Basic rules of Modar script

1. One single line of script can only take one Modar command or statement. But one command or statement can be splited in several lines. Character “\” in the end of command line means continuous line following.
2. Character “#” serves as a comments marker. Comments cannot be resided in the middle a sentence, only can
3. Modar script is case insensitive except the filename used in some internal command.

 Variable and array

• Variables in Modar scrip can be a string or a real number type, Modar can determine the type automatically according to the expression, user don’t need to declared it with a type name.
• Modar supports one dimension array only and the member index can be negative. The array exported by Modar commands always start from 0.
• For example:
  

  outputfile=”test.out”        # initiate a file name string istepstart=1000000           # initiate a number nstepmore=100000         # assign nstepmore a value 100000 x[0]=10         # assign nstepmore a value 100000 x[1]=20         # assign nstepmore a value 100000 echo $istepstart                  #print the value of istepstart echo $x[0] $x[1]                  #print the value of istepstart echo $nstepmore > $outputfile     #print the value of nstepmore to file “test.out”

  where, “$” is the character for variable substitution, i.e. for getting the value of variable. Since many Modar intrinsic commands export variables (this is one of features of Modar, through those variables, user can talk with MD system), it’s better to avoid using simple variable name and to keep in mind that your variables may be overwritten by some Modar internal commands.

 Expression

• Modar supports both math expression and string expression, but they are only valid in assignment statement, if statement and while statement.
• For example:
  

  #assign the sum of istepstart and nstepmore to nsteptot nsteptot=$istepstart+$nstepmore   i=rand(1.0)  j=int(rand(1000000))   wd=/home/mengen/villin trjfn=$wd/villin.trj

• Additionally, Modar supports selection expression in many intrinsic commands.
  For example:
  

  #define a atoms cluster defcls pocket select="segid proa && seq 26 82 99 59 56 55 46 && ! type N C O HN CA HA*"   #to calculate the distance between a ligand and the binding pocket calc dist select=”pocket” select=”resname DMS”

• Math expression
  

  Please see here

• Bool expression
  

  Please see here

• String functions
  

  Please see here

  
  

 If statement

• There are two forms of “if” statement. The short form is typed on a single line and but can specify only a single command if the expression is true.
  

  if ( expression ) command

  for example:
  

  outputfile=”test.out”    # initiate a file name string if(-f $outputfile) exec rm ¨Crf $outputfile

   

• The long form uses else and braces to allow for blocks of commands to be nested inside the condition.
  

  if ( bool expression1 ) { command } else if ( bool expression2 ) { command ... } else { command }

• For example:
  

  include “size.inc”             #feed a,b,c,boxl   #get a box type from user getText boxtype default=”cubic” msg=”please tell the box type”   #process the boxtype if($boxtype .head. "cubi") {        #cubic   boxl=$a   if($boxl<$b) boxl=$b   if($boxl<$c) boxl=$c   a=$boxl   b=$boxl   c=$boxl } else if($boxtype .head. "tetr") {   #tetragonal   boxl=$a   if($boxl<$b) boxl=$b   a=$boxl   b=$boxl } else if($boxtype .head. "octa") {   #octahidralt   boxl=$a   if($boxl<$b) boxl=$b   if($boxl<$c) boxl=$c   a=$boxl   b=$boxl   c=$boxl } else{   echo -hs "|  ** unknown boxtype: $boxtype"   goto tellboxtype_and_abort }

 While statement (loop)

• The while statement evaluates an expression, if it is true, the shell runs the nested commands and then repeats for as long as the expression remains true. Please note that there is no short form of while statement supported, only long form as shown bellow is available.
  

  while ( bool expression){ command ... }

• For example:
  

  #load a trajectory trjin file="step9_harvest.trj" ifrm=0 while($ifrm<$ntotframes){   trjreadnextframe   mdtime=$curmdtime     #print progress for every 10ps   tmod=$mdtime%10   if($tmod==0) echo -hs "current MD time: $mdtime ps"     #calculate RMSD for main chain atoms   calc rmsd fitgroup="mainpro and name C CA N O" \ calcgroup="mainpro and name C CA N O"   echo "$mdtime $value" >> mainrmsd.txt     #calculate distance between terminals   calc dist group1="residue PROA 41" group2="residue PROA 76"   echo "$mdtime $value" >> dist.txt     #calculate PHI,PSI for residue 50   calc dihe group1="atom PROA 49 C" \ group2="atom PROA 50 N"  \ group3="atom PROA 50 CA" \ group4="atom PROA 50 C"   phi=$value   calc dihe group1="atom PROA 50 N" \ group2="atom PROA 50 CA" \ group3="atom PROA 50 C" \ group4="atom PROA 51 N"   psi=$value   echo "$mdtime $PHI $PSI" >> phipsi.txt     #calculate Radius of Gyration   calc rgy  select="all"   echo "$mdtime $value" >> rgy.txt     ifrm=$ifrm+1 }

 Goto statement and label

• Modar script supports label and goto statement, which also can serve as a loop, a switch or a psudo-routine.
• For example:
  

  if(!-var boxtype) {   echo -hs "|  ** please specify the boxtype in command line"   echo -hs "|  for example: $scmdline boxtype=cubic"   goto tellboxtype_and_abort } ...   # command blocks skipeed stop   :tellboxtype_and_abort echo -hs valid boxtype are: echo -hs "  cubic        a=b=c   alpha=beta=gamma=90 ndgf=1" echo -hs "  tetragonal  a=b          alpha=beta=gamma=90 ndgf=2" echo -hs "  rectangular a/A=b/B=c/C alpha=beta=gamma=90 ndgf=1" echo -hs "  orthorhombic    a,b,c       alpha=beta=gamma=90 ndgf=3" echo -hs "  octahidralt      a=b=c        alpha=beta=gamma=ACOS(-1/3) ndgf=1" abort

  
  

 Include statement

• Modar provides include command for loading a sub-script
• For example:
  

  #load force field include "loadff.inc"

    The contents of file “loadff.inc”:
  

  #load force field loadmtf fmt=chm file="top_all27_prot_na.rtf" loadprm fmt=chm file="par_all27_prot_na.prm" tell ff_info