|
0
|
1 .\" Automatically generated by Pod::Man 2.25 (Pod::Simple 3.22)
|
|
|
2 .\"
|
|
|
3 .\" Standard preamble:
|
|
|
4 .\" ========================================================================
|
|
|
5 .de Sp \" Vertical space (when we can't use .PP)
|
|
|
6 .if t .sp .5v
|
|
|
7 .if n .sp
|
|
|
8 ..
|
|
|
9 .de Vb \" Begin verbatim text
|
|
|
10 .ft CW
|
|
|
11 .nf
|
|
|
12 .ne \\$1
|
|
|
13 ..
|
|
|
14 .de Ve \" End verbatim text
|
|
|
15 .ft R
|
|
|
16 .fi
|
|
|
17 ..
|
|
|
18 .\" Set up some character translations and predefined strings. \*(-- will
|
|
|
19 .\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left
|
|
|
20 .\" double quote, and \*(R" will give a right double quote. \*(C+ will
|
|
|
21 .\" give a nicer C++. Capital omega is used to do unbreakable dashes and
|
|
|
22 .\" therefore won't be available. \*(C` and \*(C' expand to `' in nroff,
|
|
|
23 .\" nothing in troff, for use with C<>.
|
|
|
24 .tr \(*W-
|
|
|
25 .ds C+ C\v'-.1v'\h'-1p'\s-2+\h'-1p'+\s0\v'.1v'\h'-1p'
|
|
|
26 .ie n \{\
|
|
|
27 . ds -- \(*W-
|
|
|
28 . ds PI pi
|
|
|
29 . if (\n(.H=4u)&(1m=24u) .ds -- \(*W\h'-12u'\(*W\h'-12u'-\" diablo 10 pitch
|
|
|
30 . if (\n(.H=4u)&(1m=20u) .ds -- \(*W\h'-12u'\(*W\h'-8u'-\" diablo 12 pitch
|
|
|
31 . ds L" ""
|
|
|
32 . ds R" ""
|
|
|
33 . ds C` ""
|
|
|
34 . ds C' ""
|
|
|
35 'br\}
|
|
|
36 .el\{\
|
|
|
37 . ds -- \|\(em\|
|
|
|
38 . ds PI \(*p
|
|
|
39 . ds L" ``
|
|
|
40 . ds R" ''
|
|
|
41 'br\}
|
|
|
42 .\"
|
|
|
43 .\" Escape single quotes in literal strings from groff's Unicode transform.
|
|
|
44 .ie \n(.g .ds Aq \(aq
|
|
|
45 .el .ds Aq '
|
|
|
46 .\"
|
|
|
47 .\" If the F register is turned on, we'll generate index entries on stderr for
|
|
|
48 .\" titles (.TH), headers (.SH), subsections (.SS), items (.Ip), and index
|
|
|
49 .\" entries marked with X<> in POD. Of course, you'll have to process the
|
|
|
50 .\" output yourself in some meaningful fashion.
|
|
|
51 .ie \nF \{\
|
|
|
52 . de IX
|
|
|
53 . tm Index:\\$1\t\\n%\t"\\$2"
|
|
|
54 ..
|
|
|
55 . nr % 0
|
|
|
56 . rr F
|
|
|
57 .\}
|
|
|
58 .el \{\
|
|
|
59 . de IX
|
|
|
60 ..
|
|
|
61 .\}
|
|
|
62 .\"
|
|
|
63 .\" Accent mark definitions (@(#)ms.acc 1.5 88/02/08 SMI; from UCB 4.2).
|
|
|
64 .\" Fear. Run. Save yourself. No user-serviceable parts.
|
|
|
65 . \" fudge factors for nroff and troff
|
|
|
66 .if n \{\
|
|
|
67 . ds #H 0
|
|
|
68 . ds #V .8m
|
|
|
69 . ds #F .3m
|
|
|
70 . ds #[ \f1
|
|
|
71 . ds #] \fP
|
|
|
72 .\}
|
|
|
73 .if t \{\
|
|
|
74 . ds #H ((1u-(\\\\n(.fu%2u))*.13m)
|
|
|
75 . ds #V .6m
|
|
|
76 . ds #F 0
|
|
|
77 . ds #[ \&
|
|
|
78 . ds #] \&
|
|
|
79 .\}
|
|
|
80 . \" simple accents for nroff and troff
|
|
|
81 .if n \{\
|
|
|
82 . ds ' \&
|
|
|
83 . ds ` \&
|
|
|
84 . ds ^ \&
|
|
|
85 . ds , \&
|
|
|
86 . ds ~ ~
|
|
|
87 . ds /
|
|
|
88 .\}
|
|
|
89 .if t \{\
|
|
|
90 . ds ' \\k:\h'-(\\n(.wu*8/10-\*(#H)'\'\h"|\\n:u"
|
|
|
91 . ds ` \\k:\h'-(\\n(.wu*8/10-\*(#H)'\`\h'|\\n:u'
|
|
|
92 . ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'^\h'|\\n:u'
|
|
|
93 . ds , \\k:\h'-(\\n(.wu*8/10)',\h'|\\n:u'
|
|
|
94 . ds ~ \\k:\h'-(\\n(.wu-\*(#H-.1m)'~\h'|\\n:u'
|
|
|
95 . ds / \\k:\h'-(\\n(.wu*8/10-\*(#H)'\z\(sl\h'|\\n:u'
|
|
|
96 .\}
|
|
|
97 . \" troff and (daisy-wheel) nroff accents
|
|
|
98 .ds : \\k:\h'-(\\n(.wu*8/10-\*(#H+.1m+\*(#F)'\v'-\*(#V'\z.\h'.2m+\*(#F'.\h'|\\n:u'\v'\*(#V'
|
|
|
99 .ds 8 \h'\*(#H'\(*b\h'-\*(#H'
|
|
|
100 .ds o \\k:\h'-(\\n(.wu+\w'\(de'u-\*(#H)/2u'\v'-.3n'\*(#[\z\(de\v'.3n'\h'|\\n:u'\*(#]
|
|
|
101 .ds d- \h'\*(#H'\(pd\h'-\w'~'u'\v'-.25m'\f2\(hy\fP\v'.25m'\h'-\*(#H'
|
|
|
102 .ds D- D\\k:\h'-\w'D'u'\v'-.11m'\z\(hy\v'.11m'\h'|\\n:u'
|
|
|
103 .ds th \*(#[\v'.3m'\s+1I\s-1\v'-.3m'\h'-(\w'I'u*2/3)'\s-1o\s+1\*(#]
|
|
|
104 .ds Th \*(#[\s+2I\s-2\h'-\w'I'u*3/5'\v'-.3m'o\v'.3m'\*(#]
|
|
|
105 .ds ae a\h'-(\w'a'u*4/10)'e
|
|
|
106 .ds Ae A\h'-(\w'A'u*4/10)'E
|
|
|
107 . \" corrections for vroff
|
|
|
108 .if v .ds ~ \\k:\h'-(\\n(.wu*9/10-\*(#H)'\s-2\u~\d\s+2\h'|\\n:u'
|
|
|
109 .if v .ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'\v'-.4m'^\v'.4m'\h'|\\n:u'
|
|
|
110 . \" for low resolution devices (crt and lpr)
|
|
|
111 .if \n(.H>23 .if \n(.V>19 \
|
|
|
112 \{\
|
|
|
113 . ds : e
|
|
|
114 . ds 8 ss
|
|
|
115 . ds o a
|
|
|
116 . ds d- d\h'-1'\(ga
|
|
|
117 . ds D- D\h'-1'\(hy
|
|
|
118 . ds th \o'bp'
|
|
|
119 . ds Th \o'LP'
|
|
|
120 . ds ae ae
|
|
|
121 . ds Ae AE
|
|
|
122 .\}
|
|
|
123 .rm #[ #] #H #V #F C
|
|
|
124 .\" ========================================================================
|
|
|
125 .\"
|
|
|
126 .IX Title "SDFILESTOHTML 1"
|
|
|
127 .TH SDFILESTOHTML 1 "2015-03-29" "perl v5.14.2" "MayaChemTools"
|
|
|
128 .\" For nroff, turn off justification. Always turn off hyphenation; it makes
|
|
|
129 .\" way too many mistakes in technical documents.
|
|
|
130 .if n .ad l
|
|
|
131 .nh
|
|
|
132 .SH "NAME"
|
|
|
133 SDFilesToHTML.pl \- Generate HTML table file(s) from SDFile(s)
|
|
|
134 .SH "SYNOPSIS"
|
|
|
135 .IX Header "SYNOPSIS"
|
|
|
136 SDFilesToHTML.pl SDFiles(s)...
|
|
|
137 .PP
|
|
|
138 SDFilesToHTML.pl [\fB\-a, \-\-align\fR left | center | right,[top | middle | bottom]] [\fB\-b, \-\-border\fR borderwidth] [\fB\-\-cellpadding\fR padding]
|
|
|
139 [\fB\-\-cellspacing\fR spacing] [\fB\-\-cmpddatafield\fR \*(L"fieldlabel,[label,position,alignment]\*(R"] [\fB\-\-datafields\fR \*(L"fieldlabel,[fieldlabel]...\*(R" | Common | All]
|
|
|
140 [\fB\-\-footer\fR string] [\fB\-d, \-\-displaylinks\fR top | bottom | both] [\fB\-\-displaylinksinfo\fR compound | table | both] [\fB\-h, \-\-help\fR]
|
|
|
141 [\fB\-\-headeralign\fR left | center | right,[top | middle | bottom]] [\fB\-\-headercolor\fR \*(L"#RRGGBB\*(R"]
|
|
|
142 [\fB\-\-highlight\fR \*(L"fieldlabel,datatype,criterion,value,[fieldlabel,datatype,criterion,value,...]\*(R"]
|
|
|
143 [\fB\-\-highlightcolor\fR \*(L"#RRGGBB,#RRGGBB\*(R"] [\fB\-\-highlightstyle\fR text | background]
|
|
|
144 [\fB\-m, \-\-mode\fR plain | shade | highlight | shadedhighlight | structuresonly | shadedstructuresonly]
|
|
|
145 [\fB\-n, \-\-numcmpds\fR number] [\fB\-o, \-\-overwrite\fR] [\fB\-r, \-\-root\fR rootname] [\fB\-s, \-\-structure\fR display | link]
|
|
|
146 [\fB\-\-strlinkmode\fR plain | shaded] [\fB\-\-strlinknavigation\fR yes | no]
|
|
|
147 [\fB\-\-strlinkshadecolor\fR \*(L"#RRGGBB\*(R"] [\fB\-\-strlinktitle\fR string] [\fB\-\-strlinktitledisplay\fR yes | no] [\fB\-\-strlinktype\fR href | button]
|
|
|
148 [\fB\-\-strviewertype\fR Chem3DActiveX | ChemDrawActiveX | ChemDrawPlugIn | Chime | \s-1JME\s0 | Jmol | MarvinView | ViewerActiveX]
|
|
|
149 [\fB\-\-strviewerconfig\fR codebase[,archive,code]] [\fB\-\-strviewerparams\fR \*(L"name=value [name=value ...]\*(R"]
|
|
|
150 [\fB\-\-strviewerembed\fR direct | javascript] [\fB\-\-strviewerjsfile\fR javascriptfilename]
|
|
|
151 [\fB\-\-strtablesize\fR \*(L"numrows,numcols\*(R"] [\fB\-\-stylesheet\fR old | new | none]
|
|
|
152 [\fB\-\-stylesheetname\fR filename] [\fB\-\-shadecolor\fR \*(L"#RRGGBB,#RRGGBB\*(R"] [\fB\-t, \-\-title\fR string] [\fB\-\-titledisplay\fR yes | no]
|
|
|
153 [\fB\-w, \-\-workingdir\fR dirname] SDFiles(s)...
|
|
|
154 .SH "DESCRIPTION"
|
|
|
155 .IX Header "DESCRIPTION"
|
|
|
156 Generate \s-1HTML\s0 file(s) from \fISDFile(s)\fR. The \s-1HTML\s0 file(s) contain data tables
|
|
|
157 and appropriate navigational links to view other tables; navigational links are also
|
|
|
158 provided on compound \s-1HTML\s0 pages. These files can be generated for local viewing or
|
|
|
159 deployment on a web server. A variety of options are provided to control style and
|
|
|
160 appearance of tables. And for viewing structures, options are available to use any one of
|
|
|
161 these viewers: Chem3DActiveX, ChemDrawActiveX, ChemDrawPlugIn, Chime, Jmol, \s-1JME\s0,
|
|
|
162 MarvinView, or ViewerActiveX. Jmol is the default structure viewer and it is also distributed
|
|
|
163 along with this package; however, to use any other supported viewers, make sure it's available
|
|
|
164 in your environment.
|
|
|
165 .PP
|
|
|
166 Multiple \fISDFile(s)\fR names are separated by space. The valid file extensions are
|
|
|
167 \&\fI.sdf\fR and \fI.sd\fR. All other file names are ignored. All the \s-1SD\s0 files in a current directory can
|
|
|
168 be specified either by \fI*.sdf\fR or the current directory name.
|
|
|
169 .SH "OPTIONS"
|
|
|
170 .IX Header "OPTIONS"
|
|
|
171 .IP "\fB\-a, \-\-align\fR \fIleft | center | right,[top | middle | bottom]\fR" 4
|
|
|
172 .IX Item "-a, --align left | center | right,[top | middle | bottom]"
|
|
|
173 Horizontal and vertical alignment for table rows except for header row which is specified
|
|
|
174 using \fB\-\-headeralign\fR option. Possible horizontal alignment values: \fIleft, center, or right\fR.
|
|
|
175 Possible vertical alignment values: \fItop, middle, or bottom\fR.
|
|
|
176 .Sp
|
|
|
177 Default values: \fIleft,middle\fR
|
|
|
178 .IP "\fB\-b, \-\-border\fR \fIborderwidth\fR" 4
|
|
|
179 .IX Item "-b, --border borderwidth"
|
|
|
180 Table border width. Default value: 1 for \fIplain\fR and \fIhighlight\fR mode; 0 for \fIshade\fR
|
|
|
181 and \fIshadedhightlight\fR mode. Zero indicates no border.
|
|
|
182 .IP "\fB\-\-cellpadding\fR \fIpadding\fR" 4
|
|
|
183 .IX Item "--cellpadding padding"
|
|
|
184 Table cell padding. Default value: \fI2\fR.
|
|
|
185 .IP "\fB\-\-cellspacing\fR \fIspacing\fR" 4
|
|
|
186 .IX Item "--cellspacing spacing"
|
|
|
187 Table cell spacing. Default value: \fI1\fR.
|
|
|
188 .IP "\fB\-\-cmpddatafield\fR \fIfieldlabel,[label,position,alignment]\fR" 4
|
|
|
189 .IX Item "--cmpddatafield fieldlabel,[label,position,alignment]"
|
|
|
190 This value is mode specific. It indicates data field value to be displayed with the structure along
|
|
|
191 with its label, position and alignment during \fIstructuresonly | shadedstructuresonly\fR value of \fB\-m, \-\-mode\fR
|
|
|
192 option. Possible values: feldlabel \- valid data field label; label \- yes or no; position \- \fItop or bottom\fR; alignment
|
|
|
193 \&\- \fIleft, center, or right\fR. Default: \fInone,no,bottom,center\fR. Example:
|
|
|
194 .Sp
|
|
|
195 .Vb 1
|
|
|
196 \& MolWt,no,bottom,middle
|
|
|
197 .Ve
|
|
|
198 .Sp
|
|
|
199 \&\fB\-\-cmpddatafield\fR option value is also linked to compound summary page.
|
|
|
200 .ie n .IP "\fB\-\-datafields\fR \fI""fieldlabel,[fieldlabel]..."" | Common | All\fR" 4
|
|
|
201 .el .IP "\fB\-\-datafields\fR \fI``fieldlabel,[fieldlabel]...'' | Common | All\fR" 4
|
|
|
202 .IX Item "--datafields fieldlabel,[fieldlabel]... | Common | All"
|
|
|
203 Data fields to display in \s-1HTML\s0 table(s). Possible values: list of comma separated data field
|
|
|
204 labels, data fields common to all records, or all data fields. Default value: \fIAll\fR.
|
|
|
205 Examples:
|
|
|
206 .Sp
|
|
|
207 .Vb 2
|
|
|
208 \& ALogP,MolWeight,EC50
|
|
|
209 \& "MolWeight,PSA"
|
|
|
210 .Ve
|
|
|
211 .IP "\fB\-\-footer\fR \fIstring\fR" 4
|
|
|
212 .IX Item "--footer string"
|
|
|
213 Text string to be included at bottom of each \s-1HTML\s0 file. Default: none.
|
|
|
214 .IP "\fB\-d \-\-displaylinks\fR \fItop | bottom | both\fR" 4
|
|
|
215 .IX Item "-d --displaylinks top | bottom | both"
|
|
|
216 Specify where to display navigation links in each \s-1HTML\s0 file for accessing all other \s-1HTML\s0
|
|
|
217 files. Possible values: \fItop, bottom, or both\fR. Default: \fIboth\fR. This option is
|
|
|
218 only valid during multiple \s-1HTML\s0 files generation for an input file.
|
|
|
219 .IP "\fB\-\-displaylinksinfo\fR \fIcompound | table | both\fR" 4
|
|
|
220 .IX Item "--displaylinksinfo compound | table | both"
|
|
|
221 Control display of additional information along with navigational links: Showing compound
|
|
|
222 n of m is displyed for compound and showing table n of m for table. Possible values: \fIcompound
|
|
|
223 | table | both\fR. Default: \fIboth\fR. This option is only valid during multiple \s-1HTML\s0 files generation.
|
|
|
224 .IP "\fB\-h, \-\-help\fR" 4
|
|
|
225 .IX Item "-h, --help"
|
|
|
226 Print this help message.
|
|
|
227 .IP "\fB\-\-headeralign\fR \fIleft | center | right,[top | middle | bottom\fR" 4
|
|
|
228 .IX Item "--headeralign left | center | right,[top | middle | bottom"
|
|
|
229 Horizontal and vertical alignment for table header rows. Possible horizontal alignment
|
|
|
230 values: \fIleft, center, or right\fR. Possible vertical alignment values: \fItop, middle, or bottom\fR.
|
|
|
231 .Sp
|
|
|
232 Default values: \fIcenter,middle\fR
|
|
|
233 .IP "\fB\-\-headercolor\fR \fI#RRGGBB\fR" 4
|
|
|
234 .IX Item "--headercolor #RRGGBB"
|
|
|
235 Color used to fill background of table header row containing column labels
|
|
|
236 represented as a hexadecimal string. Default value: None for \fB\-m, \-\-mode\fR option
|
|
|
237 value of \fIplain\fR and \fI#ccccff\fR, light blue, for others.
|
|
|
238 .ie n .IP "\fB\-\-highlight\fR \fI""fieldlabel,datatype,criterion,value,[fieldlabel,datatype,criterion,value,...]""\fR" 4
|
|
|
239 .el .IP "\fB\-\-highlight\fR \fI``fieldlabel,datatype,criterion,value,[fieldlabel,datatype,criterion,value,...]''\fR" 4
|
|
|
240 .IX Item "--highlight fieldlabel,datatype,criterion,value,[fieldlabel,datatype,criterion,value,...]"
|
|
|
241 Highlighting methodology used to highlight various SDFile(s) data field values in
|
|
|
242 \&\s-1HTML\s0 file(s). Same set of quartets values are applied to all SDFile(s).
|
|
|
243 .Sp
|
|
|
244 Input text contains these quartets: \fIfieldlabel,datatype,criterion,value,...\fR.
|
|
|
245 Possible datatype values: \fInumeric or text\fR. Possible criterion values: \fIle, ge, or eq\fR.
|
|
|
246 Examples:
|
|
|
247 .Sp
|
|
|
248 .Vb 3
|
|
|
249 \& "MolWt,numeric,le,450"
|
|
|
250 \& "MolWt,numeric,le,450,LogP,numeric,le,5"
|
|
|
251 \& Name,text,eq,Aspirin
|
|
|
252 .Ve
|
|
|
253 .ie n .IP "\fB\-\-highlightcolor\fR \fI""#RRGGBB,#RRGGBB""\fR" 4
|
|
|
254 .el .IP "\fB\-\-highlightcolor\fR \fI``#RRGGBB,#RRGGBB''\fR" 4
|
|
|
255 .IX Item "--highlightcolor #RRGGBB,#RRGGBB"
|
|
|
256 Colors used to highlight column values during \fIhighlight\fR and \fIshadedhightlight\fR
|
|
|
257 mode represented as hexadecimal strings.
|
|
|
258 .Sp
|
|
|
259 For \fB\-\-highlighstyle\fR option values of \fItext\fR and \fIbackground\fR, these colors represent
|
|
|
260 text or background colors respectively. For a specific column, first color string is used for
|
|
|
261 values which meet criterion indicated by \fB\-\-highlight\fR option; the second color is used for
|
|
|
262 rest of the values.
|
|
|
263 .Sp
|
|
|
264 Default values for \fIbackground\fR \fB\-\-highlightstyle\fR: \fI\*(L"#0fff0f,#ff0f0f\*(R"\fR. And default values for
|
|
|
265 \&\fItext\fR \fB\-\-highlightstyle\fR: \fI\*(L"#0fbb0f,#ff0f0f\*(R"\fR. Hexadecimal strings for both \fB\-\-highlightstyle\fR
|
|
|
266 colors correspond to \fIreddish\fR and \fIgreenish\fR.
|
|
|
267 .IP "\fB\-\-highlightstyle\fR \fItext | background\fR" 4
|
|
|
268 .IX Item "--highlightstyle text | background"
|
|
|
269 This value is mode specific. It indicates highlight style used to differentiate column
|
|
|
270 values which meet a specified criterion in \fB\-\-highlight\fR option. Possible values: \fItext or
|
|
|
271 background\fR. Default: \fIbackground\fR.
|
|
|
272 .IP "\fB\-m, \-\-mode\fR \fIplain | shade | highlight | shadedhighlight | structuresonly | shadedstructuresonly\fR" 4
|
|
|
273 .IX Item "-m, --mode plain | shade | highlight | shadedhighlight | structuresonly | shadedstructuresonly"
|
|
|
274 Specify how to generate \s-1HTML\s0 table(s): plain tables with line borders, background of
|
|
|
275 alternate rows filled with a specified color, column values highlighted using a specified
|
|
|
276 criteria, combination of previous two styles, tables containing only structures, or tables
|
|
|
277 containing only structures with filled background of alternate rows.
|
|
|
278 .Sp
|
|
|
279 Possible values: \fIplain, shade, highlight, shadedhighlight, structuresonly, or
|
|
|
280 shadedstructuresonly\fR. Default: \fIshade\fR.
|
|
|
281 .IP "\fB\-n, \-\-numcmpds\fR \fInumber\fR" 4
|
|
|
282 .IX Item "-n, --numcmpds number"
|
|
|
283 Maximum number of compounds per table. Default value: \fI15\fR for tables with structures and
|
|
|
284 \&\fI50\fR for tables with links to structures. Use 0 to put all compounds into one table. For SDFile(s)
|
|
|
285 with more than maximum number of specified compounds, multiple \s-1HTML\s0 tables, with appropriate
|
|
|
286 navigation links, are created.
|
|
|
287 .IP "\fB\-o, \-\-overwrite\fR" 4
|
|
|
288 .IX Item "-o, --overwrite"
|
|
|
289 Overwrite existing files.
|
|
|
290 .IP "\fB\-r, \-\-root\fR \fIrootname\fR" 4
|
|
|
291 .IX Item "-r, --root rootname"
|
|
|
292 New file or directory name is generated using the root: <root>.html or <root>\-html.
|
|
|
293 Default new file name: <InitialSDFileName>.html. Default directory name:
|
|
|
294 <InitialSDFileName>\-html.
|
|
|
295 .Sp
|
|
|
296 For SDFile(s) with more than maximum number of specified compounds per table,
|
|
|
297 this directory tree is generated using <Name> where <Name> corresponds to <root>
|
|
|
298 or <InitialSDFileName>: Top dir \- <Name>\-html; Sub dirs \- html and mols. <Top dir> contains
|
|
|
299 <Name>.html and <Name>.css files and <sub dir> html conatins various
|
|
|
300 <Name>Lines<Start>To<End>.html files; <sub dir> mols is created as needed and contains
|
|
|
301 \&\s-1MOL\s0 files.
|
|
|
302 .Sp
|
|
|
303 This option is ignored for multiple input files.
|
|
|
304 .IP "\fB\-s, \-\-structure\fR \fIdisplay | link\fR" 4
|
|
|
305 .IX Item "-s, --structure display | link"
|
|
|
306 Structure display control: display structures in a table column or set up a link for each
|
|
|
307 structure which opens up a new \s-1HTML\s0 page containing structure and other appropriate
|
|
|
308 information. Possible values: \fIdisplay or link\fR. Default value: \fIdisplay\fR
|
|
|
309 .IP "\fB\-\-strlinkmode\fR \fIplain | shaded\fR" 4
|
|
|
310 .IX Item "--strlinkmode plain | shaded"
|
|
|
311 Specify how to display compound \s-1HTML\s0 page: plain or background of data field
|
|
|
312 field labels is filled with a specified color. Possible values: \fIplain or shad\fR.
|
|
|
313 Default value: \fIplane\fR.
|
|
|
314 .Sp
|
|
|
315 Structure viewer background color is white. Use \fB\-\-strviewerparams\fR option to change
|
|
|
316 default behavior of structure viewers.
|
|
|
317 .IP "\fB\-\-strlinknavigation\fR \fIyes | no\fR" 4
|
|
|
318 .IX Item "--strlinknavigation yes | no"
|
|
|
319 Display navigation links to other compounds in compound \s-1HTML\s0 page. Possible values:
|
|
|
320 \&\fIyes or no\fR. Default value: \fIyes\fR.
|
|
|
321 .ie n .IP "\fB\-\-strlinkshadecolor\fR \fI""#RRGGBB""\fR" 4
|
|
|
322 .el .IP "\fB\-\-strlinkshadecolor\fR \fI``#RRGGBB''\fR" 4
|
|
|
323 .IX Item "--strlinkshadecolor #RRGGBB"
|
|
|
324 This value is \fB\-\-strlinkmode\fR specific. For \fIshade\fR value of \fB\-\-strlinkmode\fR option, it
|
|
|
325 represents colors used to fill background of data field labels.
|
|
|
326 .Sp
|
|
|
327 Default value: \fI\*(L"#e0e9eb\*(R"\fR \- it's a very light blue color.
|
|
|
328 .IP "\fB\-\-strlinktitle\fR \fIstring\fR" 4
|
|
|
329 .IX Item "--strlinktitle string"
|
|
|
330 Title for compound \s-1HTML\s0 page. Default value: \fICompound Summary\fR.
|
|
|
331 .IP "\fB\-\-strlinktitledisplay\fR \fIyes | no\fR" 4
|
|
|
332 .IX Item "--strlinktitledisplay yes | no"
|
|
|
333 Display title for compound \s-1HTML\s0 page. Possible values: \fIyes or no\fR. Default value: \fIno\fR.
|
|
|
334 .IP "\fB\-\-strlinktype\fR \fIhref | button\fR" 4
|
|
|
335 .IX Item "--strlinktype href | button"
|
|
|
336 Type of structure link. Possible values: \fIhref or button\fR. Default: \fIhref\fR.
|
|
|
337 .IP "\fB\-\-strviewertype\fR \fIChem3DActiveX | ChemDrawActiveX | ChemDrawPlugIn | Chime | \s-1JME\s0 | Jmol | MarvinView | ViewerActiveX\fR" 4
|
|
|
338 .IX Item "--strviewertype Chem3DActiveX | ChemDrawActiveX | ChemDrawPlugIn | Chime | JME | Jmol | MarvinView | ViewerActiveX"
|
|
|
339 Structure viewer supported for viewing structures. Possible values: \fIChem3DActiveX,
|
|
|
340 ChemDrawActiveX, ChemDrawPlugIn, Chime, \s-1JME\s0, Jmol, MarvinView, or ViewerActiveX\fR.
|
|
|
341 Default value: \fIJmol\fR.
|
|
|
342 .Sp
|
|
|
343 Assuming you have access to one of these viewers on your machine, you are all set
|
|
|
344 to use this script. Otherwise, visit one of these web sites to download and install
|
|
|
345 your favorite viewer:
|
|
|
346 .Sp
|
|
|
347 .Vb 7
|
|
|
348 \& accelrys.com: Viewer ActiveX 5.0
|
|
|
349 \& cambridgesoft.com: Chem3DActiveX 8.0, ChemDrawActiveX 8.0,
|
|
|
350 \& ChemDrawPlugIn
|
|
|
351 \& chemaxon.com: MarvinView applet
|
|
|
352 \& mdli.com: Chime plug\-in
|
|
|
353 \& jmol.sourceforge.net: JmolApplet V10
|
|
|
354 \& molinspiration.com: JME applet
|
|
|
355 .Ve
|
|
|
356 .Sp
|
|
|
357 The default viewer, JmolApplet V10, is distributed with MayaChemTools package.
|
|
|
358 Earlier versions of JmolApplet are not supported: due to applet security issues related to
|
|
|
359 reading files, this script uses in-line loading of \s-1MOL\s0 files and this option doesn't exist in
|
|
|
360 earlier version of JmolApplet.
|
|
|
361 .IP "\fB\-\-strviewerconfig\fR \fIcodebase[,archive,code]\fR" 4
|
|
|
362 .IX Item "--strviewerconfig codebase[,archive,code]"
|
|
|
363 Configuration information for structure viewers. This option is only valid for structure
|
|
|
364 viewers which are applets: Jmol, \s-1JME\s0 and MarvinView. For other viewer types available via
|
|
|
365 \&\fB\-\-strviewertype\fR option \- \s-1MDL\s0 Chime, ChemDrawActiveX, ChemDrawPlugIn, and
|
|
|
366 Chem3DActiveX \- this value is ignored.
|
|
|
367 .Sp
|
|
|
368 Input text format: \fIcodebase[,archive,code]\fR. For an applet viewer, \fIcodebase\fR must be
|
|
|
369 specified; \fIarchive\fR and \fIcode\fR values are optional. Here are default \fIarchive\fR and
|
|
|
370 \&\fIcodebase\fR values for various applets: Jmol \- JmolApplet, JmolApplet.jar; \s-1JME\s0 \- \s-1JME\s0, \s-1JME\s0.jar;
|
|
|
371 MarvinView: MView, marvin.jar
|
|
|
372 .Sp
|
|
|
373 For local deployment of \s-1HTML\s0 files, \fIcodebase\fR must correspond to a complete path to
|
|
|
374 the local directory containing appropriate \fIarchive\fR file and the complete path is converted
|
|
|
375 into appropriate relative path during generation of \s-1HTML\s0 files.
|
|
|
376 .Sp
|
|
|
377 By default, \fIcodebase\fR value of <this script dir>/../lib/Jmol is used for \fIJmol\fR applet viewer, and
|
|
|
378 \&\s-1HTML\s0 file(s) are generated for local deployment; however, you can specify any supported
|
|
|
379 applet viewer and generate \s-1HTML\s0 file(s) for deploying on a web server.
|
|
|
380 .Sp
|
|
|
381 For deploying the \s-1HTML\s0 file(s) on a web server, specify a valid \fIcodebase\fR directory name
|
|
|
382 relative to <WWWRootDir>. Example when \s-1JME\s0 archive file, \s-1JME\s0.jar, is available in
|
|
|
383 \&\fI/jme\fR directory on the web server:
|
|
|
384 .Sp
|
|
|
385 .Vb 1
|
|
|
386 \& /jme
|
|
|
387 .Ve
|
|
|
388 .Sp
|
|
|
389 For local deployment of \s-1HTML\s0 file(s), specify a complete \fIcodebase\fR directory name.
|
|
|
390 Example when JmolApplet archive file, JmolApplet.jar, is present in <\s-1JMOLROOT\s0> directory:
|
|
|
391 .Sp
|
|
|
392 .Vb 1
|
|
|
393 \& <JMOLROOT>
|
|
|
394 .Ve
|
|
|
395 .Sp
|
|
|
396 In addition to \fIcodebase\fR, you can also specify \fIarchive\fR file name. Example for web
|
|
|
397 deployment:
|
|
|
398 .Sp
|
|
|
399 .Vb 2
|
|
|
400 \& "/jme,JME.jar"
|
|
|
401 \& "/jme"
|
|
|
402 .Ve
|
|
|
403 .Sp
|
|
|
404 Example for local deployment:
|
|
|
405 .Sp
|
|
|
406 .Vb 2
|
|
|
407 \& "<JMEROOT>,JME.jar"
|
|
|
408 \& "<JMEROOT>"
|
|
|
409 .Ve
|
|
|
410 .ie n .IP "\fB\-\-strviewerparams\fR \fI""name=value [name=value ...]""\fR" 4
|
|
|
411 .el .IP "\fB\-\-strviewerparams\fR \fI``name=value [name=value ...]''\fR" 4
|
|
|
412 .IX Item "--strviewerparams name=value [name=value ...]"
|
|
|
413 Parameters name and value pairs for structure viewers. These name and value pairs
|
|
|
414 are used to control the appearance and behavior of structure viewers in tables and
|
|
|
415 compound \s-1HTML\s0 page during \fIlink\fR value for \fB\-s \-\-structure\fR option.
|
|
|
416 .Sp
|
|
|
417 The parameter names, along with their values, are just passed to each structure viewer
|
|
|
418 in appropriate format without checking their validity. Check documentation of appropriate
|
|
|
419 structure viewers to figure out valid parameter names.
|
|
|
420 .Sp
|
|
|
421 Input text format: \fIname=value name=value ...\fR Example:
|
|
|
422 .Sp
|
|
|
423 .Vb 1
|
|
|
424 \& "width=250 height=170"
|
|
|
425 .Ve
|
|
|
426 .Sp
|
|
|
427 Default for all structure viewers: \fIwidth=250 height=170\fR for displaying structures in
|
|
|
428 tables, and \fIstrlinkwidth=500 strlinkheight=295\fR for compound \s-1HTML\s0 page during \fIlink\fR value
|
|
|
429 for \fB\-s \-\-structure\fR option.
|
|
|
430 .Sp
|
|
|
431 Default background color for all structure viewers: same as \fB\-\-shadecolor\fR value for
|
|
|
432 displaying structures in tables and \fIstrlinkbgcolor=#ffffff\fR for compound \s-1HTML\s0 page;
|
|
|
433 however, explicit specification of background color in this option overrides default value.
|
|
|
434 To use black background for structures in tables and compound \s-1HTML\s0 page, specify \fIbgcolor=#000000\fR
|
|
|
435 and \fIstrlinkbgcolor=#000000\fR respectively. Keep this in mind: Some structure viewers
|
|
|
436 don't appear to support background color parameter.
|
|
|
437 .Sp
|
|
|
438 Additional structure viewer specific default values:
|
|
|
439 .Sp
|
|
|
440 .Vb 12
|
|
|
441 \& Chem3DActiveX: "displaytype=Ball&Stick rotationbars=false
|
|
|
442 \& moviecontroller=false"
|
|
|
443 \& ChemDrawActiveX: "ViewOnly=1 ShrinkToFit=1 ShowToolsWhenVisible=1"
|
|
|
444 \& ChemDrawPlugIn: "type=chemical/x\-mdl\-molfile ViewOnly=1
|
|
|
445 \& ShrinkToFit=1 ShowToolsWhenVisible=1"
|
|
|
446 \& Chime: "display2d=true"
|
|
|
447 \& JME: "options=depict"
|
|
|
448 \& Jmol: "progressbar=true progresscolor=#0000ff boxbgcolor=#000000
|
|
|
449 \& boxfgcolor=#ffffff script="select *; set frank off;
|
|
|
450 \& wireframe on; spacefill off""
|
|
|
451 \& MarvinView: "navmode=zoom"
|
|
|
452 \& ViewerActiveX:"Mouse=4 Convert2Dto3D=0"
|
|
|
453 .Ve
|
|
|
454 .Sp
|
|
|
455 Try overriding default values or specify additional valid parameter/value pairs to get desired
|
|
|
456 results. Example for using \s-1CPK\s0 rendering scheme with Jmol viewer:
|
|
|
457 .Sp
|
|
|
458 .Vb 1
|
|
|
459 \& "script="select *; set frank off; wireframe off; spacefill on""
|
|
|
460 .Ve
|
|
|
461 .IP "\fB\-\-strviewerembed\fR \fIdirect | javascript\fR" 4
|
|
|
462 .IX Item "--strviewerembed direct | javascript"
|
|
|
463 Specify how to embed structure viewers in \s-1HTML\s0 pages. Possible values: \fIdirect\fR \- use applet/object
|
|
|
464 tags to emded structure viewer; \fIjavascript\fR \- use vendor supplied java scripts. Default value:
|
|
|
465 direct.
|
|
|
466 .Sp
|
|
|
467 This option only applies to these vieweres: \fIChem3DActiveX, ChemDrawActiveX, ChemDrawPlugIn,
|
|
|
468 Jmol, and MarvinView\fR.
|
|
|
469 .Sp
|
|
|
470 For marvin.js to work correctly on your browser, you may need to set \fImarvin_jvm=builtin\fR or
|
|
|
471 \&\fImarvin_jvm=plugin\fR using \fB\-\-strviewerparams\fR option. Additionally, MarvinView \- at least
|
|
|
472 in my hands \- also has problems during usage of JavaScript for local deployment; however, it
|
|
|
473 does work via web server.
|
|
|
474 .Sp
|
|
|
475 As far as I can tell, Jmol.js supplied with Jmol10 release has these issues: jmolSetAppletColor
|
|
|
476 doesn't support background color; jmolInitialize disables relative specification of codebase
|
|
|
477 directroy which works okay. So, use Jmol.js supplied with MayaChemTools.
|
|
|
478 .IP "\fB\-\-strviewerjsfile\fR \fIjava script file name\fR" 4
|
|
|
479 .IX Item "--strviewerjsfile java script file name"
|
|
|
480 Name of vendor supplied java script file. Default values: Chem3DActiveX: \fIchem3d.js\fR; ChemDrawActiveX,
|
|
|
481 and ChemDrawPlugIn: \fIchemdraw.js\fR; Jmol: \fIJmol.js\fR, MarvinView: \fImarvin.js\fR.
|
|
|
482 .Sp
|
|
|
483 Directory location for these files is specified via \fIcodebase\fR value of \fB\-\-strviewerconfig\fR option.
|
|
|
484 .ie n .IP "\fB\-\-strtablesize\fR \fI""numrows,numcols""\fR" 4
|
|
|
485 .el .IP "\fB\-\-strtablesize\fR \fI``numrows,numcols''\fR" 4
|
|
|
486 .IX Item "--strtablesize numrows,numcols"
|
|
|
487 This option is only valid for \fIstructuresonly\fR and \fIshadedstructuresonly\fR modes. And it indicates
|
|
|
488 maximum number of rows and columns per structure table. Default value:\fI6,4\fR.
|
|
|
489 .IP "\fB\-\-stylesheet\fR \fIold | new | none\fR" 4
|
|
|
490 .IX Item "--stylesheet old | new | none"
|
|
|
491 Controls usage of stylesheet for newly generated \s-1HTML\s0 file(s). Possible values: \fIold,
|
|
|
492 new, or none\fR. Default value: \fInew\fR.
|
|
|
493 .Sp
|
|
|
494 Stylesheet file contains various properties which control appearance of \s-1HTML\s0 pages:
|
|
|
495 type, size, and color of fonts; background color; and so on.
|
|
|
496 .Sp
|
|
|
497 For \fIold\fR value, an existing stylesheet file specified by \fB\-\-stylesheetname\fR option is
|
|
|
498 used for each \s-1HTML\s0 file; no new stylesheet file is created. This option is quite handy
|
|
|
499 for deploying \s-1HTML\s0 file(s) on a web server: assuming you specify a valid stylesheet
|
|
|
500 file location relative to your WWWRoot, a reference to this stylesheet is added to each
|
|
|
501 \&\s-1HTML\s0 file. For local deployment of \s-1HTML\s0 file(s), a complete path to a local stylesheet
|
|
|
502 is fine as well.
|
|
|
503 .Sp
|
|
|
504 For \fIcreate\fR value, a new stylesheet is created and reference to this local stylesheet
|
|
|
505 is added to each \s-1HTML\s0 file. Use option \fB\-\-stylesheetname\fR to specify name.
|
|
|
506 .Sp
|
|
|
507 For \fInone\fR value, stylesheet usage is completely ignored.
|
|
|
508 .IP "\fB\-\-stylesheetname\fR \fIfilename\fR" 4
|
|
|
509 .IX Item "--stylesheetname filename"
|
|
|
510 Stylesheet file name to be used in conjunction with \fB\-s \-\-stylesheet\fR option. It is only
|
|
|
511 valid for \fIold\fR value of \fB\-s \-\-stylesheet\fR option. Specify a valid stylesheet file location
|
|
|
512 relative to your WWWRoot and a reference to this stylesheet is added to each \s-1HTML\s0
|
|
|
513 file. Example: \fI\*(L"/stylesheets/MyStyleSheet.css\*(R"\fR. Or a complete path name to a local
|
|
|
514 stylesheet file.
|
|
|
515 .Sp
|
|
|
516 For \fIcreate\fR value of \fB\-s \-\-stylesheet\fR option, a new stylesheet file is created using
|
|
|
517 \&\fB\-r \-\-root\fR option. And value of \fB\-\-stylesheetname\fR is simply ignored.
|
|
|
518 .ie n .IP "\fB\-\-shadecolor\fR \fI""#RRGGBB,#RRGGBB""\fR" 4
|
|
|
519 .el .IP "\fB\-\-shadecolor\fR \fI``#RRGGBB,#RRGGBB''\fR" 4
|
|
|
520 .IX Item "--shadecolor #RRGGBB,#RRGGBB"
|
|
|
521 Colors used to fill background of rows during \fIshade\fR and \fIshadedhightlight\fR mode
|
|
|
522 represented as a pair of hexadecimal string; the first and second color values
|
|
|
523 are used for odd and even number rows respectively.
|
|
|
524 .Sp
|
|
|
525 Default value: \fI\*(L"#ffffff,#e0e9eb\*(R"\fR \- it's white and very light blue for odd and even number rows.
|
|
|
526 .IP "\fB\-t, \-\-title\fR \fIstring\fR" 4
|
|
|
527 .IX Item "-t, --title string"
|
|
|
528 Title for \s-1HTML\s0 table(s). Default value: \fISDFileName\fR. This option is ignored for
|
|
|
529 multiple input files. And \fB\-r \-\-root\fR option is used to generate appropriate
|
|
|
530 titles.
|
|
|
531 .IP "\fB\-\-titledisplay\fR \fIyes | no\fR" 4
|
|
|
532 .IX Item "--titledisplay yes | no"
|
|
|
533 Display title for \s-1HTML\s0 table(s). Possible values: \fIyes or no\fR. Default value: \fIyes\fR.
|
|
|
534 .IP "\fB\-w, \-\-workingdir\fR \fIdirname\fR" 4
|
|
|
535 .IX Item "-w, --workingdir dirname"
|
|
|
536 Location of working directory. Default: current directory.
|
|
|
537 .SH "EXAMPLES"
|
|
|
538 .IX Header "EXAMPLES"
|
|
|
539 \&\s-1HTML\s0 table file(s), containing structures, can be used in two different ways: browsing on a
|
|
|
540 local machine or deployment via a web server. By default, \s-1HTML\s0 file(s) are created for viewing
|
|
|
541 on a local machine using Jmol viewer through a browser; however, you can specify any
|
|
|
542 supported applet viewer and generate \s-1HTML\s0 file(s) for deploying on a web server.
|
|
|
543 .PP
|
|
|
544 First two sets of examples show generation of \s-1HTML\s0 file(s) using different applet viewers
|
|
|
545 and a variety of options for local browsing; last set deals with web deployment.
|
|
|
546 .PP
|
|
|
547 \&\fBLocal deployment: Usage of default JMol viewer distributed with MayaChemTools:\fR
|
|
|
548 .PP
|
|
|
549 To generate \s-1HTML\s0 tables with structure display using JMol viewer, rows background filled
|
|
|
550 with white and light blue colors, navigation links on top and botton of each page, type:
|
|
|
551 .PP
|
|
|
552 .Vb 1
|
|
|
553 \& % SDFilesToHTML.pl \-o Sample1.sdf
|
|
|
554 .Ve
|
|
|
555 .PP
|
|
|
556 To generate \s-1HTML\s0 tables with structure display using JMol viewer, rows background filled
|
|
|
557 with white and light blue colors, navigation links on top and botton of each page, and
|
|
|
558 only containing MolWeight and Mol_ID \s-1SD\s0 data fields, type:
|
|
|
559 .PP
|
|
|
560 .Vb 1
|
|
|
561 \& % SDFilesToHTML.pl \-\-datafields "MolWeight,Mol_ID" \-o Sample1.sdf
|
|
|
562 .Ve
|
|
|
563 .PP
|
|
|
564 To generate \s-1HTML\s0 tables with \s-1CPK\s0 structure display using JMol viewer, rows
|
|
|
565 background filled with white and light blue colors, navigation links on top and botton of
|
|
|
566 each page, type:
|
|
|
567 .PP
|
|
|
568 .Vb 2
|
|
|
569 \& % SDFilesToHTML.pl \-\-strviewerparams "script=\e"select *; set frank off;
|
|
|
570 \& wireframe off; spacefill on\e"" \-o Sample1.sdf
|
|
|
571 .Ve
|
|
|
572 .PP
|
|
|
573 To generate \s-1HTML\s0 tables with structure display using JMol viewer and black background, rows
|
|
|
574 background filled with light golden and greyish colors, navigation links on top and botton of
|
|
|
575 each page, 10 rows in each table, greyish header row color, and cell spacing of 1, type:
|
|
|
576 .PP
|
|
|
577 .Vb 3
|
|
|
578 \& % SDFilesToHTML.pl \-o \-n 10 \-\-headeralign "center" \-\-headercolor
|
|
|
579 \& "#a1a1a1" \-\-shadecolor "#fafad2,#d1d1d1" \-\-cellspacing 1
|
|
|
580 \& \-\-strviewerparams "bgcolor=#000000" Sample1.sdf
|
|
|
581 .Ve
|
|
|
582 .PP
|
|
|
583 To highlight molecular weight values using specified highlight criteria and fill in default background
|
|
|
584 colors, type:
|
|
|
585 .PP
|
|
|
586 .Vb 2
|
|
|
587 \& % SDFilesToHTML.pl \-n 10 \-\-highlight "MolWeight,numeric,le,450"
|
|
|
588 \& \-\-highlightstyle background \-m shadedhighlight \-o Sample1.sdf
|
|
|
589 .Ve
|
|
|
590 .PP
|
|
|
591 To highlight molecular weight values using specified highlight criteria, color the text using
|
|
|
592 default colors, and add a footer message in every page, type:
|
|
|
593 .PP
|
|
|
594 .Vb 3
|
|
|
595 \& % SDFilesToHTML.pl \-n 4 \-\-highlight "MolWeight,numeric,le,500"
|
|
|
596 \& \-\-highlightstyle text \-m shadedhighlight \-o
|
|
|
597 \& \-\-footer "Copyright (C) MayaChemTools" \-\-cellspacing 1 Sample1.sdf
|
|
|
598 .Ve
|
|
|
599 .PP
|
|
|
600 To generate tables containing only structures, type:
|
|
|
601 .PP
|
|
|
602 .Vb 2
|
|
|
603 \& % SDFilesToHTML.pl \-d both \-m shadedstructuresonly \-\-strtablesize "6,4"
|
|
|
604 \& \-\-cellspacing 1 \-b 1 \-o Sample1.sdf
|
|
|
605 .Ve
|
|
|
606 .PP
|
|
|
607 To generate tables containing only structures with molecular weight displayed above the
|
|
|
608 structure, type:
|
|
|
609 .PP
|
|
|
610 .Vb 3
|
|
|
611 \& % SDFilesToHTML.pl \-d both \-m shadedstructuresonly \-\-strtablesize "6,4"
|
|
|
612 \& \-\-cmpddatafield "MolWeight,no,top,center" \-\-cellspacing 1 \-b 1
|
|
|
613 \& \-o Sample1.sdf
|
|
|
614 .Ve
|
|
|
615 .PP
|
|
|
616 To generate tables containing links to structures and highlight molecular weight data field values
|
|
|
617 using specified highlight criteria , type:
|
|
|
618 .PP
|
|
|
619 .Vb 4
|
|
|
620 \& % SDFilesToHTML.pl \-n 4 \-\-footer "Copyright (C) MayaChemTools"
|
|
|
621 \& \-\-highlight "MolWeight,numeric,le,450" \-\-highlightstyle background
|
|
|
622 \& \-d both \-m shadedhighlight \-s link \-\-strlinktype button
|
|
|
623 \& \-o Sample1.sdf
|
|
|
624 .Ve
|
|
|
625 .PP
|
|
|
626 \&\fBLocal deployment: Usage of other structure viewers:\fR
|
|
|
627 .PP
|
|
|
628 .Vb 2
|
|
|
629 \& % SDFilesToHTML.pl \-\-strviewertype MarvinView \-\-strviewerconfig
|
|
|
630 \& "<Marvin dir path>" \-o Sample1.sdf
|
|
|
631 \&
|
|
|
632 \& % SDFilesToHTML.pl \-o \-n 10 \-\-headeralign "center" \-\-headercolor
|
|
|
633 \& "#a1a1a1" \-\-shadecolor "#fafad2,#d1d1d1" \-\-cellspacing 1
|
|
|
634 \& \-\-strviewerparams "bgcolor=#000000" \-\-strviewertype Chime
|
|
|
635 \& Sample1.sdf
|
|
|
636 \&
|
|
|
637 \& % SDFilesToHTML.pl \-n 10 \-\-highlight "MolWeight,numeric,le,450"
|
|
|
638 \& \-\-highlightstyle background \-m shadedhighlight \-\-strviewertype
|
|
|
639 \& Chime \-o Sample1.sdf
|
|
|
640 \&
|
|
|
641 \& % SDFilesToHTML.pl \-d both \-m shadedstructuresonly \-\-strtablesize "6,4"
|
|
|
642 \& \-\-cellspacing 1 \-b 1 \-strviewertype JME \-strviewerconfig "<JME dir
|
|
|
643 \& path>" \-o Sample1.sdf
|
|
|
644 .Ve
|
|
|
645 .PP
|
|
|
646 \&\fBWeb deployment: Usage of different structure viewers and options:\fR
|
|
|
647 .PP
|
|
|
648 For deploying \s-1HTML\s0 file(s) on a web server, specify a valid \fIcodebase\fR directory name
|
|
|
649 relative to <WWWRootDir>. In addition to \fIcodebase\fR, you can also specify \fIarchive\fR file
|
|
|
650 name.
|
|
|
651 .PP
|
|
|
652 .Vb 3
|
|
|
653 \& % SDFilesToHTML.pl \-m plain \-s display \-\-strviewertype Jmol
|
|
|
654 \& \-strviewerconfig "/jmol" \-n 5 \-d both \-r PlainTable \-t "Example
|
|
|
655 \& using Jmol: Plain Table" \-o Sample1.sdf
|
|
|
656 \&
|
|
|
657 \& % SDFilesToHTML.pl \-n 5 \-m shade \-s display \-strviewertype JME
|
|
|
658 \& \-strviewerconfig "/jme,JME.jar" \-r ShadeTable \-t "Example using JME:
|
|
|
659 \& Shaded Table" \-o Sample.sdf
|
|
|
660 \&
|
|
|
661 \& % SDFilesToHTML.pl \-n 5 \-\-highlight "MolWeight,numeric,le,450"
|
|
|
662 \& \-\-highlightstyle background \-d both \-m shadedhighlight \-s display
|
|
|
663 \& \-strviewertype MarvinView \-strviewerconfig "/marvin" \-r
|
|
|
664 \& ShadedHightlightTable \-t "Example using MarvinView: Shaded and
|
|
|
665 \& Highlighted Table" \-o Sample.sdf
|
|
|
666 \&
|
|
|
667 \& % SDFilesToHTML.pl \-n 4 \-\-highlight "MolWeight,numeric,le,450" \-s link
|
|
|
668 \& \-\-strlinktype href \-\-strviewertype ChemDrawPlugIn \-\-highlightstyle
|
|
|
669 \& background \-m shadedhighlight \-t "Example using ChemDrawPlugIn:
|
|
|
670 \& Shaded and Highlighted Table" \-r ShadedHightlightTable \-o Sample1.sdf
|
|
|
671 .Ve
|
|
|
672 .SH "AUTHOR"
|
|
|
673 .IX Header "AUTHOR"
|
|
|
674 Manish Sud <msud@san.rr.com>
|
|
|
675 .SH "SEE ALSO"
|
|
|
676 .IX Header "SEE ALSO"
|
|
|
677 FilterSDFiles.pl, InfoSDFiles.pl, SplitSDFiles.pl, MergeTextFilesWithSD.pl
|
|
|
678 .SH "COPYRIGHT"
|
|
|
679 .IX Header "COPYRIGHT"
|
|
|
680 Copyright (C) 2015 Manish Sud. All rights reserved.
|
|
|
681 .PP
|
|
|
682 This file is part of MayaChemTools.
|
|
|
683 .PP
|
|
|
684 MayaChemTools is free software; you can redistribute it and/or modify it under
|
|
|
685 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
|
|
|
686 Software Foundation; either version 3 of the License, or (at your option)
|
|
|
687 any later version.
|
