Difference between revisions of "Transform odb.py"

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from pymol import cmd
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#REDIRECT [[Transform_odb]]
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import pymol
 
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import os
 
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import re
 
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import string
 
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def __init__(self):
 
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cmd.extend('transform_odb', transform_odb)
 
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# Creates a new object name from selection after transforming it with O-style matrix
 
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# found in matrix_file
 
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# Author: Mark Saper <saper@umich.edu>
 
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def transform_odb( name, selection, matrix_file='matrix.odb',  transpose=0):
 
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# open the file for reading
 
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matrix_file = os.path.expanduser(matrix_file)
 
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matrix_file = os.path.expandvars(matrix_file)
 
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theInFile = open ( matrix_file,"r")
 
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# what we'll store the results in
 
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theMatrix = []
 
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# read every line in the file and ...
 
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for theCurrLine in theInFile.readlines():
 
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#print theCurrLine[0]
 
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  if (theCurrLine) and (theCurrLine[0] != '!') and (theCurrLine[0] != '.'):
 
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  # if the line isn't blank, make a list of items seperated by tabs
 
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  theNewRow = string.split (theCurrLine)
 
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  # add it in the matrix
 
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  theMatrix.extend ( theNewRow )
 
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# change matrix to pymol unsupported format
 
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theMatrix = [ theMatrix[0], theMatrix[3], theMatrix[6], theMatrix[9],
 
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  theMatrix[1], theMatrix[4], theMatrix[7], theMatrix[10],
 
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  theMatrix [2], theMatrix [5], theMatrix[8], theMatrix[11],
 
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  0.0, 0.0, 0.0, 0.0 ]
 
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theMatrix = [ float(x) for x in theMatrix]
 
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# close the file
 
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theInFile.close ()
 
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#
 
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r = cmd.create ( name, selection)
 
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r = cmd.transform_object( name, theMatrix, transpose=transpose)
 
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return r
 
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cmd.extend('transform_odb', transform_odb)
 

Latest revision as of 13:01, 3 November 2011

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