newprot.pepd

LET %test = $arg17

IF %test >= 260 GOTO _haveparams
ECHO "Usage: bin/pepteditor newprot.pepd /path/to/file.pdb PROTNAME {set of 14 integers representing start and end residues of TMR1 through TMR7 domains}
EXIT
_haveparams:

LOAD $arg2

CENTER [0,0,0]

REGION TMR1 $arg4 $arg5
REGION TMR2 $arg6 $arg7
REGION TMR3 $arg8 $arg9
REGION TMR4 $arg10 $arg11
REGION TMR5 $arg12 $arg13
REGION TMR6 $arg14 $arg15
REGION TMR7 $arg16 $arg17

UPRIGHT

LET $pdbname = $arg3

LET $fam = $pdbname FROM 1 FOR 2
IF $fam != "OR" LET $fam = $pdbname FROM 1 FOR 4
IF $fam != "OR" GOTO _not_or
LET $sub = $pdbname FROM 3 FOR 2
LET %sub = $sub
LET $fam += %sub
_not_or:

LET $path = "pdbs/" + $fam
LET $path += "/"
LET $pdbname = $path + $arg3
LET $pdbname += ".upright.pdb"

SAVE $pdbname