Transform odb.py: Difference between revisions

From PyMOLWiki
Jump to navigation Jump to search
No edit summary
 
m (duplicated content)
 
(3 intermediate revisions by 2 users not shown)
Line 1: Line 1:
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 12:01, 3 November 2011

Redirect to:

Retrieved from "https://pymolwiki.org/index.php?title=Transform_odb.py&oldid=9521"