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Cchem: 1 revision

2018-07-25T05:40:11Z

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Speleo3: Python 3

2018-06-29T06:03:21Z

Python 3

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2015-08-14T17:32:00Z

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2015-08-05T19:10:50Z

rework page

Pyadmin: 8 revisions

2014-03-28T02:00:39Z

8 revisions

TakanoriNakane: auto_arg

2012-08-21T14:45:17Z

auto_arg

Baker1 at 16:05, 25 August 2010

2010-08-25T16:05:23Z

New page

[[Extend]] is an API-only function which binds a new external function as a command into the PyMOL scripting language. In other words, when you write a function and want PyMOL to recognize the new command, you '''extend''' the command into PyMOL. Once extended, the function name is recognized like other function names (example below). Typically, '''extend''' is the last line of a PyMOL script.

===PYMOL API===
<source lang="python">
cmd.extend(string name,function function)
</source>

===PYTHON EXAMPLE===
<source lang="python">
def foo(moo=2): print moo
cmd.extend('foo',foo)
</source>

The following would now work within PyMOL:
<source lang="python">
PyMOL>foo
2
PyMOL>foo 3
3
PyMOL>foo moo=5
5
PyMOL>foo ?

Usage: foo [ moo ]
</source>

===NOTES===
For security reasons, new PyMOL commands created using "extend" are not saved or restored in sessions.

===SEE ALSO===
*[[Alias]]
*[[Api]]
*[[Category:Scripting]]

[[Category:Commands|Extend]]

<hr>
=== "extend" used in selections ===
"extend" can also be used in selection statements to grow a selection based on covalent bonds. This behavior is illustrated on residue 64 of PDB file 1KAO where we initially select one atom and then "extend" that selection by one and three covalent bonds.

<table border="1">
<tr>
<td>[[Image:Extend0.png|250px]]</td>
<td>[[Image:Extend1.png|250px]]</td>
<td>[[Image:Extend3.png|250px]]</td>
</tr>
<tr>
<td>select (resi 64 and n. cz)</td>
<td>select (resi 64 and n. cz) extend 1</td>
<td>select (resi 64 and n. cz) extend 3</td>
</tr>
</table>
<hr>

Vinnyrose at 13:47, 20 June 2009

2009-06-20T13:47:48Z

New page

===DESCRIPTION===
[[Extend]] is an API-only function which binds a new external function as a command into the PyMOL scripting language. In other words, when you write a function and want PyMOL to recognize the new command, you '''extend''' the command into PyMOL. Once extended, the function name is recognized like other function names (example below). Typically, '''extend''' is the last line of a PyMOL script.

===PYMOL API===
<source lang="python">
cmd.extend(string name,function function)
</source>

===PYTHON EXAMPLE===
<source lang="python">
def foo(moo=2): print moo
cmd.extend('foo',foo)
</source>

The following would now work within PyMOL:
<source lang="python">
PyMOL>foo
2
PyMOL>foo 3
3
PyMOL>foo moo=5
5
PyMOL>foo ?

Usage: foo [ moo ]
</source>

===NOTES===
For security reasons, new PyMOL commands created using "extend" are not saved or restored in sessions.

===SEE ALSO===
*[[Alias]]
*[[Api]]
*[[Category:Scripting]]

[[Category:Commands|Extend]]

Cmoad at 17:07, 17 February 2005

2005-02-17T17:07:32Z

New page

===DESCRIPTION===
"extend" is an API-only function which binds a new external
function as a command into the PyMOL scripting language.

===PYMOL API===
cmd.extend(string name,function function)

===PYTHON EXAMPLE===
def foo(moo=2): print moo
cmd.extend('foo',foo)

The following would now work within PyMOL:
PyMOL>foo
2
PyMOL>foo 3
3
PyMOL>foo moo=5
5
PyMOL>foo ?

Usage: foo [ moo ]

===NOTES===
For security reasons, new PyMOL commands created using "extend" are
not saved or restored in sessions.

===SEE ALSO===
[[Cmd alias|alias]], [[Cmd api|api]]

[[Category:Commands|extend]]

@@ Line 31: / Line 31: @@
 def foo(moo=2):
-     print moo
+     print(moo)
 cmd.extend('foo', foo)
@@ Line 43: / Line 43: @@
 @cmd.extend
 def foo(moo=2):
-     print moo
+     print(moo)
 </source>
@@ Line 84: / Line 84: @@
      if not quiet:
          if n == 0:
-             print " No atoms in selection"
+             print(" No atoms in selection")
          else:
-             print " Updated VDW radii of %d atoms by factor %.2f" % (n, factor)
+             print(" Updated VDW radii of %d atoms by factor %.2f" % (n, factor))
 </source>

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@@ Line 1: / Line 1: @@
-[[Extend]] is an API-only function which binds a new external function as a command into the PyMOL scripting language.  In other words, when you write a function and want PyMOL to recognize the new command, you '''extend''' the command into PyMOL. Once extended, the function name is recognized like other function names (example below).  Typically, '''extend''' is the last line of a PyMOL script.
+<div style="padding: 5px 0 5px 20px; font-style: italic">
 <source lang="python">
-cmd.extend(string name,function function)
+pymol.cmd.extend(function function)
 </source>
-===PYTHON EXAMPLE===
+== Simple Example ==
 <source lang="python">
-def foo(moo=2): print moo
+from pymol import cmd
 cmd.extend('foo',foo)
 </source>
-The following would now work within PyMOL:
+Or with decorator syntax (since PyMOL 1.6):
 <source lang="python">
 PyMOL>foo
@@ Line 21: / Line 56: @@
 PyMOL>foo ?
 Usage: foo [ moo ]
 </source>
-===NOTES===
+== Advanced Example ==
-For security reasons, new PyMOL commands created using "extend" are not saved or restored in sessions.
-You may want to set [[auto_arg]] to enable auto-completion for your command's arguments.
+    The "adjust_vdw" command alters all vdw radii in the given selection
-===SEE ALSO===
+    n = _self.alter(selection, "vdw = vdw * %f" % (factor))
-*[[Alias]]
-*[[Api]]
+    if n > 0:
-*[[auto_arg]]
+      _self.rebuild()
-[[Category:Scripting]]
+* So far reasonable, provide default values for arguments (like '''selection="all"''').
-[[Category:Commands|Extend]]
+* Provide a [https://en.wikipedia.org/wiki/Docstring#Python docstring] in the same format like all other PyMOL core commands (with DESCRIPTION, USAGE, etc.), that will make calling "[[help]] yourcommand" a familiar experience for a user.
-<hr>
+*[[alias]]
-=== "extend" used in selections ===
+*[[Set_Key|set_key]]
-"extend" can also be used in selection statements to grow a selection based on covalent bonds.  This behavior is illustrated on residue 64 of PDB file 1KAO where we initially select one atom and then "extend" that selection by one and three covalent bonds.
+*[[api]]
-<table border="1">
+[[Category:Scripting]]

← Older revision	Revision as of 02:00, 28 March 2014
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