HappyDoc Generated Documentation .\chimera

. / chimera 

Chimera module

exports all symbols from C++ _chimera module

Functions   
  deleteRemoveHandler 
deleteRemoveHandler ( self,  handler )

Delete trigger handler for removing models

  addAddHandler 
addAddHandler (
        self,
        func,
        data,
        )

Add trigger handler for adding models

  registerPostGraphicsFunc 
registerPostGraphicsFunc ( func )

Register a function to execute when the graphics state is ready

  close 
close (
        self,
        models,
        checkForChanges=True,
        )

Close models and remove from list of open models.

close(models) => None

  open 
open (
        self,
        filename,
        type=None,
        baseId=OpenModels.Default,
        subid=OpenModels.Default,
        sameAs=None,
        shareXform=1,
        hidden=0,
        defaultType=None,
        prefixableType=0,
        skipViewAll=0,
        checkForChanges=True,
        *args,
        *kw,
        )

Read in a file and add the models within.

open(filename, type=None, [add arguments,] args, *kw) -> [model(s)]

If the type is given, then then open handler for that type is used. Otherwise the filename suffix is examined to determine which open function to call. See the add documentation above.

Exceptions   

ValueError, "unknown default type"
IOError, "Compressed %s files are not handled automatically.\n" "You need to decompress such files manually before using them." % type
ValueError, "Unknown model type"

  findfile 
findfile ( filename,  category="" )
  isModel 
isModel ( obj )

Return if obj is a model.

  testDrawMode 
testDrawMode (
        e,
        op,
        value,
        )

add draw mode testing capability to OSL

  makePseudoBondsToMetals 
makePseudoBondsToMetals ( models )

Replace normal bonds with pseudobonds for coordinated metals.

makePseudoBondsToMetals(models) => numAtoms, deletedBonds

  testElement 
testElement (
        e,
        op,
        value,
        )

add element testing capability to OSL

Exceptions   

SyntaxError, 'comma not allowed in element name'

  add 
add (
        self,
        models,
        baseId=OpenModels.Default,
        subid=OpenModels.Default,
        sameAs=None,
        shareXform=1,
        hidden=0,
        skipViewAll=0,
        checkForChanges=False,
        )

Add models to the list of open models.

add(models, sameAs=None, hidden=0) => None

baseId is the base model id to start numbering models with.

sameAs is an existing model that all of the new models should share the same id and subid.

If shareXform is true, then initialize the model's transformation matrix to be the same as the lowest positively numbered model (if not baseId specified) or the lowest numbered model with the same baseId. (Using sameAs overrides shareXform).

If hidden is true, that means that the given models do not normally appear when listed.

  registerOSLTests 
registerOSLTests ()
  deleteAddHandler 
deleteAddHandler ( self,  handler )

Delete trigger handler for adding models

  makePythonAtomsBondsResidues 
makePythonAtomsBondsResidues ( models )

Create Python objects for atoms, bonds and residues.

makePythonAtomsBondsResidues(models) => None

  testColor 
testColor (
        c,
        op,
        s,
        )

import oslParser

add color testing capability to OSL

Exceptions   

SyntaxError, 'comma not allowed in color name'

  addOpenFinishedHandler 
addOpenFinishedHandler (
        self,
        func,
        data,
        )

Add trigger handler for when a model is finished opening

  addRemoveHandler 
addRemoveHandler (
        self,
        func,
        data,
        )

Add trigger handler for removing models

  addModelClosedCallback 
addModelClosedCallback ( model,  callback )

Invoke a callback when a specified model is closed. The callback is only called when the given model is closed. The callback is automattically removed after it is called. The callback is passed one argument, the closed model.

  runCommand 
runCommand ( *args,  *kw )

convenience for programming...

  closeAllModels 
closeAllModels (
        self,
        trigger=None,
        closure=None,
        triggerData=None,
        )

close non-hidden models first, so that "internal chain" pseudobond groups can get removed by callbacks from the C++ layer. Then close all remaining models.

also, delay closure to the end of APPQUIT triggers, so that other modules have opportunity to de-register from model- closing triggers via APPQUIT

  selectionOperation 
selectionOperation ( sel )
  checkKsdssp 
checkKsdssp (
        trigName,
        myData,
        models,
        )
  countAtomsAndResidues 
countAtomsAndResidues ( models )

Count the total number of atoms and residues in the given models.

countAtomsAndResidues(models) => numAtoms, numResidues

  list 
list (
        self,
        id=OpenModels.Default,
        subid=OpenModels.Default,
        modelTypes=[],
        hidden=0,
        all=0,
        )

List models from the list of open models.

list(id = None, hidden=0, all=0, modelTypes=[]) => [models]

id is a model identifier (an integer). If hidden is true, then the hidden models are returned. If all is true, then both hidden and non-hidden models are returned. modelTypes is a list of model types (see the global list modelTypes) that restricts the types of the models returned.

  remove 
remove ( self,  models )

Remove models from the list of open models.

remove(models) => None

  systemPDBdir 
systemPDBdir ()
  initializeGraphics 
initializeGraphics ()
  oslLevel 
oslLevel ( obj )

Return OSL level of object or None.

The OSL level is one of SelGraph, SelSubgraph, SelVertex, SelEdge.

  delOpenFinishedHandler 
delOpenFinishedHandler ( self,  handler )

Delete trigger handler when model is finished opening

Classes   

UserError

An error that results from a wrongful action taken by a user;

ChimeraSystemExit

Used to allow Chimera to exit faster

LimitationError

An error that results from a limitation within Chimera;

NotABug

Base-class for anticipated errors. When these errors

ChimeraExit

Use this exception for known exit error states

NonChimeraError

An error that results from circumstances beyond our control,

FileInfo

Python files   

HighlightLens.py

HtmlText.py

Inspector.py

LensInspector.py

LensTreeNode.py

SearchDocs.py

Sequence.py

TreeWidget.py

WizShell.py

WriteSelDialog.py

ZoneDialog.py

ZoomHeight.py

actions.py

baseDialog.py

baseDialog
provide dialog framework for chimera dialogs

bgprefs.py

background preferences

bondGeom.py

Bond geometry utilities

chimage.py

colorTable.py

coloreditor.py

dialogs.py

Chimera Dialog Support

elements.py

exportDialog.py

exports.py

keep track of export file formats for 3D scenes

gprof.py

help.py

Chimera GUI Help Support

idatm.py

initprefs.py

lenses.py

Lenses represent an area of the screen and the graphical attributes of

match.py

misc.py

molEdit.py

mousemodes.py

oslLexer.py

oslParser.py

oslUtil.py

Miscellaneous utilities for OSL identifiers

pbgPanel.py

printer.py

register.py

registration.py

replyobj.py

Reply Object
python interface to manage reply log

resCode.py

specifier.py

splash.py

statusline.py

texture.py

tkgui.py

Chimera Graphical User Interface using Tk

tkoptions.py

Publishes Option/BooleanOption/StringOption/EnumOption.

togl.py

Tk OpenGL Widget support

toolbar.py

Toolbar interface

triggerSet.py

triggerSet module

update.py

version.py

viewing.py

widgets.py

various useful chimera-specific widgets

writeSel.py

Subdirectories   

Icons

extension

images

preferences

selection

The selection module provides tools for managing selection set and

session


This document was automatically generated Thu Feb 02 15:18:22 2006 by HappyDoc version 3.0.a1