Annotation of loncom/html/adm/jmol/README.txt, revision 1.3
1.2 albertel 1: ==============================================================================
2: === Jmol ===
3: ==============================================================================
1.3 ! raeburn 4: Jmol: an open-source Java viewer for chemical structures in 3D,
! 5: with features for chemicals, crystals, materials and biomolecules.
! 6: ==============================================================================
1.2 albertel 7:
8: Jmol is an open-source molecule viewer and editor written in Java.
9:
10: Full information is available at http://www.jmol.org/
11:
12: Usage questions and comments should be posted to jmol-users@lists.sourceforge.net
13:
14: Development questions, suggestions and comments should be posted
15: to jmol-developers@lists.sf.net
16:
17:
18: List of files included:
19: -------------------
20:
21:
1.3 ! raeburn 22: 1 == Files with information ==
! 23:
! 24: 1.1 === README.txt ===
! 25: This file.
! 26:
! 27: 1.2 === LEAME.txt ===
! 28: The Spanish version of README.txt
! 29:
! 30: 1.3 === COPYRIGHT.txt ===
! 31: The copyright explanations regarding Jmol and its 3rd-party components.
! 32:
! 33: 1.4 === LICENSE.txt ===
! 34: The GNU Lesser General Public License, under which Jmol is released.
! 35:
! 36: 1.5 === CHANGES.txt ===
! 37: A list with a history of the feature additions in each version of Jmol.
! 38:
! 39: 1.6 === README-CHEMDOODLE.txt ===
! 40: Instructions about using the ChemDoodle plug-in together with Jmol applets,
! 41: and about the license for ChemDoodle (which is different from the Jmol license).
! 42:
! 43:
! 44: 2 == Batch and shell files ==
! 45: These can be used to start Jmol application from a command line and,
! 46: particularly, to impose a certain combination of parameters
! 47: (see http://wiki.jmol.org/index.php/Jmol_Application#Command_line_options).
! 48:
! 49: 2.1 === jmol ===
! 50: ???? (Some kind of batch file)
! 51:
! 52: 2.2 === jmol.bat ===
! 53: A batch file to start Jmol application under Windows.
! 54:
! 55: 2.3 === jmol.mac ===
! 56: ??? (Some kind of batch file, for the MacOS)
! 57:
! 58: 2.4 === jmol.sh ===
! 59: A shell script to start Jmol application under Unix-like systems, like Linux,
! 60: BSD, Solaris and Cygwin for Windows.
! 61:
! 62:
! 63: 3 == Files of Jmol application ==
! 64: This is used as a standalone program.
! 65:
! 66: 3.1 === Jmol.jar ===
! 67: The application executable file (a program written in Java). This works as any
! 68: other program: opens in its own window, can be resized or minimized, admits
! 69: drag-and-drop of files over it, has a top menu bar, can open and save files,
! 70: etc. It can be open from the command line (particulary, using the shell or batch
! 71: files described above), but if Java is properly configured in your system, it's
! 72: usually enough to double-click on the file
! 73: (see http://wiki.jmol.org/index.php/Jmol_Application#Starting_Jmol_Application
! 74: for more details).
! 75:
! 76: 3.2 === JmolData.jar ===
! 77: This is a slimmed down version of Jmol.jar that lacks all visualization
! 78: capabilities. So, it betrays the whole (classic) concept of what Jmol is, but
! 79: with JmolData and some clever scripting you can get just about any information
! 80: you want out of a model and output it any way you want.
! 81:
! 82: It operates only from the command line, designed for extracting data from a
! 83: model or set of models. You are limited to commands that don't have to do with
! 84: visualization: there are bonds but no "sticks", atoms but no "dots", helices but
! 85: no "cartoons".
! 86:
! 87:
! 88: 4 == Files of Jmol applet ==
! 89: These are used inside web pages, and include:
! 90: Applet files | Core Javascript libraries | Optional Javascript libraries
! 91:
! 92: 4.1 === Applet files ===
! 93:
! 94: 4.1.1 ==== JmolApplet0.jar, JmolApplet0(severalSuffixes).jar ====
! 95: The applet, i.e. a version of the program that will only run when embedded in
! 96: a web page.
! 97:
! 98: The applet is divided up into several pieces according to their function, so
! 99: that if a page does not require a component, that component is not downloaded
! 100: from the server.
! 101: It is still recommended that you put all JmolApplet0*.jar files on your server
! 102: even if your page does not use the capabilities provided by some of the files,
! 103: because the pop-up menu and Jmol console both allow users to access parts of
! 104: Jmol you might not have considered.
! 105:
! 106: This split version is the one that will be used by default if you use Jmol.js
! 107: (which is the recommended method).
! 108: For that, use the simplest form of jmolInitialize(), just indicating the
! 109: directory or folder containing the set of jar files:
! 110: jmolInitialize("directory-containing-jar-files")
! 111: for example,
! 112: jmolInitialize(".")
! 113: (if jar files are in the same folder as the web page)
! 114: jmolInitialize("../jmol")
! 115: (if jar files are in a parallel folder, named 'jmol')
! 116:
! 117: 4.1.2 ==== JmolAppletSigned0.jar, JmolAppletSigned0(severalSuffixes).jar ====
! 118: An equivalent version of the applet, but this is a "signed" applet (a term in
! 119: Java security language). This means it must be authorized by the web
! 120: page visitor for it to run, but then it will have less security restrictions for
! 121: file access. For example, it can access files on any part of the user's hard
! 122: disk or from any other web server.
! 123:
! 124: Typically users get a message asking if they want to accept the "certificate" or
! 125: if they "trust" the applet (''see notes below''). JmolAppletSigned.jar should
! 126: be used with this in mind. Other than reading files, Jmol does not currently
! 127: use other capabilities of signed applets, such as accessing the system
! 128: clipboard or writing files. Use only if you know what you are doing and have
! 129: considered the security issues.
! 130:
! 131: To use this with Jmol.js, use the form:
! 132: jmolInitialize("directory-containing-jar-files", true)
! 133: or
! 134: jmolInitialize("directory-containing-jar-files", "JmolAppletSigned0.jar")
! 135:
! 136: Notes:
! 137: * The security feature requesting to trust the applet may not always be enabled
! 138: on users' systems.
! 139: * The message requesting permission will be displayed for each of the 14 (or
! 140: more) loadable files.
! 141: * The user may have the option to trust the applet permanently and so avoid
! 142: having to give permission every time (s)he visits a page that uses Jmol.
! 143:
! 144: 4.1.3 ==== JmolApplet.jar ====
! 145: This is an all-in-one or monolithic file, kept mainly for compatibility with old
! 146: pages that call it explicitly.
! 147: This single file is equivalent to the whole set of JmolApplet0*.jar files,
! 148: explained above.
! 149: The recommended procedure is not to use this monolithic file, but the split
! 150: version (JmolApplet0.jar etc.). In particular, Jmol.js uses the split version
! 151: by default.
! 152:
! 153: You may wish to use this if you want to keep your website simple or you just
! 154: want to upload a single jar file whenever new versions are released.
! 155: However, this will load Jmol slower than the split versions (described above),
! 156: as all the modules (adding up to 2.4 MB), needed or not, must get loaded onto a
! 157: user's machine before any structure is displayed.
! 158:
! 159: To invoke JmolApplet.jar from Jmol.js, either:
! 160:
! 161: a) put it in the directory containing the HTML page requiring it and do not use
! 162: jmolInitialize(),
! 163:
! 164: or
! 165:
! 166: b) identify it explicitly in jmolInitialize(), for example:
! 167: jmolInitialize("directory-containing-jar-files", "JmolApplet.jar")
! 168:
! 169: 4.1.4 ==== JmolAppletSigned.jar ====
! 170: An equivalent version of the monolithic applet, but this is a "signed" applet
! 171: (a term in Java security language). This means it must be authorized by the web
! 172: page visitor for it to run, but then it will have less security restrictions for
! 173: file access. For example, it can access files on any part of the user's hard
! 174: disk or from any other web server.
! 175:
! 176: Typically users get a message asking if they want to accept the "certificate" or
! 177: if they "trust" the applet, but this security feature is not always enabled.
! 178: JmolAppletSigned.jar should be used with this in mind. Other than reading files,
! 179: Jmol does not currently utilize other capabilities of signed applets, such as
! 180: accessing the System clipboard or writing files. Use only if you know what you
! 181: are doing and have considered the security issues.
! 182:
! 183: To invoke JmolAppletSigned.jar from Jmol.js, use:
! 184: jmolInitialize("directory-containing-jar-files", "JmolAppletSigned.jar")
! 185:
! 186: 4.1.5 ==== Notes ====
! 187: # Given the descriptions, you will realize that the distribution package
! 188: contains 4 full copies of the applet (signed or unsigned, split or not).
1.2 albertel 189:
190:
1.3 ! raeburn 191: 4.2 === Core Javascript libraries ===
! 192:
! 193: 4.2.1 ==== Jmol.js ====
! 194: The classic library, written in JavaScript language, that assists in the
! 195: programming of web pages that use Jmol applet, without the need to know and
! 196: write detailed JmolApplet code.
! 197:
! 198: This library uses by default the split version of the applet (unsigned or
! 199: signed).
! 200:
! 201: Fully documented at http://jmol.org/jslibrary/
! 202:
! 203: Jmol.js is phased out in Jmol v13, in favour of the object-oriented method
! 204: and set of .js files (described next).
! 205:
! 206: 4.2.2 ==== JmolApplet.js ====
! 207: Creates the object for a Jmol applet.
! 208:
! 209: 4.2.3 ==== JmolCore.js ====
! 210: Contains functions that make the Jmol applets work but are not to be used by
! 211: the webpage author (private functions).
! 212:
! 213: 4.2.4 ==== JmolControls.js ====
! 214: Support for user-interface controls like buttons, links, checkboxes, etc.
! 215:
! 216: 4.2.5 ==== JmolApi.js ====
! 217: Contains the Application Programming Interface, that is, functions that may be
! 218: used by the webpage author to interface with the Jmol applets.
! 219:
! 220:
! 221: 4.3 === Optional Javascript libraries ===
! 222:
! 223: 4.3.1 ==== JmolCD.js ====
! 224: The ChemDoodle extension: provides the means for using ChemDoodle Web Components
! 225: (that uses JavaScript + HTML5 canvas or WebGL) instead of the
! 226: Jmol applets, for systems where Java is not available.
! 227:
! 228: 4.3.2 ==== JmolGLmol.js ====
! 229: The GLmol extension: provides the means for using GLmol (that uses WebGL +
! 230: JavaScript) instead of the Jmol applets, for systems where Java is not available.
! 231:
! 232: 4.3.3 ==== JmolJME.js ====
! 233: Provides the means for adding a JME applet in the webpage (drawing of 2D chemical
! 234: formulas) and communicate with Jmol applets.
! 235:
! 236: 4.3.4 ==== JmolJSV.js ====
! 237: Provides the means for adding a JSpecView applet (viewer for spectral data) in
! 238: the webpage and communicate with Jmol applets.
! 239:
! 240:
! 241: 5 == Accessory apps and applets ==
! 242:
! 243: 5.1 === ChimeToJmol.jar ===
! 244: Undocumented and experimental.
! 245: An application to convert Chime-using html pages into pages with JmolApplets.
! 246:
! 247: 5.2 === JSpecViewApplet, JSpecViewAppletSigned ===
! 248: Unsigned and signed versions of the JSpecView applet, a viewer for spectral data
! 249: that may be intercommunicated with Jmol applets.
! 250: (See supporting .js file above)
! 251:
! 252: 5.3 === JmolSmilesApplet.jar ===
! 253: This is currently not included in the distribution, but may be obtained from the
! 254: development site.
! 255:
! 256: This is a lightweight applet, with no visible interface, that allows to check
! 257: SMILES strings. This is particularly useful for comparison of stereochemistry,
! 258: for example from structures drawn using the JME applet.
! 259:
! 260: The same functionality is included in the regular JmolApplet.
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