libtbx.phil
index
/net/chevy/raid1/nat/src/cctbx_project/libtbx/phil/__init__.py

Documentation: http://cctbx.sourceforge.net/libtbx_phil.html

 
Package Contents
       
command_line
experimental
gui_objects
interface
parser
tokenizer
tst
tst_experimental
tst_interface
tst_tokenizer

 
Classes
       
__builtin__.list(__builtin__.object)
scope_extract_list
__builtin__.object
bool_converters
choice_converters
object_locator
qstr_converters
scope_extract
scope_extract_attribute_error
scope_extract_call_proxy_object
scope_extract_is_disabled
str_converters
key_converters
path_converters
strings_converters
try_extract_proxy
try_format_proxy
try_tokenize_proxy
words_converters
exceptions.DeprecationWarning(exceptions.Warning)
PhilDeprecationWarning
libtbx.slots_getstate_setstate(__builtin__.object)
definition
scope
variable_substitution_fragment
variable_substitution_proxy
_check_value_base(__builtin__.object)
number_converters_base
float_converters
int_converters
numbers_converters_base
floats_converters
ints_converters

 
class PhilDeprecationWarning(exceptions.DeprecationWarning)
    
Method resolution order:
PhilDeprecationWarning
exceptions.DeprecationWarning
exceptions.Warning
exceptions.Exception
exceptions.BaseException
__builtin__.object

Data descriptors defined here:
__weakref__
list of weak references to the object (if defined)

Methods inherited from exceptions.DeprecationWarning:
__init__(...)
x.__init__(...) initializes x; see help(type(x)) for signature

Data and other attributes inherited from exceptions.DeprecationWarning:
__new__ = <built-in method __new__ of type object>
T.__new__(S, ...) -> a new object with type S, a subtype of T

Methods inherited from exceptions.BaseException:
__delattr__(...)
x.__delattr__('name') <==> del x.name
__getattribute__(...)
x.__getattribute__('name') <==> x.name
__getitem__(...)
x.__getitem__(y) <==> x[y]
__getslice__(...)
x.__getslice__(i, j) <==> x[i:j]
 
Use of negative indices is not supported.
__reduce__(...)
__repr__(...)
x.__repr__() <==> repr(x)
__setattr__(...)
x.__setattr__('name', value) <==> x.name = value
__setstate__(...)
__str__(...)
x.__str__() <==> str(x)
__unicode__(...)

Data descriptors inherited from exceptions.BaseException:
__dict__
args
message

 
class bool_converters(__builtin__.object)
     Methods defined here:
__str__(self)
as_words(self, python_object, master)
from_words(self, words, master)

Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

Data and other attributes defined here:
phil_type = 'bool'

 
class choice_converters(__builtin__.object)
     Methods defined here:
__init__(self, multi=False)
__str__(self)
as_words(self, python_object, master)
fetch(self, source_words, master, ignore_errors=False)
from_words(self, words, master)

Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

Data and other attributes defined here:
phil_type = 'choice'

 
class definition(libtbx.slots_getstate_setstate)
    
Method resolution order:
definition
libtbx.slots_getstate_setstate
__builtin__.object

Methods defined here:
__init__(self, name, words, primary_id=None, primary_parent_scope=None, is_disabled=False, is_template=0, where_str='', merge_names=False, tmp=None, help=None, caption=None, short_caption=None, optional=None, type=None, multiple=None, input_size=None, style=None, expert_level=None, deprecated=None, alias=None)
__setstate__(self, *args, **kwds)
alias_path(self)
as_str(self, prefix='', expert_level=None, attributes_level=0, print_width=None)
assign_attribute(self, name, words, converter_registry, converter_cache)
assign_tmp(self, value, active_only=False)
copy(self)
customized_copy(self, name=None, words=None)
extract(self, parent=None)
extract_format(self, source=None)
fetch(self, source, diff=False, skip_incompatible_objects=False)
fetch_diff(self, source, skip_incompatible_objects=False)
fetch_value(self, source, diff_mode=False, skip_incompatible_objects=False)
format(self, python_object)
full_path(self)
get_without_substitution(self, path, alias_path=None)
has_attribute_with_name(self, name)
resolve_variables(self, diff_mode=False)
show(self, out=None, merged_names=[], prefix='', expert_level=None, attributes_level=0, print_width=None)
try_extract(self)
try_extract_format(self)
try_tokenize(self, input_string, source_info=None)
unique(self)
validate(self, input_string, source_info=None)
validate_and_format(self, input_string, source_info=None)

Data descriptors defined here:
alias
caption
deprecated
expert_level
help
input_size
is_disabled
is_template
merge_names
multiple
name
optional
primary_id
primary_parent_scope
short_caption
style
tmp
type
where_str
words

Data and other attributes defined here:
attribute_names = ['help', 'caption', 'short_caption', 'optional', 'type', 'multiple', 'input_size', 'style', 'expert_level', 'deprecated', 'alias']
is_definition = True
is_scope = False

Methods inherited from libtbx.slots_getstate_setstate:
__getstate__(self)

 
class float_converters(number_converters_base)
    
Method resolution order:
float_converters
number_converters_base
_check_value_base
__builtin__.object

Data and other attributes defined here:
phil_type = 'float'

Methods inherited from number_converters_base:
__init__(self, value_min=None, value_max=None)
__str__(self)
as_words(self, python_object, master)
from_words(self, words, master)

Data descriptors inherited from _check_value_base:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class floats_converters(numbers_converters_base)
    
Method resolution order:
floats_converters
numbers_converters_base
_check_value_base
__builtin__.object

Data and other attributes defined here:
phil_type = 'floats'

Methods inherited from numbers_converters_base:
__init__(self, size=None, size_min=None, size_max=None, value_min=None, value_max=None, allow_none_elements=False, allow_auto_elements=False)
__str__(self)
as_words(self, python_object, master)
from_words(self, words, master)

Data descriptors inherited from _check_value_base:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class int_converters(number_converters_base)
    
Method resolution order:
int_converters
number_converters_base
_check_value_base
__builtin__.object

Data and other attributes defined here:
phil_type = 'int'

Methods inherited from number_converters_base:
__init__(self, value_min=None, value_max=None)
__str__(self)
as_words(self, python_object, master)
from_words(self, words, master)

Data descriptors inherited from _check_value_base:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class ints_converters(numbers_converters_base)
    
Method resolution order:
ints_converters
numbers_converters_base
_check_value_base
__builtin__.object

Data and other attributes defined here:
phil_type = 'ints'

Methods inherited from numbers_converters_base:
__init__(self, size=None, size_min=None, size_max=None, value_min=None, value_max=None, allow_none_elements=False, allow_auto_elements=False)
__str__(self)
as_words(self, python_object, master)
from_words(self, words, master)

Data descriptors inherited from _check_value_base:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class key_converters(str_converters)
    
Method resolution order:
key_converters
str_converters
__builtin__.object

Methods defined here:
__str__(self)

Data and other attributes defined here:
phil_type = 'key'

Methods inherited from str_converters:
as_words(self, python_object, master)
from_words(self, words, master)

Data descriptors inherited from str_converters:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class number_converters_base(_check_value_base)
    
Method resolution order:
number_converters_base
_check_value_base
__builtin__.object

Methods defined here:
__init__(self, value_min=None, value_max=None)
__str__(self)
as_words(self, python_object, master)
from_words(self, words, master)

Data descriptors inherited from _check_value_base:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class numbers_converters_base(_check_value_base)
    
Method resolution order:
numbers_converters_base
_check_value_base
__builtin__.object

Methods defined here:
__init__(self, size=None, size_min=None, size_max=None, value_min=None, value_max=None, allow_none_elements=False, allow_auto_elements=False)
__str__(self)
as_words(self, python_object, master)
from_words(self, words, master)

Data descriptors inherited from _check_value_base:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class object_locator(__builtin__.object)
     Methods defined here:
__init__(self, parent, path, object)
__str__(self)

Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class path_converters(str_converters)
    
Method resolution order:
path_converters
str_converters
__builtin__.object

Methods defined here:
__str__(self)
from_words(self, words, master)

Data and other attributes defined here:
phil_type = 'path'

Methods inherited from str_converters:
as_words(self, python_object, master)

Data descriptors inherited from str_converters:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class qstr_converters(__builtin__.object)
     Methods defined here:
__str__(self)
as_words(self, python_object, master)
from_words(self, words, master)

Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

Data and other attributes defined here:
phil_type = 'qstr'

 
class scope(libtbx.slots_getstate_setstate)
    
Method resolution order:
scope
libtbx.slots_getstate_setstate
__builtin__.object

Methods defined here:
__init__(self, name, objects=None, primary_id=None, primary_parent_scope=None, is_disabled=False, is_template=0, where_str='', merge_names=False, style=None, help=None, caption=None, short_caption=None, optional=None, call=None, multiple=None, sequential_format=None, disable_add=None, disable_delete=None, expert_level=None, alias=None)
active_objects(self)
adopt(self, object)
adopt_scope(self, other)
alias_path(self)
all_definitions(self, suppress_multiple=False, select_tmp=None)
as_str(self, prefix='', expert_level=None, attributes_level=0, print_width=None)
assign_attribute(self, name, words, scope_extract_call_proxy_cache)
assign_tmp(self, value, active_only=False)
change_primary_parent_scope(self, new_value)
clone(self, python_object, converter_registry=None)
command_line_argument_interpreter(self, home_scope=None, argument_description=None)
copy(self)
customized_copy(self, name=None, objects=None)
extract(self, parent=None)
extract_format(self, source=None)
fetch(self, source=None, sources=None, track_unused_definitions=False, diff=False, skip_incompatible_objects=False, warn_deprecated=True)
fetch_diff(self, source=None, sources=None, track_unused_definitions=False, skip_incompatible_objects=False)
format(self, python_object)
full_path(self)
get(self, path, with_substitution=True, alias_path=None)
get_without_substitution(self, path, alias_path=None)
has_attribute_with_name(self, name)
is_empty(self)
lexical_get(self, path, stop_id, search_up=True)
master_active_objects(self)
process_includes(self, converter_registry, reference_directory, include_stack=None)
resolve_variables(self)
show(self, out=None, merged_names=[], prefix='', expert_level=None, attributes_level=0, print_width=None)
unique(self)

Data descriptors defined here:
alias
call
caption
disable_add
disable_delete
expert_level
help
is_disabled
is_template
merge_names
multiple
name
objects
optional
primary_id
primary_parent_scope
sequential_format
short_caption
style
where_str

Data and other attributes defined here:
attribute_names = ['style', 'help', 'caption', 'short_caption', 'optional', 'call', 'multiple', 'sequential_format', 'disable_add', 'disable_delete', 'expert_level', 'alias']
deprecated = False
is_definition = False
is_scope = True

Methods inherited from libtbx.slots_getstate_setstate:
__getstate__(self)
__setstate__(self, state)

 
class scope_extract(__builtin__.object)
     Methods defined here:
__call__(self, **keyword_args)
__init__(self, name, parent, call)
__inject__(self, name, value)
__phil_get__(self, name)
__phil_join__(self, other)
__phil_path__(self, object_name=None)
__phil_path_and_value__(self, object_name)
__phil_set__(self, name, optional, multiple, value)
__setattr__(self, name, value)

Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class scope_extract_attribute_error(__builtin__.object)
     Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class scope_extract_call_proxy_object(__builtin__.object)
     Methods defined here:
__init__(self, where_str, expression, callable, keyword_args)
__str__(self)

Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class scope_extract_is_disabled(__builtin__.object)
     Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class scope_extract_list(__builtin__.list)
    
Method resolution order:
scope_extract_list
__builtin__.list
__builtin__.object

Methods defined here:
__init__(self, optional)

Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

Methods inherited from __builtin__.list:
__add__(...)
x.__add__(y) <==> x+y
__contains__(...)
x.__contains__(y) <==> y in x
__delitem__(...)
x.__delitem__(y) <==> del x[y]
__delslice__(...)
x.__delslice__(i, j) <==> del x[i:j]
 
Use of negative indices is not supported.
__eq__(...)
x.__eq__(y) <==> x==y
__ge__(...)
x.__ge__(y) <==> x>=y
__getattribute__(...)
x.__getattribute__('name') <==> x.name
__getitem__(...)
x.__getitem__(y) <==> x[y]
__getslice__(...)
x.__getslice__(i, j) <==> x[i:j]
 
Use of negative indices is not supported.
__gt__(...)
x.__gt__(y) <==> x>y
__iadd__(...)
x.__iadd__(y) <==> x+=y
__imul__(...)
x.__imul__(y) <==> x*=y
__iter__(...)
x.__iter__() <==> iter(x)
__le__(...)
x.__le__(y) <==> x<=y
__len__(...)
x.__len__() <==> len(x)
__lt__(...)
x.__lt__(y) <==> x<y
__mul__(...)
x.__mul__(n) <==> x*n
__ne__(...)
x.__ne__(y) <==> x!=y
__repr__(...)
x.__repr__() <==> repr(x)
__reversed__(...)
L.__reversed__() -- return a reverse iterator over the list
__rmul__(...)
x.__rmul__(n) <==> n*x
__setitem__(...)
x.__setitem__(i, y) <==> x[i]=y
__setslice__(...)
x.__setslice__(i, j, y) <==> x[i:j]=y
 
Use  of negative indices is not supported.
__sizeof__(...)
L.__sizeof__() -- size of L in memory, in bytes
append(...)
L.append(object) -- append object to end
count(...)
L.count(value) -> integer -- return number of occurrences of value
extend(...)
L.extend(iterable) -- extend list by appending elements from the iterable
index(...)
L.index(value, [start, [stop]]) -> integer -- return first index of value.
Raises ValueError if the value is not present.
insert(...)
L.insert(index, object) -- insert object before index
pop(...)
L.pop([index]) -> item -- remove and return item at index (default last).
Raises IndexError if list is empty or index is out of range.
remove(...)
L.remove(value) -- remove first occurrence of value.
Raises ValueError if the value is not present.
reverse(...)
L.reverse() -- reverse *IN PLACE*
sort(...)
L.sort(cmp=None, key=None, reverse=False) -- stable sort *IN PLACE*;
cmp(x, y) -> -1, 0, 1

Data and other attributes inherited from __builtin__.list:
__hash__ = None
__new__ = <built-in method __new__ of type object>
T.__new__(S, ...) -> a new object with type S, a subtype of T

 
class str_converters(__builtin__.object)
     Methods defined here:
__str__(self)
as_words(self, python_object, master)
from_words(self, words, master)

Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

Data and other attributes defined here:
phil_type = 'str'

 
class strings_converters(__builtin__.object)
     Methods defined here:
__str__(self)
as_words(self, python_object, master)
from_words(self, words, master)

Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

Data and other attributes defined here:
phil_type = 'strings'

 
class try_extract_proxy(__builtin__.object)
     Methods defined here:
__init__(self, error_message, extracted)

Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class try_format_proxy(__builtin__.object)
     Methods defined here:
__init__(self, error_message, formatted)

Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class try_tokenize_proxy(__builtin__.object)
     Methods defined here:
__init__(self, error_message, tokenized)

Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class variable_substitution_fragment(libtbx.slots_getstate_setstate)
    
Method resolution order:
variable_substitution_fragment
libtbx.slots_getstate_setstate
__builtin__.object

Methods defined here:
__init__(self, is_variable, value)

Data descriptors defined here:
is_variable
result
value

Methods inherited from libtbx.slots_getstate_setstate:
__getstate__(self)
__setstate__(self, state)

 
class variable_substitution_proxy(libtbx.slots_getstate_setstate)
    
Method resolution order:
variable_substitution_proxy
libtbx.slots_getstate_setstate
__builtin__.object

Methods defined here:
__init__(self, word)
get_new_words(self)

Data descriptors defined here:
force_string
fragments
have_variables
word

Methods inherited from libtbx.slots_getstate_setstate:
__getstate__(self)
__setstate__(self, state)

 
class words_converters(__builtin__.object)
     Methods defined here:
__str__(self)
as_words(self, python_object, master)
from_words(self, words, master)

Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

Data and other attributes defined here:
phil_type = 'words'

 
Functions
       
StringIO(...)
StringIO([s]) -- Return a StringIO-like stream for reading or writing
alias_path(self)
bool_from_words(words, path)
definition_converters_from_words(words, converter_registry, converter_cache)
extended_converter_registry(additional_converters, base_registry=None)
extract_args(*args, **keyword_args)
find_scope(current_phil, scope_name)
float_from_number(number, words, path)
float_from_words(words, path)
full_path(self)
get_converters_phil_type(converters)
int_from_number(number, words, path)
int_from_words(words, path)
is_plain_auto(words)
is_plain_none(words)
is_reserved_identifier(string)
is_standard_identifier(string)
normalize_call_expression(expression)
number_from_value_string(value_string, words, path)
number_from_words(words, path)
numbers_from_words(words, path)
parse(input_string=None, source_info=None, file_name=None, converter_registry=None, process_includes=False, include_stack=None)
process_command_line(args, master_string, parse=None)
process_include_scope(converter_registry, include_stack, object, import_path, phil_path)
read_default(caller_file_name, params_extension='.params', converter_registry=None, process_includes=True)
scope_extract_call_proxy(full_path, words, cache)
show_attributes(self, out, prefix, attributes_level, print_width)
str_from_words(words)
strings_as_words(python_object)
strings_from_words(words)
tokenize_value_literal(input_string, source_info)

 
Data
        Auto = <libtbx.AutoType object>
c = '9'
default_converter_registry = {'bool': <class 'libtbx.phil.bool_converters'>, 'choice': <class 'libtbx.phil.choice_converters'>, 'float': <class 'libtbx.phil.float_converters'>, 'floats': <class 'libtbx.phil.floats_converters'>, 'int': <class 'libtbx.phil.int_converters'>, 'ints': <class 'libtbx.phil.ints_converters'>, 'key': <class 'libtbx.phil.key_converters'>, 'path': <class 'libtbx.phil.path_converters'>, 'qstr': <class 'libtbx.phil.qstr_converters'>, 'str': <class 'libtbx.phil.str_converters'>, ...}
default_print_width = 79
division = _Feature((2, 2, 0, 'alpha', 2), (3, 0, 0, 'alpha', 0), 8192)
standard_identifier_continuation_characters = set(['.', '0', '1', '2', '3', '4', ...])
standard_identifier_start_characters = set(['A', 'B', 'C', 'D', 'E', 'F', ...])