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3 <title>MayaChemTools:Documentation:SDFilesToHTML.pl</title>
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13 <div class="DocNav">
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14 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./PathLengthFingerprints.html" title="PathLengthFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./SDToMolFiles.html" title="SDToMolFiles.html">Next</a></td><td width="34%" align="middle"><strong>SDFilesToHTML.pl</strong></td><td width="33%" align="right"><a href="././code/SDFilesToHTML.html" title="View source code">Code</a> | <a href="./../pdf/SDFilesToHTML.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/SDFilesToHTML.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/SDFilesToHTML.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/SDFilesToHTML.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr>
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16 </table>
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17 </div>
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18 <p>
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19 </p>
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20 <h2>NAME</h2>
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21 <p>SDFilesToHTML.pl - Generate HTML table file(s) from SDFile(s)</p>
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22 <p>
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23 </p>
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24 <h2>SYNOPSIS</h2>
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25 <p>SDFilesToHTML.pl SDFiles(s)...</p>
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26 <p>SDFilesToHTML.pl [<strong>-a, --align</strong> left | center | right,[top | middle | bottom]] [<strong>-b, --border</strong> borderwidth] [<strong>--cellpadding</strong> padding]
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27 [<strong>--cellspacing</strong> spacing] [<strong>--cmpddatafield</strong> "fieldlabel,[label,position,alignment]"] [<strong>--datafields</strong> "fieldlabel,[fieldlabel]..." | Common | All]
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28 [<strong>--footer</strong> string] [<strong>-d, --displaylinks</strong> top | bottom | both] [<strong>--displaylinksinfo</strong> compound | table | both] [<strong>-h, --help</strong>]
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29 [<strong>--headeralign</strong> left | center | right,[top | middle | bottom]] [<strong>--headercolor</strong> "#RRGGBB"]
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30 [<strong>--highlight</strong> "fieldlabel,datatype,criterion,value,[fieldlabel,datatype,criterion,value,...]"]
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31 [<strong>--highlightcolor</strong> "#RRGGBB,#RRGGBB"] [<strong>--highlightstyle</strong> text | background]
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32 [<strong>-m, --mode</strong> plain | shade | highlight | shadedhighlight | structuresonly | shadedstructuresonly]
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33 [<strong>-n, --numcmpds</strong> number] [<strong>-o, --overwrite</strong>] [<strong>-r, --root</strong> rootname] [<strong>-s, --structure</strong> display | link]
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34 [<strong>--strlinkmode</strong> plain | shaded] [<strong>--strlinknavigation</strong> yes | no]
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35 [<strong>--strlinkshadecolor</strong> "#RRGGBB"] [<strong>--strlinktitle</strong> string] [<strong>--strlinktitledisplay</strong> yes | no] [<strong>--strlinktype</strong> href | button]
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36 [<strong>--strviewertype</strong> Chem3DActiveX | ChemDrawActiveX | ChemDrawPlugIn | Chime | JME | Jmol | MarvinView | ViewerActiveX]
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37 [<strong>--strviewerconfig</strong> codebase[,archive,code]] [<strong>--strviewerparams</strong> "name=value [name=value ...]"]
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38 [<strong>--strviewerembed</strong> direct | javascript] [<strong>--strviewerjsfile</strong> javascriptfilename]
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39 [<strong>--strtablesize</strong> "numrows,numcols"] [<strong>--stylesheet</strong> old | new | none]
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40 [<strong>--stylesheetname</strong> filename] [<strong>--shadecolor</strong> "#RRGGBB,#RRGGBB"] [<strong>-t, --title</strong> string] [<strong>--titledisplay</strong> yes | no]
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41 [<strong>-w, --workingdir</strong> dirname] SDFiles(s)...</p>
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42 <p>
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43 </p>
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44 <h2>DESCRIPTION</h2>
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45 <p>Generate HTML file(s) from <em>SDFile(s)</em>. The HTML file(s) contain data tables
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46 and appropriate navigational links to view other tables; navigational links are also
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47 provided on compound HTML pages. These files can be generated for local viewing or
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48 deployment on a web server. A variety of options are provided to control style and
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49 appearance of tables. And for viewing structures, options are available to use any one of
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50 these viewers: Chem3DActiveX, ChemDrawActiveX, ChemDrawPlugIn, Chime, Jmol, JME,
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51 MarvinView, or ViewerActiveX. Jmol is the default structure viewer and it is also distributed
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52 along with this package; however, to use any other supported viewers, make sure it's available
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53 in your environment.</p>
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54 <p>Multiple <em>SDFile(s)</em> names are separated by space. The valid file extensions are
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55 <em>.sdf</em> and <em>.sd</em>. All other file names are ignored. All the SD files in a current directory can
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56 be specified either by <em>*.sdf</em> or the current directory name.</p>
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57 <p>
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58 </p>
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59 <h2>OPTIONS</h2>
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60 <dl>
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61 <dt><strong><strong>-a, --align</strong> <em>left | center | right,[top | middle | bottom]</em></strong></dt>
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62 <dd>
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63 <p>Horizontal and vertical alignment for table rows except for header row which is specified
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64 using <strong>--headeralign</strong> option. Possible horizontal alignment values: <em>left, center, or right</em>.
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65 Possible vertical alignment values: <em>top, middle, or bottom</em>.</p>
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66 <p>Default values: <em>left,middle</em></p>
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67 </dd>
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68 <dt><strong><strong>-b, --border</strong> <em>borderwidth</em></strong></dt>
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69 <dd>
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70 <p>Table border width. Default value: 1 for <em>plain</em> and <em>highlight</em> mode; 0 for <em>shade</em>
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71 and <em>shadedhightlight</em> mode. Zero indicates no border.</p>
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72 </dd>
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73 <dt><strong><strong>--cellpadding</strong> <em>padding</em></strong></dt>
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74 <dd>
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75 <p>Table cell padding. Default value: <em>2</em>.</p>
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76 </dd>
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77 <dt><strong><strong>--cellspacing</strong> <em>spacing</em></strong></dt>
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78 <dd>
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79 <p>Table cell spacing. Default value: <em>1</em>.</p>
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80 </dd>
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81 <dt><strong><strong>--cmpddatafield</strong> <em>fieldlabel,[label,position,alignment]</em></strong></dt>
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82 <dd>
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83 <p>This value is mode specific. It indicates data field value to be displayed with the structure along
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84 with its label, position and alignment during <em>structuresonly | shadedstructuresonly</em> value of <strong>-m, --mode</strong>
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85 option. Possible values: feldlabel - valid data field label; label - yes or no; position - <em>top or bottom</em>; alignment
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86 - <em>left, center, or right</em>. Default: <em>none,no,bottom,center</em>. Example:</p>
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87 <div class="OptionsBox">
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88 MolWt,no,bottom,middle</div>
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89 <p><strong>--cmpddatafield</strong> option value is also linked to compound summary page.</p>
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90 </dd>
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91 <dt><strong><strong>--datafields</strong> <em>"fieldlabel,[fieldlabel]..." | Common | All</em></strong></dt>
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92 <dd>
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93 <p>Data fields to display in HTML table(s). Possible values: list of comma separated data field
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94 labels, data fields common to all records, or all data fields. Default value: <em>All</em>.
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95 Examples:</p>
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96 <div class="OptionsBox">
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97 ALogP,MolWeight,EC50
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98 <br/> "MolWeight,PSA"</div>
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99 </dd>
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100 <dt><strong><strong>--footer</strong> <em>string</em></strong></dt>
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101 <dd>
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102 <p>Text string to be included at bottom of each HTML file. Default: none.</p>
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103 </dd>
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104 <dt><strong><strong>-d --displaylinks</strong> <em>top | bottom | both</em></strong></dt>
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105 <dd>
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106 <p>Specify where to display navigation links in each HTML file for accessing all other HTML
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107 files. Possible values: <em>top, bottom, or both</em>. Default: <em>both</em>. This option is
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108 only valid during multiple HTML files generation for an input file.</p>
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109 </dd>
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110 <dt><strong><strong>--displaylinksinfo</strong> <em>compound | table | both</em></strong></dt>
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111 <dd>
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112 <p>Control display of additional information along with navigational links: Showing compound
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113 n of m is displyed for compound and showing table n of m for table. Possible values: <em>compound
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114 | table | both</em>. Default: <em>both</em>. This option is only valid during multiple HTML files generation.</p>
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115 </dd>
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116 <dt><strong><strong>-h, --help</strong></strong></dt>
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117 <dd>
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118 <p>Print this help message.</p>
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119 </dd>
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120 <dt><strong><strong>--headeralign</strong> <em>left | center | right,[top | middle | bottom</em></strong></dt>
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121 <dd>
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122 <p>Horizontal and vertical alignment for table header rows. Possible horizontal alignment
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123 values: <em>left, center, or right</em>. Possible vertical alignment values: <em>top, middle, or bottom</em>.</p>
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124 <p>Default values: <em>center,middle</em></p>
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125 </dd>
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126 <dt><strong><strong>--headercolor</strong> <em>#RRGGBB</em></strong></dt>
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127 <dd>
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128 <p>Color used to fill background of table header row containing column labels
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129 represented as a hexadecimal string. Default value: None for <strong>-m, --mode</strong> option
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130 value of <em>plain</em> and <em>#ccccff</em>, light blue, for others.</p>
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131 </dd>
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132 <dt><strong><strong>--highlight</strong> <em>"fieldlabel,datatype,criterion,value,[fieldlabel,datatype,criterion,value,...]"</em></strong></dt>
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133 <dd>
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134 <p>Highlighting methodology used to highlight various SDFile(s) data field values in
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135 HTML file(s). Same set of quartets values are applied to all SDFile(s).</p>
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136 <p>Input text contains these quartets: <em>fieldlabel,datatype,criterion,value,...</em>.
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137 Possible datatype values: <em>numeric or text</em>. Possible criterion values: <em>le, ge, or eq</em>.
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138 Examples:</p>
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139 <div class="OptionsBox">
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140 "MolWt,numeric,le,450"
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141 <br/> "MolWt,numeric,le,450,LogP,numeric,le,5"
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142 <br/> Name,text,eq,Aspirin</div>
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143 </dd>
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144 <dt><strong><strong>--highlightcolor</strong> <em>"#RRGGBB,#RRGGBB"</em></strong></dt>
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145 <dd>
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146 <p>Colors used to highlight column values during <em>highlight</em> and <em>shadedhightlight</em>
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147 mode represented as hexadecimal strings.</p>
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148 <p>For <strong>--highlighstyle</strong> option values of <em>text</em> and <em>background</em>, these colors represent
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149 text or background colors respectively. For a specific column, first color string is used for
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150 values which meet criterion indicated by <strong>--highlight</strong> option; the second color is used for
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151 rest of the values.</p>
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152 <p>Default values for <em>background</em> <strong>--highlightstyle</strong>: <em>"#0fff0f,#ff0f0f"</em>. And default values for
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153 <em>text</em> <strong>--highlightstyle</strong>: <em>"#0fbb0f,#ff0f0f"</em>. Hexadecimal strings for both <strong>--highlightstyle</strong>
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154 colors correspond to <em>reddish</em> and <em>greenish</em>.</p>
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155 </dd>
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156 <dt><strong><strong>--highlightstyle</strong> <em>text | background</em></strong></dt>
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157 <dd>
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158 <p>This value is mode specific. It indicates highlight style used to differentiate column
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159 values which meet a specified criterion in <strong>--highlight</strong> option. Possible values: <em>text or
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160 background</em>. Default: <em>background</em>.</p>
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161 </dd>
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162 <dt><strong><strong>-m, --mode</strong> <em>plain | shade | highlight | shadedhighlight | structuresonly | shadedstructuresonly</em></strong></dt>
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163 <dd>
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164 <p>Specify how to generate HTML table(s): plain tables with line borders, background of
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165 alternate rows filled with a specified color, column values highlighted using a specified
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166 criteria, combination of previous two styles, tables containing only structures, or tables
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167 containing only structures with filled background of alternate rows.</p>
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168 <p>Possible values: <em>plain, shade, highlight, shadedhighlight, structuresonly, or
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169 shadedstructuresonly</em>. Default: <em>shade</em>.</p>
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170 </dd>
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171 <dt><strong><strong>-n, --numcmpds</strong> <em>number</em></strong></dt>
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172 <dd>
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173 <p>Maximum number of compounds per table. Default value: <em>15</em> for tables with structures and
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174 <em>50</em> for tables with links to structures. Use 0 to put all compounds into one table. For SDFile(s)
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175 with more than maximum number of specified compounds, multiple HTML tables, with appropriate
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176 navigation links, are created.</p>
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177 </dd>
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178 <dt><strong><strong>-o, --overwrite</strong></strong></dt>
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179 <dd>
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180 <p>Overwrite existing files.</p>
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181 </dd>
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182 <dt><strong><strong>-r, --root</strong> <em>rootname</em></strong></dt>
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183 <dd>
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184 <p>New file or directory name is generated using the root: <root>.html or <root>-html.
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185 Default new file name: <InitialSDFileName>.html. Default directory name:
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186 <InitialSDFileName>-html.</p>
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187 <p>For SDFile(s) with more than maximum number of specified compounds per table,
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188 this directory tree is generated using <Name> where <Name> corresponds to <root>
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189 or <InitialSDFileName>: Top dir - <Name>-html; Sub dirs - html and mols. <Top dir> contains
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190 <Name>.html and <Name>.css files and <sub dir> html conatins various
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191 <Name>Lines<Start>To<End>.html files; <sub dir> mols is created as needed and contains
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192 MOL files.</p>
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193 <p>This option is ignored for multiple input files.</p>
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194 </dd>
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195 <dt><strong><strong>-s, --structure</strong> <em>display | link</em></strong></dt>
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196 <dd>
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197 <p>Structure display control: display structures in a table column or set up a link for each
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198 structure which opens up a new HTML page containing structure and other appropriate
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199 information. Possible values: <em>display or link</em>. Default value: <em>display</em></p>
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200 </dd>
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201 <dt><strong><strong>--strlinkmode</strong> <em>plain | shaded</em></strong></dt>
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202 <dd>
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203 <p>Specify how to display compound HTML page: plain or background of data field
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204 field labels is filled with a specified color. Possible values: <em>plain or shad</em>.
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205 Default value: <em>plane</em>.</p>
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206 <p>Structure viewer background color is white. Use <strong>--strviewerparams</strong> option to change
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207 default behavior of structure viewers.</p>
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208 </dd>
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209 <dt><strong><strong>--strlinknavigation</strong> <em>yes | no</em></strong></dt>
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210 <dd>
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211 <p>Display navigation links to other compounds in compound HTML page. Possible values:
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212 <em>yes or no</em>. Default value: <em>yes</em>.</p>
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213 </dd>
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214 <dt><strong><strong>--strlinkshadecolor</strong> <em>"#RRGGBB"</em></strong></dt>
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215 <dd>
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216 <p>This value is <strong>--strlinkmode</strong> specific. For <em>shade</em> value of <strong>--strlinkmode</strong> option, it
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217 represents colors used to fill background of data field labels.</p>
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218 <p>Default value: <em>"#e0e9eb"</em> - it's a very light blue color.</p>
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219 </dd>
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220 <dt><strong><strong>--strlinktitle</strong> <em>string</em></strong></dt>
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221 <dd>
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222 <p>Title for compound HTML page. Default value: <em>Compound Summary</em>.</p>
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223 </dd>
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224 <dt><strong><strong>--strlinktitledisplay</strong> <em>yes | no</em></strong></dt>
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225 <dd>
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226 <p>Display title for compound HTML page. Possible values: <em>yes or no</em>. Default value: <em>no</em>.</p>
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227 </dd>
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228 <dt><strong><strong>--strlinktype</strong> <em>href | button</em></strong></dt>
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229 <dd>
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230 <p>Type of structure link. Possible values: <em>href or button</em>. Default: <em>href</em>.</p>
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231 </dd>
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232 <dt><strong><strong>--strviewertype</strong> <em>Chem3DActiveX | ChemDrawActiveX | ChemDrawPlugIn | Chime | JME | Jmol | MarvinView | ViewerActiveX</em></strong></dt>
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233 <dd>
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234 <p>Structure viewer supported for viewing structures. Possible values: <em>Chem3DActiveX,
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235 ChemDrawActiveX, ChemDrawPlugIn, Chime, JME, Jmol, MarvinView, or ViewerActiveX</em>.
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236 Default value: <em>Jmol</em>.</p>
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237 <p>Assuming you have access to one of these viewers on your machine, you are all set
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238 to use this script. Otherwise, visit one of these web sites to download and install
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239 your favorite viewer:</p>
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240 <div class="OptionsBox">
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241 accelrys.com: Viewer ActiveX 5.0
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242 <br/> cambridgesoft.com: Chem3DActiveX 8.0, ChemDrawActiveX 8.0,
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243 ChemDrawPlugIn
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244 <br/> chemaxon.com: MarvinView applet
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245 <br/> mdli.com: Chime plug-in
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246 <br/> jmol.sourceforge.net: JmolApplet V10
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247 <br/> molinspiration.com: JME applet</div>
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248 <p>The default viewer, JmolApplet V10, is distributed with MayaChemTools package.
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249 Earlier versions of JmolApplet are not supported: due to applet security issues related to
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250 reading files, this script uses in-line loading of MOL files and this option doesn't exist in
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251 earlier version of JmolApplet.</p>
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252 </dd>
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253 <dt><strong><strong>--strviewerconfig</strong> <em>codebase[,archive,code]</em></strong></dt>
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254 <dd>
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255 <p>Configuration information for structure viewers. This option is only valid for structure
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256 viewers which are applets: Jmol, JME and MarvinView. For other viewer types available via
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257 <strong>--strviewertype</strong> option - MDL Chime, ChemDrawActiveX, ChemDrawPlugIn, and
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258 Chem3DActiveX - this value is ignored.</p>
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259 <p>Input text format: <em>codebase[,archive,code]</em>. For an applet viewer, <em>codebase</em> must be
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260 specified; <em>archive</em> and <em>code</em> values are optional. Here are default <em>archive</em> and
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261 <em>codebase</em> values for various applets: Jmol - JmolApplet, JmolApplet.jar; JME - JME, JME.jar;
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262 MarvinView: MView, marvin.jar</p>
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263 <p>For local deployment of HTML files, <em>codebase</em> must correspond to a complete path to
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264 the local directory containing appropriate <em>archive</em> file and the complete path is converted
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265 into appropriate relative path during generation of HTML files.</p>
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266 <p>By default, <em>codebase</em> value of <this script dir>/../lib/Jmol is used for <em>Jmol</em> applet viewer, and
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267 HTML file(s) are generated for local deployment; however, you can specify any supported
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268 applet viewer and generate HTML file(s) for deploying on a web server.</p>
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269 <p>For deploying the HTML file(s) on a web server, specify a valid <em>codebase</em> directory name
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270 relative to <WWWRootDir>. Example when JME archive file, JME.jar, is available in
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271 <em>/jme</em> directory on the web server:</p>
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272 <div class="OptionsBox">
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273 /jme</div>
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274 <p>For local deployment of HTML file(s), specify a complete <em>codebase</em> directory name.
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275 Example when JmolApplet archive file, JmolApplet.jar, is present in <JMOLROOT> directory:</p>
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276 <div class="OptionsBox">
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277 <JMOLROOT></div>
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278 <p>In addition to <em>codebase</em>, you can also specify <em>archive</em> file name. Example for web
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279 deployment:</p>
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280 <div class="OptionsBox">
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281 "/jme,JME.jar"
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282 <br/> "/jme"</div>
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283 <p>Example for local deployment:</p>
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284 <div class="OptionsBox">
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285 "<JMEROOT>,JME.jar"
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286 <br/> "<JMEROOT>"</div>
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287 </dd>
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288 <dt><strong><strong>--strviewerparams</strong> <em>"name=value [name=value ...]"</em></strong></dt>
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289 <dd>
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290 <p>Parameters name and value pairs for structure viewers. These name and value pairs
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291 are used to control the appearance and behavior of structure viewers in tables and
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292 compound HTML page during <em>link</em> value for <strong>-s --structure</strong> option.</p>
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293 <p>The parameter names, along with their values, are just passed to each structure viewer
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294 in appropriate format without checking their validity. Check documentation of appropriate
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295 structure viewers to figure out valid parameter names.</p>
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296 <p>Input text format: <em>name=value name=value ...</em> Example:</p>
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297 <div class="OptionsBox">
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298 "width=250 height=170"</div>
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299 <p>Default for all structure viewers: <em>width=250 height=170</em> for displaying structures in
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300 tables, and <em>strlinkwidth=500 strlinkheight=295</em> for compound HTML page during <em>link</em> value
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301 for <strong>-s --structure</strong> option.</p>
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302 <p>Default background color for all structure viewers: same as <strong>--shadecolor</strong> value for
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303 displaying structures in tables and <em>strlinkbgcolor=#ffffff</em> for compound HTML page;
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304 however, explicit specification of background color in this option overrides default value.
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305 To use black background for structures in tables and compound HTML page, specify <em>bgcolor=#000000</em>
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306 and <em>strlinkbgcolor=#000000</em> respectively. Keep this in mind: Some structure viewers
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307 don't appear to support background color parameter.</p>
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308 <p>Additional structure viewer specific default values:</p>
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309 <div class="OptionsBox">
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310 Chem3DActiveX: "displaytype=Ball&Stick rotationbars=false
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311 moviecontroller=false"
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312 <br/> ChemDrawActiveX: "ViewOnly=1 ShrinkToFit=1 ShowToolsWhenVisible=1"
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313 <br/> ChemDrawPlugIn: "type=chemical/x-mdl-molfile ViewOnly=1
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314 ShrinkToFit=1 ShowToolsWhenVisible=1"
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315 <br/> Chime: "display2d=true"
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316 <br/> JME: "options=depict"
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317 <br/> Jmol: "progressbar=true progresscolor=#0000ff boxbgcolor=#000000
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318 boxfgcolor=#ffffff script="select *; set frank off;
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319 wireframe on; spacefill off""
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320 <br/> MarvinView: "navmode=zoom"
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321 <br/> ViewerActiveX:"Mouse=4 Convert2Dto3D=0"</div>
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322 <p>Try overriding default values or specify additional valid parameter/value pairs to get desired
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323 results. Example for using CPK rendering scheme with Jmol viewer:</p>
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324 <div class="OptionsBox">
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325 "script="select *; set frank off; wireframe off; spacefill on""</div>
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326 </dd>
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327 <dt><strong><strong>--strviewerembed</strong> <em>direct | javascript</em></strong></dt>
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328 <dd>
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329 <p>Specify how to embed structure viewers in HTML pages. Possible values: <em>direct</em> - use applet/object
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330 tags to emded structure viewer; <em>javascript</em> - use vendor supplied java scripts. Default value:
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331 direct.</p>
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332 <p>This option only applies to these vieweres: <em>Chem3DActiveX, ChemDrawActiveX, ChemDrawPlugIn,
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333 Jmol, and MarvinView</em>.</p>
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334 <p>For marvin.js to work correctly on your browser, you may need to set <em>marvin_jvm=builtin</em> or
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335 <em>marvin_jvm=plugin</em> using <strong>--strviewerparams</strong> option. Additionally, MarvinView - at least
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336 in my hands - also has problems during usage of JavaScript for local deployment; however, it
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337 does work via web server.</p>
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338 <p>As far as I can tell, Jmol.js supplied with Jmol10 release has these issues: jmolSetAppletColor
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339 doesn't support background color; jmolInitialize disables relative specification of codebase
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340 directroy which works okay. So, use Jmol.js supplied with MayaChemTools.</p>
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341 </dd>
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342 <dt><strong><strong>--strviewerjsfile</strong> <em>java script file name</em></strong></dt>
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343 <dd>
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344 <p>Name of vendor supplied java script file. Default values: Chem3DActiveX: <em>chem3d.js</em>; ChemDrawActiveX,
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345 and ChemDrawPlugIn: <em>chemdraw.js</em>; Jmol: <em>Jmol.js</em>, MarvinView: <em>marvin.js</em>.</p>
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346 <p>Directory location for these files is specified via <em>codebase</em> value of <strong>--strviewerconfig</strong> option.</p>
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347 </dd>
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348 <dt><strong><strong>--strtablesize</strong> <em>"numrows,numcols"</em></strong></dt>
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349 <dd>
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350 <p>This option is only valid for <em>structuresonly</em> and <em>shadedstructuresonly</em> modes. And it indicates
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351 maximum number of rows and columns per structure table. Default value:<em>6,4</em>.</p>
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352 </dd>
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353 <dt><strong><strong>--stylesheet</strong> <em>old | new | none</em></strong></dt>
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354 <dd>
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355 <p>Controls usage of stylesheet for newly generated HTML file(s). Possible values: <em>old,
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356 new, or none</em>. Default value: <em>new</em>.</p>
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357 <p>Stylesheet file contains various properties which control appearance of HTML pages:
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358 type, size, and color of fonts; background color; and so on.</p>
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359 <p>For <em>old</em> value, an existing stylesheet file specified by <strong>--stylesheetname</strong> option is
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360 used for each HTML file; no new stylesheet file is created. This option is quite handy
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361 for deploying HTML file(s) on a web server: assuming you specify a valid stylesheet
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362 file location relative to your WWWRoot, a reference to this stylesheet is added to each
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363 HTML file. For local deployment of HTML file(s), a complete path to a local stylesheet
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364 is fine as well.</p>
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365 <p>For <em>create</em> value, a new stylesheet is created and reference to this local stylesheet
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366 is added to each HTML file. Use option <strong>--stylesheetname</strong> to specify name.</p>
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367 <p>For <em>none</em> value, stylesheet usage is completely ignored.</p>
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368 </dd>
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369 <dt><strong><strong>--stylesheetname</strong> <em>filename</em></strong></dt>
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370 <dd>
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371 <p>Stylesheet file name to be used in conjunction with <strong>-s --stylesheet</strong> option. It is only
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372 valid for <em>old</em> value of <strong>-s --stylesheet</strong> option. Specify a valid stylesheet file location
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373 relative to your WWWRoot and a reference to this stylesheet is added to each HTML
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374 file. Example: <em>"/stylesheets/MyStyleSheet.css"</em>. Or a complete path name to a local
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375 stylesheet file.</p>
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376 <p>For <em>create</em> value of <strong>-s --stylesheet</strong> option, a new stylesheet file is created using
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377 <strong>-r --root</strong> option. And value of <strong>--stylesheetname</strong> is simply ignored.</p>
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378 </dd>
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379 <dt><strong><strong>--shadecolor</strong> <em>"#RRGGBB,#RRGGBB"</em></strong></dt>
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380 <dd>
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381 <p>Colors used to fill background of rows during <em>shade</em> and <em>shadedhightlight</em> mode
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382 represented as a pair of hexadecimal string; the first and second color values
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383 are used for odd and even number rows respectively.</p>
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384 <p>Default value: <em>"#ffffff,#e0e9eb"</em> - it's white and very light blue for odd and even number rows.</p>
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385 </dd>
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386 <dt><strong><strong>-t, --title</strong> <em>string</em></strong></dt>
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387 <dd>
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388 <p>Title for HTML table(s). Default value: <em>SDFileName</em>. This option is ignored for
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389 multiple input files. And <strong>-r --root</strong> option is used to generate appropriate
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390 titles.</p>
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391 </dd>
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392 <dt><strong><strong>--titledisplay</strong> <em>yes | no</em></strong></dt>
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393 <dd>
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394 <p>Display title for HTML table(s). Possible values: <em>yes or no</em>. Default value: <em>yes</em>.</p>
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395 </dd>
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396 <dt><strong><strong>-w, --workingdir</strong> <em>dirname</em></strong></dt>
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397 <dd>
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398 <p>Location of working directory. Default: current directory.</p>
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399 </dd>
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400 </dl>
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401 <p>
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402 </p>
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403 <h2>EXAMPLES</h2>
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404 <p>HTML table file(s), containing structures, can be used in two different ways: browsing on a
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405 local machine or deployment via a web server. By default, HTML file(s) are created for viewing
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406 on a local machine using Jmol viewer through a browser; however, you can specify any
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407 supported applet viewer and generate HTML file(s) for deploying on a web server.</p>
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408 <p>First two sets of examples show generation of HTML file(s) using different applet viewers
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409 and a variety of options for local browsing; last set deals with web deployment.</p>
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410 <p><strong>Local deployment: Usage of default JMol viewer distributed with MayaChemTools:</strong></p>
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411 <p>To generate HTML tables with structure display using JMol viewer, rows background filled
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412 with white and light blue colors, navigation links on top and botton of each page, type:</p>
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413 <div class="ExampleBox">
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414 % SDFilesToHTML.pl -o Sample1.sdf</div>
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415 <p>To generate HTML tables with structure display using JMol viewer, rows background filled
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416 with white and light blue colors, navigation links on top and botton of each page, and
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417 only containing MolWeight and Mol_ID SD data fields, type:</p>
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418 <div class="ExampleBox">
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419 % SDFilesToHTML.pl --datafields "MolWeight,Mol_ID" -o Sample1.sdf</div>
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420 <p>To generate HTML tables with CPK structure display using JMol viewer, rows
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421 background filled with white and light blue colors, navigation links on top and botton of
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422 each page, type:</p>
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423 <div class="ExampleBox">
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424 % SDFilesToHTML.pl --strviewerparams "script=\"select *; set frank off;
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425 wireframe off; spacefill on\"" -o Sample1.sdf</div>
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426 <p>To generate HTML tables with structure display using JMol viewer and black background, rows
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427 background filled with light golden and greyish colors, navigation links on top and botton of
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428 each page, 10 rows in each table, greyish header row color, and cell spacing of 1, type:</p>
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429 <div class="ExampleBox">
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430 % SDFilesToHTML.pl -o -n 10 --headeralign "center" --headercolor
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431 "#a1a1a1" --shadecolor "#fafad2,#d1d1d1" --cellspacing 1
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432 --strviewerparams "bgcolor=#000000" Sample1.sdf</div>
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433 <p>To highlight molecular weight values using specified highlight criteria and fill in default background
|
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434 colors, type:</p>
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435 <div class="ExampleBox">
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436 % SDFilesToHTML.pl -n 10 --highlight "MolWeight,numeric,le,450"
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437 --highlightstyle background -m shadedhighlight -o Sample1.sdf</div>
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438 <p>To highlight molecular weight values using specified highlight criteria, color the text using
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439 default colors, and add a footer message in every page, type:</p>
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440 <div class="ExampleBox">
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441 % SDFilesToHTML.pl -n 4 --highlight "MolWeight,numeric,le,500"
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442 --highlightstyle text -m shadedhighlight -o
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443 --footer "Copyright (C) MayaChemTools" --cellspacing 1 Sample1.sdf</div>
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|
444 <p>To generate tables containing only structures, type:</p>
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445 <div class="ExampleBox">
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446 % SDFilesToHTML.pl -d both -m shadedstructuresonly --strtablesize "6,4"
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447 --cellspacing 1 -b 1 -o Sample1.sdf</div>
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448 <p>To generate tables containing only structures with molecular weight displayed above the
|
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449 structure, type:</p>
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450 <div class="ExampleBox">
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451 % SDFilesToHTML.pl -d both -m shadedstructuresonly --strtablesize "6,4"
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452 --cmpddatafield "MolWeight,no,top,center" --cellspacing 1 -b 1
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453 -o Sample1.sdf</div>
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454 <p>To generate tables containing links to structures and highlight molecular weight data field values
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455 using specified highlight criteria , type:</p>
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456 <div class="ExampleBox">
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457 % SDFilesToHTML.pl -n 4 --footer "Copyright (C) MayaChemTools"
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458 --highlight "MolWeight,numeric,le,450" --highlightstyle background
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459 -d both -m shadedhighlight -s link --strlinktype button
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460 -o Sample1.sdf</div>
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461 <p><strong>Local deployment: Usage of other structure viewers:</strong></p>
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462 <div class="ExampleBox">
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463 % SDFilesToHTML.pl --strviewertype MarvinView --strviewerconfig
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464 "<Marvin dir path>" -o Sample1.sdf</div>
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465 <div class="ExampleBox">
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466 % SDFilesToHTML.pl -o -n 10 --headeralign "center" --headercolor
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467 "#a1a1a1" --shadecolor "#fafad2,#d1d1d1" --cellspacing 1
|
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468 --strviewerparams "bgcolor=#000000" --strviewertype Chime
|
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|
469 Sample1.sdf</div>
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470 <div class="ExampleBox">
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471 % SDFilesToHTML.pl -n 10 --highlight "MolWeight,numeric,le,450"
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472 --highlightstyle background -m shadedhighlight --strviewertype
|
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|
473 Chime -o Sample1.sdf</div>
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474 <div class="ExampleBox">
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475 % SDFilesToHTML.pl -d both -m shadedstructuresonly --strtablesize "6,4"
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476 --cellspacing 1 -b 1 -strviewertype JME -strviewerconfig "<JME dir
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477 path>" -o Sample1.sdf</div>
|
|
|
478 <p><strong>Web deployment: Usage of different structure viewers and options:</strong></p>
|
|
|
479 <p>For deploying HTML file(s) on a web server, specify a valid <em>codebase</em> directory name
|
|
|
480 relative to <WWWRootDir>. In addition to <em>codebase</em>, you can also specify <em>archive</em> file
|
|
|
481 name.</p>
|
|
|
482 <div class="ExampleBox">
|
|
|
483 % SDFilesToHTML.pl -m plain -s display --strviewertype Jmol
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484 -strviewerconfig "/jmol" -n 5 -d both -r PlainTable -t "Example
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485 using Jmol: Plain Table" -o Sample1.sdf</div>
|
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486 <div class="ExampleBox">
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487 % SDFilesToHTML.pl -n 5 -m shade -s display -strviewertype JME
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488 -strviewerconfig "/jme,JME.jar" -r ShadeTable -t "Example using JME:
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489 Shaded Table" -o Sample.sdf</div>
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490 <div class="ExampleBox">
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491 % SDFilesToHTML.pl -n 5 --highlight "MolWeight,numeric,le,450"
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492 --highlightstyle background -d both -m shadedhighlight -s display
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|
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493 -strviewertype MarvinView -strviewerconfig "/marvin" -r
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494 ShadedHightlightTable -t "Example using MarvinView: Shaded and
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495 Highlighted Table" -o Sample.sdf</div>
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496 <div class="ExampleBox">
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497 % SDFilesToHTML.pl -n 4 --highlight "MolWeight,numeric,le,450" -s link
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498 --strlinktype href --strviewertype ChemDrawPlugIn --highlightstyle
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499 background -m shadedhighlight -t "Example using ChemDrawPlugIn:
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500 Shaded and Highlighted Table" -r ShadedHightlightTable -o Sample1.sdf</div>
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501 <p>
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502 </p>
|
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503 <h2>AUTHOR</h2>
|
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504 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
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505 <p>
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506 </p>
|
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507 <h2>SEE ALSO</h2>
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508 <p><a href="./FilterSDFiles.html">FilterSDFiles.pl</a>, <a href="./InfoSDFiles.html">InfoSDFiles.pl</a>, <a href="./SplitSDFiles.html">SplitSDFiles.pl</a>, <a href="./MergeTextFilesWithSD.html">MergeTextFilesWithSD.pl</a>
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509 </p>
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510 <p>
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511 </p>
|
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512 <h2>COPYRIGHT</h2>
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513 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
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514 <p>This file is part of MayaChemTools.</p>
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515 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
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516 the terms of the GNU Lesser General Public License as published by the Free
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517 Software Foundation; either version 3 of the License, or (at your option)
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518 any later version.</p>
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519 <p> </p><p> </p><div class="DocNav">
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520 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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521 <tr align="left" valign="top"><td width="33%" align="left"><a href="./PathLengthFingerprints.html" title="PathLengthFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./SDToMolFiles.html" title="SDToMolFiles.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>SDFilesToHTML.pl</strong></td></tr>
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522 </table>
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523 </div>
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524 <br />
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525 <center>
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526 <img src="../../images/h2o2.png">
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527 </center>
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528 </body>
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529 </html>
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