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Difference between revisions of "Transform odb.py"

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from pymol import cmd
+
#REDIRECT [[Transform_odb]]
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():
 
 
 
#print theCurrLine[0]
 
  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)
 

Latest revision as of 01:44, 28 March 2014

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