java.lang.Object
- org.jmol.adapter.readers.pymol.PickleReader

```
class PickleReader
extends java.lang.Object
```
generic Python Pickle file reader only utilizing records needed for PyMOL. It appears we must read integers littleEndian and doubles bigEndian. 2013.04.06 -- added memo functions. PyMOL pickling is using LONG_BINPUT way too often. This results in a huge unnecessary memory overhead. My only solution is to only cache Strings in memo, and then only selectively -- not parts of movie; not when markCount > 5 (residues). This seems to work, but it is still way overkill, since each atom generates several items. see http://www.picklingtools.com/

Author:

Bob Hanson hansonr@stolaf.edu

Field Summary

Fields
Modifier and Type	Field	Description
`private static byte`	`APPEND`
`private static byte`	`APPENDS`
`(package private) byte[]`	`aTemp`
`private javajs.api.GenericBinaryDocument`	`binaryDoc`
`private static byte`	`BINFLOAT`
`private static byte`	`BINGET`
`private static byte`	`BININT`
`private static byte`	`BININT1`
`private static byte`	`BININT2`
`private static byte`	`BINPUT`
`private static byte`	`BINSTRING`
`private static byte`	`BINUNICODE`
`private javajs.util.Lst<java.lang.Object>`	`build`
`private static byte`	`BUILD`
`private static byte`	`EMPTY_DICT`
`private static byte`	`EMPTY_LIST`
`private int`	`emptyListPt`
`private int`	`filePt`
`private static byte`	`GLOBAL`
`private int`	`id`
`private boolean`	`inMovie`
`private boolean`	`inNames`
`private static byte`	`INT`
`private int`	`ipt`
`private int`	`lastMark`
`private boolean`	`logging`
`private static byte`	`LONG_BINGET`
`private static byte`	`LONG_BINPUT`
`private static byte`	`MARK`
`private int`	`markCount`
`private javajs.util.Lst<java.lang.Integer>`	`marks`
`private java.util.Map<java.lang.Object,java.lang.Object>`	`memo`
`private static byte`	`NONE`
`private static byte`	`OBJ`
`private int`	`retrieveCount`
`private static byte`	`SETITEM`
`private static byte`	`SETITEMS`
`private static byte`	`SHORT_BINSTRING`
`private javajs.util.Lst<java.lang.Object>`	`stack`
`private static byte`	`STOP`
`private java.lang.String`	`thisName`
`private java.lang.Object`	`thisSection`
`private static byte`	`TUPLE`
`private Viewer`	`vwr`

Constructor Summary

Constructors
Constructor Description

PickleReader(javajs.api.GenericBinaryDocument doc, Viewer vwr)

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`private java.lang.String`	`bytesToString(java.lang.Object o)`
`(package private) java.util.Map<java.lang.String,java.lang.Object>`	`getMap(boolean logging)`
`private int`	`getMark()`
`private java.lang.Object`	`getMemo(int i)`
`private javajs.util.Lst<java.lang.Object>`	`getObjects(int mark)`
`private void`	`log(java.lang.String s)`
`private java.lang.Object`	`peek()`
`private java.lang.Object`	`pop()`
`private void`	`push(java.lang.Object o)`
`private void`	`putMark(int i)`
`private void`	`putMemo(int i, boolean doCheck)`
`private byte[]`	`readStringAsBytes()`

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

Field Detail

vwr
```
private Viewer vwr
```

binaryDoc

private javajs.api.GenericBinaryDocument binaryDoc

stack

private javajs.util.Lst<java.lang.Object> stack

marks

private javajs.util.Lst<java.lang.Integer> marks

build

private javajs.util.Lst<java.lang.Object> build

memo

private java.util.Map<java.lang.Object,java.lang.Object> memo

logging
```
private boolean logging
```

id
```
private int id
```

markCount
```
private int markCount
```

filePt
```
private int filePt
```

emptyListPt
```
private int emptyListPt
```

thisSection
```
private java.lang.Object thisSection
```

inMovie
```
private boolean inMovie
```

inNames
```
private boolean inNames
```

thisName
```
private java.lang.String thisName
```

lastMark
```
private int lastMark
```

retrieveCount
```
private int retrieveCount
```

APPEND
```
private static final byte APPEND
```
See Also:

Constant Field Values

APPENDS
```
private static final byte APPENDS
```
See Also:

Constant Field Values

BINFLOAT
```
private static final byte BINFLOAT
```
See Also:

Constant Field Values

BININT
```
private static final byte BININT
```
See Also:

Constant Field Values

BININT1
```
private static final byte BININT1
```
See Also:

Constant Field Values

BININT2
```
private static final byte BININT2
```
See Also:

Constant Field Values

BINPUT
```
private static final byte BINPUT
```
See Also:

Constant Field Values

BINSTRING
```
private static final byte BINSTRING
```
See Also:

Constant Field Values

BINUNICODE
```
private static final byte BINUNICODE
```
See Also:

Constant Field Values

BUILD
```
private static final byte BUILD
```
See Also:

Constant Field Values

EMPTY_DICT
```
private static final byte EMPTY_DICT
```
See Also:

Constant Field Values

EMPTY_LIST
```
private static final byte EMPTY_LIST
```
See Also:

Constant Field Values

GLOBAL
```
private static final byte GLOBAL
```
See Also:

Constant Field Values

LONG_BINPUT
```
private static final byte LONG_BINPUT
```
See Also:

Constant Field Values

MARK
```
private static final byte MARK
```
See Also:

Constant Field Values

NONE
```
private static final byte NONE
```
See Also:

Constant Field Values

OBJ
```
private static final byte OBJ
```
See Also:

Constant Field Values

SETITEM
```
private static final byte SETITEM
```
See Also:

Constant Field Values

SETITEMS
```
private static final byte SETITEMS
```
See Also:

Constant Field Values

SHORT_BINSTRING
```
private static final byte SHORT_BINSTRING
```
See Also:

Constant Field Values

STOP
```
private static final byte STOP
```
See Also:

Constant Field Values

BINGET
```
private static final byte BINGET
```
See Also:

Constant Field Values

LONG_BINGET
```
private static final byte LONG_BINGET
```
See Also:

Constant Field Values

TUPLE
```
private static final byte TUPLE
```
See Also:

Constant Field Values

INT
```
private static final byte INT
```
See Also:

Constant Field Values

ipt
```
private int ipt
```

aTemp
```
byte[] aTemp
```

Constructor Detail

PickleReader

PickleReader(javajs.api.GenericBinaryDocument doc,
             Viewer vwr)

Method Detail

log

private void log(java.lang.String s)

getMap

java.util.Map<java.lang.String,java.lang.Object> getMap(boolean logging)
                                                       throws java.lang.Exception

Throws:: java.lang.Exception

bytesToString

private java.lang.String bytesToString(java.lang.Object o)

putMemo

private void putMemo(int i,
                     boolean doCheck)

getMemo

private java.lang.Object getMemo(int i)

getObjects

private javajs.util.Lst<java.lang.Object> getObjects(int mark)

readStringAsBytes

private byte[] readStringAsBytes()
                          throws java.lang.Exception

Throws:: java.lang.Exception

putMark
```
private void putMark(int i)
```

getMark
```
private int getMark()
```

push

private void push(java.lang.Object o)

peek
```
private java.lang.Object peek()
```

pop
```
private java.lang.Object pop()
```

Class PickleReader

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

vwr

binaryDoc

stack

marks

build

memo

logging

id

markCount

filePt

emptyListPt

thisSection

inMovie

inNames

thisName

lastMark

retrieveCount

APPEND

APPENDS

BINFLOAT

BININT

BININT1

BININT2

BINPUT

BINSTRING

BINUNICODE

BUILD

EMPTY_DICT

EMPTY_LIST

GLOBAL

LONG_BINPUT

MARK

NONE

OBJ

SETITEM

SETITEMS

SHORT_BINSTRING

STOP

BINGET

LONG_BINGET

TUPLE

INT

ipt

aTemp

Constructor Detail

PickleReader

Method Detail

log

getMap

bytesToString

putMemo

getMemo

getObjects

readStringAsBytes

putMark

getMark

push

peek

pop