[ ecepp | fasta | grob | Filter functions | Gui functions ]

grob

an abbreviation for a general GRaphics OBject, which contains dots, and/or lines and/or solid surfaces; it can be a geometrical body, a contoured electron density, 3D plot, an arrow, etc. If the graphics object contains triangles, it can be represented by solid surfaces. The order of points in the triangles defines the direction of the normals which in turn defines which of the two sides are lit. Grob-file format is straightforward and editable.
To merge two or several grobs, use the double-slash operator (e.g. g = g1//g2//g3 ) or the write grob append command.

The default file format for grobs is Object File Format, .off the native format of the Wavefront application.
Example:

 
 read grob "icos"             # several example graphics objects 
 read grob "cube"             # are read in ... 
 read grob "oblate" 
 read grob "prolate" 
 gAll = g_cube//g_icos 
 
 display g_cube red           # ... and displayed 
 display solid g_icos blue 
 display g_oblate green 
 display g_prolate magenta 
 center 

Setting property masks Creating grobs from molecular surface.This is done with the make grob skin command. In this command one can also specify the transparency level of the grob, e.g.

make grob skin a_2 a_2 0.6

Comparing grob shapes

One method is to compare the distance histograms. For example, if one has two grobs, g1 and g2 , the code looks like this:

  dh1 = Histogram(Sort(Rarray( Distance( Xyz(g1)))),0.,20.,0.5)[?,2]
  dh2 = Histogram(Sort(Rarray( Distance( Xyz(g2)))),0.,20.,0.5)[?,2]
  Corr(dh1,dh2)

It goes through the following steps:

1. computes the distance matrix between all nodes
2. converts the distance matrix into one array and sorts it
3. computes a histogram in fixed bins from 0. to 20. A (adjust this as needed), and takes the second column of this matrix (the first contains the distance bin position, the second contains the number of distances in this bin)

Grob functions:

• Area ( g_solid [ error ] ) (only for triangulated grobs)
• Color ( g ) &arrow; M_rgb
• Grob ( g R6_colorRanges )
• Image ( g_with_texture texture ) ⇒ P_array_of_images
• Label ( g ) , e.g. gg = Grob("label",{0. 1. 2.},"Okidoki"); Label(gg)
• Matrix( g wire )
• Name ( g )
• Nof( g {1|2|3} ) returns the number of vertexes, lines or triangles
• Parray( g ) returns an array of grobs for tables
• : Property( full|surface|texture|grid ) =>
• Trim ( g R6_xyzXYZ ) quick fix to select points with certain coordinate ranges
• Volume( g_solid )
• Xyz ( g [gradient] )

Supported 3D graphical object file formats

• .gro old limited internal ICM format (obsolete)
• .obj Wavefront .obj format, see Wiki obj
• .off Object File Format
• .dae (digital asset exchange ): the Collada file format.
• .kmz (.zip) the extended Collada zipped set of files containing additional texture files.
• .3dxml from Dassault Systemes

Several ICM commands use functions to filter out table rows or database entries by an expression applied to a column/field value. For example: UNFINISHED

Built-in GUI functions for dynamic and user-defined dialogs in ICM.

To see how these functions are used, open the icm.gui file and search for a function of interest. Most of those functions are just used for internal ICM purposes and we were even hesitant to document or even list those. However some of them, e.g. nIcmObj are quite general and are frequently used.

These functions can be used in different expressions

• AnimateViewMenu :
• Apply : generates a so called 'modal' dialog with an Apply button, rather than the default Close button.
• Atom : indicates if the level of selection (or a right click object for a popup menu) is atomic (see also Res , Mol , Obj )
• AtomMenu :
• canRestoreAutosave :
• Cell :
• CheckItem :
• CheckModified :
• ChemProperties :
• ChemSearch :
• ClusterDialog :
• ConnectDB :
• connected :
• DisconnectDB :
• Docking : yes, if the docking (D) license is present
• EditLabelGrob :
• EditMenu :
• Energy : yes, if the energy (E) license is present
• FileNew : a dialog
• FileOpen : a dialog
• hasLigandRedo : checks if the LIGAND.selection in 3D editor has 'redo' states.
• hasLigandUndo : same for 'undo' states.
• hasReceptor :
• hasSwissID : see also set swiss
• HelpBrowser :
• Hidden :
• Homology :
• icongf :
• isAmino :
• isChemTable :
• isCurIcm :
• isDsGBox :
• isDsMol :
• isDsObj :
• isGrobDot :
• isGrobLabel :
• isGrobSmooth :
• isGrobTransparent :
• isGrobWire :
• isHet :
• isHetnRes :
• isIcmObj :
• isLigandEdit :
• isMini :
• isNucl :
• isObjFolder :
• isPharm :
• isReadOnlyMode :
• isSeqNucl :
• LearnDialog :
• ligandUndo :
• Mol :
• molcartCanModify :
• molcartCanRebuildIndex :
• molcartconnected :
• molcartHave3D :
• MolEdit :
• mysqldb : see also other molcart functions
• nAsGraph :
• nAtomInMol :
• nBiomtMol :
• nChemTable :
• nDots :
• nDsObj :
• nDsSelObj :
• Neighbors :
• nGrob :
• nLigAsGraph :
• nLigAsGraphTerm :
• nLigFrag :
• nLines :
• nMap :
• nModel :
• nObj :
• nResInMol :
• nSelSeq :
• nSeq :
• nStackConf :
• nTable :
• nTrianges :
• nTriangles :
• nUserObj :
• Obj :
• okToConvert :
• PredictDialog :
• Preferences :
• QuickImage :
• Quit : dialog :
• Rebel :
• RecentFilesMenu :
• RecentPDBsMenu :
• Res :
• ResAtom :
• SaveDir :
• SaveProject :
• Sel :
• Selection :
• SelectionLevelMenu :
• SelectionModeMenu :
• Seq :
• TableToolsMenu :
• Terms :
• Toggle :
• ToggleButton :
• Upgrade :
• Version :
• Vls :
• WindowsMenu :