field Values
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SPIN_SAW_AY
private static final int SPIN_SAW_AY
- See Also:
- Constant Field Values
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SPIN_SAW_AZ
private static final int SPIN_SAW_AZ
- See Also:
- Constant Field Values
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SPIN_SAW_C
private static final int SPIN_SAW_C
- See Also:
- Constant Field Values
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SPIN_SAW_W
private static final int SPIN_SAW_W
- See Also:
- Constant Field Values
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LEG_DISP_LABEL
private static final int LEG_DISP_LABEL
- See Also:
- Constant Field Values
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LEG_DISP_AXIS
private static final int LEG_DISP_AXIS
- See Also:
- Constant Field Values
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LEG_DISP_ORDER
private static final int LEG_DISP_ORDER
- See Also:
- Constant Field Values
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LEG_DISP_COEF
private static final int LEG_DISP_COEF
- See Also:
- Constant Field Values
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LEG_U_LABEL
private static final int LEG_U_LABEL
- See Also:
- Constant Field Values
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LEG_U_TENS
private static final int LEG_U_TENS
- See Also:
- Constant Field Values
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LEG_U_ORDER
private static final int LEG_U_ORDER
- See Also:
- Constant Field Values
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LEG_U_COEF
private static final int LEG_U_COEF
- See Also:
- Constant Field Values
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LEG_OCC_LABEL
private static final int LEG_OCC_LABEL
- See Also:
- Constant Field Values
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LEG_OCC_ORDER
private static final int LEG_OCC_ORDER
- See Also:
- Constant Field Values
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LEG_OCC_COEF
private static final int LEG_OCC_COEF
- See Also:
- Constant Field Values
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DEPR_FD_COS
private static final int DEPR_FD_COS
- See Also:
- Constant Field Values
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DEPR_FD_SIN
private static final int DEPR_FD_SIN
- See Also:
- Constant Field Values
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DEPR_FO_COS
private static final int DEPR_FO_COS
- See Also:
- Constant Field Values
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DEPR_FO_SIN
private static final int DEPR_FO_SIN
- See Also:
- Constant Field Values
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DEPR_FU_COS
private static final int DEPR_FU_COS
- See Also:
- Constant Field Values
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DEPR_FU_SIN
private static final int DEPR_FU_SIN
- See Also:
- Constant Field Values
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modulationFields
private static final java.lang.String[] modulationFields
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NONE
private static final int NONE
- See Also:
- Constant Field Values
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comSSMat
private javajs.util.M3 comSSMat
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Method Detail
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processEntry
public void processEntry() throws java.lang.Exception
- Throws:
java.lang.Exception
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processLoopBlock
public int processLoopBlock() throws java.lang.Exception
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:
java.lang.Exception
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addMod
private void addMod(java.lang.String id, java.lang.String fid, double[] params)
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processSubsystemLoopBlock
private int processSubsystemLoopBlock() throws java.lang.Exception
- Throws:
java.lang.Exception
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getSparseMatrix
private javajs.util.Matrix getSparseMatrix(CifReader cr, java.lang.String term, int i, int dim)
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fieldProperty
private int fieldProperty(CifReader cr, int i)
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