: T

Jul 1 2004

Contents


Introduction
Reference Guide
User's guide
References
Glossary
A
B
C
D
E-H
S
T
U-Z

Index

5.7 T

!- table 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 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).

Tables can be read, written, and shown. Tables can also be created by
group table obj1 obj2 ...
command and returned by some functions such as:

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

One can inserted to empty rows, or duplicate rows or , insert rows from a different table with the add table command.
Tables can be merged with the append column command.
!- Pairwise table expressions:

!(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] & ... )

The result of the pairwise expression is a subset of the table involved. The pairwise expressions can be further combined with the & (AND) or | (OR) operations. A full expression can be assigned to a new table or used on the fly in a number of commands and functions. String comparison can use patterns (e.g. t.NA=="*_MOUSE"). The pattern may contain more sophisticated \{n,m\} expressions, if the first symbol is '*' or '^'.
The Index( tableExpression ) function will return integer array of selected row-numbers.
Example:

 
 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

!- 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}]

Index arrays are returned by some commands or the Iarray(T_) function.
Look at this example of operations with tables. We read a database of secondary structures foldbank.db dump arrays into a table, add sequence length to a table, extract entries of interest, sort them and save the result.

 
 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"

!- Plotting table data
The ICM tables can have built-in plots. To add an automatically generated plot to a table, follow these steps:

append the plot header field with a sarray of plots (e.g. group table append t header {"x=A;y=B"} "plot" ).
specify a subset of following options separated by semincolons and without space.

Syntax of a plotString, ( f is the name of a column of the table, e.g. A ) x=f;y=f;[label=f;][color=f;][shape=SHAPE;][size=f;] [xbarFrom=f;xbarTo=f;|ybarFrom=f;ybarTo=f;] [title=text;][xScale=from,to,nMajorTics,nMinorTics][yScale=from,to,nMajorTics,nMinorTics] [regression={yes|no};][connect_dots;][rainbow=slash_separated_colors;] [element=element_specs] <>
The element section descrives additional sub-plots which can be added to the main plot. The element specifications are similar to the main plot specifications, but the fields for each element are separated by commas, rather than by semicolons.

 
element={rectangle|RECTANGLE},x=,y=,{x2=,y2=|w=,h=},color=,fillPattern=PATTERN,label=,labelPos={top|bottom|left|right|center}

The following shape types are possible: None (i.e. dot), Ellipse , Rect , Diamond , Triangle , DTriangle , UTriangle , LTriangle , RTriangle
The following fillPattern styles are available:

Solid	solid color
Dense1	the most dense pattern
Dense2
..
Dense7	the lightest pattern
Hor	horizontal lines
Ver	vertical lines
Cross	cross pattern
BDiag	diagonal pattern
FDiag	another diagonal pattern
DiagCross	diagonal cross pattern
Custom	pixmap

Example:

 
S_plots = Sarray(1) 
S_plots[1] = "x=i;y=MaxDev;color=Entropy;size=8;title=Quick plot" 
# t has the following columns: i, MaxDev, Entropy,  
group table append t header S_plots "plot"

!- 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).

!- tif files Tag(ged) Image File Format, used by default in the ICM commands write image and display movie. See also: rgb, png, targa.

!- transformation vector an elementary space transformation is defined by a rarray where values {a1,a2,...,a12} define 3x3 rotation matrix and translation vector {a4,a8,a12}. The complete augmented affine 4x4 transformation matrix in direct space can be presented as:

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

The commands and functions related to transformation vector (referred to as R_tv):

transform ms_ R_tv applies transformation to an object;
Symgroup( 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.

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