EntDetect 1.2.0__py3-none-any.whl

EntDetect/resources/__init__.py

@@ -0,0 +1,11 @@
+"""Bundled resource files shipped with EntDetect.
+
+This package exists so :mod:`importlib.resources` can locate bundled helper
+executables/scripts (e.g., ``calc_Q.pl``, ``calc_K.pl``, ``stride``, ``pulchra``)
+and supporting data files.
+"""
+"""Packaged resource files for EntDetect.
+
+This subpackage exists so `importlib.resources` can locate bundled helper
+executables/scripts (e.g., `calc_Q.pl`, `stride`, `pulchra`) and data files.
+"""

EntDetect/resources/calc_K.pl

@@ -0,0 +1,712 @@
+#!/usr/bin/perl
+
+use Getopt::Long;
+use Data::Dumper;
+
+my ($help, $input_cor, $sec_def, $dom_def, $traj, $start, $end, $output_dir);
+GetOptions(
+ 'help|h!' => \$help,
+ 'input|i=s' => \$input_cor,
+ 'secs|s=s' => \$sec_def,
+ 'domain|d=s' => \$dom_def,
+ 'traj|t=s' => \$traj,
+ 'begin|b=s' => \$start,
+ 'end|e=s' => \$end,
+ 'outdir|o=s' => \$output_dir,
+);
+
+my $usage = "
+  Usage: perl calc_chirality_number.pl 
+              --input | -i <INPUT.COR> for identify native contacts
+              --domain | -d <DOMAIN.DAT> for domain defination
+              [--secs | -s] <SECONDARY STRUCTURE> for secondary 
+                          structure defination. If no file specified,
+                          it will calculate all residues regardless
+                          of the secondary structure.
+              --traj | -t <TRAJ.DCD> for simulation trajectory
+              [--begin | -b] <START STEP> to split trajectory. 
+                                  Default is 1
+              [--end | -e] <END STEP> to split trajectory. 
+                                Default is the end frame.
+              [--outdir | -o] <DIRECTORY> for the outputs. Default is the directory
+                                          of your trajectories
+              [--help | -h]\n
+  Example for DOMAIN.DAT:
+  1:96 302:350 a #Domain 1 is from resid 1 to 96 and 302 to 350, and in
+                 #alpha-helix class
+  97:155 b #Domain 2 is from resid 97 to 155 and in beta-sheet class
+  156:301 c #Domain 3 is from resid 156 to 301 and in alpha-beta class\n\n";
+
+if($help)
+{
+  die($usage);
+}
+elsif(!(defined($input_cor) && defined($dom_def) && defined($traj)))
+{
+  die($usage);
+}
+
+if(!defined($sec_def))
+{
+  $sec_def = "";
+}
+if(!defined($start))
+{
+  $start = 1;
+}
+if(!defined($end))
+{
+  $end = 9999999999999999999;
+}
+
+my @str = ();
+if($traj =~ /\.cor$/)
+{
+  @str = split(/\.cor/, $traj);
+}
+else
+{
+  @str = split(/\.dcd/, $traj);
+}
+@str = split(/\//, $str[0]);
+my $name = $str[$#str];
+my $dir = join("/", @str[0...$#str-1]);
+if(@str eq 1)
+{
+  $dir = './';
+}
+
+if(!defined($output_dir))
+{
+  $output_dir = $dir;
+}
+
+my $cutoff = 0;
+
+my @domain = parse_domain($dom_def);
+
+my @native_cor = parse_cor($input_cor);
+my $native_natom = @native_cor;
+
+my @sec_struc = parse_secondary_structure($sec_def);
+
+my @native_c_list = calc_traj_c_list(\@native_cor, \@domain, \@sec_struc);
+#print "@{$native_c_list[$#native_c_list]} \n";
+
+if($traj =~ /\.cor$/)
+{
+  open(DAT, ">${output_dir}/K_${name}.dat")||die("Error: cannot create ${output_dir}/K_${name}.dat\n\n");
+  for(my $i = 1; $i <= @domain; $i++)
+  {
+    my $dom = $domain[$i-1];
+    if($dom->{"class"} eq "i")
+    {
+      printf DAT ("%10s ", $dom->{"range"}->[0]."|".$dom->{"range"}->[1]);
+    }
+    else
+    {
+      printf DAT ("%10s ", "D_$i");
+    }
+  }
+  printf DAT ("%10s\n", "total");
+  my @traj_cor = parse_cor($traj);
+  my $natom = @traj_cor;
+  if($natom ne $native_natom)
+  {
+    print("Warning: atom numbers mismatch in $input_cor ($native_natom) and $traj ($natom)\n")
+  }
+  my @traj_c_list = calc_traj_c_list(\@traj_cor, \@domain, \@sec_struc);
+
+  for(my $i = 0; $i < @traj_c_list; $i++)
+  {
+    my $K = calc_K($native_c_list[$i], $traj_c_list[$i], $cutoff);
+    my $fraction = sprintf("%.4f", $K);
+    printf DAT ("%10s ", $fraction);
+  }
+  printf DAT ("\n");
+  exit;
+}
+
+open(my $dcdfile, "<$traj") || die("Error: Cannot find $traj\n\n");
+binmode($dcdfile);
+my ($natom, $tstep, $nframe, $first, $delta, $crystal, $fixed) = read_DCD_head($dcdfile);
+
+if($natom ne $native_natom)
+{
+  print("Warning: atom numbers mismatch in $input_cor ($native_natom) and $traj ($natom)\n")
+}
+
+open(DAT, ">${output_dir}/K_${name}.dat")||die("Error: cannot create ${output_dir}/K_${name}.dat\n\n");
+for(my $i = 1; $i <= @domain; $i++)
+{
+  my $dom = $domain[$i-1];
+  if($dom->{"class"} eq "i")
+  {
+    printf DAT ("%10s ", $dom->{"range"}->[0]."|".$dom->{"range"}->[1]);
+  }
+  else
+  {
+    printf DAT ("%10s ", "D_$i");
+  }
+}
+printf DAT ("%10s\n", "total");
+
+my $deltat = $delta * $tstep;
+my $firstframe = $first / $delta;
+for(my $i_frame = 1; $i_frame <= $nframe; $i_frame++)
+{
+  my @traj_cor = read_DCD_frame($dcdfile, $crystal);
+  if($i_frame >= $start && $i_frame <= $end)
+  {
+    my @traj_c_list = calc_traj_c_list(\@traj_cor, \@domain, \@sec_struc);
+    #print "@{$traj_c_list[$#traj_c_list]} \n";
+
+    for(my $i = 0; $i < @traj_c_list; $i++)
+    {
+      my $K = calc_K($native_c_list[$i], $traj_c_list[$i], $cutoff);
+      my $fraction = sprintf("%.4f", $K);
+      printf DAT ("%10s ", $fraction);
+    }
+    printf DAT ("\n");
+  }
+}
+close(DAT);
+
+######################################################
+sub parse_domain
+{
+  my $dom_def = $_[0];
+
+  my @domain = ();
+
+  my %class = ("a" => "Alpha-helix",
+               "b" => "Beta-sheet",
+               "c" => "Alpha-Beta");
+
+  print "-> Domain defination:\n";
+
+  open(DAT, "<$dom_def") || die("Error: Cannot find $dom_def\n\n");
+  my $n = 1;
+  my $start_min = 10000;
+  while(my $line = <DAT>)
+  {
+    chomp($line);
+    $line =~ s/^\s+|\s+$//g;
+    if($line !~ /^#/)
+    {
+      my @str = split(/\s*#/, $line);
+      my @data = split(/\s+/, $str[0]);
+      my @res_range = @data[0..$#data-1];
+      my $sec_class = $data[$#data];
+      print "   Domain $n: ";
+      if($sec_class ne "a" && $sec_class ne "b" && $sec_class ne "c")
+      {
+        die("Error: Forget to specify class as a, b or c?\n\n");
+      }
+      my %dom = ("range" => [],
+                 "class" => $sec_class);
+      foreach my $d (@res_range)
+      {
+        my @data = split(/\s*:\s*/, $d);
+        my $start = $data[0];
+        my $end = $data[1];
+        print "$start ~ $end; ";
+        if($start < $start_min)
+        {
+          $start_min = $start;
+        }
+        push@{$dom{"range"}}, [$start, $end];
+      }
+      print "Class: ".$class{$sec_class}."\n";
+      push@domain, \%dom;
+      $n++;
+    }
+  }
+  close(DAT);
+
+  my $offset = $start_min - 1;
+  foreach my $d (@domain)
+  {
+    foreach my $r (@{$d->{"range"}})
+    {
+      $r->[0] -= $offset;
+      $r->[1] -= $offset;
+    }
+  }
+
+  for(my $i = 1; $i < $n-1; $i++)
+  {
+    for(my $j = $i+1; $j < $n; $j++)
+    {
+      my %hash = ("range" => [$i, $j],
+                  "class" => "i",);
+      push@domain, \%hash;
+    }
+  }
+  return @domain;
+}
+
+######################################################
+sub parse_mask
+{
+  my $mask = $_[0];
+  my @sel_idx = ();
+  $mask =~ s/^\s+|\s+$//g;
+  if($mask eq "all")
+  {
+    @sel_idx = ("all");
+  }
+  else
+  {
+    my @str = split(/,\s*/, $mask);
+    foreach my $s (@str)
+    {
+      if($s =~ /\-/)
+      {
+        my @str_1 = split(/\s*\-\s*/, $s);
+        for(my $i = $str_1[0]; $i <= $str_1[1]; $i++)
+        {
+          push@sel_idx, $i;
+        }
+      }
+      else
+      {
+        push@sel_idx, $s;
+      }
+    }
+  }
+  return @sel_idx;
+}
+
+######################################################
+sub parse_cor
+{
+  my $cor = $_[0];
+  
+  my @native_cor = ();
+  my $num_atom = 0;
+  my $if_ext = 0;
+  open(COR, "<$cor") || die("Error: cannot find $cor\n\n");
+  while(my $line = <COR>)
+  {
+  	chomp($line);
+  	if($line !~ /^\*/)
+  	{
+  	  if($line =~ /^\s*[0-9]+$/)
+  	  {
+  	  	$line =~ s/^\s+|\s+$//g;
+  	  	$num_atom = $line;
+  	  }
+  	  elsif($line =~ /^\s*[0-9]+\s+EXT$/)
+  	  {
+  	    $line =~ s/^\s+|\s+$//g;
+  	    $if_ext = 1;
+  	    my @str = split(/\s+/, $line);
+  	    $num_atom = $str[0];
+  	  }
+  	  else
+  	  {
+  	    my ($x, $y, $z) = (0, 0, 0);
+  	    if($if_ext eq 0)
+  	    {
+  	      ($x, $y, $z) = unpack("x5 x5 x6 x1 x3 a10 a10 a10 x20", $line);
+  	    }
+  	  	else
+  	  	{
+  	  	  ($x, $y, $z) = unpack("x10 x10 x10 x10 a20 a20 a20 x10 x10 x20", $line);
+  	  	}
+  	  	$x =~ s/^\s+|\s+$//g;
+  	  	$y =~ s/^\s+|\s+$//g;
+  	  	$z =~ s/^\s+|\s+$//g;
+  	  	push@native_cor, [$x, $y, $z];
+  	  }
+  	}
+  }
+  close(COR);
+
+  return @native_cor;
+}
+
+######################################################
+sub parse_secondary_structure
+{
+  my $sec_def = $_[0];
+  my @sec_struc = ();
+  print "-> Secondary structure defination:\n";
+  print "   ";
+  if($sec_def eq "")
+  {
+    print "None\n";
+    return ([1, 99999999999999]);
+  }
+  open(DAT, "<$sec_def") || die("Error: cannot find $sec_def\n\n");
+  while(my $line = <DAT>)
+  {
+  	chomp($line);
+  	my @str = split(/\s+/, $line);
+  	push@sec_struc, [$str[1], $str[2]];
+    print $str[1]." ~ ".$str[2]."; ";
+  }
+  close(DAT);
+  print "\n";
+  return @sec_struc;
+}
+
+#########################################################
+sub V_dot
+{
+  my @V1 = @{$_[0]};
+  my @V2 = @{$_[1]};
+  
+  my $result = 0;
+  for(my $i = 0; $i < @V1; $i++)
+  {
+    $result += $V1[$i] * $V2[$i];
+  }
+  
+  return $result;
+}
+
+#########################################################
+sub V_cross
+{
+  my @V1 = @{$_[0]};
+  my @V2 = @{$_[1]};
+  
+  my @result = ();
+  $result[0] = $V1[1]*$V2[2]-$V1[2]*$V2[1];
+  $result[1] = $V1[2]*$V2[0]-$V1[0]*$V2[2];
+  $result[2] = $V1[0]*$V2[1]-$V1[1]*$V2[0];
+  
+  return @result;
+}
+
+#########################################################
+sub V_norm
+{
+  my @V1 = @{$_[0]};
+  
+  my $result = sqrt(V_dot(\@V1, \@V1));
+  
+  return $result;
+}
+
+#########################################################
+sub V_add
+{
+  my @V1 = @{$_[0]};
+  my @V2 = @{$_[1]};
+  
+  my @result = ();
+  for(my $i = 0; $i < @V1; $i++)
+  {
+    $result[$i] = $V1[$i] + $V2[$i];
+  }
+  
+  return @result;
+}
+
+#########################################################
+sub V_minus
+{
+  my @V1 = @{$_[0]};
+  my @V2 = @{$_[1]};
+  
+  my @result = ();
+  for(my $i = 0; $i < @V1; $i++)
+  {
+    $result[$i] = $V1[$i] - $V2[$i];
+  }
+  
+  return @result;
+}
+
+#########################################################
+sub calc_c_list
+{
+  my @coor = @{$_[0]};
+  my @sel = @{$_[1]};
+
+  my @c_list = ();
+
+  for(my $i = 0; $i < @sel-3; $i++)
+  {
+    my @v1 = V_minus($coor[$sel[$i+1]], $coor[$sel[$i]]);
+    my @v2 = V_minus($coor[$sel[$i+2]], $coor[$sel[$i+1]]);
+    my @v3 = V_minus($coor[$sel[$i+3]], $coor[$sel[$i+2]]);
+    my @a = V_cross(\@v1, \@v2);
+    my $c = V_dot(\@a, \@v3);
+    my $cn = V_norm(\@v1) * V_norm(\@v2) * V_norm(\@v3);
+    if($cn == 0)
+    {
+      $c = 'nan';
+    }
+    else
+    {
+      # $c = $c / (V_norm(\@v1) * V_norm(\@v2) * V_norm(\@v3));
+      $c = $c / $cn;
+    }
+    push@c_list, $c;
+  }
+
+  return @c_list;
+}
+
+#########################################################
+sub calc_traj_c_list
+{
+  my @coor = @{$_[0]};
+  my @domain = @{$_[1]};
+  my @sec_struc = @{$_[2]};
+  
+  my @result = ();
+  foreach my $dom (@domain)
+  {
+    my @range = @{$dom->{"range"}};
+    if($dom->{"class"} eq "i")
+    {
+      my @range_1 = @{$domain[$range[0]-1]->{"range"}};
+      my @range_2 = @{$domain[$range[1]-1]->{"range"}};
+      @range = (@range_1, @range_2);
+    }
+    
+    my @sel = ();
+    foreach my $rd (@range)
+    {
+      for(my $i = $rd->[0]; $i <= $rd->[1]; $i++)
+      {
+        my $tag_i = 0;
+        foreach my $rs (@sec_struc)
+        {
+          #if($i >= $rs->[0] && $i <= $rs->[1])
+          if($i == $rs->[0] || $i == $rs->[1])
+          {
+            $tag_i = 1;
+            last;
+          }
+        }
+
+        if($tag_i eq 1)
+        {
+          push@sel, $i-1;
+        }
+      }
+    }
+    my @c_list = calc_c_list(\@coor, \@sel);
+    push@result, \@c_list;
+  }
+  my @sel = ();
+  for(my $i = 1; $i <= $sec_struc[$#sec_struc]->[1]; $i++)
+  {
+    my $tag_i = 0;
+    foreach my $rs (@sec_struc)
+    {
+      #if($i >= $rs->[0] && $i <= $rs->[1])
+      if($i == $rs->[0] || $i == $rs->[1])
+      {
+        $tag_i = 1;
+        last;
+      }
+    }
+
+    if($tag_i eq 1)
+    {
+      push@sel, $i-1;
+    }
+  }
+  my @c_list = calc_c_list(\@coor, \@sel);
+  push@result, \@c_list;
+  return @result;
+}
+
+#########################################################
+sub calc_K
+{
+  my @native_c_list = @{$_[0]};
+  my @traj_c_list = @{$_[1]};
+  my $cutoff = $_[2];
+  
+  my $K = 0;
+  my $not_nan = 0;
+  for(my $i = 0; $i < @native_c_list; $i++)
+  {
+    if($traj_c_list[$i] ne 'nan' && $traj_c_list[$i]*$native_c_list[$i] >= 0)
+    {
+      $K += 1;
+    }
+    if($native_c_list[$i] ne 'nan')
+    {
+      $not_nan += 1;
+    }
+  }
+  if($not_nan == 0)
+  {
+    $K = -1;
+  }
+  else
+  {
+    $K /= $not_nan;
+  }
+  return $K;
+}
+
+#########################################################
+sub calc_K_2
+{
+  my @native_c_list = @{$_[0]};
+  my @traj_c_list = @{$_[1]};
+  my $cutoff = $_[2];
+  
+  my $K_0 = 0;
+  my $K_1 = 0;
+  for(my $i = 0; $i < @native_c_list; $i++)
+  {
+    $K_0 += $native_c_list[$i];
+    $K_1 += $traj_c_list[$i];
+  }
+  if($K_0 * $K_1 < 0)
+  {
+    return 1;
+  }
+  else
+  {
+    return 0;
+  }
+}
+
+#########################################################
+sub readFortran 
+{
+  my $handle=shift;
+
+  my $dat;
+  my $tdat;
+
+  read($handle,$tdat,4) || die "cannot read data";
+  my $len=unpack("L",$tdat);
+  read($handle,$dat,$len) || die "cannot read data";
+  read($handle,$tdat,4) || die "cannot read data";
+
+#  printf STDERR "Fread %d bytes\n",$len;
+
+  return ($dat,$len);
+}
+
+################################################################
+sub read_DCD
+{
+  my $traj = $_[0];
+  my $boxsize = $_[1];
+  my $from = 1;
+  my $to = 999999999999999;
+  my $step = 1;
+
+  open(my $dcdfile, "<$traj") || die("Error: Cannot find $traj\n\n");
+  binmode($dcdfile);
+  my $buffer;
+  my $len;
+  ($buffer,$len)=readFortran($dcdfile);
+  my ($tag,@icontrol)=unpack("A4L*",$buffer);
+  
+  ($buffer,$len)=readFortran($dcdfile);
+  ($buffer,$len)=readFortran($dcdfile);
+  my $natom=unpack("L",$buffer);
+  
+  my $tstep=unpack("f",pack("L",$icontrol[9]))*4.88882129E-02;
+  my $nfiles=$icontrol[0];
+  my $first=$icontrol[1];
+  my $delta=$icontrol[2];
+  my $deltat=$icontrol[2]*$tstep;
+  my $crystal=$icontrol[10];
+  my $fixed=$icontrol[8];
+
+  my $firstframe=$first/$delta;
+
+  my ($xbuf,$ybuf,$zbuf);
+  
+  my $itot = 0;
+  for (my $i=1; $itot<=$to && $i<=$nfiles; $i++) 
+  {
+    $itot++;
+    if ($crystal) 
+    {
+      my ($tbuf,$tlen)=readFortran($dcdfile);
+      if ($boxsize)
+      {
+        my @cdat=unpack("d*",$tbuf);
+        printf "%f %f %f\n",$cdat[0],$cdat[2],$cdat[5];
+      }
+    }
+
+    ($xbuf,$len)=readFortran($dcdfile); # printf STDERR "%d ",$len;
+    ($ybuf,$len)=readFortran($dcdfile); # printf STDERR "%d ",$len;
+    ($zbuf,$len)=readFortran($dcdfile); # printf STDERR "%d \n",$len;
+      
+    if ($itot>=$from && $itot<=$to && ($itot%$step)==0 && !$boxsize)
+    {
+      my @xcoor=unpack("f*",$xbuf);
+      my @ycoor=unpack("f*",$ybuf);
+      my @zcoor=unpack("f*",$zbuf);
+      for(my $j = 0; $j < @xcoor; $j++)
+      {
+        print "$xcoor[$j] $ycoor[$j] $zcoor[$j]\n";
+      }
+      print "\n";
+    }
+  }
+  close($dcdfile);
+}
+
+################################################################
+sub read_DCD_head
+{
+  my $dcdfile = $_[0];
+  my $buffer;
+  my $len;
+  ($buffer,$len)=readFortran($dcdfile);
+  my ($tag,@icontrol)=unpack("A4L*",$buffer);
+  
+  ($buffer,$len)=readFortran($dcdfile);
+  ($buffer,$len)=readFortran($dcdfile);
+  my $natom=unpack("L",$buffer);
+  
+  my $tstep=unpack("f",pack("L",$icontrol[9]))*4.88882129E-02;
+  my $nframe=$icontrol[0];
+  my $first=$icontrol[1];
+  my $delta=$icontrol[2];
+  my $crystal=$icontrol[10];
+  my $fixed=$icontrol[8];
+
+  my @results = ($natom, $tstep, $nframe, $first, $delta, $crystal, $fixed);
+  return @results;
+}
+
+################################################################
+sub read_DCD_frame
+{
+  my $dcdfile = $_[0];
+  my $crystal = $_[1];
+
+  my @coor = ();
+
+  my ($xbuf,$ybuf,$zbuf);
+  
+  if ($crystal) 
+  {
+    my ($tbuf,$tlen)=readFortran($dcdfile);
+  }
+
+  ($xbuf,$len)=readFortran($dcdfile);
+  ($ybuf,$len)=readFortran($dcdfile);
+  ($zbuf,$len)=readFortran($dcdfile);
+      
+  my @xcoor=unpack("f*",$xbuf);
+  my @ycoor=unpack("f*",$ybuf);
+  my @zcoor=unpack("f*",$zbuf);
+  for(my $j = 0; $j < @xcoor; $j++)
+  {
+    push@coor, [$xcoor[$j], $ycoor[$j], $zcoor[$j]];
+  }
+  
+  return @coor;
+}