.. _api-constants: ******************* Enums and Constants ******************* Orientation =========== | Orientation of a Complex. * | **DOWN** = -1 * | **NONE** = 0 * | **UP** = 1 * | **NOT_SET** = 2 * | **ANY** = 3 * | **DEFAULT** = 4 | Value DEFAULT means NONE for volume complexes and UP for surface complexes. Notification ============ * | **NONE** = 0 * | **BRIEF** = 1 * | **FULL** = 2 WarningLevel ============ * | **IGNORE** = 0 | Do something sensible and continue silently. * | **WARNING** = 1 | Do something sensible but emit a warning message. * | **ERROR** = 2 | Treat the warning as an error and stop. VizMode ======= * | **ASCII** = 0 | Readable molecule visualization output. * | **CELLBLENDER_V1** = 1 | Binary molecule visualization output used by MCell3, format v1. | Allows only limited length of species name (256 chars) and | does not contain molecule IDs. * | **CELLBLENDER** = 2 | Binary molecule visualization output, format v2. Shape ===== * | **UNSET** = 0 * | **SPHERICAL** = 1 * | **REGION_EXPR** = 2 * | **LIST** = 3 * | **COMPARTMENT** = 4 SurfacePropertyType =================== * | **UNSET** = 0 * | **REACTIVE** = 1 | This surface class does not do anything by itself, but it can be used as a reactant in | reaction rules. * | **REFLECTIVE** = 2 | If used as a surface property for a volume molecule it is reflected by any surface with | this surface class. This is the default behavior for volume molecules. | If used for a surface molecule it is reflected by the border of the | surface with this surface class. | Setting orientation in affected_complex_pattern allows selective reflection of volume | molecules from only the front or back of a surface or selective reflection of surface | molecules with only a certain orientation from the surface’s border. | Using m.ALL_MOLECULES as affected_complex_pattern has the effect that all | volume molecules are reflected by surfaces with this surface class and all surface molecules | are reflected by the border of the surfaces with this surface class. | Using m.ALL_VOLUME_MOLECULES as affected_complex_pattern has the effect that all | volume molecules are reflected by surfaces with this surface class. | Using m.ALL_SURFACE_MOLECULES as affected_complex_pattern has the effect that all | surface molecules are reflected by the border of the surface with this surface class. * | **TRANSPARENT** = 3 | If used as a surface property for a volume molecule it passes through all surfaces with | this surface class. | If used for a surface molecule it passes through the border of the surface with this surface | class. This is the default behavior for surface molecules. | Setting orientation in affected_complex_pattern allows selective transparency of volume | molecules from only the front or back of a surface or selective transparency for surface | molecules with only a certain orientation from the surface’s border. | To make a surface with this surface class transparent to all volume molecules, | use m.ALL_VOLUME_MOLECULES for affected_complex_pattern. | To make a border of the surface with this surface class transparent to all surface molecules, | use m.ALL_SURFACE_MOLECULES for the affected_complex_pattern. | Using m.ALL_MOLECULES for affected_complex_pattern has the effect that surfaces with this surface class | are transparent to all volume molecules and borders of the surfaces with this surface class are | transparent to all surface molecules. * | **ABSORPTIVE** = 4 | If affected_complex_pattern refers to a volume molecule it is destroyed if it touches surfaces with this surface class. | If affected_complex_pattern refers to a surface molecule it is destroyed if it touches the border of the surface with | this surface class, i.e., it is allowed to release surface molecules on absorptive surfaces, they get destroyed only | when they touch the border of this surface. | Tick marks on name allow destruction from only one side of the surface for volume molecules or selective destruction | for surface molecules on the surfaces’s border based on their orientation. | To make a surface with this surface class absorptive to all volume molecules, m.ALL_VOLUME_MOLECULES | can be used for affected_complex_pattern. | To make a border of the surface with this surface class absorptive to all surface molecules, | m.ALL_SURFACE_MOLECULES can be used for name. | Using m.ALL_MOLECULES as affected_complex_pattern has the effect that surfaces with this surface | class are absorptive for all volume molecules and borders of the surfaces with this surface class | are absorptive for all surface molecules. * | **CONCENTRATION_CLAMP** = 5 | Clamps concentration at a surface by periodically releasing molecules that correspond | to the wall being a transparent boundary to the area with given concentration, | and by absorbing all molecules that hit this surface. | The molecules matching affected_complex_pattern are destroyed if they touch the surface (as if they | had passed through), and new molecules are created at the surface, as if molecules had passed through | from the other side at a concentration value (units = M). | Orientation marks may be used; in this case, the other side of the surface is reflective. | Note that this command is only used to set the effective concentration of a volume molecule at a surface; | it is not valid to specify a surface molecule. * | **FLUX_CLAMP** = 6 | Clamps flux at a surface by periodically releasing molecules that correspond | to the wall being a transparent boundary to the area with given concentration. | The clamped surface reflects these molecules. ExprNodeType ============ | Used internally to represent expression trees. * | **UNSET** = 0 * | **LEAF** = 1 * | **ADD** = 2 * | **SUB** = 3 RegionNodeType ============== | Used internally to represent region trees. * | **UNSET** = 0 * | **LEAF_GEOMETRY_OBJECT** = 1 * | **LEAF_SURFACE_REGION** = 2 * | **UNION** = 3 * | **DIFFERENCE** = 4 * | **INTERSECT** = 5 ReactionType ============ | Used in reaction callbacks. * | **UNSET** = 0 * | **UNIMOL_VOLUME** = 1 * | **UNIMOL_SURFACE** = 2 * | **VOLUME_VOLUME** = 3 * | **VOLUME_SURFACE** = 4 * | **SURFACE_SURFACE** = 5 MoleculeType ============ | Used in molecule introspection and internally in checkpointing. * | **UNSET** = 0 * | **VOLUME** = 1 * | **SURFACE** = 2 BNGSimulationMethod =================== | Specifies simulation method in exported BNGL, used in Model.export_to_bngl. * | **NONE** = 0 * | **ODE** = 1 * | **SSA** = 2 * | **PLA** = 3 * | **NF** = 4 CountOutputFormat ================= * | **UNSET** = 0 | Invalid value. * | **AUTOMATIC_FROM_EXTENSION** = 1 | Output format is determined fom extension - .dat selects DAT file format | and .gdat selects GDAT file format. * | **DAT** = 2 | A two-column file with columns time and observable value is created. | Each count must have its own unique file name. * | **GDAT** = 3 | A multi-column file with time and observable values is created. | The first line of the file is a header that starts with a comment | character followed by time and then by the observable names. | The order of observables is given by the order in which they were added | to the model. | Can specify the same output file name for multiple observables. Constants ========= * | **STATE_UNSET**: str = STATE_UNSET * | **STATE_UNSET_INT**: int = -1 * | **BOND_UNBOUND**: int = -1 | Represents cases when a component must not be bound in a pattern. * | **BOND_BOUND**: int = -2 | Represents bond type !+ in a pattern. * | **BOND_ANY**: int = -3 | Represents bond type !? in a pattern. * | **PARTITION_EDGE_EXTRA_MARGIN_UM**: float = 0.01 | Internal constant used to match partition setup when comparing models against their MDL variant. * | **DEFAULT_COUNT_BUFFER_SIZE**: int = 100 | Internal constant used to initialize buffer size for molecule and reaction counts. * | **ALL_MOLECULES**: str = ALL_MOLECULES * | **ALL_VOLUME_MOLECULES**: str = ALL_VOLUME_MOLECULES * | **ALL_SURFACE_MOLECULES**: str = ALL_SURFACE_MOLECULES * | **DEFAULT_CHECKPOINTS_DIR**: str = checkpoints * | **DEFAULT_SEED_DIR_PREFIX**: str = seed_ * | **DEFAULT_SEED_DIR_DIGITS**: int = 5 * | **DEFAULT_ITERATION_DIR_PREFIX**: str = it_ * | **AllMolecules**: Species = AllMolecules * | **AllVolumeMolecules**: Species = AllVolumeMolecules * | **AllSurfaceMolecules**: Species = AllSurfaceMolecules * | **ID_INVALID**: int = -1 * | **NUMBER_OF_TRAINS_UNLIMITED**: int = -1 * | **TIME_INFINITY**: float = 1e140 * | **INT_UNSET**: int = INT32_MAX | This is a special integer value that means that an argument was not set, | its value is 2147483647. * | **FLT_UNSET**: float = FLT_MAX | This is a special floating-point value that means that an argument was not set, | its value is 3.40282346638528859812e+38F. * | **RNG_SIZE**: int = 256 | Size of arrays of