Transform selection - Revision history

Bell: 1 revision

2015-07-09T20:24:05Z

1 revision

Sbliven: Added description from 1.7.0 docstring

2015-06-01T10:56:31Z

Added description from 1.7.0 docstring

Bell: 5 revisions

2014-03-28T03:36:20Z

5 revisions

Karo at 11:13, 7 September 2010

2010-09-07T11:13:07Z

New page

== Overview ==
'''transform_selection''' applies a transformation matrix to a selection. The matrix should actually be passed in as a single list -- not a list of lists.

=== Details ===
When '''homogenous == 0''': the matrix needed is a 4x4 matrix, where the upper-left 3x3 quadrant is a typical rotation matrix. The 4th row and 4th column specify the pre- and post-translation vectors. So, you can translate+rotate+translate with this one matrix.

== Example ==
=== Basic Syntax ===
<source lang="python">
cmd.transform_selection("a", [x,x,x,x, x,x,x,x, x,x,x,x, x,x,x,x],
homogenous=1)
</source>

=== Real-World Example ===
I wrote a structure alignment program that needs to update the coordinates of the 2nd protein by translating it, rotating it and then translating it on top of the other molecule. It's done as follows:
<source lang="c">
//
// C code
//
// ...after the magic is done, pack all the values into the TTT matrix.
PyObject* pyU = Py_BuildValue( "[f,f,f,f, f,f,f,f, f,f,f,f, f,f,f,f]",
bestU[0][0], bestU[1][0], bestU[2][0], bestCOM1[0],
bestU[0][1], bestU[1][1], bestU[2][1], bestCOM1[1],
bestU[0][2], bestU[1][2], bestU[2][2], bestCOM1[2],
-bestCOM2[0], -bestCOM2[1], -bestCOM2[2], 1.);
</source>
where bestU is the transpose of the best rotation matrix, bestCOM1 is the center of mass (COM) for molecule 1, and bestCOM2 is for two. '''pyU''' becomes '''rotMat'''. The call in Python is then,
<source lang="python">
#
# Python code.
#
cmd.transform_selection( mol2, rotMat, homogenous=0 );
</source>

Were I '''not''' to use bestCOM1 or bestCOM2, each of those entries would be 0. The last element should always be 1.

== See Also ==
[[transform_odb]]

← Older revision	Revision as of 20:24, 9 July 2015
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@@ Line 1: / Line 1: @@
 == Overview ==
 '''transform_selection''' applies a transformation matrix to a selection.  The matrix should actually be passed in as a single list -- not a list of lists.
 === Details ===
-When '''homogenous == 0''': the matrix needed is a 4x4 matrix, where the upper-left 3x3 quadrant is a typical rotation matrix.  The 4th row and 4th column specify the pre- and post-translation vectors.  So, you can translate+rotate+translate with this one matrix.
 == Example ==
 === Real-World Example ===
@@ Line 25: / Line 49: @@
                            -bestCOM2[0], -bestCOM2[1], -bestCOM2[2], 1.);
 </source>
-where bestU is the transpose of the best rotation matrix, bestCOM1 is the center of mass (COM) for molecule 1, and bestCOM2 is for two.  '''pyU''' becomes '''rotMat'''.  The call in Python is then,
+where bestU is the transpose of the best rotation matrix, bestCOM1 is the center of mass (COM) for molecule 1, and bestCOM2 is for molecule two.  '''pyU''' becomes '''rotMat'''.  The call in Python is then,
 <source lang="python">
+#

← Older revision	Revision as of 03:36, 28 March 2014
(No difference)