proteindf_tools.basisset module

class proteindf_tools.basisset.BasisSet(*args, **kwargs)

Bases: list

>>> bs = BasisSet('sample', 3)
>>> bs.name
'sample'
>>> len(bs)
3
>>> bs[0] = ContractedGTO('p', 3)
>>> bs[0][0] = PrimitiveGTO(2.80806400E+03, 2.01783000E-03)
>>> bs[0][1] = PrimitiveGTO(4.21138300E+02, 1.54332000E-02)
>>> bs[0][2] = PrimitiveGTO(9.55866200E+01, 7.55815500E-02)

expand()

Expand the case where shell_type is e.g. ‘spd’.

get_basis2()

get_num_of_CGTOs(shell_type)

get_number_of_AOs()

get_raw_data()

property max_shell_type

property max_shell_type_id

property name

set_by_raw_data(odict)

sort()

Sort the list in ascending order and return None.

The sort is in-place (i.e. the list itself is modified) and stable (i.e. the order of two equal elements is maintained).

If a key function is given, apply it once to each list item and sort them, ascending or descending, according to their function values.

The reverse flag can be set to sort in descending order.

class proteindf_tools.basisset.ContractedGTO(*args, **kwargs)

Bases: list

>>> cgto = ContractedGTO('p', 3)
>>> cgto[0] = PrimitiveGTO(2.80806400E+03, 2.01783000E-03)
>>> cgto[1] = PrimitiveGTO(4.21138300E+02, 1.54332000E-02)
>>> cgto[2] = PrimitiveGTO(9.55866200E+01, 7.55815500E-02)
>>> cgto.shell_type
'p'
>>> len(cgto)
3

expand()

Expand the case where shell_type is e.g. ‘spd’.

classmethod get_basis_type(shell_type_id, basis_id)

Return the orbital type string. shell_type_id=0, basis_id=0: s shell_type_id=1, basis_id=0: px shell_type_id=1, basis_id=1: py shell_type_id=1, basis_id=2: pz shell_type_id=2, basis_id=0: dxy shell_type_id=2, basis_id=1: dyz shell_type_id=2, basis_id=2: dzx shell_type_id=2, basis_id=3: dxx-yy shell_type_id=2, basis_id=4: dzz

get_raw_data()

classmethod get_shell_type(id)

classmethod get_shell_type_id(shell_type)

Return the id corresponding to shell_type.

s: 0, p: 1, d: 2

classmethod get_supported_shell_types()

normalize()

property scale_factor

set_by_raw_data(odict)

property shell_type

property shell_type_id

class proteindf_tools.basisset.PrimitiveGTO(*args, **kwargs)

Bases: object

>>> pgto = PrimitiveGTO(2.80806400E+03, 2.01783000E-03)
>>> math.fabs(pgto.exp - 2.80806400E+03) < 1.0E-15
True
>>> math.fabs(pgto.coef - 2.01783000E-03) < 1.0E-15
True

property coef

property exp

get_raw_data()

normalize(shell_type)

set_by_raw_data(odict)