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Difference between revisions of "Transform odb"
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* matrix_file = file name or path of .odb file containing a transformation matrix data block | * matrix_file = file name or path of .odb file containing a transformation matrix data block | ||
* transpose (default 0] | * transpose (default 0] | ||
| − | |||
===EXAMPLES=== | ===EXAMPLES=== | ||
| Line 15: | Line 14: | ||
===USER COMMENTS=== | ===USER COMMENTS=== | ||
| + | Contact | ||
| + | |||
| + | ===Source=== | ||
| + | from pymol import cmd | ||
| + | import pymol | ||
| + | import os | ||
| + | import re | ||
| + | import string | ||
| + | |||
| + | 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 = string.split (theCurrLine) | ||
| + | # 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) | ||
===SEE ALSO=== | ===SEE ALSO=== | ||
Revision as of 04:17, 2 August 2005
DESCRIPTION
"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 = object to contain transformed coordinates
- selection = atoms to transform
- matrix_file = file name or path of .odb file containing a transformation matrix data block
- transpose (default 0]
EXAMPLES
transform moved_helix, ( mol1 and resi 200:220 ), move_helix.odb
USER COMMENTS
Contact
Source
from pymol import cmd import pymol import os import re import string
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 = string.split (theCurrLine) # 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)
SEE ALSO
transform_selection, transform_object