'''
(c) 2011 Thomas Holder, MPI for Developmental Biology
License: BSD-2-Clause
'''
from pymol import cmd
[docs]
def save_settings(filename='~/.pymolrc-settings.py', quiet=1, *, _self=cmd):
'''
DESCRIPTION
Dumps all settings with non-default values to ~/.pymolrc-settings.py
Feature Request: Save settings for later use - ID: 1009951
https://sourceforge.net/tracker/?func=detail&aid=1009951&group_id=4546&atid=354546
'''
from pymol.setting import get_name_list
quiet = int(quiet)
if not filename.endswith('.py'):
print('Warning: filename should end with ".py"')
# temporatily load default settings and remember them
_self.reinitialize('store_defaults')
_self.reinitialize('original_settings')
original = [(name, _self.get(name)) for name in get_name_list()]
_self.reinitialize('settings')
# dump to file
filename = cmd.exp_path(filename)
f = open(filename, 'w')
f.write('# AUTOGENERATED FILE\n')
f.write('from pymol import cmd, invocation\n')
f.write('if invocation.options.show_splash: ') # no newline
f.write(' print("Loading settings from " + ' + repr(filename) + ')\n')
count = 0
for name, o_value in original:
value = _self.get(name)
if value != o_value:
f.write('cmd.set("%s", %s)\n' % (name, repr(value)))
if not quiet:
print('set %s, %s # default: %s' % (name, value, o_value))
count += 1
f.close()
if not quiet:
print('Dumped %d settings to %s' % (count, filename))
[docs]
def paper_settings(fancy=0, quiet=0, *, _self=cmd):
'''
DESCRIPTION
Set rendering quality high and some stuff good for printing:
* Side chain helper (cartoon_side_chain_helper = 1)
* No shadows (ray_shadows = 0)
ARGUMENTS
fancy = 0 or 1: set cartoon_fancy_helices and cartoon_highlight_color
{default: 0}
NOTES
You may also try "set ray_trace_mode, 1"
'''
fancy, quiet = int(fancy), int(quiet)
if fancy == 1:
_self.set('cartoon_fancy_helices', 1, quiet=quiet)
_self.set('cartoon_highlight_color', 'grey50', quiet=quiet)
_self.set('cartoon_side_chain_helper', 1, quiet=quiet)
_self.set('ray_shadows', 0, quiet=quiet)
_self.set('opaque_background', 0, quiet=quiet)
_self.bg_color('white')
[docs]
class set_temporary(object):
'''
DESCRIPTION
API only. Supports the following pattern:
>>> with set_temporary(pdb_retain_ids=1):
... cmd.save('out.pdb')
'''
def __init__(self, *args, _self=cmd, **kwargs):
self._self = _self
self.sele = kwargs.pop('selection', '')
self.args = args + tuple(kwargs.items())
def __enter__(self):
self.saved = []
for k, v in self.args:
v_saved = self._self.get(k, self.sele)
if v != v_saved:
self.saved.append((k, v_saved))
self._self.set(k, v, self.sele)
return self
def __exit__(self, type, value, traceback):
for k, v in self.saved:
self._self.set(k, v, self.sele)
cmd.extend('save_settings', save_settings)
cmd.extend('paper_settings', paper_settings)
# vi:expandtab:smarttab