proteindf_tools package

class proteindf_tools.Basis2(basis2_path='')[ソース]

ベースクラス: object

read ProteinDF basis2 file

>>> bs2 = Basis2("data/basis2.sample")
>>> print(bs2.get_basis2())
O-CARBON (621/41) by FS
 3 2 0 0 0 0 0 0 0 0 0
 6
     2.808064e+03  2.017830e-03
     4.211383e+02  1.543320e-02
     9.558662e+01  7.558155e-02
     2.673900e+01  2.478282e-01
     8.432827e+00  4.793725e-01
     2.760582e+00  3.338344e-01
 2
     5.447004e+00 -7.784077e-02
     4.792422e-01  5.689560e-01
 1
     1.461565e-01  1.000000e+00
 4
     1.813085e+01  1.585473e-02
     4.099883e+00  9.568277e-02
     1.185837e+00  3.049119e-01
     3.685974e-01  4.935017e-01
 1
     1.097200e-01  1.000000e+00

A-CARBON (7/2;7/2) by FS
 7 2 0 0 0 0 0 0 0 0 0
 1
     3.467611e+02  1.000000e+00
 1
     7.966888e+01  1.000000e+00
 1
     2.201073e+01  1.000000e+00
 1
     6.473901e+00  1.000000e+00
 1
     2.508147e+00  1.000000e+00
 1
     7.781041e-01  1.000000e+00
 1
     2.288027e-01  1.000000e+00
 1
     2.508147e+00  1.000000e+00
 1
     2.288027e-01  1.000000e+00
A-CARBON (7/2;7/2) by FS
 7 2 0 0 0 0 0 0 0 0 0
 1
     1.160000e+02  1.000000e+00
 1
     2.655629e+01  1.000000e+00
 1
     7.336909e+00  1.000000e+00
 1
     2.157967e+00  1.000000e+00
 1
     8.360489e-01  1.000000e+00
 1
     2.593680e-01  1.000000e+00
 1
     7.626760e-02  1.000000e+00
 1
     8.360489e-01  1.000000e+00
 1
     7.626760e-02  1.000000e+00
get_basis2()[ソース]
get_basisset(name)[ソース]
get_basisset_j(name)[ソース]
get_basisset_xc(name)[ソース]
class proteindf_tools.BasisSet(*args, **kwargs)[ソース]

ベースクラス: 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()[ソース]

shell_typeが'spd'などの場合に分解する

get_basis2()[ソース]
get_num_of_CGTOs(shell_type)[ソース]
get_number_of_AOs()[ソース]
get_raw_data()[ソース]
property max_shell_type
property max_shell_type_id
property name
set_by_raw_data(odict)[ソース]
sort()[ソース]

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.ContractedGTO(*args, **kwargs)[ソース]

ベースクラス: 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()[ソース]

shell_typeが'spd'などの場合に分解する

classmethod get_basis_type(shell_type_id, basis_id)[ソース]

軌道種類の文字列を返す 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()[ソース]
classmethod get_shell_type(id)[ソース]
classmethod get_shell_type_id(shell_type)[ソース]

shell_typeに対応するidを返す

s: 0, p: 1, d: 2

classmethod get_supported_shell_types()[ソース]
normalize()[ソース]
property scale_factor
set_by_raw_data(odict)[ソース]
property shell_type
property shell_type_id
class proteindf_tools.GaussianParam[ソース]

ベースクラス: QmSim

Gaussianの計算条件を設定する

property basisset
property charge
property ext_basisset
get_inputfile_contents()[ソース]
property jobtype
property title
class proteindf_tools.Matrix(*args, **kwargs)[ソース]

ベースクラス: Matrix

classmethod find_header_struct(file_path)[ソース]
classmethod get_size(file_path)[ソース]
classmethod is_loadable(file_path)[ソース]
load(file_path)[ソース]

Load the matrix. True is returned if the reading is successful.

save(file_path, matrix_type=1)[ソース]
class proteindf_tools.OrbInfo(obj=None)[ソース]

ベースクラス: object

軌道情報を管理する

get_atom(orb_index)[ソース]
get_atom_id(orb_index)[ソース]
get_basis_type(orb_index)[ソース]
get_num_of_orbitals()[ソース]
get_shell_type(orb_index)[ソース]
class proteindf_tools.PdfParam(rhs=None)[ソース]

ベースクラス: PdfParamObject

class proteindf_tools.PdfSim(*args, **kwargs)[ソース]

ベースクラス: object

numerical_grad(pdfparam, workdir='.', accuracy=0.001, delta=0.001)[ソース]
opt(pdfparam, workdir='.', max_cycle=100)[ソース]
pop(iteration=-1, *args, **kwargs)[ソース]

calc population

setup(pdfparam=None, workdir='.')[ソース]

setup to run ProteinDF

sp(pdfparam, *args, **kwargs)[ソース]

calc single-point

Keyword arguments: pdfparam --- PdfParam object represented the calculation condition. workdir --- working directory. db_path --- ProteinDF ArchiveDB path (default: pdfresults.db) dry_run --- if True, the calculation is NOT carried out. Default is False.

Returns: tuple of the number of iterations and the total energy.

total_energy(pdfparam, workdir='.')[ソース]
class proteindf_tools.PopEspUtils[ソース]

ベースクラス: PopUtils

Population Utilities for ESP

get_RRMS(mpac_path, atoms)[ソース]
class proteindf_tools.PopUtils[ソース]

ベースクラス: object

Population Utilities

static get_atomlist_by_param(param_path)[ソース]
static set_atomlist(atom_charges, atomlist)[ソース]

substitute atom_charges for atomlist

class proteindf_tools.PrimitiveGTO(*args, **kwargs)[ソース]

ベースクラス: 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()[ソース]
normalize(shell_type)[ソース]
set_by_raw_data(odict)[ソース]
class proteindf_tools.QmSim[ソース]

ベースクラス: object

QmSimulatorの基本クラス

property method
class proteindf_tools.SymmetricMatrix(*args, **kwargs)[ソース]

ベースクラス: SymmetricMatrix

classmethod find_header_struct(file_path)[ソース]
classmethod get_size(file_path)[ソース]
classmethod is_loadable(file_path)[ソース]
load(file_path)[ソース]
save(file_path, is_little_endian=True)[ソース]
class proteindf_tools.Vector(obj=[])[ソース]

ベースクラス: Vector

classmethod find_header_struct(file_path)[ソース]
classmethod is_loadable(file_path)[ソース]
load(file_path)[ソース]

Load the vector. True is returned if the reading is successful.

save(file_path)[ソース]

Submodules