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
FDPARAM_ID
private java.lang.String
field
private static int
FO_ID
private static int
FOPARAM_ID
private static int
FPARAM_DISP_COS
private static int
FPARAM_DISP_MODULUS
private static int
FPARAM_DISP_PHASE
private static int
FPARAM_DISP_SIN
private static int
FPARAM_OCC_COS
private static int
FPARAM_OCC_MODULUS
private static int
FPARAM_OCC_PHASE
private static int
FPARAM_OCC_SIN
private static int
FPARAM_SPIN_COS
private static int
FPARAM_SPIN_MODULUS
private static int
FPARAM_SPIN_PHASE
private static int
FPARAM_SPIN_SIN
private static int
FPARAM_U_COS
private static int
FPARAM_U_MODULUS
private static int
FPARAM_U_PHASE
private static int
FPARAM_U_SIN
private static int
FU_ID
private static int
FUPARAM_ID
private static int
FWV_DISP_AXIS
private static int
FWV_DISP_LABEL
private static int
FWV_DISP_SEQ_ID
private static int
FWV_ID
private static int
FWV_OCC_LABEL
private static int
FWV_OCC_SEQ_ID
private static int
FWV_Q_COEF
private static int
FWV_SPIN_AXIS
private static int
FWV_SPIN_LABEL
private static int
FWV_SPIN_SEQ_ID
private static int
FWV_U_LABEL
private static int
FWV_U_SEQ_ID
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
(package private) static java.lang.String
SEP
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, modCoord, 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 key, java.lang.String id, java.lang.String fid, double[] params)
private int
fieldProperty(CifReader cr, int i)
private double
fixDouble(double d)
private javajs.util.Matrix
getSparseMatrix(CifReader cr, java.lang.String term, int i, int dim)
private double
parseDouble(java.lang.String field)
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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FPARAM_DISP_COS
private static final int FPARAM_DISP_COS
- See Also:
- Constant Field Values
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FPARAM_DISP_SIN
private static final int FPARAM_DISP_SIN
- See Also:
- Constant Field Values
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FPARAM_DISP_MODULUS
private static final int FPARAM_DISP_MODULUS
- See Also:
- Constant Field Values
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FPARAM_DISP_PHASE
private static final int FPARAM_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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FPARAM_OCC_COS
private static final int FPARAM_OCC_COS
- See Also:
- Constant Field Values
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FPARAM_OCC_SIN
private static final int FPARAM_OCC_SIN
- See Also:
- Constant Field Values
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FPARAM_OCC_MODULUS
private static final int FPARAM_OCC_MODULUS
- See Also:
- Constant Field Values
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FPARAM_OCC_PHASE
private static final int FPARAM_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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FPARAM_U_COS
private static final int FPARAM_U_COS
- See Also:
- Constant Field Values
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FPARAM_U_SIN
private static final int FPARAM_U_SIN
- See Also:
- Constant Field Values
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FPARAM_U_MODULUS
private static final int FPARAM_U_MODULUS
- See Also:
- Constant Field Values
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FPARAM_U_PHASE
private static final int FPARAM_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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FDPARAM_ID
private static final int FDPARAM_ID
- See Also:
- Constant Field Values
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FOPARAM_ID
private static final int FOPARAM_ID
- See Also:
- Constant Field Values
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FUPARAM_ID
private static final int FUPARAM_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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FPARAM_SPIN_COS
private static final int FPARAM_SPIN_COS
- See Also:
- Constant Field Values
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FPARAM_SPIN_SIN
private static final int FPARAM_SPIN_SIN
- See Also:
- Constant Field Values
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FPARAM_SPIN_MODULUS
private static final int FPARAM_SPIN_MODULUS
- See Also:
- Constant Field Values
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FPARAM_SPIN_PHASE
private static final int FPARAM_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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SEP
static final java.lang.String SEP
- 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 key, 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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parseDouble
private double parseDouble(java.lang.String field)
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fixDouble
private double fixDouble(double d)
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fieldProperty
private int fieldProperty(CifReader cr, int i)
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