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.
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)
