set pdbLine ""
set previousResidueNumber 1
set isFirstResidue 1
set isLastResidue 0
set pdbBlock ""
set isAtEndOfResidueBlock 0

set inputPdbFile [open "/Users/charlesjanac/desktop/URL050.txt" r]
proc readOneBlock {inputPdbFile} {
	global pdbLine
	global isAtEndOfResidueBlock
	global previousResidueNumber
	global isLastResidue
	global pdbBlock
	set pdbBlock ""
	while {![eof $inputPdbFile]}  {
		 if {$isAtEndOfResidueBlock} {
		set pdbLine [gets $inputPdbFile]	
		} else {set isAtEndOfResidueBlock 1}
		if {[regexp {^TER    } $pdbLine]} {
				set isLastResidue 1
				set pdbLine ""
				return $pdbBlock		
		} elseif {[regexp {^ATOM \s*} $pdbLine] || [regexp {^HETATM \s*} $pdbLine]} {
			if {![regexp "ATOM\(.*?\)\[AUCG\]\\s\\w...$previousResidueNumber\\s\\s\\s" $pdbLine]} { 
				set previousResidueNumber [string range $pdbLine 25 25]
				set isAtEndOfResidueBlock 0
				return $pdbBlock
			} else {set pdbBlock "$pdbBlock \n$pdbLine"
				#puts $pdbBlock 
			}
		}
	}	
}
  
while {!$isAtEndOfResidueBlock} {

	readOneBlock $inputPdbFile

	regsub -lineanchor -all {(?!(^ATOM)(.*))[AUCG]\s\w} $pdbBlock R& pdbBlock



if {$isLastResidue & $isFirstResidue} {
		regsub -lineanchor -all {(?!(^ATOM)(.*))R[AUCG]} $pdbBlock &N pdbBlock
		set isFirstResidue 1
		#puts $outputPdbFile $pdbBlock
		puts $pdbBlock
} elseif {$isFirstResidue} {
		regsub -lineanchor -all {(?!(^ATOM)(.*))R[AUCG]} $pdbBlock &5 pdbBlock
		set isFirstResidue 0
		#puts $outputPdbFile $pdbBlock
		puts $pdbBlock  
} elseif {$isLastResidue} {
		regsub -lineanchor -all {(?!(^ATOM)(.*))R[AUCG]} $pdbBlock &3 pdbBlock
		set isFirstResidue 1
		#set isLastResidue 0
		#puts $outputPdbFile $pdbBlock
		set isAtEndOfResidueBlock 0
		puts $pdbBlock
} else {puts $pdbBlock} }