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