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, na, nb, nc, nx, nxyzStart, ny, nz, origin, vectors
ac, boundingBox, canDownsample, downsampleFactor, downsampleRemainders, endOfData, isAngstroms, negativeAtomCount, nSkipX, nSkipY, nSkipZ, nSurfaces
allowSigma, 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) |
getVectorsAndOrigin, init2MFR
checkAtomLine, closeReader, getNextVoxelValue, getPlane, getPlaneProcessed, getSPFv, getSurfacePointAndFraction, getValue, getVoxelBitSet, gotoData, init2VFR, initializeSurfaceData, readSurfaceData, readSurfaceDataVFR, readVolumeData, readVolumeDataVFR, readVolumeParameters, readVoxelVector, recordData, skipComments, skipDataVFR, swapXZ
closeReaderSFR, discardTempData, getQuotedStringNext, getTokens, init, init2SFR, newBinaryDocument, parseFloat, parseFloatArray, parseFloatArrayStr, parseFloatRange, parseFloatStr, parseInt, parseIntNext, parseIntStr, rd, setOutputChannel, setStream, skipTo
addTriangleCheck, addVC, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, discardTempDataSR, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getPlane2, 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, updateTriangles
private 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 MapFileReader
private 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 VolumeFileReader
java.lang.Exception
protected float nextVoxel() throws java.lang.Exception
nextVoxel
in class VolumeFileReader
java.lang.Exception
private float getFloat(javajs.util.Lst<java.lang.Object> list, int i)
protected void skipData(int nPoints) throws java.lang.Exception
skipData
in class VolumeFileReader
java.lang.Exception
protected void setCutoffAutomatic()
setCutoffAutomatic
in class MapFileReader
private float calculateCutoff()