def _docArg(self, doc, arg):
"""Add documentation string for *arg* to *doc*."""
kwargs = self._args[arg]
dest = kwargs.get('dest', arg[0])
desc = ':arg {0}: {1}'.format(dest, kwargs['help'])
choices = kwargs.get('choices')
if choices:
desc += ', one of ' + ', '.join(['``' + repr(ch) + '``'
for ch in choices])
default = kwargs.get('default')
if default:
desc += ', default is ``{0}``'.format(repr(default))
doc.extend(wrapText(desc, join=False, subsequent_indent=' '))
try:
type = kwargs['type']
except KeyError:
try:
action = kwargs['action']
except KeyError:
type = None
else:
if action.startswith('store') and action.endswith('e'):
type = bool
else:
type = None
if type is not None:
doc.append(':type {0}: {1}'.format(dest, type.__name__))
doc.append('')
def _docArg(self, doc, arg):
"""Add documentation string for *arg* to *doc*."""
kwargs = self._args[arg]
dest = kwargs.get('dest', arg[0])
desc = ':arg {0}: {1}'.format(dest, kwargs['help'])
choices = kwargs.get('choices')
if choices:
desc += ', one of ' + ', '.join(['``' + repr(ch) + '``'
for ch in choices])
default = kwargs.get('default')
if default:
desc += ', default is ``{0}``'.format(repr(default))
doc.extend(wrapText(desc, join=False, subsequent_indent=' '))
try:
type = kwargs['type']
except KeyError:
try:
action = kwargs['action']
except KeyError:
type = None
else:
if action.startswith('store') and action.endswith('e'):
type = bool
else:
type = None
if type is not None:
doc.append(':type {0}: {1}'.format(dest, type.__name__))
doc.append('')
def getDocstr(self, meth, plural=True, selex=True):
"""Return documentation string for the field."""
assert meth in ('set', 'get', '_get'), "meth must be 'set' or 'get'"
assert isinstance(plural, bool), 'plural must be a boolean'
assert isinstance(selex, bool), 'selex must be a boolean'
if meth == 'get':
if plural:
docstr = 'Return a copy of {0}.'.format(self.doc_pl)
else:
docstr = 'Return {0} of the atom.'.format(self.doc)
elif meth == 'set':
if plural:
docstr = 'Set {0}.'.format(self.doc_pl)
else:
docstr = 'Set {0} of the atom.'.format(self.doc)
else:
selex = False
if plural:
docstr = 'Return {0} array.'.format(self.doc_pl)
if self.desc:
docstr += ' ' + self.desc
selstr = self.selstr
if selex and selstr:
if plural:
doc = self.doc_pl
else:
doc = self.doc
if '(' in doc:
doc = doc[:doc.index('(')]
selex = "``, ``".join([repr(s) for s in selstr])
selex = (" {0} can be used in atom selections, e.g. "
"``{1}``.").format(doc.capitalize(), selex)
if self.synonym is not None:
selex = selex + (' Note that *{0}* is a synonym for '
'*{1}*.').format(self.synonym, self.name)
return wrapText(docstr + selex)
else:
return wrapText(docstr)
backbonefull
bbfull
backbone atoms of :term:`protein` residues, same as selection
``'name CA C O N H H1 H2 H3 OXT and protein'``
sidechain
sc
side-chain atoms of :term:`protein` residues, same as selection
``'protein and not backbonefull'``
""".format(
stdaa = wrapText('indicates the standard amino acid residues: ' +
joinLinks(DEFAULTS['stdaa'], last=', and ', sort=True),
subsequent_indent=' '*6),
)
cats = list(CATEGORIZED)
cats.sort()
for cat in cats:
res = CATEGORIZED[cat]
res.sort()
__doc__ += """
{cat:s}
{res:s}
backbonefull
bbfull
backbone atoms of :term:`protein` residues, same as selection
``'name CA C O N H H1 H2 H3 OXT and protein'``
sidechain
sc
side-chain atoms of :term:`protein` residues, same as selection
``'protein and not backbonefull'``
""".format(
stdaa=wrapText('indicates the standard amino acid residues: ' +
joinLinks(DEFAULTS['stdaa'], last=', and ', sort=True),
subsequent_indent=' ' * 6))
cats = list(CATEGORIZED)
cats.sort()
for cat in cats:
res = CATEGORIZED[cat]
res.sort()
__doc__ += """
{cat}
{res}
""".format(cat=cat,
res=wrapText('residues ' + ', '.join(res),
subsequent_indent=' ' * 6))
"""
keys = list(ATOMIC_FIELDS.keys())
keys.sort()
for key in keys:
field = ATOMIC_FIELDS[key]
__doc__ += '\n\n ' + key + '\n'
if field.synonym:
__doc__ += ' ' + field.synonym + '\n'
__doc__ += wrapText(field.doc + (' *(read only)*' if field.readonly
else ''), indent=6)
if field.selstr:
sel = "\n ``'" + "'``,\n ``'".join(field.selstr) + "'``"
__doc__ += '\n\n *E.g.:* ' + sel
for key in FLAG_FIELDS.keys():
ATOMIC_FIELDS[key].flags = True
def wrapGetMethod(fn):
def getMethod(self):
return fn(self)
return getMethod
