pytraj.datasets.c_datasets.Dataset¶Bases: object
Attributes
aspect |
|
data |
mostly memoryview |
dtype |
|
key |
|
name |
|
scalar_type |
|
size |
|
values |
return a copy or non-copy, depending on data |
Methods
to_dict(self[, use_numpy]) |
|
to_ndarray(self[, copy]) |
return ndarray view of self.data |
tolist(self) |
aspect¶data¶mostly memoryview
dtype¶key¶name¶scalar_type¶size¶to_dict(self, use_numpy=False)¶to_ndarray(self, copy=False)¶return ndarray view of self.data
tolist(self)¶values¶return a copy or non-copy, depending on data
pytraj.datasets.c_datasets.Dataset1D¶Bases: pytraj.datasets.c_datasets.Dataset
Attributes
aspect |
|
data |
mostly memoryview |
dtype |
|
key |
|
name |
|
scalar_type |
|
shape |
|
size |
|
values |
return a copy or non-copy, depending on data |
Methods
from_array_like(self, array_like) |
Notes: require numpy |
to_dict(self[, use_numpy]) |
|
to_ndarray(self[, copy]) |
return ndarray view of self.data |
tolist(self) |
aspect¶data¶mostly memoryview
dtype¶from_array_like(self, array_like)¶Notes: require numpy
key¶name¶scalar_type¶shape¶size¶to_dict(self, use_numpy=False)¶to_ndarray(self, copy=False)¶return ndarray view of self.data
tolist(self)¶values¶return a copy or non-copy, depending on data
pytraj.datasets.c_datasets.Dataset2D¶Bases: pytraj.datasets.c_datasets.Dataset
Attributes
aspect |
|
data |
mostly memoryview |
dtype |
|
key |
|
kind |
|
n_cols |
|
n_rows |
|
name |
|
scalar_type |
|
size |
|
values |
return a copy or non-copy, depending on data |
Methods
get_element(self, int x, int y) |
|
get_full_matrix(self) |
|
to_dataframe(self) |
|
to_dict(self[, use_numpy]) |
|
to_ndarray(self[, copy]) |
return ndarray view of self.data |
tolist(self) |
aspect¶data¶mostly memoryview
dtype¶get_element(self, int x, int y)¶get_full_matrix(self)¶key¶kind¶n_cols¶n_rows¶name¶scalar_type¶size¶to_dataframe(self)¶to_dict(self, use_numpy=False)¶to_ndarray(self, copy=False)¶return ndarray view of self.data
tolist(self)¶values¶return a copy or non-copy, depending on data
pytraj.datasets.c_datasets.Dataset3D¶Bases: pytraj.datasets.c_datasets.Dataset
Attributes
aspect |
|
data |
mostly memoryview |
dtype |
|
key |
|
name |
|
scalar_type |
|
size |
|
values |
return a copy or non-copy, depending on data |
Methods
to_dict(self[, use_numpy]) |
|
to_ndarray(self[, copy]) |
return ndarray view of self.data |
tolist(self) |
aspect¶data¶mostly memoryview
dtype¶key¶name¶scalar_type¶size¶to_dict(self, use_numpy=False)¶to_ndarray(self, copy=False)¶return ndarray view of self.data
tolist(self)¶values¶return a copy or non-copy, depending on data
pytraj.datasets.c_datasets.DatasetCoords¶Bases: pytraj.datasets.c_datasets.Dataset
Attributes
aspect |
|
data |
mostly memoryview |
dtype |
|
key |
|
n_atoms |
used for frame_iter |
n_frames |
|
name |
|
scalar_type |
|
size |
|
top |
|
values |
return a copy or non-copy, depending on data |
xyz |
return a copy of xyz coordinates (ndarray, shape=(n_frames, n_atoms, 3) |
Methods
add_frame(self, Frame frame) |
|
allocate_frame(self) |
|
append(self, frame) |
alis of addframe |
get_frame(self, int idx, Frame frameout) |
|
to_dataframe(self) |
|
to_dict(self[, use_numpy]) |
|
to_ndarray(self[, copy]) |
return ndarray view of self.data |
tolist(self) |
return flatten list for traj-like object |
add_frame(self, Frame frame)¶allocate_frame(self)¶append(self, frame)¶alis of addframe
aspect¶data¶mostly memoryview
dtype¶get_frame(self, int idx, Frame frameout)¶key¶n_atoms¶used for frame_iter
n_frames¶name¶scalar_type¶size¶to_dataframe(self)¶to_dict(self, use_numpy=False)¶to_ndarray(self, copy=False)¶return ndarray view of self.data
tolist(self)¶return flatten list for traj-like object
top¶values¶return a copy or non-copy, depending on data
xyz¶return a copy of xyz coordinates (ndarray, shape=(n_frames, n_atoms, 3) We can not return a memoryview since Trajectory is a C++ vector of Frame object
pytraj.datasets.c_datasets.DatasetCoordsCRD¶Bases: pytraj.datasets.c_datasets.DatasetCoords
Attributes
aspect |
|
data |
|
dtype |
|
key |
|
n_atoms |
used for frame_iter |
n_frames |
|
name |
|
scalar_type |
|
size |
|
top |
|
values |
|
xyz |
return a copy of xyz coordinates (ndarray, shape=(n_frames, n_atoms, 3) |
Methods
add_frame(self, Frame frame) |
|
allocate_frame(self) |
|
append(self, frame) |
alis of addframe |
get_frame(self, int idx, Frame frameout) |
|
load(self, filename) |
|
to_dataframe(self) |
|
to_dict(self[, use_numpy]) |
|
to_ndarray(self[, copy]) |
return ndarray view of self.data |
tolist(self) |
return flatten list for traj-like object |
add_frame(self, Frame frame)¶allocate_frame(self)¶append(self, frame)¶alis of addframe
aspect¶data¶dtype¶get_frame(self, int idx, Frame frameout)¶key¶load(self, filename)¶n_atoms¶used for frame_iter
n_frames¶name¶scalar_type¶size¶to_dataframe(self)¶to_dict(self, use_numpy=False)¶to_ndarray(self, copy=False)¶return ndarray view of self.data
tolist(self)¶return flatten list for traj-like object
top¶values¶xyz¶return a copy of xyz coordinates (ndarray, shape=(n_frames, n_atoms, 3) We can not return a memoryview since Trajectory is a C++ vector of Frame object
pytraj.datasets.c_datasets.DatasetCoordsRef¶Bases: pytraj.datasets.c_datasets.DatasetCoords
Attributes
aspect |
|
data |
|
dtype |
|
key |
|
n_atoms |
used for frame_iter |
n_frames |
|
name |
|
scalar_type |
|
size |
|
top |
|
values |
|
xyz |
Methods
add_frame(self, Frame frame) |
|
allocate_frame(self) |
|
append(self, frame) |
alis of addframe |
get_frame(self) |
|
to_dataframe(self) |
|
to_dict(self[, use_numpy]) |
|
to_ndarray(self[, copy]) |
return ndarray view of self.data |
tolist(self) |
return flatten list for traj-like object |
add_frame(self, Frame frame)¶allocate_frame(self)¶append(self, frame)¶alis of addframe
aspect¶data¶dtype¶get_frame(self)¶key¶n_atoms¶used for frame_iter
n_frames¶name¶scalar_type¶size¶to_dataframe(self)¶to_dict(self, use_numpy=False)¶to_ndarray(self, copy=False)¶return ndarray view of self.data
tolist(self)¶return flatten list for traj-like object
top¶values¶xyz¶pytraj.datasets.c_datasets.DatasetDouble¶Bases: pytraj.datasets.c_datasets.Dataset1D
Attributes
aspect |
|
data |
|
dtype |
|
key |
|
name |
|
scalar_type |
|
shape |
|
size |
|
values |
return a copy or non-copy, depending on data |
Methods
append(self, double d) |
|
from_array_like(self, array_like) |
Notes: require numpy |
resize(self, size_t sizeIn) |
|
to_dict(self[, use_numpy]) |
|
to_ndarray(self[, copy]) |
return ndarray view of self.data |
tolist(self) |
append(self, double d)¶aspect¶data¶dtype¶from_array_like(self, array_like)¶Notes: require numpy
key¶name¶resize(self, size_t sizeIn)¶scalar_type¶shape¶size¶to_dict(self, use_numpy=False)¶to_ndarray(self, copy=False)¶return ndarray view of self.data
tolist(self)¶values¶return a copy or non-copy, depending on data
pytraj.datasets.c_datasets.DatasetFloat¶Bases: pytraj.datasets.c_datasets.Dataset1D
Attributes
aspect |
|
data |
|
dtype |
|
key |
|
name |
|
scalar_type |
|
shape |
|
size |
|
values |
return a copy or non-copy, depending on data |
Methods
append(self, ds) |
|
from_array_like(self, array_like) |
Notes: require numpy |
resize(self, size_t sizeIn) |
|
to_dict(self[, use_numpy]) |
|
to_ndarray(self[, copy]) |
return ndarray view of self.data |
tolist(self) |
append(self, ds)¶aspect¶data¶dtype¶from_array_like(self, array_like)¶Notes: require numpy
key¶name¶resize(self, size_t sizeIn)¶scalar_type¶shape¶size¶to_dict(self, use_numpy=False)¶to_ndarray(self, copy=False)¶return ndarray view of self.data
tolist(self)¶values¶return a copy or non-copy, depending on data
pytraj.datasets.c_datasets.DatasetGridDouble¶Bases: pytraj.datasets.c_datasets.Dataset3D
Attributes
aspect |
|
data |
|
dtype |
|
key |
|
name |
|
nx |
|
ny |
|
nz |
|
scalar_type |
|
shape |
|
size |
|
values |
return a copy or non-copy, depending on data |
Methods
resize(self, size_t x, size_t y, size_t z) |
|
to_dict(self[, use_numpy]) |
|
to_ndarray(self[, copy]) |
|
tolist(self) |
aspect¶data¶dtype¶key¶name¶nx¶ny¶nz¶resize(self, size_t x, size_t y, size_t z)¶scalar_type¶shape¶size¶to_dict(self, use_numpy=False)¶to_ndarray(self, copy=True)¶tolist(self)¶values¶return a copy or non-copy, depending on data
pytraj.datasets.c_datasets.DatasetGridFloat¶Bases: pytraj.datasets.c_datasets.Dataset3D
Attributes
aspect |
|
data |
|
dtype |
|
key |
|
name |
|
nx |
|
ny |
|
nz |
|
scalar_type |
|
shape |
|
size |
|
values |
return a copy or non-copy, depending on data |
Methods
resize(self, size_t x, size_t y, size_t z) |
|
to_dict(self[, use_numpy]) |
|
to_ndarray(self[, copy]) |
|
tolist(self) |
aspect¶data¶dtype¶key¶name¶nx¶ny¶nz¶resize(self, size_t x, size_t y, size_t z)¶scalar_type¶shape¶size¶to_dict(self, use_numpy=False)¶to_ndarray(self, copy=True)¶tolist(self)¶values¶return a copy or non-copy, depending on data
pytraj.datasets.c_datasets.DatasetInteger¶Bases: pytraj.datasets.c_datasets.Dataset1D
Attributes
aspect |
|
data |
|
dtype |
|
key |
|
name |
|
scalar_type |
|
shape |
|
size |
|
values |
return a copy or non-copy, depending on data |
Methods
append(self, val) |
|
from_array_like(self, array_like) |
Notes: require numpy |
resize(self, size_t sizeIn) |
|
to_dict(self[, use_numpy]) |
|
to_ndarray(self[, copy]) |
return ndarray view of self.data |
tolist(self) |
append(self, val)¶aspect¶data¶dtype¶from_array_like(self, array_like)¶Notes: require numpy
key¶name¶resize(self, size_t sizeIn)¶scalar_type¶shape¶size¶to_dict(self, use_numpy=False)¶to_ndarray(self, copy=False)¶return ndarray view of self.data
tolist(self)¶values¶return a copy or non-copy, depending on data
pytraj.datasets.c_datasets.DatasetMatrix3x3¶Bases: pytraj.datasets.c_datasets.Dataset
Attributes
aspect |
|
data |
|
dtype |
|
key |
|
name |
|
scalar_type |
|
size |
|
values |
return a copy or non-copy, depending on data |
Methods
append(self, Matrix_3x3 mat) |
|
to_dict(self[, use_numpy]) |
|
to_ndarray(self[, copy]) |
return a copy |
tolist(self) |
append(self, Matrix_3x3 mat)¶aspect¶data¶dtype¶key¶name¶scalar_type¶size¶to_dict(self, use_numpy=False)¶to_ndarray(self, copy=True)¶return a copy
tolist(self)¶values¶return a copy or non-copy, depending on data
pytraj.datasets.c_datasets.DatasetMatrixDouble¶Bases: pytraj.datasets.c_datasets.Dataset2D
Attributes
aspect |
|
data |
|
dtype |
|
key |
|
kind |
|
mass |
|
n_cols |
|
n_rows |
|
n_snapshots |
|
name |
|
scalar_type |
|
size |
|
values |
return a copy or non-copy, depending on data |
Methods
append(self, double d) |
|
element(self, size_t x, size_t y) |
|
get_element(self, int x, int y) |
|
get_full_matrix(self) |
return python array with length = n_rows*n_cols |
set_element(self, size_t x, size_t y, double d) |
|
store_mass(self, Darray mIn) |
|
to_dataframe(self) |
|
to_dict(self[, use_numpy]) |
|
to_half_matrix(self) |
|
to_ndarray(self[, copy]) |
use copy=True to be the same as Dataset1D |
tolist(self) |
|
vect(self) |
append(self, double d)¶aspect¶data¶dtype¶element(self, size_t x, size_t y)¶get_element(self, int x, int y)¶get_full_matrix(self)¶return python array with length = n_rows*n_cols
key¶kind¶mass¶n_cols¶n_rows¶n_snapshots¶name¶scalar_type¶set_element(self, size_t x, size_t y, double d)¶size¶store_mass(self, Darray mIn)¶to_dataframe(self)¶to_dict(self, use_numpy=False)¶to_half_matrix(self)¶to_ndarray(self, copy=True)¶use copy=True to be the same as Dataset1D
tolist(self)¶values¶return a copy or non-copy, depending on data
vect(self)¶pytraj.datasets.c_datasets.DatasetMatrixFloat¶Bases: pytraj.datasets.c_datasets.Dataset2D
Attributes
aspect |
|
data |
|
dtype |
|
key |
|
kind |
|
n_cols |
|
n_rows |
|
name |
|
scalar_type |
|
size |
|
values |
return a copy or non-copy, depending on data |
Methods
get_element(self, int x, int y) |
|
get_full_matrix(self) |
|
to_dataframe(self) |
|
to_dict(self[, use_numpy]) |
|
to_half_matrix(self) |
|
to_ndarray(self[, copy]) |
|
tolist(self) |
aspect¶data¶dtype¶get_element(self, int x, int y)¶get_full_matrix(self)¶key¶kind¶n_cols¶n_rows¶name¶scalar_type¶size¶to_dataframe(self)¶to_dict(self, use_numpy=False)¶to_half_matrix(self)¶to_ndarray(self, copy=True)¶tolist(self)¶values¶return a copy or non-copy, depending on data
pytraj.datasets.c_datasets.DatasetMesh¶Bases: pytraj.datasets.c_datasets.Dataset1D
Attributes
aspect |
|
data |
|
dtype |
|
key |
|
name |
|
scalar_type |
|
shape |
|
size |
|
values |
return a copy or non-copy, depending on data |
Methods
from_array_like(self, array_like) |
Notes: require numpy |
to_dict(self[, use_numpy]) |
|
to_ndarray(self[, copy]) |
use copy=True to make consistent with Dataset1D |
tolist(self) |
return 2D list with format [index, value] |
aspect¶data¶dtype¶from_array_like(self, array_like)¶Notes: require numpy
key¶name¶scalar_type¶shape¶size¶to_dict(self, use_numpy=False)¶to_ndarray(self, copy=True)¶use copy=True to make consistent with Dataset1D
tolist(self)¶return 2D list with format [index, value]
values¶return a copy or non-copy, depending on data
pytraj.datasets.c_datasets.DatasetModes¶Bases: pytraj.datasets.c_datasets.Dataset
Attributes
aspect |
|
data |
|
dtype |
|
eigenvalues |
|
eigenvectors |
|
key |
|
n_modes |
|
name |
|
scalar_type |
|
size |
|
values |
|
vector_size |
Methods
eigval_to_freq(self, x) |
|
to_dict(self[, use_numpy]) |
|
to_ndarray(self[, copy]) |
return ndarray view of self.data |
tolist(self) |
aspect¶data¶dtype¶eigenvalues¶eigenvectors¶eigval_to_freq(self, x)¶key¶n_modes¶name¶scalar_type¶size¶to_dict(self, use_numpy=False)¶to_ndarray(self, copy=False)¶return ndarray view of self.data
tolist(self)¶values¶vector_size¶pytraj.datasets.c_datasets.DatasetString¶Bases: pytraj.datasets.c_datasets.Dataset1D
Attributes
aspect |
|
data |
|
dtype |
|
key |
|
name |
|
scalar_type |
|
shape |
|
size |
|
values |
return a copy or non-copy, depending on data |
Methods
from_array_like(self, array_like) |
Notes: require numpy |
resize(self, size_t sizeIn) |
|
to_dict(self[, use_numpy]) |
|
to_ndarray(self[, copy]) |
return ndarray view of self.data |
tolist(self) |
aspect¶data¶dtype¶from_array_like(self, array_like)¶Notes: require numpy
key¶name¶resize(self, size_t sizeIn)¶scalar_type¶shape¶size¶to_dict(self, use_numpy=False)¶to_ndarray(self, copy=False)¶return ndarray view of self.data
tolist(self)¶values¶return a copy or non-copy, depending on data
pytraj.datasets.c_datasets.DatasetTopology¶Bases: pytraj.datasets.c_datasets.Dataset
Attributes
aspect |
|
data |
|
dtype |
|
key |
|
name |
|
scalar_type |
|
size |
|
values |
Methods
to_dict(self[, use_numpy]) |
|
to_ndarray(self[, copy]) |
return ndarray view of self.data |
tolist(self) |
aspect¶data¶dtype¶key¶name¶scalar_type¶size¶to_dict(self, use_numpy=False)¶to_ndarray(self, copy=False)¶return ndarray view of self.data
tolist(self)¶values¶pytraj.datasets.c_datasets.DatasetVector¶Bases: pytraj.datasets.c_datasets.Dataset
Attributes
aspect |
|
data |
|
dtype |
|
key |
|
name |
|
scalar_type |
|
shape |
|
size |
|
values |
return a copy or non-copy, depending on data |
Methods
append(self, Vec3 vec) |
|
resize(self, size_t sizeIn) |
|
to_dataframe(self) |
|
to_dict(self[, use_numpy]) |
|
to_ndarray(self[, copy]) |
|
tolist(self) |
append(self, Vec3 vec)¶aspect¶data¶dtype¶key¶name¶resize(self, size_t sizeIn)¶scalar_type¶shape¶size¶to_dataframe(self)¶to_dict(self, use_numpy=False)¶to_ndarray(self, copy=True)¶tolist(self)¶values¶return a copy or non-copy, depending on data