py_atomsel.C File Reference

static PyObject *funcname(PyObject *self) { \
  VMDApp *app = get_vmdapp(); \
  PyObject *result = PyList_New(0); \
  SymbolTable *table = app->atomSelParser; \
  int i, n = table->fctns.num(); \
  for (i=0; i<n; i++) \
    if (table->fctns.data(i)->is_a == elemtype) \
      PyList_Append(result, PyString_FromString(table->fctns.name(i))); \
  return result; \
}

 (char *)
    "atomsel( selection, molid = top, frame = now) -> new selection object\n"

 {
  { (char *)"frame", (getter)getframe, (setter)setframe, frame_doc, NULL },
  { (char *)"bonds", (getter)getbonds, (setter)setbonds, bonds_doc, NULL },
  { (char *)"molid", (getter)getmolid, (setter)NULL, molid_doc, NULL },
  { NULL },
}

 {
  atomselection_length,
  (binaryfunc)atomselection_subscript,
  0
}

 {
  {"macro", (PyCFunction)macro, METH_VARARGS | METH_KEYWORDS,
    "macro(name=None, selection=None) -- create and query selection macros.\n"
    "If both name and selection are None, return list of macro names.\n"
    "If selection is None, return definition for name.\n"
    "If both name and selection are given, define new macro.\n" },
  {"delmacro", (vmdPyMethod)delmacro, METH_VARARGS, 
    "delmacro(name) -> Delete atom selection macro with given name." },
  {"inverse", (PyCFunction)inverse, METH_O,
    "inverse(matrix) -> Inverse of matrix returned by atomsel.fit(...)"},
  {"keywords", (PyCFunction)keywords, METH_NOARGS,
    "keywords() -> List of available atom selection keywords."},
  {"booleans", (PyCFunction)booleans, METH_NOARGS,
    "booleans() -> List of available atom selection boolean tokens."},
  {"functions", (PyCFunction)functions, METH_NOARGS,
    "functions() -> List of available atom selection functions."},
  {"stringfunctions", (PyCFunction)stringfunctions, METH_NOARGS,
    "stringfunctions() -> List of available atom selection string functions."},
  { NULL, NULL }
}

 {
  { "get", (PyCFunction)atomsel_get, METH_O, get_doc  },
  { "set", (PyCFunction)atomsel_set, METH_VARARGS, set_doc },
  { "update", (PyCFunction)py_update, METH_NOARGS, update_doc },
  { "write", (PyCFunction)py_write, METH_VARARGS|METH_KEYWORDS, write_doc },
  { "minmax", (PyCFunction)minmax, METH_VARARGS, minmax_doc },
  { "center", (PyCFunction)center, METH_VARARGS|METH_KEYWORDS, center_doc },
  { "rmsd", (PyCFunction)py_rmsd, METH_VARARGS, rmsd_doc, },
  { "fit", (PyCFunction)py_fit, METH_VARARGS, fit_doc, },
  { "move", (PyCFunction)py_move, METH_O, move_doc },
  { "moveby", (PyCFunction)py_moveby, METH_O, moveby_doc },
  { "contacts", (PyCFunction)contacts, METH_VARARGS, contacts_doc },
  { "sasa", (PyCFunction)sasa, METH_VARARGS | METH_KEYWORDS, sasa_doc },
  { NULL, NULL }
}

 (char *)
    "bonds - for each atom in selection, a list of the indices\n"
    "  of the bonded atoms.\n"

 (char *)
  "center(weight=None) -> (x, y, z)\n"
  "Return a tuple corresponding to the center of the selection,\n"
  "optionally weighted by weight."

 (char *)
  "contacts(sel, cutoff) -> contact pairs\n"
  "Return two lists, whose corresponding elements contain atom indices\n"
  "in selection that are within cutoff of sel, but not directly bonded.\n"

 (char *)
    "fit(sel, weight=None) -> transformation matrix\n"
    "  Compute and return the transformation matrix for the RMS alignment\n"
    "  of the selection to sel.  The format of the matrix is a 16-element\n"
    "  tuple suitable for passing to the move() method.\n"
    "  Weight must be None or list of same size as selections."

 (char *)
    "frame -- the animation frame referenced by the selection.\n"
    "   Special values: -1 = current frame, -2 = last frame.\n"
    "NOTE: changing the frame does not update the selection;\n"
    "   use update() to do that.\n"

 (char *)
    "get( attrib ) -> corresponding attrib values for selected atoms."

 {
    {"__length_hint__", (PyCFunction)iter_len, METH_NOARGS },
    {NULL, NULL}
  }

 (char *)
  "minmax() -> (min, max)\n"
  "Return minimum and maximum coordinates for selected atoms."

 (char *)
    "Methods for creating, updating, querying, and modifying\n"
    "selections of atoms.\n"
    "\n"
    "Example of usage:\n"
    ">>> from atomsel import *\n"
    ">>> s1 = atomsel('residue 1 to 10 and backbone')\n"
    ">>> s1.get('resid')\n"
    " <snip> \n"
    ">>> s1.set('beta', 5') # set B value to 5 for atoms in s1\n"
    ">>> # Mass-weighted RMS alignment:\n"
    ">>> mass = s1.get('mass')\n"
    ">>> s2 = atomsel('residue 21 to 30 and backbone')\n"
    ">>> mat = s1.fit(s2, mass)\n"
    ">>> s1.move(mat)\n"
    ">>> print s1.rmsd(s2)\n"

 (char *)
    "molid - The id of the molecule this selection is associated with.\n"

 (char *)
    "move( matrix ) -> apply coordinate transformation to selection.\n"
    "  matrix should be of the form returned by fit()."

 (char *)
    "moveby( vec ) -> shift the selection by the three-element vector vec."

 (char *)
  "rmsd(sel, weight=None) -> rms distance between selections.\n"
  "  Selections must have the same number of atoms.\n"
  "  Weight must be None or list of same size as selections."

 (char *)
    "sasa(srad, sel, ... ) -> solvent accessible surface area.\n"
    "srad gives solvent radius.\n"
    "Optional keyword arguments:\n"
    "  samples=500 -- specifies number of sample points used per atom.\n"
    "  points=None -- If points is a list, coordinates of surface points\n"
    "    will be appended to the list.\n"
    "  restrict=None -- Pass an atom selection as argument to restrict\n"
    "    to find contributions coming from just atoms in restrict.\n"

 (char *)
    "set( attrib, val ) -> set attrib values for selected atoms.\n"
    "  val must be either a single value, or a sequence of values, one for\n"
    "   each atom in selection.\n"

 (char *)
    "update() -> Recompute atoms in selection; if the selection is\n"
       "distance-based (e.g., if it uses 'within'), changes to the frame\n"
       "will not be reflected in the selected atoms until this method\n"
       "is called.\n"

 (char *)
  "write(filetype, filename) -> None\n"
  "Write the atoms in the selection to a file of the given type."

Compounds
struct	iterobject
struct	PyAtomSelObject
Defines
#define	SYMBOL_TABLE_FUNC(funcname, elemtype)
Typedefs
typedef int	Py_ssize_t
Functions
int	atomsel_Check (PyObject *obj)
DrawMolecule *	get_molecule (PyAtomSelObject *a)
void	atomsel_dealloc (PyAtomSelObject *obj)
PyObject *	atomsel_repr (PyAtomSelObject *obj)
PyObject *	atomsel_str (PyAtomSelObject *obj)
PyObject *	atomsel_new (PyTypeObject type, PyObject args, PyObject *kwds)
PyObject *	atomsel_get (PyAtomSelObject a, PyObject keyobj)
PyObject *	atomsel_set (PyAtomSelObject a, PyObject args)
PyObject *	getframe (PyAtomSelObject a, void )
int	setframe (PyAtomSelObject a, PyObject frameobj, void *)
PyObject *	py_update (PyAtomSelObject *a)
PyObject *	py_write (PyAtomSelObject a, PyObject args, PyObject *kwds)
PyObject *	getbonds (PyAtomSelObject a, void )
int	setbonds (PyAtomSelObject a, PyObject obj, void *)
PyObject *	getmolid (PyAtomSelObject a, void )
PyObject *	macro (PyObject self, PyObject args, PyObject *keywds)
PyObject *	delmacro (PyObject self, PyObject args)
int	py_get_vector (PyObject matobj, int n, float vec)
PyObject *	inverse (PyObject self, PyObject matobj)
float *	parse_weight (AtomSel sel, PyObject wtobj)
PyObject *	minmax (PyAtomSelObject a, PyObject withradii)
PyObject *	center (PyAtomSelObject a, PyObject args, PyObject *kwds)
float *	parse_two_selections_return_weight (PyAtomSelObject a, PyObject args, AtomSel **othersel)
PyObject *	py_rmsd (PyAtomSelObject a, PyObject args)
PyObject *	py_fit (PyAtomSelObject a, PyObject args)
PyObject *	py_moveby (PyAtomSelObject a, PyObject vecobj)
PyObject *	py_move (PyAtomSelObject a, PyObject matobj)
PyObject *	contacts (PyAtomSelObject a, PyObject args)
PyObject *	sasa (PyAtomSelObject a, PyObject args, PyObject *keywds)
Py_ssize_t	atomselection_length (PyObject *a)
PyObject *	atomselection_subscript (PyAtomSelObject a, PyObject keyobj)
PyObject *	atomsel_iter (PyObject *)
PyObject *	iter_next (iterobject *it)
void	iter_dealloc (iterobject *it)
PyObject *	iter_len (iterobject *it)
PyObject *	atomsel_iter (PyObject *self)
AtomSel *	atomsel_AsAtomSel (PyObject *obj)
void	initatomsel (void)
Variables
char *	atomsel_doc
char *	get_doc
char *	set_doc
char *	frame_doc
char *	update_doc
char *	write_doc
char *	bonds_doc
char *	molid_doc
PyGetSetDef	atomsel_getset []
char *	minmax_doc
char *	center_doc
char *	rmsd_doc
char *	fit_doc
char *	moveby_doc
char *	move_doc
char *	contacts_doc
char *	sasa_doc
PyMappingMethods	atomsel_mapping
PyMethodDef	atomselection_methods []
PyMethodDef	iter_methods []
PyTypeObject	itertype
PyTypeObject	atomsel_type
PyMethodDef	atomsel_methods []
char *	module_doc

py_atomsel.C File Reference

Compounds

Defines

Typedefs

Functions

Variables

Define Documentation

Typedef Documentation

Function Documentation

Variable Documentation