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Formal charges in functional groups can be changed in chemical arrays with the modify command.

The following variables and commands are related to charges in 3D objects or chemical arrays:

• set charge formal
• set charge
• set chargemmff
• Charge ( .. [formal] )
• GRAPHICS.formalChargeDisplay
• modify : find and replace charge and uncharged chemical functional groups

 
#>  a   b   c 
   1.  15  "alpha"  
   2.  18  "beta"  
   5.  10  "gamma"  

Collection is composed of a array of unique keys and a array of values, where each key is associated with one value. Each value can either be of basic type or other collection or array of collections.

A collection can be created in different ways:

• using Collection function
• from JSON format. (`read-json Collection)
• -- read xml from XML source ( read xml file.xml or Collection )

Examples:

c = Collection( "firstName", "John", "lastName", "Snith", "age" 25 ) # from key/value pairs 
c = Collection( "{ 'firstName': 'John', 'lastName': 'Smith', 'age': 25 }" ) # from JSON string
c = Collection( "<firstName>John</firstName><lastName>Smith</lastName><age>25</age>" )  # from XML string
c["age"]
c["firstName"]
write xml c "c.xml"

Elements can be added, modified and removed dynamically

c = Collection()   # empty collection
c["count"] += 1    # accumulates count (when used the first time, creates a new key
c["name"] = "John"  # creates a new element
c["name"] = "Jack"  # overwrites an existing element
c["addressBook"] = Array()
c["addressBook",1] = Collection( "name" "Jack" "tel" "858-3452238" "cell" "858-8872676" )
c["addressBook",2] = Collection( "name" "John" "tel" "858-7878795" "cell" "858-6373913" )
# index access
c["addressBook",1]  #  first entry of the addressbook
c["addressBook",1:2]  #  first two entries of the addressbook
c["addressBook",1:2,"tel"]  #  first two 'tel' fields
# deletion
delete c["addressBook",2]  # deletes second element of the adderssbook
delete c["addressBook"]

See: Collection read xml , read json , write-xml, String( xml), xml drugbank example

current map

usually is the last map loaded by the read map command or created by the make map family of commands. The current map may be changed by the set map command. To find out which one is the current, use list maps.

an instruction one can execute in the ICM-shell interactively or from an ICM script file. Typically a command consists of a verb (like read or delete ) and a bunch of arguments.

The word order in the argument list is not important, if arguments have different types. For example:

 
 display a_//ca,c,n yellow # is as good as ...  
 display yellow a_//ca,c,n # ... inverse  

If two or more argument of the same type are present the order becomes important, e.g.

• if two or more arguments are of the same type, e.g. write "This line" "filename" or superimpose as_select1 as_select2 ,
• a complex argument consists of two parts: e.g. delete label i_number or grid["x"] in the plot command. In the latter case if the "x" string is not preceded by grid word, it will not be considered.

Redefining global preferences and parameters temporarily for one command.

Sometimes you want to run a command with different values of global preference and global shell variables of the following type: integer, real, string and logical . Their values will be automatically restored after the completion of the command. E.g.

show surface area surfaceAccuracy=10 vwExpand=1.4
show energy electroMethod = "Coulomb"

 
Cij_norm = Cij/Sqrt(Cii*Cjj) 

See also:

• Index( compare)

Individual properties, such as energies, number of visits and the total numbers of visits can be re-set with the set stack command.
Example:

 
% icm 
 build string "ala his trp"   
 montecarlo 
 show stack 
 iconf>       1       2       3       4       5       6       7 
 ener>    -15.1   -14.6   -14.6   -14.2   -13.9   -11.4    -1.7 
 rmsd>      0.3    39.2    48.0    44.1    27.4    56.6    39.3 
 naft>        1       0       0       1       1       1       0 
 nvis>        4       1       1       4       4       4       1 
 print Nof(conf) 
 7 
 print Iarray(stack)  # returns {4 1 1 4 4 4 1} 
 t = Table(stack)     # more conf parameters 
 for i=1,Nof(conf) 
   load conf i 
   center 
   pause  # hit return 
 endfor 

The stack can also be stored in the object it is associated with. It enables multiple object sessions, each object with its own stack, and ability to save the object with multiple conformations to a file. To store the stack in the object use the store conf a_ command.

If cpk and xstick are displayed simultaneously the cpk sphere becomes transparent. Undisplay xstick to make the spk solid again.

The spheres sliced by a clipping plane can be displayed in several ways, see GRAPHICS.cpkClipCaps .