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RNApath.pl
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RNApath.pl
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#!/usr/bin/env perl
# -*- perl -*-
#
# RNApath.pl
#
# Written by Cody Geary, 2019
#
# Requires RNA_nts.pdb datafile
#
# Usage: perl RNApath.pl input.file
#
# Input file is a traceable text map with >Name as the first line
# Outputs Name.pdb PDB file keyframes and Chimera .cmd script for making morph movies.
#
#Copyright 2019 Cody Geary and Ebbe S. Andersen
#Permission is hereby granted, free of charge, to any person obtaining
#a copy of this software and associated documentation files (the
#"Software"), \ to deal in the Software without restriction, including
#without limitation the rights to use, copy, modify, merge, publish,
#distribute, sublicense, \ and/or sell copies of the Software, and to
#permit persons to whom the Software is furnished to do so, subject to
#the following conditions:
#The above copyright notice and this permission notice shall be
#included in all copies or substantial portions of the Software.
#THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
# EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
# MERCHANTABILITY,\ FITNESS FOR A PARTICULAR PURPOSE AND
# NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
# BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\ LIABILITY, WHETHER IN AN
# ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
# CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALIN\ GS IN THE
# SOFTWARE.
use strict;
use warnings FATAL => qw ( all );
#use Data::Dumper;
use Math::Trig ':radial';
use Math::Trig;
use Cwd; #to get the current working directory
my $dir = getcwd;
####################
###Begin Program
####################
my $file1 = "";
my $synthesis_step_size;
my $KL_delay;
my $output_file_path;
($file1, $synthesis_step_size, $KL_delay, $output_file_path ) = @ARGV;
########################
## User Specified Variables
########################
if ( !defined $synthesis_step_size ) { $synthesis_step_size=15; } # Default number of nts between keyframes
if ( !defined $KL_delay ) { $KL_delay=150; } # Default number of nts delay before KLs snap closed
my $eccentricity=.35; #Determines how much single-stranded regions wobble around (0.5 looks like very random motion)
my $frozen = 0; #this var finds the first base-pair, and freezes the nascent chain before this position so it doesn't wobble too much.
my $nascent_chain = 20;
my $stacking_delay = 60;
my $hidden_offset=.001; #this sets the offset for both x,y,z for the 'hidden' superimposed residues.
# an offset of 0 leads to divide by zero errors in some ribbon-models in PDB viewers, so it's important
# to have his set to a small, but non-zero amount, so the ribbon will have a clear directionality.
my $pmode = 1; #pmode =0 is all-atom, pmode=1 is P-trace only. pmode=1 saves a lot of rendering time and storage space.
my $max_design_size = 0; #0 sets unlimited size, otherwise sets the max accepted length in nts (for the webserver)
#################################################################################
my $synthesized = 0;
my $timesteps= 0;
my @nt_step = (); my @angles = (); my @point = (); my @moved = ();
my @ref_frame = (); my @ref_frame_angle = (); my @ref_trans = ();
my @motif = (); #is each nt_pos a motif, 1 or 0
my $roundedx =0; my $roundedy=0; my $roundedz=0;
my $ref_frame_position = 1;
my $cross_rand_a = rand(1)*$eccentricity-$eccentricity/2; #randomize variables related to the relaxed crossover (use same random number for the whole construct each pdb iteration)
my $cross_rand_b = rand(1)*$eccentricity-$eccentricity/2;
my $cross_rand_c = rand(1)*$eccentricity-$eccentricity/2;
#################################
#Trace the Strandpath Input
#################################
sub read_file
{
my ( $file ) = @_;
my ( @lines, $content );
if ( not open FILE, $file ) {
die "Not readable: $file";
}
{
# Reads the whole file by temporarily undefining the
# record separator,
local $/ = undef;
$content = <FILE>;
# Make Unix line ends from either Mac or DOS,
$content =~ s/\r\n/\n/g;
$content =~ s/\r/\n/g;
}
close FILE;
@lines = split "\n", $content;
return wantarray ? @lines : \@lines;
}
my $input_structure = "";
my $barriers_input_structure = "";
my $input_sequence = "";
my $name = 'mytestoutput';
my @m = ( ); my @n = ( );
my @strand_dir= ( );
&trace; #trace the strandpath
my @input_seq = split(//,$input_sequence);
my $find = " ";
my $replace = "";
$name =~ s/$find/$replace/g;
#$name=$name.".pdb";
my ( $file, $line, @lines, @cols, $seq, @seq, $ATOM, @ATOM );
my @map = (); #stores the dot_paren map
( $file ) = @ARGV;
my @pat = split(//, $input_structure);
if ( not open FILE, "< RNA_lib.pdb" ) { die "file not found!";} #some error checking stuff
if ( defined $input_sequence ) { @seq = split(//, $input_sequence);}
else { die "no sequence provided";}
my @PDB = (); my $PDB = 0; #this will store the final PDB file that we build
###Scan in the PDB library file
$ATOM = 0;
@ATOM = ( ); #this hash stores the PDB coords of the nt and motif library
while ( $line = <FILE> ) { #This parses the information from the FILE into $lines. Each line that begins with ATOM is further parsed into substrings that are stored into vars of ATOM hash-file.
@cols = ( );
@cols = split(/\s+/, $line);
if ( defined $cols[0] ) {
if ( $cols[0] eq "ATOM") {
push @ATOM, {
"a" => substr("$line", 13, 3), #atom type
"n" => substr("$line", 19, 1), #residue type
"i" => int(substr("$line", 22, 4)), #residue number
"h" => substr("$line", 21, 1), #chain name
"x" => substr("$line", 30, 8),
"y" => substr("$line", 38, 8),
"z" => substr("$line", 46, 8),
}
}
}
}
close FILE || die "couldn't close file.";
###Additional Variable Declarations
my $i = 0; my $p = 0; my $x = 1; my $y = 1; my $z = 1;
my $c = $ATOM[0]->{i};
my $strand_length = scalar(@seq);
my $pattern_length = scalar(@pat);
my $nt_pos = 1;
####Variables for mapping multiloops
my $multiloops = 0;
my @multi = ();
my @multi_mask = ();
my @multi_type = ();
#########
# Check strand-length for the server
if ($max_design_size > 0){ #0 sets unlimited design size
if($strand_length>$max_design_size){
die "Strand Length is greater than $max_design_size, try a smaller design.";
}
}
my $keyframes = int(($strand_length+$KL_delay)/$synthesis_step_size)+1;
my $framecount=0;
#######
# Make the Working DIR and write a Command file for Chimera
######
if ( !defined $output_file_path ){
qx(mkdir data\_$name);
$output_file_path = "data\_$name";
} else {
$output_file_path = $output_file_path."\/";
}
open(my $output_spool, '>', "$output_file_path\/$name\_commands.cmd"); ##Output buffer for the screen/file outputs. Spool will hold all screen outputs and send them to a file at the end.
open(my $output_spool2, '>', "$output_file_path\/$name\_Substructures.txt"); ##Output buffer for the screen/file outputs. Spool will hold all screen outputs and send them to a file at the end.
########
# Show the Structural Barriers
#########
print $output_spool2 "\n\nHighlighting Structural Barriers\n\n";
print $output_spool2 " Plot of delay = $KL_delay nts before closing KL interactions. \n\n";
#now parse out the ^ symbols
my $dot_paren = $input_structure;
$find = "^";
$replace = "";
$find = quotemeta $find; # escape regex metachars if present
$dot_paren =~ s/$find/$replace/g;
&map($dot_paren); #generate the nt pairing map with no ^ symbols first, to initialize the random sequences right
&map($input_structure);
my @struc_array = split(//, $input_structure);
my $length=scalar @struc_array;
my @barriers = ();
my $topo_count =0;
my $k=0; my $j=0;
my $orange_list = "";
my $red_list = "";
my $crossover_count=0;
for ($i=0; $i<$length; $i++){
$barriers[$i]="\342\227\246"; #blank
if ($struc_array[$i]eq"^"){$barriers[$i]="^";}
if ($struc_array[$i]eq"."){$barriers[$i]="\342\227\246"; $topo_count=0;} #unpaired are not marked
if ($struc_array[$i]eq"("){$barriers[$i]="x"; $topo_count=0;} #mark open pairs as potential barriers
if ($struc_array[$i]eq")"){
if ($barriers[$map[$i]] eq "x"){ #closing pairs remove barriers
$barriers[$i]="\342\227\246";
$barriers[$map[$i]]="\342\227\246";
$topo_count=0;
}
if ($barriers[$map[$i]] eq "X"){ #if the closing pair is already blocked, then we mark the barrier reached and start counting
if($topo_count>5){
$barriers[$i]="X";
$barriers[$map[$i]]="~";
} else { $barriers[$i]="~"; $barriers[$map[$i]]="~";}
$topo_count++; #increment the topology counter
}
}
if ($i>$KL_delay){
if ($struc_array[$i-$KL_delay]eq"]"){ #closing KLs marks all the intervening sequence is blocked
$barriers[$i-$KL_delay]="\342\227\246";
$barriers[$map[$i-$KL_delay]]="\342\227\246";
for($k=$map[$i-$KL_delay]; $k<$i-$KL_delay; $k++){
if ($barriers[$k]eq"x"){$barriers[$k]="X"; } #mark all the blocked residues
}
}
}
}
my $offsetnum = 0;
for ($i=0; $i<$length; $i++){ #scan through and find the positions to color orange and red
if ($barriers[$i] eq "^"){$crossover_count++}
$offsetnum = $i-$crossover_count;
if ($barriers[$i] eq "~"){ $orange_list=$orange_list."$offsetnum,"}
if ($barriers[$i] eq "X"){ $red_list=$red_list."$offsetnum,"}
}
chop($orange_list); #chop off the tailing comma
chop($red_list);
sub num2range { #regex code to convert series of numbers to ranges of numbers
local $_ = join ',' => @_;
s/(?<!\d)(\d+)(?:,((??{$++1}))(?!\d))+/$1-$+/g;
return $_;
}
$orange_list = num2range($orange_list);
$red_list = num2range($red_list);
for ($i=0;$i<1000;$i++) {
for ($j=0;$j<1000;$j++) {
if ( defined $m[$i][$j] || defined $n[$i][$j] ) {
if ( $m[$i][$j] =~ /[NXACGURYKMSTWVHBD]/ ) { print $output_spool2 "$barriers[$n[$i][$j]-1]"; }
if ( $m[$i][$j] =~ /[35]/ ) { print $output_spool2 "$m[$i][$j]"; }
if ( $m[$i][$j] eq "T" ) { print $output_spool2 "\342\224\200"; }
if ( $m[$i][$j] eq "\n" ) { print $output_spool2 "$m[$i][$j]"; }
if ( $m[$i][$j] eq " " ) { print $output_spool2 "$m[$i][$j]"; }
if ( $m[$i][$j] eq "^" ) { print $output_spool2 "^"; }
if ( $m[$i][$j] eq "7" ) { print $output_spool2 "\342\225\256"; }
if ( $m[$i][$j] eq "-" ) { print $output_spool2 "\342\224\200"; }
if ( $m[$i][$j] eq "r" ) { print $output_spool2 "\342\225\255"; }
if ( $m[$i][$j] eq "L" ) { print $output_spool2 "\342\225\260"; }
if ( $m[$i][$j] eq "J" ) { print $output_spool2 "\342\225\257"; }
if ( $m[$i][$j] eq "x" ) { print $output_spool2 "\342\224\274"; }
if ( $m[$i][$j] eq "i" ) { print $output_spool2 "\342\224\202"; }
if ( $m[$i][$j] eq "b" ) { print $output_spool2 "\342\224\200"; }
if (defined $strand_dir[$i][$j] ) {
if ( $strand_dir[$i][$j] eq "down" || $strand_dir[$i][$j] eq "up" ){
if ( $m[$i][$j] eq "p" ) { print $output_spool2 "\342\224\200"; }
if ( $m[$i][$j] eq "!" ) { print $output_spool2 "\342\224\200"; }
if ( $m[$i][$j] eq "\*") { print $output_spool2 "\342\224\200"; }
} else {
if ( $m[$i][$j] eq "p" ) { print $output_spool2 "\342\224\202"; }
if ( $m[$i][$j] eq "!" ) { print $output_spool2 "\342\224\202"; }
if ( $m[$i][$j] eq "\*") { print $output_spool2 "\342\224\202"; }
}
}
}
}
}
#####################
# Make the Chimera Script
#####################
my $numbercount =0;
my $models_created = 0;
for ($numbercount=$synthesis_step_size; $numbercount<($keyframes*$synthesis_step_size+1); $numbercount += $synthesis_step_size ){
&printer ("open $name\_$numbercount.pdb\n");
$models_created++;
}
if ($pmode==1){ ###in pmode=1, the phosphate trace gives a bug and doesn't render unless we use the final-model as the first frame.
$models_created+= -1;
&printer ("morph start \#$models_created\n"); ##sloppy way to show $models-created -1 in the text (decrement, print, increment)
&printer ("morph interpolate \#0\n");
$models_created++;
} else {
&printer ("morph start \#0\n");
}
for ($i=1; $i<$models_created; $i++){
&printer ("morph interpolate \#$i\n");
}
&printer ("~modeldisp #0-$models_created\n");
&printer ("morph movie\n");
&printer ("color blue #$models_created\n");
if($orange_list ne "" ){&printer ("color orange #$models_created:$orange_list \n");}
if($red_list ne "" ){&printer ("color red #$models_created:$red_list \n");}
#&printer ("roll y 1\n");
#&printer ("perframe \"center \#$models_created:$strand_length\"");
##### Optionally, you can add (in Chimera) this per-frame script to add a polymerase model and center on the 3' end.
###
### close <morph model# +1>
### center <morph model>:<strand_length>
### cofr <model>:<strand_length>
### shape sphere radius 10 center <model>:<strand_length>
###
close $output_spool;
for ($framecount=0; $framecount<$keyframes; $framecount++){
$timesteps+=$synthesis_step_size; #keep track of this separately since $synthesized maxes at the strand-length.
$synthesized+=$synthesis_step_size;
if ($synthesized>$strand_length){
$synthesized=$strand_length;
}
#################################
#Setup Output Spool
#################################
open($output_spool, '>', "$output_file_path\/$name\_$timesteps.pdb"); ##Output buffer for the screen/file outputs. Spool will hold all screen outputs and send them to a file at the end.
&printer("REMARK - File Generated by RNA_vis.pl - written by Cody Geary \n");
&printer("REMARK - Building a total of $strand_length nts. \n");
##&printer("REMARK - Sequence 5- @seq -3 \n");
##&printer("REMARK - $input_structure\n");
for ($i=0; $i<$strand_length; $i++){$motif[$i]=1;} #pre-block all sites, and uncheck them as clean helix is produced.
my $sub_structure = ""; #this will contain the current substructure
@struc_array = split(//, $input_structure);
#now parse out the ^ symbols
$dot_paren = $input_structure;
$find = "^";
$replace = "";
$find = quotemeta $find; # escape regex metachars if present
$dot_paren =~ s/$find/$replace/g;
&map($dot_paren); #generate the nt pairing map with no ^ symbols first, to initialize the random sequences right
&map($input_structure); #next re-generate the nt pairing map with ^ symbols added back for making the structural array
my @dot_paren_array = split(//,$dot_paren);
my $crossover_symbol_count = scalar(@struc_array)-scalar(@dot_paren_array);
my $first_pair = 0;
for ($i=0; $i<scalar( @struc_array ); $i++){
if ($struc_array[$i] eq "(" && $map[$i]<($synthesized+$crossover_symbol_count) ){$first_pair = 1;}
if ($i>($synthesized+$crossover_symbol_count)) {
$sub_structure = $sub_structure."-";
} elsif ( ( $struc_array[$i]eq"(" || $struc_array[$i]eq"[" ) && $map[$i]>($synthesized+$crossover_symbol_count) ){
if ($first_pair==0){
$sub_structure = $sub_structure.","; #make this "." if you want the start strand to be rigid helix
$frozen=$i;
}elsif($first_pair==1){
$sub_structure = $sub_structure.",";
}
} elsif ( $struc_array[$i]eq"^" ) {
$sub_structure = $sub_structure."^";
} else {
$sub_structure = $sub_structure.$struc_array[$i];
}
}
&printer2($synthesized,"$sub_structure\n");
$find = "-";
$replace = ".";
$find = quotemeta $find; # escape regex metachars if present
$sub_structure =~ s/$find/$replace/g;
&map($dot_paren); #generate the nt pairing map without ^ symbols for RNA building
@dot_paren_array = split(//,$dot_paren);
########
### Find Multiloops
########
my $mpos = 0;
$multiloops = 1;
for ($i=0; $i<$strand_length;$i++){$multi_mask[$i]="-";}
for ($i=0; $i<($strand_length-1); $i++){
if ( ($map[$i] ne ($map[$i+1]+1) ) && ( $map[$i] ne $i ) && $dot_paren_array[$i+1]ne"[" && $dot_paren_array[$i+1]ne"]" && $dot_paren_array[$i+1]ne"." ) {
if (defined $multi[$i]){
#&printer(".");
}else{
$mpos = $i;
for (my $j=0; $j<20; $j++){ #this is more awkward than a do-while but safer since it will only count to a max of 20!
$mpos = $map[$mpos+1];
$multi[$mpos]="$multiloops";
$multi_mask[$mpos] = "X";
#&printer("$mpos ");
if ($mpos eq ($strand_length-1)){$multi[$i]="0"; $j=21;}
if ($mpos == $i){$multiloops++; $j=21;}
}
#&printer("- ");
}
} else {
$multi[$i]="-";
$multi_mask[$mpos]="-";
}
}
my @closed_structure = ();
for ($i=0; $i<$strand_length; $i++){ #the strand starts pre-blocked as 'O' unfolded
$closed_structure[$i] = "O";
}
my $l=0;
for ($i=0; $i<($strand_length-1); $i++){
if (defined $multi[$i]){ #go again and make sure all $multi positions are defined with something
}else{
$multi[$i]="-";
}
}
for ($i=0; $i<$strand_length; $i++){
if ( $dot_paren_array[$i]eq"]" && ( $timesteps > ($i + $KL_delay) ) ) {
for ($p=$map[$i];$p<$i;$p++){
if ($multi[$p]ne"-"){
for (my $l=0; $l<($strand_length-1); $l++){
if ($multi[$p] eq $multi[$l]){$closed_structure[$l]="M";}
}
}
if ($multi[$map[$p]]ne"-"){
for (my $l=0; $l<($strand_length-1); $l++){
if ($multi[$map[$p]] eq $multi[$l]){$closed_structure[$l]="m";}
}
}
$closed_structure[$p]="L";
}
}
}
for ($i=0; $i<$strand_length; $i++){ #now look at the pairs of anything marked closed, and close that and the neighbors of it too.
if ( $closed_structure[$i] eq "O" && $closed_structure[$map[$i]] ne "O"){
$closed_structure[$i] = "D";
}
}
if($framecount==$keyframes){ #if it's the last time around, all sites are marked 'X' as closed
#$name=$name."\_Final";
for(my $z=0; $z<$strand_length; $z++){$closed_structure[$z]="X";}
}
#Parse the input structure into motif chunks. This method is rather clumsy.
# Initially find all the loops and KLs, these are terminal to hairpins, and thus easiest to identify. KLs motif placement inlcludes the closing bp.
# BEWARE: Loops of lengths that are not 4,7 or 9 will not be recognized and modeled as loops!!! We can add other loop lengths to the motif library to correct this.
my $parsed_struc = $sub_structure;
$find = "((((((.(.((((....)))))))))))"; #Tar/Tat RNA length28
$replace = "R";
$find = quotemeta $find; # escape regex metachars if present
$parsed_struc =~ s/$find/$replace/g;
$find = "(((((.((((......)))))))))"; #PP7 length25
$replace = "N";
$find = quotemeta $find;
$parsed_struc =~ s/$find/$replace/g;
$find = "((.((....))))"; #MS2 length13
$replace = "M";
$find = quotemeta $find;
$parsed_struc =~ s/$find/$replace/g;
$find = "(((..((............(.("; #iSpinach A Length22
$replace = "S";
$find = quotemeta $find;
$parsed_struc =~ s/$find/$replace/g;
$find = ")))..))............).)"; #iSpinach A
$replace = "S";
$find = quotemeta $find;
$parsed_struc =~ s/$find/$replace/g;
$find = "(((..((..............("; #iSpinach A
$replace = "S";
$find = quotemeta $find;
$parsed_struc =~ s/$find/$replace/g;
$find = ")))..))..............)"; #iSpinach A
$replace = "S";
$find = quotemeta $find;
$parsed_struc =~ s/$find/$replace/g;
$find = ").).........)))))"; #iSpinach B Length17
$replace = "U";
$find = quotemeta $find;
$parsed_struc =~ s/$find/$replace/g;
$find = "(.(.........((((("; #iSpinach B
$replace = "U";
$find = quotemeta $find;
$parsed_struc =~ s/$find/$replace/g;
$find = "(((.......................)))"; #Mango length29
$replace = "Q";
$find = quotemeta $find;
$parsed_struc =~ s/$find/$replace/g;
#Tetraloops
$find = "(....)";
$replace = "T";
$find = quotemeta $find; # escape regex metachars if present
$parsed_struc =~ s/$find/$replace/g;
#180KL loops
$find = qr/\(\.\.(\[|.|\]){6}\.\)/; # (..[[[[[[.) (..]]]]]].) or (.........)
$replace = "K";
$parsed_struc =~ s/$find/$replace/g;
#120KL loops
$find = "(.......)";
$replace = "L";
$find = quotemeta $find; # escape regex metachars if present
$parsed_struc =~ s/$find/$replace/g;
$find = "([[[[[[[)";
$replace = "L";
$find = quotemeta $find; # escape regex metachars if present
$parsed_struc =~ s/$find/$replace/g;
$find = "(]]]]]]])";
$replace = "L";
$find = quotemeta $find; # escape regex metachars if present
$parsed_struc =~ s/$find/$replace/g;
$find = "(...(("; #search for K-turn, note that this actually reads any 3nt or 6nt bulge as a Kturn pattern, but no other motifs use 3nt or 6nt at this stage.
$replace = "B";
$find = quotemeta $find;
$parsed_struc =~ s/$find/$replace/g;
$find = ")...))";
$replace = "B";
$find = quotemeta $find;
$parsed_struc =~ s/$find/$replace/g;
$find = "((......("; # B is the 2nd side of the Kturn
$replace = "C";
$find = quotemeta $find;
$parsed_struc =~ s/$find/$replace/g;
$find = "))......)";
$replace = "C";
$find = quotemeta $find;
$parsed_struc =~ s/$find/$replace/g;
#Crossover Symbols are specially recognized
$find = qr/.[\^]../;
$replace = "E";
$parsed_struc =~ s/$find/$replace/g;
$find = ",";
$replace = "A";
$find = quotemeta $find;
$parsed_struc =~ s/$find/$replace/g;
$find = ".";
$replace = "A";
$find = quotemeta $find;
$parsed_struc =~ s/$find/$replace/g;
#Everything remaining is modeled as a nt stacked on helix
$find = qr/\W/;
$replace = "H";
$parsed_struc =~ s/$find/$replace/g;
$nt_pos = 1;
### Code conversion table
### T=6nts
### K=11nts
### L=9nts
### E=3nts
### H=1nt
#&printer("REMARK - $parsed_struc \n"); ##Structures larger than 1000nts can crash SwissPDB by overflowing the remark buffer, so I am commenting this line out. It is for debugging the parser on smaller designs.
my @assembly_instructions = split(//, $parsed_struc);
#&printer("REMARK - $parsed_struc\n");
## Scan over the assembly instruction list and the map and add in 'O' everywhere we have a multi-junction.
my $index=0; #index is where the build is currently, tracked separately from synthesized
my $k =0; my $count=0;
$cross_rand_a = rand(1)*$eccentricity-$eccentricity/2; #randomize variables related to the relaxed crossover (use same random number for the whole construct each pdb iteration)
$cross_rand_b = rand(1)*$eccentricity-$eccentricity/2;
$cross_rand_c = rand(1)*$eccentricity-$eccentricity/2;
for ( $k=0; $k< scalar(@assembly_instructions) ; $k++){
if ($index< $synthesized ){
if ($index > $timesteps-$nascent_chain){
if ($assembly_instructions[$k] eq 'H') { &add_nascent; $index++;}
if ($assembly_instructions[$k] eq 'A') { &add_nascent; $index++;} #A is single-strand or unpaired
if ($assembly_instructions[$k] eq 'T') { &add_tetraloop; $index+=6;}
if ($assembly_instructions[$k] eq 'K') { &add_KL; $index+=11;}
if ($assembly_instructions[$k] eq 'L') { &add_KLbend; $index+=9;}
if ($assembly_instructions[$k] eq 'E') { for($count=0; $count<3; $count++){&add_nascent;} $index+=3;}
if ($assembly_instructions[$k] eq 'O') { for($count=0; $count<3; $count++){&add_nascent;} $index+=3;}
if ($assembly_instructions[$k] eq 'R') { &add_tar; $index+=28;} #TAR
if ($assembly_instructions[$k] eq 'N') { &add_pp7; $index+=25;} #PP7
if ($assembly_instructions[$k] eq 'M') { &add_ms2; $index+=13;} #MS2
if ($assembly_instructions[$k] eq 'S') { for($count=0; $count<22; $count++){&add_nascent;} $index+=22;} #SpinachA
if ($assembly_instructions[$k] eq 'U') { for($count=0; $count<17; $count++){&add_nascent;} $index+=17;} #SpinachB
if ($assembly_instructions[$k] eq 'B') { for($count=0; $count<6; $count++){&add_nascent;} $index+=6;} #KturnA
if ($assembly_instructions[$k] eq 'C') { for($count=0; $count<9; $count++){&add_nascent;} $index+=9;} #KturnB
if ($assembly_instructions[$k] eq 'Q') {&add_mango; $index+=29;} #Mango
} else {
if ($closed_structure[$index]eq"O"){
if ($assembly_instructions[$k] eq 'H') { &add_nts; $index++;}
if ($assembly_instructions[$k] eq 'A') { &add_nascent; $index++;}
if ($assembly_instructions[$k] eq 'T') { &add_tetraloop; $index+=6;}
if ($assembly_instructions[$k] eq 'K') { &add_KL; $index+=11;}
if ($assembly_instructions[$k] eq 'L') { &add_KLbend; $index+=9;}
if ($assembly_instructions[$k] eq 'E' ) {
if($index>($timesteps-$stacking_delay) ) {&opened; $index+=3;
} else {
&crossover_relaxed; $index+=3;
}
}
if ($assembly_instructions[$k] eq 'O') {
if($map[$index+3]>$synthesized){
&add_nascent; &add_nascent; &add_nascent; $index+=3;
} else {
if ($index > ($timesteps-$stacking_delay) ){
&add_nts; &add_nts; &add_nts; $index+=3;
} else {
&opened;
$index+=3;
}
}
}
if ($assembly_instructions[$k] eq 'R') { &add_tar; $index+=28;}
if ($assembly_instructions[$k] eq 'M') { &add_ms2; $index+=13;}
if ($assembly_instructions[$k] eq 'N') { &add_pp7; $index+=25; }
if ($assembly_instructions[$k] eq 'S') { &add_spinacha; $index+=22;}
if ($assembly_instructions[$k] eq 'U') { &add_spinachb; $index+=17;}
if ($assembly_instructions[$k] eq 'B') { &add_kturna; $index+=6;}
if ($assembly_instructions[$k] eq 'C') { &add_kturnb; $index+=9;}
if ($assembly_instructions[$k] eq 'Q') { &add_mango; $index+=29;}
} else {
if ($assembly_instructions[$k] eq 'H') { &add_nts; $index++;}
if ($assembly_instructions[$k] eq 'A') { &add_nts; $index++;}
if ($assembly_instructions[$k] eq 'T') { &add_tetraloop; $index+=6;}
if ($assembly_instructions[$k] eq 'K') { &add_KL; $index+=11;}
if ($assembly_instructions[$k] eq 'L') { &add_KLbend; $index+=9;}
if ($assembly_instructions[$k] eq 'E') { &crossover; $index+=3;}
if ($assembly_instructions[$k] eq 'O') { &add_nts; &add_nts; &add_nts; $index+=3;}
if ($assembly_instructions[$k] eq 'R') { &add_tar; $index+=28;}
if ($assembly_instructions[$k] eq 'M') { &add_ms2; $index+=13;}
if ($assembly_instructions[$k] eq 'N') { &add_pp7; $index+=25; }
if ($assembly_instructions[$k] eq 'S') { &add_spinacha; $index+=22;}
if ($assembly_instructions[$k] eq 'U') { &add_spinachb; $index+=17;}
if ($assembly_instructions[$k] eq 'B') { &add_kturna; $index+=6;}
if ($assembly_instructions[$k] eq 'C') { &add_kturnb; $index+=9;}
if ($assembly_instructions[$k] eq 'Q') { &add_mango; $index+=29;}
}
}
} else {
if ($assembly_instructions[$k] eq 'H') { &add_hidden; $index++;}
if ($assembly_instructions[$k] eq 'A') { &add_hidden; $index++;}
if ($assembly_instructions[$k] eq 'T') { for($count=0; $count<6; $count++){&add_hidden;} $index+=6;}
if ($assembly_instructions[$k] eq 'K') { for($count=0; $count<11; $count++){&add_hidden;} $index+=11;}
if ($assembly_instructions[$k] eq 'L') { for($count=0; $count<9; $count++){&add_hidden;} $index+=9;}
if ($assembly_instructions[$k] eq 'E') { &add_hidden; &add_hidden; &add_hidden; $index+=3;}
if ($assembly_instructions[$k] eq 'O') { &add_hidden; &add_hidden; &add_hidden; $index+=3;}
if ($assembly_instructions[$k] eq 'R') { for($count=0; $count<28; $count++){&add_hidden;} $index+=28;} #TAR
if ($assembly_instructions[$k] eq 'M') { for($count=0; $count<13; $count++){&add_hidden;} $index+=13;} #MS2
if ($assembly_instructions[$k] eq 'N') { for($count=0; $count<25; $count++){&add_hidden;} $index+=25;} #PP7
if ($assembly_instructions[$k] eq 'S') { for($count=0; $count<22; $count++){&add_hidden;} $index+=22;} #SpinachA
if ($assembly_instructions[$k] eq 'U') { for($count=0; $count<17; $count++){&add_hidden;} $index+=17;} #SpinachB
if ($assembly_instructions[$k] eq 'B') { for($count=0; $count<6; $count++){&add_hidden;} $index+=6;} #KturnA
if ($assembly_instructions[$k] eq 'C') { for($count=0; $count<9; $count++){&add_hidden;} $index+=9;} #KturnB
if ($assembly_instructions[$k] eq 'Q') { for($count=0; $count<29; $count++){&add_hidden;} $index+=29;} #Mango
}
}
my $t = 1;
my $seam = 0;
my $filecount=1;
@input_seq = split(//,$input_sequence);
foreach $PDB ( @PDB ) { #print out the PDB file
if ($t<99000){$seam = $PDB->{i};}
if ($PDB->{i}<=$seam){
if($pmode==0 || $PDB->{a} eq 'P '){
printf $output_spool "%-6s", "ATOM";
printf $output_spool "%5s", $t;
print $output_spool " ";
print $output_spool $PDB->{a};
print $output_spool " ";
#print $output_spool $PDB->{n}; #eliminating residue names simplifies some problems that can occur with animations
print $output_spool "A"; #just put A for each nucleotide
print $output_spool " ";
print $output_spool $PDB->{h}; #Retain chain names
printf $output_spool "%4s", $PDB->{i};
print $output_spool " ";
printf $output_spool ("%8s",$PDB->{x});
printf $output_spool ("%8s",$PDB->{y});
printf $output_spool ("%8s",$PDB->{z});
print $output_spool " 1.00100.00 ";
print $output_spool "\n";
$t++;
}
} else {
close $output_spool;
substr $name, length($name)-4 , 4, "";
open( $output_spool, '>', "$name\_$synthesized\_$filecount.pdb"); #open a new file buffer
$t=1;
if($pmode==0 || $PDB->{a} eq 'P '){
printf $output_spool "%-6s", "ATOM";
printf $output_spool "%5s", $t;
print $output_spool " ";
print $output_spool $PDB->{a};
print $output_spool " ";
#print $output_spool $PDB->{n}; #eliminating atom names simplifies some problems that can occur with animations
print $output_spool "A"; #just put A for each nucleotide
print $output_spool " ";
print $output_spool $PDB->{h}; #Retain chain names
printf $output_spool "%4s", $PDB->{i};
print $output_spool " ";
printf $output_spool ("%8s",$PDB->{x});
printf $output_spool ("%8s",$PDB->{y});
printf $output_spool ("%8s",$PDB->{z});
print $output_spool " 1.00100.00 ";
print $output_spool "\n";
$t++;
}
}
}
close $output_spool;
@PDB = (); ##very important! Flush out the PDB buffer before the next file is started.
}
close $output_spool2; #closes the spool with the substructure outputs
#################################################
## >>>>>>>>>>>>>>>>>> SUB ROUTINES <<<<<<<<<<<<<<<<<<<<
#################################################
sub translate_matrix {
my @r_tr1 = split(' ',$_[0]);
my @r_tr2 = split(' ',$_[1]);
my $tx=$r_tr2[0];
my $ty=$r_tr2[1];
my $tz=$r_tr2[2];
my @Translate=(
1, 0, 0, 0,
0, 1, 0, 0,
0, 0, 1, 0,
$tx, $ty, $tz, 1);
transform ("@r_tr1","@Translate");
}
sub rotate_x { #point followed by theta in rad
my @r_tr1 = split(' ',$_[0]);
my $theta = $_[1];
my @Translate=(
1, 0, 0, 0,
0, cos($theta), -sin($theta), 0,
0, sin($theta), cos($theta), 0,
0, 0, 0, 1);
transform ("@r_tr1","@Translate");
}
sub rotate_y { #point followed by theta in rad
my @r_tr1 = split(' ',$_[0]);
my $theta = $_[1];
my @Translate=(
cos($theta), 0, sin($theta), 0,
0, 1, 0, 0,
-sin($theta), 0, cos($theta), 0,
0, 0, 0, 1);
transform ("@r_tr1","@Translate");
}
sub rotate_z { #point followed by theta in rad
my @r_tr1 = split(' ',$_[0]);
my $theta = $_[1];
my @Translate=(
cos($theta), -sin($theta), 0, 0,
sin($theta), cos($theta), 0, 0,
0, 0, 1, 0,
0, 0, 0, 1);
transform ("@r_tr1","@Translate");
}
sub transform { #point (x,y,z,1) multiplied by the transform_matrix (16 elements long)
my @m1 = split(' ',$_[0]);
my @m2 = split(' ',$_[1]);
my $result = [];
my $xout=$m1[0]*$m2[0] + $m1[1]*$m2[4] + $m1[2]*$m2[8] + $m1[3]*$m2[12];
my $yout=$m1[0]*$m2[1] + $m1[1]*$m2[5] + $m1[2]*$m2[9] + $m1[3]*$m2[13];
my $zout=$m1[0]*$m2[2] + $m1[1]*$m2[6] + $m1[2]*$m2[10] + $m1[3]*$m2[14];
my $vout=$m1[0]*$m2[3] + $m1[1]*$m2[7] + $m1[2]*$m2[11] + $m1[3]*$m2[15];
($xout, $yout, $zout, $vout);
}
sub add_nts {
my $no = 1;
if ($map[$nt_pos-1]<($nt_pos-1) && $motif[$map[$nt_pos-1]]==0 ) { #if map<nt_pos then we are a closing nt, and we calculate from the partner's ref-frame (later we may average the two options)
$ref_frame_position = $map[$nt_pos-1]+2;
@ref_frame_angle = &update_ref_frame($ref_frame_position);
foreach $ATOM ( @ATOM ) { #paste in the nt as paired to the map[nt_pos]
if ( ($ATOM->{n} eq $seq[$nt_pos-1]) && ($ATOM->{h} eq 'A')) { #$c is the current resi, atom(i) is the resi number element in the PDB file.
$nt_step[0]=2.2260; $nt_step[1]=2.0800; $nt_step[2]=-10.4200; $nt_step[3]=1; #flip strand
$angles[0]=2.00510013; $angles[1]=2.95283932; $angles[2]=1.1652;
$point[0]=$ATOM->{x}; $point[1]=$ATOM->{y}; $point[2]=$ATOM->{z}; $point[3]=1;
@moved = &rotate_z ("@point",-$angles[2]); #first rotation -we move the nt to the untranslocated pos
@moved = &rotate_y ("@moved",-$angles[1]); #second rotation
@moved = &rotate_z ("@moved",-$angles[0]); #final rotation
@moved = &translate_matrix ("@moved","@nt_step"); #POINT followed by translation vector
@moved = &rotate_z ("@moved",-$ref_frame_angle[2]); #first rotation -now we rotate aout
@moved = &rotate_y ("@moved",-$ref_frame_angle[1]); #second rotation
@moved = &rotate_z ("@moved",-$ref_frame_angle[0]); #final rotation
@moved = &translate_matrix ("@moved","@ref_trans"); # Now moving to add to the 3prime end
$roundedx = sprintf("%4.3f", $moved[0]); $roundedy = sprintf("%4.3f", $moved[1]); $roundedz = sprintf("%4.3f", $moved[2]);
push @PDB, {
"a" => $ATOM->{a}, #atom type
"n" => $ATOM->{n}, #residue type
"i" => $nt_pos, #residue number
"h" => "A", #chain name
"x" => sprintf("%8s",$roundedx),
"y" => sprintf("%8s",$roundedy),
"z" => sprintf("%8s",$roundedz),
}
}
}
$nt_pos += 1; #increment nt_counter
} else {
$ref_frame_position = $nt_pos;
@ref_frame_angle = &update_ref_frame($ref_frame_position);
foreach $ATOM ( @ATOM ) { #we scan the datafile for the nt type and paste it into the active site
if ( ($ATOM->{n} eq $seq[$nt_pos-1]) && ($ATOM->{h} eq 'A')) { #$c is the current resi, atom(i) is the resi number element in the PDB file.
$nt_step[0]=5.05026531; $nt_step[1]=0.63351020; $nt_step[2]=-2.27143878; $nt_step[3]=1; #these were measured by nt_diff.pl, averaged from 50bp of A-form generated in Assemble/Chimera
$angles[0]=-1.05152505; $angles[1]=0.46918242; $angles[2]=1.37954160;
$point[0]=$ATOM->{x}; $point[1]=$ATOM->{y}; $point[2]=$ATOM->{z}; $point[3]=1;
@moved = &rotate_z ("@point",-$angles[2]); #first rotation -we move the nt to the untranslocated pos
@moved = &rotate_y ("@moved",-$angles[1]); #second rotation
@moved = &rotate_z ("@moved",-$angles[0]); #final rotation
@moved = &translate_matrix ("@moved","@nt_step"); #POINT followed by translation vector
@moved = &rotate_z ("@moved",-$ref_frame_angle[2]); #first rotation -now we rotate aout
@moved = &rotate_y ("@moved",-$ref_frame_angle[1]); #second rotation
@moved = &rotate_z ("@moved",-$ref_frame_angle[0]); #final rotation
@moved = &translate_matrix ("@moved","@ref_trans"); # Now moving to add to the 3prime end
$roundedx = sprintf("%4.3f", $moved[0]); $roundedy = sprintf("%4.3f", $moved[1]); $roundedz = sprintf("%4.3f", $moved[2]);
push @PDB, {
"a" => $ATOM->{a}, #atom type
"n" => $ATOM->{n}, #residue type
"i" => $nt_pos, #residue number
"h" => "A", #chain name
"x" => sprintf("%8s",$roundedx),
"y" => sprintf("%8s",$roundedy),
"z" => sprintf("%8s",$roundedz),
}
}
}
$nt_pos += 1; #increment nt_counter
}
$motif[$nt_pos-2] = 0;
}