Changes between Version 17 and Version 18 of ChimeraAnimationState

Timestamp:

Jan 7, 2011, 10:59:57 AM (15 years ago)

Author:

Darren Weber

Comment:

--

ChimeraAnimationState

@@ -91 +91 @@
 }}}
 
+See also the [http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html Chimera BILD] commands.
+
+==== 'Active' models ====
+
+{{{
+#!python
+#
+# 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
+
+}}}
+
+
 
 === Atoms ===
@@ -100 +139 @@
 }}}
 
-==== Color ====
+==== Representations ====
+
+Each atom in a molecule has a drawMode attribute, with possible values: 0 = 'dot', 1 = 'sphere', 2 = 'endcap', 3 = 'ball'.  These values can be compared with the equivalent 'enum' values in chimera.Atom, i.e.:
+
+{{{
+#!python
+>>> chimera.Atom.Dot
+0
+>>> chimera.Atom.Sphere
+1
+>>> chimera.Atom.EndCap
+2
+>>> chimera.Atom.Ball
+3
+}}}
+
+{{{
+#!python
+molecules = chimera.openModels.list(modelTypes=[chimera.Molecule])
+for m in molecules:
+    for a in m.atoms:
+        print a.drawMode == chimera.Atom.Sphere
+}}}
+
+
+==== Color and Material Attributes ====
+
+See [http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/Main_ColorWellUI.html Main_ColorWellUI example].
 
 {{{
@@ -167 +233 @@
 
 
-==== Representations ====
-
-Each atom in a molecule has a drawMode attribute, with possible values: 0 = 'dot', 1 = 'sphere', 2 = 'endcap', 3 = 'ball'.  These values can be compared with the equivalent 'enum' values in chimera.Atom, i.e.:
-
-{{{
-#!python
->>> chimera.Atom.Dot
-0
->>> chimera.Atom.Sphere
-1
->>> chimera.Atom.EndCap
-2
->>> chimera.Atom.Ball
-3
-}}}
-
-{{{
-#!python
-molecules = chimera.openModels.list(modelTypes=[chimera.Molecule])
-for m in molecules:
-    for a in m.atoms:
-        print a.drawMode == chimera.Atom.Sphere
-}}}
-
-
-=== Parameter Access Methods ===
-
-Something like this gains access to a lot of view parameters:
-{{{
-#!python
-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.
-{{{
-#!python
->>> 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:
@@ -274 +285 @@
 
 
+=== Parameter Access Methods ===
+
+Something like this gains access to a lot of view parameters:
+{{{
+#!python
+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.
+{{{
+#!python
+>>> 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.
+
+
 ==== openState attributes ====
 
@@ -281 +318 @@
 
 
-
-==== 'Active' models ====
-
-{{{
-#!python
-#
-# 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
-
-}}}