Get Coordinates I - Revision history

Bell: 6 revisions

2016-01-03T07:02:33Z

6 revisions

Speleo3: updated

2015-12-29T01:40:30Z

updated

Pyadmin: 1 revision

2014-03-28T02:16:25Z

1 revision

Speleo3 at 12:29, 2 April 2012

2012-04-02T12:29:29Z

Speleo3: alternatives

2011-04-10T16:28:31Z

alternatives

New page

<source lang="python">
# This script gets a copy of the coordinates in Python,
# rotates the object about the Z axis, and then
# updates the coordinates in the original object.

from pymol import cmd

model = cmd.get_model("pept")
for a in model.atom:
a.coord=[ -a.coord[1], a.coord[0], a.coord[2]]

cmd.load_model(model,"tmp")
cmd.update("pept","tmp")
cmd.delete("tmp")
</source>

The same result can be achieved also like this:

<source lang="python">
alter_state 1, pept, (x,y,z) = (-y,x,z)
</source>

or like this:

<source lang="python">
rotate z, 90, pept, camera=0, origin=[0,0,0]
</source>

[[Category:Script_Library|Get Coordinates I]]
[[Category:ObjSel_Scripts]]

Warren at 00:36, 4 March 2005

2005-03-04T00:36:49Z

Krother at 15:15, 23 February 2005

2005-02-23T15:15:20Z

New page

<source lang="python">
from pymol import cmd

model = cmd.get_model("pept")
for a in model.atom:
a.coord=[ -a.coord[1], a.coord[0], a.coord[2]]

cmd.load_model(model,"tmp")
cmd.update("pept","tmp")
cmd.delete("tmp")
</source>

[[Category:Scripting_Script_Library|Get Coordinates I]]

@@ Line 1: / Line 1: @@
 There are several ways to extract or load atomic coordinates in PyMOL using the python API.
 == Extract coordinates using [[Get_Model|get_model]] ==
-This is the fastest method to extract coordinates. It considers the object rotation matrix.
+Before 1.7.4, this was the fastest method to extract coordinates. It considers the object rotation matrix.
 <source lang="python">
@@ Line 42: / Line 58: @@
 </source>
-== Load coordinates using load_coords ==
+== Load coordinates using [[load_coords]] ==
-This method is experimental and buggy, but it's the fastest method to load coordinates. There is a count mistake in the state argument (must use state+1). The xyz argument '''must''' be a list of lists (no tuples). It only works for complete objects, not atom selections.
+''New in PyMOL 1.7.4''. The [[get_coordset]] function can also return a memory view instead of a copy. This allows modifying the coordinates in place.
 <source lang="python">
-import pymol.experimenting
+xyz = cmd.get_coordset(objectname, 1, copy=0)
-pymol.experimenting.loadable = cmd.loadable
+xyz[:] = newxyz
 </source>
 [[Category:Script_Library|Get Coordinates I]]
 [[Category:ObjSel_Scripts]]

← Older revision	Revision as of 07:02, 3 January 2016
(No difference)

← Older revision	Revision as of 02:16, 28 March 2014
(No difference)

@@ Line 1: / Line 1: @@
 <source lang="python">
-# This script gets a copy of the coordinates in Python,
+xyz = cmd.get_model('sele', 1).get_coord_list()
-# rotates the object about the Z axis, and then
+</source>
-# updates the coordinates in the original object.
-from pymol import cmd
+<source lang="python">
-model = cmd.get_model("pept")
+== Load coordinates using [[Alter_State|alter_state]] ==
-for a in model.atom:
-   a.coord=[ -a.coord[1], a.coord[0], a.coord[2]]
+This is the most convenient way to load coordinates and works equivalent to '''iterate_state'''.
-cmd.load_model(model,"tmp")
+<source lang="python">
-cmd.update("pept","tmp")
+xyz = [...] # some Nx3 list with coordinates
-cmd.delete("tmp")
+xyz_iter = iter(xyz)
 </source>
-The same result can be achieved also like this:
+== Load coordinates using [[update]] ==
 <source lang="python">
-alter_state 1, pept, (x,y,z) = (-y,x,z)
+model = cmd.get_model('pept')
 </source>
-or like this:
+== Load coordinates using load_coords ==
 <source lang="python">
-rotate z, 90, pept, camera=0, origin=[0,0,0]
+import pymol.experimenting
 </source>
 [[Category:Script_Library|Get Coordinates I]]
 [[Category:ObjSel_Scripts]]

← Older revision		Revision as of 00:36, 4 March 2005
Line 1:		Line 1:
	<source lang="python">		<source lang="python">
		+	# This script gets a copy of the coordinates in Python,
		+	# rotates the object about the Z axis, and then
		+	# updates the coordinates in the original object.
		+
	from pymol import cmd		from pymol import cmd