/*
* $Header: /cx5/bioroot/rcs/catalyst/v450/source/agen_in/system.in,v 450.22 1999/05/18 21:34:13 hong Exp $
*
* System Configuration Variables
*/
privateColormap (boolean TRUE
"If set, Catalyst will use its own colormap rather than share the global one"
public)
displayLibrary (enum(automatic gl xlib) automatic
"Forces catalyst to use a particular display engine."
protected)
useOverlayMenus (boolean TRUE
"If set, Catalyst will place menus in overlay planes to prevent spurious redraws" public)
db.license.attempts (int(1 100) 5
"Number of times to attempt to get a
database before giving up." public)
db.file.extension (string ".bdb" "File type extension for big db files" private)
db.catdb (string "catDB.bdb" "File name for catDB config file" private)
db.userdb (string "StockroomDB" "Name of user database" private)
db.run1DFree (boolean FALSE
"Operate as though no 1D server/data is available at all." protected)
remoteRepository.timeout (int(1 *) 600
"Amount of time to wait for a remote server to respond to a request
for a remote resource (in seconds)." protected)
data.dir (string "catdata" "Subdirectory where Catalyst maintains data files" private)
units.distance (enum(picometers angstroms nanometers)
angstroms "Units for distance measurements" protected)
units.angle (enum(radians degrees)
degrees "Units for angle measurements" protected)
paradigm.mouseButtons(enum(ONEBUTTON THREEBUTTON) THREEBUTTON "Description" protected)
windowLayout(
enum("2D Top/3D Bottom"
"3D Top/2D Bottom"
"2D Left/3D Right"
"3D Left/2D Right"
"Small 2D at Top Left"
"Small 2D at Top Right"
"Small 2D at Bottom Left"
"Small 2D at Bottom Right"
"Small 3D at Top Left"
"Small 3D at Top Right"
"Small 3D at Bottom Left"
"Small 3D at Bottom Right"
"Only 2D"
"Only 3D")
"2D Left/3D Right" "Default window layout for multi-window workbenches" protected)
exportType.compound(
enum(CPD TPL SMI MOL SKC HIN MMOD MOL2)
CPD
"Default type for compound export" protected)
exportType.hypothesis(
enum(CHM)
CHM
"Default type for hypothesis export" protected)
exportType.spreadsheet(
enum(SPST ESP SD)
SPST
"Default type for spreadsheet export" protected)
importMOL.realCompoundNameProperty (string "Name"
"For MOL/SD import, what 1D property overrides header compound name"
protected)
importMOL.ignoreChiralityInSmiles (boolean TRUE
"For SD file import, if set to TRUE, will ignore the chirality in the canonical SMILES strings when using them to determine if conformers belong to the same compound. Set to FALSE for 400 behavior"
protected)
import.keepMolFileChirality (boolean FALSE
"For MDL files import, if TRUE, set chirality to known if it can be determined and when a compound has a single conformer. The default is set to FALSE, which is the 310 behavior"
protected)
import.useISISChirality (boolean TRUE
"For MDL files import, if TRUE, try and determine the chiralities as if the file is generated from ISIS"
protected)
import.transformToOrigin (boolean TRUE
"For MDL files import, if the variable is FALSE, no transformation to the origin of the imported geoms will be done. Setting the variable to TRUE will transform the geom to the origin. Setting the variable to TRUE will revert back to 310 behavior" protected)
import.doNotCreateQuery (boolean FALSE
"For MDL files import, if TRUE, would not create the query fragment. This will save some time if we know for sure that the .sd file is meant as compounds and not queries." protected)
importSMILES.explicitChirality (
boolean
FALSE
"If TRUE, SMILES import interprets @ and @@ to explicitly set chirality, overriding Catalyst default behavior which uses bond directions to imply chirality." protected)
export.ConvertToRGroupsMDLFormat (boolean TRUE
"For the Convert to R Groups command, if set to FALSE, will have Catalyst 310 behavior, that is, write out files in .msi format. The default is TRUE in Catalyst400, which writes out one large .sd file" protected)
export.SDMirrorConfs (boolean FALSE
"When exporting SD files from the ui or from catConf, export the mirror image of each conformation as well" protected)
export.alwaysReorient (boolean TRUE
"For exporting of MDL files, if the variable to TRUE (default for 400), the exported geoms will always be re-oriented so that what the user sees in the graphics area should be the confInst being exported. Setting the variable to FALSE will revert back to the 310 behavior" protected)
grid.type(enum(SQUARE HEXAGONAL TRIGONAL) HEXAGONAL
"Default grid style in 2D drawing windows" protected)
style.3d.rendering(
enum(WIRE
DOTS
MESH
TUBE
BALLTUBE
SPHEREROD
SPACEFILLING)
TUBE "Default rendering style in 3D Windows" protected)
style.3d.constraint(
enum(INVISIBLE
MESH
TRANSPARENT
SOLID
DOTS)
MESH "Default style for 3D constraints" protected)
style.3d.geomObject(
enum(INVISIBLE
MESH
TRANSPARENT
SOLID
DOTS)
MESH "Default style for 3D geometric objects" protected)
units.energy(
enum(KCALS
KJOULE)
KCALS "Energy will be presented in these units" protected)
maximumLabMenu(
int(0 50) 10 "If there are more than this number
of labs, the choice of lab in the save dialog will be displayed
as a list rather than a menu." public)
units.force(
enum(DYNES
NEWTONS)
DYNES "Force will be presented in these units" protected)
forceField.energyReport(enum(NONE VERBOSE) NONE "Debugging level for forceField"
protected)
forceField.paramReport(enum (NONE VERBOSE) NONE
"Enables the printing (to the log file) of all matched parameters." protected)
toolboxLayout(
enum(VERTICAL_TOOLBOX HORIZONTAL_TOOLBOX) HORIZONTAL_TOOLBOX
"Sets the layout for the toolbox as horizontal or vertical" protected)
paradigm.behavior(
enum(MOTIF OPENLOOK MACINTOSH) MACINTOSH "General interface style" protected)
ViewCompound.style.3d.rendering(
enum(WIRE
DOTS
MESH
TUBE
BALLTUBE
SPHEREROD
SPACEFILLING)
BALLTUBE "Graphic style in the View Compound Workbench" protected)
ViewCompound.style.3d.constraint(
from style.3d.constraint
"Style of constraints in View Compound Workbench")
ViewCompound.style.3d.geomObject(
from style.3d.geomObject
"Style of geometric objects in the View Compound Workbench")
ViewCompound.grid.type(from grid.type
"Default grid style in the View Compound Workbench")
ViewCompound.windowLayout(
enum("2D Top/3D Bottom"
"3D Top/2D Bottom"
"3D Left/2D Right"
"2D Left/3D Right"
"Small 2D at Top Left"
"Small 2D at Top Right"
"Small 2D at Bottom Left"
"Small 2D at Bottom Right"
"Small 3D at Top Left"
"Small 3D at Top Right"
"Small 3D at Bottom Left"
"Small 3D at Bottom Right"
"Only 2D"
"Only 3D")
"2D Left/3D Right" "Window layout in View Compound Workbench" protected)
ViewDatabase.style.3d.rendering(
enum(WIRE
DOTS
MESH
TUBE
BALLTUBE
SPHEREROD
SPACEFILLING)
TUBE "Geometric rendering style in the View Database Workbench" protected)
ViewDatabase.style.3d.constraint(
from style.3d.constraint
"Constraint style in View Database Workbench")
ViewDatabase.style.3d.geomObject(
from style.3d.geomObject
"Style of geometric objects in the View Database Workbench")
ViewDatabaseHit.style.3d.constraint(
from style.3d.constraint
"Style of constraints in View Database Hit Dialog")
ViewDatabaseHit.style.3d.geomObject(
from style.3d.geomObject
"Style of geometric objects in the View Database Hit Dialog")
GenerateHypo.style.3d.rendering(
enum(WIRE
DOTS
MESH
TUBE
BALLTUBE
SPHEREROD
SPACEFILLING)
TUBE "General style of rendering in the Generate Hypothesis Workbench" protected)
GenerateHypo.style.3d.constraint(
from style.3d.constraint
"Style of constraints in the Generate Hypothesis Workbench")
GenerateHypo.style.3d.geomObject(
from style.3d.geomObject
"Style of geometric objects in Generate Hypothesis Workbench")
GenerateHypo.overlay.colorize(
enum(BINARY SPECTRUM) SPECTRUM
"How to color overlays in the Generate Hypothesis Workbench" protected)
GenerateHypo.overlay.atomsToColor(
enum(ALL_ATOMS NON_HETERO_ATOMS NO_ATOMS)
NON_HETERO_ATOMS
"What atoms to color in overlays in the Generate Hypothesis Workbench"
protected)
ViewHypothesis.style.3d.rendering(
enum(WIRE
DOTS
MESH
TUBE
BALLTUBE
SPHEREROD
SPACEFILLING)
BALLTUBE "General style of 3D drawing in the View Hypothesis Workbench"
protected)
ViewHypothesis.style.3d.constraint(
from style.3d.constraint
"Style of constraints in the View Hypothesis Workbench")
ViewHypothesis.style.3d.geomObject(
from style.3d.geomObject
"Style of geometric objects in the View Hypothesis Workbench")
ViewHypothesis.windowLayout(
enum("2D Top/3D Bottom"
"3D Top/2D Bottom"
"3D Left/2D Right"
"2D Left/3D Right"
"Small 2D at Top Left"
"Small 2D at Top Right"
"Small 2D at Bottom Left"
"Small 2D at Bottom Right"
"Small 3D at Top Left"
"Small 3D at Top Right"
"Small 3D at Bottom Left"
"Small 3D at Bottom Right"
"Only 2D"
"Only 3D")
"Small 2D at Top Left" "Description" protected)
FuntionMapping.Hydrophobe.Ring.NoOtherHeavyAtom (boolean FALSE
"This is to address the problem that cyclohexanol ring of para-methyl-cyclohexanol mapped as a hydrophobe and para-ethyl-cyclohexanol does not" protected)
FuntionMapping.Hydrophobe.Ring.OtherHeavyAtom (int 1
"This is to address the problem that cyclohexanol ring of para-methyl-cyclohexanol mapped as a hydrophobe and para-ethyl-cyclohexanol does not" protected)
FunctionMapping.Hydrophobe.Ring.NoOtherHeavyAtom (boolean FALSE
"This is to address the problem that cyclohexanol ring of para-methyl-cyclohexanol mapped as a hydrophobe and para-ethyl-cyclohexanol does not" protected)
FunctionMapping.Hydrophobe.Ring.OtherHeavyAtom (int 1
"This is to address the problem that cyclohexanol ring of para-methyl-cyclohexanol mapped as a hydrophobe and para-ethyl-cyclohexanol does not" protected)
FunctionMapping.Hydrophobe.Ring.HydrophobicityLimit
(real 60.0 "This specifies the minimum value that the sum of the hydrophobicity values for each atom in a small ring (size 7 or less) has to exceed to be considered a hydrophobe. The value has to be larger than 0." protected)
FunctionMapping.Hydrophobe.Group.HydrophobicityLimit
(real 47.0 "This specifies the minimum value that the sum of the hydrophobicity values for each atom in a group has to exceed to be considered a hydrophobe. The value has to be larger than 0." protected)
FunctionMapping.Hydrophobe.Chain.HydrophobicityLimit
(real 100.0 "This specifies the minimum value that the sum of the hydrophobicity values for each atom in a chain group has to exceed to be considered a hydrophobe. The value has to be larger than 0." protected)
FunctionMapping.Hydrophobe.Neighbor.numBondLessEqualFromChargedAtom
(int 2 "Number of bonds, less than or equal to, from a charged atom. The allowed values are 0, 1, or 2." protected)
FunctionMapping.Hydrophobe.Neighbor.numBondLessEqualFromOHNH
(int 2 "Number of bonds, less than or equal to, from OH or NH with no delocalized electrons. The allowed values are 0, 1, or 2." protected)
FunctionMapping.Hydrophobe.Neighbor.numBondLessEqualFromSH
(int 1 "Number of bonds, less than or equal to, from SH with no delocalized electrons. The allowed values are 0 or 1." protected)
FunctionMapping.Hydrophobe.Neighbor.numBondLessEqualFromOWithDoubleBond
(int 2 "Number of bonds, less than or equal to, from O with double bond. The allowed values are 0, 1, or 2." protected)
FunctionMapping.Hydrophobe.Neighbor.numBondLessEqualFromSWithValLargerThanTwo
(int 1 "Number of bonds, less than or equal to, from S with valence > 2. The allowed values are 0 or 1." protected)
FunctionMapping.Hydrophobe.Atom.factorNNeighborsAwayFromOSS
(real 0.6
"Factor for atoms (1) n4+1 bonds away from O with double bond; (2) n5+1 bonds away from S with valence larger than 3; or (3) one bond away from S with double bond. n4 can be 0, 1, or 2, and can be set by the variable FunctionMapping.Hydrophobe.Neighbor.numBondLessEqualFromOWithDoubleBond. n5 can be 0 or 1 and can be set by the variable FunctionMapping.Hydrophobe.Neighbor.numBondLessEqualFromSWithValLargerThanTwo. The factor is to be larger than or equal to zero." protected)
FunctionMapping.Hydrophobe.Atom.factorOneNeighboringOOrN
(real 0.25
"Factor for atom with 1 neighboring O or N with no delocalized electrons. The factor is to be larger than or equal to zero." protected)
FunctionMapping.Hydrophobe.Atom.factorTwoOrMoreNeighboringOOrN
(real 0.0
"Factor for atom with 2 or more neighboring O or N with no delocalized electrons. The factor is to be larger than or equal to zero." protected)
lab.view.type(
enum(TEXTUAL SMALL_ICONS LARGE_ICONS)
TEXTUAL "Icon appearance inside Labs" protected)
date.format(
enum("7-20-1969"=1
"Jul-20-1969"=2
"July 20, 1969"=3
"20-7-1969"=-1
"20-Jul-1969"=-2
"20 July 1969"=-3)
"Jul-20-1969"
"Formatting preference of the user for dates within Catalyst" protected)
bin.dir
(string "$CATALYST_BIN"
"Directory containing programs and scripts for biocad system" private)
conf.dir
(string "$CATALYST_CONF"
"Directory containing configuration files for Catalyst" private)
wconf.dir
(string "$CATALYST_WCONF"
"Directory containing writable configuration files for Catalyst"
private)
binary.dir
(string "$CATALYST_DATA"
"Directory containing binary data files for Catalyst"
private)
selection.color
(color RGB(1.0 1.0 1.0)
"Controls the color of selected objects" protected)
selection.restore
(boolean TRUE
"Restores color of selected objects to normal" protected)
background.2d
(color RGB(0.78 0.78 0.78)
"Controls the background color in 2D graphics windows" protected)
background.3d
(color RGB(0.5 0.5 0.5)
"Controls the background color in 3D graphics windows" protected)
highlightColor.2d
(color RGB(1.0 0.204 0.0)
"Controls the color used for highlighting 2d objects" protected)
highlightColor.3d
(color RGB(1.0 0.8 0.0)
"Controls the color used for highlighting 3d objects" protected)
commandLine
(boolean FALSE
"Description" protected)
view.2d.atomLabels
(boolean FALSE
"Display atom labels in 2D window" protected)
view.2d.charges
(boolean TRUE
"Display charges in 2D Window" protected)
view.2d.chirality
(boolean TRUE
"Display chirality in 2D Window" protected)
view.2d.hydrogens
(boolean FALSE
"Display Hydrogens in 2D Window" protected)
view.2d.lonepairs
(boolean FALSE
"Display lone pairs in 2D Windows" protected)
view.2d.compoundName
(boolean FALSE
"Display compound names below drawing in 2D Windows" protected)
view.2d.constraintNames
(boolean FALSE
"Display constraint names in 2D Windows" protected)
view.2d.constraintTolerance
(boolean FALSE
"Display constraint tolerances in 2D Windows" protected)
view.2d.geomObjectNames
(boolean FALSE
"Display names of function/feature objects in 2D Windows" protected)
view.2d.monochrome
(boolean TRUE
"Render drawings in 2D Windows in monochrome" protected)
view.3d.atomLabels
(boolean FALSE
"Display atom labels in 3D Graphics Windows" protected)
view.3d.charges
(boolean TRUE
"Display charges in 3D Windows" protected)
view.3d.chirality
(boolean TRUE
"Display chirality in 3D Windows" protected)
view.3d.hydrogens
(boolean TRUE
"Display Hydrogens in 3D Graphics Windows" protected)
view.3d.lonepairs
(boolean FALSE
"Display lone pairs in 3D Graphics Windows" protected)
view.3d.compoundName
(boolean FALSE
"Display compound name below drawing in 3D Windows" protected)
view.3d.constraintNames
(boolean FALSE
"Display constraint names in 3D Graphics Windows" protected)
view.3d.constraintTolerance
(boolean FALSE
"Display constraint tolerances in 3D graphic windows" protected)
view.3d.geomObjectNames
(boolean FALSE
"Display names of features/blobs in 3D graphic windows" protected)
view.noCenter
(boolean FALSE
"If set to TRUE, do not tile the compounds and hypotheses in the display area by default. The 400 behavior is FALSE." protected)
grid
(boolean FALSE
"Display a grid in 2D Windows" protected)
grid.snap
(boolean FALSE
"Snap mouse input to grid in 2D Window" protected)
grid.spacing
(real 500.0
"Grid spacing (in picometers) of the 2D grid" protected)
rubberbandLength.2d
(real 90000.0
"Length of the 2D rubber band cursor (in picometers)" protected)
lineWidth.2d
(real 1.0
"Width of lines in 2D Windows" protected)
hashSpacing.2d
(real 1.0
"Distance between hash marks for hash style lines" protected)
bondSpacing.doubleBond.2d
(real 1.0
"Distance between lines for double bonds" protected)
bondSpacing.tripleBond.2d
(real 1.0
"Distance between lines for triple bonds" protected)
ball.size
(real 0.15
"Size of atoms in Ball/Tube representation as a percentage of Van Der Waals radius" protected)
sphere.size
(real 0.225
"Size of atoms in Sphere/Rod representation as a percentage of Van Der Waals radius" protected)
tube.ballTube.size
(real 0.05
"Default atom size as a percentage of Van Der Waals radius" protected)
tube.tube.size
(real 0.05
"Default bond radius for ball tube render style" protected)
rod.size
(real 0.10
"Default bond radius for sphere rod render style" protected)
rod.color
(color RGB(0.77 0.77 0.77)
"Default color for rods in sphere rod render style" protected)
constraint.transparency
(real 0.35
"Degree of transparency of constraints" protected)
geomObject.transparency
(real 0.35
"Degree of transparency for geometric objects" protected)
shape.transparency
(real 0.75
"Degree of transparency for shapes" protected)
minimize.energyConvergence
(real 1.0e-03
"Minimization will converge when the function change is less than this value (Joules)"
protected)
minimize.gradientConvergence
(real 0.05
"Minimization will converge when the gradient change is less than this value"
protected)
minimize.maxCycles
(int 100
"Estimated number of cycles to complete minimization (for UI purposes)"
protected)
forceField.filename
(string "$CATALYST_CONF/forceField.data"
"Force field data file" protected)
forceField.ignorePhase
(boolean FALSE
"Set all dihedral parameter phase terms equal to zero degrees."
protected)
forceField.dm.maxStressEnergy
(real 200.0
"Maximum stress energy the user is permitted to introduce." protected)
forceField.dm.stepSize
(real 0.30
"Single dynamic modeling step size in radians" protected)
forceField.dm.mouseScaleFactor
(real 7.5
"Scale factor for mouse motions contolling dynamic modeling." protected)
forceField.dm.displacementUpdate
(real 1.0
"Update nonbond pair list when total displacement greater than this." protected)
forceField.dm.iterationUpdate
(int 16
"Update nonbond pair list after this number of steps" protected)
forceField.dm.cartMinimizationCycles
(int 5
"Number of cartesian minimization cycles per dynamic modelling step" protected)
forceField.dm.torMinimizationCycles
(int 2
"Number of cartesian minimization cycles per dynamic modelling step" protected)
forceField.dm.nonBondCutOff
(real 500.0
"Nonbond cutoff parameter" protected)
forceField.dm.nonBondRadiusFactor
(real 1.00
"Nonbond radius factor" protected)
confAnalysis.minimizationCycles
(int 500
"Iteration count for structure generation" protected)
confAnalysis.poleHydrogenOnRingNitrogen
(boolean FALSE
"Add poling to H atom attached to a Nitrogen on a ring" protected)
confAnalysis.treatAcyclicNitrogenAsChiralCenter
(boolean FALSE
"Find conformers for both inversions of acyclic N atoms" protected)
confAnalysis.systematicFlipAxialEquatorial
(boolean TRUE
"Flip Axial/Equatorial substituents in rings systematically" protected)
confAnalysis.systematicFlipAxialEquatorialMinRingSize
(int 4
"Minimum ring size for checking Axial/Equatorial substituents" protected)
confAnalysis.systematicFlipAxialEquatorialMaxRingSize
(int 7
"Maximum ring size for checking Axial/Equatorial substituents" protected)
confAnalysis.dbstd
(boolean FALSE
"Set the Best confAnalysis to the dbstd method" protected)
confAnalysis.best.torsion.factor
(int 1
"Sets the number of minimization cycles in torsional space to 20 times this factor" protected)
confAnalysis.best.cg.factor
(int 3
"Sets the number of conjugate gradient minimization cycles in cartesian space to ku_max(1,((2*nCycles*cg.factor)/9))" protected)
confAnalysis.best.qn.factor
(int 1
"Sets the number of quasi newton minimization cycles in cartesian space to ku_max(0,(nCycles * cartQNFactor - nCGCycles))" protected)
confAnalysis.fast.printMarks
(int(0 *) 0
"Print a mark for this multiple of conformers generated." protected)
confAnalysis.fast.printProgress
(boolean FALSE
"Print info about progress of conformational analysis." protected)
confAnalysis.fast.printAlgorithmChange
(boolean FALSE
"Print out a message when switching algorithm from systematic search to others." protected)
confAnalysis.fast.minimizationCycles
(int(0 *) 10
"Iteration count for structure generation" protected)
confAnalysis.fast.granularity
(int 1
"Controls granularity for fast conformational analysis" protected)
confAnalysis.fast.minHoleSize
(real 70.0
"Convergence parameter for fast, measuring minimum hole sizes" protected)
confAnalysis.fast.slopeFactor
(real 1.0
"Convergence parameter for fast, measuring change in hole sizes" protected)
confAnalysis.fast.maxEnergySpread
(real 83680.0
"Default allowed energy range for fast conformational analysis." protected)
confAnalysis.fast.energyIncrementCount
(int 400
"Allowed energy range grows linearly for molecules with more atoms than this value." protected)
confAnalysis.fast.convergenceSlope
(real -0.3
"Controls convergence in fast conformational analysis." protected)
confAnalysis.fast.convergenceIterations
(int 10
"Controls convergence in fast conformational analysis." protected)
confAnalysis.fast.useFragments
(boolean TRUE
"Controls usage of the fragment database in fast conformational analysis." public)
confAnalysis.fast.readFragments
(boolean FALSE
"Controls reading in the fragment database in fast conformational analysis." public)
confAnalysis.fast.writeFragments
(boolean FALSE
"Controls writing out the fragment database in fast conformational analysis." public)
confAnalysis.fast.systematic.upperbound
(int(0 *) 750
"Maximum theoretical number of conformers for a molecule to be searched systematically." protected)
confAnalysis.fast.random.nAttempt
(int(1 *) 5
"Number of times to attempt random search." protected)
confAnalysis.fast.maxRotatableBonds
(int 30
"Only a single conformer is returned for compounds with greater than this many rotatable bonds." protected)
confAnalysis.catDB.fast.readFragments
(boolean TRUE
"Controls reading in the fragment database in fast conformational analysis in catDB." public)
confAnalysis.catDB.fast.writeFragments
(boolean TRUE
"Controls writing out the fragment database in fast conformational analysis in catDB." public)
confAnalysis.catDB.time
(boolean FALSE
"If true, print timing information for catDB." protected)
confAnalysis.catDB.fast.minHoleSize
(real 70.0
"Convergence parameter for fast in catDB, measuring minimum hole sizes" protected)
confAnalysis.catDB.fast.slopeFactor
(real 1.0
"Convergence parameter for fast in catDB, measuring change in hole sizes" protected)
confAnalysis.catDB.minimizationCycles
(int 10
"Controls amount of minimization for the fast option in catDB." protected)
confAnalysis.catDB.maxEnergySpread
(real 83680.0
"Default allowed energy spread in catDB is 20 kcals." protected)
confAnalysis.catDB.energyIncrementCount
(int 400
"Allowed energy range grows linearly for molecules with more atoms than this value." protected)
confAnalysis.catDB.convergenceSlope
(real -0.3
"Controls convergence in catDB with the fast option." protected)
confAnalysis.catDB.convergenceIterations
(int 10
"Controls convergence in catDB with the fast option." protected)
confAnalysis.best.slopeFactor
(real 5.0e-03
"Convergence parameter for best, measuring change in hole sizes" protected)
confAnalysis.best.min.rms.for.pole.confs
(real 175.0
"Only pole on conformers with an RMS (pole distance space) less than this" protected)
confAnalysis.best.min.rms.for.good.conf
(real 0.60
"Reject conformer if RMS (pole dist. space) to neighbors is less than this." protected)
confAnalysis.best.max.successive.failures
(int 5
"Quit best analysis if this many successive fail to generate a good conf." protected)
confAnalysis.best.pole.power
(int 2
"Raise the polling error to this power." protected)
confAnalysis.best.pole.weight
(real 20.0
"Pole weight for each neighboring pole conformer." protected)
confAnalysis.best.pole.pain.barrier
(real 100.0
"Pole rises rapidly when RMS difference in pole confs is less than this." protected)
confAnalysis.best.min.pole.weight
(real 15.0
"Minimum permitted weight for poles." protected)
confAnalysis.best.conf.energy.for.pole.proximity
(real 30.0
"Default weight for auto-scaling of poles." protected)
confAnalysis.best.min.rms.for.conf.rejection
(real 40.0
"Reject conformer if minimum hole size in distance space is less than this." protected)
confAnalysis.best.lookback.for.pole.proximity
(int 5
"Controls how much history is considered when updating pole weights." protected)
confAnalysis.best.conf.count.for.pole.proximity
(int 6
"Auto-scaling for poles kicks in after this many confs." protected)
confAnalysis.best.max.poleDist.per.feature
(int 3
"Maximum number of pole distances per feature." protected)
confAnalysis.best.no.poling
(boolean FALSE
"If true, poling is switched off." protected)
confAnalysis.best.cisPeptideRatio
(real(0.0 1.0) 0.1
"Target value for (# cis bonds)/(# trans bonds) for non-proline, non-n-alkylated peptides" protected)
confAnalysis.best.cisPeptideRatio.proline
(real(0.0 1.0) 0.4
"Target value for (# cis bonds)/(# trans bonds) for proline peptides" protected)
confAnalysis.best.cisPeptideRatio.nAlkylated
(real(0.0 1.0) 0.4
"Target value for (# cis bonds)/(# trans confs) for n-alkylated peptides" protected)
fragDatabase.name
(string "fragments.data"
"The name of the fragment database data file" protected)
fragDatabase.version
(int 1
"The version of the fragment database data file" private)
fragDatabase.coordMax
(real 6400.0
"The maximum value (in pm) for any coordinate to be stored in the fragment database" protected)
constraintColor.2d
(color RGB(0.9 0.9 0.9)
"Controls the color used for 2d constraint lines" protected)
constraintColor.3d
(color RGB(0.9 0.9 0.9)
"Controls the color used for 3d constraint lines" protected)
infoHighlightColor.2d
(color RGB(0.5 0.75 0.0)
"Controls the color used for 2d info objects (mesh)" protected)
infoHighlightColor.3d
(color RGB(0.7 1.0 0.0)
"Controls the color used for 3d info objects (mesh)" protected)
geomObjectColor.2d
(color RGB(0.5 0.7 1.0)
"Controls the color used for 2d geomobjects(points, vectors, planes, ...)" protected)
geomObjectColor.3d
(color RGB(0.5 0.7 1.0)
"Controls the color used for 3d geomobjects(points, vectors, planes, ...)" protected)
labelColor.2d
(color RGB(0.9 0.9 0.9)
"Controls the color used for labeling 2d objects" protected)
labelColor.3d
(color RGB(0.9 0.9 0.9)
"Controls the color used for labeling 3d objects" protected)
mapping.color
(color RGB(0.9 0.9 0.0)
"Controls the color of the 'show function map' mapping on a compound" protected)
font.2d.topologyLabels.color
(color RGB(1.00 1.00 1.00)
"Color for 2D atoms, charge, chirality, constraints, geomObjects... labels" protected)
font.3d.topologyLabels.color
(color RGB(1.00 1.00 1.00)
"Color for 3D atoms, charge, chirality, constraints, geomObjects... labels" protected)
font.2d.compoundNameLabels.color
(color RGB(0.0 0.0 0.0)
"Color for 2D compound name labels." protected)
font.3d.compoundNameLabels.color
(color RGB(0.0 0.0 0.0)
"Color for 3D compound name labels." protected)
dihedral.reportRange0to360
(boolean FALSE
"If on, angles will be reported as unsigned" protected)
chiralityOnNonCarbon
(boolean FALSE
"Report chirality on non-carbon atoms" protected)
confGen.fastType
(boolean TRUE
"Whether default is Fast Analysis, or Best, in dialog box" protected)
confGen.numConfs
(int 250
"Default number of conformers to generate, for dialog box" protected)
confGen.removeTopSymDuplicate
(boolean TRUE
"Whether to check duplicate using topological symmetry" protected)
confGen.topSymHeavyAtomOnly
(boolean TRUE
"Whether to check topological symmetry on heavy atoms only" protected)
confGen.topSymRmsTol
(real(0.0 10000.0) 0.03
"RMS tol for topological symmetry checking" protected)
confGen.topSymMaxSymMappings
(int 8000
"Maximum number of symmetry mappings for topological symmetry checking" protected)
confSort.byEnergy
(int 1
"A value of one will sort the conformers by energy after import, saving from a database, etc." protected)
ViewCompound.background.2d
(color RGB(0.78 0.78 0.78)
"Controls the background color in 2D graphics windows" protected)
ViewCompound.background.3d
(color RGB(0.5 0.5 0.5)
"Controls the background color in 3D graphics windows" protected)
ViewCompound.view.2d.atomLabels
(from view.2d.atomLabels "Display atom labels in View Compound 2D Window")
ViewCompound.view.2d.charges
(from view.2d.charges "Display charges in View Compound 2D Window")
ViewCompound.view.2d.chirality
(from view.2d.chirality "Display chirality in View Compound 2D Window")
ViewCompound.view.2d.hydrogens
(from view.2d.hydrogens "Display hydrogens in View Compound 2D Window")
ViewCompound.view.2d.lonepairs
(from view.2d.lonepairs "Display lone pairs in View Compound 2D Window")
ViewCompound.view.2d.monochrome
(from view.2d.monochrome "Display 2D drawings in View Compound in monochrome")
ViewCompound.view.3d.atomLabels
(from view.3d.atomLabels "Display atom labels in View Compound 3D Window")
ViewCompound.view.3d.charges
(from view.3d.charges "Display charges in View Compound 3D Window")
ViewCompound.view.3d.chirality
(from view.3d.chirality "Display chirality in View Compound 3D Window")
ViewCompound.view.3d.hydrogens
(from view.3d.hydrogens "Display hydrogens in View Compound 3D Window")
ViewCompound.view.3d.lonepairs
(from view.3d.lonepairs "Display lone pairs in View Compound 3D Window")
ViewCompound.view.3d.constraintNames
(from view.3d.constraintNames "Display constraint names in View Compound 3D Window")
ViewCompound.view.3d.constraintTolerance
(from view.3d.constraintTolerance "Display constraint tolerances in View Compound 3D Window")
ViewCompound.view.3d.geomObjectNames
(from view.3d.geomObjectNames "Display names of features/blobs in View Compound 3D Window")
ViewCompound.grid
(from grid "Display a grid in View Compound 2D Window")
ViewCompound.grid.snap
(from grid.snap "Snap mouse input to grid in View Compound 2D Window")
ViewCompound.grid.spacing
(from grid.spacing "Grid spacing (in picometers) in the View Compound 2D Window")
ViewCompound.commandLine
(boolean FALSE
"Display command line in View Compound Workbench" protected)
ViewCompound.2d.rubberbandLength
(from rubberbandLength.2d "Length (in picometers) of the rubberband cursor in View Compound 2D Window")
ViewCompound.dm.restoringForces
(boolean FALSE
"Use restoring forces in dynamic modelling" protected)
ViewCompound.dm.useElectrostatics
(boolean FALSE
"Use electrostatic forces in dynamic modelling" protected)
ViewCompound.dm.useVDW
(boolean TRUE
"Use Van Der Waals forces in dynamic modelling" protected)
ViewCompound.dm.allowAngleBend
(boolean FALSE
"Allow angle bend in dynamic modelling" protected)
ViewCompound.dm.allowBondStretch
(boolean FALSE
"Allow bond stretch in dynamic modelling" protected)
ViewCompound.dm.allowDistortion
(boolean FALSE
"Allow geometric distortion in dynamic modelling" protected)
ViewCompound.dm.AllowTranslation
(boolean FALSE
"Allow compound to move during dynamic modelling" protected)
ViewDatabase.background.2d
(color RGB(0.78 0.78 0.78)
"Controls the background color in 2D graphics windows" protected)
ViewDatabase.background.3d
(color RGB(0.5 0.5 0.5)
"Controls the background color in 3D graphics windows" protected)
ViewDatabase.view.3d.atomLabels
(from view.3d.atomLabels "Display atom labels in View Database 3D Window")
ViewDatabase.view.3d.charges
(from view.3d.charges "Display charges in View Database 3D Window")
ViewDatabase.view.3d.chirality
(from view.3d.chirality "Display chirality in View Database 3D Window")
ViewDatabase.view.3d.hydrogens
(from view.3d.hydrogens "Display hydrogens in View Database 3D Window")
ViewDatabase.view.3d.lonepairs
(from view.3d.lonepairs "Display lone pairs in View Database 3D Window")
ViewDatabase.view.3d.constraintNames
(from view.3d.constraintNames "Display constraint names in View Database 3D Window")
ViewDatabase.view.3d.constraintTolerance
(from view.3d.constraintTolerance "Display constraint tolerances in View Database 3D Window")
ViewDatabase.view.3d.geomObjectNames
(from view.3d.geomObjectNames "Display names of features/blobs in View Database 3D Window")
ViewDatabase.commandLine
(boolean FALSE
"Display command line in View Database Workbench" protected)
ViewDatabase.report.filename
(string "Compound-Table"
"Name of default report in View Database Workbench" protected)
ViewDatabase.maxHits
(int(1 *) 300
"Maximum number of DB Search hits returned to the user" protected)
ViewDatabase.2D.IndexingProcessTimeout
(int 1200
"2D indexing process timeout" protected)
ViewDatabase.3D.IndexingProcessTimeout
(int 1800
"3D indexing process timeout" protected)
ViewDatabase.4D.IndexingProcessTimeout
(int 1800
"4D indexing process timeout" protected)
ViewDatabase.3D.IndexingCandThreshold
(int 200
"Minimum number of rows in the spreadsheet to do 3D indexing" protected)
ViewDatabase.4D.IndexingThreshold
(int 200
"Minimum number of rows in the spreadsheet to do 4D indexing" protected)
ViewDatabaseHit.view.3d.constraintNames
(from view.3d.constraintNames "Display constraint names in View Database Hit Dialog 3D Window")
ViewDatabaseHit.view.3d.constraintTolerance
(from view.3d.constraintTolerance "Display constraint tolerances in View Database Hit Dialog 3D Window")
ViewDatabaseHit.view.3d.constraintValue
(boolean TRUE
"Description" protected)
ViewDatabaseHit.view.3d.geomObjectNames
(from view.3d.geomObjectNames "Display names of features/blobs in View Database Hit Dialog 3D Window")
ViewDatabase.1dSelectSize
(int 65535
"Number of compounds to be considered in one 1D select" protected)
ViewDatabase.2D.IndexingBufferSize
(int 500
"2D indexing buffer size" protected)
ViewDatabase.3D.IndexingBufferSize
(int 500
"3D indexing buffer size" protected)
Search.LeastSquaresPlaneNormalLength
(int 300
"Least Squares Plane normal vector length in picometers" protected)
Search.server.hosts
(string "DefaultHost"
"List of catDisk server hosts for paraller database search" public)
GenerateHypo.background.2d
(color RGB(0.78 0.78 0.78)
"Controls the background color in 2D graphics windows" protected)
GenerateHypo.background.3d
(color RGB(0.5 0.5 0.5)
"Controls the background color in 3D graphics windows" protected)
GenerateHypo.view.3d.atomLabels
(from view.3d.atomLabels "Display atom labels in Generate Hypothesis 3D Window")
GenerateHypo.view.3d.charges
(from view.3d.charges "Display charges in Generate Hypothesis 3D Window")
GenerateHypo.view.3d.chirality
(from view.3d.chirality "Display chirality in Generate Hypothesis 3D Window")
GenerateHypo.view.3d.hydrogens
(from view.3d.hydrogens "Display hydrogens in Generate Hypothesis 3D Window")
GenerateHypo.view.3d.lonepairs
(from view.3d.lonepairs "Display lone pairs in Generate Hypothesis 3D Window")
GenerateHypo.view.3d.constraintNames
(from view.3d.constraintNames "Display constraint names in Generate Hypothesis 3D Window")
GenerateHypo.view.3d.constraintTolerance
(from view.3d.constraintTolerance "Display constraint tolerances in Generate Hypothesis 3D Window")
GenerateHypo.view.3d.geomObjectNames
(from view.3d.geomObjectNames "Display names of features/blobs in Generate Hypothesis 3D Window")
GenerateHypo.commandLine
(boolean FALSE
"Display command line in Generate Hypothesis Workbench" protected)
GenerateHypo.filename
(string "$CATALYST_CONF/hypo.data"
"Name of file from which Hypothesis Generation parameters are read" protected)
GenerateHypo.inactive.spread
(real 3.5
"Difference from most active in order to be used in subtractive phase" protected)
GenerateHypo.sortInputDefinitions
(boolean TRUE
"Sort input function definitions so that results are independent of order" protected)
GenerateHypo.overlay.together
(boolean TRUE
"Description" protected)
GenerateHypo.overlay.activesColor
(color RGB(0.78 0.20 0.20)
"Default color of active compounds in overlay display" protected)
GenerateHypo.overlay.inactivesColor
(color RGB(0.20 0.78 0.20)
"Default color of inactive compounds in overlay display" protected)
GenerateHypo.overlay.activesThreshold
(real 0.01
"Compounds with activity above this threshold are considered active" protected)
GenerateHypo.overlay.colorAllAtoms
(boolean FALSE
"If TRUE, atoms will be colored in the overlay display" protected)
GenerateHypo.report.filename
(string "Hypothesis-Data"
"Default report style in Generate Hypothesis Workbench" protected)
fx.hbondCollisionScaleFactor
(real 0.95
"Radius of atom and of probe sphere are scaled by this factor prior to check\ that hydrogen bond projected points do not collide with ligand atoms.\ If 0, no collision check. Does not affect molecules already in database." protected)
ViewHypothesis.background.2d
(color RGB(0.78 0.78 0.78)
"Controls the background color in 2D graphics windows" protected)
ViewHypothesis.background.3d
(color RGB(0.5 0.5 0.5)
"Controls the background color in 3D graphics windows" protected)
ViewHypothesis.view.2d.atomLabels
(from view.2d.atomLabels "Display atom labels in View Hypothesis 2D Window")
ViewHypothesis.view.2d.charges
(from view.2d.charges "Display charges in View Hypothesis 2D Window")
ViewHypothesis.view.2d.chirality
(from view.2d.chirality "Display chirality in View Hypothesis 2D Window")
ViewHypothesis.view.2d.hydrogens
(from view.2d.hydrogens "Display Hydrogens in View Hypothesis 2D Window")
ViewHypothesis.view.2d.lonepairs
(from view.2d.lonepairs "Display lone pairs in View Hypothesis 2D Window")
ViewHypothesis.view.2d.monochrome
(from view.2d.monochrome "Display drawings in View Hypothesis 2D Window in monochrome")
ViewHypothesis.view.3d.atomLabels
(from view.3d.atomLabels "Display atom labels in View Hypothesis 3D Window")
ViewHypothesis.view.3d.charges
(from view.3d.charges "Display charges in View Hypothesis 3D Window")
ViewHypothesis.view.3d.chirality
(from view.3d.chirality "Display chirality in View Hypothesis 3D Window")
ViewHypothesis.view.3d.hydrogens
(from view.3d.hydrogens "Display hydrogens in View Hypothesis 3D Window")
ViewHypothesis.view.3d.lonepairs
(from view.3d.lonepairs "Display lone pairs in View Hypothesis 3D Window")
ViewHypothesis.view.3d.constraintNames
(from view.3d.constraintNames "Display constraint names in View Hypothesis 3D Window")
ViewHypothesis.view.3d.constraintTolerance
(from view.3d.constraintTolerance "Display constraint tolerances in View Hypothesis 3D Window")
ViewHypothesis.view.3d.geomObjectNames
(from view.3d.geomObjectNames "Display names of features/blobs in View Hypothesis 3D Window")
ViewHypothesis.commandLine
(boolean FALSE
"Description" protected)
lab.commandLine
(boolean FALSE
"Display command line in lab windows" protected)
process.remote.basedir
(string "/usr/tmp"
"Directory to place temporary remote data files" protected)
process.remote.host
(string "madonna"
"Default host name for running remote jobs" protected)
process.remote.dirPrefix
(string ""
"Prefix for remote job temporary files" protected)
process.runRemote
(boolean FALSE
"Default value of run remote option" protected)
maxDatabaseHits
(int 300
"Maximum number of DB Search hits returned to the user" protected)
maxFindHits
(int 300
"Maximum number of Find hits returned to the user" protected)
useWedgeHash
(boolean FALSE
"Determines whether wedges or bold lines are used in 2D" protected)
dirtyCell.color
(color RGB(0.7 0.7 0.7)
"Controls the background color of a 'dirty' report cell" protected)
nullCell.color
(color RGB(0.5 0.5 0.5)
"Controls the color of a 'NULL' report cell indicator" protected)
constraint.minMaxDisplay
(boolean TRUE
"Whether constraint dialog employs max/min or value +/- tolerance display" protected)
compare.initialWeakenFactor
(real 1.0
"When doing flex compare, use this weaken factor in initial try" protected)
compare.weakenFactor
(real 1.4
"if we can't find a mapping with initial weaken factor, use this one" protected)
compare.maxMappings
(int 100
"ignore mappings beyond this many top mappings" protected)
compare.maxConfsPerMapping
(int 12
"ignore confs beyond this many top confs per mapping" protected)
compare.maxFitDifference
(real 2.0
"ignore mappings whose fit is this different than best fit" protected)
compare.initialFlexMappings
(int 100
"how many of top rigid mappings should be flex fit before sort" protected)
compare.minInterBlobDistance
(real 200.0
"the minimum distance required between two blobs in a hypothesis." protected)
compare.maxOmittedFeaturesFast
(int -1
"Maximum number of omitted features allowed for fast compare. Set to 0 to ignore mappings involving a subset of features. Set to -1 to consider all mappings." protected)
compare.maxOmittedFeaturesBest
(int 2
"Maximum number of omitted features allowed for best compare. Set to 0 to ignore mappings involving a subset of features. Set to -1 to consider all mappings." protected)
compare.energyPerFitUnit
(real 1.0e+06
"Estimate of number of joules it is worth to improve the fit by 1 unit." protected)
compare.ignoreSymmetricMappings
(boolean TRUE
"If set, db search and compare ignore redundant symmetric mappings" protected)
compare.considerMirror
(int 1
"1 considers mirror image during fit, 0 will not " protected)
compare.considerWeight
(int 0
"1 considers differences in feature weights in a query-query compare" protected)
compare.considerTolerance
(int 0
"1 considers differences in feature tolerances in a query-query compare" protected)
cluster.catalyst400Behavior
(int 0
"1 will use picometers instead of angstroms for the rms value used to compute the cluster distance" protected)
flexfit.includeExcludedVolumes
(boolean TRUE
"If FALSE, reverts to pre-4.0 behavior of eliminating excluded volumes from flexible searching." protected)
flexfit.minimMaxItersNoVDW
(int 20
"Maximum number of minimization cycles ignoring VDW during flexible fit." protected)
flexfit.minimMaxItersVDW
(int 40
"Maximum number of minimization cycles with VDW during flexible fit." protected)
flexfit.percentConfsSearch
(int 30
"Percent of conformers to consider for flexible search." protected)
flexfit.maxMappingsPerConf
(int 20
"Maximum number of mappings per conformer." protected)
flexfit.excessEnergyPerConf
(real 40000.0
"Maximum permitted excess energy permitted during flexible fit." protected)
flexfit.ignoreEnergy
(boolean FALSE
"Ignore energy when doing flexible search." protected)
flexfit.ignoreEnergyMinimization
(boolean FALSE
"Ignore energy minimization when doing flexible search." protected)
flexfit.hydrophobMinDist
(int 50
"Flexible search hydrophob min distance." protected)
flexfit.hydrophobRadiusDist
(int 175
"Flexible search hydrophob radius distance." protected)
flexfit.filterDistHalfTolerance
(int 100
"Flexible search filtering distance half tolerance." protected)
flexfit.distHalfTolerance
(int 100
"Flexible search distance half tolerance." protected)
flexfit.angleHalfTolerance
(int 30
"Flexible search angle half tolerance." protected)
flexfit.torsionHalfTolerance
(int 30
"Flexible search torsion half tolerance." protected)
fit.doBestMapping
(boolean FALSE
"Will get the conformer and mapping with the largest fit value when set to TRUE." protected)
sysSearch.sp3sp3SearchIncrement
(real 120.0
"Systematic search increment for sp3-sp3 rotatable bonds (degrees)." protected)
sysSearch.sp3sp3SearchOffset
(real 60.0
"Systematic search offset for sp3-sp3 rotatable bonds (degrees)." protected)
sysSearch.sp2sp2SearchIncrement
(real 180.0
"Systematic search increment for sp2-sp2 rotatable bonds (degrees)." protected)
sysSearch.sp2sp2SearchOffset
(real 0.0
"Systematic search offset for sp2-sp2 rotatable bonds (degrees)." protected)
sysSearch.sp3sp2SearchIncrement
(real 60.0
"Systematic search increment for sp3-sp2 rotatable bonds (degrees)." protected)
sysSearch.sp3sp2SearchOffset
(real 60.0
"Systematic search offset for sp3-sp2 rotatable bonds (degrees)." protected)
sysSearch.sysSearch1NVDWScale
(real 0.7
"VDW scaling for 1-N interactions during systematic search." protected)
sysSearch.sysSearch14VDWScale
(real 0.5
"VDW scaling for 1-4 interactions during systematic search." protected)
indexing.max3configs
(int 3375
"Max 3 configs in db indexing" protected)
indexing.max2configs
(int 500
"Max 2 configs in db indexing" protected)
export.kekule
(boolean TRUE
"Attempt to export aromatic structures in kekule form for MOL" protected)
catHypo.forceAbsoluteStereochemistry
(int 0
"1 forces absolute stereochemistry, will not consider mirror image " protected)
catDB.compoundBufferSize
(int 10
"Number of compounds stored in memory before writing to disk" protected)
catDisk.singleProcess
(boolean FALSE
"If set, run in single-process mode" protected)
catDisk.remoteDataTimeout
(int 180
"Time the database is kept in cache by catDisk, with no client processes accessing the database" public)
default.printer
(string "lp1"
"Name of default printer for Print dialog" protected)
hipHop.calculate.hypoFit
(int 0
"Calculate the fit values for each compound/hypo compare" protected)
hipHop.extended.output
(int 0
"Print catHypo style information in log file." protected)
hipHop.memory.virtPhysRatio
(real 2.0
"Ratio of virtual to physical memory. Used for alg choice and bailout if needed." protected)
DontSaveDB
(boolean FALSE
"If set, do not save DB" protected)
Core
(boolean FALSE
"Causes program to dump core on error if true" protected)
Verbose
(boolean FALSE
"Causes program to output verbose diagnostic messages" protected)
Timeout
(int 100
"Sets time in ms for GL event management" protected)
RemoteHost
(string ""
"Remote hostname for DGL graphics, obsolete under Cypress" protected)
mailProgram
(string "/usr/sbin/Mail"
"Where to find the program for mailing comments" protected)
This page was last modified in February 2000. Maintained
by the MSI Documentation Group.
Copyright 1999-2000 Molecular Simulations Inc, a subsidiary of Pharmacopeia, Inc.
All rights reserved.