Changes between Initial Version and Version 1 of ChimeraProgrammingResources

Timestamp:

Dec 21, 2010, 2:20:50 PM (15 years ago)

Author:

Darren Weber

Comment:

--

ChimeraProgrammingResources

@@ +1 @@
+
+== 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