Changes between Version 19 and Version 20 of ChimeraAnimationTasks


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Timestamp:
Dec 21, 2010, 2:23:12 PM (15 years ago)
Author:
Darren Weber
Comment:

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  • ChimeraAnimationTasks

    v19 v20  
    11
    2  * [wiki:ChimeraProgrammingResources Programming resources], including commonly used modules for access to molecular data attributes
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    … …  
    87Need to identify all the possible state parameters that can be changed between two states. All of those parameters need to be retained, probably in some form of immutable data type (tuple) within a dictionary for easy access to several parameter groups (viewer, volumes, surfaces, models, labels, etc.). Some of the elements in a state may have shared spatial parameters (e.g., molecular surfaces, molecules, and atoms may share a common spatial transform).
    98
    10 
    11 
    12 === State Parameters: Categories ===
    13 
    14  * Elements
    15    * 2D Labels
    16    * Models (Molecules, Atoms)
    17    * Surfaces
    18    * Volumes
    19    * Selections
    20  * Display State
    21    * Hidden
    22    * Active for Motion
    23  * Spatial
    24    * Camera
    25    * Model Geometry (Center of Rotation, Xform, etc.)
    26    * Clipping Planes
    27  * Lighting
    28    * Background
    29    * Directional Lights
    30  * Surfacing
    31    * Textures
    32    * Materials (Color, Specular reflection, etc.)
    33    * Transparency
    34  * Rendering
    35    * Model and ribbon styles
    36    * Motion Blur
    37 
    38 
    39 === State Parameters: initial work based on {{{savepos}}} and {{{reset}}} ===
    40 
    41 The savepos/reset functionality works with a tuple:
    42 {{{
    43 #
    44 # savepos returns a tuple of various parameters (my comments added)
    45 #
    46         return (
    47             chimera.viewer.scaleFactor, #cam
    48             chimera.viewer.viewSize, #cam
    49             cam.center, #cam
    50             cam.nearFar, #cam
    51             cam.focal, #cam
    52             xforms, # spatial/geometry
    53             clips, # per-model clipping
    54             chimera.openModels.cofrMethod, # spatial/geometry
    55             cofr, # spatial/geometry
    56             chimera.viewer.clipping #cam
    57         )
    58 }}}
    59 
    60 
    61 
    62 === Parameter Access Methods ===
    63 
    64 Something like this gains access to a lot of view parameters:
    65 {{{
    66 for n in dir(chimera.viewer):
    67     print n, eval('type(chimera.viewer.%s)' % n)
    68 }}}
    69 
    70 Some tips in the [http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html programming FAQ] are useful (esp, items 4, 5, 7-10).
    71 
    72 
    73 
    74 ==== Attributes: To Copy or Not to Copy, that is the question! ====
    75 
    76 From the [http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html FAQ], item (7): Some attributes return a copy of an object.
    77 {{{
    78 >>> xf = model.openState.xform  # xf is a copy of the model's Xform matrix.
    79 >>> xf.zRotate(45)              # This will not rotate the model.
    80 
    81 >>> c = model.atoms[0].color    # c is the MaterialColor object for the atom
    82 >>> c.ambientDiffuse = (1,0,0)  # The Atom color changes immediately to red.
    83 }}}
    84 
    85 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.
    86 
    87 
    88 
    89 ==== Color and Material Attributes ====
    90 
    91 See http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/Main_ColorWellUI.html
    92 
    93 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).
    94 
    95 Get a PDB molecule to play with:
    96 {{{
    97 chimera.runCommand('open 2por')
    98 om = chimera.openModels.list(all=True)
    99 por2 = om[1]
    100 }}}
    101 
    102 Exploring color properties:
    103 {{{
    104 >>> por2.color
    105 <_chimera.MaterialColor object at 0x3d50dc8>
    106 >>> por2.color.name()
    107 u'_openColor00'
    108 >>> por2.color.rgba()
    109 (1.0, 1.0, 1.0, 1.0)
    110 >>> por2.color.ambientDiffuse
    111 (1.0, 1.0, 1.0)
    112 >>> por2.color.isTranslucent()
    113 False
    114 >>> por2.color.opacity
    115 1.0
    116 }}}
    117 
    118 Chimera material attributes are collected with color attributes.
    119 {{{
    120 # chimera.Material object
    121 >>> por2.color.material
    122 <_chimera.Material object at 0x2fd7c60>
    123 >>> por2.color.material.name()  # material name (unicode str)
    124 u'default'
    125 >>> por2.color.material.shininess
    126 30.0
    127 >>> por2.color.material.specular
    128 (0.85, 0.85, 0.85)
    129 >>> por2.color.material.opacity
    130 1.0
    131 >>> por2.color.material.ambientDiffuse
    132 (1.0, 1.0, 1.0)
    133 >>> por2.color.material.isTexture()
    134 False
    135 >>> por2.color.material.isTranslucent()
    136 False
    137 }}}
    138 
    139 
    140 
    141 ==== openState attributes ====
    142 
    143 Get the !OpenState attributes of a model: {{{chimera.openModels.openState(id: int, subid: int)}}}
    144 
    145 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.
    146 
    147 
    148 
    149 ==== 'Active' models ====
    150 
    151 {{{
    152 #
    153 # Working with a specific active model:
    154 # openState(id: int, subid: int)
    155 modelID = chimera.openModels.listIds()[0]
    156 model_openState = chimera.openModels.openState(*modelID)
    157 if model_openState.active:
    158     # do something useful with it
    159     print model_openState.xform
    160     print model_openState.xform.getRotation()
    161     print model_openState.xform.getTranslation()
    162 #
    163 # looping over all open-active models
    164 #
    165 if chimera.openModels.hasActiveModels():
    166     om = chimera.openModels.list(all=True)
    167     for m in om:
    168         if m.openState.active:
    169             # do something useful with it
    170             print m.openState.xform
    171 #
    172 # Setting 'active' models:
    173 # chimera.openModels.setActive(id: int, active: bool)
    174 #
    175 chimera.openModels.setActive(modelID[0], False)
    176 model_openState.active
    177 # False
    178 chimera.openModels.setActive(modelID[0], True)
    179 model_openState.active
    180 # True
    181 
    182 }}}
    183 
    184 
    185 
    186 ==== openState.xform ====
    187 
    188 {{{
    189 
    190 >>> dir(model_openState.xform)
    191 ['__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']
    192 
    193 >>> help(model_openState.xform)
    194 Help on Xform object:
    195 
    196 ...
    197 
    198 }}}
     9 * [wiki:ChimeraProgrammingResources Programming resources], including commonly used modules for access to molecular data attributes
     10 * [wiki:ChimeraAnimationState Animation State Parameters]
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