"Fossies" - the Fresh Open Source Software Archive  

Source code changes of the file "modules/pymol/fitting.py" between
pymol-v2.1.0.tar.bz2 and pymol-open-source-2.2.0.tar.gz

About: PyMOL is a Python-enhanced molecular graphics tool. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies. Open Source version.

fitting.py  (pymol-v2.1.0.tar.bz2)	:	fitting.py  (pymol-open-source-2.2.0)
skipping to change at line 113		skipping to change at line 113
(aliLen, RMSD, rotMat, i1, i2) = r		(aliLen, RMSD, rotMat, i1, i2) = r
if quiet==-1:		if quiet==-1:
import pprint		import pprint
print("RMSD %f over %i residues" % (float(RMSD), int(aliLen)))		print("RMSD %f over %i residues" % (float(RMSD), int(aliLen)))
print("TTT Matrix:")		print("TTT Matrix:")
pprint.pprint(rotMat)		pprint.pprint(rotMat)
elif quiet==0:		elif quiet==0:
print("RMSD %f over %i residues" % (float(RMSD), int(aliLen)))		print("RMSD %f over %i residues" % (float(RMSD), int(aliLen)))
if int(transform):		if int(transform):
for model in cmd.get_object_list("(" + mobile + ")") :		for model in _self.get_object_list("(" + mobile + ") "):
_self.transform_object(model, rotMat, state=0)		_self.transform_object(model, rotMat, state=0)
if object is not None:		if object is not None:
obj1 = cmd.get_object_list("(" + target + ")")		obj1 = _self.get_object_list("(" + target + ")")
obj2 = cmd.get_object_list("(" + mobile + ")")		obj2 = _self.get_object_list("(" + mobile + ")")
if len(obj1) > 1 or len(obj2) > 1:		if len(obj1) > 1 or len(obj2) > 1:
print(' CEalign-Error: selection spans multiple' + \		print(' CEalign-Error: selection spans multiple' + \
' objects, cannot create alignment objec t')		' objects, cannot create alignment objec t')
raise pymol.CmdException		raise pymol.CmdException
tmp1 = _self.get_unused_name('_1')		tmp1 = _self.get_unused_name('_1')
tmp2 = _self.get_unused_name('_2')		tmp2 = _self.get_unused_name('_2')
_self.select_list(tmp1, obj1[0], [ids1[j] for i in i 1 for j in range(i, i+window)])		_self.select_list(tmp1, obj1[0], [ids1[j] for i in i 1 for j in range(i, i+window)])
_self.select_list(tmp2, obj2[0], [ids2[j] for i in i 2 for j in range(i, i+window)])		_self.select_list(tmp2, obj2[0], [ids2[j] for i in i 2 for j in range(i, i+window)])
_self.rms_cur(tmp2, tmp1, cycles=0, matchmaker=4, ob ject=object)		_self.rms_cur(tmp2, tmp1, cycles=0, matchmaker=4, ob ject=object)
_self.delete(tmp1)		_self.delete(tmp1)
skipping to change at line 228		skipping to change at line 228
# align them to 1cll using cealign		# align them to 1cll using cealign
alignto 1cll, method=cealign		alignto 1cll, method=cealign
alignto 1cll, object=all_to_1cll		alignto 1cll, object=all_to_1cll
SEE ALSO		SEE ALSO
extra_fit, align, super, cealign, fit, rms, rms_cur, intra_fit		extra_fit, align, super, cealign, fit, rms, rms_cur, intra_fit
"""		"""
if not selection:		if not selection:
names = cmd.get_names("public_objects", 1)		names = _self.get_names("public_objects", 1)
if not names:		if not names:
raise pymol.CmdException('no public objects')		raise pymol.CmdException('no public objects')
selection = '%' + ' %'.join(names)		selection = '%' + ' %'.join(names)
return extra_fit(selection, target, method, 0, quiet, _self, **k wargs)		return extra_fit(selection, target, method, 0, quiet, _self, **k wargs)
def super(mobile, target, cutoff=2.0, cycles=5,		def super(mobile, target, cutoff=2.0, cycles=5,
gap=-1.5, extend=-0.7, max_gap=50, object=None,		gap=-1.5, extend=-0.7, max_gap=50, object=None,
matrix="BLOSUM62", mobile_state=0, target_state=0,		matrix="BLOSUM62", mobile_state=0, target_state=0,
quiet=1, max_skip=0, transform=1, reset=0,		quiet=1, max_skip=0, transform=1, reset=0,
seq=0.0, radius=12.0, scale=17.0, base=0.65,		seq=0.0, radius=12.0, scale=17.0, base=0.65,
End of changes. 3 change blocks.
4 lines changed or deleted		4 lines changed or added

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