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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 11:55:01 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mayachemtools/docs/scripts/html/SDFilesToHTML.html Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,529 @@ +<html> +<head> +<title>MayaChemTools:Documentation:SDFilesToHTML.pl</title> +<meta http-equiv="content-type" content="text/html;charset=utf-8"> +<link rel="stylesheet" type="text/css" href="../../css/MayaChemTools.css"> +</head> +<body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> +<br/> +<center> +<a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> +</center> +<br/> +<div class="DocNav"> +<table width="100%" border=0 cellpadding=0 cellspacing=2> +<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> +</table> +</div> +<p> +</p> +<h2>NAME</h2> +<p>SDFilesToHTML.pl - Generate HTML table file(s) from SDFile(s)</p> +<p> +</p> +<h2>SYNOPSIS</h2> +<p>SDFilesToHTML.pl SDFiles(s)...</p> +<p>SDFilesToHTML.pl [<strong>-a, --align</strong> left | center | right,[top | middle | bottom]] [<strong>-b, --border</strong> borderwidth] [<strong>--cellpadding</strong> padding] +[<strong>--cellspacing</strong> spacing] [<strong>--cmpddatafield</strong> "fieldlabel,[label,position,alignment]"] [<strong>--datafields</strong> "fieldlabel,[fieldlabel]..." | Common | All] +[<strong>--footer</strong> string] [<strong>-d, --displaylinks</strong> top | bottom | both] [<strong>--displaylinksinfo</strong> compound | table | both] [<strong>-h, --help</strong>] +[<strong>--headeralign</strong> left | center | right,[top | middle | bottom]] [<strong>--headercolor</strong> "#RRGGBB"] +[<strong>--highlight</strong> "fieldlabel,datatype,criterion,value,[fieldlabel,datatype,criterion,value,...]"] +[<strong>--highlightcolor</strong> "#RRGGBB,#RRGGBB"] [<strong>--highlightstyle</strong> text | background] +[<strong>-m, --mode</strong> plain | shade | highlight | shadedhighlight | structuresonly | shadedstructuresonly] +[<strong>-n, --numcmpds</strong> number] [<strong>-o, --overwrite</strong>] [<strong>-r, --root</strong> rootname] [<strong>-s, --structure</strong> display | link] +[<strong>--strlinkmode</strong> plain | shaded] [<strong>--strlinknavigation</strong> yes | no] +[<strong>--strlinkshadecolor</strong> "#RRGGBB"] [<strong>--strlinktitle</strong> string] [<strong>--strlinktitledisplay</strong> yes | no] [<strong>--strlinktype</strong> href | button] +[<strong>--strviewertype</strong> Chem3DActiveX | ChemDrawActiveX | ChemDrawPlugIn | Chime | JME | Jmol | MarvinView | ViewerActiveX] +[<strong>--strviewerconfig</strong> codebase[,archive,code]] [<strong>--strviewerparams</strong> "name=value [name=value ...]"] +[<strong>--strviewerembed</strong> direct | javascript] [<strong>--strviewerjsfile</strong> javascriptfilename] +[<strong>--strtablesize</strong> "numrows,numcols"] [<strong>--stylesheet</strong> old | new | none] +[<strong>--stylesheetname</strong> filename] [<strong>--shadecolor</strong> "#RRGGBB,#RRGGBB"] [<strong>-t, --title</strong> string] [<strong>--titledisplay</strong> yes | no] +[<strong>-w, --workingdir</strong> dirname] SDFiles(s)...</p> +<p> +</p> +<h2>DESCRIPTION</h2> +<p>Generate HTML file(s) from <em>SDFile(s)</em>. The HTML file(s) contain data tables +and appropriate navigational links to view other tables; navigational links are also +provided on compound HTML pages. These files can be generated for local viewing or +deployment on a web server. A variety of options are provided to control style and +appearance of tables. And for viewing structures, options are available to use any one of +these viewers: Chem3DActiveX, ChemDrawActiveX, ChemDrawPlugIn, Chime, Jmol, JME, +MarvinView, or ViewerActiveX. Jmol is the default structure viewer and it is also distributed +along with this package; however, to use any other supported viewers, make sure it's available +in your environment.</p> +<p>Multiple <em>SDFile(s)</em> names are separated by space. The valid file extensions are +<em>.sdf</em> and <em>.sd</em>. All other file names are ignored. All the SD files in a current directory can +be specified either by <em>*.sdf</em> or the current directory name.</p> +<p> +</p> +<h2>OPTIONS</h2> +<dl> +<dt><strong><strong>-a, --align</strong> <em>left | center | right,[top | middle | bottom]</em></strong></dt> +<dd> +<p>Horizontal and vertical alignment for table rows except for header row which is specified +using <strong>--headeralign</strong> option. Possible horizontal alignment values: <em>left, center, or right</em>. +Possible vertical alignment values: <em>top, middle, or bottom</em>.</p> +<p>Default values: <em>left,middle</em></p> +</dd> +<dt><strong><strong>-b, --border</strong> <em>borderwidth</em></strong></dt> +<dd> +<p>Table border width. Default value: 1 for <em>plain</em> and <em>highlight</em> mode; 0 for <em>shade</em> +and <em>shadedhightlight</em> mode. Zero indicates no border.</p> +</dd> +<dt><strong><strong>--cellpadding</strong> <em>padding</em></strong></dt> +<dd> +<p>Table cell padding. Default value: <em>2</em>.</p> +</dd> +<dt><strong><strong>--cellspacing</strong> <em>spacing</em></strong></dt> +<dd> +<p>Table cell spacing. Default value: <em>1</em>.</p> +</dd> +<dt><strong><strong>--cmpddatafield</strong> <em>fieldlabel,[label,position,alignment]</em></strong></dt> +<dd> +<p>This value is mode specific. It indicates data field value to be displayed with the structure along +with its label, position and alignment during <em>structuresonly | shadedstructuresonly</em> value of <strong>-m, --mode</strong> +option. Possible values: feldlabel - valid data field label; label - yes or no; position - <em>top or bottom</em>; alignment +- <em>left, center, or right</em>. Default: <em>none,no,bottom,center</em>. Example:</p> +<div class="OptionsBox"> + MolWt,no,bottom,middle</div> +<p><strong>--cmpddatafield</strong> option value is also linked to compound summary page.</p> +</dd> +<dt><strong><strong>--datafields</strong> <em>"fieldlabel,[fieldlabel]..." | Common | All</em></strong></dt> +<dd> +<p>Data fields to display in HTML table(s). Possible values: list of comma separated data field +labels, data fields common to all records, or all data fields. Default value: <em>All</em>. +Examples:</p> +<div class="OptionsBox"> + ALogP,MolWeight,EC50 +<br/> "MolWeight,PSA"</div> +</dd> +<dt><strong><strong>--footer</strong> <em>string</em></strong></dt> +<dd> +<p>Text string to be included at bottom of each HTML file. Default: none.</p> +</dd> +<dt><strong><strong>-d --displaylinks</strong> <em>top | bottom | both</em></strong></dt> +<dd> +<p>Specify where to display navigation links in each HTML file for accessing all other HTML +files. Possible values: <em>top, bottom, or both</em>. Default: <em>both</em>. This option is +only valid during multiple HTML files generation for an input file.</p> +</dd> +<dt><strong><strong>--displaylinksinfo</strong> <em>compound | table | both</em></strong></dt> +<dd> +<p>Control display of additional information along with navigational links: Showing compound +n of m is displyed for compound and showing table n of m for table. Possible values: <em>compound +| table | both</em>. Default: <em>both</em>. This option is only valid during multiple HTML files generation.</p> +</dd> +<dt><strong><strong>-h, --help</strong></strong></dt> +<dd> +<p>Print this help message.</p> +</dd> +<dt><strong><strong>--headeralign</strong> <em>left | center | right,[top | middle | bottom</em></strong></dt> +<dd> +<p>Horizontal and vertical alignment for table header rows. Possible horizontal alignment +values: <em>left, center, or right</em>. Possible vertical alignment values: <em>top, middle, or bottom</em>.</p> +<p>Default values: <em>center,middle</em></p> +</dd> +<dt><strong><strong>--headercolor</strong> <em>#RRGGBB</em></strong></dt> +<dd> +<p>Color used to fill background of table header row containing column labels +represented as a hexadecimal string. Default value: None for <strong>-m, --mode</strong> option +value of <em>plain</em> and <em>#ccccff</em>, light blue, for others.</p> +</dd> +<dt><strong><strong>--highlight</strong> <em>"fieldlabel,datatype,criterion,value,[fieldlabel,datatype,criterion,value,...]"</em></strong></dt> +<dd> +<p>Highlighting methodology used to highlight various SDFile(s) data field values in +HTML file(s). Same set of quartets values are applied to all SDFile(s).</p> +<p>Input text contains these quartets: <em>fieldlabel,datatype,criterion,value,...</em>. +Possible datatype values: <em>numeric or text</em>. Possible criterion values: <em>le, ge, or eq</em>. +Examples:</p> +<div class="OptionsBox"> + "MolWt,numeric,le,450" +<br/> "MolWt,numeric,le,450,LogP,numeric,le,5" +<br/> Name,text,eq,Aspirin</div> +</dd> +<dt><strong><strong>--highlightcolor</strong> <em>"#RRGGBB,#RRGGBB"</em></strong></dt> +<dd> +<p>Colors used to highlight column values during <em>highlight</em> and <em>shadedhightlight</em> +mode represented as hexadecimal strings.</p> +<p>For <strong>--highlighstyle</strong> option values of <em>text</em> and <em>background</em>, these colors represent +text or background colors respectively. For a specific column, first color string is used for +values which meet criterion indicated by <strong>--highlight</strong> option; the second color is used for + rest of the values.</p> +<p>Default values for <em>background</em> <strong>--highlightstyle</strong>: <em>"#0fff0f,#ff0f0f"</em>. And default values for +<em>text</em> <strong>--highlightstyle</strong>: <em>"#0fbb0f,#ff0f0f"</em>. Hexadecimal strings for both <strong>--highlightstyle</strong> +colors correspond to <em>reddish</em> and <em>greenish</em>.</p> +</dd> +<dt><strong><strong>--highlightstyle</strong> <em>text | background</em></strong></dt> +<dd> +<p>This value is mode specific. It indicates highlight style used to differentiate column +values which meet a specified criterion in <strong>--highlight</strong> option. Possible values: <em>text or +background</em>. Default: <em>background</em>.</p> +</dd> +<dt><strong><strong>-m, --mode</strong> <em>plain | shade | highlight | shadedhighlight | structuresonly | shadedstructuresonly</em></strong></dt> +<dd> +<p>Specify how to generate HTML table(s): plain tables with line borders, background of +alternate rows filled with a specified color, column values highlighted using a specified +criteria, combination of previous two styles, tables containing only structures, or tables +containing only structures with filled background of alternate rows.</p> +<p>Possible values: <em>plain, shade, highlight, shadedhighlight, structuresonly, or +shadedstructuresonly</em>. Default: <em>shade</em>.</p> +</dd> +<dt><strong><strong>-n, --numcmpds</strong> <em>number</em></strong></dt> +<dd> +<p>Maximum number of compounds per table. Default value: <em>15</em> for tables with structures and +<em>50</em> for tables with links to structures. Use 0 to put all compounds into one table. For SDFile(s) +with more than maximum number of specified compounds, multiple HTML tables, with appropriate +navigation links, are created.</p> +</dd> +<dt><strong><strong>-o, --overwrite</strong></strong></dt> +<dd> +<p>Overwrite existing files.</p> +</dd> +<dt><strong><strong>-r, --root</strong> <em>rootname</em></strong></dt> +<dd> +<p>New file or directory name is generated using the root: <root>.html or <root>-html. +Default new file name: <InitialSDFileName>.html. Default directory name: +<InitialSDFileName>-html.</p> +<p>For SDFile(s) with more than maximum number of specified compounds per table, +this directory tree is generated using <Name> where <Name> corresponds to <root> +or <InitialSDFileName>: Top dir - <Name>-html; Sub dirs - html and mols. <Top dir> contains +<Name>.html and <Name>.css files and <sub dir> html conatins various +<Name>Lines<Start>To<End>.html files; <sub dir> mols is created as needed and contains +MOL files.</p> +<p>This option is ignored for multiple input files.</p> +</dd> +<dt><strong><strong>-s, --structure</strong> <em>display | link</em></strong></dt> +<dd> +<p>Structure display control: display structures in a table column or set up a link for each +structure which opens up a new HTML page containing structure and other appropriate +information. Possible values: <em>display or link</em>. Default value: <em>display</em></p> +</dd> +<dt><strong><strong>--strlinkmode</strong> <em>plain | shaded</em></strong></dt> +<dd> +<p>Specify how to display compound HTML page: plain or background of data field +field labels is filled with a specified color. Possible values: <em>plain or shad</em>. +Default value: <em>plane</em>.</p> +<p>Structure viewer background color is white. Use <strong>--strviewerparams</strong> option to change +default behavior of structure viewers.</p> +</dd> +<dt><strong><strong>--strlinknavigation</strong> <em>yes | no</em></strong></dt> +<dd> +<p>Display navigation links to other compounds in compound HTML page. Possible values: +<em>yes or no</em>. Default value: <em>yes</em>.</p> +</dd> +<dt><strong><strong>--strlinkshadecolor</strong> <em>"#RRGGBB"</em></strong></dt> +<dd> +<p>This value is <strong>--strlinkmode</strong> specific. For <em>shade</em> value of <strong>--strlinkmode</strong> option, it +represents colors used to fill background of data field labels.</p> +<p>Default value: <em>"#e0e9eb"</em> - it's a very light blue color.</p> +</dd> +<dt><strong><strong>--strlinktitle</strong> <em>string</em></strong></dt> +<dd> +<p>Title for compound HTML page. Default value: <em>Compound Summary</em>.</p> +</dd> +<dt><strong><strong>--strlinktitledisplay</strong> <em>yes | no</em></strong></dt> +<dd> +<p>Display title for compound HTML page. Possible values: <em>yes or no</em>. Default value: <em>no</em>.</p> +</dd> +<dt><strong><strong>--strlinktype</strong> <em>href | button</em></strong></dt> +<dd> +<p>Type of structure link. Possible values: <em>href or button</em>. Default: <em>href</em>.</p> +</dd> +<dt><strong><strong>--strviewertype</strong> <em>Chem3DActiveX | ChemDrawActiveX | ChemDrawPlugIn | Chime | JME | Jmol | MarvinView | ViewerActiveX</em></strong></dt> +<dd> +<p>Structure viewer supported for viewing structures. Possible values: <em>Chem3DActiveX, +ChemDrawActiveX, ChemDrawPlugIn, Chime, JME, Jmol, MarvinView, or ViewerActiveX</em>. +Default value: <em>Jmol</em>.</p> +<p>Assuming you have access to one of these viewers on your machine, you are all set +to use this script. Otherwise, visit one of these web sites to download and install +your favorite viewer:</p> +<div class="OptionsBox"> + accelrys.com: Viewer ActiveX 5.0 +<br/> cambridgesoft.com: Chem3DActiveX 8.0, ChemDrawActiveX 8.0, + ChemDrawPlugIn +<br/> chemaxon.com: MarvinView applet +<br/> mdli.com: Chime plug-in +<br/> jmol.sourceforge.net: JmolApplet V10 +<br/> molinspiration.com: JME applet</div> +<p>The default viewer, JmolApplet V10, is distributed with MayaChemTools package. +Earlier versions of JmolApplet are not supported: due to applet security issues related to +reading files, this script uses in-line loading of MOL files and this option doesn't exist in +earlier version of JmolApplet.</p> +</dd> +<dt><strong><strong>--strviewerconfig</strong> <em>codebase[,archive,code]</em></strong></dt> +<dd> +<p>Configuration information for structure viewers. This option is only valid for structure +viewers which are applets: Jmol, JME and MarvinView. For other viewer types available via +<strong>--strviewertype</strong> option - MDL Chime, ChemDrawActiveX, ChemDrawPlugIn, and +Chem3DActiveX - this value is ignored.</p> +<p>Input text format: <em>codebase[,archive,code]</em>. For an applet viewer, <em>codebase</em> must be +specified; <em>archive</em> and <em>code</em> values are optional. Here are default <em>archive</em> and +<em>codebase</em> values for various applets: Jmol - JmolApplet, JmolApplet.jar; JME - JME, JME.jar; + MarvinView: MView, marvin.jar</p> +<p>For local deployment of HTML files, <em>codebase</em> must correspond to a complete path to +the local directory containing appropriate <em>archive</em> file and the complete path is converted +into appropriate relative path during generation of HTML files.</p> +<p>By default, <em>codebase</em> value of <this script dir>/../lib/Jmol is used for <em>Jmol</em> applet viewer, and +HTML file(s) are generated for local deployment; however, you can specify any supported +applet viewer and generate HTML file(s) for deploying on a web server.</p> +<p>For deploying the HTML file(s) on a web server, specify a valid <em>codebase</em> directory name +relative to <WWWRootDir>. Example when JME archive file, JME.jar, is available in +<em>/jme</em> directory on the web server:</p> +<div class="OptionsBox"> + /jme</div> +<p>For local deployment of HTML file(s), specify a complete <em>codebase</em> directory name. +Example when JmolApplet archive file, JmolApplet.jar, is present in <JMOLROOT> directory:</p> +<div class="OptionsBox"> + <JMOLROOT></div> +<p>In addition to <em>codebase</em>, you can also specify <em>archive</em> file name. Example for web +deployment:</p> +<div class="OptionsBox"> + "/jme,JME.jar" +<br/> "/jme"</div> +<p>Example for local deployment:</p> +<div class="OptionsBox"> + "<JMEROOT>,JME.jar" +<br/> "<JMEROOT>"</div> +</dd> +<dt><strong><strong>--strviewerparams</strong> <em>"name=value [name=value ...]"</em></strong></dt> +<dd> +<p>Parameters name and value pairs for structure viewers. These name and value pairs +are used to control the appearance and behavior of structure viewers in tables and +compound HTML page during <em>link</em> value for <strong>-s --structure</strong> option.</p> +<p>The parameter names, along with their values, are just passed to each structure viewer +in appropriate format without checking their validity. Check documentation of appropriate +structure viewers to figure out valid parameter names.</p> +<p>Input text format: <em>name=value name=value ...</em> Example:</p> +<div class="OptionsBox"> + "width=250 height=170"</div> +<p>Default for all structure viewers: <em>width=250 height=170</em> for displaying structures in +tables, and <em>strlinkwidth=500 strlinkheight=295</em> for compound HTML page during <em>link</em> value +for <strong>-s --structure</strong> option.</p> +<p>Default background color for all structure viewers: same as <strong>--shadecolor</strong> value for +displaying structures in tables and <em>strlinkbgcolor=#ffffff</em> for compound HTML page; +however, explicit specification of background color in this option overrides default value. +To use black background for structures in tables and compound HTML page, specify <em>bgcolor=#000000</em> +and <em>strlinkbgcolor=#000000</em> respectively. Keep this in mind: Some structure viewers +don't appear to support background color parameter.</p> +<p>Additional structure viewer specific default values:</p> +<div class="OptionsBox"> + Chem3DActiveX: "displaytype=Ball&Stick rotationbars=false + moviecontroller=false" +<br/> ChemDrawActiveX: "ViewOnly=1 ShrinkToFit=1 ShowToolsWhenVisible=1" +<br/> ChemDrawPlugIn: "type=chemical/x-mdl-molfile ViewOnly=1 + ShrinkToFit=1 ShowToolsWhenVisible=1" +<br/> Chime: "display2d=true" +<br/> JME: "options=depict" +<br/> Jmol: "progressbar=true progresscolor=#0000ff boxbgcolor=#000000 + boxfgcolor=#ffffff script="select *; set frank off; + wireframe on; spacefill off"" +<br/> MarvinView: "navmode=zoom" +<br/> ViewerActiveX:"Mouse=4 Convert2Dto3D=0"</div> +<p>Try overriding default values or specify additional valid parameter/value pairs to get desired +results. Example for using CPK rendering scheme with Jmol viewer:</p> +<div class="OptionsBox"> + "script="select *; set frank off; wireframe off; spacefill on""</div> +</dd> +<dt><strong><strong>--strviewerembed</strong> <em>direct | javascript</em></strong></dt> +<dd> +<p>Specify how to embed structure viewers in HTML pages. Possible values: <em>direct</em> - use applet/object +tags to emded structure viewer; <em>javascript</em> - use vendor supplied java scripts. Default value: +direct.</p> +<p>This option only applies to these vieweres: <em>Chem3DActiveX, ChemDrawActiveX, ChemDrawPlugIn, +Jmol, and MarvinView</em>.</p> +<p>For marvin.js to work correctly on your browser, you may need to set <em>marvin_jvm=builtin</em> or +<em>marvin_jvm=plugin</em> using <strong>--strviewerparams</strong> option. Additionally, MarvinView - at least +in my hands - also has problems during usage of JavaScript for local deployment; however, it +does work via web server.</p> +<p>As far as I can tell, Jmol.js supplied with Jmol10 release has these issues: jmolSetAppletColor +doesn't support background color; jmolInitialize disables relative specification of codebase +directroy which works okay. So, use Jmol.js supplied with MayaChemTools.</p> +</dd> +<dt><strong><strong>--strviewerjsfile</strong> <em>java script file name</em></strong></dt> +<dd> +<p>Name of vendor supplied java script file. Default values: Chem3DActiveX: <em>chem3d.js</em>; ChemDrawActiveX, +and ChemDrawPlugIn: <em>chemdraw.js</em>; Jmol: <em>Jmol.js</em>, MarvinView: <em>marvin.js</em>.</p> +<p>Directory location for these files is specified via <em>codebase</em> value of <strong>--strviewerconfig</strong> option.</p> +</dd> +<dt><strong><strong>--strtablesize</strong> <em>"numrows,numcols"</em></strong></dt> +<dd> +<p>This option is only valid for <em>structuresonly</em> and <em>shadedstructuresonly</em> modes. And it indicates +maximum number of rows and columns per structure table. Default value:<em>6,4</em>.</p> +</dd> +<dt><strong><strong>--stylesheet</strong> <em>old | new | none</em></strong></dt> +<dd> +<p>Controls usage of stylesheet for newly generated HTML file(s). Possible values: <em>old, +new, or none</em>. Default value: <em>new</em>.</p> +<p>Stylesheet file contains various properties which control appearance of HTML pages: +type, size, and color of fonts; background color; and so on.</p> +<p>For <em>old</em> value, an existing stylesheet file specified by <strong>--stylesheetname</strong> option is +used for each HTML file; no new stylesheet file is created. This option is quite handy +for deploying HTML file(s) on a web server: assuming you specify a valid stylesheet +file location relative to your WWWRoot, a reference to this stylesheet is added to each +HTML file. For local deployment of HTML file(s), a complete path to a local stylesheet +is fine as well.</p> +<p>For <em>create</em> value, a new stylesheet is created and reference to this local stylesheet +is added to each HTML file. Use option <strong>--stylesheetname</strong> to specify name.</p> +<p>For <em>none</em> value, stylesheet usage is completely ignored.</p> +</dd> +<dt><strong><strong>--stylesheetname</strong> <em>filename</em></strong></dt> +<dd> +<p>Stylesheet file name to be used in conjunction with <strong>-s --stylesheet</strong> option. It is only +valid for <em>old</em> value of <strong>-s --stylesheet</strong> option. Specify a valid stylesheet file location +relative to your WWWRoot and a reference to this stylesheet is added to each HTML +file. Example: <em>"/stylesheets/MyStyleSheet.css"</em>. Or a complete path name to a local +stylesheet file.</p> +<p>For <em>create</em> value of <strong>-s --stylesheet</strong> option, a new stylesheet file is created using +<strong>-r --root</strong> option. And value of <strong>--stylesheetname</strong> is simply ignored.</p> +</dd> +<dt><strong><strong>--shadecolor</strong> <em>"#RRGGBB,#RRGGBB"</em></strong></dt> +<dd> +<p>Colors used to fill background of rows during <em>shade</em> and <em>shadedhightlight</em> mode +represented as a pair of hexadecimal string; the first and second color values +are used for odd and even number rows respectively.</p> +<p>Default value: <em>"#ffffff,#e0e9eb"</em> - it's white and very light blue for odd and even number rows.</p> +</dd> +<dt><strong><strong>-t, --title</strong> <em>string</em></strong></dt> +<dd> +<p>Title for HTML table(s). Default value: <em>SDFileName</em>. This option is ignored for +multiple input files. And <strong>-r --root</strong> option is used to generate appropriate +titles.</p> +</dd> +<dt><strong><strong>--titledisplay</strong> <em>yes | no</em></strong></dt> +<dd> +<p>Display title for HTML table(s). Possible values: <em>yes or no</em>. Default value: <em>yes</em>.</p> +</dd> +<dt><strong><strong>-w, --workingdir</strong> <em>dirname</em></strong></dt> +<dd> +<p>Location of working directory. Default: current directory.</p> +</dd> +</dl> +<p> +</p> +<h2>EXAMPLES</h2> +<p>HTML table file(s), containing structures, can be used in two different ways: browsing on a +local machine or deployment via a web server. By default, HTML file(s) are created for viewing +on a local machine using Jmol viewer through a browser; however, you can specify any +supported applet viewer and generate HTML file(s) for deploying on a web server.</p> +<p>First two sets of examples show generation of HTML file(s) using different applet viewers +and a variety of options for local browsing; last set deals with web deployment.</p> +<p><strong>Local deployment: Usage of default JMol viewer distributed with MayaChemTools:</strong></p> +<p>To generate HTML tables with structure display using JMol viewer, rows background filled +with white and light blue colors, navigation links on top and botton of each page, type:</p> +<div class="ExampleBox"> + % SDFilesToHTML.pl -o Sample1.sdf</div> +<p>To generate HTML tables with structure display using JMol viewer, rows background filled +with white and light blue colors, navigation links on top and botton of each page, and +only containing MolWeight and Mol_ID SD data fields, type:</p> +<div class="ExampleBox"> + % SDFilesToHTML.pl --datafields "MolWeight,Mol_ID" -o Sample1.sdf</div> +<p>To generate HTML tables with CPK structure display using JMol viewer, rows +background filled with white and light blue colors, navigation links on top and botton of +each page, type:</p> +<div class="ExampleBox"> + % SDFilesToHTML.pl --strviewerparams "script=\"select *; set frank off; + wireframe off; spacefill on\"" -o Sample1.sdf</div> +<p>To generate HTML tables with structure display using JMol viewer and black background, rows +background filled with light golden and greyish colors, navigation links on top and botton of +each page, 10 rows in each table, greyish header row color, and cell spacing of 1, type:</p> +<div class="ExampleBox"> + % SDFilesToHTML.pl -o -n 10 --headeralign "center" --headercolor + "#a1a1a1" --shadecolor "#fafad2,#d1d1d1" --cellspacing 1 + --strviewerparams "bgcolor=#000000" Sample1.sdf</div> +<p>To highlight molecular weight values using specified highlight criteria and fill in default background +colors, type:</p> +<div class="ExampleBox"> + % SDFilesToHTML.pl -n 10 --highlight "MolWeight,numeric,le,450" + --highlightstyle background -m shadedhighlight -o Sample1.sdf</div> +<p>To highlight molecular weight values using specified highlight criteria, color the text using +default colors, and add a footer message in every page, type:</p> +<div class="ExampleBox"> + % SDFilesToHTML.pl -n 4 --highlight "MolWeight,numeric,le,500" + --highlightstyle text -m shadedhighlight -o + --footer "Copyright (C) MayaChemTools" --cellspacing 1 Sample1.sdf</div> +<p>To generate tables containing only structures, type:</p> +<div class="ExampleBox"> + % SDFilesToHTML.pl -d both -m shadedstructuresonly --strtablesize "6,4" + --cellspacing 1 -b 1 -o Sample1.sdf</div> +<p>To generate tables containing only structures with molecular weight displayed above the +structure, type:</p> +<div class="ExampleBox"> + % SDFilesToHTML.pl -d both -m shadedstructuresonly --strtablesize "6,4" + --cmpddatafield "MolWeight,no,top,center" --cellspacing 1 -b 1 + -o Sample1.sdf</div> +<p>To generate tables containing links to structures and highlight molecular weight data field values +using specified highlight criteria , type:</p> +<div class="ExampleBox"> + % SDFilesToHTML.pl -n 4 --footer "Copyright (C) MayaChemTools" + --highlight "MolWeight,numeric,le,450" --highlightstyle background + -d both -m shadedhighlight -s link --strlinktype button + -o Sample1.sdf</div> +<p><strong>Local deployment: Usage of other structure viewers:</strong></p> +<div class="ExampleBox"> + % SDFilesToHTML.pl --strviewertype MarvinView --strviewerconfig + "<Marvin dir path>" -o Sample1.sdf</div> +<div class="ExampleBox"> + % SDFilesToHTML.pl -o -n 10 --headeralign "center" --headercolor + "#a1a1a1" --shadecolor "#fafad2,#d1d1d1" --cellspacing 1 + --strviewerparams "bgcolor=#000000" --strviewertype Chime + Sample1.sdf</div> +<div class="ExampleBox"> + % SDFilesToHTML.pl -n 10 --highlight "MolWeight,numeric,le,450" + --highlightstyle background -m shadedhighlight --strviewertype + Chime -o Sample1.sdf</div> +<div class="ExampleBox"> + % SDFilesToHTML.pl -d both -m shadedstructuresonly --strtablesize "6,4" + --cellspacing 1 -b 1 -strviewertype JME -strviewerconfig "<JME dir + path>" -o Sample1.sdf</div> +<p><strong>Web deployment: Usage of different structure viewers and options:</strong></p> +<p>For deploying HTML file(s) on a web server, specify a valid <em>codebase</em> directory name +relative to <WWWRootDir>. In addition to <em>codebase</em>, you can also specify <em>archive</em> file +name.</p> +<div class="ExampleBox"> + % SDFilesToHTML.pl -m plain -s display --strviewertype Jmol + -strviewerconfig "/jmol" -n 5 -d both -r PlainTable -t "Example + using Jmol: Plain Table" -o Sample1.sdf</div> +<div class="ExampleBox"> + % SDFilesToHTML.pl -n 5 -m shade -s display -strviewertype JME + -strviewerconfig "/jme,JME.jar" -r ShadeTable -t "Example using JME: + Shaded Table" -o Sample.sdf</div> +<div class="ExampleBox"> + % SDFilesToHTML.pl -n 5 --highlight "MolWeight,numeric,le,450" + --highlightstyle background -d both -m shadedhighlight -s display + -strviewertype MarvinView -strviewerconfig "/marvin" -r + ShadedHightlightTable -t "Example using MarvinView: Shaded and + Highlighted Table" -o Sample.sdf</div> +<div class="ExampleBox"> + % SDFilesToHTML.pl -n 4 --highlight "MolWeight,numeric,le,450" -s link + --strlinktype href --strviewertype ChemDrawPlugIn --highlightstyle + background -m shadedhighlight -t "Example using ChemDrawPlugIn: + Shaded and Highlighted Table" -r ShadedHightlightTable -o Sample1.sdf</div> +<p> +</p> +<h2>AUTHOR</h2> +<p><a href="mailto:msud@san.rr.com">Manish Sud</a></p> +<p> +</p> +<h2>SEE ALSO</h2> +<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> +</p> +<p> +</p> +<h2>COPYRIGHT</h2> +<p>Copyright (C) 2015 Manish Sud. All rights reserved.</p> +<p>This file is part of MayaChemTools.</p> +<p>MayaChemTools is free software; you can redistribute it and/or modify it under +the terms of the GNU Lesser General Public License as published by the Free +Software Foundation; either version 3 of the License, or (at your option) +any later version.</p> +<p> </p><p> </p><div class="DocNav"> +<table width="100%" border=0 cellpadding=0 cellspacing=2> +<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> +</table> +</div> +<br /> +<center> +<img src="../../images/h2o2.png"> +</center> +</body> +</html>