ICM Manual v.3.8
by Ruben Abagyan,Eugene Raush and Max Totrov
Copyright © 2018, Molsoft LLC
Oct 18 2018

Contents
 
Introduction
Reference Guide
Command Line User's Guide
 ICM-shell
 ICM graphics
 Str.Analysis
 Sequence
 Molcart
  Database file
  Molcart connection options
 Pharmacophores
 Energy
 Molecules
 Animation
 Symmetry
 X-ray
 Plotting
 Docking/VLS
 Examples
 _chemSuper
 Chemical Conformation Generator
References
Glossary
 
Index
PrevICM Language Reference
Molcart
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[ Database file | Molcart connection options ]

Molcart is a chemical extension for two relational databases, namely Mysql and sqllite, and a set of tools to work with it. It efficiently supports special ICM types, such as chemicals. ICM provides command-level interface and GUI to work with Molcart.

The same interface is used for the Molsoft local database files.

ICM commands for Molcart databases and database files:


Molsoft database files


Molsoft table database files are a specialized file format optimized for fast search and other operations. It plays very well with advanced ICM types, such as chemicals. At the command level database files are almost undistinguishable from database server connections. It makes scaling solutions from individual to organization level much easier.

Creating a .molt file with a single table.


 # just a mock-up chem table
 add column t1 Chemical({"CCO","CCCO"})  {1. 2.}  
 make molcart table name="t" t1 filename="db.molt"
 # or read an SDF file and convert it to the database format
 read table mol "file.sdf" name="t2"
 make molcart table name="t2" t2 filename="db2.molt"

See also: molcart


Specifying database in commands


ICM commands working with Molcart support multiple connections to databases and multiple open database files. To specify the database, almost all ICM database access commands support the following options:

filename=s_database_file

- specifies a Molsoft local database location in the file system.

connect=s_connectionID

- specifies a connectionID. For each open database file and server connection ICM creates a unique connectionID which may be used to specify the connection in ICM commands. To list available database connections use the list molcart connect command. It is possible to request the current connection's connectionID using Name(sql) function.

If no connection is specified, the current connection is used. If no current connection is available, ICM tries to connect to the database server using connection parameters saved in user's ICM settings.

See also: molcart, list molcart, Name molcart.


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