Transform odb.py - Revision history

Pyadmin: 5 revisions

2014-03-28T01:44:37Z

5 revisions

Speleo3: duplicated content

2011-11-03T17:01:30Z

duplicated content

Newacct at 08:16, 27 November 2009

2009-11-27T08:16:53Z

New page

<source lang="python">
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():

#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 = 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)
</source>
[[Category:Script_Library|Transform_ODB]]
[[Category:Math_Scripts]]
[[Category:ThirdParty_Scripts]]

Saper at 04:22, 2 August 2005

2005-08-02T04:22:42Z

New page

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():

#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)

← Older revision		Revision as of 17:01, 3 November 2011
Line 1:		Line 1:
−	~~<source lang="python">~~	+	#REDIRECT [[Transform_odb]]
−	~~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():~~
−
−	~~#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 = 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)~~
−	~~</source>~~
−	~~[[Category:Script_Library\|Transform_ODB]]~~
−	~~[[Category:Math_Scripts]]~~
−	[[~~Category:ThirdParty_Scripts~~]]

← Older revision	Revision as of 01:44, 28 March 2014
(No difference)