cellblender_initialization.py

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# <pep8 compliant>

"""
This file contains the classes for CellBlender's Reactions.

"""

import cellblender

# blender imports
import bpy
from bpy.props import BoolProperty, CollectionProperty, EnumProperty, \
                      FloatProperty, FloatVectorProperty, IntProperty, \
                      IntVectorProperty, PointerProperty, StringProperty

#from bpy.app.handlers import persistent
#import math
#import mathutils

# python imports
import re

# CellBlender imports
import cellblender
from . import parameter_system
from . import cellblender_utils



class MCellInitializationPropertyGroup(bpy.types.PropertyGroup):

    def __init__(self):
        print ( "\n\nMCellInitializationPropertyGroup.__init__() called\n\n" )

    iterations: PointerProperty ( name="iterations", type=parameter_system.Parameter_Reference )
    time_step:  PointerProperty ( name="Time Step", type=parameter_system.Parameter_Reference )

    status: StringProperty(name="Status")
    advanced: BoolProperty(default=False)
    warnings: BoolProperty(default=False)
    notifications: BoolProperty(default=False)

    # Advanced/Optional Commands

    time_step_max: PointerProperty ( name="Time Step Max", type=parameter_system.Parameter_Reference )
    space_step: PointerProperty ( name="Space Step", type=parameter_system.Parameter_Reference )
    interaction_radius: PointerProperty ( name="Interaction Radius", type=parameter_system.Parameter_Reference )
    radial_directions: PointerProperty ( name="Radial Directions", type=parameter_system.Parameter_Reference )
    radial_subdivisions: PointerProperty ( name="Radial Subdivisions", type=parameter_system.Parameter_Reference )
    vacancy_search_distance: PointerProperty ( name="Radial Subdivisions", type=parameter_system.Parameter_Reference )
    surface_grid_density: PointerProperty ( name="Surface Grid Density", type=parameter_system.Parameter_Reference )

    command_options: StringProperty(name="Command Options", default="")

    def init_properties ( self, parameter_system ):
        helptext = "Number of iterations to run"
        self.iterations.init_ref    ( parameter_system,
                                      user_name="Iterations",
                                      user_expr="1000",
                                      user_units="",
                                      user_descr=helptext,
                                      user_int=True )

        helptext = "Simulation Time Step\n1e-6 is a common value."
        self.time_step.init_ref     ( parameter_system,
                                      user_name="Time Step",
                                      user_expr="1e-6",
                                      user_units="seconds",
                                      user_descr=helptext )

        helptext = """The longest possible time step.  MCell3 will move longer
than the specified simulation time step if it seems safe. This command makes
sure that the longest possible time step is no longer than this value (in
seconds), even if MCell3 thinks a longer step would be safe.  The default is no
limit."""
        self.time_step_max.init_ref ( parameter_system,
                                      user_name="Maximum Time Step",
                                      user_expr="",
                                      user_units="seconds",
                                      user_descr=helptext )

        helptext = """Have molecules take the same mean diffusion distance.
Have all diffusing molecules take time steps of different duration, chosen so
that the mean diffusion distance is N microns for each molecule. By default,
all molecules move the same time step."""
        self.space_step.init_ref    ( parameter_system,
                                      user_name="Space Step",
                                      user_expr="",
                                      user_units="microns",
                                      user_descr=helptext )

        helptext = """Diffusing Volume Molecules will interact when they get
within N microns of each other. The default is:  1 / sqrt(Pi *
SurfaceGridDensity)"""
        self.interaction_radius.init_ref ( parameter_system,
                                           user_name="Interaction Radius",
                                           user_expr="", user_units="microns",
                                           user_descr=helptext )

        helptext = """Specifies how many different directions to put in the
lookup table.  The default is sensible. Don’t use this unless you know what
you’re doing.  Instead of a number, you can specify FULLY_RANDOM in MDL to
generate the directions directly from double precision numbers (but this is
slower)."""
        self.radial_directions.init_ref   ( parameter_system,
                                            user_name="Radial Directions",
                                            user_expr="", user_units="microns",
                                            user_descr=helptext )

        helptext = """Specifies how many distances to put in the diffusion
look-up table. The default is sensible. FULLY_RANDOM is not implemented."""
        self.radial_subdivisions.init_ref ( parameter_system,
                                            user_name="Radial Subdivisions",
                                            user_expr="",
                                            user_descr=helptext )

        helptext = """Surface molecule products can be created at r distance.
Normally, a reaction will not proceed on a surface unless there is room to
place all products on the single grid element where the reaction is initiated.
By increasing r from its default value of 0, one can specify how far from the
reaction’s location, in microns, the reaction can place its products. To be
useful, r must be larger than the longest axis of the grid element on the
triangle in question. The reaction will then proceed if there is room to place
its products within a radius r, and will place those products as close as
possible to the place where the reaction occurs (deterministically, so
small-scale directional bias is possible)."""
        self.vacancy_search_distance.init_ref ( parameter_system,
                                                user_name="Vacancy Search Distance",
                                                user_expr="",
                                                user_units="microns",
                                                user_descr=helptext )

        helptext = """Number of molecules that can be stored per square micron.
Tile all surfaces so that they can hold molecules at N different positions per
square micron. The default is 10000. For backwards compatibility,
EFFECTOR_GRID_DENSITY works also in MCell MDL."""
        self.surface_grid_density.init_ref ( parameter_system,
                                             user_name="Surface Grid Density",
                                             user_expr="10000",
                                             user_units="count / sq micron",
                                             user_descr=helptext )

    def remove_properties ( self, context ):
        ps = context.scene.mcell.parameter_system
        # It's not needed to remove these properties because there is only one copy? Mostly yes.

        # It appears that removing some of the "original 16" panel parameters causes a problem.
        # This was fixed by commenting out the removal code. However, that causes some of the
        # other "original 16" to be recreated when reading from a data model (or using the
        # "Clear Project" scripting button). These duplicate parameters appear to not be a
        # problem because the RNA properties only store a reference to the most current one.
        # However, they do leave a trail of ID property "ghosts" which show multiple versions
        # of the same panel parameters.

        # But if they were to be removed, here's what it would look like:
        """
        self.iterations.clear_ref ( ps )
        self.time_step.clear_ref ( ps )
        self.time_step_max.clear_ref ( ps )
        self.space_step.clear_ref ( ps )
        self.interaction_radius.clear_ref ( ps )
        self.radial_directions.clear_ref ( ps )
        self.radial_subdivisions.clear_ref ( ps )
        self.vacancy_search_distance.clear_ref ( ps )
        self.surface_grid_density.clear_ref ( ps )
        """


    def build_data_model_from_properties ( self, context ):
        mcell4_mode = context.scene.mcell.cellblender_preferences.mcell4_mode

        dm_dict = {}

        dm_dict['data_model_version'] = "DM_2017_11_18_0130"

        dm_dict['iterations'] = self.iterations.get_expr()
        dm_dict['time_step'] = self.time_step.get_expr()
        dm_dict['time_step_max'] = self.time_step_max.get_expr()
        dm_dict['space_step'] = self.space_step.get_expr()
        dm_dict['interaction_radius'] = self.interaction_radius.get_expr()
        dm_dict['radial_directions'] = self.radial_directions.get_expr()
        dm_dict['radial_subdivisions'] = self.radial_subdivisions.get_expr()
        dm_dict['vacancy_search_distance'] = self.vacancy_search_distance.get_expr()
        dm_dict['surface_grid_density'] = self.surface_grid_density.get_expr()
        dm_dict['microscopic_reversibility'] = str(self.microscopic_reversibility)
        dm_dict['accurate_3d_reactions'] = self.accurate_3d_reactions==True
        dm_dict['center_molecules_on_grid'] = self.center_molecules_grid==True
        dm_dict['export_all_ascii'] = self.export_all_ascii==True
        dm_dict['command_options'] = self.command_options

        notify_dict = {}
        notify_dict['all_notifications'] = str(self.all_notifications)
        notify_dict['species_reactions_report'] = self.species_reactions_report
        notify_dict['diffusion_constant_report'] = str(self.diffusion_constant_report)
        notify_dict['file_output_report'] = self.file_output_report==True
        notify_dict['final_summary'] = self.final_summary==True
        notify_dict['iteration_report'] = self.iteration_report==True
        notify_dict['partition_location_report'] = self.partition_location_report==True
        notify_dict['probability_report'] = str(self.probability_report)
        notify_dict['probability_report_threshold'] = "%g" % (self.probability_report_threshold)
        notify_dict['varying_probability_report'] = self.varying_probability_report==True
        notify_dict['progress_report'] = self.progress_report==True
        notify_dict['release_event_report'] = self.release_event_report==True
        notify_dict['molecule_collision_report'] = self.molecule_collision_report==True
        notify_dict['box_triangulation_report'] = False
        dm_dict['notifications'] = notify_dict

        warn_dict = {}
        warn_dict['all_warnings'] = str(self.all_warnings)
        warn_dict['large_molecular_displacement'] = str(self.large_molecular_displacement)
        warn_dict['degenerate_polygons'] = str(self.degenerate_polygons)
        if not mcell4_mode:
            warn_dict['high_reaction_probability'] = str(self.high_reaction_probability)
        else:
            warn_dict['high_reaction_probability'] = str(self.high_reaction_probability_mcell4)
        warn_dict['high_probability_threshold'] = "%g" % (self.high_probability_threshold)
        warn_dict['lifetime_too_short'] = str(self.lifetime_too_short)
        warn_dict['lifetime_threshold'] = str(self.lifetime_threshold)
        warn_dict['missed_reactions'] = str(self.missed_reactions)
        warn_dict['missed_reaction_threshold'] = "%g" % (self.missed_reaction_threshold)
        warn_dict['negative_diffusion_constant'] = str(self.negative_diffusion_constant)
        warn_dict['missing_surface_orientation'] = str(self.missing_surface_orientation)
        warn_dict['negative_reaction_rate'] = str(self.negative_reaction_rate)
        warn_dict['useless_volume_orientation'] = str(self.useless_volume_orientation)
        dm_dict['warnings'] = warn_dict

        return dm_dict


    @staticmethod
    def upgrade_data_model ( dm ):
        # Upgrade the data model as needed. Return updated data model or None if it can't be upgraded.
        print ( "------------------------->>> Upgrading MCellInitializationPropertyGroup Data Model" )
        if not ('data_model_version' in dm):
            # Make changes to move from unversioned to DM_2014_10_24_1638
            dm['data_model_version'] = "DM_2014_10_24_1638"

        if dm['data_model_version'] == "DM_2014_10_24_1638":
            # Change on November 18, 2017: Add the large_molecular_displacement field with the current MCell default of warning:
            dm['large_molecular_displacement'] = "WARNING"
            dm['data_model_version'] = "DM_2017_11_18_0130"

        if dm['data_model_version'] != "DM_2017_11_18_0130":
            data_model.flag_incompatible_data_model ( "Error: Unable to upgrade MCellInitializationPropertyGroup data model to current version." )
            return None

        return dm


    def build_properties_from_data_model ( self, context, dm_dict ):
        mcell4_mode = context.scene.mcell.cellblender_preferences.mcell4_mode
        
        print ( "Top of MCellInitializationPropertyGroup.build_properties_from_data_model" )

        if dm_dict['data_model_version'] != "DM_2017_11_18_0130":
            data_model.handle_incompatible_data_model ( "Error: Unable to upgrade MCellInitializationPropertyGroup data model to current version." )

        #__import__('code').interact(local={k: v for ns in (globals(), locals()) for k, v in ns.items()})

        if "iterations" in dm_dict: self.iterations.set_expr ( dm_dict["iterations"] )
        if "time_step" in dm_dict: self.time_step.set_expr ( dm_dict["time_step"] )
        if "time_step_max" in dm_dict: self.time_step_max.set_expr ( dm_dict["time_step_max"] )
        if "space_step" in dm_dict: self.space_step.set_expr ( dm_dict["space_step"] )
        if "interaction_radius" in dm_dict: self.interaction_radius.set_expr ( dm_dict["interaction_radius"] )
        if "radial_directions" in dm_dict: self.radial_directions.set_expr ( dm_dict["radial_directions"] )
        if "radial_subdivisions" in dm_dict: self.radial_subdivisions.set_expr ( dm_dict["radial_subdivisions"] )
        if "vacancy_search_distance" in dm_dict: self.vacancy_search_distance.set_expr ( dm_dict["vacancy_search_distance"] )
        if "surface_grid_density" in dm_dict: self.surface_grid_density.set_expr ( dm_dict["surface_grid_density"] )
        if "microscopic_reversibility" in dm_dict: self.microscopic_reversibility = dm_dict["microscopic_reversibility"]
        if "accurate_3d_reactions" in dm_dict: self.accurate_3d_reactions = dm_dict["accurate_3d_reactions"]
        if "center_molecules_on_grid" in dm_dict: self.center_molecules_grid = dm_dict["center_molecules_on_grid"]
        if "export_all_ascii" in dm_dict: self.export_all_ascii = dm_dict["export_all_ascii"]
        if "command_options" in dm_dict: self.command_options = dm_dict["command_options"]

        if "notifications" in dm_dict:
            note_dict = dm_dict['notifications']
            if "all_notifications" in note_dict: self.all_notifications = note_dict['all_notifications']
            if "diffusion_constant_report" in note_dict: self.diffusion_constant_report = note_dict['diffusion_constant_report']
            if "species_reactions_report" in note_dict: self.species_reactions_report = note_dict['species_reactions_report']
            if "file_output_report" in note_dict: self.file_output_report = note_dict['file_output_report']
            if "final_summary" in note_dict: self.final_summary = note_dict['final_summary']
            if "iteration_report" in note_dict: self.iteration_report = note_dict['iteration_report']
            if "partition_location_report" in note_dict: self.partition_location_report = note_dict['partition_location_report']
            if "probability_report" in note_dict: self.probability_report = note_dict['probability_report']
            if "probability_report_threshold" in note_dict: self.probability_report_threshold = float(note_dict['probability_report_threshold'])
            if "varying_probability_report" in note_dict: self.varying_probability_report = note_dict['varying_probability_report']
            if "progress_report" in note_dict: self.progress_report = note_dict['progress_report']
            if "release_event_report" in note_dict: self.release_event_report = note_dict['release_event_report']
            if "molecule_collision_report" in note_dict: self.molecule_collision_report = note_dict['molecule_collision_report']

        ##notify_dict[box_triangulation_report'] = False

        if "warnings" in dm_dict:
            warn_dict = dm_dict['warnings']
            if "all_warnings" in warn_dict: self.all_warnings = warn_dict['all_warnings']
            if "large_molecular_displacement" in warn_dict: self.large_molecular_displacement = warn_dict['large_molecular_displacement']
            if "degenerate_polygons" in warn_dict: self.degenerate_polygons = warn_dict['degenerate_polygons']
            if "high_reaction_probability" in warn_dict: 
                self.high_reaction_probability = warn_dict['high_reaction_probability']
                self.high_reaction_probability_mcell4 = warn_dict['high_reaction_probability']
            
            if "high_probability_threshold" in warn_dict: self.high_probability_threshold = float(warn_dict['high_probability_threshold'])
            if "lifetime_too_short" in warn_dict: self.lifetime_too_short = warn_dict['lifetime_too_short']
            if "lifetime_threshold" in warn_dict: self.lifetime_threshold = float(warn_dict['lifetime_threshold'])
            if "missed_reactions" in warn_dict: self.missed_reactions = warn_dict['missed_reactions']
            if "missed_reaction_threshold" in warn_dict: self.missed_reaction_threshold = float(warn_dict['missed_reaction_threshold'])
            if "negative_diffusion_constant" in warn_dict: self.negative_diffusion_constant = warn_dict['negative_diffusion_constant']
            if "missing_surface_orientation" in warn_dict: self.missing_surface_orientation = warn_dict['missing_surface_orientation']
            if "negative_reaction_rate" in warn_dict: self.negative_reaction_rate = warn_dict['negative_reaction_rate']
            if "useless_volume_orientation" in warn_dict: self.useless_volume_orientation = warn_dict['useless_volume_orientation']

        print ( "Bottom of MCellInitializationPropertyGroup.build_properties_from_data_model" )


    def check_properties_after_building ( self, context ):
        print ( "check_properties_after_building not implemented for " + str(self) )


    accurate_3d_reactions: BoolProperty(
        name="Accurate 3D Reaction",
        description="If selected, molecules will look through partitions to "
                    "react.",
        default=True)
    center_molecules_grid: BoolProperty(
        name="Center Molecules on Grid",
        description="If selected, surface molecules will be centered on the "
                    "grid.",
        default=False)


    microscopic_reversibility_enum = [
        ('ON', "On", ""),
        ('OFF', "Off", ""),
        ('SURFACE_ONLY', "Surface Only", ""),
        ('VOLUME_ONLY', "Volume Only", "")]
    microscopic_reversibility: EnumProperty(
        items=microscopic_reversibility_enum, name="Microscopic Reversibility",
        description="If false, more efficient but less accurate reactions",
        default='OFF')

    # Export all ascii
    export_all_ascii: BoolProperty(
        name="ASCII Molecule Files",
        description="Positions of all molecules are also exported in ASCII format",
        default=False)

    # Notifications
    all_notifications_enum = [
        ('INDIVIDUAL', "Set Individually", ""),
        ('ON', "On", ""),
        ('OFF', "Off", "")]
    all_notifications: EnumProperty(
        items=all_notifications_enum, name="All Notifications",
        description="If on/off, all notifications will be set to on/off "
                    "respectively.",
        default='INDIVIDUAL')
    diffusion_constant_report_enum = [
        ('BRIEF', "Brief", ""),
        ('ON', "On", ""),
        ('OFF', "Off", "")]
    diffusion_constant_report: EnumProperty(
        items=diffusion_constant_report_enum, name="Diffusion Constant Report",
        description="If brief, Mcell will report average diffusion distance "
                    "per step for each molecule.")
    species_reactions_report: BoolProperty( # MCell4-specific
        name="Species and Reactions Report",
        description="If enabled, MCell will generate report files containing information on species and reactions used during simulation.",
        default=False)
    file_output_report: BoolProperty(
        name="File Output Report",
        description="If selected, MCell will report every time that reaction "
                    "data is written.",
        default=False)
    final_summary: BoolProperty(
        name="Final Summary",
        description="If selected, MCell will report about the CPU time used",
        default=True)
    iteration_report: BoolProperty(
        name="Iteration Report",
        description="If selected, MCell will report how many iterations have "
                    "completed based on total.",
        default=True)
    partition_location_report: BoolProperty(
        name="Partition Location Report",
        description="If selected, the partition locations will be printed.",
        default=False)
    probability_report_enum = [
        ('ON', "On", ""),
        ('OFF', "Off", ""),
        ('THRESHOLD', "Threshold", "")]
    probability_report: EnumProperty(
        items=probability_report_enum, name="Probability Report", default='ON',
        description="If on, MCell will report reaction probabilites for each "
                    "reaction.")
    probability_report_threshold: FloatProperty(
        name="Threshold", min=0.0, max=1.0, precision=2)
    varying_probability_report: BoolProperty(
        name="Varying Probability Report",
        description="If selected, MCell will print out the reaction "
                    "probabilites for time-varying reaction.",
        default=True)
    progress_report: BoolProperty(
        name="Progress Report",
        description="If selected, MCell will print out messages indicating "
                    "which part of the simulation is underway.",
        default=True)
    release_event_report: BoolProperty(
        name="Release Event Report",
        description="If selected, MCell will print a message every time "
                    "molecules are released through a release site.",
        default=True)
    molecule_collision_report: BoolProperty(
        name="Molecule Collision Report",
        description="If selected, MCell will print the number of "
                    "bi/trimolecular collisions that occured.",
        default=False)


    # Warnings
    all_warnings_enum = [
        ('INDIVIDUAL', "Set Individually", ""),
        ('IGNORED', "Ignored", ""),
        ('WARNING', "Warning", ""),
        ('ERROR', "Error", "")]
    all_warnings: EnumProperty(
        items=all_warnings_enum, name="All Warnings",
        description="If not \"Set Individually\", all warnings will be set "
                    "the same.",
        default='INDIVIDUAL')
    large_molecular_displacement_enum = [
        ('IGNORED', "Ignored", ""),
        ('WARNING', "Warning", ""),
        ('ERROR', "Error", "")]
    large_molecular_displacement: EnumProperty(
        items=large_molecular_displacement_enum, name="Large Molecular Displacement",
        description="Generate warnings or errors for large molecular displacement.",
        default='WARNING')
    degenerate_polygons_enum = [
        ('IGNORED', "Ignored", ""),
        ('WARNING', "Warning", ""),
        ('ERROR', "Error", "")]
    degenerate_polygons: EnumProperty(
        items=degenerate_polygons_enum, name="Degenerate Polygons",
        description="Degenerate polygons have zero area and must be removed.",
        default='WARNING')
    high_reaction_probability_enum = [
        ('IGNORED', "Ignored", ""),
        ('WARNING', "Warning", ""),
        ('ERROR', "Error", "")]
    high_reaction_probability: EnumProperty(
        items=high_reaction_probability_enum, name="High Reaction Probability",
        description="Generate warnings or errors if probability reaches a "
                    "specified threshold.",
        default='IGNORED')
    high_reaction_probability_enum_mcell4 = [
        ('IGNORED', "Ignored", ""),
        ('WARNING', "Warning", "")]
    high_reaction_probability_mcell4: EnumProperty(
        items=high_reaction_probability_enum_mcell4, name="High Reaction Probability",
        description="Generate warnings if bimolecular reaction probability reaches 50%, "
            "warnings when reaction probability reaches 100% are always printed.",
        default='IGNORED')
    high_probability_threshold: FloatProperty(
        name="High Probability Threshold", min=0.0, max=1.0, default=1.0,
        precision=2)
    lifetime_too_short_enum = [
        ('IGNORED', "Ignored", ""),
        ('WARNING', "Warning", "")]
    lifetime_too_short: EnumProperty(
        items=lifetime_too_short_enum, name="Lifetime Too Short",
        description="Generate warning if molecules have short lifetimes.",
        default='WARNING')
    lifetime_threshold: IntProperty(
        name="Threshold", min=0, default=50)
    missed_reactions_enum = [
        ('IGNORED', "Ignored", ""),
        ('WARNING', "Warning", "")]
    missed_reactions: EnumProperty(
        items=missed_reactions_enum, name="Missed Reactions",
        description="Generate warning if there are missed reactions.",
        default='WARNING')
    missed_reaction_threshold: FloatProperty(
        name="Threshold", min=0.0, max=1.0, default=0.001,
        precision=4)
    negative_diffusion_constant_enum = [
        ('IGNORED', "Ignored", ""),
        ('WARNING', "Warning", ""),
        ('ERROR', "Error", "")]
    negative_diffusion_constant: EnumProperty(
        items=negative_diffusion_constant_enum,
        description="Diffusion constants cannot be negative and will be set "
                    "to zero.",
        name="Negative Diffusion Constant", default='WARNING')
    missing_surface_orientation_enum = [
        ('IGNORED', "Ignored", ""),
        ('WARNING', "Warning", ""),
        ('ERROR', "Error", "")]
    missing_surface_orientation: EnumProperty(
        items=missing_surface_orientation_enum,
        description="Generate errors/warnings if molecules are placed on "
                    "surfaces or reactions occur at surfaces without "
                    "specified orientation.",
        name="Missing Surface Orientation",
        default='ERROR')
    negative_reaction_rate_enum = [
        ('IGNORED', "Ignored", ""),
        ('WARNING', "Warning", ""),
        ('ERROR', "Error", "")]
    negative_reaction_rate: EnumProperty(
        items=negative_reaction_rate_enum, name="Negative Reaction Rate",
        description="Reaction rates cannot be negative and will be set "
                    "to zero.",
        default='WARNING')
    useless_volume_orientation_enum = [
        ('IGNORED', "Ignored", ""),
        ('WARNING', "Warning", ""),
        ('ERROR', "Error", "")]
    useless_volume_orientation: EnumProperty(
        items=useless_volume_orientation_enum,
        description="Generate errors/warnings if molecules are released in a "
                    "volume or reactions occur in a volume with specified "
                    "orientation.",
        name="Useless Volume Orientation", default='WARNING')


    acc3D_show_help: BoolProperty ( default=False, description="Toggle more information about this parameter" )
    center_on_grid_show_help: BoolProperty ( default=False, description="Toggle more information about this parameter" )
    micro_rev_show_help: BoolProperty ( default=False, description="Toggle more information about this parameter" )
    export_ascii_show_help: BoolProperty ( default=False, description="Toggle more information about this parameter" )
    command_options_show_help: BoolProperty ( default=False, description="Toggle more information about this parameter" )

    def draw_layout(self, context, layout):
        mcell = context.scene.mcell
        mcell4_mode = mcell.cellblender_preferences.mcell4_mode

        if not mcell.initialized:
            mcell.draw_uninitialized ( layout )
        else:
            ps = mcell.parameter_system
            self.iterations.draw(layout,ps)
            self.time_step.draw(layout,ps)


            # Note that the run_simulation panel is effectively being drawn in the middle of this model_initialization panel!!!
            mcell.run_simulation.draw_layout_queue(context,layout)


            # Advanced Options
            box = layout.box()
            row = box.row(align=True)
            row.alignment = 'LEFT'
            if self.advanced:
                row.prop(mcell.initialization, "advanced", icon='TRIA_DOWN',
                         text="Advanced Options", emboss=False)

                self.time_step_max.draw(box,ps)
                self.space_step.draw(box,ps)
                self.interaction_radius.draw(box,ps)
                if not mcell4_mode:
                    self.radial_directions.draw(box,ps)
                    self.radial_subdivisions.draw(box,ps)
                self.vacancy_search_distance.draw(box,ps)
                self.surface_grid_density.draw(box,ps)

                if not mcell4_mode:
                    helptext = """Specifies which method to use for computing 3D
molecule-molecule interactions. If value is TRUE, then molecules will look
through partition boundaries for potential interacting partners – this is
slower but more accurate. If boolean is FALSE, then molecule interaction disks
will be clipped at partition boundaries and probabilities adjusted to get the
correct rate – this is faster but can be less accurate. The default is TRUE."""
                    ps.draw_prop_with_help ( box, "Accurate 3D Reactions", mcell.initialization, "accurate_3d_reactions", "acc3D_show_help", self.acc3D_show_help, helptext )

                helptext = """If boolean is set to TRUE, then all molecules on
a surface will be located exactly at the center of their grid element. If
FALSE, the molecules will be randomly located when placed, and reactions will
take place at the location of the target (or the site of impact in the case of
3D molecule/surface reactions). The default is FALSE."""
                ps.draw_prop_with_help ( box, "Center Molecules on Grid", mcell.initialization, "center_molecules_grid", "center_on_grid_show_help", self.center_on_grid_show_help, helptext )

                if not mcell4_mode:
                    helptext = """If value is set to OFF, then binding- unbinding
reactions between molecules will be somewhat more efficient but may not be
accurate if the probability of binding is high (close to 1).  If ON, a more
computationally demanding routine will be used to make sure binding- unbinding
is more similar in both directions.  If value is set to SURFACE_ONLY or
VOLUME_ONLY, the more accurate routines will be used only for reactions at
surfaces or only for those in the volume. OFF is the default."""
                    ps.draw_prop_with_help ( box, "Microscopic Reversibility", mcell.initialization, "microscopic_reversibility", "micro_rev_show_help", self.micro_rev_show_help, helptext )

                helptext = """Generate visualization data in ASCII format. The default is OFF."""
                ps.draw_prop_with_help ( box, "ASCII Molecule Files", mcell.initialization, "export_all_ascii", "export_ascii_show_help", self.export_ascii_show_help, helptext )

                if not mcell4_mode:
                    helptext = "Command Line Parameters - \n" \
                               "These options are passed directly to the program.\n" \
                               "Use -h to print MCell's help to console or text overlay.\n" \
                               "Visualization options (-z) are defined in viz_output.c.\n" \
                               "\n" \
                               "  0x01=All_components_share_name\n" \
                               "  0x02=All_components_by_global_name\n" \
                               "  0x03=All_components_by_mol_comp_name\n" \
                               "  0x08=Force_output_of_proxy_molecules\n" \
                               "  0x10=Generate_Text_BNGL_Viz_Files\n" \
                               "  0x20=Generate_JSON_BNGL_Viz_Files\n" \
                               "\n" \
                               "Debug output with -d # (between 0 and 100)"
                    ps.draw_prop_with_help ( box, "Command Options", mcell.initialization, "command_options", "command_options_show_help", self.command_options_show_help, helptext )

            else:
                row.prop(mcell.initialization, "advanced", icon='TRIA_RIGHT',
                         text="Advanced Options", emboss=False)

            # Notifications
            box = layout.box()
            row = box.row(align=True)
            row.alignment = 'LEFT'
            if self.notifications:
                row.prop(mcell.initialization, "notifications", icon='TRIA_DOWN',
                         text="Notifications", emboss=False)
                if not mcell4_mode:
                    row = box.row()
                    row.prop(mcell.initialization, "all_notifications")
                if self.all_notifications == 'INDIVIDUAL':
                    if not mcell4_mode:
                        row = box.row(align=True)
                        row.prop(mcell.initialization, "probability_report")
                        if self.probability_report == 'THRESHOLD':
                            row.prop(
                                mcell.initialization, "probability_report_threshold",
                                slider=True)
                    
                        row = box.row()
                        row.prop(mcell.initialization, "diffusion_constant_report")

                    if mcell4_mode:
                        row = box.row()
                        row.prop(mcell.initialization, "species_reactions_report")
                    
                    if not mcell4_mode:
                        row = box.row()
                        row.prop(mcell.initialization, "file_output_report")
                        row = box.row()
                        row.prop(mcell.initialization, "final_summary")
                        row = box.row()
                        row.prop(mcell.initialization, "iteration_report")
                        row = box.row()
                        row.prop(mcell.initialization, "partition_location_report")
                        
                    row = box.row()
                    row.prop(mcell.initialization, "varying_probability_report")
                        
                    if not mcell4_mode:
                        row = box.row()
                        row.prop(mcell.initialization, "progress_report")
                        row = box.row()
                        row.prop(mcell.initialization, "release_event_report")
                        row = box.row()
                        row.prop(mcell.initialization, "molecule_collision_report")
            else:
                row.prop(mcell.initialization, "notifications", icon='TRIA_RIGHT',
                         text="Notifications", emboss=False)

            # Warnings
            box = layout.box()
            row = box.row(align=True)
            row.alignment = 'LEFT'
            if self.warnings:
                row.prop(mcell.initialization, "warnings", icon='TRIA_DOWN',
                         text="Warnings", emboss=False)
                row = box.row()
                if not mcell4_mode:
                    row.prop(mcell.initialization, "all_warnings")
                    if self.all_warnings == 'INDIVIDUAL':
                        row = box.row()
                        row.prop(mcell.initialization, "large_molecular_displacement")
                        row = box.row()
                        row.prop(mcell.initialization, "degenerate_polygons")
                        row = box.row()
                        row.prop(mcell.initialization, "missing_surface_orientation")
                        row = box.row()
                        row.prop(mcell.initialization, "negative_diffusion_constant")
                        row = box.row()
                        row.prop(mcell.initialization, "negative_reaction_rate")
                        row = box.row()
                        row.prop(mcell.initialization, "useless_volume_orientation")
                        row = box.row(align=True)
                        row.prop(mcell.initialization, "high_reaction_probability")
                        if self.high_reaction_probability != 'IGNORED':
                            row.prop(mcell.initialization,
                                     "high_probability_threshold", slider=True)
                        row = box.row(align=True)
                        row.prop(mcell.initialization, "lifetime_too_short")
                        if self.lifetime_too_short == 'WARNING':
                            row.prop(mcell.initialization, "lifetime_threshold")
                        row = box.row(align=True)
                        row.prop(mcell.initialization, "missed_reactions")
                        if self.missed_reactions == 'WARNING':
                            row.prop(mcell.initialization, "missed_reaction_threshold")
                else: # mcell4   
                    row = box.row()
                    row.prop(mcell.initialization, "high_reaction_probability_mcell4")
            else:
                row.prop(mcell.initialization, "warnings", icon='TRIA_RIGHT',
                         text="Warnings", emboss=False)                    
            if (self.status != ""):
                row = layout.row()
                row.label(text=self.status, icon='ERROR')


    def draw_panel ( self, context, panel ):
        """ Create a layout from the panel and draw into it """
        layout = panel.layout
        self.draw_layout ( context, layout )


classes = (
            MCellInitializationPropertyGroup,
          )

def register():
    for cls in classes:
      bpy.utils.register_class(cls)

def unregister():
    for cls in reversed(classes):
      bpy.utils.unregister_class(cls)