"Fossies" - the Fresh Open Source Software Archive  

Source code changes of the file "modules/pymol/exporting.py" between
pymol-v1.8.6.0.tar.bz2 and pymol-v2.1.0.tar.bz2

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-v1.8.6.0.tar.bz2)	:	exporting.py  (pymol-v2.1.0.tar.bz2)
skipping to change at line 22		skipping to change at line 22
#-*		#-*
#Z* -------------------------------------------------------------------		#Z* -------------------------------------------------------------------
from __future__ import print_function, absolute_import		from __future__ import print_function, absolute_import
if __name__=='pymol.exporting':		if __name__=='pymol.exporting':
import os		import os
import sys		import sys
if sys.version_info[0] == 2:		if sys.version_info[0] == 2:
import thread		import thread
import cPickle
else:		else:
import _thread as thread		import _thread as thread
import pickle as cPickle
from . import selector		from . import selector
import re		import re
import copy		import copy
import pymol		import pymol
cmd = sys.modules["pymol.cmd"]		cmd = sys.modules["pymol.cmd"]
from .cmd import _cmd,lock,unlock,Shortcut,QuietException		from .cmd import _cmd,lock,unlock,Shortcut,QuietException
from chempy import io		from chempy import io
		from chempy.pkl import cPickle
from chempy.sdf import SDF,SDFRec		from chempy.sdf import SDF,SDFRec
from .cmd import _feedback,fb_module,fb_mask, \		from .cmd import _feedback,fb_module,fb_mask, \
DEFAULT_ERROR, DEFAULT_SUCCESS, _raising, is_ok, is_error, \		DEFAULT_ERROR, DEFAULT_SUCCESS, _raising, is_ok, is_error, \
is_list, is_dict, is_tuple, loadable		is_list, is_dict, is_tuple, loadable
import traceback		import traceback
def copy_image(quiet=1,_self=cmd): # incentive feature / proprietary		def copy_image(quiet=1,_self=cmd): # incentive feature / proprietary
r = DEFAULT_ERROR		r = DEFAULT_ERROR
if thread.get_ident() == pymol.glutThread:		if thread.get_ident() == pymol.glutThread:
r = _self._copy_image(_self,int(quiet))		r = _self._copy_image(_self,int(quiet))
else:		else:
r = _self.do('cmd._copy_image(quiet=%d,_self=cmd)'%int(quiet))		r = _self.do('cmd._copy_image(quiet=%d)'%int(quiet))
if _self._raising(r,_self): raise QuietException		if _self._raising(r,_self): raise QuietException
return r		return r
cache_action_dict = {		cache_action_dict = {
'enable' : 0,		'enable' : 0,
'disable' : 1,		'disable' : 1,
'read_only' : 2,		'read_only' : 2,
'clear' : 3,		'clear' : 3,
'optimize' : 4,		'optimize' : 4,
}		}
skipping to change at line 362		skipping to change at line 361
def get_session(names='', partial=0, quiet=1, compress=-1, cache=-1, _self=c md):		def get_session(names='', partial=0, quiet=1, compress=-1, cache=-1, _self=c md):
session = {}		session = {}
r = DEFAULT_SUCCESS		r = DEFAULT_SUCCESS
cache = int(cache)		cache = int(cache)
compress = int(compress)		compress = int(compress)
partial = int(partial)		partial = int(partial)
pse_export_version = round(_self.get_setting_float('pse_export_version') , 4)		pse_export_version = round(_self.get_setting_float('pse_export_version') , 4)
legacyscenes = (0 < pse_export_version < 1.76) and _self.get_scene_list( )		legacyscenes = (0 < pse_export_version < 1.76) and _self.get_scene_list( )
		if sys.version_info[0] > 2:
		legacypickle = (0 < pse_export_version < 1.9)
		if legacypickle:
		print(' Warning: pse_export_version with Python 3 is experimenta
		l')
		cPickle.configure_legacy_dump(legacypickle)
if legacyscenes:		if legacyscenes:
_self.pymol._scene_dict = {}		_self.pymol._scene_dict = {}
scene_current_name = _self.get('scene_current_name')		scene_current_name = _self.get('scene_current_name')
tempname = '_scene_db96724c3cef00875c3bebb4f348f711'		tempname = '_scene_db96724c3cef00875c3bebb4f348f711'
_self.scene(tempname, 'store')		_self.scene(tempname, 'store')
for name in legacyscenes:		for name in legacyscenes:
_self.scene(name, 'recall', animate=0)		_self.scene(name, 'recall', animate=0)
wizard = _self.get_wizard()		wizard = _self.get_wizard()
skipping to change at line 632		skipping to change at line 637
ref_state = int: state of ref object {default: -1}		ref_state = int: state of ref object {default: -1}
multi = int: for multi-entry file formats, 0 = single entry,		multi = int: for multi-entry file formats, 0 = single entry,
1 = by object, 2 = by object-state, -1 = format default {default: -1}		1 = by object, 2 = by object-state, -1 = format default {default: -1}
'''		'''
with _self.lockcm:		with _self.lockcm:
return _cmd.get_str(_self._COb, str(format), str(selection),		return _cmd.get_str(_self._COb, str(format), str(selection),
int(state) - 1, str(ref), int(ref_state),		int(state) - 1, str(ref), int(ref_state),
int(multi), int(quiet))		int(multi), int(quiet))
		def multifilesave(filename, selection='*', state=-1, format='', ref='',
		ref_state=-1, quiet=1, _self=cmd):
		'''
		DESCRIPTION
		For a selection that spans multiple molecular objects and/or states,
		save each object and/or state to a separate file. Takes a filename
		argument with placeholders:
		{name} : object name
		{state} : state number
		{title} : state title
		{num} : file number
		{} : object name (first) or state (second)
		EXAMPLES
		multifilesave /tmp/{name}.pdb
		multifilesave /tmp/{name}-{state}.cif, state=0
		multifilesave /tmp/{}-{}.cif, state=0
		multifilesave /tmp/{}-{title}.sdf, state=0
		'''
		for (fname, osele, ostate) in multifilenamegen(
		filename, selection, int(state), _self):
		r = _self.save(fname, osele, ostate, format, ref, ref_state, quiet)
		return r
		def multifilenamegen(filename, selection, state, _self=cmd):
		'''Given a filename pattern, atom selection and state argument,
		Generate object-state specific filenames and selections.
		'''
		import string
		filename = _self.exp_path(filename)
		fmt_keys = [v[1]
		for v in string.Formatter().parse(filename)
		if v[1] is not None]
		nindexed = fmt_keys.count('')
		multiobject = nindexed > 0 or 'name' in fmt_keys or 'num' in fmt_keys
		multistate = nindexed > 1 or 'state' in fmt_keys or 'title' in fmt_keys
		if not (multiobject or multistate):
		raise ValueError('need one or more of {name}, {num}, {state}, {title
		}')
		odata = []
		for oname in _self.get_object_list(selection):
		osele = '(%s) & ?%s' % (selection, oname)
		first = last = state
		if multistate:
		if state < 0:
		first = last = _self.get_object_state(oname)
		if first == 0:
		first = 1
		last = _self.count_states('%' + oname)
		for ostate in range(first, last + 1):
		odata.append((oname, osele, ostate))
		# pad {state} and {num} with zeros
		swidth = len(str(max(v[2] for v in odata)))
		nwidth = len(str(len(odata)))
		filename = filename.replace('{state}', '{state:0%d}' % swidth)
		filename = filename.replace('{num}', '{num:0%d}' % nwidth)
		for num, (oname, osele, ostate) in enumerate(odata, 1):
		fname = filename.format(oname, ostate,
		name=oname, state=ostate, num=num,
		title=_self.get_title(oname, ostate))
		yield fname, osele, ostate
def save(filename, selection='(all)', state=-1, format='', ref='',		def save(filename, selection='(all)', state=-1, format='', ref='',
ref_state=-1, quiet=1, partial=0,_self=cmd):		ref_state=-1, quiet=1, partial=0,_self=cmd):
'''		'''
DESCRIPTION		DESCRIPTION
"save" writes content to a file.		"save" writes content to a file.
USAGE		USAGE
save filename [, selection [, state [, format ]]]		save filename [, selection [, state [, format ]]]
skipping to change at line 683		skipping to change at line 762
load, get_model		load, get_model
'''		'''
quiet = int(quiet)		quiet = int(quiet)
# preprocess selection		# preprocess selection
selection = selector.process(selection)		selection = selector.process(selection)
#		#
r = DEFAULT_ERROR		r = DEFAULT_ERROR
# analyze filename		# analyze filename
from pymol.importing import filename_to_format		from pymol.importing import filename_to_format, _eval_func
_, _, format_guessed, zipped = filename_to_format(filename)		_, _, format_guessed, zipped = filename_to_format(filename)
filename = _self.exp_path(filename)		filename = _self.exp_path(filename)
# file format		# file format
if not format:		if not format:
if not format_guessed:		if not format_guessed:
raise pymol.CmdException('Unrecognized file format')		raise pymol.CmdException('Unrecognized file format')
format = format_guessed		format = format_guessed
# PyMOL session		# PyMOL session
skipping to change at line 712		skipping to change at line 791
'mmod': io.mmd.toFile,		'mmod': io.mmd.toFile,
'pkl': io.pkl.toFile, # binary pickle		'pkl': io.pkl.toFile, # binary pickle
'pkla': lambda model, filename: io.pkl.toFile(model, filename, bin=0 ), # ascii pickle		'pkla': lambda model, filename: io.pkl.toFile(model, filename, bin=0 ), # ascii pickle
}		}
contents = None		contents = None
if format in savefunctions:		if format in savefunctions:
# generic forwarding to format specific save functions		# generic forwarding to format specific save functions
func = savefunctions[format]		func = savefunctions[format]
		func = _eval_func(func)
kw = {		kw = {
'filename': filename,		'filename': filename,
'selection': selection,		'selection': selection,
'name': selection, # alt (get_ccp4str)		'name': selection, # alt (get_ccp4str)
'state': state,		'state': state,
'format': format,		'format': format,
'ref': ref,		'ref': ref,
'ref_state': ref_state,		'ref_state': ref_state,
'quiet': quiet,		'quiet': quiet,
'partial': partial,		'partial': partial,
skipping to change at line 817		skipping to change at line 897
return get_str('mae', selection, state, ref, ref_state, -1, quiet, _self )		return get_str('mae', selection, state, ref, ref_state, -1, quiet, _self )
def get_ccp4str(name, state=1, quiet=1, _self=cmd):		def get_ccp4str(name, state=1, quiet=1, _self=cmd):
with _self.lockcm:		with _self.lockcm:
return _cmd.get_ccp4str(_self._COb, str(name),		return _cmd.get_ccp4str(_self._COb, str(name),
int(state) - 1, int(quiet))		int(state) - 1, int(quiet))
def get_psestr(selection, partial, quiet, _self):		def get_psestr(selection, partial, quiet, _self):
if '(' in selection: # ignore selections		if '(' in selection: # ignore selections
selection = ''		selection = ''
return cPickle.dumps(_self.get_session(selection, partial, quiet), 1)		session = _self.get_session(selection, partial, quiet)
		return cPickle.dumps(session, 1)
def _get_mtl_obj(format, _self):		def _get_mtl_obj(format, _self):
# TODO mtl not implemented, always returns empty string		# TODO mtl not implemented, always returns empty string
		if format == 'mtl':
		raise pymol.CmdException('.MTL export not implemented')
i = {'mtl': 0, 'obj': 1}.get(format)		i = {'mtl': 0, 'obj': 1}.get(format)
return _self.get_mtl_obj()[i]		return _self.get_mtl_obj()[i]
from . import querying
savefunctions = {		savefunctions = {
'cif': get_str, # mmCIF		'cif': get_str, # mmCIF
'xyz': get_str,		'xyz': get_str,
'pdb': get_str,		'pdb': get_str,
'pqr': get_str,		'pqr': get_str,
'sdf': get_str,		'sdf': get_str,
'mol2': get_str,		'mol2': get_str,
'mae': get_str,		'mae': get_str,
'mol': get_str,		'mol': get_str,
		'mmtf': 'pymol.lazyio:get_mmtfstr',
'pse': get_psestr,		'pse': get_psestr,
'psw': get_psestr,		'psw': get_psestr,
'fasta': get_fastastr,		'fasta': get_fastastr,
'aln': get_alnstr,		'aln': get_alnstr,
'ccp4': get_ccp4str,		'ccp4': get_ccp4str,
'png': png,		'png': png,
# no arguments (some have a "version" argument)		# no arguments (some have a "version" argument)
'dae': querying.get_collada,		'dae': 'pymol.querying:get_collada',
'wrl': querying.get_vrml,		'wrl': 'pymol.querying:get_vrml',
'pov': querying.get_povray,		'pov': 'pymol.querying:get_povray',
'idtf': querying.get_idtf,		'idtf': 'pymol.querying:get_idtf',
'mtl': _get_mtl_obj, # TODO not implemented		'mtl': _get_mtl_obj, # TODO not implemented
'obj': _get_mtl_obj,		'obj': _get_mtl_obj,
}		}
End of changes. 13 change blocks.
11 lines changed or deleted		95 lines changed or added

---