ICM Manual v.3.8
by Ruben Abagyan,Eugene Raush and Max Totrov
Copyright © 2018, Molsoft LLC
Apr 11 2018

Contents
 
Introduction
Reference Guide
 ICM options
 Editing
 Graph.Controls
 Alignment Editor
 Constants
 Subsets
 Molecules
 Selections
 Fingerprints
 Regexp
 Cgi programming with icm
 Xml drugbank example
 Tree cluster
 Arithmetics
 Flow control
 MolObjects
 Energy Terms
 Integers
 Reals
 Logicals
 Strings
 Preferences
 Tables
 Other
 Chemical
 Smiles
 Soap
 Gui programming
 Commands
 Functions
 Icm shell functions
 Macros
 Files
Command Line User's Guide
References
Glossary
 
Index
PrevICM Language Reference
Chemical arrays and tables. Operations, virtual chemistry.
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Chemical arrays can be read from multiple external formats (e.g. .sdf , ml2 ) either as standalone arrays, or columns in chemical spreadsheets. These arrays are abbreviated as X_

Reading/Writing Chemical Arrays and Tables

read table mol reads chemical table from file

write table mol writes chemical table to file

InChI conversion

converts chemicals to InChI or InChI_key converts InChI to chemical array

Smiles conversion

converts smiles to chemical array

converts chemical array to smiles

Conversion from loaded 3D objects

converts 3D selection to chemical array

converts chemical to 3D

converts chemical to 3D and optimize

converts loaded object to 3D and optimize

converts loaded object to 3D ICM object, preserve coordinates

Modifying chemicals

modify chemical perform chemical group modifications on chemical arrays

apply 2D depiction

Generating chemicals. Virtual chemistry

Markush library generation

Chemical reactions

Comparing, Searching and Chemical Matching

searching in chemical tables

search in Molcart databases

search in loaded 3D objects

chemical distance/similarity

Other chemical search related functions

Nof chemical

Index chemical

Predicting chemical properties

Predict

Chemical superposistion

superimpose Rmsd Srmsd

chemSuper3D

Pharmacophore analysis

pharmacophore search

superimpose

Rmsd

create pharmacophore

Batch chemical processing,

_chemBatch


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