Changes between Initial Version and Version 1 of ChimeraAnimationState

Timestamp:

Dec 21, 2010, 2:23:25 PM (15 years ago)

Author:

Darren Weber

Comment:

--

ChimeraAnimationState

@@ +1 @@
+
+=== State Parameters: Categories ===
+
+ * Elements
+   * 2D Labels
+   * Models (Molecules, Atoms)
+   * Surfaces
+   * Volumes
+   * Selections
+ * Display State
+   * Hidden
+   * Active for Motion
+ * Spatial
+   * Camera
+   * Model Geometry (Center of Rotation, Xform, etc.)
+   * Clipping Planes
+ * Lighting
+   * Background
+   * Directional Lights
+ * Surfacing
+   * Textures
+   * Materials (Color, Specular reflection, etc.)
+   * Transparency
+ * Rendering
+   * Model and ribbon styles
+   * Motion Blur
+
+
+=== State Parameters: initial work based on {{{savepos}}} and {{{reset}}} ===
+
+The savepos/reset functionality works with a tuple:
+{{{
+#
+# savepos returns a tuple of various parameters (my comments added)
+#
+        return (
+            chimera.viewer.scaleFactor, #cam
+            chimera.viewer.viewSize, #cam
+            cam.center, #cam
+            cam.nearFar, #cam
+            cam.focal, #cam
+            xforms, # spatial/geometry
+            clips, # per-model clipping
+            chimera.openModels.cofrMethod, # spatial/geometry
+            cofr, # spatial/geometry
+            chimera.viewer.clipping #cam
+        )
+}}}
+
+
+
+=== Parameter Access Methods ===
+
+Something like this gains access to a lot of view parameters:
+{{{
+for n in dir(chimera.viewer):
+    print n, eval('type(chimera.viewer.%s)' % n)
+}}}
+
+Some tips in the [http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html programming FAQ] are useful (esp, items 4, 5, 7-10).
+
+
+
+==== Attributes: To Copy or Not to Copy, that is the question! ====
+
+From the [http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html FAQ], item (7): Some attributes return a copy of an object.
+{{{
+>>> xf = model.openState.xform  # xf is a copy of the model's Xform matrix.
+>>> xf.zRotate(45)              # This will not rotate the model.
+
+>>> c = model.atoms[0].color    # c is the MaterialColor object for the atom
+>>> c.ambientDiffuse = (1,0,0)  # The Atom color changes immediately to red.
+}}}
+
+Some Chimera objects returned as attributes are always copies, some are always references to the uncopied object. Objects that are always copied include {{{Xform, Vector, Point, Sphere, Element, MolResId, Coord,}}} .... Objects that are never copied include {{{Atom, Bond, PseudoBond, CoordSet, Molecule, Residue, RibbonStyle,}}} .... Object that can be copied have a {{{__copy__}}} method. In order to know if an object type is passed by value is to look at the Chimera C++ header files. Classes without a !WrapPy base class are always copied. This base class is part of the C++ to Python interface generation.
+
+
+
+==== Color and Material Attributes ====
+
+See http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/Main_ColorWellUI.html
+
+Also need a function for color interpolations (linear may suffice).  This may be a simple function to interpolate each component of the RGBA tuple from stateA to stateB over N frames (the range of values is between 0-1, so it's a floating point interpolation).
+
+Get a PDB molecule to play with:
+{{{
+chimera.runCommand('open 2por')
+om = chimera.openModels.list(all=True)
+por2 = om[1]
+}}}
+
+Exploring color properties:
+{{{
+>>> por2.color
+<_chimera.MaterialColor object at 0x3d50dc8>
+>>> por2.color.name()
+u'_openColor00'
+>>> por2.color.rgba()
+(1.0, 1.0, 1.0, 1.0)
+>>> por2.color.ambientDiffuse
+(1.0, 1.0, 1.0)
+>>> por2.color.isTranslucent()
+False
+>>> por2.color.opacity
+1.0
+}}}
+
+Chimera material attributes are collected with color attributes.
+{{{
+# chimera.Material object
+>>> por2.color.material
+<_chimera.Material object at 0x2fd7c60>
+>>> por2.color.material.name()  # material name (unicode str)
+u'default'
+>>> por2.color.material.shininess
+30.0
+>>> por2.color.material.specular
+(0.85, 0.85, 0.85)
+>>> por2.color.material.opacity
+1.0
+>>> por2.color.material.ambientDiffuse
+(1.0, 1.0, 1.0)
+>>> por2.color.material.isTexture()
+False
+>>> por2.color.material.isTranslucent()
+False
+}}}
+
+
+
+==== openState attributes ====
+
+Get the !OpenState attributes of a model: {{{chimera.openModels.openState(id: int, subid: int)}}}
+
+From the [http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html FAQ], item (10):  The openState attribute of a Model controls whether that model is active for motion ('.active'), and contains the model's transformation matrix ('.xform') and center of rotation ('.cofr'). Since some models must move in synchrony (e.g. a molecule and its surface), !OpenState instances may be shared among multiple models. If you create a model that needs a shared openState with another model, then when adding your model to the list of open models with chimera.openModels.add(), you should use the 'sameAs' keyword to specify the other model.
+
+
+
+==== 'Active' models ====
+
+{{{
+#
+# Working with a specific active model:
+# openState(id: int, subid: int)
+modelID = chimera.openModels.listIds()[0]
+model_openState = chimera.openModels.openState(*modelID)
+if model_openState.active:
+    # do something useful with it
+    print model_openState.xform
+    print model_openState.xform.getRotation()
+    print model_openState.xform.getTranslation()
+#
+# looping over all open-active models
+#
+if chimera.openModels.hasActiveModels():
+    om = chimera.openModels.list(all=True)
+    for m in om:
+        if m.openState.active:
+            # do something useful with it
+            print m.openState.xform
+#
+# Setting 'active' models:
+# chimera.openModels.setActive(id: int, active: bool)
+#
+chimera.openModels.setActive(modelID[0], False)
+model_openState.active
+# False
+chimera.openModels.setActive(modelID[0], True)
+model_openState.active
+# True
+
+}}}
+
+
+
+==== openState.xform ====
+
+{{{
+
+>>> dir(model_openState.xform)
+['__class__', '__copy__', '__delattr__', '__dict__', '__doc__', '__eq__', '__format__', '__ge__', '__getattribute__', '__gt__', '__hash__', '__init__', '__le__', '__lt__', '__ne__', '__new__', '__reduce__', '__reduce_ex__', '__repr__', '__setattr__', '__sizeof__', '__str__', '__subclasshook__', 'apply', 'coordFrame', 'getCoordFrame', 'getOpenGLMatrix', 'getRotation', 'getTranslation', 'identity', 'inverse', 'invert', 'isIdentity', 'lookAt', 'makeOrthogonal', 'multiply', 'premultiply', 'rotate', 'rotation', 'translate', 'translation', 'xRotate', 'xRotation', 'xform', 'yRotate', 'yRotation', 'zAlign', 'zRotate', 'zRotation']
+
+>>> help(model_openState.xform)
+Help on Xform object:
+
+...
+
+}}}
+