Daylight Summer School 2001, June 5-7, Santa Fe, NM

MCL-Merlin Control Language

Daylight's Merlin Control Language. Simple English interface to Merlin, found as the MCL program

MCL-

An English language interface to Merlin
Automates Merlin searches
Generates HTML output
Integrable with Daycgi tools and thorfilters
Daycgi Wizard application provides interactive means of generating MCL scripts

MCL Commands (Verbs):

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.

MCL 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.

MCL Program 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
===============================================================================

Daylight Chemical Information Systems Inc.