.. _api-introspection: ************* Introspection ************* Introspection ============= Only internal. This class is used only as a base class to Model, it is not provided through API. Defines interface to introspect simulation state. Methods: ********* .. _Introspection__get_molecule_ids: get_molecule_ids (pattern: Complex=None) -> List[int] ----------------------------------------------------- | Returns a list of ids of molecules. | If the arguments pattern is not set, the list of all molecule ids is returned. | If the argument pattern is set, the list of all molecule ids whose species match | the pattern is returned. * | pattern: Complex = None | BNGL pattern to select molecules based on their species, might use compartments. | Example: `1910_get_molecule_ids_w_pattern/model.py `_ .. _Introspection__get_molecule: get_molecule (id: int) -> Molecule ---------------------------------- | Returns a information on a molecule from the simulated environment, | None if the molecule does not exist. * | id: int | Unique id of the molecule to be retrieved. | Example: `1900_molecule_introspection/model.py `_ .. _Introspection__get_species_name: get_species_name (species_id: int) -> str ----------------------------------------- | Returns a string representing canonical species name in the BNGL format. * | species_id: int | Id of the species. | Example: `1850_run_unimol_rxn_in_callback/model.py `_ .. _Introspection__get_vertex: get_vertex (object: GeometryObject, vertex_index: int) -> List[float] --------------------------------------------------------------------- | Returns coordinates of a vertex. * | object: GeometryObject * | vertex_index: int | This is the index of the vertex in the geometry object's walls (wall_list). | Example: `1340_get_vertex/model.py `_ .. _Introspection__get_wall: get_wall (object: GeometryObject, wall_index: int) -> Wall ---------------------------------------------------------- | Returns information about a wall belonging to a given object. * | object: GeometryObject | Geometry object whose wall to retrieve. * | wall_index: int | This is the index of the wall in the geometry object's walls (wall_list). | Example: `1330_get_wall/model.py `_ .. _Introspection__get_vertex_unit_normal: get_vertex_unit_normal (object: GeometryObject, vertex_index: int) -> List[float] --------------------------------------------------------------------------------- | Returns sum of all wall normals that use this vertex converted to a unit vector of | length 1 um (micrometer). | This represents the unit vector pointing outwards from the vertex. * | object: GeometryObject | Geometry object whose vertex to retrieve. * | vertex_index: int | This is the index of the vertex in the geometry object's vertex_list. | Example: `1320_get_vertex_unit_normal/model.py `_ .. _Introspection__get_wall_unit_normal: get_wall_unit_normal (object: GeometryObject, wall_index: int) -> List[float] ----------------------------------------------------------------------------- | Returns wall normal converted to a unit vector of length 1um. * | object: GeometryObject | Geometry object whose wall's normal to retrieve. * | wall_index: int | This is the index of the vertex in the geometry object's walls (wall_list). | Example: `1310_get_wall_unit_normal/model.py `_ .. _Introspection__get_wall_color: get_wall_color (object: GeometryObject, wall_index: int) -> Color ----------------------------------------------------------------- | Returns color of a wall. * | object: GeometryObject | Geometry object whose wall's color to retrieve. * | wall_index: int | This is the index of the vertex in the geometry object's walls (wall_list). .. _Introspection__set_wall_color: set_wall_color (object: GeometryObject, wall_index: int, color: Color) ---------------------------------------------------------------------- | Sets color of a wall. * | object: GeometryObject | Geometry object whose wall's color to retrieve. * | wall_index: int | This is the index of the vertex in the geometry object's walls (wall_list). * | color: Color | Color to be set. Molecule ======== Representation of a molecule obtained from Model during simulation obtained through Model.get_molecule. Changes through changing attributes of this object are not allowed except for complete removal of this molecule. Example: `1900_molecule_introspection/model.py `_ Attributes: *********** .. _Molecule__id: id: int ------- | Unique id of this molecule. MCell assigns this unique id to each created | molecule. All reactions change ID of molecules even in reactions such as | A\@CP -> A\@EC. | - default argument value in constructor: ID_INVALID .. _Molecule__type: type: MoleculeType ------------------ | Type of this molecule, either volume or surface. | - default argument value in constructor: MoleculeType.UNSET .. _Molecule__species_id: species_id: int --------------- | Species id of this molecule. | The species_id value is only temporary. Species ids are created and removed as needed | automatically and if this species is removed, this particular species_id value | won't be valid. This can happen when a following iteration is simulated. | - default argument value in constructor: ID_INVALID .. _Molecule__pos3d: pos3d: List[float] ------------------ | Contains position of a molecule in 3D space. | - default argument value in constructor: None .. _Molecule__orientation: orientation: Orientation ------------------------ | Contains orientation for surface molecule. Volume molecules | have always orientation set to Orientation.NONE. | - default argument value in constructor: Orientation.NOT_SET .. _Molecule__pos2d: pos2d: List[float] ------------------ | Set only for surface molecules. Position on a wall in UV coordinates | relative to the triangle of the wall. | - default argument value in constructor: None .. _Molecule__geometry_object: geometry_object: GeometryObject ------------------------------- | Set only for surface molecules. | Is set to a reference to the geometry object on whose surface is the molecule located. | - default argument value in constructor: None .. _Molecule__wall_index: wall_index: int --------------- | Set only for surface molecules. | Index of wall belonging to the geometry_object where is the | molecule located. | - default argument value in constructor: -1 Methods: ********* .. _Molecule__remove: remove () --------- | Removes this molecule from simulation. Any subsequent modifications | of this molecule won't have any effect. | Example: `1920_molecule_remove/model.py `_ Wall ==== Constant representation of wall of a geometry object. Changes through changing attributes of this object are not allowed except for the attribute is_movable. Example: `1330_get_wall/model.py `_ Attributes: *********** .. _Wall__geometry_object: geometry_object: GeometryObject ------------------------------- | Object to which this wall belongs. .. _Wall__wall_index: wall_index: int --------------- | Index of this wall in the object to which this wall belongs. .. _Wall__vertices: vertices: List[List[float]] --------------------------- | Vertices of the triangle that represents this wall. .. _Wall__area: area: float ----------- | Area of the wall in um^2. .. _Wall__unit_normal: unit_normal: List[float] ------------------------ | Normal of this wall with unit length of 1 um. | There is also a method Model.get_wall_unit_normal that allows to | retrieve just the normal value without the need to prepare this | whole Wall object. .. _Wall__is_movable: is_movable: bool ---------------- | If True, whis wall can be moved through Model.apply_vertex_moves, | if False, wall moves are ignored. | Can be set during simulation. | - default argument value in constructor: True WallWallHitInfo =============== This class is used in the return type of Model.apply_vertex_moves. Contains pair of walls that collided. Example: `1515_tetrahedron_box_collision_moving_3_w_wall_wall_hit/model.py `_ Attributes: *********** .. _WallWallHitInfo__wall1: wall1: Wall ----------- | First colliding wall. .. _WallWallHitInfo__wall2: wall2: Wall ----------- | Second colliding wall.