####       Basic Rules
####    1  All the flags must start at the first row
####    2  TMPFILE and MOLNAME in the command lines and add_line lines will be
####       replaced with the defined tmparatory file name and molecular record name
####    3  Commands are running in a sequential order.
####    4  Additional lines are appended in a sequential order.
####    5  Up to to MAXCOMMAND commands, MAXLINE add_lines and MAXLINE omit_lines can
####       be defined.
####    6  RECORD_BEGIN, RECORD_END, MOLNAME_FIELD, IMMEDIATE_STOP, OMIT_LINE, ADD_LINE
####       must be placed in a pair of double quotas.
****RECORD_BEGIN and RECORD_END****
	Define the start and end points of each record.
	eg RECORD_BEGIN  "########## Number      :" 
	eg RECORD_END    "1   ****   1" 
 	RECORD_BEGIN and RECORD_END can not be space or '\0'
****SEPARATOR****
	SEPARATOR defines the separator between two records, it is suppressed by 
	RECORD_BEGIN and RECORD_END
	eg SEPARATOR  "@<TRIPOS>MOLECULE"  
****SEPA_TYPE****
	=0:  the SEPARATOR line is at the beginning of a record (may not necessary the
	     first line for the first record, such as "@<TRIPOS>MOLECULE" in a multiple 
	     mol2 file, it is the default)  
	=1:  the SEPARATOR line is at the end of a record(such as "$$$$" in a sdf file)
	eg SEPA_TYPE  0 
****MOLNAME_DEF**** 
 	Define the prefex of record names
	eg MOLNAME_DEF  COMP    
****MOLNAME_ID**** 
 	Define the starting ID, default is 1   
 	If MOLNAME_DEF="comp" and MOLNAME_ID is 1, then record names are comp1, comp2, 
	comp3 etc.	 
	eg MOLNAME_ID   100
****MOLNAME_FIELD****
	MOLNAME_FIELD defines a reference line to be used to read in record names from 
	the input, it is suppressed by MOLNAME_DEF 
	eg MOLNAME_FIELD "ZINC"
****MOLNAME_FL****
	=1: The first line of each record is taken as the reference line. For example,
	    some sdf files places the record name at the first line of each record. 
	=0: not applied (the default).
	eg MOLNAME_FL 0 
****MOLNAME_FR****
	=n: It is used when MOLANME_FL is set to 1. For the first record, the nth line is
	    taken as the reference line. 
	=0: not applied (the default).
	eg MOLNAME_FR 0 
****MOLNAME_LD****
	MOLNAME_LD (line distance) specifies from which line the record names are read in 
	The first integar specifies the line ID and the second specifies the start column 	
	For the first integar, 
		 0, read record name from the reference line defined by MOLNAME_FIELD or 
		    MOLNAME_FL and MOLNAME_FR.
 		-1, read record name from the immediate above reference line
 		-2, read record name from the second immediate above reference line
 		-3, read record name from the third immediate above reference line
 		-4, read record name from the fourth immediate above reference line
 		-5, read record name from the fifth immediate above reference line
		 1, read record name from the immediate next reference line (the default)
		 2, read record name from the second immediate next reference line
		 3, read record name from the third immediate next reference line
		 4, read record name from the fourth immediate next reference line
		 5, read record name from the fifth immediate next reference line
	eg MOLNAME_LD 0 0, read molecular name from the current line starting 
	from the first column
****TMPFILE****
	TMPFILE specifies the name of a temparatory file that holds all lines extraced 
	from the input for each record
	eg TMPFILE TMP 
****PROC_BEGIN****
	The starting record to be handled (commands are to be executed). If PROC_BEGIN  
	is smaller than 1, it is reset to 1 (the default is 1).
	eg PROC_BEGIN 0
****PROC_END****
	The ending record to be handled. If PROC_END is smaller than 1, this 
	restriction is ignored (the default is 0).
	eg PROC_END 0
****PROC_FREQ****
	The frequency to handle records bewteen PROC_BEGIN and PROC_END (or the 
	last record), the default is 1.
	eg PROC_FREQ 1
****PROC_PROB****
	The probability of handling a record bewteen PROC_BEGIN and PROC_END 
	(or the last record). This parameter should be larger than 0 and smaller than 1. 
	It is activated only if PROC_FREQ equals to 1. The default is not applied(=-1). 
	eg PROC_PROB 0.1
****IMMEDIATE_STOP*****
	Stop running if a line contains the defined string. 
	eg IMMEDIATE_STOP "END"
****OMIT_LINE***
	Omit lines that contain the defined string
	eg OMIT_LINE "RENARK"
****ADD_LINE***
	Add lines to records, it takes two variables (the type and content)
	For the type flag,	
	 1: to the beginning of each record
	-1: to the end of the each record
	eg. ADD_LINE -1 "End Of Record"
****COMMAND****
	Define commands to be executed.
	eg COMMAND  "cp TMPFILE MOLNAME.mol2"
	eg COMMAND  "$AMBERHOME/bin/antechamber -fi mol2 -fo prepi -i MOLNAME.mol2 -o MOLNAME.prepi -j 4 -pf yes"
	eg COMMAND  "cat MOLNAME.prepi >>total.prepi"
	eg COMMAND  "$AMBERHOME/bin/parmchk -i MOLNAME.prepi -o MOLNAME.frcmod -f prepi"
	eg COMMAND  "cat MOLNAME.frcmod >>total.frcmod"
	eg COMMAND  "rm -f TMPFILE"
	eg COMMAND  "rm -f MOLNAME.*"
#### end of definition