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[ ecepp | fasta | grob | Filter functions | Gui functions | Gamess | Hbond | Html ]
ecepp |
fasta |
grob |
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:
Grob functions:
Supported 3D graphical object file formats
Built-in filter functions for arrays, chemicals and table rows |
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
Gamess |
The General Atomic and Molecular Electronic Structure System (GAMESS) is a general ab initio quantum chemistry package.
http://www.msg.chem.iastate.edu/gamess/ http://www.msg.ameslab.gov/gamess/download.htmlA few comments for those of us who have never been exposed to the quantum chemistry programs:
* The energies produced by the Gamess program include the interaction energies of electrons with its own nuclei. Therefore the values of energies could be very large. To get a more useful value of the bonding and conformational energy the individual atomic contributions can be subtracted. These contributions, however, need to calculated consistently with the method and the basis set.
ICM can generate input files for this publically available program and parse its output. See commands:
The following approximations in Gamess can currently be interfaced from ICM: h3-- RHF (restricted Hartree-Fock) see wiki Limitations : This method in Gamess will not work for radicals (molecules, ions or atoms with unpaired electrons ).
hbond- hydrogen bonds |
There are three ways in which hydrogen bonds are evaluated or displayed in ICM.
The pairs of hbonded atoms found during methods 1. and 2.
are calculated according to ECEPP/3 potential.
One can also display hbonds with their distances, deviations from linearity,
colored by the strength parameter which takes the angle into account.
Related commands are show hbond, display hbond,
color, and undisplay .
See also the following parameters changing the graphics representation of
static hbonds:
HTML documents in ICM |
ICM can contain any number of html-pages. These pages appear in the shell as strings of the html property . To create an html document follow one of two possible routes:
read html "a.html" # reads and sets the property mask # s = "<html><h1>TITLE</h1></html>" set property html s
Internal tagsThe internal html documents can contain links to icm slides , viewpoints , images( both .jpg and .png ) and scripts with icm commands .
The shell objects representing slides, viewpoints, images and scripts can be linked to the html document with the following tags.
<a href="#icm/slide/slideshow.slides/1"> Link text</a> <a href="#icm/script/scriptShellName"> Link text</a> <a href="#icm/viewpoint/vpShellName"> Link text</a> <img src="imgfileName" /> # the image needs to be in Workspace album
In the graphics editor, these tags are automatically created when images, slides, viewpoints, scripts are dragged and dropped to the Edit Source window.
Input elements
The internal html documents can contain this following input elements :
Checkboxes.
The general syntax is:
<input type="checkbox" checked={<icmVariableName>|<os><ms>} [oncheck=s_scriptOnCheck] [onuncheck=s_scriptOnUnckeck] []/>The state of the checkbox is evaluated from the state of ICM shell variable or selection. For molecular objects or meshes 'checked' means that object or mesh is displayed. For logicals and integers - 'yes' or non-zero value.
The default 'oncheck' and 'onuncheck' actions for molecular objects and meshes are display / undisplay commands. Example:
Show Receptor: <input type="checkbox" checked="a_2jav.a" /> <br> Show Ligand: <input type="checkbox" checked="a_2jav.a5z5" /> <br> Show Pocket: <input type="checkbox" checked="g_2jav_a" /> <br> <!--icmscript name="dsSurf" display wire g_recPocketSurface --> <!--icmscript name="undsSurf" undisplay checked=g_recPocketSurface --> Show Ligand Surface: <input type="checkbox" checked="g_recPocketSurface" oncheck="dsSurf" onunckeck="undsSurf" /> <br> Custom Action: <!--icmscript name="onchk" if (! %1) then print %1 %1 = ! %1 endif --><!--icmscript name="onunchk" if ( %1) then print %1 %1 = ! %1 endif --> <input type="checkbox" checked="l_info" oncheck="onchk" onuncheck="onunchk" />
See also gui .
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