ICM Manual v.3.9
by Ruben Abagyan,Eugene Raush and Max Totrov
Copyright © 2020, Molsoft LLC
Jun 5 2024

Reference Guide
 ICM options
 Alignment Editor
 Cgi programming with icm
 Xml drugbank example
 Tree cluster
 Flow control
 Energy Terms
 Chemical Functions
 Gui programming
 Icm shell functions
Command Line User's Guide
PrevICM Language Reference
Subsets and Index Expressions

one can refer to an element or a subset of ten kinds of ICM-shell variables:
Variable type Expression Result type Example
string string[i] string lastChar=str[Length(str)]
string[i1:i2] string resName=pdbStr[18:21]
iarray iarray[i] integer CurrSize=sizes[i]
iarray[i1:i2] iarray frag=list[4:nitems]
iarray[I_] iarray sublist=list[{1,3,5}]
rarray rarray[i] real the=same[i]
rarray[i1:i2] rarray all=as[for:iarr]
rarray[I_] rarray Part=R1[{1,2,3}]
sarray sarray[i] string best=menu[ibest]
sarray[i1:i2] sarray fish=list[4:8]
sarray[I_] sarray some=all[{1,2,3}]
matrix matrix[i1,i2] real Element=M[4,5]
matrix[i1] rarray atomCaVec=CoordMatr[15]
matrix[i1,i2:i3] rarray thirdRow=M[3,1:5]
matrix[i1,?] rarray thirdRow=M[3,?]
matrix[i1:i2,i3] rarray firstColumn=mm[1:3,1]
matrix[?,i3] rarray firstColumn=mm[?,1]
matrix[i1:i2,i3:i4] matrix upperSqr=rot[1:2,1:2]
sequence sequence[i] string amino4=bpti[4]
sequence[i1:i2] sequence domain=seq[139:302]
alignment alignment[i] alignment column4=globins[4]
alignment[i1,i2] string AminoAcIn2ndSeq=globins[4,2]
alignment[i1:i2] alignment motif=EFhand[15:27]
profile profile[i] profile His=prof[18:18]
profile[i1:i2] profile motif=prf[14:35]
selection selection[i] selection ca18=ca[18]
selection[i1:i2] selection frag=ca[14:35]
table table[i] table show t[3]
table[i1:i2] table delete t[3:5]

Important note. When both lower and upper limits are explicitly specified, even if they are equal (e.g. list [3:3] ), the type of the subset object remains the same. If only one element is specified, the rank may be reduced. The upper limit may be larger than the actual limit (e.g. t[3:9999]). You may also use 0 instead of the last element number (e.g. t[3:0]).


Copyright© 1989-2024, Molsoft,LLC - All Rights Reserved. Copyright© 1989-2024, Molsoft,LLC - All Rights Reserved. This document contains proprietary and confidential information of Molsoft, LLC. The content of this document may not be disclosed to third parties, copied or duplicated in any form, in whole or in part, without the prior written permission from Molsoft, LLC.