Mercurial > repos > deepakjadmin > mayatool3_test2

comparison docs/scripts/html/SDFilesToHTML.html @ 0:4816e4a8ae95 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author deepakjadmin
date Wed, 20 Jan 2016 09:23:18 -0500
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:4816e4a8ae95
1 <html>
2 <head>
3 <title>MayaChemTools:Documentation:SDFilesToHTML.pl</title>
4 <meta http-equiv="content-type" content="text/html;charset=utf-8">
5 <link rel="stylesheet" type="text/css" href="../../css/MayaChemTools.css">
6 </head>
7 <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10">
8 <br/>
9 <center>
10 <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a>
11 </center>
12 <br/>
13 <div class="DocNav">
14 <table width="100%" border=0 cellpadding=0 cellspacing=2>
15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./PathLengthFingerprints.html" title="PathLengthFingerprints.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<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>&nbsp;|&nbsp;<a href="./../pdf/SDFilesToHTML.pdf" title="PDF US Letter Size">PDF</a>&nbsp;|&nbsp;<a href="./../pdfgreen/SDFilesToHTML.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a>&nbsp;|&nbsp;<a href="./../pdfa4/SDFilesToHTML.pdf" title="PDF A4 Size">PDFA4</a>&nbsp;|&nbsp;<a href="./../pdfa4green/SDFilesToHTML.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr>
16 </table>
17 </div>
18 <p>
19 </p>
20 <h2>NAME</h2>
21 <p>SDFilesToHTML.pl - Generate HTML table file(s) from SDFile(s)</p>
22 <p>
23 </p>
24 <h2>SYNOPSIS</h2>
25 <p>SDFilesToHTML.pl SDFiles(s)...</p>
26 <p>SDFilesToHTML.pl [<strong>-a, --align</strong> left | center | right,[top | middle | bottom]] [<strong>-b, --border</strong> borderwidth] [<strong>--cellpadding</strong> padding]
27 [<strong>--cellspacing</strong> spacing] [<strong>--cmpddatafield</strong> &quot;fieldlabel,[label,position,alignment]&quot;] [<strong>--datafields</strong> &quot;fieldlabel,[fieldlabel]...&quot; | Common | All]
28 [<strong>--footer</strong> string] [<strong>-d, --displaylinks</strong> top | bottom | both] [<strong>--displaylinksinfo</strong> compound | table | both] [<strong>-h, --help</strong>]
29 [<strong>--headeralign</strong> left | center | right,[top | middle | bottom]] [<strong>--headercolor</strong> &quot;#RRGGBB&quot;]
30 [<strong>--highlight</strong> &quot;fieldlabel,datatype,criterion,value,[fieldlabel,datatype,criterion,value,...]&quot;]
31 [<strong>--highlightcolor</strong> &quot;#RRGGBB,#RRGGBB&quot;] [<strong>--highlightstyle</strong> text | background]
32 [<strong>-m, --mode</strong> plain | shade | highlight | shadedhighlight | structuresonly | shadedstructuresonly]
33 [<strong>-n, --numcmpds</strong> number] [<strong>-o, --overwrite</strong>] [<strong>-r, --root</strong> rootname] [<strong>-s, --structure</strong> display | link]
34 [<strong>--strlinkmode</strong> plain | shaded] [<strong>--strlinknavigation</strong> yes | no]
35 [<strong>--strlinkshadecolor</strong> &quot;#RRGGBB&quot;] [<strong>--strlinktitle</strong> string] [<strong>--strlinktitledisplay</strong> yes | no] [<strong>--strlinktype</strong> href | button]
36 [<strong>--strviewertype</strong> Chem3DActiveX | ChemDrawActiveX | ChemDrawPlugIn | Chime | JME | Jmol | MarvinView | ViewerActiveX]
37 [<strong>--strviewerconfig</strong> codebase[,archive,code]] [<strong>--strviewerparams</strong> &quot;name=value [name=value ...]&quot;]
38 [<strong>--strviewerembed</strong> direct | javascript] [<strong>--strviewerjsfile</strong> javascriptfilename]
39 [<strong>--strtablesize</strong> &quot;numrows,numcols&quot;] [<strong>--stylesheet</strong> old | new | none]
40 [<strong>--stylesheetname</strong> filename] [<strong>--shadecolor</strong> &quot;#RRGGBB,#RRGGBB&quot;] [<strong>-t, --title</strong> string] [<strong>--titledisplay</strong> yes | no]
41 [<strong>-w, --workingdir</strong> dirname] SDFiles(s)...</p>
42 <p>
43 </p>
44 <h2>DESCRIPTION</h2>
45 <p>Generate HTML file(s) from <em>SDFile(s)</em>. The HTML file(s) contain data tables
46 and appropriate navigational links to view other tables; navigational links are also
47 provided on compound HTML pages. These files can be generated for local viewing or
48 deployment on a web server. A variety of options are provided to control style and
49 appearance of tables. And for viewing structures, options are available to use any one of
50 these viewers: Chem3DActiveX, ChemDrawActiveX, ChemDrawPlugIn, Chime, Jmol, JME,
51 MarvinView, or ViewerActiveX. Jmol is the default structure viewer and it is also distributed
52 along with this package; however, to use any other supported viewers, make sure it's available
53 in your environment.</p>
54 <p>Multiple <em>SDFile(s)</em> names are separated by space. The valid file extensions are
55 <em>.sdf</em> and <em>.sd</em>. All other file names are ignored. All the SD files in a current directory can
56 be specified either by <em>*.sdf</em> or the current directory name.</p>
57 <p>
58 </p>
59 <h2>OPTIONS</h2>
60 <dl>
61 <dt><strong><strong>-a, --align</strong> <em>left | center | right,[top | middle | bottom]</em></strong></dt>
62 <dd>
63 <p>Horizontal and vertical alignment for table rows except for header row which is specified
64 using <strong>--headeralign</strong> option. Possible horizontal alignment values: <em>left, center, or right</em>.
65 Possible vertical alignment values: <em>top, middle, or bottom</em>.</p>
66 <p>Default values: <em>left,middle</em></p>
67 </dd>
68 <dt><strong><strong>-b, --border</strong> <em>borderwidth</em></strong></dt>
69 <dd>
70 <p>Table border width. Default value: 1 for <em>plain</em> and <em>highlight</em> mode; 0 for <em>shade</em>
71 and <em>shadedhightlight</em> mode. Zero indicates no border.</p>
72 </dd>
73 <dt><strong><strong>--cellpadding</strong> <em>padding</em></strong></dt>
74 <dd>
75 <p>Table cell padding. Default value: <em>2</em>.</p>
76 </dd>
77 <dt><strong><strong>--cellspacing</strong> <em>spacing</em></strong></dt>
78 <dd>
79 <p>Table cell spacing. Default value: <em>1</em>.</p>
80 </dd>
81 <dt><strong><strong>--cmpddatafield</strong> <em>fieldlabel,[label,position,alignment]</em></strong></dt>
82 <dd>
83 <p>This value is mode specific. It indicates data field value to be displayed with the structure along
84 with its label, position and alignment during <em>structuresonly | shadedstructuresonly</em> value of <strong>-m, --mode</strong>
85 option. Possible values: feldlabel - valid data field label; label - yes or no; position - <em>top or bottom</em>; alignment
86 - <em>left, center, or right</em>. Default: <em>none,no,bottom,center</em>. Example:</p>
87 <div class="OptionsBox">
88 MolWt,no,bottom,middle</div>
89 <p><strong>--cmpddatafield</strong> option value is also linked to compound summary page.</p>
90 </dd>
91 <dt><strong><strong>--datafields</strong> <em>&quot;fieldlabel,[fieldlabel]...&quot; | Common | All</em></strong></dt>
92 <dd>
93 <p>Data fields to display in HTML table(s). Possible values: list of comma separated data field
94 labels, data fields common to all records, or all data fields. Default value: <em>All</em>.
95 Examples:</p>
96 <div class="OptionsBox">
97 ALogP,MolWeight,EC50
98 <br/> &quot;MolWeight,PSA&quot;</div>
99 </dd>
100 <dt><strong><strong>--footer</strong> <em>string</em></strong></dt>
101 <dd>
102 <p>Text string to be included at bottom of each HTML file. Default: none.</p>
103 </dd>
104 <dt><strong><strong>-d --displaylinks</strong> <em>top | bottom | both</em></strong></dt>
105 <dd>
106 <p>Specify where to display navigation links in each HTML file for accessing all other HTML
107 files. Possible values: <em>top, bottom, or both</em>. Default: <em>both</em>. This option is
108 only valid during multiple HTML files generation for an input file.</p>
109 </dd>
110 <dt><strong><strong>--displaylinksinfo</strong> <em>compound | table | both</em></strong></dt>
111 <dd>
112 <p>Control display of additional information along with navigational links: Showing compound
113 n of m is displyed for compound and showing table n of m for table. Possible values: <em>compound
114 | table | both</em>. Default: <em>both</em>. This option is only valid during multiple HTML files generation.</p>
115 </dd>
116 <dt><strong><strong>-h, --help</strong></strong></dt>
117 <dd>
118 <p>Print this help message.</p>
119 </dd>
120 <dt><strong><strong>--headeralign</strong> <em>left | center | right,[top | middle | bottom</em></strong></dt>
121 <dd>
122 <p>Horizontal and vertical alignment for table header rows. Possible horizontal alignment
123 values: <em>left, center, or right</em>. Possible vertical alignment values: <em>top, middle, or bottom</em>.</p>
124 <p>Default values: <em>center,middle</em></p>
125 </dd>
126 <dt><strong><strong>--headercolor</strong> <em>#RRGGBB</em></strong></dt>
127 <dd>
128 <p>Color used to fill background of table header row containing column labels
129 represented as a hexadecimal string. Default value: None for <strong>-m, --mode</strong> option
130 value of <em>plain</em> and <em>#ccccff</em>, light blue, for others.</p>
131 </dd>
132 <dt><strong><strong>--highlight</strong> <em>&quot;fieldlabel,datatype,criterion,value,[fieldlabel,datatype,criterion,value,...]&quot;</em></strong></dt>
133 <dd>
134 <p>Highlighting methodology used to highlight various SDFile(s) data field values in
135 HTML file(s). Same set of quartets values are applied to all SDFile(s).</p>
136 <p>Input text contains these quartets: <em>fieldlabel,datatype,criterion,value,...</em>.
137 Possible datatype values: <em>numeric or text</em>. Possible criterion values: <em>le, ge, or eq</em>.
138 Examples:</p>
139 <div class="OptionsBox">
140 &quot;MolWt,numeric,le,450&quot;
141 <br/> &quot;MolWt,numeric,le,450,LogP,numeric,le,5&quot;
142 <br/> Name,text,eq,Aspirin</div>
143 </dd>
144 <dt><strong><strong>--highlightcolor</strong> <em>&quot;#RRGGBB,#RRGGBB&quot;</em></strong></dt>
145 <dd>
146 <p>Colors used to highlight column values during <em>highlight</em> and <em>shadedhightlight</em>
147 mode represented as hexadecimal strings.</p>
148 <p>For <strong>--highlighstyle</strong> option values of <em>text</em> and <em>background</em>, these colors represent
149 text or background colors respectively. For a specific column, first color string is used for
150 values which meet criterion indicated by <strong>--highlight</strong> option; the second color is used for
151 rest of the values.</p>
152 <p>Default values for <em>background</em> <strong>--highlightstyle</strong>: <em>&quot;#0fff0f,#ff0f0f&quot;</em>. And default values for
153 <em>text</em> <strong>--highlightstyle</strong>: <em>&quot;#0fbb0f,#ff0f0f&quot;</em>. Hexadecimal strings for both <strong>--highlightstyle</strong>
154 colors correspond to <em>reddish</em> and <em>greenish</em>.</p>
155 </dd>
156 <dt><strong><strong>--highlightstyle</strong> <em>text | background</em></strong></dt>
157 <dd>
158 <p>This value is mode specific. It indicates highlight style used to differentiate column
159 values which meet a specified criterion in <strong>--highlight</strong> option. Possible values: <em>text or
160 background</em>. Default: <em>background</em>.</p>
161 </dd>
162 <dt><strong><strong>-m, --mode</strong> <em>plain | shade | highlight | shadedhighlight | structuresonly | shadedstructuresonly</em></strong></dt>
163 <dd>
164 <p>Specify how to generate HTML table(s): plain tables with line borders, background of
165 alternate rows filled with a specified color, column values highlighted using a specified
166 criteria, combination of previous two styles, tables containing only structures, or tables
167 containing only structures with filled background of alternate rows.</p>
168 <p>Possible values: <em>plain, shade, highlight, shadedhighlight, structuresonly, or
169 shadedstructuresonly</em>. Default: <em>shade</em>.</p>
170 </dd>
171 <dt><strong><strong>-n, --numcmpds</strong> <em>number</em></strong></dt>
172 <dd>
173 <p>Maximum number of compounds per table. Default value: <em>15</em> for tables with structures and
174 <em>50</em> for tables with links to structures. Use 0 to put all compounds into one table. For SDFile(s)
175 with more than maximum number of specified compounds, multiple HTML tables, with appropriate
176 navigation links, are created.</p>
177 </dd>
178 <dt><strong><strong>-o, --overwrite</strong></strong></dt>
179 <dd>
180 <p>Overwrite existing files.</p>
181 </dd>
182 <dt><strong><strong>-r, --root</strong> <em>rootname</em></strong></dt>
183 <dd>
184 <p>New file or directory name is generated using the root: &lt;root&gt;.html or &lt;root&gt;-html.
185 Default new file name: &lt;InitialSDFileName&gt;.html. Default directory name:
186 &lt;InitialSDFileName&gt;-html.</p>
187 <p>For SDFile(s) with more than maximum number of specified compounds per table,
188 this directory tree is generated using &lt;Name&gt; where &lt;Name&gt; corresponds to &lt;root&gt;
189 or &lt;InitialSDFileName&gt;: Top dir - &lt;Name&gt;-html; Sub dirs - html and mols. &lt;Top dir&gt; contains
190 &lt;Name&gt;.html and &lt;Name&gt;.css files and &lt;sub dir&gt; html conatins various
191 &lt;Name&gt;Lines&lt;Start&gt;To&lt;End&gt;.html files; &lt;sub dir&gt; mols is created as needed and contains
192 MOL files.</p>
193 <p>This option is ignored for multiple input files.</p>
194 </dd>
195 <dt><strong><strong>-s, --structure</strong> <em>display | link</em></strong></dt>
196 <dd>
197 <p>Structure display control: display structures in a table column or set up a link for each
198 structure which opens up a new HTML page containing structure and other appropriate
199 information. Possible values: <em>display or link</em>. Default value: <em>display</em></p>
200 </dd>
201 <dt><strong><strong>--strlinkmode</strong> <em>plain | shaded</em></strong></dt>
202 <dd>
203 <p>Specify how to display compound HTML page: plain or background of data field
204 field labels is filled with a specified color. Possible values: <em>plain or shad</em>.
205 Default value: <em>plane</em>.</p>
206 <p>Structure viewer background color is white. Use <strong>--strviewerparams</strong> option to change
207 default behavior of structure viewers.</p>
208 </dd>
209 <dt><strong><strong>--strlinknavigation</strong> <em>yes | no</em></strong></dt>
210 <dd>
211 <p>Display navigation links to other compounds in compound HTML page. Possible values:
212 <em>yes or no</em>. Default value: <em>yes</em>.</p>
213 </dd>
214 <dt><strong><strong>--strlinkshadecolor</strong> <em>&quot;#RRGGBB&quot;</em></strong></dt>
215 <dd>
216 <p>This value is <strong>--strlinkmode</strong> specific. For <em>shade</em> value of <strong>--strlinkmode</strong> option, it
217 represents colors used to fill background of data field labels.</p>
218 <p>Default value: <em>&quot;#e0e9eb&quot;</em> - it's a very light blue color.</p>
219 </dd>
220 <dt><strong><strong>--strlinktitle</strong> <em>string</em></strong></dt>
221 <dd>
222 <p>Title for compound HTML page. Default value: <em>Compound Summary</em>.</p>
223 </dd>
224 <dt><strong><strong>--strlinktitledisplay</strong> <em>yes | no</em></strong></dt>
225 <dd>
226 <p>Display title for compound HTML page. Possible values: <em>yes or no</em>. Default value: <em>no</em>.</p>
227 </dd>
228 <dt><strong><strong>--strlinktype</strong> <em>href | button</em></strong></dt>
229 <dd>
230 <p>Type of structure link. Possible values: <em>href or button</em>. Default: <em>href</em>.</p>
231 </dd>
232 <dt><strong><strong>--strviewertype</strong> <em>Chem3DActiveX | ChemDrawActiveX | ChemDrawPlugIn | Chime | JME | Jmol | MarvinView | ViewerActiveX</em></strong></dt>
233 <dd>
234 <p>Structure viewer supported for viewing structures. Possible values: <em>Chem3DActiveX,
235 ChemDrawActiveX, ChemDrawPlugIn, Chime, JME, Jmol, MarvinView, or ViewerActiveX</em>.
236 Default value: <em>Jmol</em>.</p>
237 <p>Assuming you have access to one of these viewers on your machine, you are all set
238 to use this script. Otherwise, visit one of these web sites to download and install
239 your favorite viewer:</p>
240 <div class="OptionsBox">
241 accelrys.com: Viewer ActiveX 5.0
242 <br/> cambridgesoft.com: Chem3DActiveX 8.0, ChemDrawActiveX 8.0,
243 ChemDrawPlugIn
244 <br/> chemaxon.com: MarvinView applet
245 <br/> mdli.com: Chime plug-in
246 <br/> jmol.sourceforge.net: JmolApplet V10
247 <br/> molinspiration.com: JME applet</div>
248 <p>The default viewer, JmolApplet V10, is distributed with MayaChemTools package.
249 Earlier versions of JmolApplet are not supported: due to applet security issues related to
250 reading files, this script uses in-line loading of MOL files and this option doesn't exist in
251 earlier version of JmolApplet.</p>
252 </dd>
253 <dt><strong><strong>--strviewerconfig</strong> <em>codebase[,archive,code]</em></strong></dt>
254 <dd>
255 <p>Configuration information for structure viewers. This option is only valid for structure
256 viewers which are applets: Jmol, JME and MarvinView. For other viewer types available via
257 <strong>--strviewertype</strong> option - MDL Chime, ChemDrawActiveX, ChemDrawPlugIn, and
258 Chem3DActiveX - this value is ignored.</p>
259 <p>Input text format: <em>codebase[,archive,code]</em>. For an applet viewer, <em>codebase</em> must be
260 specified; <em>archive</em> and <em>code</em> values are optional. Here are default <em>archive</em> and
261 <em>codebase</em> values for various applets: Jmol - JmolApplet, JmolApplet.jar; JME - JME, JME.jar;
262 MarvinView: MView, marvin.jar</p>
263 <p>For local deployment of HTML files, <em>codebase</em> must correspond to a complete path to
264 the local directory containing appropriate <em>archive</em> file and the complete path is converted
265 into appropriate relative path during generation of HTML files.</p>
266 <p>By default, <em>codebase</em> value of &lt;this script dir&gt;/../lib/Jmol is used for <em>Jmol</em> applet viewer, and
267 HTML file(s) are generated for local deployment; however, you can specify any supported
268 applet viewer and generate HTML file(s) for deploying on a web server.</p>
269 <p>For deploying the HTML file(s) on a web server, specify a valid <em>codebase</em> directory name
270 relative to &lt;WWWRootDir&gt;. Example when JME archive file, JME.jar, is available in
271 <em>/jme</em> directory on the web server:</p>
272 <div class="OptionsBox">
273 /jme</div>
274 <p>For local deployment of HTML file(s), specify a complete <em>codebase</em> directory name.
275 Example when JmolApplet archive file, JmolApplet.jar, is present in &lt;JMOLROOT&gt; directory:</p>
276 <div class="OptionsBox">
277 &lt;JMOLROOT&gt;</div>
278 <p>In addition to <em>codebase</em>, you can also specify <em>archive</em> file name. Example for web
279 deployment:</p>
280 <div class="OptionsBox">
281 &quot;/jme,JME.jar&quot;
282 <br/> &quot;/jme&quot;</div>
283 <p>Example for local deployment:</p>
284 <div class="OptionsBox">
285 &quot;&lt;JMEROOT&gt;,JME.jar&quot;
286 <br/> &quot;&lt;JMEROOT&gt;&quot;</div>
287 </dd>
288 <dt><strong><strong>--strviewerparams</strong> <em>&quot;name=value [name=value ...]&quot;</em></strong></dt>
289 <dd>
290 <p>Parameters name and value pairs for structure viewers. These name and value pairs
291 are used to control the appearance and behavior of structure viewers in tables and
292 compound HTML page during <em>link</em> value for <strong>-s --structure</strong> option.</p>
293 <p>The parameter names, along with their values, are just passed to each structure viewer
294 in appropriate format without checking their validity. Check documentation of appropriate
295 structure viewers to figure out valid parameter names.</p>
296 <p>Input text format: <em>name=value name=value ...</em> Example:</p>
297 <div class="OptionsBox">
298 &quot;width=250 height=170&quot;</div>
299 <p>Default for all structure viewers: <em>width=250 height=170</em> for displaying structures in
300 tables, and <em>strlinkwidth=500 strlinkheight=295</em> for compound HTML page during <em>link</em> value
301 for <strong>-s --structure</strong> option.</p>
302 <p>Default background color for all structure viewers: same as <strong>--shadecolor</strong> value for
303 displaying structures in tables and <em>strlinkbgcolor=#ffffff</em> for compound HTML page;
304 however, explicit specification of background color in this option overrides default value.
305 To use black background for structures in tables and compound HTML page, specify <em>bgcolor=#000000</em>
306 and <em>strlinkbgcolor=#000000</em> respectively. Keep this in mind: Some structure viewers
307 don't appear to support background color parameter.</p>
308 <p>Additional structure viewer specific default values:</p>
309 <div class="OptionsBox">
310 Chem3DActiveX: &quot;displaytype=Ball&amp;Stick rotationbars=false
311 moviecontroller=false&quot;
312 <br/> ChemDrawActiveX: &quot;ViewOnly=1 ShrinkToFit=1 ShowToolsWhenVisible=1&quot;
313 <br/> ChemDrawPlugIn: &quot;type=chemical/x-mdl-molfile ViewOnly=1
314 ShrinkToFit=1 ShowToolsWhenVisible=1&quot;
315 <br/> Chime: &quot;display2d=true&quot;
316 <br/> JME: &quot;options=depict&quot;
317 <br/> Jmol: &quot;progressbar=true progresscolor=#0000ff boxbgcolor=#000000
318 boxfgcolor=#ffffff script=&quot;select *; set frank off;
319 wireframe on; spacefill off&quot;&quot;
320 <br/> MarvinView: &quot;navmode=zoom&quot;
321 <br/> ViewerActiveX:&quot;Mouse=4 Convert2Dto3D=0&quot;</div>
322 <p>Try overriding default values or specify additional valid parameter/value pairs to get desired
323 results. Example for using CPK rendering scheme with Jmol viewer:</p>
324 <div class="OptionsBox">
325 &quot;script=&quot;select *; set frank off; wireframe off; spacefill on&quot;&quot;</div>
326 </dd>
327 <dt><strong><strong>--strviewerembed</strong> <em>direct | javascript</em></strong></dt>
328 <dd>
329 <p>Specify how to embed structure viewers in HTML pages. Possible values: <em>direct</em> - use applet/object
330 tags to emded structure viewer; <em>javascript</em> - use vendor supplied java scripts. Default value:
331 direct.</p>
332 <p>This option only applies to these vieweres: <em>Chem3DActiveX, ChemDrawActiveX, ChemDrawPlugIn,
333 Jmol, and MarvinView</em>.</p>
334 <p>For marvin.js to work correctly on your browser, you may need to set <em>marvin_jvm=builtin</em> or
335 <em>marvin_jvm=plugin</em> using <strong>--strviewerparams</strong> option. Additionally, MarvinView - at least
336 in my hands - also has problems during usage of JavaScript for local deployment; however, it
337 does work via web server.</p>
338 <p>As far as I can tell, Jmol.js supplied with Jmol10 release has these issues: jmolSetAppletColor
339 doesn't support background color; jmolInitialize disables relative specification of codebase
340 directroy which works okay. So, use Jmol.js supplied with MayaChemTools.</p>
341 </dd>
342 <dt><strong><strong>--strviewerjsfile</strong> <em>java script file name</em></strong></dt>
343 <dd>
344 <p>Name of vendor supplied java script file. Default values: Chem3DActiveX: <em>chem3d.js</em>; ChemDrawActiveX,
345 and ChemDrawPlugIn: <em>chemdraw.js</em>; Jmol: <em>Jmol.js</em>, MarvinView: <em>marvin.js</em>.</p>
346 <p>Directory location for these files is specified via <em>codebase</em> value of <strong>--strviewerconfig</strong> option.</p>
347 </dd>
348 <dt><strong><strong>--strtablesize</strong> <em>&quot;numrows,numcols&quot;</em></strong></dt>
349 <dd>
350 <p>This option is only valid for <em>structuresonly</em> and <em>shadedstructuresonly</em> modes. And it indicates
351 maximum number of rows and columns per structure table. Default value:<em>6,4</em>.</p>
352 </dd>
353 <dt><strong><strong>--stylesheet</strong> <em>old | new | none</em></strong></dt>
354 <dd>
355 <p>Controls usage of stylesheet for newly generated HTML file(s). Possible values: <em>old,
356 new, or none</em>. Default value: <em>new</em>.</p>
357 <p>Stylesheet file contains various properties which control appearance of HTML pages:
358 type, size, and color of fonts; background color; and so on.</p>
359 <p>For <em>old</em> value, an existing stylesheet file specified by <strong>--stylesheetname</strong> option is
360 used for each HTML file; no new stylesheet file is created. This option is quite handy
361 for deploying HTML file(s) on a web server: assuming you specify a valid stylesheet
362 file location relative to your WWWRoot, a reference to this stylesheet is added to each
363 HTML file. For local deployment of HTML file(s), a complete path to a local stylesheet
364 is fine as well.</p>
365 <p>For <em>create</em> value, a new stylesheet is created and reference to this local stylesheet
366 is added to each HTML file. Use option <strong>--stylesheetname</strong> to specify name.</p>
367 <p>For <em>none</em> value, stylesheet usage is completely ignored.</p>
368 </dd>
369 <dt><strong><strong>--stylesheetname</strong> <em>filename</em></strong></dt>
370 <dd>
371 <p>Stylesheet file name to be used in conjunction with <strong>-s --stylesheet</strong> option. It is only
372 valid for <em>old</em> value of <strong>-s --stylesheet</strong> option. Specify a valid stylesheet file location
373 relative to your WWWRoot and a reference to this stylesheet is added to each HTML
374 file. Example: <em>&quot;/stylesheets/MyStyleSheet.css&quot;</em>. Or a complete path name to a local
375 stylesheet file.</p>
376 <p>For <em>create</em> value of <strong>-s --stylesheet</strong> option, a new stylesheet file is created using
377 <strong>-r --root</strong> option. And value of <strong>--stylesheetname</strong> is simply ignored.</p>
378 </dd>
379 <dt><strong><strong>--shadecolor</strong> <em>&quot;#RRGGBB,#RRGGBB&quot;</em></strong></dt>
380 <dd>
381 <p>Colors used to fill background of rows during <em>shade</em> and <em>shadedhightlight</em> mode
382 represented as a pair of hexadecimal string; the first and second color values
383 are used for odd and even number rows respectively.</p>
384 <p>Default value: <em>&quot;#ffffff,#e0e9eb&quot;</em> - it's white and very light blue for odd and even number rows.</p>
385 </dd>
386 <dt><strong><strong>-t, --title</strong> <em>string</em></strong></dt>
387 <dd>
388 <p>Title for HTML table(s). Default value: <em>SDFileName</em>. This option is ignored for
389 multiple input files. And <strong>-r --root</strong> option is used to generate appropriate
390 titles.</p>
391 </dd>
392 <dt><strong><strong>--titledisplay</strong> <em>yes | no</em></strong></dt>
393 <dd>
394 <p>Display title for HTML table(s). Possible values: <em>yes or no</em>. Default value: <em>yes</em>.</p>
395 </dd>
396 <dt><strong><strong>-w, --workingdir</strong> <em>dirname</em></strong></dt>
397 <dd>
398 <p>Location of working directory. Default: current directory.</p>
399 </dd>
400 </dl>
401 <p>
402 </p>
403 <h2>EXAMPLES</h2>
404 <p>HTML table file(s), containing structures, can be used in two different ways: browsing on a
405 local machine or deployment via a web server. By default, HTML file(s) are created for viewing
406 on a local machine using Jmol viewer through a browser; however, you can specify any
407 supported applet viewer and generate HTML file(s) for deploying on a web server.</p>
408 <p>First two sets of examples show generation of HTML file(s) using different applet viewers
409 and a variety of options for local browsing; last set deals with web deployment.</p>
410 <p><strong>Local deployment: Usage of default JMol viewer distributed with MayaChemTools:</strong></p>
411 <p>To generate HTML tables with structure display using JMol viewer, rows background filled
412 with white and light blue colors, navigation links on top and botton of each page, type:</p>
413 <div class="ExampleBox">
414 % SDFilesToHTML.pl -o Sample1.sdf</div>
415 <p>To generate HTML tables with structure display using JMol viewer, rows background filled
416 with white and light blue colors, navigation links on top and botton of each page, and
417 only containing MolWeight and Mol_ID SD data fields, type:</p>
418 <div class="ExampleBox">
419 % SDFilesToHTML.pl --datafields &quot;MolWeight,Mol_ID&quot; -o Sample1.sdf</div>
420 <p>To generate HTML tables with CPK structure display using JMol viewer, rows
421 background filled with white and light blue colors, navigation links on top and botton of
422 each page, type:</p>
423 <div class="ExampleBox">
424 % SDFilesToHTML.pl --strviewerparams &quot;script=\&quot;select *; set frank off;
425 wireframe off; spacefill on\&quot;&quot; -o Sample1.sdf</div>
426 <p>To generate HTML tables with structure display using JMol viewer and black background, rows
427 background filled with light golden and greyish colors, navigation links on top and botton of
428 each page, 10 rows in each table, greyish header row color, and cell spacing of 1, type:</p>
429 <div class="ExampleBox">
430 % SDFilesToHTML.pl -o -n 10 --headeralign &quot;center&quot; --headercolor
431 &quot;#a1a1a1&quot; --shadecolor &quot;#fafad2,#d1d1d1&quot; --cellspacing 1
432 --strviewerparams &quot;bgcolor=#000000&quot; Sample1.sdf</div>
433 <p>To highlight molecular weight values using specified highlight criteria and fill in default background
434 colors, type:</p>
435 <div class="ExampleBox">
436 % SDFilesToHTML.pl -n 10 --highlight &quot;MolWeight,numeric,le,450&quot;
437 --highlightstyle background -m shadedhighlight -o Sample1.sdf</div>
438 <p>To highlight molecular weight values using specified highlight criteria, color the text using
439 default colors, and add a footer message in every page, type:</p>
440 <div class="ExampleBox">
441 % SDFilesToHTML.pl -n 4 --highlight &quot;MolWeight,numeric,le,500&quot;
442 --highlightstyle text -m shadedhighlight -o
443 --footer &quot;Copyright (C) MayaChemTools&quot; --cellspacing 1 Sample1.sdf</div>
444 <p>To generate tables containing only structures, type:</p>
445 <div class="ExampleBox">
446 % SDFilesToHTML.pl -d both -m shadedstructuresonly --strtablesize &quot;6,4&quot;
447 --cellspacing 1 -b 1 -o Sample1.sdf</div>
448 <p>To generate tables containing only structures with molecular weight displayed above the
449 structure, type:</p>
450 <div class="ExampleBox">
451 % SDFilesToHTML.pl -d both -m shadedstructuresonly --strtablesize &quot;6,4&quot;
452 --cmpddatafield &quot;MolWeight,no,top,center&quot; --cellspacing 1 -b 1
453 -o Sample1.sdf</div>
454 <p>To generate tables containing links to structures and highlight molecular weight data field values
455 using specified highlight criteria , type:</p>
456 <div class="ExampleBox">
457 % SDFilesToHTML.pl -n 4 --footer &quot;Copyright (C) MayaChemTools&quot;
458 --highlight &quot;MolWeight,numeric,le,450&quot; --highlightstyle background
459 -d both -m shadedhighlight -s link --strlinktype button
460 -o Sample1.sdf</div>
461 <p><strong>Local deployment: Usage of other structure viewers:</strong></p>
462 <div class="ExampleBox">
463 % SDFilesToHTML.pl --strviewertype MarvinView --strviewerconfig
464 &quot;&lt;Marvin dir path&gt;&quot; -o Sample1.sdf</div>
465 <div class="ExampleBox">
466 % SDFilesToHTML.pl -o -n 10 --headeralign &quot;center&quot; --headercolor
467 &quot;#a1a1a1&quot; --shadecolor &quot;#fafad2,#d1d1d1&quot; --cellspacing 1
468 --strviewerparams &quot;bgcolor=#000000&quot; --strviewertype Chime
469 Sample1.sdf</div>
470 <div class="ExampleBox">
471 % SDFilesToHTML.pl -n 10 --highlight &quot;MolWeight,numeric,le,450&quot;
472 --highlightstyle background -m shadedhighlight --strviewertype
473 Chime -o Sample1.sdf</div>
474 <div class="ExampleBox">
475 % SDFilesToHTML.pl -d both -m shadedstructuresonly --strtablesize &quot;6,4&quot;
476 --cellspacing 1 -b 1 -strviewertype JME -strviewerconfig &quot;&lt;JME dir
477 path&gt;&quot; -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 &lt;WWWRootDir&gt;. 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
484 -strviewerconfig &quot;/jmol&quot; -n 5 -d both -r PlainTable -t &quot;Example
485 using Jmol: Plain Table&quot; -o Sample1.sdf</div>
486 <div class="ExampleBox">
487 % SDFilesToHTML.pl -n 5 -m shade -s display -strviewertype JME
488 -strviewerconfig &quot;/jme,JME.jar&quot; -r ShadeTable -t &quot;Example using JME:
489 Shaded Table&quot; -o Sample.sdf</div>
490 <div class="ExampleBox">
491 % SDFilesToHTML.pl -n 5 --highlight &quot;MolWeight,numeric,le,450&quot;
492 --highlightstyle background -d both -m shadedhighlight -s display
493 -strviewertype MarvinView -strviewerconfig &quot;/marvin&quot; -r
494 ShadedHightlightTable -t &quot;Example using MarvinView: Shaded and
495 Highlighted Table&quot; -o Sample.sdf</div>
496 <div class="ExampleBox">
497 % SDFilesToHTML.pl -n 4 --highlight &quot;MolWeight,numeric,le,450&quot; -s link
498 --strlinktype href --strviewertype ChemDrawPlugIn --highlightstyle
499 background -m shadedhighlight -t &quot;Example using ChemDrawPlugIn:
500 Shaded and Highlighted Table&quot; -r ShadedHightlightTable -o Sample1.sdf</div>
501 <p>
502 </p>
503 <h2>AUTHOR</h2>
504 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
505 <p>
506 </p>
507 <h2>SEE ALSO</h2>
508 <p><a href="./FilterSDFiles.html">FilterSDFiles.pl</a>,&nbsp<a href="./InfoSDFiles.html">InfoSDFiles.pl</a>,&nbsp<a href="./SplitSDFiles.html">SplitSDFiles.pl</a>,&nbsp<a href="./MergeTextFilesWithSD.html">MergeTextFilesWithSD.pl</a>
509 </p>
510 <p>
511 </p>
512 <h2>COPYRIGHT</h2>
513 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
514 <p>This file is part of MayaChemTools.</p>
515 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
516 the terms of the GNU Lesser General Public License as published by the Free
517 Software Foundation; either version 3 of the License, or (at your option)
518 any later version.</p>
519 <p>&nbsp</p><p>&nbsp</p><div class="DocNav">
520 <table width="100%" border=0 cellpadding=0 cellspacing=2>
521 <tr align="left" valign="top"><td width="33%" align="left"><a href="./PathLengthFingerprints.html" title="PathLengthFingerprints.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<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>
522 </table>
523 </div>
524 <br />
525 <center>
526 <img src="../../images/h2o2.png">
527 </center>
528 </body>
529 </html>