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diff mayachemtools/docs/scripts/man1/SDFilesToHTML.1 @ 0:73ae111cf86f draft
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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/man1/SDFilesToHTML.1 Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,687 @@ +.\" Automatically generated by Pod::Man 2.25 (Pod::Simple 3.22) +.\" +.\" Standard preamble: +.\" ======================================================================== +.de Sp \" Vertical space (when we can't use .PP) +.if t .sp .5v +.if n .sp +.. +.de Vb \" Begin verbatim text +.ft CW +.nf +.ne \\$1 +.. +.de Ve \" End verbatim text +.ft R +.fi +.. +.\" Set up some character translations and predefined strings. \*(-- will +.\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left +.\" double quote, and \*(R" will give a right double quote. \*(C+ will +.\" give a nicer C++. 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Always turn off hyphenation; it makes +.\" way too many mistakes in technical documents. +.if n .ad l +.nh +.SH "NAME" +SDFilesToHTML.pl \- Generate HTML table file(s) from SDFile(s) +.SH "SYNOPSIS" +.IX Header "SYNOPSIS" +SDFilesToHTML.pl SDFiles(s)... +.PP +SDFilesToHTML.pl [\fB\-a, \-\-align\fR left | center | right,[top | middle | bottom]] [\fB\-b, \-\-border\fR borderwidth] [\fB\-\-cellpadding\fR padding] +[\fB\-\-cellspacing\fR spacing] [\fB\-\-cmpddatafield\fR \*(L"fieldlabel,[label,position,alignment]\*(R"] [\fB\-\-datafields\fR \*(L"fieldlabel,[fieldlabel]...\*(R" | Common | All] +[\fB\-\-footer\fR string] [\fB\-d, \-\-displaylinks\fR top | bottom | both] [\fB\-\-displaylinksinfo\fR compound | table | both] [\fB\-h, \-\-help\fR] +[\fB\-\-headeralign\fR left | center | right,[top | middle | bottom]] [\fB\-\-headercolor\fR \*(L"#RRGGBB\*(R"] +[\fB\-\-highlight\fR \*(L"fieldlabel,datatype,criterion,value,[fieldlabel,datatype,criterion,value,...]\*(R"] +[\fB\-\-highlightcolor\fR \*(L"#RRGGBB,#RRGGBB\*(R"] [\fB\-\-highlightstyle\fR text | background] +[\fB\-m, \-\-mode\fR plain | shade | highlight | shadedhighlight | structuresonly | shadedstructuresonly] +[\fB\-n, \-\-numcmpds\fR number] [\fB\-o, \-\-overwrite\fR] [\fB\-r, \-\-root\fR rootname] [\fB\-s, \-\-structure\fR display | link] +[\fB\-\-strlinkmode\fR plain | shaded] [\fB\-\-strlinknavigation\fR yes | no] +[\fB\-\-strlinkshadecolor\fR \*(L"#RRGGBB\*(R"] [\fB\-\-strlinktitle\fR string] [\fB\-\-strlinktitledisplay\fR yes | no] [\fB\-\-strlinktype\fR href | button] +[\fB\-\-strviewertype\fR Chem3DActiveX | ChemDrawActiveX | ChemDrawPlugIn | Chime | \s-1JME\s0 | Jmol | MarvinView | ViewerActiveX] +[\fB\-\-strviewerconfig\fR codebase[,archive,code]] [\fB\-\-strviewerparams\fR \*(L"name=value [name=value ...]\*(R"] +[\fB\-\-strviewerembed\fR direct | javascript] [\fB\-\-strviewerjsfile\fR javascriptfilename] +[\fB\-\-strtablesize\fR \*(L"numrows,numcols\*(R"] [\fB\-\-stylesheet\fR old | new | none] +[\fB\-\-stylesheetname\fR filename] [\fB\-\-shadecolor\fR \*(L"#RRGGBB,#RRGGBB\*(R"] [\fB\-t, \-\-title\fR string] [\fB\-\-titledisplay\fR yes | no] +[\fB\-w, \-\-workingdir\fR dirname] SDFiles(s)... +.SH "DESCRIPTION" +.IX Header "DESCRIPTION" +Generate \s-1HTML\s0 file(s) from \fISDFile(s)\fR. The \s-1HTML\s0 file(s) contain data tables +and appropriate navigational links to view other tables; navigational links are also +provided on compound \s-1HTML\s0 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, \s-1JME\s0, +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. +.PP +Multiple \fISDFile(s)\fR names are separated by space. The valid file extensions are +\&\fI.sdf\fR and \fI.sd\fR. All other file names are ignored. All the \s-1SD\s0 files in a current directory can +be specified either by \fI*.sdf\fR or the current directory name. +.SH "OPTIONS" +.IX Header "OPTIONS" +.IP "\fB\-a, \-\-align\fR \fIleft | center | right,[top | middle | bottom]\fR" 4 +.IX Item "-a, --align left | center | right,[top | middle | bottom]" +Horizontal and vertical alignment for table rows except for header row which is specified +using \fB\-\-headeralign\fR option. Possible horizontal alignment values: \fIleft, center, or right\fR. +Possible vertical alignment values: \fItop, middle, or bottom\fR. +.Sp +Default values: \fIleft,middle\fR +.IP "\fB\-b, \-\-border\fR \fIborderwidth\fR" 4 +.IX Item "-b, --border borderwidth" +Table border width. Default value: 1 for \fIplain\fR and \fIhighlight\fR mode; 0 for \fIshade\fR +and \fIshadedhightlight\fR mode. Zero indicates no border. +.IP "\fB\-\-cellpadding\fR \fIpadding\fR" 4 +.IX Item "--cellpadding padding" +Table cell padding. Default value: \fI2\fR. +.IP "\fB\-\-cellspacing\fR \fIspacing\fR" 4 +.IX Item "--cellspacing spacing" +Table cell spacing. Default value: \fI1\fR. +.IP "\fB\-\-cmpddatafield\fR \fIfieldlabel,[label,position,alignment]\fR" 4 +.IX Item "--cmpddatafield fieldlabel,[label,position,alignment]" +This value is mode specific. It indicates data field value to be displayed with the structure along +with its label, position and alignment during \fIstructuresonly | shadedstructuresonly\fR value of \fB\-m, \-\-mode\fR +option. Possible values: feldlabel \- valid data field label; label \- yes or no; position \- \fItop or bottom\fR; alignment +\&\- \fIleft, center, or right\fR. Default: \fInone,no,bottom,center\fR. Example: +.Sp +.Vb 1 +\& MolWt,no,bottom,middle +.Ve +.Sp +\&\fB\-\-cmpddatafield\fR option value is also linked to compound summary page. +.ie n .IP "\fB\-\-datafields\fR \fI""fieldlabel,[fieldlabel]..."" | Common | All\fR" 4 +.el .IP "\fB\-\-datafields\fR \fI``fieldlabel,[fieldlabel]...'' | Common | All\fR" 4 +.IX Item "--datafields fieldlabel,[fieldlabel]... | Common | All" +Data fields to display in \s-1HTML\s0 table(s). Possible values: list of comma separated data field +labels, data fields common to all records, or all data fields. Default value: \fIAll\fR. +Examples: +.Sp +.Vb 2 +\& ALogP,MolWeight,EC50 +\& "MolWeight,PSA" +.Ve +.IP "\fB\-\-footer\fR \fIstring\fR" 4 +.IX Item "--footer string" +Text string to be included at bottom of each \s-1HTML\s0 file. Default: none. +.IP "\fB\-d \-\-displaylinks\fR \fItop | bottom | both\fR" 4 +.IX Item "-d --displaylinks top | bottom | both" +Specify where to display navigation links in each \s-1HTML\s0 file for accessing all other \s-1HTML\s0 +files. Possible values: \fItop, bottom, or both\fR. Default: \fIboth\fR. This option is +only valid during multiple \s-1HTML\s0 files generation for an input file. +.IP "\fB\-\-displaylinksinfo\fR \fIcompound | table | both\fR" 4 +.IX Item "--displaylinksinfo compound | table | both" +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: \fIcompound +| table | both\fR. Default: \fIboth\fR. This option is only valid during multiple \s-1HTML\s0 files generation. +.IP "\fB\-h, \-\-help\fR" 4 +.IX Item "-h, --help" +Print this help message. +.IP "\fB\-\-headeralign\fR \fIleft | center | right,[top | middle | bottom\fR" 4 +.IX Item "--headeralign left | center | right,[top | middle | bottom" +Horizontal and vertical alignment for table header rows. Possible horizontal alignment +values: \fIleft, center, or right\fR. Possible vertical alignment values: \fItop, middle, or bottom\fR. +.Sp +Default values: \fIcenter,middle\fR +.IP "\fB\-\-headercolor\fR \fI#RRGGBB\fR" 4 +.IX Item "--headercolor #RRGGBB" +Color used to fill background of table header row containing column labels +represented as a hexadecimal string. Default value: None for \fB\-m, \-\-mode\fR option +value of \fIplain\fR and \fI#ccccff\fR, light blue, for others. +.ie n .IP "\fB\-\-highlight\fR \fI""fieldlabel,datatype,criterion,value,[fieldlabel,datatype,criterion,value,...]""\fR" 4 +.el .IP "\fB\-\-highlight\fR \fI``fieldlabel,datatype,criterion,value,[fieldlabel,datatype,criterion,value,...]''\fR" 4 +.IX Item "--highlight fieldlabel,datatype,criterion,value,[fieldlabel,datatype,criterion,value,...]" +Highlighting methodology used to highlight various SDFile(s) data field values in +\&\s-1HTML\s0 file(s). Same set of quartets values are applied to all SDFile(s). +.Sp +Input text contains these quartets: \fIfieldlabel,datatype,criterion,value,...\fR. +Possible datatype values: \fInumeric or text\fR. Possible criterion values: \fIle, ge, or eq\fR. +Examples: +.Sp +.Vb 3 +\& "MolWt,numeric,le,450" +\& "MolWt,numeric,le,450,LogP,numeric,le,5" +\& Name,text,eq,Aspirin +.Ve +.ie n .IP "\fB\-\-highlightcolor\fR \fI""#RRGGBB,#RRGGBB""\fR" 4 +.el .IP "\fB\-\-highlightcolor\fR \fI``#RRGGBB,#RRGGBB''\fR" 4 +.IX Item "--highlightcolor #RRGGBB,#RRGGBB" +Colors used to highlight column values during \fIhighlight\fR and \fIshadedhightlight\fR +mode represented as hexadecimal strings. +.Sp +For \fB\-\-highlighstyle\fR option values of \fItext\fR and \fIbackground\fR, these colors represent +text or background colors respectively. For a specific column, first color string is used for +values which meet criterion indicated by \fB\-\-highlight\fR option; the second color is used for + rest of the values. +.Sp +Default values for \fIbackground\fR \fB\-\-highlightstyle\fR: \fI\*(L"#0fff0f,#ff0f0f\*(R"\fR. And default values for +\&\fItext\fR \fB\-\-highlightstyle\fR: \fI\*(L"#0fbb0f,#ff0f0f\*(R"\fR. Hexadecimal strings for both \fB\-\-highlightstyle\fR +colors correspond to \fIreddish\fR and \fIgreenish\fR. +.IP "\fB\-\-highlightstyle\fR \fItext | background\fR" 4 +.IX Item "--highlightstyle text | background" +This value is mode specific. It indicates highlight style used to differentiate column +values which meet a specified criterion in \fB\-\-highlight\fR option. Possible values: \fItext or +background\fR. Default: \fIbackground\fR. +.IP "\fB\-m, \-\-mode\fR \fIplain | shade | highlight | shadedhighlight | structuresonly | shadedstructuresonly\fR" 4 +.IX Item "-m, --mode plain | shade | highlight | shadedhighlight | structuresonly | shadedstructuresonly" +Specify how to generate \s-1HTML\s0 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. +.Sp +Possible values: \fIplain, shade, highlight, shadedhighlight, structuresonly, or +shadedstructuresonly\fR. Default: \fIshade\fR. +.IP "\fB\-n, \-\-numcmpds\fR \fInumber\fR" 4 +.IX Item "-n, --numcmpds number" +Maximum number of compounds per table. Default value: \fI15\fR for tables with structures and +\&\fI50\fR 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 \s-1HTML\s0 tables, with appropriate +navigation links, are created. +.IP "\fB\-o, \-\-overwrite\fR" 4 +.IX Item "-o, --overwrite" +Overwrite existing files. +.IP "\fB\-r, \-\-root\fR \fIrootname\fR" 4 +.IX Item "-r, --root rootname" +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. +.Sp +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 +\&\s-1MOL\s0 files. +.Sp +This option is ignored for multiple input files. +.IP "\fB\-s, \-\-structure\fR \fIdisplay | link\fR" 4 +.IX Item "-s, --structure display | link" +Structure display control: display structures in a table column or set up a link for each +structure which opens up a new \s-1HTML\s0 page containing structure and other appropriate +information. Possible values: \fIdisplay or link\fR. Default value: \fIdisplay\fR +.IP "\fB\-\-strlinkmode\fR \fIplain | shaded\fR" 4 +.IX Item "--strlinkmode plain | shaded" +Specify how to display compound \s-1HTML\s0 page: plain or background of data field +field labels is filled with a specified color. Possible values: \fIplain or shad\fR. +Default value: \fIplane\fR. +.Sp +Structure viewer background color is white. Use \fB\-\-strviewerparams\fR option to change +default behavior of structure viewers. +.IP "\fB\-\-strlinknavigation\fR \fIyes | no\fR" 4 +.IX Item "--strlinknavigation yes | no" +Display navigation links to other compounds in compound \s-1HTML\s0 page. Possible values: +\&\fIyes or no\fR. Default value: \fIyes\fR. +.ie n .IP "\fB\-\-strlinkshadecolor\fR \fI""#RRGGBB""\fR" 4 +.el .IP "\fB\-\-strlinkshadecolor\fR \fI``#RRGGBB''\fR" 4 +.IX Item "--strlinkshadecolor #RRGGBB" +This value is \fB\-\-strlinkmode\fR specific. For \fIshade\fR value of \fB\-\-strlinkmode\fR option, it +represents colors used to fill background of data field labels. +.Sp +Default value: \fI\*(L"#e0e9eb\*(R"\fR \- it's a very light blue color. +.IP "\fB\-\-strlinktitle\fR \fIstring\fR" 4 +.IX Item "--strlinktitle string" +Title for compound \s-1HTML\s0 page. Default value: \fICompound Summary\fR. +.IP "\fB\-\-strlinktitledisplay\fR \fIyes | no\fR" 4 +.IX Item "--strlinktitledisplay yes | no" +Display title for compound \s-1HTML\s0 page. Possible values: \fIyes or no\fR. Default value: \fIno\fR. +.IP "\fB\-\-strlinktype\fR \fIhref | button\fR" 4 +.IX Item "--strlinktype href | button" +Type of structure link. Possible values: \fIhref or button\fR. Default: \fIhref\fR. +.IP "\fB\-\-strviewertype\fR \fIChem3DActiveX | ChemDrawActiveX | ChemDrawPlugIn | Chime | \s-1JME\s0 | Jmol | MarvinView | ViewerActiveX\fR" 4 +.IX Item "--strviewertype Chem3DActiveX | ChemDrawActiveX | ChemDrawPlugIn | Chime | JME | Jmol | MarvinView | ViewerActiveX" +Structure viewer supported for viewing structures. Possible values: \fIChem3DActiveX, +ChemDrawActiveX, ChemDrawPlugIn, Chime, \s-1JME\s0, Jmol, MarvinView, or ViewerActiveX\fR. +Default value: \fIJmol\fR. +.Sp +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: +.Sp +.Vb 7 +\& accelrys.com: Viewer ActiveX 5.0 +\& cambridgesoft.com: Chem3DActiveX 8.0, ChemDrawActiveX 8.0, +\& ChemDrawPlugIn +\& chemaxon.com: MarvinView applet +\& mdli.com: Chime plug\-in +\& jmol.sourceforge.net: JmolApplet V10 +\& molinspiration.com: JME applet +.Ve +.Sp +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 \s-1MOL\s0 files and this option doesn't exist in +earlier version of JmolApplet. +.IP "\fB\-\-strviewerconfig\fR \fIcodebase[,archive,code]\fR" 4 +.IX Item "--strviewerconfig codebase[,archive,code]" +Configuration information for structure viewers. This option is only valid for structure +viewers which are applets: Jmol, \s-1JME\s0 and MarvinView. For other viewer types available via +\&\fB\-\-strviewertype\fR option \- \s-1MDL\s0 Chime, ChemDrawActiveX, ChemDrawPlugIn, and +Chem3DActiveX \- this value is ignored. +.Sp +Input text format: \fIcodebase[,archive,code]\fR. For an applet viewer, \fIcodebase\fR must be +specified; \fIarchive\fR and \fIcode\fR values are optional. Here are default \fIarchive\fR and +\&\fIcodebase\fR values for various applets: Jmol \- JmolApplet, JmolApplet.jar; \s-1JME\s0 \- \s-1JME\s0, \s-1JME\s0.jar; + MarvinView: MView, marvin.jar +.Sp +For local deployment of \s-1HTML\s0 files, \fIcodebase\fR must correspond to a complete path to +the local directory containing appropriate \fIarchive\fR file and the complete path is converted +into appropriate relative path during generation of \s-1HTML\s0 files. +.Sp +By default, \fIcodebase\fR value of <this script dir>/../lib/Jmol is used for \fIJmol\fR applet viewer, and +\&\s-1HTML\s0 file(s) are generated for local deployment; however, you can specify any supported +applet viewer and generate \s-1HTML\s0 file(s) for deploying on a web server. +.Sp +For deploying the \s-1HTML\s0 file(s) on a web server, specify a valid \fIcodebase\fR directory name +relative to <WWWRootDir>. Example when \s-1JME\s0 archive file, \s-1JME\s0.jar, is available in +\&\fI/jme\fR directory on the web server: +.Sp +.Vb 1 +\& /jme +.Ve +.Sp +For local deployment of \s-1HTML\s0 file(s), specify a complete \fIcodebase\fR directory name. +Example when JmolApplet archive file, JmolApplet.jar, is present in <\s-1JMOLROOT\s0> directory: +.Sp +.Vb 1 +\& <JMOLROOT> +.Ve +.Sp +In addition to \fIcodebase\fR, you can also specify \fIarchive\fR file name. Example for web +deployment: +.Sp +.Vb 2 +\& "/jme,JME.jar" +\& "/jme" +.Ve +.Sp +Example for local deployment: +.Sp +.Vb 2 +\& "<JMEROOT>,JME.jar" +\& "<JMEROOT>" +.Ve +.ie n .IP "\fB\-\-strviewerparams\fR \fI""name=value [name=value ...]""\fR" 4 +.el .IP "\fB\-\-strviewerparams\fR \fI``name=value [name=value ...]''\fR" 4 +.IX Item "--strviewerparams name=value [name=value ...]" +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 \s-1HTML\s0 page during \fIlink\fR value for \fB\-s \-\-structure\fR option. +.Sp +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. +.Sp +Input text format: \fIname=value name=value ...\fR Example: +.Sp +.Vb 1 +\& "width=250 height=170" +.Ve +.Sp +Default for all structure viewers: \fIwidth=250 height=170\fR for displaying structures in +tables, and \fIstrlinkwidth=500 strlinkheight=295\fR for compound \s-1HTML\s0 page during \fIlink\fR value +for \fB\-s \-\-structure\fR option. +.Sp +Default background color for all structure viewers: same as \fB\-\-shadecolor\fR value for +displaying structures in tables and \fIstrlinkbgcolor=#ffffff\fR for compound \s-1HTML\s0 page; +however, explicit specification of background color in this option overrides default value. +To use black background for structures in tables and compound \s-1HTML\s0 page, specify \fIbgcolor=#000000\fR +and \fIstrlinkbgcolor=#000000\fR respectively. Keep this in mind: Some structure viewers +don't appear to support background color parameter. +.Sp +Additional structure viewer specific default values: +.Sp +.Vb 12 +\& Chem3DActiveX: "displaytype=Ball&Stick rotationbars=false +\& moviecontroller=false" +\& ChemDrawActiveX: "ViewOnly=1 ShrinkToFit=1 ShowToolsWhenVisible=1" +\& ChemDrawPlugIn: "type=chemical/x\-mdl\-molfile ViewOnly=1 +\& ShrinkToFit=1 ShowToolsWhenVisible=1" +\& Chime: "display2d=true" +\& JME: "options=depict" +\& Jmol: "progressbar=true progresscolor=#0000ff boxbgcolor=#000000 +\& boxfgcolor=#ffffff script="select *; set frank off; +\& wireframe on; spacefill off"" +\& MarvinView: "navmode=zoom" +\& ViewerActiveX:"Mouse=4 Convert2Dto3D=0" +.Ve +.Sp +Try overriding default values or specify additional valid parameter/value pairs to get desired +results. Example for using \s-1CPK\s0 rendering scheme with Jmol viewer: +.Sp +.Vb 1 +\& "script="select *; set frank off; wireframe off; spacefill on"" +.Ve +.IP "\fB\-\-strviewerembed\fR \fIdirect | javascript\fR" 4 +.IX Item "--strviewerembed direct | javascript" +Specify how to embed structure viewers in \s-1HTML\s0 pages. Possible values: \fIdirect\fR \- use applet/object +tags to emded structure viewer; \fIjavascript\fR \- use vendor supplied java scripts. Default value: +direct. +.Sp +This option only applies to these vieweres: \fIChem3DActiveX, ChemDrawActiveX, ChemDrawPlugIn, +Jmol, and MarvinView\fR. +.Sp +For marvin.js to work correctly on your browser, you may need to set \fImarvin_jvm=builtin\fR or +\&\fImarvin_jvm=plugin\fR using \fB\-\-strviewerparams\fR 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. +.Sp +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. +.IP "\fB\-\-strviewerjsfile\fR \fIjava script file name\fR" 4 +.IX Item "--strviewerjsfile java script file name" +Name of vendor supplied java script file. Default values: Chem3DActiveX: \fIchem3d.js\fR; ChemDrawActiveX, +and ChemDrawPlugIn: \fIchemdraw.js\fR; Jmol: \fIJmol.js\fR, MarvinView: \fImarvin.js\fR. +.Sp +Directory location for these files is specified via \fIcodebase\fR value of \fB\-\-strviewerconfig\fR option. +.ie n .IP "\fB\-\-strtablesize\fR \fI""numrows,numcols""\fR" 4 +.el .IP "\fB\-\-strtablesize\fR \fI``numrows,numcols''\fR" 4 +.IX Item "--strtablesize numrows,numcols" +This option is only valid for \fIstructuresonly\fR and \fIshadedstructuresonly\fR modes. And it indicates +maximum number of rows and columns per structure table. Default value:\fI6,4\fR. +.IP "\fB\-\-stylesheet\fR \fIold | new | none\fR" 4 +.IX Item "--stylesheet old | new | none" +Controls usage of stylesheet for newly generated \s-1HTML\s0 file(s). Possible values: \fIold, +new, or none\fR. Default value: \fInew\fR. +.Sp +Stylesheet file contains various properties which control appearance of \s-1HTML\s0 pages: +type, size, and color of fonts; background color; and so on. +.Sp +For \fIold\fR value, an existing stylesheet file specified by \fB\-\-stylesheetname\fR option is +used for each \s-1HTML\s0 file; no new stylesheet file is created. This option is quite handy +for deploying \s-1HTML\s0 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 +\&\s-1HTML\s0 file. For local deployment of \s-1HTML\s0 file(s), a complete path to a local stylesheet +is fine as well. +.Sp +For \fIcreate\fR value, a new stylesheet is created and reference to this local stylesheet +is added to each \s-1HTML\s0 file. Use option \fB\-\-stylesheetname\fR to specify name. +.Sp +For \fInone\fR value, stylesheet usage is completely ignored. +.IP "\fB\-\-stylesheetname\fR \fIfilename\fR" 4 +.IX Item "--stylesheetname filename" +Stylesheet file name to be used in conjunction with \fB\-s \-\-stylesheet\fR option. It is only +valid for \fIold\fR value of \fB\-s \-\-stylesheet\fR option. Specify a valid stylesheet file location +relative to your WWWRoot and a reference to this stylesheet is added to each \s-1HTML\s0 +file. Example: \fI\*(L"/stylesheets/MyStyleSheet.css\*(R"\fR. Or a complete path name to a local +stylesheet file. +.Sp +For \fIcreate\fR value of \fB\-s \-\-stylesheet\fR option, a new stylesheet file is created using +\&\fB\-r \-\-root\fR option. And value of \fB\-\-stylesheetname\fR is simply ignored. +.ie n .IP "\fB\-\-shadecolor\fR \fI""#RRGGBB,#RRGGBB""\fR" 4 +.el .IP "\fB\-\-shadecolor\fR \fI``#RRGGBB,#RRGGBB''\fR" 4 +.IX Item "--shadecolor #RRGGBB,#RRGGBB" +Colors used to fill background of rows during \fIshade\fR and \fIshadedhightlight\fR mode +represented as a pair of hexadecimal string; the first and second color values +are used for odd and even number rows respectively. +.Sp +Default value: \fI\*(L"#ffffff,#e0e9eb\*(R"\fR \- it's white and very light blue for odd and even number rows. +.IP "\fB\-t, \-\-title\fR \fIstring\fR" 4 +.IX Item "-t, --title string" +Title for \s-1HTML\s0 table(s). Default value: \fISDFileName\fR. This option is ignored for +multiple input files. And \fB\-r \-\-root\fR option is used to generate appropriate +titles. +.IP "\fB\-\-titledisplay\fR \fIyes | no\fR" 4 +.IX Item "--titledisplay yes | no" +Display title for \s-1HTML\s0 table(s). Possible values: \fIyes or no\fR. Default value: \fIyes\fR. +.IP "\fB\-w, \-\-workingdir\fR \fIdirname\fR" 4 +.IX Item "-w, --workingdir dirname" +Location of working directory. Default: current directory. +.SH "EXAMPLES" +.IX Header "EXAMPLES" +\&\s-1HTML\s0 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, \s-1HTML\s0 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 \s-1HTML\s0 file(s) for deploying on a web server. +.PP +First two sets of examples show generation of \s-1HTML\s0 file(s) using different applet viewers +and a variety of options for local browsing; last set deals with web deployment. +.PP +\&\fBLocal deployment: Usage of default JMol viewer distributed with MayaChemTools:\fR +.PP +To generate \s-1HTML\s0 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: +.PP +.Vb 1 +\& % SDFilesToHTML.pl \-o Sample1.sdf +.Ve +.PP +To generate \s-1HTML\s0 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 \s-1SD\s0 data fields, type: +.PP +.Vb 1 +\& % SDFilesToHTML.pl \-\-datafields "MolWeight,Mol_ID" \-o Sample1.sdf +.Ve +.PP +To generate \s-1HTML\s0 tables with \s-1CPK\s0 structure display using JMol viewer, rows +background filled with white and light blue colors, navigation links on top and botton of +each page, type: +.PP +.Vb 2 +\& % SDFilesToHTML.pl \-\-strviewerparams "script=\e"select *; set frank off; +\& wireframe off; spacefill on\e"" \-o Sample1.sdf +.Ve +.PP +To generate \s-1HTML\s0 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: +.PP +.Vb 3 +\& % SDFilesToHTML.pl \-o \-n 10 \-\-headeralign "center" \-\-headercolor +\& "#a1a1a1" \-\-shadecolor "#fafad2,#d1d1d1" \-\-cellspacing 1 +\& \-\-strviewerparams "bgcolor=#000000" Sample1.sdf +.Ve +.PP +To highlight molecular weight values using specified highlight criteria and fill in default background +colors, type: +.PP +.Vb 2 +\& % SDFilesToHTML.pl \-n 10 \-\-highlight "MolWeight,numeric,le,450" +\& \-\-highlightstyle background \-m shadedhighlight \-o Sample1.sdf +.Ve +.PP +To highlight molecular weight values using specified highlight criteria, color the text using +default colors, and add a footer message in every page, type: +.PP +.Vb 3 +\& % SDFilesToHTML.pl \-n 4 \-\-highlight "MolWeight,numeric,le,500" +\& \-\-highlightstyle text \-m shadedhighlight \-o +\& \-\-footer "Copyright (C) MayaChemTools" \-\-cellspacing 1 Sample1.sdf +.Ve +.PP +To generate tables containing only structures, type: +.PP +.Vb 2 +\& % SDFilesToHTML.pl \-d both \-m shadedstructuresonly \-\-strtablesize "6,4" +\& \-\-cellspacing 1 \-b 1 \-o Sample1.sdf +.Ve +.PP +To generate tables containing only structures with molecular weight displayed above the +structure, type: +.PP +.Vb 3 +\& % SDFilesToHTML.pl \-d both \-m shadedstructuresonly \-\-strtablesize "6,4" +\& \-\-cmpddatafield "MolWeight,no,top,center" \-\-cellspacing 1 \-b 1 +\& \-o Sample1.sdf +.Ve +.PP +To generate tables containing links to structures and highlight molecular weight data field values +using specified highlight criteria , type: +.PP +.Vb 4 +\& % 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 +.Ve +.PP +\&\fBLocal deployment: Usage of other structure viewers:\fR +.PP +.Vb 2 +\& % SDFilesToHTML.pl \-\-strviewertype MarvinView \-\-strviewerconfig +\& "<Marvin dir path>" \-o Sample1.sdf +\& +\& % SDFilesToHTML.pl \-o \-n 10 \-\-headeralign "center" \-\-headercolor +\& "#a1a1a1" \-\-shadecolor "#fafad2,#d1d1d1" \-\-cellspacing 1 +\& \-\-strviewerparams "bgcolor=#000000" \-\-strviewertype Chime +\& Sample1.sdf +\& +\& % SDFilesToHTML.pl \-n 10 \-\-highlight "MolWeight,numeric,le,450" +\& \-\-highlightstyle background \-m shadedhighlight \-\-strviewertype +\& Chime \-o Sample1.sdf +\& +\& % SDFilesToHTML.pl \-d both \-m shadedstructuresonly \-\-strtablesize "6,4" +\& \-\-cellspacing 1 \-b 1 \-strviewertype JME \-strviewerconfig "<JME dir +\& path>" \-o Sample1.sdf +.Ve +.PP +\&\fBWeb deployment: Usage of different structure viewers and options:\fR +.PP +For deploying \s-1HTML\s0 file(s) on a web server, specify a valid \fIcodebase\fR directory name +relative to <WWWRootDir>. In addition to \fIcodebase\fR, you can also specify \fIarchive\fR file +name. +.PP +.Vb 3 +\& % 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 +\& +\& % 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 +\& +\& % 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 +\& +\& % 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 +.Ve +.SH "AUTHOR" +.IX Header "AUTHOR" +Manish Sud <msud@san.rr.com> +.SH "SEE ALSO" +.IX Header "SEE ALSO" +FilterSDFiles.pl, InfoSDFiles.pl, SplitSDFiles.pl, MergeTextFilesWithSD.pl +.SH "COPYRIGHT" +.IX Header "COPYRIGHT" +Copyright (C) 2015 Manish Sud. All rights reserved. +.PP +This file is part of MayaChemTools. +.PP +MayaChemTools is free software; you can redistribute it and/or modify it under +the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free +Software Foundation; either version 3 of the License, or (at your option) +any later version.