PyMOLMeshReader

java.lang.Object
- org.jmol.jvxl.readers.SurfaceReader
- - org.jmol.jvxl.readers.SurfaceFileReader
  - - org.jmol.jvxl.readers.VolumeFileReader
    - - org.jmol.jvxl.readers.MapFileReader
      - org.jmol.jvxl.readers.PyMOLMeshReader

All Implemented Interfaces:

VertexDataServer
```
class PyMOLMeshReader
extends MapFileReader
```
PyMOL surface/mesh reader. PyMOL "mesh": Describes a cutoff and "carving" distance around a set of points PyMOL "map": Volume data used by mesh (HupA_2) or direct visualization (HupA_LC)

Author:

Bob Hanson

Field Summary

Fields
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<Object>`	`data`
`private boolean`	`isMesh`
`(package private) static int`	`OBJECT_MAPDATA`
`(package private) static int`	`OBJECT_MAPMESH`
`private int`	`pt`
`private int`	`pymolType`
`private String`	`surfaceName`
`private javajs.util.Lst<Object>`	`voxelList`

Fields inherited from class org.jmol.jvxl.readers.MapFileReader
a, alpha, b, beta, c, dmax, dmean, dmin, drange, gamma, mapc, mapr, maps, mode, na, nb, nc, nx, nxyzStart, ny, nz, origin, vectors

Fields inherited from class org.jmol.jvxl.readers.VolumeFileReader
ac, boundingBox, canDownsample, downsampleFactor, downsampleRemainders, endOfData, isAngstroms, nData, negativeAtomCount, nSkipX, nSkipY, nSkipZ, nSurfaces

Fields inherited from class org.jmol.jvxl.readers.SurfaceFileReader
binarydoc, br, line, next, out

Fields inherited from class org.jmol.jvxl.readers.SurfaceReader
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 Summary

Constructors
Constructor and Description

PyMOLMeshReader()

Constructors
Constructor and Description
`PyMOLMeshReader()`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`private float`	`calculateCutoff()`
`private float`	`getFloat(javajs.util.Lst<Object> list, int i)`
`private static javajs.util.Lst<Object>`	`getList(javajs.util.Lst<Object> list, int i)`
`(package private) void`	`init2(SurfaceGenerator sg, BufferedReader brNull)`
`protected float`	`nextVoxel()`
`protected void`	`readParameters()`
`protected void`	`setCutoffAutomatic()`
`protected void`	`skipData(int nPoints)`

Methods inherited from class org.jmol.jvxl.readers.MapFileReader
getVectorsAndOrigin, init2MFR

Methods inherited from class org.jmol.jvxl.readers.VolumeFileReader
checkAtomLine, closeReader, getNextVoxelValue, getPlane, getPlaneNCI, getSPFv, getSurfacePointAndFraction, getValue, getVoxelBitSet, gotoData, init2VFR, initializeSurfaceData, readSurfaceData, readSurfaceDataVFR, readVolumeData, readVolumeDataVFR, readVolumeParameters, readVoxelVector, recordData, skipComments, skipDataVFR, swapXZ

Methods inherited from class org.jmol.jvxl.readers.SurfaceFileReader
closeReaderSFR, discardTempData, getQuotedStringNext, getTokens, init, init2SFR, newBinaryDocument, parseFloat, parseFloatArray, parseFloatArrayStr, parseFloatRange, parseFloatStr, parseInt, parseIntNext, parseIntStr, rd, setOutputChannel, setStream, skipTo

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail
- data
```
private javajs.util.Lst<Object> data
```
- voxelList
```
private javajs.util.Lst<Object> voxelList
```
- surfaceName
```
private String surfaceName
```
- pymolType
```
private int pymolType
```
- isMesh
```
private boolean isMesh
```
- cMapSourceCrystallographic
```
static final int cMapSourceCrystallographic
```
  See Also:
  
  Constant Field Values
- cMapSourceCCP4
```
static final int cMapSourceCCP4
```
  See Also:
  
  Constant Field Values
- cMapSourceGeneralPurpose
```
static final int cMapSourceGeneralPurpose
```
  See Also:
  
  Constant Field Values
- cMapSourceDesc
```
static final int cMapSourceDesc
```
  See Also:
  
  Constant Field Values
- cMapSourceFLD
```
static final int cMapSourceFLD
```
  See Also:
  
  Constant Field Values
- cMapSourceBRIX
```
static final int cMapSourceBRIX
```
  See Also:
  
  Constant Field Values
- cMapSourceGRD
```
static final int cMapSourceGRD
```
  See Also:
  
  Constant Field Values
- cMapSourceChempyBrick
```
static final int cMapSourceChempyBrick
```
  See Also:
  
  Constant Field Values
- cMapSourceVMDPlugin
```
static final int cMapSourceVMDPlugin
```
  See Also:
  
  Constant Field Values
- cMapSourceObsolete
```
static final int cMapSourceObsolete
```
  See Also:
  
  Constant Field Values
- OBJECT_MAPDATA
```
static final int OBJECT_MAPDATA
```
  See Also:
  
  Constant Field Values
- OBJECT_MAPMESH
```
static final int OBJECT_MAPMESH
```
  See Also:
  
  Constant Field Values
- pt
```
private int pt
```

Constructor Detail
- PyMOLMeshReader
```
PyMOLMeshReader()
```

Method Detail

init2

void init2(SurfaceGenerator sg,
           BufferedReader brNull)

Overrides:: init2 in class MapFileReader

getList

private static javajs.util.Lst<Object> getList(javajs.util.Lst<Object> list,
                                               int i)

readParameters
```
protected void readParameters()
                       throws Exception
```
Specified by:

readParameters in class VolumeFileReader

Throws:

Exception

nextVoxel
```
protected float nextVoxel()
                   throws Exception
```
Overrides:

nextVoxel in class VolumeFileReader

Throws:

Exception

getFloat

private float getFloat(javajs.util.Lst<Object> list,
                       int i)

skipData

protected void skipData(int nPoints)
                 throws Exception

Overrides:: skipData in class VolumeFileReader
Throws:: Exception

setCutoffAutomatic
```
protected void setCutoffAutomatic()
```
Overrides:

setCutoffAutomatic in class MapFileReader

calculateCutoff
```
private float calculateCutoff()
```

Class PyMOLMeshReader

Field Summary

Fields inherited from class org.jmol.jvxl.readers.MapFileReader

Fields inherited from class org.jmol.jvxl.readers.VolumeFileReader

Fields inherited from class org.jmol.jvxl.readers.SurfaceFileReader

Fields inherited from class org.jmol.jvxl.readers.SurfaceReader

Constructor Summary

Method Summary

Methods inherited from class org.jmol.jvxl.readers.MapFileReader

Methods inherited from class org.jmol.jvxl.readers.VolumeFileReader

Methods inherited from class org.jmol.jvxl.readers.SurfaceFileReader

Methods inherited from class org.jmol.jvxl.readers.SurfaceReader

Methods inherited from class java.lang.Object

Field Detail

data

voxelList

surfaceName

pymolType

isMesh

cMapSourceCrystallographic

cMapSourceCCP4

cMapSourceGeneralPurpose

cMapSourceDesc

cMapSourceFLD

cMapSourceBRIX

cMapSourceGRD

cMapSourceChempyBrick

cMapSourceVMDPlugin

cMapSourceObsolete

OBJECT_MAPDATA

OBJECT_MAPMESH

pt

Constructor Detail

PyMOLMeshReader

Method Detail

init2

getList

readParameters

nextVoxel

getFloat

skipData

setCutoffAutomatic

calculateCutoff