Migrating from `diffpy.srfit.structure`

diffpy.cmistructure holds the code that used to live in diffpy.srfit.structure. The behavior is the same, but the names follow the Python style: camelCase methods are now snake_case, and abbreviated attribute and argument names are spelled out.

diffpy.srfit 3.5.0 warns when you use an old method or attribute and names its replacement. Renamed function arguments can’t be warned about, so check the Renamed arguments table if your script passes arguments by keyword.

Update your imports

Replace diffpy.srfit.structure with diffpy.cmistructure. The module names are unchanged:

# Before
from diffpy.srfit.structure import constrainAsSpaceGroup
from diffpy.srfit.structure.objcrystparset import ObjCrystCrystalParSet

# After
from diffpy.cmistructure import constrain_as_space_group
from diffpy.cmistructure.objcrystparset import ObjCrystCrystalParSet

`constrain_as_space_group` accepts a generator

constrain_as_space_group now also accepts a generator, such as a PDFGenerator, in place of its .phase. Both of these calls work:

constrain_as_space_group(generator.phase, "Fm-3m")
constrain_as_space_group(generator, "Fm-3m")

Anything that is neither a structure parameter set nor an object with one as its .phase raises a TypeError.

What has not changed

Class names, such as DiffpyStructureParSet and ObjCrystCrystalParSet.
The space group containers .sgpars, .latpars, .xyzpars and .adppars. They also name Parameters in fit results, for example sgpars.latpars.a.
The constrainadps and periodic keyword arguments.

Renamed functions and methods

diffpy.srfit.structure	diffpy.cmistructure
`struToParameterSet(name, stru)`	`structure_to_parameter_set(name, structure)`
`constrainAsSpaceGroup`	`constrain_as_space_group`
`canAdapt` (all adapters)	`can_adapt`
`getLattice` (all adapters)	`get_lattice`
`getScatterers` (all adapters)	`get_scatterers`
`CCTBXCrystalParSet.getSpaceGroup`	`get_space_group`
`SrRealParSet.restrainBVS`	`restrain_bvs`
`useSymmetry`	`use_symmetry`
`usingSymmetry`	`using_symmetry`
`isDummy`	`is_dummy`
`ObjCrystScattererParSet.hasScatterers`	`has_scatterers`
`ObjCrystMoleculeParSet.wrapRestraints`	`wrap_restraints`
`ObjCrystMoleculeParSet.wrapStretchModeParameters`	`wrap_stretch_mode_parameters`
`ObjCrystMoleculeParSet.restrainBondLength`	`restrain_bond_length`
`ObjCrystMoleculeParSet.restrainBondLengthParameter`	`restrain_bond_length_parameter`
`ObjCrystMoleculeParSet.restrainBondAngle`	`restrain_bond_angle`
`ObjCrystMoleculeParSet.restrainBondAngleParameter`	`restrain_bond_angle_parameter`
`ObjCrystMoleculeParSet.restrainDihedralAngle`	`restrain_dihedral_angle`
`ObjCrystMoleculeParSet.restrainDihedralAngleParameter`	`restrain_dihedral_angle_parameter`
`ObjCrystMoleculeParSet.addBondLengthParameter`	`add_bond_length_parameter`
`ObjCrystMoleculeParSet.addBondAngleParameter`	`add_bond_angle_parameter`
`ObjCrystMoleculeParSet.addDihedralAngleParameter`	`add_dihedral_angle_parameter`
`StretchModeParameter.addAtoms`	`add_atoms`
`setConst` on the bond length, bond angle and dihedral angle Parameters	`set_constant`
`BaseSpaceGroupParameters.addParameter`	`add_parameter`

Renamed attributes

Class	diffpy.srfit.structure	diffpy.cmistructure
`SrRealParSet`, `DiffpyStructureParSet`, `ObjCrystCrystalParSet`, `ObjCrystMoleculeParSet`, `CCTBXCrystalParSet`	`.stru`	`.structure`
`DiffpyLatticeParSet`, `ObjCrystCrystalParSet`	`.angunits`	`.angle_units`
`ObjCrystScattererParSet`	`.scat`	`.scatterer`
`ObjCrystMoleculeRestraint`	`.res`	`.restraint`
Bond length, bond angle and dihedral angle Parameters	`.matoms`	`.mutated_atoms`
`SpaceGroupParameters`	`.sg`	`.space_group`
`CCTBXScattererParSet`, `CCTBXUnitCellParSet`	`.strups`	`.structure_parameter_set`
`CCTBXScattererParSet`	`.idx`	`.index`

Renamed arguments

These only matter if you pass the argument by keyword. Positional calls keep working, because no argument has moved.

Function or class	diffpy.srfit.structure	diffpy.cmistructure
`structure_to_parameter_set`, `can_adapt`, `DiffpyStructureParSet`, `CCTBXCrystalParSet`	`stru`	`structure`
`ObjCrystCrystalParSet`	`cryst`	`crystal`
`ObjCrystScattererParSet`, `ObjCrystMolAtomParSet`	`scat`	`scatterer`
`ObjCrystMoleculeRestraint`	`res`	`restraint`
`BVSRestraint`	`parset`	`parameter_set`
`CCTBXScattererParSet`, `CCTBXUnitCellParSet`	`strups`	`structure_parameter_set`
`CCTBXScattererParSet`	`idx`	`index`
`SpaceGroupParameters`	`sg`	`space_group`
`restrain_bond_length_parameter`, `restrain_bond_angle_parameter`, `restrain_dihedral_angle_parameter`, `BaseSpaceGroupParameters.add_parameter`	`par`	`parameter`
`StretchModeParameter.set_value`	`val`	`value`

Migrating from diffpy.srfit.structure