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Table of Contents

1. Introduction
2. Commands
3. Syntax
4. Structure

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ドル.
Create hitlist "hits". Clear "hits".
Create column of datatype "SIMILARITY" named "SIMILARITY".
Add structures at least 0.50 similar to 2ドル.
Sort by similarity to 2ドル.
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

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