An object to read and write PDB files to or from the current Simulation. 
 
If there is a possibility that atom naming is inconsistent with
Xplor-NIH standards, the protocol.initCoords() helper should be
used, as it can handling naming translations.
 
Constructor:
 
  PDBTool(filename, atomSel) 
    both arguments are optional. If the selection is omitted, it defaults
    to all atoms of the current simulation.Simulation. If the filename is 
    blank, the contents string buffer is used for reading/writing.
 
The primary methods of the class are:
  read(model)      - read the pdb file. If the model argument is present, the
                     specified PDB MODEL entry is read, else the first MODEL
                     is read. The return value is a list of unmatched ATOM
                     entries, if any. If the specified model number is not 
                     found, an exception is thrown. ATOM entries with non-
                     allowed AltLoc entries or entries with the insertion code
                     column set are ignored.
  write(coords)    - write the file. Make a backup if makeBackup()==1.
                     If the coords argument is present it should specify a 
                     sequence of CDSVectors of atom positions, one for each 
                     atom in the Simulation. These are written as separate
                     MODEL entries. If this argument is absent, the current
                     Simulation's coordinates are written with no MODEL entry.
  models()         - return the number of MODEL records in the PDB entry.
 
REMARK fields are manipulated using the following methods:
  addRemark(string) - add a remark field (one line).
  addRemarks(arg)   - in this case, arg is a multiline string.
                      Each line is successively added as a remark.
  clearRemarks()    - remove all remark fields.
  remarks()         - return the current remark fields in a list.
 
The following accessors are available:
 
  selection     - an atomSel.AtomSel which specifies atoms to be read or 
                  written.
  filename      - the file name to be read or written.
  contents      - string buffer used if the filename is blank. To read from a
                  string, first use setContents(string), then call read(). To
                  get the PDB record as a string, first call write(), then
                  getContents().
  makeBackup    - boolean. If true, make a backup of the current pdb file
                  before writing. Default value: true.
  verbose       - whether to print a warning when unknown atoms are read in.
                  Default: true if simWorld.logLevel is not NONE.
  aux1(atom)    - the aux1 (occupancy) field for the specified atom.
                  This member can be set using setAux1(atom,value).
  occupancy()   - synonym for aux1.
  aux2(atom)    - the aux2 (bfactor) field for the specified atom.
                  This member can be set using setAux2(atom,value).
  bfactor()     - synonym for aux2(atom).
 
  occupancies() - return a list of occupancies of all atoms.
  bfactors()    - return a list of bfactors of all atoms.
 
  allowedAltLoc - ATOM entries with one of these values will be read- 
                  otherwise the entry will be ignored. 
                  default value: [' ', 'A']
  useChainID    - overwrite the segment name with the chainID PDB field, if
                  the chainID field is not blank. This is only used when 
                  reading a PDB record.
  writeChainID  - write the segment name to the chainID pdb field and leave
                  the segment name field blank. An exception will be thrown
                  if the segment name is longer than one character.
 
For a given member, values can be read using the method member() and set via
setMember(val).
 
The atom name field is controlled by the following methods:
  useXplorNames() - use the XPLOR naming convention. This includes
                    changing the "*" character to a "'".
  useIupacNames() - use the IUPAC naming conventions.
 
The following is a low-level helper routine:
 
  readAtoms() - array for each atom (by index) specifying whether it
                was read in the last call to read().
 
 
 
 
 
# This file was created automatically by SWIG.
# Don't modify this file, modify the SWIG interface instead.
# This file is compatible with both classic and new-style classes.

Classes
		__builtin__.object AltLocRecord AltLocRecordPtr CDSList_AltLocRecord CDSList_AltLocRecordPtr CDSList_char CDSList_charPtr PDBTool PDBToolPtr   class AltLocRecord(__builtin__.object)           Methods defined here: __del__(self, destroy=<built-in function delete_AltLocRecord>)   __getattr__ lambda self, name   __init__(self, *args)   __repr__(self)   __setattr__ lambda self, name, value   Properties defined here: bfactor   get = AltLocRecord_bfactor_get(...)   set = AltLocRecord_bfactor_set(...)   occupancy   get = AltLocRecord_occupancy_get(...)   set = AltLocRecord_occupancy_set(...)   pos   get = AltLocRecord_pos_get(...)   set = AltLocRecord_pos_set(...)   Data and other attributes defined here: __dict__ = <dictproxy object at 0x250e280>   dictionary for instance variables (if defined) __swig_getmethods__ = {'bfactor': <built-in function AltLocRecord_bfactor_get>, 'occupancy': <built-in function AltLocRecord_occupancy_get>, 'pos': <built-in function AltLocRecord_pos_get>} __swig_setmethods__ = {'bfactor': <built-in function AltLocRecord_bfactor_set>, 'occupancy': <built-in function AltLocRecord_occupancy_set>, 'pos': <built-in function AltLocRecord_pos_set>} __weakref__ = <attribute '__weakref__' of 'AltLocRecord' objects>   list of weak references to the object (if defined)   class AltLocRecordPtr(AltLocRecord)           Method resolution order: AltLocRecordPtr AltLocRecord __builtin__.object Methods defined here: __init__(self, this)   Methods inherited from AltLocRecord: __del__(self, destroy=<built-in function delete_AltLocRecord>)   __getattr__ lambda self, name   __repr__(self)   __setattr__ lambda self, name, value   Properties inherited from AltLocRecord: bfactor   get = AltLocRecord_bfactor_get(...)   set = AltLocRecord_bfactor_set(...)   occupancy   get = AltLocRecord_occupancy_get(...)   set = AltLocRecord_occupancy_set(...)   pos   get = AltLocRecord_pos_get(...)   set = AltLocRecord_pos_set(...)   Data and other attributes inherited from AltLocRecord: __dict__ = <dictproxy object at 0x250e2b8>   dictionary for instance variables (if defined) __swig_getmethods__ = {'bfactor': <built-in function AltLocRecord_bfactor_get>, 'occupancy': <built-in function AltLocRecord_occupancy_get>, 'pos': <built-in function AltLocRecord_pos_get>} __swig_setmethods__ = {'bfactor': <built-in function AltLocRecord_bfactor_set>, 'occupancy': <built-in function AltLocRecord_occupancy_set>, 'pos': <built-in function AltLocRecord_pos_set>} __weakref__ = <attribute '__weakref__' of 'AltLocRecord' objects>   list of weak references to the object (if defined)   class CDSList_AltLocRecord(__builtin__.object)           Methods defined here: __del__(self, destroy=<built-in function delete_CDSList_AltLocRecord>)   __delitem__(*args)   __getattr__ lambda self, name   __getitem__(*args)   __getslice__(*args)   __init__(self, *args)   __len__(*args)   __repr__(self)   __setattr__ lambda self, name, value   __setitem__(*args)   help(*args)   Data and other attributes defined here: __dict__ = <dictproxy object at 0x250e280>   dictionary for instance variables (if defined) __swig_getmethods__ = {} __swig_setmethods__ = {} __weakref__ = <attribute '__weakref__' of 'CDSList_AltLocRecord' objects>   list of weak references to the object (if defined)   class CDSList_AltLocRecordPtr(CDSList_AltLocRecord)           Method resolution order: CDSList_AltLocRecordPtr CDSList_AltLocRecord __builtin__.object Methods defined here: __init__(self, this)   Methods inherited from CDSList_AltLocRecord: __del__(self, destroy=<built-in function delete_CDSList_AltLocRecord>)   __delitem__(*args)   __getattr__ lambda self, name   __getitem__(*args)   __getslice__(*args)   __len__(*args)   __repr__(self)   __setattr__ lambda self, name, value   __setitem__(*args)   help(*args)   Data and other attributes inherited from CDSList_AltLocRecord: __dict__ = <dictproxy object at 0x250e1a0>   dictionary for instance variables (if defined) __swig_getmethods__ = {} __swig_setmethods__ = {} __weakref__ = <attribute '__weakref__' of 'CDSList_AltLocRecord' objects>   list of weak references to the object (if defined)   class CDSList_char(__builtin__.object)           Methods defined here: __del__(self, destroy=<built-in function delete_CDSList_char>)   __delitem__(*args)   __getattr__ lambda self, name   __getitem__(*args)   __getslice__(*args)   __init__(self, *args)   __len__(*args)   __repr__(self)   __setattr__ lambda self, name, value   __setitem__(*args)   help(*args)   Data and other attributes defined here: __dict__ = <dictproxy object at 0x250e2b8>   dictionary for instance variables (if defined) __swig_getmethods__ = {} __swig_setmethods__ = {} __weakref__ = <attribute '__weakref__' of 'CDSList_char' objects>   list of weak references to the object (if defined)   class CDSList_charPtr(CDSList_char)           Method resolution order: CDSList_charPtr CDSList_char __builtin__.object Methods defined here: __init__(self, this)   Methods inherited from CDSList_char: __del__(self, destroy=<built-in function delete_CDSList_char>)   __delitem__(*args)   __getattr__ lambda self, name   __getitem__(*args)   __getslice__(*args)   __len__(*args)   __repr__(self)   __setattr__ lambda self, name, value   __setitem__(*args)   help(*args)   Data and other attributes inherited from CDSList_char: __dict__ = <dictproxy object at 0x250e280>   dictionary for instance variables (if defined) __swig_getmethods__ = {} __swig_setmethods__ = {} __weakref__ = <attribute '__weakref__' of 'CDSList_char' objects>   list of weak references to the object (if defined)   class PDBTool(__builtin__.object)           Methods defined here: __del__(self, destroy=<built-in function delete_PDBTool>)   __getattr__ lambda self, name   __init__(self, *args)   __repr__(self)   __setattr__ lambda self, name, value   addRemark(*args)   addRemarks(self, remarks)   add multiline string as multiple remarks          allowedAltLoc(*args)   aux1(*args)   aux2(*args)   bfactor(*args)   bfactors(*args)   clearRemarks(*args)   contents(*args)   filename(*args)   help(*args)   makeBackup(*args)   models(*args)   occupancies(*args)   occupancy(*args)   read(*args)   readAtoms(*args)   remarks(*args)   selection(*args)   setAllowedAltLoc(*args)   setAux1(*args)   setAux2(*args)   setContents(*args)   setFilename(*args)   setMakeBackup(*args)   setSelection(*args)   setStrictResNames(*args)   setUseChainID(*args)   setVerbose(*args)   setWriteChainID(*args)   strictResNames(*args)   useChainID(*args)   useIupacNames(*args)   useXplorNames(*args)   verbose(*args)   write(*args)   writeAltLoc(*args)   writeChainID(*args)   Data and other attributes defined here: __dict__ = <dictproxy object at 0x250e520>   dictionary for instance variables (if defined) __swig_getmethods__ = {} __swig_setmethods__ = {} __weakref__ = <attribute '__weakref__' of 'PDBTool' objects>   list of weak references to the object (if defined)   class PDBToolPtr(PDBTool)           Method resolution order: PDBToolPtr PDBTool __builtin__.object Methods defined here: __init__(self, this)   Methods inherited from PDBTool: __del__(self, destroy=<built-in function delete_PDBTool>)   __getattr__ lambda self, name   __repr__(self)   __setattr__ lambda self, name, value   addRemark(*args)   addRemarks(self, remarks)   add multiline string as multiple remarks          allowedAltLoc(*args)   aux1(*args)   aux2(*args)   bfactor(*args)   bfactors(*args)   clearRemarks(*args)   contents(*args)   filename(*args)   help(*args)   makeBackup(*args)   models(*args)   occupancies(*args)   occupancy(*args)   read(*args)   readAtoms(*args)   remarks(*args)   selection(*args)   setAllowedAltLoc(*args)   setAux1(*args)   setAux2(*args)   setContents(*args)   setFilename(*args)   setMakeBackup(*args)   setSelection(*args)   setStrictResNames(*args)   setUseChainID(*args)   setVerbose(*args)   setWriteChainID(*args)   strictResNames(*args)   useChainID(*args)   useIupacNames(*args)   useXplorNames(*args)   verbose(*args)   write(*args)   writeAltLoc(*args)   writeChainID(*args)   Data and other attributes inherited from PDBTool: __dict__ = <dictproxy object at 0x250e360>   dictionary for instance variables (if defined) __swig_getmethods__ = {} __swig_setmethods__ = {} __weakref__ = <attribute '__weakref__' of 'PDBTool' objects>   list of weak references to the object (if defined)

Functions
		help(...)

Data
		__package__ = None pyXplorHelp = Type help() for interactive help, or help(object) for help about object.