MCL Tutorial

Table of Contents

Introduction

MCL...

...means Merlin Control Language.
...is an English language interface to Merlin.
...automates Merlin searches.
...is interopperable with thorfilters.
...is capable of generating HTML output.

2. Commands

    Add
    add results of a search to hitlist, or add one hitlist to another.
    Copy
    copy one hitlist to another.
    Clear
    set current or specified hitlist to all off.
    Create
    create a column for a hitlist, or create a hitlist.
    Exchange
    exchange two hitlists.
    Free
    free a column, hitlist or database.
    Invert
    invert hitlist, off becomes on and vice
    versa.
    Move to
    set current row of hitlist
    Print
    write data to terminal
    Put
    puts search hits into hitlist
    Read
    read saved hitlist from file
    Remove
    reverse order of hitlist
    Reverse
    reverse order of hitlist
    Select
    intersection of 2 hitlsits.
    Set
    set default hitlist.
    Sort
    sort hitlist by a variety of means.
    Write
    write hitlist to file.

3. Syntax

MCL is made up of single statements ( no blocks).
Statements start with a capitalized verb(command).
Statements end with a period.
Correct MCL grammar is correct English grammar.
Whitespace outside quoted text is ignored, including newlines.
Non-reserved text does not need to be quoted.

4. Structure

Programs generally must follow this sequence:

Open Database

Select

Allocate columns

Create

Allocate hitlist(s)

Create

Manipulate hitlist(s)

Add,Put,Remove,Sort, etc.

Output Results

Print

Example:

% mcl -i topten.mcl medchem98demo@sun1 'NCc1ccc(O)c(O)c1'

"topten.mcl":
 
 

Select database $1.
Create hitlist "hits".  Clear "hits".
Create column of datatype "SIMILARITY" named "SIMILARITY".
Add structures at least 0.50 similar to $2.
Sort by similarity to $2.
Create column of datatype "$NAM" named "$NAM".
Create column of datatype "CR" named "CR".
Print table of hits from row 1 to row 10 containing "$NAM" "CR".
 
 
OUTPUT: 


===============================================================================

hits 1 to 10 of 2895 in hitlist "hits", database "medchem98@origin.daylight.com:thor:norah"
-------------------------------------------------------------------------------
 hit Name                                 CMR
 --- ------------------------------------ ------------------------------------
   1 BENZYLAMINE3METHOXY4HYDROXY          4.291
   2 BENZYLAMINE2METHOXY3HYDROXY          4.291
   3 BENZENEMETHANAMINE34DIMETHOXY        4.755
   4 TRIMETHYLBENZYLAMMONIUMIODIDE3HYDROX ~
   5 BENZENEMETHANEAMINENNDIMETHYL3HYDROX 4.602
   6 BENZENEMETHANAMINE3METHOXY           4.138
   7 BENZENEMETHANAMINE4METHOXY           4.138
   8 BENZYLAMINE2HYDROXY3METHOXY          4.291
   9 TRIMETHYLBENZYLAMMONIUMIODIDE4HYDROX ~
  10 BENZENEMETHANEAMINENNDIMETHYL4HYDROX 4.602
===============================================================================
MCL User Guide