class PyMOLMeshReader extends MapFileReader
| Modifier and Type | Field and Description |
|---|---|
(package private) static int |
cMapSourceBRIX |
(package private) static int |
cMapSourceCCP4 |
(package private) static int |
cMapSourceChempyBrick |
(package private) static int |
cMapSourceCrystallographic |
(package private) static int |
cMapSourceDesc |
(package private) static int |
cMapSourceFLD |
(package private) static int |
cMapSourceGeneralPurpose |
(package private) static int |
cMapSourceGRD |
(package private) static int |
cMapSourceObsolete |
(package private) static int |
cMapSourceVMDPlugin |
private javajs.util.Lst<java.lang.Object> |
data |
private boolean |
isMesh |
(package private) static int |
OBJECT_MAPDATA |
(package private) static int |
OBJECT_MAPMESH |
private int |
pt |
private int |
pymolType |
private java.lang.String |
surfaceName |
private javajs.util.Lst<java.lang.Object> |
voxelList |
a, alpha, b, beta, c, dmax, dmean, dmin, drange, gamma, mapc, mapr, maps, mode, n0, n1, n2, na, nb, nc, origin, p3, vectors, xIndex, xyzStart, yIndex, zIndexac, boundingBox, canDownsample, downsampleFactor, downsampleRemainders, endOfData, isAngstroms, nData, negativeAtomCount, nSkipX, nSkipY, nSkipZ, nSurfaces, readerClosedallowSigma, ANGSTROMS_PER_BOHR, anisotropy, center, cJvxlEdgeNaN, colorFractionBase, colorFractionRange, contourVertexCount, dataMax, dataMean, dataMin, defaultCutoff, defaultMappedDataMax, defaultMappedDataMin, eccentricityMatrix, eccentricityMatrixInverse, eccentricityRatio, eccentricityScale, edgeFractionBase, edgeFractionRange, fractionData, hasColorData, haveSurfaceAtoms, isAnisotropic, isEccentric, isJvxl, isPeriodic, isProgressive, isQuiet, isXLowToHigh, jvxlColorDataRead, jvxlCutoff, jvxlData, jvxlDataIs2dContour, jvxlDataIsColorDensity, jvxlDataIsColorMapped, jvxlDataIsPrecisionColor, jvxlEdgeDataRead, jvxlFileHeaderBuffer, jvxlNSurfaceInts, jvxlVoxelBitSet, marchingCubes, marchingSquares, meshData, meshDataServer, minMax, nBytes, nDataPoints, nPointsX, nPointsY, nPointsZ, params, ptTemp, qpc, sg, vertexDataOnly, volumeData, volumetricOrigin, volumetricVectors, voxelCounts, voxelData, xyzMax, xyzMin, yzCount, yzPlanes| Constructor and Description |
|---|
PyMOLMeshReader() |
| Modifier and Type | Method and Description |
|---|---|
private float |
calculateCutoff() |
private float |
getFloat(javajs.util.Lst<java.lang.Object> list,
int i) |
private static javajs.util.Lst<java.lang.Object> |
getList(javajs.util.Lst<java.lang.Object> list,
int i) |
(package private) void |
init2(SurfaceGenerator sg,
java.io.BufferedReader brNull) |
protected float |
nextVoxel() |
protected void |
readParameters() |
protected void |
setCutoffAutomatic() |
protected void |
skipData(int nPoints) |
checkInsideOut, getVectorsAndOrigin, init2MFRcheckAtomLine, closeReader, getNextVoxelValue, getPlane, getPlaneNCI, getSPFv, getSurfacePointAndFraction, getValue, getVoxelBitSet, gotoData, init2VFR, initializeSurfaceData, readSurfaceData, readSurfaceDataVFR, readVolumeData, readVolumeDataVFR, readVolumeParameters, readVoxelVector, recordData, skipComments, skipDataVFR, swapXZcloseReaderSFR, discardTempData, getQuotedStringNext, getTokens, init, init2SFR, newBinaryDocument, parseFloat, parseFloatArray, parseFloatArrayStr, parseFloatRange, parseFloatStr, parseInt, parseIntNext, parseIntStr, rd, setOutputChannel, setStream, skipToaddTriangleCheck, addVC, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, discardTempDataSR, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getPlaneSR, getSPF, getSurfaceAtomIndex, getSurfacePointIndexAndFraction, getValue2, getValueAtPoint, gotoAndReadVoxelData, initializeMapping, initializeVolumetricData, initPlanes, initSR, jvxlUpdateInfo, newVoxelDataCube, postProcessVertices, readAndSetVolumeParameters, readColorData, resetIsosurface, selectPocket, setBBox, setVectorAnisotropy, setVertexAnisotropy, setVolumeDataV, setVolumetricAnisotropy, setVolumetricOriginAnisotropy, slabIsosurface, updateSurfaceData, updateTrianglesprivate javajs.util.Lst<java.lang.Object> data
private javajs.util.Lst<java.lang.Object> voxelList
private java.lang.String surfaceName
private int pymolType
private boolean isMesh
static final int cMapSourceCrystallographic
static final int cMapSourceCCP4
static final int cMapSourceGeneralPurpose
static final int cMapSourceDesc
static final int cMapSourceFLD
static final int cMapSourceBRIX
static final int cMapSourceGRD
static final int cMapSourceChempyBrick
static final int cMapSourceVMDPlugin
static final int cMapSourceObsolete
static final int OBJECT_MAPDATA
static final int OBJECT_MAPMESH
private int pt
void init2(SurfaceGenerator sg, java.io.BufferedReader brNull)
init2 in class MapFileReaderprivate static javajs.util.Lst<java.lang.Object> getList(javajs.util.Lst<java.lang.Object> list,
int i)
protected void readParameters()
throws java.lang.Exception
readParameters in class VolumeFileReaderjava.lang.Exceptionprotected float nextVoxel()
throws java.lang.Exception
nextVoxel in class VolumeFileReaderjava.lang.Exceptionprivate float getFloat(javajs.util.Lst<java.lang.Object> list,
int i)
protected void skipData(int nPoints)
throws java.lang.Exception
skipData in class VolumeFileReaderjava.lang.Exceptionprotected void setCutoffAutomatic()
setCutoffAutomatic in class MapFileReaderprivate float calculateCutoff()