Class FitStructure

Initialize FitDataSet.

name         -- name of the data set.  The same name is used for
                self.initial and self.final.
args, kwargs -- optional arguments passed to parent PDFStructure

Overrides: pdfstructure.PDFStructure.__init__

Load structure from a file, raise ControlFileError for invalid
or unknown structure format.  Overloads PDFStructure.read()
to handle custom_spacegroup attribute.

filename -- file to be loaded
format   -- structure format such as 'pdffit', 'pdb', 'xyz'.  When
            'auto' all available formats are tried in a row.

Return instance of StructureParser used to load the data.
See Structure.read() for more info.

Overrides: pdfstructure.PDFStructure.read

Same as PDFStructure.readStr, but handle the
custom_spacegroup data.

Return instance of StructureParser used to load the data.
See Structure.readStr() for more info.

Overrides: Structure.pdffitstructure.PDFFitStructure.readStr

Map self.initial to self.
This is called only when normal attribute lookup fails.

Upload refined phase from PdfFit server instance.

server -- instance of PdfFit server
iphase -- index of this phase in server

Obtain dictionary of parameters used by self.constraints.
The keys of returned dictionary are integer parameter indices, and
the values are Parameter instances, with guessed initial values.

returns dictionary of indices and Parameter instances

Evaluate constraint formulas and adjust initial PDFStructure.

parameters -- dictionary of parameter indices with Parameter
              instance values.  Values may also be float type.

Change a parameter index to a new value.

This will replace all instances of one parameter name with another in
this fit.

Insert list of atoms before index and adjust self.constraints.

index    -- position in the initial structure, atoms are appended
            when larger than len(self.initial).
atomlist -- list of atom instances.

Removed atoms at given indices and adjust self.constraints.

indices -- list of integer indices of atoms to be deleted

Perform supercell expansion for this structure and adjust
constraints for positions and lattice parameters.  New lattice
parameters are multiplied and fractional coordinates divided by
corresponding multiplier.  New atoms are grouped with their source
in the original cell.

mno -- tuple or list of three positive integer cell multipliers along
the a, b, c axis

Check if space group is consistent with lattice parameters.

spacegroup -- instance of SpaceGroup

Return bool.

Return a list of SpaceGroup instances sorted by International
Tables number.  When custom_spacegroup is defined, the list starts
with custom_spacegroup.

Find space group in getSpaceGroupList() by short_name or number.
Use P1 when nothing else matches.

Return instance of SpaceGroup.
Raise ValueError if sgname cannot be found or when it is not present
in getSpaceGroupList().

Perform symmetry expansion for atoms at given indices.
Temperature factors may be corrected to reflect the symmetry.
All constraints for expanded atoms are erased with the exception
of the occupancy("occ".  Constraints of unaffected atoms are adjusted
for new positions self.initial.

spacegroup  -- instance of Structure.SpaceGroup
indices     -- list of integer indices of atoms to be expanded
sgoffset    -- optional offset of space group origin [0,0,0]

Generate symmetry constraints for positions and thermal factors.
Both positions and thermal factors may get corrected to reflect
space group symmetry.  Old positional and thermal constraints get
erased.  New parameter indices start at fist decade after the last
used parameter.

spacegroup  -- instance of Structure.SpaceGroup
indices     -- list of integer indices of atoms to be expanded
posflag     -- required bool flag for constraining positions
Uijflag     -- required bool flag for Uij constrainment
sgoffset    -- optional offset of space group origin [0,0,0]

Set the value of selected_pairs to s, raise ControlValueError when
s has invalid syntax.  The selected_pairs is a comma separated list of
words formatted as

    [!]{element|indexOrRange|all}-[!]{element|indexOrRange|all}

where '!' excludes the given atoms from first or second pair.

Examples:

    all-all              all possible pairs
    Na-Na                only Na-Na pairs
    all-all, !Na-        all pairs except Na-Na (first index skips Na)
    all-all, -!Na        same as previous (second index skips Na)
    Na-1:4               pairs of Na and first 4 atoms
    all-all, !Cl-!Cl     exclude any pairs containing Cl
    all-all, !Cl-, -!Cl  same as previous
    1-all                only pairs including the first atom

Use getPairSelectionFlags() method to get a list of included values
for first and second pair index.

Translate string s to a list of allowed values for first and second
pair index.  Raise ControlValueError for invalid syntax of s.  See
setSelectedPairs() docstring for a definition of pair selection syntax.

s -- string describing selected pairs (default: self.selected_pairs)

Return a dictionary with following keys:

firstflags  -- list of selection flags for first indices
secondflags -- list of selection flags for second indices
fixed_pair_string -- argument corrected to standard syntax

Apply pair selection for calculations of partial PDF.

server   -- instance of PdfFit engine
phaseidx -- phase index in PdfFit engine starting from 1

copy self to other. if other is None, create new instance

other -- reference to other object

returns reference to copied object

Overrides: pdfstructure.PDFStructure.copy

Load structure from a zipped project file.

z       -- zipped project file
subpath -- path to its own storage within project file

Save structure to a zipped project file.

z       -- zipped project file
subpath -- path to its own storage within project file

get names of data item which can be plotted as y

returns a name str list

get names of data item which can be plotted as x

returns a name str list

get self's data member

name -- data item name
step -- step info, it can be:
        (1) a number ( -1 means latest step ): for single step
        (2) a list of numbers: for multiple steps
        (3) None: for all steps

returns data object, be it a single number, a list, or a list of list