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CaGe.ini
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CaGe.ini
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# CaGe, the Chemical & abstract Graph environment
#
# - configuration file -
# There is a substitution mechanism for configuration values --
# substitutions start with $, then some opening bracket, then the
# corresponding closing bracket.
#
# To substitute environment variables, such as PATH, use the format
# (e.g.) ${PATH} for PATH, the braces {} are required.
#
# To substitute Java system properties, use angle brackets [] -- note:
# the 'cage.sh' script tries to set a system property called CaGe.InstallDir
# to the installation directory.
#
# To substitute other configuration values from this file, use parentheses ()
# -- be sure to avoid circular substitutions.
# If this is true (or yes or 1), let user edit generator and embedder commands
# and suppress the warning about Rasmol's unreliability.
CaGe.ExpertMode: false
# If this is true (or yes or 1), print detailed information to standard error.
CaGe.DebugMode: false
# In the following settings (those starting with "CaGe."), three
# directories are frequently mentioned:
# - The "install directory", where CaGe is installed (this very file
# is in the install directory). 'cage.sh' finds out where this is and
# creates a system property that contains an absolute path to it.
# This is used wherever $[CaGe.InstallDir] is mentioned in this file.
# (Should CaGe not find out its install directory, which we only
# expect if CaGe is not started by the "cage.sh" script, the
# start directory is assumed to be the install directory.)
# - The "start directory", from where the call to start CaGe is issued.
# - "RunDir", which CaGe subprocesses change into before generators and
# embedders are run, and where CaGe also looks for files to read or save.
# This is the next configuration option in this file.
# Keep these three places in mind and don't be confused by the fact
# that by default, RunDir is set to "." which makes it equal to the
# start directory.
# RunDir is where generator and embedder processes are run --
# saved data files, log or error output files are also found here.
# - This directory is relative to the start directory (cf. above).
# - The default "." is probably what users expect -- they can save
# files and after finishing CaGe will find them in the directory
# where they made the call. The programmer would however recommend
# some absolute location below the install directory, as CaGe can
# create quite a few files with quite long names rather quickly.
# The installation includes an empty subdirectory called "Data"
# and here, commented out, is a setting for RunDir that uses it.
# CaGe.Generators.RunDir: $[CaGe.InstallDir]/Data
CaGe.Generators.RunDir: .
# The search path used for generator and embedder processes, as well as
# any other pipes started by entering file names starting with '|'.
# - Separate path entries by space, not by ':' or ';' or whatever.
# - The search path is relative to RunDir, not to the start directory.
CaGe.Generators.Path: $[CaGe.InstallDir]/Generators ${PATH}
# A file for generators' stderr output, relative to the start directory.
# CaGe tries to delete this at the end, even if no generator was ever run.
# If you ever want to keep a generator's stderr output, copy or move this
# file before starting another generator or exiting CaGe.
CaGe.Generators.ErrFile: $(CaGe.Generators.RunDir)/generation.log
# LibDir is the directory where the Java native libraries are stored --
# actually not directly there, but in a subdirectory whose name is
# returned by the method SysInfo.get("os.name").
# You won't normally have to change this value.
# LibDir must not contain ${...} substitutions.
CaGe.Native.LibDir: $[CaGe.InstallDir]/Native
# The number of digits to expect in a graph number.
CaGe.GraphNoDigits: 6
# Should the settings in steps 2 (generator options) and 3 (output options)
# be remembered? (output options seperately for each generator)
CaGe.RememberSettings: true
# The number of graphs and the maximum time (in milliseconds)
# after which the graph number in the results window should be updated
# while "flowing".
CaGe.GraphNoFireInterval.Foreground: 100
CaGe.GraphNoFirePeriod.Foreground: 1000
# The same for background tasks.
CaGe.GraphNoFireInterval.Background: 10
CaGe.GraphNoFirePeriod.Background: 10000
# The output formats known to CaGe.
CaGe.Writers.2D: Writegraph CML
CaGe.Writers.3D: Writegraph CML PDB OFF Spinput Scad
CaGe.Writers.Adjacency: Planar Writegraph
# The cage.writer.WriterFactory class creates writers
# out of these format - by searching for classes named
# cage.writer.[Native?]<format>Writer extending cage.writer.CaGeWriter,
# or <format> itself as a class name.
# Embedding type factories
# These classes should implement cage.EmbeddingTypeFactory
# Each factory may return an unlimited number of embedding types.
CaGe.EmbeddingTypeFactory: cage.CaGeEmbeddingTypeFactory
# The generators used by CaGe.
CaGe.Generators: ThreeRegularPlaneGraphs FourRegularPlaneGraphs HCgen TubesCones PlantriT PlantriQ PlantriP External
# Each entry in this list must be further described in this file -
# caution: the same "name space" is used here for generators and viewers.
# Each generator must be desribed futher by a set of options named
# after the generator -- here are the required options:
# - its title in the selection window
##Fullgen.Title: general fullerenes
# - the Java class that communicates the generator's options to CaGe
# (must extend CaGe.GeneratorPanel)
##Fullgen.ConfigPanel: cage.generator.FullgenPanel
# - 2D and 3D viewers suitable for this generator
##Fullgen.Viewers.2D: TwoView
##Fullgen.Viewers.3D: CaGeJmolViewer RasmolViewer
# - "xD" viewers are displayed for both 2D and 3D
##Fullgen.Viewers.xD: TextViewer
# The three viewer lists must be present even if empty.
TubesCones.Title: tubes, cones and joins
TubesCones.ConfigPanel: cage.generator.TubesConesPanel
TubesCones.Viewers.2D: TwoView
TubesCones.Viewers.3D: CaGeJmolViewer RasmolViewer
TubesCones.Viewers.xD: TextViewer
ThreeRegularPlaneGraphs.Title: 3-regular plane graphs
ThreeRegularPlaneGraphs.ConfigPanel: cage.generator.ThreeRegularPlaneGraphsPanel
ThreeRegularPlaneGraphs.Viewers.2D: TwoView
ThreeRegularPlaneGraphs.Viewers.3D: CaGeJmolViewer RasmolViewer
ThreeRegularPlaneGraphs.Viewers.xD: TextViewer
FourRegularPlaneGraphs.Title: 4-regular plane graphs
FourRegularPlaneGraphs.ConfigPanel: cage.generator.FourRegularPlaneGraphsPanel
FourRegularPlaneGraphs.Viewers.2D: TwoView
FourRegularPlaneGraphs.Viewers.3D: CaGeJmolViewer RasmolViewer
FourRegularPlaneGraphs.Viewers.xD: TextViewer
HCgen.Title: hydrocarbons
HCgen.ConfigPanel: cage.generator.HCgenPanel
HCgen.Viewers.2D: TwoView
HCgen.Viewers.3D: CaGeJmolViewer RasmolViewer
HCgen.Viewers.xD: TextViewer
# This extra option is read by the HCgen generator panel.
# It affects the TwoView viewer's ability to react to mouse clicks
# inside a face, asking for a new embedding in which this face
# becomes the exterior one. The default for HCgen is false.
# For generators not having this option, expect the default to be true,
# but this actually depends on the generator panel's implementation.
HCgen.EnableReembed2D: false
PlantriT.Title: triangulations
PlantriT.ConfigPanel: cage.generator.TriangulationsPanel
PlantriT.Viewers.2D: TwoView
PlantriT.Viewers.3D: CaGeJmolViewer RasmolViewer
PlantriT.Viewers.xD: TextViewer
# See HCgen above for an explanation of this option.
PlantriT.Disk.EnableReembed2D: false
PlantriQ.Title: quadrangulations
PlantriQ.ConfigPanel: cage.generator.QuadrangulationsPanel
PlantriQ.Viewers.2D: TwoView
PlantriQ.Viewers.3D: CaGeJmolViewer RasmolViewer
PlantriQ.Viewers.xD: TextViewer
# See HCgen above for an explanation of this option.
PlantriQ.Disk.EnableReembed2D: false
PlantriP.Title: general plane graphs
PlantriP.ConfigPanel: cage.generator.GeneralPlaneGraphsPanel
PlantriP.Viewers.2D: TwoView
PlantriP.Viewers.3D: CaGeJmolViewer RasmolViewer
PlantriP.Viewers.xD: TextViewer
External.Title: external generator
External.ConfigPanel: cage.generator.ExternalPanel
External.Viewers.2D: TwoView
External.Viewers.3D: CaGeJmolViewer RasmolViewer
External.Viewers.xD: TextViewer
# A viewer -- again we need some more information about each one:
# - its Java class -- must implement cage.CaGeViewer
TextViewer.Class: cage.viewer.TextViewer
# - its name as used in the output selection window
TextViewer.Title: text viewer
# - more options may of course be used by the viewer itself
# The 3D viewer called "Jmol viewer" in CaGe.
CaGeJmolViewer.Class: cage.viewer.CaGeJmolViewer
CaGeJmolViewer.Title: Jmol Viewer
CaGeJmolViewer.Width: 550
CaGeJmolViewer.Height: 500
# CaGe's own 2D viewer.
TwoView.Class: cage.viewer.TwoView
TwoView.Title: TwoView
# The size of the TwoView diagram panel (the display without controls)
TwoView.Width: 550
TwoView.Height: 400
# Should vertex numbers be shown? If yes, TwoView might increase the
# vertex size until displaying numbers makes sense.
TwoView.ShowNumbers: false
# The default edge brightness (0.0 to 0.75)
TwoView.EdgeBrightness: 0.75
# The default edge width (0 to 9)
TwoView.EdgeWidth: 4
# The default vertex size (3 to 25)
TwoView.VertexSize: 11
# The following values are used in the PS code written by TwoView,
# they have no effect in the on-screen display. They are default
# values for the three colours used when painting vertices:
# the first two define the blending fill in the interior of vertex symbols,
# the third is the font colour of vertex numbers.
# The colour system used is RGB, values range from 0 to 1, 0 being "dark".
TwoView.VertexColor1: 1.0 0.650 0.395
TwoView.VertexColor2: 1.0 0.775 0.620
TwoView.VertexNumberColor: 0.25 0.25 1.0
# The following setting determines whether the PostScript output uses
# a gradient for the vertex color.
TwoView.PostScript.VertexGradient: false
# CaGe's rasmol integration.
RasmolViewer.Class: cage.viewer.RasmolViewer
RasmolViewer.Title: Rasmol
# the interval, in milliseconds, in which Rasmol's output
# is to be checked for questions requiring a user response
RasmolViewer.WatchInterval: 500
# Spinput writer configuration
# if the following property is set to true, then all vertices
# are of the same element type
Spinput.UseSingleElement: false
# if the property above is true, then the following two properties
# specify the specific element to use for each vertex
Spinput.ElementNumber: 6
Spinput.ElementName: C
# the next property specify the scaling that needs to be done.
# Each coordinate will be multiplied with this factor.
Spinput.scaling: 1.0
# Scad writer configuration
# The following property specifies the class for the default type
Scad.type: cage.writer.scad.BallStickType
# The next property specifies the default resolution to use for SCAD outputs
Scad.resolution: medium