Changes between Version 18 and Version 19 of ChimeraAnimationTasks


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Timestamp:
Dec 21, 2010, 2:20:33 PM (15 years ago)
Author:
Darren Weber
Comment:

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  • ChimeraAnimationTasks

    v18 v19  
    11
    2 == Resources ==
    3 
    4  * [http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/ Programmer's Guide] (http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/)
    5  * [http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts Example scripts] (http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts)
    6  * IDLE (Tools > General Controls): help(object), dir(object)
    7  * [http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev Chimera developer mailing list] (http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev)
    8  * Source code:
    9    * [http://plato.cgl.ucsf.edu/trac/chimera/browser subversion browser] (http://plato.cgl.ucsf.edu/trac/chimera/browser)
    10    * [http://www.cgl.ucsf.edu/chimera/sourcecode.html download] (http://www.cgl.ucsf.edu/chimera/sourcecode.html)
    11    * C++ headers are available in distributions (see $CHIMERA/include)
    12    * Python source code is included with distributions (see $CHIMERA/share)
    13  * [http://docs.python.org/ Python documentation] (http://docs.python.org/)
    14  * [http://www.scipy.org/Numpy_Example_List_With_Doc Numpy examples] (http://www.scipy.org/Numpy_Example_List_With_Doc)
    15 
    16 == Chimera Molecular Data ==
    17 
    18 {{{
    19 # a list of open models
    20 models = chimera.openModels.list()
    21 
    22 # restrict list to Molecules
    23 molecules = chimera.openModels.list(modelTypes=[chimera.Molecule])
    24 
    25 # a Molecule's residues, atoms, or bonds
    26 if len(molecules):
    27   r = molecules[0].residues
    28   a = molecules[0].atoms
    29   b = molecules[0].bonds
    30 }}}
    31 
    32 === Residues ===
    33 
    34  * type: LYS, HEM, etc.
    35  * id.position / id.chainId / id.insertionCode: number / chain ID / insertion code
    36  * molecule: parent Molecule
    37  * atoms: list of atoms
    38  * atomsMap: dict of {atom-name: [list of atoms]}
    39  * isHelix / isStrand: in helix / strand
    40 
    41 === Atoms ===
    42 
    43  * name: name
    44  * coord() / xformCoord(): untransformed / transformed coordinates
    45  * residue / molecule: parent Residue / Molecule
    46  * bonds: list of bonds
    47  * neighbors: list of bonded atoms
    48  * primaryBonds() / primaryNeighbors(): same as above but only primary altlocs
    49  * bondsMap: dict of {bonded-atom: bond}
    50  * color: Color
    51  * display: True if shown
    52  * drawMode: one of chimera.Atom.X with X being Dot, Sphere, EndCap, or Ball
    53  * element: chemical element (type chimera.Element, settable with string or number)
    54  * label: label shown in graphics window
    55  * radius: VdW radius
    56 
    57 === Bonds ===
    58 
    59  * atoms: 2-tuple of atoms
    60  * otherAtom(a): [a is one of the bond's atoms] other atom in bond
    61  * drawMode: one of chimera.Bond.X with X being Wire or Stick
    62  * label: label shown in graphics window
    63  * molecule: parent Molecule
    64  * length(): length
    65 
    66 === Molecular Measurements ===
    67 
    68 chimera module functions use Points, which are returned by Atom's coord() or xformCoord() methods
    69  * distance / sqdistance
    70  * also: a1.coord().[sq]distance(a2.coord()) [similar for xformCoord]
    71  * angle (in degrees)
    72  * dihedral (in degrees)
    73 
    74 === Molecular Editing ===
    75 
    76 Look in {{{$CHIMERA/share/BuildStructure/__init__.py}}} for examples of creating new molecules and residues.
    77 
    78 Using the {{{chimera.molEdit}}} module:
    79  * addAtom
    80     * if adding in bulk, make sure to specify optional serialNumber keyword
    81  * addBond
    82  * addDihedralAtom -- add atom given a bond length / angle / dihedral
    83 
    84 === Setting or Querying Selections ===
    85 
    86 Using the {{{chimera.selection}}} module:
    87  * currentAtoms / currentBonds / currentResidues / currentMolecules: currently selected Atoms / Bonds / Residues / Molecules
    88  * setCurrent: set current selection to given items
    89  * addCurrent / addImpliedCurrent: add given items to current selection
    90  * the "implied" version also selects endpoint Atoms of added Bonds and connecting Bonds of added Atoms
    91  * removeCurrent: remove items from current selection, if present
    92 
    93 === Miscellaneous ===
    94 
    95  * chimera.runCommand: execute any command-line command (arg is a string)
    96     * direct Python equivalent usually in Midas module
    97  * chimera.colorTable module:
    98     * getColorByName: get a Color by name
    99  * !OpenSave module:
    100     * osOpen: open a file or HTTP URL, with or without compression
    101  * chimera.extension module
    102     * manager.instances: running dialogs listed at end of Tools menu
     2 * [wiki:ChimeraProgrammingResources Programming resources], including commonly used modules for access to molecular data attributes
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