Mercurial > repos > marpiech > norwich_tools_dock

annotate tools/rdock/lib/run_rbfuncs.pl @ 0:75f2b4087722 draft

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author marpiech
date Tue, 30 Aug 2016 03:18:58 -0400
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1 #!/usr/bin/perl
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2 # Perl functions for the run_rb* collection of automated docking scripts
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3
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4 use strict;
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5
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6 ################################################################################
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7 # sub get_prm_table
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8 #
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9 # Purpose: return a hash table of
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10 # key=parameter file name, value = file title
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11 # for all .prm files in a directory
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12 #
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13 # Usage: %prm_table = get_prm_table($dir)
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14 #
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15 # Arguments:
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16 # $prmDir - directory to search for .prm files
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17 #
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18 # Return parameters:
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19 # %prm_table - hash table
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20 #
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21 sub get_prm_table {
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22 #Arguments
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23 my $prm_dir = shift;
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24
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25 #Local variables
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26 my @prm_list;
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27 my %prm_table;
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28 my $TITLEREC = "TITLE ";
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29 my $file;
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30 my $title;
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31 my @titleLines;
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32
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33 #Get the list of files ending in .prm
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34 @prm_list = glob "$prm_dir/*.prm";
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35
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36 #Read each file and extract the title record
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37 foreach $file (@prm_list) {
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38 open PRMHANDLE,$file;
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39 @titleLines = grep /^$TITLEREC/,<PRMHANDLE>;
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40 close PRMHANDLE;
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41 #Extract just the file name from the full path
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42 my $prmName = substr($file, rindex($file,"/")+1);
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43 #Check if a title record was found
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44 if (scalar @titleLines) {
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45 $title = substr $titleLines[0],length($TITLEREC);
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46 chomp $title;
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47 $prm_table{$prmName} = $title;
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48 }
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49 else {
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50 $prm_table{$prmName} = "No title";
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51 }
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52 }
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53 return %prm_table;
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54 }
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55 ################################################################################
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56 # sub get_dock_table
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57 #
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58 # Purpose: Modified version of get_prm_table
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59 # specific for the RBT_LIGDB docking database
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60 # Return a hash table of
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61 # key=docking library, value = expression for all sd files in that library
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62 #
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63 # Assumes that all subdirs within $db_dir are separate vendor libraries,
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64 # and that each subdir contains a set of compressed .sd.gz files
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65 #
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66 # Usage: %dock_table = get_dock_table($dir)
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67 #
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68 # Arguments:
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69 # $db_dir - directory to search for docking libraries
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70 #
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71 # Return parameters:
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72 # %dock_table - hash table#
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73 #
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74 sub get_dock_table {
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75 #Arguments
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76 my $db_dir = shift;
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77
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78 #Local variables
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79 my ($lib,$sdfiles);
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80 my (@lib_list,@sd_list);
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81 my %dock_table;
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82
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83 opendir DBDIR,$db_dir;
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84 @lib_list = readdir DBDIR;
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85 closedir DBDIR;
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86
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87 foreach $lib (sort @lib_list) {
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88 if (-d "$db_dir/$lib") {
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89 $sdfiles = "$db_dir/$lib/*.sd*";
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90 @sd_list = glob $sdfiles;
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91 my $n = scalar(@sd_list);
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92 if ($n > 0) {
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93 $dock_table{"$lib ($n files)"} = $sdfiles;
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94 }
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95 }
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96 }
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97
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98 return %dock_table;
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99 }
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100 #
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101 ################################################################################
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102 # sub get_selection
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103 #
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104 # Purpose: allow a user to select from
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105 # a list of parameter files.
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106 #
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107 # Usage: $receptor = get_selection(\%prm_table,"receptor")
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108 #
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109 # Arguments:
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110 # $prm_table_ref - reference to hash table returned by get_prm_table
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111 # $name - descriptive name for items (e.g. "receptor" or "script"
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112 #
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113 # Return parameters:
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114 # $item - selected items (key into %prm_table)
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115 #
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116 sub get_selection {
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117 #Arguments
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118 my $prm_table_ref = shift;
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119 my $name = shift;
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120
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121 #Local variables
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122 my @items = sort keys %$prm_table_ref;
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123 my $nItems = scalar @items;
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124 my ($i,$itemNum,$item);
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125 my $inRange;
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126
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127 print "\n\n$name selection:\n\n";
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128 $i=1;
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129 foreach $item (@items) {
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130 print "$i\t$item\t$$prm_table_ref{$item}\n";
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131 $i++;
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132 }
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133 do {
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134 print "\nEnter the $name number: ";
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135 $itemNum = <STDIN>;
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136 chomp $itemNum;
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137 print "\n";
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138 $inRange = (($itemNum >= 1) && ($itemNum <= $nItems));
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139 print "$itemNum is out of range\n" if (!$inRange);
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140 } until ($inRange);
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141
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142 print "\nYou have selected the following $name\n";
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143 $item = $items[$itemNum-1];
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144 print "$itemNum\t$item\t$$prm_table_ref{$item}\n";
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145 return $item;
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146 }
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147
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148 ################################################################################
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149 # sub get_multiple_selection
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150 #
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151 # Purpose: allow a user to multiply select from the docking library list
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152 #
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153 # Usage: $receptor = get_selection(\%prm_table,"receptor")
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154 #
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155 # Arguments:
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156 # $prm_table_ref - reference to hash table returned by get_prm_table
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157 # $name - descriptive name for items (e.g. "receptor" or "script"
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158 #
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159 # Return parameters:
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160 # $item - selected items (key into %prm_table)
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161 #
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162 sub get_multiple_selection {
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163 #Arguments
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164 my $prm_table_ref = shift;
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165 my $name = shift;
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166
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167 #Local variables
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168 my @items = sort keys %$prm_table_ref;
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169 my $nItems = scalar @items;
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170 my ($i,$idstring,$itemNum,$item);
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171 my @itemNums;
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172 my @selectedItems;
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173 my $inRange;
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174 my $allInRange;
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175
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176 print "\n\n$name selection:\n\n";
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177 $i=1;
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178 foreach $item (@items) {
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179 print "$i\t$item\t$$prm_table_ref{$item}\n";
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180 $i++;
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181 }
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182 do {
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183 print "\nEnter the $name number(s): ";
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184 my $idstring = <STDIN>;
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185 chomp $idstring;
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186 @itemNums = get_ids($idstring);
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187 print "\n";
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188 $allInRange = 1;
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189 foreach $itemNum (@itemNums) {
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190 $inRange = (($itemNum >= 1) && ($itemNum <= $nItems));
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191 print "$itemNum is out of range\n" if (!$inRange);
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192 $allInRange = $allInRange && $inRange;
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193 }
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194 } until ($allInRange);
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195
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196 print "\nYou have selected the following $name(s)\n";
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197 foreach $itemNum (@itemNums) {
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198 $item = $items[$itemNum-1];
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199 push @selectedItems,$item;
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200 print "$itemNum\t$item\t$$prm_table_ref{$item}\n";
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201 }
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202 return @selectedItems;
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203 }
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204
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205 ################################################################################
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206 # sub get_input
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207 #
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208 # Purpose: get user input, or returns default if no response given
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209 #
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210 # Usage: $nRuns = get_input("Enter no. of runs per ligand",10)
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211 #
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212 # Arguments:
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213 # $question - text of question to ask
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214 # $defResponse - default answer
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215 #
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216 # Return parameters:
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217 # $response - user response, or default
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218
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219 sub get_input {
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220 #Arguments
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221 my $question = shift;
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222 my $defResponse = shift;
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223 print "$question [$defResponse]: ";
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224 my $response = <STDIN>;
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225 chomp $response;
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226 $response = $defResponse if ($response eq "");
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227 return $response;
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228 }
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229
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230 # Based on //depot/intranet/1.0/lib/rbt_func.pl#1
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231 # this function converts a list of ids in one string
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232 # in the format 1,2,4-6,8,15-20
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233 # and returns an @array with the unique ids
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234 sub get_ids {
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235 my $idstring = shift;
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236 my %ids;
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237
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238 foreach my $id (split (',',$idstring)){
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239 if ( grep (/-/,$id)){
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240 (my $low, my $up) = split ('-',$id);
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241 for ( my $co = $low; $co <= $up; $co++ ){
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242 $ids{$co}=$co;
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243 }
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244 }
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245 else {
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246 $ids{$id}=$id;
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247 }
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248 }
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249
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250 return (sort {$a<=>$b} keys %ids);
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251 }
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252 ################################################################################
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253 # sub get_filter_table
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254 #
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255 # Purpose: return a hash table of
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256 # key=filter file name, value = file title
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257 # for all .filter files in a directory
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258 #
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259 # Usage: %filter_table = get_filter_table($dir)
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260 #
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261 # Arguments:
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262 # $filterDir - directory to search for .filter files
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263 # $tmp - temperature for first filter
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264 # Note:
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265 # The first two filters are not in a file, but are created here
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266 #
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267 # Return parameters:
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268 # %filter_table - hash table
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269 #
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270 sub get_filter_table {
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271 #Arguments
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272 my $filter_dir = shift;
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273 my $tmp = shift;
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274
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275 #Local variables
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276 my $pwd = $ENV{"PWD"};
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277 my @filter_list;
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278 my %filter_table;
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279 my $file;
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280
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281 #Get the list of files ending in .filter
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282 @filter_list = ((glob "$pwd/*.filter"), (glob "$filter_dir/*.filter"));
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283 $filter_table{"1no_other_filters"} = "";
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284 # $filter_table{"1threshold"} = "\tSCORE.INTER < $tmp";
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285 # $filter_table{"2cavity"} = "\t\tSCORE.RESTR.CAVITY < 1 ";
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286
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287 #Read each file and extract the title record
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288 foreach $file (@filter_list) {
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289 #Extract just the file name from the full path
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290 my $filterName = substr($file, rindex($file,"/")+1);
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291 #Check if a title record was found
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292 $filter_table{$filterName} = "No title";
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293 }
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294 return %filter_table;
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295 }
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296 1;