"Fossies" - the Fresh Open Source Software Archive  

Source code changes of the file "modules/pymol/exporting.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.

exporting.py  (pymol-v2.1.0.tar.bz2)	:	exporting.py  (pymol-open-source-2.2.0)
skipping to change at line 124		skipping to change at line 124
scenes = str(scenes)		scenes = str(scenes)
scene_list = scenes.split()		scene_list = scenes.split()
cache_mode = int(_self.get('cache_mode'))		cache_mode = int(_self.get('cache_mode'))
_self.set('cache_mode',2)		_self.set('cache_mode',2)
if not len(scene_list):		if not len(scene_list):
scene_list = _self.get_scene_list()		scene_list = _self.get_scene_list()
for scene in scene_list:		for scene in scene_list:
scene = scene.strip()		scene = scene.strip()
if not quiet:		if not quiet:
print(" cache: optimizing scene '%s'."%scene)		print(" cache: optimizing scene '%s'."%scene)
cmd.scene(scene,animate=0)		_self.scene(scene,animate=0)
cmd.rebuild()		_self.rebuild()
cmd.refresh()		_self.refresh()
if len(cur_scene):		if len(cur_scene):
cmd.scene(cur_scene,animate=0)		_self.scene(cur_scene,animate=0)
else:		else:
scene_list = _self.get_scene_list()		scene_list = _self.get_scene_list()
if len(scene_list):		if len(scene_list):
cmd.scene(scene_list[0],animate=0)		_self.scene(scene_list[0],animate=0)
else:		else:
if not quiet:		if not quiet:
print(" cache: no scenes defined -- optimizing current d isplay.")		print(" cache: no scenes defined -- optimizing current d isplay.")
cmd.rebuild()		_self.rebuild()
cmd.refresh()		_self.refresh()
usage = _self._cache_purge(-1,_self=_self)		usage = _self._cache_purge(-1,_self=_self)
if cache_mode:		if cache_mode:
_self.set('cache_mode',cache_mode)		_self.set('cache_mode',cache_mode)
else:		else:
_self.set('cache_mode',2) # hmm... could use 1 here instead.		_self.set('cache_mode',2) # hmm... could use 1 here instead.
_self.set('cache_max',cache_max) # restore previous limits		_self.set('cache_max',cache_max) # restore previous limits
if not quiet:		if not quiet:
print(" cache: optimization complete (~%0.1f MB)."%(usage*4/1000 000.0))		print(" cache: optimization complete (~%0.1f MB)."%(usage*4/1000 000.0))
try:		try:
_self.lock(_self)		_self.lock(_self)
skipping to change at line 174		skipping to change at line 174
'MET' : 'M',		'MET' : 'M',
'ASN' : 'N',		'ASN' : 'N',
'PRO' : 'P',		'PRO' : 'P',
'GLN' : 'Q',		'GLN' : 'Q',
'ARG' : 'R',		'ARG' : 'R',
'SER' : 'S',		'SER' : 'S',
'THR' : 'T',		'THR' : 'T',
'VAL' : 'V',		'VAL' : 'V',
'TRP' : 'W',		'TRP' : 'W',
'TYR' : 'Y',		'TYR' : 'Y',
		# RNA
		'A' : 'A',
		'U' : 'U',
		'G' : 'G',
		'C' : 'C',
		# DNA
		'DA' : 'A',
		'DT' : 'T',
		'DG' : 'G',
		'DC' : 'C',
}		}
def get_fastastr(selection="all", state=-1, quiet=1, _self=cmd):		def get_fastastr(selection="all", state=-1, quiet=1, key='', _self=cmd):
dict = { 'seq' : {} }		'''
# we use (alt '' or alt 'A') because 'guide' picks up		DESCRIPTION
# non-canonical structures: eg, 1ejg has residue 22 as a SER and
# PRO, which guide will report twice		API only. Get protein and nucleic acid sequences in fasta format.
_self.iterate("("+selection+") and polymer and name CA and alt +A",
"seq[model]=seq.get(model,[]);seq[model].append(resn)",space		Used for saving:
=dict)		PyMOL> save foo.fasta
seq = dict['seq']
result = []		New in PyMOL 2.2:
for obj in _self.get_names("objects",selection='('+selection+')'):		- chain specific keys (key argument)
if obj in seq:		- nucleic acid support
cur_seq = [_resn_to_aa.get(x,'?') for x in seq[obj]]
result.append(">%s"%obj)		ARGUMENTS
cur_seq = ''.join(cur_seq)
while len(cur_seq):		selection = str: atom selection (reduced to "guide & alt +A") {default: all}
if len(cur_seq)>=70:
result.append(cur_seq[0:70])		state = int: (only used if state > 0)
cur_seq=cur_seq[70:]
else:		quiet = 0/1: UNUSED
result.append(cur_seq)
break		key = str: python expression {default: model + "_" + chain}
result = '\n'.join(result)		Use key=model to get the old (non-chain specific) behavior
if len(result):		'''
result = result + '\n'		import textwrap
return result		import collections
		seq = collections.OrderedDict()
		lines = []
		selection = "(" + selection + ") & guide & alt +A"
		if int(state) > 0:
		selection += ' & state {}'.format(state)
		if not key:
		key = 'model + "_" + chain'
		# for discrete objects: state specific keys
		key += ' + (":{}".format(state) if state else "")'
		_self.iterate(selection,
		"seq.setdefault((" + key + "),[]).append(resn)",
		space={'seq': seq, 'str': str})
		for key, resn_list in seq.items():
		cur_seq = ''.join(_resn_to_aa.get(x, '?') for x in resn_list)
		lines.append(">{}".format(key))
		lines.extend(textwrap.wrap(cur_seq, 70))
		if lines:
		lines.append('') # final newline
		return '\n'.join(lines)
def get_pdbstr(selection="all", state=-1, ref='', ref_state=-1, quiet=1, _se lf=cmd):		def get_pdbstr(selection="all", state=-1, ref='', ref_state=-1, quiet=1, _se lf=cmd):
'''		'''
DESCRIPTION		DESCRIPTION
"get_pdbstr" in an API-only function which returns a pdb		"get_pdbstr" in an API-only function which returns a pdb
corresponding to the atoms in the selection provided and that are		corresponding to the atoms in the selection provided and that are
present in the indicated state		present in the indicated state
PYMOL API		PYMOL API
skipping to change at line 519		skipping to change at line 555
if prior:		if prior:
# fetch the prior image, without doing any work (fast-path / non-GLU T thread-safe)		# fetch the prior image, without doing any work (fast-path / non-GLU T thread-safe)
r = _self._png(str(filename),0,0,float(dpi),0,int(quiet),1,		r = _self._png(str(filename),0,0,float(dpi),0,int(quiet),1,
int(format),_self)		int(format),_self)
if r != 1: # no prior image available -- revert to default behavior		if r != 1: # no prior image available -- revert to default behavior
if prior < 0: # default is to fall back to actual rendering		if prior < 0: # default is to fall back to actual rendering
prior = 0		prior = 0
if not prior:		if not prior:
dpi = float(dpi)		dpi = float(dpi)
if dpi < 0:		if dpi < 0:
dpi = cmd.get_setting_float('image_dots_per_inch')		dpi = _self.get_setting_float('image_dots_per_inch')
width = _unit2px(width, dpi)		width = _unit2px(width, dpi)
height = _unit2px(height, dpi)		height = _unit2px(height, dpi)
if thread.get_ident() == pymol.glutThread:		if thread.get_ident() == pymol.glutThread:
r = _self._png(str(filename),int(width),int(height),float(dpi),		r = _self._png(str(filename),int(width),int(height),float(dpi),
int(ray),int(quiet),0,int(format),_self)		int(ray),int(quiet),0,int(format),_self)
else:		else:
r = _self._do("cmd._png('''%s''',%d,%d,%1.6f,%d,%d,%d,%d)"%		r = _self._do("cmd._png('''%s''',%d,%d,%1.6f,%d,%d,%d,%d)"%
(filename,width,height,dpi,		(filename,width,height,dpi,
ray,int(quiet),0,int(format)),_self=_self)		ray,int(quiet),0,int(format)),_self=_self)
End of changes. 7 change blocks.
34 lines changed or deleted		69 lines changed or added

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