== Resources ==

 * [http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/ Programmer's Guide] (http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/)
 * [http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts Example scripts] (http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts)
 * IDLE (Tools > General Controls): help(object), dir(object)
 * [http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev Chimera developer mailing list] (http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev)
 * Source code:
   * [http://plato.cgl.ucsf.edu/trac/chimera/browser subversion browser] (http://plato.cgl.ucsf.edu/trac/chimera/browser)
   * [http://www.cgl.ucsf.edu/chimera/sourcecode.html download] (http://www.cgl.ucsf.edu/chimera/sourcecode.html)
   * C++ headers are available in distributions (see $CHIMERA/include)
   * Python source code is included with distributions (see $CHIMERA/share)
 * [http://docs.python.org/ Python documentation] (http://docs.python.org/)
 * [http://www.scipy.org/Numpy_Example_List_With_Doc Numpy examples] (http://www.scipy.org/Numpy_Example_List_With_Doc)

== Chimera Molecular Data ==

{{{
# a list of open models
models = chimera.openModels.list()

# restrict list to Molecules
molecules = chimera.openModels.list(modelTypes=[chimera.Molecule])

# a Molecule's residues, atoms, or bonds
if len(molecules):
  r = molecules[0].residues
  a = molecules[0].atoms
  b = molecules[0].bonds
}}}

=== Residues ===

 * type: LYS, HEM, etc.
 * id.position / id.chainId / id.insertionCode: number / chain ID / insertion code
 * molecule: parent Molecule
 * atoms: list of atoms
 * atomsMap: dict of {atom-name: [list of atoms]}
 * isHelix / isStrand: in helix / strand

=== Atoms ===

 * name: name
 * coord() / xformCoord(): untransformed / transformed coordinates
 * residue / molecule: parent Residue / Molecule
 * bonds: list of bonds
 * neighbors: list of bonded atoms
 * primaryBonds() / primaryNeighbors(): same as above but only primary altlocs
 * bondsMap: dict of {bonded-atom: bond}
 * color: Color
 * display: True if shown
 * drawMode: one of chimera.Atom.X with X being Dot, Sphere, EndCap, or Ball
 * element: chemical element (type chimera.Element, settable with string or number)
 * label: label shown in graphics window
 * radius: VdW radius

=== Bonds ===

 * atoms: 2-tuple of atoms
 * otherAtom(a): [a is one of the bond's atoms] other atom in bond
 * drawMode: one of chimera.Bond.X with X being Wire or Stick
 * label: label shown in graphics window
 * molecule: parent Molecule
 * length(): length

=== Molecular Measurements ===

chimera module functions use Points, which are returned by Atom's coord() or xformCoord() methods
 * distance / sqdistance
 * also: a1.coord().[sq]distance(a2.coord()) [similar for xformCoord]
 * angle (in degrees)
 * dihedral (in degrees)

=== Molecular Editing ===

Look in {{{$CHIMERA/share/BuildStructure/__init__.py}}} for examples of creating new molecules and residues.

Using the {{{chimera.molEdit}}} module:
 * addAtom
    * if adding in bulk, make sure to specify optional serialNumber keyword
 * addBond
 * addDihedralAtom -- add atom given a bond length / angle / dihedral

=== Setting or Querying Selections ===

Using the {{{chimera.selection}}} module:
 * currentAtoms / currentBonds / currentResidues / currentMolecules: currently selected Atoms / Bonds / Residues / Molecules
 * setCurrent: set current selection to given items
 * addCurrent / addImpliedCurrent: add given items to current selection
 * the "implied" version also selects endpoint Atoms of added Bonds and connecting Bonds of added Atoms
 * removeCurrent: remove items from current selection, if present

=== Miscellaneous ===

 * chimera.runCommand: execute any command-line command (arg is a string)
    * direct Python equivalent usually in Midas module
 * chimera.colorTable module:
    * getColorByName: get a Color by name
 * !OpenSave module:
    * osOpen: open a file or HTTP URL, with or without compression
 * chimera.extension module
    * manager.instances: running dialogs listed at end of Tools menu