"Fossies" - the Fresh Open Source Software Archive  

Source code changes of the file "modules/pymol/exporting.py" between
pymol-open-source-2.2.0.tar.gz and pymol-open-source-2.3.0.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-open-source-2.2.0)	:	exporting.py  (pymol-open-source-2.3.0)
skipping to change at line 17		skipping to change at line 17
#G* Please see the accompanying LICENSE file for further information.		#G* Please see the accompanying LICENSE file for further information.
#H* -------------------------------------------------------------------		#H* -------------------------------------------------------------------
#I* Additional authors of this source file include:		#I* Additional authors of this source file include:
#-*		#-*
#-*		#-*
#-*		#-*
#Z* -------------------------------------------------------------------		#Z* -------------------------------------------------------------------
from __future__ import print_function, absolute_import		from __future__ import print_function, absolute_import
if __name__=='pymol.exporting':		if True:
import os		import os
import sys		import sys
if sys.version_info[0] == 2:		if sys.version_info[0] == 2:
import thread		import thread
else:		else:
import _thread as thread		import _thread as thread
from . import selector		from . import selector
import re		import re
import copy		import copy
skipping to change at line 650		skipping to change at line 650
r = _cmd.assign_atom_types(_self._COb, selection, int(1), int(state- 1), quiet)		r = _cmd.assign_atom_types(_self._COb, selection, int(1), int(state- 1), quiet)
finally:		finally:
_self.unlock(r,_self)		_self.unlock(r,_self)
return r		return r
def get_str(format, selection='(all)', state=-1, ref='',		def get_str(format, selection='(all)', state=-1, ref='',
ref_state=-1, multi=-1, quiet=1, _self=cmd):		ref_state=-1, multi=-1, quiet=1, _self=cmd):
'''		'''
DESCRIPTION		DESCRIPTION
		Like "get_bytes" but return a unicode string.
		'''
		assert format not in ('mmtf',), 'binary format, use get_bytes'
		b = get_bytes(format, selection, state, ref, ref_state, multi, quiet, _s
		elf)
		return b.decode('utf-8')
		def get_bytes(format, selection='(all)', state=-1, ref='',
		ref_state=-1, multi=-1, quiet=1, _self=cmd):
		'''
		DESCRIPTION
API-only function which exports the selection to a molecular file		API-only function which exports the selection to a molecular file
format and returns it as a string.		format and returns it as a binary ("bytes") string.
ARGUMENTS		ARGUMENTS
format = str: pdb|cif|sdf|mol|mol2|mae|pqr|xyz		format = str: pdb|cif|sdf|mol|mol2|mae|pqr|xyz
selection = str: atom selection {default: all}		selection = str: atom selection {default: all}
state = int: object state (-1=current, 0=all) {default: -1}		state = int: object state (-1=current, 0=all) {default: -1}
ref = str: object name which defines reference frame {default: }		ref = str: object name which defines reference frame {default: }
skipping to change at line 673		skipping to change at line 684
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))
		if sys.version_info[0] == 2:
		get_str = get_bytes
def multifilesave(filename, selection='*', state=-1, format='', ref='',		def multifilesave(filename, selection='*', state=-1, format='', ref='',
ref_state=-1, quiet=1, _self=cmd):		ref_state=-1, quiet=1, _self=cmd):
'''		'''
DESCRIPTION		DESCRIPTION
For a selection that spans multiple molecular objects and/or states,		For a selection that spans multiple molecular objects and/or states,
save each object and/or state to a separate file. Takes a filename		save each object and/or state to a separate file. Takes a filename
argument with placeholders:		argument with placeholders:
{name} : object name		{name} : object name
skipping to change at line 952		skipping to change at line 966
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',		'mmtf': get_bytes,
'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,
End of changes. 5 change blocks.
3 lines changed or deleted		18 lines changed or added

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