Optimize - Revision history

Cchem: 1 revision

2019-04-29T03:23:32Z

1 revision

2019-04-07T23:46:56Z

2017-06-26T04:31:23Z

1 revision

2017-06-14T08:15:29Z

change license

2015-01-18T05:46:00Z

5 revisions

2014-12-21T01:16:20Z

PyMOL API

2014-12-21T01:15:27Z

Local optimization

2014-12-21T01:13:23Z

Installation

2014-12-21T01:09:55Z

2014-12-20T21:14:40Z

Installation

@@ Line 84: / Line 84: @@
 Noel M. O'Boyle , Michael Banck , Craig A. James , Chris Morley , Tim Vandermeersch and Geoffrey R. Hutchison. "Open Babel: An open chemical toolbox." Journal of Cheminformatics 2011, 3:33. http://www.jcheminf.com/content/3/1/33
 [[Category:Plugins]]
 [[Category:Pymol-script-repo]]

@@ Line 3: / Line 3: @@
 |filename  = plugins/optimize.py
 |author    = [[User:OsvaldoMartin|Osvaldo Martin]]
-|license   = GPL
+|license   = MIT
 }}

@@ Line 41: / Line 41: @@
 === PyMOL API ===
 <source lang="python">
-cmd.minimize(string selection="all", string forcefield="MMFF94s", string method="conjugate gradients", int nsteps=500, float conv=0.0001, bool cutoff=False, float cut_vdw=6.0, float cut_elec=8.0)
+cmd.minimize(string selection="all", string forcefield="MMFF94s", string method="conjugate gradients",
 </source>

@@ Line 20: / Line 20: @@
 == Local optimization ==
 Local optimization can be done using the <code>minimize</code> command.
@@ Line 27: / Line 26: @@
 minimize [selection [, forcefield [, method [, nsteps [, conv [, cutoff [, cut_vdw [, cut_elec]]]]]]]]
 </source>
 * '''selection''': The name of the object to be minimized.  From the command line, the default value is 'all'.  When using the GUI, the default value is the first uploaded object.
@@ Line 36: / Line 37: @@
 * '''cut_vdw''': If cutoff is True, then this parameter sets the distance (in Angstroms) beyond which two atoms do not interact through Van der Waals forces (default = 6.0).
 * '''cut_elec''': If cutoff is True, then this parameter sets the distance (in Angstroms) beyond which two atoms do not interact through electrostatic forces (default = 8.0).
 === PyMOL API ===

@@ Line 14: / Line 14: @@
 ''Optimize'' needs OpenBabel (and OpenBabel Python bindings) to be installed on your computer (see instructions [http://openbabel.org/wiki/Get_Open_Babel here]).
-'''Note to Windows users:''' If you are using a 64-bit Windows, please install OpenBabel 64-bit from [www.lfd.uci.edu/~gohlke/pythonlibs/#openbabel here]
+'''Note to Windows users:''' If you are using a 64-bit Windows, please install OpenBabel 64-bit from [http://www.lfd.uci.edu/~gohlke/pythonlibs/#openbabel here]
 = Usage =

← Older revision	Revision as of 03:23, 29 April 2019
(No difference)

← Older revision	Revision as of 04:31, 26 June 2017
(No difference)

← Older revision	Revision as of 05:46, 18 January 2015
(No difference)

@@ Line 10: / Line 10: @@
 = Installation =
-''Optimize'' was tested only on GNU/Linux but should work on other operating systems. The plugin can be downloaded through the project [[git_intro | Pymol-script-repo]]. ''Optimize'' needs OpenBabel (and OpenBabel Python bindings) to be installed on your computer (see instructions [http://openbabel.org/wiki/Get_Open_Babel here]).
+The plugin can be downloaded through the project [[git_intro | Pymol-script-repo]].
-'''Note to Windows users:''' As far as I know on Windows OpenBabel is 32-bit (not 64 bit version available) and hence you should have installed a 32-bit version of Python and PyMOL.
+''Optimize'' needs OpenBabel (and OpenBabel Python bindings) to be installed on your computer (see instructions [http://openbabel.org/wiki/Get_Open_Babel here]).
 = Usage =