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comparison docs/scripts/txt/SDFilesToHTML.txt @ 0:4816e4a8ae95 draft default tip
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author | deepakjadmin |
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date | Wed, 20 Jan 2016 09:23:18 -0500 |
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1 NAME | |
2 SDFilesToHTML.pl - Generate HTML table file(s) from SDFile(s) | |
3 | |
4 SYNOPSIS | |
5 SDFilesToHTML.pl SDFiles(s)... | |
6 | |
7 SDFilesToHTML.pl [-a, --align left | center | right,[top | middle | | |
8 bottom]] [-b, --border borderwidth] [--cellpadding padding] | |
9 [--cellspacing spacing] [--cmpddatafield | |
10 "fieldlabel,[label,position,alignment]"] [--datafields | |
11 "fieldlabel,[fieldlabel]..." | Common | All] [--footer string] [-d, | |
12 --displaylinks top | bottom | both] [--displaylinksinfo compound | table | |
13 | both] [-h, --help] [--headeralign left | center | right,[top | middle | |
14 | bottom]] [--headercolor "#RRGGBB"] [--highlight | |
15 "fieldlabel,datatype,criterion,value,[fieldlabel,datatype,criterion,valu | |
16 e,...]"] [--highlightcolor "#RRGGBB,#RRGGBB"] [--highlightstyle text | | |
17 background] [-m, --mode plain | shade | highlight | shadedhighlight | | |
18 structuresonly | shadedstructuresonly] [-n, --numcmpds number] [-o, | |
19 --overwrite] [-r, --root rootname] [-s, --structure display | link] | |
20 [--strlinkmode plain | shaded] [--strlinknavigation yes | no] | |
21 [--strlinkshadecolor "#RRGGBB"] [--strlinktitle string] | |
22 [--strlinktitledisplay yes | no] [--strlinktype href | button] | |
23 [--strviewertype Chem3DActiveX | ChemDrawActiveX | ChemDrawPlugIn | | |
24 Chime | JME | Jmol | MarvinView | ViewerActiveX] [--strviewerconfig | |
25 codebase[,archive,code]] [--strviewerparams "name=value [name=value | |
26 ...]"] [--strviewerembed direct | javascript] [--strviewerjsfile | |
27 javascriptfilename] [--strtablesize "numrows,numcols"] [--stylesheet old | |
28 | new | none] [--stylesheetname filename] [--shadecolor | |
29 "#RRGGBB,#RRGGBB"] [-t, --title string] [--titledisplay yes | no] [-w, | |
30 --workingdir dirname] SDFiles(s)... | |
31 | |
32 DESCRIPTION | |
33 Generate HTML file(s) from *SDFile(s)*. The HTML file(s) contain data | |
34 tables and appropriate navigational links to view other tables; | |
35 navigational links are also provided on compound HTML pages. These files | |
36 can be generated for local viewing or deployment on a web server. A | |
37 variety of options are provided to control style and appearance of | |
38 tables. And for viewing structures, options are available to use any one | |
39 of these viewers: Chem3DActiveX, ChemDrawActiveX, ChemDrawPlugIn, Chime, | |
40 Jmol, JME, MarvinView, or ViewerActiveX. Jmol is the default structure | |
41 viewer and it is also distributed along with this package; however, to | |
42 use any other supported viewers, make sure it's available in your | |
43 environment. | |
44 | |
45 Multiple *SDFile(s)* names are separated by space. The valid file | |
46 extensions are *.sdf* and *.sd*. All other file names are ignored. All | |
47 the SD files in a current directory can be specified either by **.sdf* | |
48 or the current directory name. | |
49 | |
50 OPTIONS | |
51 -a, --align *left | center | right,[top | middle | bottom]* | |
52 Horizontal and vertical alignment for table rows except for header | |
53 row which is specified using --headeralign option. Possible | |
54 horizontal alignment values: *left, center, or right*. Possible | |
55 vertical alignment values: *top, middle, or bottom*. | |
56 | |
57 Default values: *left,middle* | |
58 | |
59 -b, --border *borderwidth* | |
60 Table border width. Default value: 1 for *plain* and *highlight* | |
61 mode; 0 for *shade* and *shadedhightlight* mode. Zero indicates no | |
62 border. | |
63 | |
64 --cellpadding *padding* | |
65 Table cell padding. Default value: *2*. | |
66 | |
67 --cellspacing *spacing* | |
68 Table cell spacing. Default value: *1*. | |
69 | |
70 --cmpddatafield *fieldlabel,[label,position,alignment]* | |
71 This value is mode specific. It indicates data field value to be | |
72 displayed with the structure along with its label, position and | |
73 alignment during *structuresonly | shadedstructuresonly* value of | |
74 -m, --mode option. Possible values: feldlabel - valid data field | |
75 label; label - yes or no; position - *top or bottom*; alignment - | |
76 *left, center, or right*. Default: *none,no,bottom,center*. Example: | |
77 | |
78 MolWt,no,bottom,middle | |
79 | |
80 --cmpddatafield option value is also linked to compound summary | |
81 page. | |
82 | |
83 --datafields *"fieldlabel,[fieldlabel]..." | Common | All* | |
84 Data fields to display in HTML table(s). Possible values: list of | |
85 comma separated data field labels, data fields common to all | |
86 records, or all data fields. Default value: *All*. Examples: | |
87 | |
88 ALogP,MolWeight,EC50 | |
89 "MolWeight,PSA" | |
90 | |
91 --footer *string* | |
92 Text string to be included at bottom of each HTML file. Default: | |
93 none. | |
94 | |
95 -d --displaylinks *top | bottom | both* | |
96 Specify where to display navigation links in each HTML file for | |
97 accessing all other HTML files. Possible values: *top, bottom, or | |
98 both*. Default: *both*. This option is only valid during multiple | |
99 HTML files generation for an input file. | |
100 | |
101 --displaylinksinfo *compound | table | both* | |
102 Control display of additional information along with navigational | |
103 links: Showing compound n of m is displyed for compound and showing | |
104 table n of m for table. Possible values: *compound | table | both*. | |
105 Default: *both*. This option is only valid during multiple HTML | |
106 files generation. | |
107 | |
108 -h, --help | |
109 Print this help message. | |
110 | |
111 --headeralign *left | center | right,[top | middle | bottom* | |
112 Horizontal and vertical alignment for table header rows. Possible | |
113 horizontal alignment values: *left, center, or right*. Possible | |
114 vertical alignment values: *top, middle, or bottom*. | |
115 | |
116 Default values: *center,middle* | |
117 | |
118 --headercolor *#RRGGBB* | |
119 Color used to fill background of table header row containing column | |
120 labels represented as a hexadecimal string. Default value: None for | |
121 -m, --mode option value of *plain* and *#ccccff*, light blue, for | |
122 others. | |
123 | |
124 --highlight | |
125 *"fieldlabel,datatype,criterion,value,[fieldlabel,datatype,criterion,val | |
126 ue,...]"* | |
127 Highlighting methodology used to highlight various SDFile(s) data | |
128 field values in HTML file(s). Same set of quartets values are | |
129 applied to all SDFile(s). | |
130 | |
131 Input text contains these quartets: | |
132 *fieldlabel,datatype,criterion,value,...*. Possible datatype values: | |
133 *numeric or text*. Possible criterion values: *le, ge, or eq*. | |
134 Examples: | |
135 | |
136 "MolWt,numeric,le,450" | |
137 "MolWt,numeric,le,450,LogP,numeric,le,5" | |
138 Name,text,eq,Aspirin | |
139 | |
140 --highlightcolor *"#RRGGBB,#RRGGBB"* | |
141 Colors used to highlight column values during *highlight* and | |
142 *shadedhightlight* mode represented as hexadecimal strings. | |
143 | |
144 For --highlighstyle option values of *text* and *background*, these | |
145 colors represent text or background colors respectively. For a | |
146 specific column, first color string is used for values which meet | |
147 criterion indicated by --highlight option; the second color is used | |
148 for rest of the values. | |
149 | |
150 Default values for *background* --highlightstyle: | |
151 *"#0fff0f,#ff0f0f"*. And default values for *text* --highlightstyle: | |
152 *"#0fbb0f,#ff0f0f"*. Hexadecimal strings for both --highlightstyle | |
153 colors correspond to *reddish* and *greenish*. | |
154 | |
155 --highlightstyle *text | background* | |
156 This value is mode specific. It indicates highlight style used to | |
157 differentiate column values which meet a specified criterion in | |
158 --highlight option. Possible values: *text or background*. Default: | |
159 *background*. | |
160 | |
161 -m, --mode *plain | shade | highlight | shadedhighlight | structuresonly | |
162 | shadedstructuresonly* | |
163 Specify how to generate HTML table(s): plain tables with line | |
164 borders, background of alternate rows filled with a specified color, | |
165 column values highlighted using a specified criteria, combination of | |
166 previous two styles, tables containing only structures, or tables | |
167 containing only structures with filled background of alternate rows. | |
168 | |
169 Possible values: *plain, shade, highlight, shadedhighlight, | |
170 structuresonly, or shadedstructuresonly*. Default: *shade*. | |
171 | |
172 -n, --numcmpds *number* | |
173 Maximum number of compounds per table. Default value: *15* for | |
174 tables with structures and *50* for tables with links to structures. | |
175 Use 0 to put all compounds into one table. For SDFile(s) with more | |
176 than maximum number of specified compounds, multiple HTML tables, | |
177 with appropriate navigation links, are created. | |
178 | |
179 -o, --overwrite | |
180 Overwrite existing files. | |
181 | |
182 -r, --root *rootname* | |
183 New file or directory name is generated using the root: <root>.html | |
184 or <root>-html. Default new file name: <InitialSDFileName>.html. | |
185 Default directory name: <InitialSDFileName>-html. | |
186 | |
187 For SDFile(s) with more than maximum number of specified compounds | |
188 per table, this directory tree is generated using <Name> where | |
189 <Name> corresponds to <root> or <InitialSDFileName>: Top dir - | |
190 <Name>-html; Sub dirs - html and mols. <Top dir> contains | |
191 <Name>.html and <Name>.css files and <sub dir> html conatins various | |
192 <Name>Lines<Start>To<End>.html files; <sub dir> mols is created as | |
193 needed and contains MOL files. | |
194 | |
195 This option is ignored for multiple input files. | |
196 | |
197 -s, --structure *display | link* | |
198 Structure display control: display structures in a table column or | |
199 set up a link for each structure which opens up a new HTML page | |
200 containing structure and other appropriate information. Possible | |
201 values: *display or link*. Default value: *display* | |
202 | |
203 --strlinkmode *plain | shaded* | |
204 Specify how to display compound HTML page: plain or background of | |
205 data field field labels is filled with a specified color. Possible | |
206 values: *plain or shad*. Default value: *plane*. | |
207 | |
208 Structure viewer background color is white. Use --strviewerparams | |
209 option to change default behavior of structure viewers. | |
210 | |
211 --strlinknavigation *yes | no* | |
212 Display navigation links to other compounds in compound HTML page. | |
213 Possible values: *yes or no*. Default value: *yes*. | |
214 | |
215 --strlinkshadecolor *"#RRGGBB"* | |
216 This value is --strlinkmode specific. For *shade* value of | |
217 --strlinkmode option, it represents colors used to fill background | |
218 of data field labels. | |
219 | |
220 Default value: *"#e0e9eb"* - it's a very light blue color. | |
221 | |
222 --strlinktitle *string* | |
223 Title for compound HTML page. Default value: *Compound Summary*. | |
224 | |
225 --strlinktitledisplay *yes | no* | |
226 Display title for compound HTML page. Possible values: *yes or no*. | |
227 Default value: *no*. | |
228 | |
229 --strlinktype *href | button* | |
230 Type of structure link. Possible values: *href or button*. Default: | |
231 *href*. | |
232 | |
233 --strviewertype *Chem3DActiveX | ChemDrawActiveX | ChemDrawPlugIn | | |
234 Chime | JME | Jmol | MarvinView | ViewerActiveX* | |
235 Structure viewer supported for viewing structures. Possible values: | |
236 *Chem3DActiveX, ChemDrawActiveX, ChemDrawPlugIn, Chime, JME, Jmol, | |
237 MarvinView, or ViewerActiveX*. Default value: *Jmol*. | |
238 | |
239 Assuming you have access to one of these viewers on your machine, | |
240 you are all set to use this script. Otherwise, visit one of these | |
241 web sites to download and install your favorite viewer: | |
242 | |
243 accelrys.com: Viewer ActiveX 5.0 | |
244 cambridgesoft.com: Chem3DActiveX 8.0, ChemDrawActiveX 8.0, | |
245 ChemDrawPlugIn | |
246 chemaxon.com: MarvinView applet | |
247 mdli.com: Chime plug-in | |
248 jmol.sourceforge.net: JmolApplet V10 | |
249 molinspiration.com: JME applet | |
250 | |
251 The default viewer, JmolApplet V10, is distributed with | |
252 MayaChemTools package. Earlier versions of JmolApplet are not | |
253 supported: due to applet security issues related to reading files, | |
254 this script uses in-line loading of MOL files and this option | |
255 doesn't exist in earlier version of JmolApplet. | |
256 | |
257 --strviewerconfig *codebase[,archive,code]* | |
258 Configuration information for structure viewers. This option is only | |
259 valid for structure viewers which are applets: Jmol, JME and | |
260 MarvinView. For other viewer types available via --strviewertype | |
261 option - MDL Chime, ChemDrawActiveX, ChemDrawPlugIn, and | |
262 Chem3DActiveX - this value is ignored. | |
263 | |
264 Input text format: *codebase[,archive,code]*. For an applet viewer, | |
265 *codebase* must be specified; *archive* and *code* values are | |
266 optional. Here are default *archive* and *codebase* values for | |
267 various applets: Jmol - JmolApplet, JmolApplet.jar; JME - JME, | |
268 JME.jar; MarvinView: MView, marvin.jar | |
269 | |
270 For local deployment of HTML files, *codebase* must correspond to a | |
271 complete path to the local directory containing appropriate | |
272 *archive* file and the complete path is converted into appropriate | |
273 relative path during generation of HTML files. | |
274 | |
275 By default, *codebase* value of <this script dir>/../lib/Jmol is | |
276 used for *Jmol* applet viewer, and HTML file(s) are generated for | |
277 local deployment; however, you can specify any supported applet | |
278 viewer and generate HTML file(s) for deploying on a web server. | |
279 | |
280 For deploying the HTML file(s) on a web server, specify a valid | |
281 *codebase* directory name relative to <WWWRootDir>. Example when JME | |
282 archive file, JME.jar, is available in */jme* directory on the web | |
283 server: | |
284 | |
285 /jme | |
286 | |
287 For local deployment of HTML file(s), specify a complete *codebase* | |
288 directory name. Example when JmolApplet archive file, | |
289 JmolApplet.jar, is present in <JMOLROOT> directory: | |
290 | |
291 <JMOLROOT> | |
292 | |
293 In addition to *codebase*, you can also specify *archive* file name. | |
294 Example for web deployment: | |
295 | |
296 "/jme,JME.jar" | |
297 "/jme" | |
298 | |
299 Example for local deployment: | |
300 | |
301 "<JMEROOT>,JME.jar" | |
302 "<JMEROOT>" | |
303 | |
304 --strviewerparams *"name=value [name=value ...]"* | |
305 Parameters name and value pairs for structure viewers. These name | |
306 and value pairs are used to control the appearance and behavior of | |
307 structure viewers in tables and compound HTML page during *link* | |
308 value for -s --structure option. | |
309 | |
310 The parameter names, along with their values, are just passed to | |
311 each structure viewer in appropriate format without checking their | |
312 validity. Check documentation of appropriate structure viewers to | |
313 figure out valid parameter names. | |
314 | |
315 Input text format: *name=value name=value ...* Example: | |
316 | |
317 "width=250 height=170" | |
318 | |
319 Default for all structure viewers: *width=250 height=170* for | |
320 displaying structures in tables, and *strlinkwidth=500 | |
321 strlinkheight=295* for compound HTML page during *link* value for -s | |
322 --structure option. | |
323 | |
324 Default background color for all structure viewers: same as | |
325 --shadecolor value for displaying structures in tables and | |
326 *strlinkbgcolor=#ffffff* for compound HTML page; however, explicit | |
327 specification of background color in this option overrides default | |
328 value. To use black background for structures in tables and compound | |
329 HTML page, specify *bgcolor=#000000* and *strlinkbgcolor=#000000* | |
330 respectively. Keep this in mind: Some structure viewers don't appear | |
331 to support background color parameter. | |
332 | |
333 Additional structure viewer specific default values: | |
334 | |
335 Chem3DActiveX: "displaytype=Ball&Stick rotationbars=false | |
336 moviecontroller=false" | |
337 ChemDrawActiveX: "ViewOnly=1 ShrinkToFit=1 ShowToolsWhenVisible=1" | |
338 ChemDrawPlugIn: "type=chemical/x-mdl-molfile ViewOnly=1 | |
339 ShrinkToFit=1 ShowToolsWhenVisible=1" | |
340 Chime: "display2d=true" | |
341 JME: "options=depict" | |
342 Jmol: "progressbar=true progresscolor=#0000ff boxbgcolor=#000000 | |
343 boxfgcolor=#ffffff script="select *; set frank off; | |
344 wireframe on; spacefill off"" | |
345 MarvinView: "navmode=zoom" | |
346 ViewerActiveX:"Mouse=4 Convert2Dto3D=0" | |
347 | |
348 Try overriding default values or specify additional valid | |
349 parameter/value pairs to get desired results. Example for using CPK | |
350 rendering scheme with Jmol viewer: | |
351 | |
352 "script="select *; set frank off; wireframe off; spacefill on"" | |
353 | |
354 --strviewerembed *direct | javascript* | |
355 Specify how to embed structure viewers in HTML pages. Possible | |
356 values: *direct* - use applet/object tags to emded structure viewer; | |
357 *javascript* - use vendor supplied java scripts. Default value: | |
358 direct. | |
359 | |
360 This option only applies to these vieweres: *Chem3DActiveX, | |
361 ChemDrawActiveX, ChemDrawPlugIn, Jmol, and MarvinView*. | |
362 | |
363 For marvin.js to work correctly on your browser, you may need to set | |
364 *marvin_jvm=builtin* or *marvin_jvm=plugin* using --strviewerparams | |
365 option. Additionally, MarvinView - at least in my hands - also has | |
366 problems during usage of JavaScript for local deployment; however, | |
367 it does work via web server. | |
368 | |
369 As far as I can tell, Jmol.js supplied with Jmol10 release has these | |
370 issues: jmolSetAppletColor doesn't support background color; | |
371 jmolInitialize disables relative specification of codebase directroy | |
372 which works okay. So, use Jmol.js supplied with MayaChemTools. | |
373 | |
374 --strviewerjsfile *java script file name* | |
375 Name of vendor supplied java script file. Default values: | |
376 Chem3DActiveX: *chem3d.js*; ChemDrawActiveX, and ChemDrawPlugIn: | |
377 *chemdraw.js*; Jmol: *Jmol.js*, MarvinView: *marvin.js*. | |
378 | |
379 Directory location for these files is specified via *codebase* value | |
380 of --strviewerconfig option. | |
381 | |
382 --strtablesize *"numrows,numcols"* | |
383 This option is only valid for *structuresonly* and | |
384 *shadedstructuresonly* modes. And it indicates maximum number of | |
385 rows and columns per structure table. Default value:*6,4*. | |
386 | |
387 --stylesheet *old | new | none* | |
388 Controls usage of stylesheet for newly generated HTML file(s). | |
389 Possible values: *old, new, or none*. Default value: *new*. | |
390 | |
391 Stylesheet file contains various properties which control appearance | |
392 of HTML pages: type, size, and color of fonts; background color; and | |
393 so on. | |
394 | |
395 For *old* value, an existing stylesheet file specified by | |
396 --stylesheetname option is used for each HTML file; no new | |
397 stylesheet file is created. This option is quite handy for deploying | |
398 HTML file(s) on a web server: assuming you specify a valid | |
399 stylesheet file location relative to your WWWRoot, a reference to | |
400 this stylesheet is added to each HTML file. For local deployment of | |
401 HTML file(s), a complete path to a local stylesheet is fine as well. | |
402 | |
403 For *create* value, a new stylesheet is created and reference to | |
404 this local stylesheet is added to each HTML file. Use option | |
405 --stylesheetname to specify name. | |
406 | |
407 For *none* value, stylesheet usage is completely ignored. | |
408 | |
409 --stylesheetname *filename* | |
410 Stylesheet file name to be used in conjunction with -s --stylesheet | |
411 option. It is only valid for *old* value of -s --stylesheet option. | |
412 Specify a valid stylesheet file location relative to your WWWRoot | |
413 and a reference to this stylesheet is added to each HTML file. | |
414 Example: *"/stylesheets/MyStyleSheet.css"*. Or a complete path name | |
415 to a local stylesheet file. | |
416 | |
417 For *create* value of -s --stylesheet option, a new stylesheet file | |
418 is created using -r --root option. And value of --stylesheetname is | |
419 simply ignored. | |
420 | |
421 --shadecolor *"#RRGGBB,#RRGGBB"* | |
422 Colors used to fill background of rows during *shade* and | |
423 *shadedhightlight* mode represented as a pair of hexadecimal string; | |
424 the first and second color values are used for odd and even number | |
425 rows respectively. | |
426 | |
427 Default value: *"#ffffff,#e0e9eb"* - it's white and very light blue | |
428 for odd and even number rows. | |
429 | |
430 -t, --title *string* | |
431 Title for HTML table(s). Default value: *SDFileName*. This option is | |
432 ignored for multiple input files. And -r --root option is used to | |
433 generate appropriate titles. | |
434 | |
435 --titledisplay *yes | no* | |
436 Display title for HTML table(s). Possible values: *yes or no*. | |
437 Default value: *yes*. | |
438 | |
439 -w, --workingdir *dirname* | |
440 Location of working directory. Default: current directory. | |
441 | |
442 EXAMPLES | |
443 HTML table file(s), containing structures, can be used in two different | |
444 ways: browsing on a local machine or deployment via a web server. By | |
445 default, HTML file(s) are created for viewing on a local machine using | |
446 Jmol viewer through a browser; however, you can specify any supported | |
447 applet viewer and generate HTML file(s) for deploying on a web server. | |
448 | |
449 First two sets of examples show generation of HTML file(s) using | |
450 different applet viewers and a variety of options for local browsing; | |
451 last set deals with web deployment. | |
452 | |
453 Local deployment: Usage of default JMol viewer distributed with | |
454 MayaChemTools: | |
455 | |
456 To generate HTML tables with structure display using JMol viewer, rows | |
457 background filled with white and light blue colors, navigation links on | |
458 top and botton of each page, type: | |
459 | |
460 % SDFilesToHTML.pl -o Sample1.sdf | |
461 | |
462 To generate HTML tables with structure display using JMol viewer, rows | |
463 background filled with white and light blue colors, navigation links on | |
464 top and botton of each page, and only containing MolWeight and Mol_ID SD | |
465 data fields, type: | |
466 | |
467 % SDFilesToHTML.pl --datafields "MolWeight,Mol_ID" -o Sample1.sdf | |
468 | |
469 To generate HTML tables with CPK structure display using JMol viewer, | |
470 rows background filled with white and light blue colors, navigation | |
471 links on top and botton of each page, type: | |
472 | |
473 % SDFilesToHTML.pl --strviewerparams "script=\"select *; set frank off; | |
474 wireframe off; spacefill on\"" -o Sample1.sdf | |
475 | |
476 To generate HTML tables with structure display using JMol viewer and | |
477 black background, rows background filled with light golden and greyish | |
478 colors, navigation links on top and botton of each page, 10 rows in each | |
479 table, greyish header row color, and cell spacing of 1, type: | |
480 | |
481 % SDFilesToHTML.pl -o -n 10 --headeralign "center" --headercolor | |
482 "#a1a1a1" --shadecolor "#fafad2,#d1d1d1" --cellspacing 1 | |
483 --strviewerparams "bgcolor=#000000" Sample1.sdf | |
484 | |
485 To highlight molecular weight values using specified highlight criteria | |
486 and fill in default background colors, type: | |
487 | |
488 % SDFilesToHTML.pl -n 10 --highlight "MolWeight,numeric,le,450" | |
489 --highlightstyle background -m shadedhighlight -o Sample1.sdf | |
490 | |
491 To highlight molecular weight values using specified highlight criteria, | |
492 color the text using default colors, and add a footer message in every | |
493 page, type: | |
494 | |
495 % SDFilesToHTML.pl -n 4 --highlight "MolWeight,numeric,le,500" | |
496 --highlightstyle text -m shadedhighlight -o | |
497 --footer "Copyright (C) MayaChemTools" --cellspacing 1 Sample1.sdf | |
498 | |
499 To generate tables containing only structures, type: | |
500 | |
501 % SDFilesToHTML.pl -d both -m shadedstructuresonly --strtablesize "6,4" | |
502 --cellspacing 1 -b 1 -o Sample1.sdf | |
503 | |
504 To generate tables containing only structures with molecular weight | |
505 displayed above the structure, type: | |
506 | |
507 % SDFilesToHTML.pl -d both -m shadedstructuresonly --strtablesize "6,4" | |
508 --cmpddatafield "MolWeight,no,top,center" --cellspacing 1 -b 1 | |
509 -o Sample1.sdf | |
510 | |
511 To generate tables containing links to structures and highlight | |
512 molecular weight data field values using specified highlight criteria , | |
513 type: | |
514 | |
515 % SDFilesToHTML.pl -n 4 --footer "Copyright (C) MayaChemTools" | |
516 --highlight "MolWeight,numeric,le,450" --highlightstyle background | |
517 -d both -m shadedhighlight -s link --strlinktype button | |
518 -o Sample1.sdf | |
519 | |
520 Local deployment: Usage of other structure viewers: | |
521 | |
522 % SDFilesToHTML.pl --strviewertype MarvinView --strviewerconfig | |
523 "<Marvin dir path>" -o Sample1.sdf | |
524 | |
525 % SDFilesToHTML.pl -o -n 10 --headeralign "center" --headercolor | |
526 "#a1a1a1" --shadecolor "#fafad2,#d1d1d1" --cellspacing 1 | |
527 --strviewerparams "bgcolor=#000000" --strviewertype Chime | |
528 Sample1.sdf | |
529 | |
530 % SDFilesToHTML.pl -n 10 --highlight "MolWeight,numeric,le,450" | |
531 --highlightstyle background -m shadedhighlight --strviewertype | |
532 Chime -o Sample1.sdf | |
533 | |
534 % SDFilesToHTML.pl -d both -m shadedstructuresonly --strtablesize "6,4" | |
535 --cellspacing 1 -b 1 -strviewertype JME -strviewerconfig "<JME dir | |
536 path>" -o Sample1.sdf | |
537 | |
538 Web deployment: Usage of different structure viewers and options: | |
539 | |
540 For deploying HTML file(s) on a web server, specify a valid *codebase* | |
541 directory name relative to <WWWRootDir>. In addition to *codebase*, you | |
542 can also specify *archive* file name. | |
543 | |
544 % SDFilesToHTML.pl -m plain -s display --strviewertype Jmol | |
545 -strviewerconfig "/jmol" -n 5 -d both -r PlainTable -t "Example | |
546 using Jmol: Plain Table" -o Sample1.sdf | |
547 | |
548 % SDFilesToHTML.pl -n 5 -m shade -s display -strviewertype JME | |
549 -strviewerconfig "/jme,JME.jar" -r ShadeTable -t "Example using JME: | |
550 Shaded Table" -o Sample.sdf | |
551 | |
552 % SDFilesToHTML.pl -n 5 --highlight "MolWeight,numeric,le,450" | |
553 --highlightstyle background -d both -m shadedhighlight -s display | |
554 -strviewertype MarvinView -strviewerconfig "/marvin" -r | |
555 ShadedHightlightTable -t "Example using MarvinView: Shaded and | |
556 Highlighted Table" -o Sample.sdf | |
557 | |
558 % SDFilesToHTML.pl -n 4 --highlight "MolWeight,numeric,le,450" -s link | |
559 --strlinktype href --strviewertype ChemDrawPlugIn --highlightstyle | |
560 background -m shadedhighlight -t "Example using ChemDrawPlugIn: | |
561 Shaded and Highlighted Table" -r ShadedHightlightTable -o Sample1.sdf | |
562 | |
563 AUTHOR | |
564 Manish Sud <msud@san.rr.com> | |
565 | |
566 SEE ALSO | |
567 FilterSDFiles.pl, InfoSDFiles.pl, SplitSDFiles.pl, | |
568 MergeTextFilesWithSD.pl | |
569 | |
570 COPYRIGHT | |
571 Copyright (C) 2015 Manish Sud. All rights reserved. | |
572 | |
573 This file is part of MayaChemTools. | |
574 | |
575 MayaChemTools is free software; you can redistribute it and/or modify it | |
576 under the terms of the GNU Lesser General Public License as published by | |
577 the Free Software Foundation; either version 3 of the License, or (at | |
578 your option) any later version. | |
579 |