Mercurial > repos > deepakjadmin > mayatool3_test2
diff docs/scripts/txt/SDFilesToHTML.txt @ 0:4816e4a8ae95 draft default tip
Uploaded
| author | deepakjadmin |
|---|---|
| date | Wed, 20 Jan 2016 09:23:18 -0500 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/docs/scripts/txt/SDFilesToHTML.txt Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,579 @@ +NAME + SDFilesToHTML.pl - Generate HTML table file(s) from SDFile(s) + +SYNOPSIS + SDFilesToHTML.pl SDFiles(s)... + + SDFilesToHTML.pl [-a, --align left | center | right,[top | middle | + bottom]] [-b, --border borderwidth] [--cellpadding padding] + [--cellspacing spacing] [--cmpddatafield + "fieldlabel,[label,position,alignment]"] [--datafields + "fieldlabel,[fieldlabel]..." | Common | All] [--footer string] [-d, + --displaylinks top | bottom | both] [--displaylinksinfo compound | table + | both] [-h, --help] [--headeralign left | center | right,[top | middle + | bottom]] [--headercolor "#RRGGBB"] [--highlight + "fieldlabel,datatype,criterion,value,[fieldlabel,datatype,criterion,valu + e,...]"] [--highlightcolor "#RRGGBB,#RRGGBB"] [--highlightstyle text | + background] [-m, --mode plain | shade | highlight | shadedhighlight | + structuresonly | shadedstructuresonly] [-n, --numcmpds number] [-o, + --overwrite] [-r, --root rootname] [-s, --structure display | link] + [--strlinkmode plain | shaded] [--strlinknavigation yes | no] + [--strlinkshadecolor "#RRGGBB"] [--strlinktitle string] + [--strlinktitledisplay yes | no] [--strlinktype href | button] + [--strviewertype Chem3DActiveX | ChemDrawActiveX | ChemDrawPlugIn | + Chime | JME | Jmol | MarvinView | ViewerActiveX] [--strviewerconfig + codebase[,archive,code]] [--strviewerparams "name=value [name=value + ...]"] [--strviewerembed direct | javascript] [--strviewerjsfile + javascriptfilename] [--strtablesize "numrows,numcols"] [--stylesheet old + | new | none] [--stylesheetname filename] [--shadecolor + "#RRGGBB,#RRGGBB"] [-t, --title string] [--titledisplay yes | no] [-w, + --workingdir dirname] SDFiles(s)... + +DESCRIPTION + Generate HTML file(s) from *SDFile(s)*. 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. + + Multiple *SDFile(s)* names are separated by space. The valid file + extensions are *.sdf* and *.sd*. All other file names are ignored. All + the SD files in a current directory can be specified either by **.sdf* + or the current directory name. + +OPTIONS + -a, --align *left | center | right,[top | middle | bottom]* + Horizontal and vertical alignment for table rows except for header + row which is specified using --headeralign option. Possible + horizontal alignment values: *left, center, or right*. Possible + vertical alignment values: *top, middle, or bottom*. + + Default values: *left,middle* + + -b, --border *borderwidth* + Table border width. Default value: 1 for *plain* and *highlight* + mode; 0 for *shade* and *shadedhightlight* mode. Zero indicates no + border. + + --cellpadding *padding* + Table cell padding. Default value: *2*. + + --cellspacing *spacing* + Table cell spacing. Default value: *1*. + + --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 *structuresonly | shadedstructuresonly* value of + -m, --mode option. Possible values: feldlabel - valid data field + label; label - yes or no; position - *top or bottom*; alignment - + *left, center, or right*. Default: *none,no,bottom,center*. Example: + + MolWt,no,bottom,middle + + --cmpddatafield option value is also linked to compound summary + page. + + --datafields *"fieldlabel,[fieldlabel]..." | Common | All* + 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: *All*. Examples: + + ALogP,MolWeight,EC50 + "MolWeight,PSA" + + --footer *string* + Text string to be included at bottom of each HTML file. Default: + none. + + -d --displaylinks *top | bottom | both* + Specify where to display navigation links in each HTML file for + accessing all other HTML files. Possible values: *top, bottom, or + both*. Default: *both*. This option is only valid during multiple + HTML files generation for an input file. + + --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: *compound | table | both*. + Default: *both*. This option is only valid during multiple HTML + files generation. + + -h, --help + Print this help message. + + --headeralign *left | center | right,[top | middle | bottom* + Horizontal and vertical alignment for table header rows. Possible + horizontal alignment values: *left, center, or right*. Possible + vertical alignment values: *top, middle, or bottom*. + + Default values: *center,middle* + + --headercolor *#RRGGBB* + Color used to fill background of table header row containing column + labels represented as a hexadecimal string. Default value: None for + -m, --mode option value of *plain* and *#ccccff*, light blue, for + others. + + --highlight + *"fieldlabel,datatype,criterion,value,[fieldlabel,datatype,criterion,val + ue,...]"* + 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). + + Input text contains these quartets: + *fieldlabel,datatype,criterion,value,...*. Possible datatype values: + *numeric or text*. Possible criterion values: *le, ge, or eq*. + Examples: + + "MolWt,numeric,le,450" + "MolWt,numeric,le,450,LogP,numeric,le,5" + Name,text,eq,Aspirin + + --highlightcolor *"#RRGGBB,#RRGGBB"* + Colors used to highlight column values during *highlight* and + *shadedhightlight* mode represented as hexadecimal strings. + + For --highlighstyle option values of *text* and *background*, these + colors represent text or background colors respectively. For a + specific column, first color string is used for values which meet + criterion indicated by --highlight option; the second color is used + for rest of the values. + + Default values for *background* --highlightstyle: + *"#0fff0f,#ff0f0f"*. And default values for *text* --highlightstyle: + *"#0fbb0f,#ff0f0f"*. Hexadecimal strings for both --highlightstyle + colors correspond to *reddish* and *greenish*. + + --highlightstyle *text | background* + This value is mode specific. It indicates highlight style used to + differentiate column values which meet a specified criterion in + --highlight option. Possible values: *text or background*. Default: + *background*. + + -m, --mode *plain | shade | highlight | shadedhighlight | structuresonly + | shadedstructuresonly* + 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. + + Possible values: *plain, shade, highlight, shadedhighlight, + structuresonly, or shadedstructuresonly*. Default: *shade*. + + -n, --numcmpds *number* + Maximum number of compounds per table. Default value: *15* for + tables with structures and *50* 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. + + -o, --overwrite + Overwrite existing files. + + -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. + + 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. + + This option is ignored for multiple input files. + + -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 HTML page + containing structure and other appropriate information. Possible + values: *display or link*. Default value: *display* + + --strlinkmode *plain | shaded* + Specify how to display compound HTML page: plain or background of + data field field labels is filled with a specified color. Possible + values: *plain or shad*. Default value: *plane*. + + Structure viewer background color is white. Use --strviewerparams + option to change default behavior of structure viewers. + + --strlinknavigation *yes | no* + Display navigation links to other compounds in compound HTML page. + Possible values: *yes or no*. Default value: *yes*. + + --strlinkshadecolor *"#RRGGBB"* + This value is --strlinkmode specific. For *shade* value of + --strlinkmode option, it represents colors used to fill background + of data field labels. + + Default value: *"#e0e9eb"* - it's a very light blue color. + + --strlinktitle *string* + Title for compound HTML page. Default value: *Compound Summary*. + + --strlinktitledisplay *yes | no* + Display title for compound HTML page. Possible values: *yes or no*. + Default value: *no*. + + --strlinktype *href | button* + Type of structure link. Possible values: *href or button*. Default: + *href*. + + --strviewertype *Chem3DActiveX | ChemDrawActiveX | ChemDrawPlugIn | + Chime | JME | Jmol | MarvinView | ViewerActiveX* + Structure viewer supported for viewing structures. Possible values: + *Chem3DActiveX, ChemDrawActiveX, ChemDrawPlugIn, Chime, JME, Jmol, + MarvinView, or ViewerActiveX*. Default value: *Jmol*. + + 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: + + 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 + + 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. + + --strviewerconfig *codebase[,archive,code]* + 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 --strviewertype + option - MDL Chime, ChemDrawActiveX, ChemDrawPlugIn, and + Chem3DActiveX - this value is ignored. + + Input text format: *codebase[,archive,code]*. For an applet viewer, + *codebase* must be specified; *archive* and *code* values are + optional. Here are default *archive* and *codebase* values for + various applets: Jmol - JmolApplet, JmolApplet.jar; JME - JME, + JME.jar; MarvinView: MView, marvin.jar + + For local deployment of HTML files, *codebase* must correspond to a + complete path to the local directory containing appropriate + *archive* file and the complete path is converted into appropriate + relative path during generation of HTML files. + + By default, *codebase* value of <this script dir>/../lib/Jmol is + used for *Jmol* 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. + + For deploying the HTML file(s) on a web server, specify a valid + *codebase* directory name relative to <WWWRootDir>. Example when JME + archive file, JME.jar, is available in */jme* directory on the web + server: + + /jme + + For local deployment of HTML file(s), specify a complete *codebase* + directory name. Example when JmolApplet archive file, + JmolApplet.jar, is present in <JMOLROOT> directory: + + <JMOLROOT> + + In addition to *codebase*, you can also specify *archive* file name. + Example for web deployment: + + "/jme,JME.jar" + "/jme" + + Example for local deployment: + + "<JMEROOT>,JME.jar" + "<JMEROOT>" + + --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 HTML page during *link* + value for -s --structure option. + + 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. + + Input text format: *name=value name=value ...* Example: + + "width=250 height=170" + + Default for all structure viewers: *width=250 height=170* for + displaying structures in tables, and *strlinkwidth=500 + strlinkheight=295* for compound HTML page during *link* value for -s + --structure option. + + Default background color for all structure viewers: same as + --shadecolor value for displaying structures in tables and + *strlinkbgcolor=#ffffff* 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 *bgcolor=#000000* and *strlinkbgcolor=#000000* + respectively. Keep this in mind: Some structure viewers don't appear + to support background color parameter. + + Additional structure viewer specific default values: + + 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" + + Try overriding default values or specify additional valid + parameter/value pairs to get desired results. Example for using CPK + rendering scheme with Jmol viewer: + + "script="select *; set frank off; wireframe off; spacefill on"" + + --strviewerembed *direct | javascript* + Specify how to embed structure viewers in HTML pages. Possible + values: *direct* - use applet/object tags to emded structure viewer; + *javascript* - use vendor supplied java scripts. Default value: + direct. + + This option only applies to these vieweres: *Chem3DActiveX, + ChemDrawActiveX, ChemDrawPlugIn, Jmol, and MarvinView*. + + For marvin.js to work correctly on your browser, you may need to set + *marvin_jvm=builtin* or *marvin_jvm=plugin* using --strviewerparams + 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. + + 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. + + --strviewerjsfile *java script file name* + Name of vendor supplied java script file. Default values: + Chem3DActiveX: *chem3d.js*; ChemDrawActiveX, and ChemDrawPlugIn: + *chemdraw.js*; Jmol: *Jmol.js*, MarvinView: *marvin.js*. + + Directory location for these files is specified via *codebase* value + of --strviewerconfig option. + + --strtablesize *"numrows,numcols"* + This option is only valid for *structuresonly* and + *shadedstructuresonly* modes. And it indicates maximum number of + rows and columns per structure table. Default value:*6,4*. + + --stylesheet *old | new | none* + Controls usage of stylesheet for newly generated HTML file(s). + Possible values: *old, new, or none*. Default value: *new*. + + Stylesheet file contains various properties which control appearance + of HTML pages: type, size, and color of fonts; background color; and + so on. + + For *old* value, an existing stylesheet file specified by + --stylesheetname 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. + + For *create* value, a new stylesheet is created and reference to + this local stylesheet is added to each HTML file. Use option + --stylesheetname to specify name. + + For *none* value, stylesheet usage is completely ignored. + + --stylesheetname *filename* + Stylesheet file name to be used in conjunction with -s --stylesheet + option. It is only valid for *old* value of -s --stylesheet option. + Specify a valid stylesheet file location relative to your WWWRoot + and a reference to this stylesheet is added to each HTML file. + Example: *"/stylesheets/MyStyleSheet.css"*. Or a complete path name + to a local stylesheet file. + + For *create* value of -s --stylesheet option, a new stylesheet file + is created using -r --root option. And value of --stylesheetname is + simply ignored. + + --shadecolor *"#RRGGBB,#RRGGBB"* + Colors used to fill background of rows during *shade* and + *shadedhightlight* mode represented as a pair of hexadecimal string; + the first and second color values are used for odd and even number + rows respectively. + + Default value: *"#ffffff,#e0e9eb"* - it's white and very light blue + for odd and even number rows. + + -t, --title *string* + Title for HTML table(s). Default value: *SDFileName*. This option is + ignored for multiple input files. And -r --root option is used to + generate appropriate titles. + + --titledisplay *yes | no* + Display title for HTML table(s). Possible values: *yes or no*. + Default value: *yes*. + + -w, --workingdir *dirname* + Location of working directory. Default: current directory. + +EXAMPLES + 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. + + 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. + + Local deployment: Usage of default JMol viewer distributed with + MayaChemTools: + + 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: + + % SDFilesToHTML.pl -o Sample1.sdf + + 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: + + % SDFilesToHTML.pl --datafields "MolWeight,Mol_ID" -o Sample1.sdf + + 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: + + % SDFilesToHTML.pl --strviewerparams "script=\"select *; set frank off; + wireframe off; spacefill on\"" -o Sample1.sdf + + 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: + + % SDFilesToHTML.pl -o -n 10 --headeralign "center" --headercolor + "#a1a1a1" --shadecolor "#fafad2,#d1d1d1" --cellspacing 1 + --strviewerparams "bgcolor=#000000" Sample1.sdf + + To highlight molecular weight values using specified highlight criteria + and fill in default background colors, type: + + % SDFilesToHTML.pl -n 10 --highlight "MolWeight,numeric,le,450" + --highlightstyle background -m shadedhighlight -o Sample1.sdf + + To highlight molecular weight values using specified highlight criteria, + color the text using default colors, and add a footer message in every + page, type: + + % SDFilesToHTML.pl -n 4 --highlight "MolWeight,numeric,le,500" + --highlightstyle text -m shadedhighlight -o + --footer "Copyright (C) MayaChemTools" --cellspacing 1 Sample1.sdf + + To generate tables containing only structures, type: + + % SDFilesToHTML.pl -d both -m shadedstructuresonly --strtablesize "6,4" + --cellspacing 1 -b 1 -o Sample1.sdf + + To generate tables containing only structures with molecular weight + displayed above the structure, type: + + % SDFilesToHTML.pl -d both -m shadedstructuresonly --strtablesize "6,4" + --cmpddatafield "MolWeight,no,top,center" --cellspacing 1 -b 1 + -o Sample1.sdf + + To generate tables containing links to structures and highlight + molecular weight data field values using specified highlight criteria , + type: + + % 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 + + Local deployment: Usage of other structure viewers: + + % 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 + + Web deployment: Usage of different structure viewers and options: + + For deploying HTML file(s) on a web server, specify a valid *codebase* + directory name relative to <WWWRootDir>. In addition to *codebase*, you + can also specify *archive* file name. + + % 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 + +AUTHOR + Manish Sud <msud@san.rr.com> + +SEE ALSO + FilterSDFiles.pl, InfoSDFiles.pl, SplitSDFiles.pl, + MergeTextFilesWithSD.pl + +COPYRIGHT + Copyright (C) 2015 Manish Sud. All rights reserved. + + This file is part of MayaChemTools. + + 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. +