Transform odb - Revision history

Bell: 17 revisions

2014-03-28T04:07:09Z

17 revisions

Newacct at 08:13, 27 November 2009

2009-11-27T08:13:08Z

New page

'''transform_odb''' transforms the coordinates of a selection and creates a new object with the transformed coordinates. The transformation matrix is read from a specified "O"-style tranformation matrix file (.odb) written by "O" or by any of the Uppsala Software Factory programs (from Gerard Klegweit) such as LSQMAN.

===USAGE===
transform_odb name, (selection), matrix_file [, transpose]

* name = new or modified object that will contain transformed coordinates
* selection = selection of atoms to transform
* matrix_file = file name or path of .odb file containing a transformation matrix data block
* transpose (default 0]

===EXAMPLES===
transform_odb moved_helix, ( mol1 and resi 200:220 ), move_helix.odb

===USER COMMENTS===
Please send questions or bug reports to Mark Saper, mailto:saper@umich.edu

===SOURCE===

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

def __init__(self):
cmd.extend('transform_odb', transform_odb)

# Creates a new object name from selection after transforming it with O-style matrix
# found in matrix_file
# Author: Mark Saper <saper@umich.edu>

def transform_odb( name, selection, matrix_file='matrix.odb', transpose=0):

# open the file for reading
matrix_file = os.path.expanduser(matrix_file)
matrix_file = os.path.expandvars(matrix_file)
theInFile = open ( matrix_file,"r")

# what we'll store the results in
theMatrix = []

# read every line in the file and ...
for theCurrLine in theInFile.readlines():
if (theCurrLine) and (theCurrLine[0] != '!') and (theCurrLine[0] != '.'):
# if the line isn't blank, make a list of items seperated by tabs
theNewRow = theCurrLine.split ()
# add it in the matrix
theMatrix.extend ( theNewRow )

# change matrix to pymol unsupported format

theMatrix = [ theMatrix[0], theMatrix[3], theMatrix[6], theMatrix[9],
theMatrix[1], theMatrix[4], theMatrix[7], theMatrix[10],
theMatrix [2], theMatrix [5], theMatrix[8], theMatrix[11],
0.0, 0.0, 0.0, 0.0 ]
theMatrix = [ float(x) for x in theMatrix]

# close the file
theInFile.close ()

r = cmd.create ( name, selection)
r = cmd.transform_object( name, theMatrix, transpose=transpose)

return r

cmd.extend('transform_odb', transform_odb)
</source>

===SEE ALSO===
[[transform_selection]], [[transform_object]]

[[Category:Script Library|Transform odb]]
[[Category:ThirdParty_Scripts]]

Saper: Fixed error in EXAMPLES

2005-08-19T04:29:17Z

Fixed error in EXAMPLES

Saper: /* USAGE */

2005-08-02T17:52:15Z

USAGE

Saper at 17:49, 2 August 2005

2005-08-02T17:49:40Z

Saper at 17:49, 2 August 2005

2005-08-02T17:49:11Z

Saper at 04:25, 2 August 2005

2005-08-02T04:25:30Z

Saper at 04:21, 2 August 2005

2005-08-02T04:21:54Z

Saper at 04:21, 2 August 2005

2005-08-02T04:21:10Z

Saper: Includes source

2005-08-02T04:20:19Z

Includes source

← Older revision		Revision as of 17:49, 2 August 2005
Line 17:		Line 17:

	===SOURCE===		===SOURCE===
−
−	* Download

	<source lang="python">		<source lang="python">

@@ Line 18: / Line 18: @@
 ===SOURCE===
-* Download [[transform_odb.py]]
+* Download
 <source lang="python">

← Older revision	Revision as of 04:07, 28 March 2014
(No difference)

@@ Line 11: / Line 11: @@
 ===EXAMPLES===
-  transform moved_helix, ( mol1 and resi 200:220 ),  move_helix.odb
+  transform_odb moved_helix, ( mol1 and resi 200:220 ),  move_helix.odb
 ===USER COMMENTS===

@@ Line 5: / Line 5: @@
   transform_odb name, (selection), matrix_file [, transpose]
-* name = object to contain transformed coordinates
+* name = new or modified object that will contain transformed coordinates
-* selection = atoms to transform
+* selection = selection of atoms to transform
 * matrix_file = file name or path of .odb file containing a transformation matrix data block
 * transpose (default 0]

@@ Line 16: / Line 16: @@
 Contact
-===[[SOURCE]]===
+===SOURCE===
 <source lang="python">
 from pymol import cmd

@@ Line 16: / Line 16: @@
 Contact
-===Source===
+===SOURCE===
 from pymol import cmd
 import pymol
@@ Line 65: / Line 66: @@
 cmd.extend('transform_odb', transform_odb)
 ===SEE ALSO===