File formats/Chemical Structure - Revision history

AngelHerraez: /* JME */

2022-11-22T19:28:55Z

‎JME

AngelHerraez: Changing dead links to archived copies. Expanding and reorganising format description.

2022-11-22T19:17:13Z

Changing dead links to archived copies. Expanding and reorganising format description.

AngelHerraez: JME + JSME

2018-11-16T17:03:05Z

JME + JSME

AngelHerraez: insert template with links

2010-11-29T17:40:34Z

insert template with links

AngelHerraez: add to Category

2010-11-25T21:01:14Z

add to Category

AngelHerraez: SMILES demo applet

2010-09-27T18:17:36Z

SMILES demo applet

AngelHerraez: /* SMILES */

2010-09-25T19:41:59Z

‎SMILES

AngelHerraez: loading JME; combine info from File_formats/Coordinates

2010-09-24T17:38:14Z

loading JME; combine info from File_formats/Coordinates

AngelHerraez: loading SMILES and JME

2010-09-23T20:28:05Z

loading SMILES and JME

AngelHerraez: loading SMILES and JME

2010-09-23T19:29:17Z

loading SMILES and JME

New page

Some formats do not specify the 3D or 2D coordinates of atoms in a molecule, but just the chemical structure, that is a list of atoms and of connections (bonds) between them.

They can be put into text files or be just a text string.

== SMILES ==

== JME ==
This is the native format used by the [http://www.molinspiration.com/jme/ JME Molecular Editor] by Peter Ertl.

Jmol can read this format, both from file or from a text string, and make a flat 2D model out of it; then, using the built-in UFF force field minimization, Jmol generates a 3D model for the molecule, with added hydrogens (the JME format usually does not include hydrogens).

Example, for isopentane:
load inline "5 4 C 7.05 -5.74 C 8.27 -7.84 C 4.63 -7.14 C 5.84 -7.84 C 7.05 -7.14 1 5 1 2 5 1 3 4 1 4 5 1"
or
load isopentane.jme
where {{file|isopentane.jme}} is a plain-text file with this content (a single line):
5 4 C 7.05 -5.74 C 8.27 -7.84 C 4.63 -7.14 C 5.84 -7.84 C 7.05 -7.14 1 5 1 2 5 1 3 4 1 4 5 1

By default, Jmol will produce the 3D optimized model. Using the <code>filter "noMin"</code> parameter avoids that and so you will get the model, with atoms adjusted to 3D in preparation for minimization, but without added hydrogens and without the minimization.

Example, for isopentane:
load isopentane.jme filter "noMin"

@@ Line 48: / Line 48: @@
 == JME ==
-The [https://web.archive.org/web/20181203153343/http://www.molinspiration.com/jme/index.html JME Molecular Editor] (by Peter Ertl) is a Java applet which allows to draw, edit and display molecules and reactions within a web page.
+The '''[https://web.archive.org/web/20181203153343/http://www.molinspiration.com/jme/index.html JME Molecular Editor]''' (or JME Molecule Editor) is a Java applet written by Peter Ertl which allows to draw, edit and display molecules and reactions within a web page.
-Its successor, [https://jsme-editor.github.io/ JSME Molecule Editor], needs no Java and runs in any browser using just JavaScript.
+Its successor, '''[https://jsme-editor.github.io/ JSME Molecule Editor]''', needs no Java and runs in any browser using just JavaScript.
-Among their output formats there
 === JME format (file or text string)===
-This is a proprietary format designed with JME. It is formed by a single line of text, specifying atom identities, coordinates and bonds.
+It is formed by a single line of text, specifying atom identities, coordinates and bonds.
 [https://web.archive.org/web/20181203153343/http://www.molinspiration.com/jme/doc/jme_functions.html JME format]

@@ Line 48: / Line 48: @@
 == JME ==
-The [http://www.molinspiration.com/jme/ JME Molecular Editor] (by Peter Ertl) is a Java applet which allows to draw, edit and display molecules and reactions within a web page.
+The [https://web.archive.org/web/20181203153343/http://www.molinspiration.com/jme/index.html JME Molecular Editor] (by Peter Ertl) is a Java applet which allows to draw, edit and display molecules and reactions within a web page.
-[{{SVN Trunk}}Jmol-datafiles/jme/ Example files].
+Its successor, [https://jsme-editor.github.io/ JSME Molecule Editor], needs no Java and runs in any browser using just JavaScript.
 Jmol can read this format, both from file or from a text string, and make a flat 2D model out of it; then, it adjusts atoms into 3D, adds missing hydrogens and, using the built-in UFF force field minimization, generates a 3D model for the molecule. (The JME format usually does not include hydrogens).
@@ Line 60: / Line 63: @@
 or
   load isopentane.jme
-where {{file|isopentane.jme}} is a plain-text file with this content (a single line):
+where {{file|isopentane.jme}} is a plain-text file with this content (everything in a single line):
 4 C 7.05 -5.74 C 8.27 -7.84 C 4.63 -7.14 C 5.84 -7.84 C 7.05 -7.14 1 5 1 2 5 1 3 4 1 4 5 1
@@ Line 67: / Line 70: @@
 Example, for isopentane:
   load isopentane.jme filter "noMin"
 [[Category:Pages Using Jmol MW Extension]]

@@ Line 48: / Line 48: @@
 == JME ==
-The [http://www.molinspiration.com/jme/ JME Molecular Editor] (by Peter Ertl) is an applet which allows to draw, edit and display molecules and reactions within a web page.
+The [http://www.molinspiration.com/jme/ JME Molecular Editor] (by Peter Ertl) is a Java applet which allows to draw, edit and display molecules and reactions within a web page.
-Among its output formats there is a proprietary [http://www.molinspiration.com/jme/doc/jme_functions.html JME format], formed by a single line of text, specifying atom identities, coordinates and bonds.
+Its successor, JSME, needs no Java and runs in any browser using just JavaScript.
 [{{SVN Trunk}}Jmol-datafiles/jme/ Example files].

← Older revision		Revision as of 17:40, 29 November 2010
Line 1:		Line 1:
		+	{{File_Formats}}
		+	__TOC__
	Some formats do not specify the 3D or 2D coordinates of atoms in a molecule, but just the chemical structure, that is a list of atoms and of connections (bonds) between them.		Some formats do not specify the 3D or 2D coordinates of atoms in a molecule, but just the chemical structure, that is a list of atoms and of connections (bonds) between them.

← Older revision		Revision as of 21:01, 25 November 2010
Line 64:		Line 64:
	Example, for isopentane:		Example, for isopentane:
	load isopentane.jme filter "noMin"		load isopentane.jme filter "noMin"
		+
		+	[[Category:Pages Using Jmol MW Extension]]

@@ Line 15: / Line 15: @@
   load smiles "CCC(C)C"
 (quotes may not be necessary, but are recommended for safety)
 This ability was introduced in Jmol 12.0.RC15, using [http://cheminfo.wikispaces.com/smi23d the web service at Indiana University]. Starting with Jmol 12.0.15 and 12.1.6, [http://cactus.nci.nih.gov/ the NIH Cactus server] is used instead.

@@ Line 16: / Line 16: @@
 (quotes may not be necessary, but are recommended for safety)
-This ability was introduced in Jmol 12.0.RC15, using [http://cheminfo.wikispaces.com/smi23d the web service at Indiana University]. Starting with Jmol 12.1.6, [http://cactus.nci.nih.gov/ the NIH Cactus server] is used instead.
+This ability was introduced in Jmol 12.0.RC15, using [http://cheminfo.wikispaces.com/smi23d the web service at Indiana University]. Starting with Jmol 12.0.15 and 12.1.6, [http://cactus.nci.nih.gov/ the NIH Cactus server] is used instead.
 To force the use of a certain server, you can do:
   smilesUrlFormat = "  "
@@ Line 24: / Line 24: @@
   <nowiki>smilesUrlFormat="http://cheminfov.informatics.indiana.edu/rest/thread/d3.py/SMILES/%FILE";</nowiki>
   <nowiki>smilesUrlFormat="http://cactus.nci.nih.gov/chemical/structure/%FILE/file?format=sdf&get3d=True";</nowiki>
 == JME ==

@@ Line 1: / Line 1: @@
 Some formats do not specify the 3D or 2D coordinates of atoms in a molecule, but just the chemical structure, that is a list of atoms and of connections (bonds) between them.
-They can be put into text files or be just a text string.
+They can be put into text files or be just a text string fed into Jmol (inline loading).
 == SMILES ==
 == JME ==
-This is the native format used by the [http://www.molinspiration.com/jme/ JME Molecular Editor] by Peter Ertl.
+This is the native format used by the [http://www.molinspiration.com/jme/ JME Molecular Editor] by Peter Ertl. It is a  format for 2D drawing, specifying atom identities, coordinates and bonds.
-Jmol can read this format, both from file or from a text string, and make a flat 2D model out of it; then, using the built-in UFF force field minimization, Jmol generates a 3D model for the molecule, with added hydrogens (the JME format usually does not include hydrogens).
+Jmol can read this format, both from file or from a text string, and make a flat 2D model out of it; then, it adjusts atoms into 3D, adds missing hydrogens and, using the built-in UFF force field minimization, generates a 3D model for the molecule. (The JME format usually does not include hydrogens).
 Example, for isopentane: