Contents
Introduction
Reference Guide
User's Guide
References
Glossary
A
B
C
D
E-H
I-N
O-R
S
T
table
Table expression
targa
tether
tif files
transformation vector
U-Z
Index

[ table | Table expression | targa | tether | tif files | transformation vector ]

an ICM object which unite several other ICM-objects. It consists of two parts:

• a header which is a set of any ICM-objects and
• a spreadsheet (or a set of columns) composed of iarrays, rarrays, sarrays, or parrays, of the same length. A parray, or pointer-array can contain chemical structures (see read table mol command), sequences Parray( seq | sequence ), or molecular objects ( Parray(object .. ) ) .

or add column tabName col1 col2 .. [ name= S_names ]
commands (see group table and add column ).

Columns can be further added with

add column table col [ name= s_colname ]

Examples:

add column t {1 2 3} {2 3 4} #creates table t with two columns
add column t {1 2 3} name="CC"  # adds one more column
group table tt {1 2} "A" {2. 3.} "B" {"xx","yy"} "C"

Some other functions can also return tables,e.g.:

• Energy(stack) returns a table with energy values for the stack conformations
• Table(s_out) interprets an output of an HTML form.
• Find performs search in all entries and returns the matching entries

Selecting columnsColumns can be selected and copied into another table with the Table( T S_colNames ) ⇒ T_out

E.g.

add column t {1 2} {2 3} {3 4} # creates A,B,C columns
tt = Table(t,{"B","C"})

Setting the grid and table views

add header t "TABLE"|"GRID"|"GRID1"|"GRID2"|.. name="displayStyle"

Where:

• "TABLE": normal table style
• "GRID" : grid view with automatic fitting optimal number of columns.
• "GRID1","GRID2",... : number of grid columns is explicitly specified

In a grid view you may want to add a some columns to be displayed below the molecular image. You need to add a header "gridColumns" which constains string with a comma-separated column names.

add header t s_commaSeparatedColNames name="gridColumns"

Example:

add column t Chemical({"CCC", "CCO", "CCN"}) 
add column t Mass(t.mol) name="MW"
add column t Predict(t.mol,"MolLogP") name="MolLogP"
# set a grid view
add header t "GRID" name="displayStyle" 
# add more MW to grid view
add header t "MW,MolLogP" name="gridColumns"
# switch back to the table view
add header t "TABLE" name="displayStyle" 

As an addition to the views above you may open a 'form record view'. (Useful for tables with many columns). To show a form you need to append '_FORM' to displayStyle. For example the most convenient combination is GRID1_FORM.

Example:

add header t "GRID1_FORM" name="displayStyle"

Changing the color, format and name of a column
set format t.col s_format [ name=s_displayedColName ]

The format should use the C-format specifications ( e.g. "%s","%.2f", etc.) of "%1" for any data type.

group table t {1 2 3} {2.222 3.333 4.444}
set format t.B "<i>%1</i>" name="Reals" 
set format t.B "<i>%.1f</i>"  # will only show 1 sign. digit

To reset the displayed column name to its true column name, set name= argument to empty string.

Condensing or grouping the table rows by a column

Sometimes a table contains multiple rows with the same value of a particular column (see example). In this case the rows of the table can be condensed to show only one representative row. Left and right arrows would rotate through the rows. The commands leading to that view are the following:

group table tt {3 2 2 2 1 1 1 1} {"a","b","c","d","e","f","g","h"}
set group column tt.A 

Pairwise table expressions:

[ Table operations | Table subset | Table plot | Table actions ]

• !(Table selection) negation
• T.I_ ? i_ ( ? is one of: ==, !=, <=, >=, <, > )
• T.R_ ? r_ ( ? is one of: ==, !=, <=, >=, <, > )
• T.S_ ? s_ ( ? is one of: ==, !=, ~, !~, i.e. exact of fuzzy comparisons )
• T.S_ ? S_ ( ? is one of: ==, ~, equivalent to T.S_ ? S_[1] | T.S_ ? S_[2] | ... )
• T.S_ ? S_ ( ? is one of: !=, !~, a complement to what is returned by the T.S_ == S_ or T.S_ ~ S_ comparison, respectively, equivalent to T.S_ ? S_[1] & T.S_ & S_[2] & ... )

 
 group table t {"a","b","c"} "s" {1 2 3} "i" # arrays t.s, t.i 
 show t 
 show t.s == {"c","a"} # shows the 1st and the 3rd lines 
 show t.s ~ "a*" | t.i < 3 # shows the 1st and the 2nd lines 
 Index(  t.s ~ "a*" | t.i < 3 ) # returns {1,2} 

Table operations

• split column values
• appending one table to another by a shared column
• grouping table rows by a column
• add/insert table rows
• specifying actions upon clickin on table rows

table subsets:

Table subsets can also be defined explicitly through the three types of index expressions:

• T[i_element], e.g. t[3]
• T[i_from:i_to], e.g. t[3:15]
• T[I_indexArray], e.g. t[{3,14,18}]

 
 read database "foldbank.db"          # load information into arrays  
 LE=Length(SS )                       # create iarray with sequence lengths 
 group table t $s_out LE              # create table t with all info + lengths 
 show t                               # press 'q' otherwise computer will explode 
 show t.NA == {"1gec.i","5pad*"}      # find these entries 
 a=t.RZ < 2.2 & t.ER < 1. & t.LE > 35 # select entries with resolution < 2.5,  
                                      # converted with ER < 1. and longer 
                                      # than 35 residues 
 sort a.LE a.RZ                       # resort entries according to 
                                      # lengths/resolution 
 write database a "SUBSET" 

Each table may have a header section containing different ICM-shell variables in addition to a set of column-vections. Example:

add column t {1 2 3} {2 3 4}
add header t "Francis Bacon" name="author"
show t.author
 Francis Bacon

There are header strings with fixed names for three types of actions:

• cursor these commands are invoked after the cursor position is changed
• doubleClick these commands are invoked upon double click on a column row
• lockAction these commands are invokved upon clicking on a button in the column named L

The action commands are regular ICM commands, however they can use certain abbreviations to refer to the table and its row number (cursor position):

%#  # row number, e.g. t[%#]
%@  # table name, e.g. %@.name[%#] 
%^  # column name e.g: %@.%^[%#]
%1  or %COLNAME  # value of cell from column number 1 and the current row
%3 

Example:

add column t {1 2 3} {"A" "B" "C"}
add header t "print %@.%^[%#]" name="cursor"
add header t "print %@.%^[%#], \"double clicked\" " name="doubleClick"

Setting the lockAction requires the the following action.

set property display t # creates an array and activate the lock action

TARGA or TGA format is a format for describing bitmap images, TARGA can represent grey-scale bitmaps, indexed colour, and RGB colour, the format also supports various compression methods.

tether

a harmonic restraint pulling an atom in the current object to a static point in space. This point is represented by an atom in another object. Typically, it is used to relate the geometry of an ICM molecular object with that of, say, an X-ray structure whose geometry is considered as a target (see also delete tether, minimize tether, show tether, set tether ).
The restraint can also pull an atom to a z-plane (rather than to a point), if you specify tzMethod="z_only"
Atom specific weights can be imposed with tzMethod="weighted" via bfactors.
tzMethod="function" is the most flexible. It allows you to specify different strength, upper and lower boundaries for each tether, establish a flat area in which no penalty is imposed, and even exert constant force. In this case one needs to set atom properties of the "dummy" object to which the "active" atoms are tethered.
Two other types of restraints are drestraint (distance restraints), and vrestraint (multidimensional variable restraints).

 
   a1  a2  a3  | a4 
   a5  a6  a7  | a8 
   a9  a10 a11 | a12 
   ------------+---- 
   0.  0.  0.  | 1. 

• transform ms_ R_tv applies transformation to an object;
• Transform( .. ) function returns one or several cancatenated 12-vectors.
• Transform( i_spaceGroupNumber) returns a chain (R_[1:12*n]) of all n transformation vectors composing the specified space group;
• Augment( R_tv) converts 12-membered transformation vector into the augmented transformation matrix 4x4;
• Vector( M_4x4) converts a 4 by 4 transformation matrix into 12-membered transformation vector
• superimpose as_1 as_2 ... returns R_tv in R_out;
• Rmsd( as_1 as_2 [ exact]) returns R_tv in R_out;
• Axis( R_tv ) calculates the rotation axis R_3 of the transformation. Rotation angle is returned in r_out;
• Rot( R_tv ) extracts the 3x3 rotation matrix;
• Trans( R_tv ) extracts the translation 3-vector which is applied after rotation.