def test_matrix_copy(self):
cmd.fragment('ala')
cmd.fragment('gly')
cmd.rotate('x', 90, 'none', object='ala')
cmd.matrix_copy('ala', 'gly')
self.assertArrayEqual(cmd.get_object_matrix('gly'),
(1.0, 0.0, 0.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0,
1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0), 1e-4)
cmd.matrix_reset('gly', mode=1)
self.assertArrayEqual(cmd.get_object_matrix('gly'),
(1.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0,
0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 1.0), 1e-4)
def test_matrix_copy(self):
cmd.fragment('ala')
cmd.fragment('gly')
cmd.rotate('x', 90, 'none', object='ala')
cmd.matrix_copy('ala', 'gly')
self.assertArrayEqual(cmd.get_object_matrix('gly'),
(1.0, 0.0, 0.0, 0.0,
0.0, 0.0,-1.0, 0.0,
0.0, 1.0, 0.0, 0.0,
0.0, 0.0, 0.0, 1.0), 1e-4)
cmd.matrix_reset('gly', mode=1)
self.assertArrayEqual(cmd.get_object_matrix('gly'),
(1.0, 0.0, 0.0, 0.0,
0.0, 1.0, 0.0, 0.0,
0.0, 0.0, 1.0, 0.0,
0.0, 0.0, 0.0, 1.0), 1e-4)
def ColorByDisplacementAll(objSel1, objSel2, super1='all', super2='all', doColor="True", doAlign="True", AlignedWhite='yes'):
# First create backup copies; names starting with __ (underscores) are normally hidden by PyMOL
tObj1, tObj2, aln = "__tempObj1", "__tempObj2", "__aln"
if strTrue(doAlign):
# Create temp objects
cmd.create(tObj1, objSel1)
cmd.create(tObj2, objSel2)
# Align and make create an object aln which indicates which atoms were paired between the two structures
# Super is must faster than align http://www.pymolwiki.org/index.php/Super
cmd.super(tObj1 + ' and ' + str(super1), tObj2 + ' and ' + str(super2), object=aln)
# Modify the original matrix of object1 from the alignment
cmd.matrix_copy(tObj1, objSel1)
else:
# Create temp objects
cmd.create(tObj1, objSel1)
cmd.create(tObj2, objSel2)
# Align and make create an object aln which indicates which atoms were paired between the two structures
# Super is must faster than align http://www.pymolwiki.org/index.php/Super
cmd.super(tObj1 + ' and ' + str(super1), tObj2 + ' and ' + str(super2), object=aln)
# Modify the B-factor columns of the original objects,
# in order to identify the residues NOT used for alignment, later on
cmd.alter(objSel1 + " or " + objSel2, "b=-0.2")
cmd.alter(tObj1 + " or " + tObj2, "chain='A'")
cmd.alter(tObj1 + " or " + tObj2, "segi='A'")
# Update pymol internal representations; one of these should do the trick
cmd.refresh()
cmd.rebuild()
cmd.sort(tObj1)
cmd.sort(tObj2)
# Create lists for storage
stored.alnAres, stored.alnBres = [], []
# Iterate over objects and get resi
if AlignedWhite == 'yes':
cmd.iterate(tObj1 + " and not " + aln, "stored.alnAres.append((resi, name))")
cmd.iterate(tObj2 + " and not " + aln, "stored.alnBres.append((resi, name))")
else:
cmd.iterate(tObj1, "stored.alnAres.append((resi, name))")
cmd.iterate(tObj2, "stored.alnBres.append((resi, name))")
# Change the B-factors for EACH object
displacementUpdateBAll(tObj1, stored.alnAres, tObj2, stored.alnBres)
# Store the NEW B-factors
stored.alnAnb, stored.alnBnb = [], []
# Iterate over objects and get b
if AlignedWhite == 'yes':
# Iterate over objects which is not aligned
cmd.iterate(tObj1 + " and not " + aln, "stored.alnAnb.append(b)")
cmd.iterate(tObj2 + " and not " + aln, "stored.alnBnb.append(b)")
else:
# Or Iterate over all objects with CA
cmd.iterate(tObj1, "stored.alnAnb.append(b)")
cmd.iterate(tObj2, "stored.alnBnb.append(b)")
# Get rid of all intermediate objects and clean up
cmd.delete(tObj1)
cmd.delete(tObj2)
cmd.delete(aln)
# Assign the just stored NEW B-factors to the original objects
print "Sooon ready. 1 more minute"
for x in range(len(stored.alnAres)):
cmd.alter(objSel1 + " and resi " + str(stored.alnAres[x][0]) + " and name " + str(stored.alnAres[x][1]), "b = " + str(stored.alnAnb[x]))
for x in range(len(stored.alnBres)):
cmd.alter(objSel2 + " and resi " + str(stored.alnBres[x][0]) + " and name " + str(stored.alnBres[x][1]), "b = " + str(stored.alnBnb[x]))
cmd.rebuild()
cmd.refresh()
cmd.sort(objSel1)
cmd.sort(objSel2)
# Provide some useful information
stored.allRMSDval = []
stored.allRMSDval = stored.alnAnb + stored.alnBnb
print "\nColorByDisplacementAll completed successfully."
print "The MAXIMUM Displacement is: " + str(max(stored.allRMSDval)) + " residue " + str(stored.alnAres[int(stored.allRMSDval.index(max(stored.allRMSDval)))])
if strTrue(doColor):
# Showcase what we did
# cmd.orient()
# cmd.hide("all")
cmd.show("sticks", objSel1 + " or " + objSel2)
# Select the residues not used for alignment; they still have their B-factors as "-0.2"
cmd.select("notUsedForAln", "b = -0.2")
# White-wash the residues not used for alignment
cmd.color("white", "notUsedForAln")
# Select the residues not in both pdb files; they have their B-factors as "-0.01"
cmd.select("ResNotInBothPDB", "b = -0.01")
# White-wash the residues not used for alignment
cmd.color("black", "ResNotInBothPDB")
# Color the residues used for alignment according to their B-factors (Displacement values)
#cmd.spectrum("b", 'rainbow', "((" + objSel1 + ") or (" + objSel2 +" )) and not notUsedForAln+ResNotInBothPDB")
cmd.spectrum("b", 'rainbow', "((" + objSel1 + ") or (" + objSel2 + " )) and not (notUsedForAln or ResNotInBothPDB)")
# Delete the selection of atoms not used for alignment
# If you would like to keep this selection intact,
# just comment "cmd.delete" line and
# uncomment the "cmd.disable" line abowe.
cmd.disable("notUsedForAln")
cmd.delete("notUsedForAln")
cmd.disable("ResNotInBothPDB")
cmd.delete("ResNotInBothPDB")
print "\nObjects are now colored by C-alpha displacement deviation."
print "Blue is minimum and red is maximum..."
print "White is those residues used in the alignment algorithm. Can be turned off in top of algorithm."
print "Black is residues that does not exist in both files..."
