gklearn.utils.graphfiles
Utilities function to manage graph files
- loadCT(filename)[source]
load data from a Chemical Table (.ct) file.
Notes
a typical example of data in .ct is like this:
3 2 <- number of nodes and edges
0.0000 0.0000 0.0000 C <- each line describes a node (x,y,z + label)
0.0000 0.0000 0.0000 C
0.0000 0.0000 0.0000 O
1 3 1 1 <- each line describes an edge : to, from, bond type, bond stereo
2 3 1 1
Check CTFile Formats file for detailed format discription.
- loadDataset(filename, filename_y=None, extra_params=None)[source]
Read graph data from filename and load them as NetworkX graphs.
Parameters
- filenamestring
The name of the file from where the dataset is read.
- filename_ystring
The name of file of the targets corresponding to graphs.
- extra_paramsdict
Extra parameters only designated to ‘.mat’ format.
Return
data : List of NetworkX graph.
y : List
Targets corresponding to graphs.
Notes
This function supports following graph dataset formats:
‘ds’: load data from .ds file. See comments of function loadFromDS for a example.
‘cxl’: load data from Graph eXchange Language file (.cxl file). See here for detail.
‘sdf’: load data from structured data file (.sdf file). See here for details.
‘mat’: Load graph data from a MATLAB (up to version 7.1) .mat file. See README in downloadable file for details.
‘txt’: Load graph data from a special .txt file. See here for details. Note here filename is the name of either .txt file in the dataset directory.
- loadFromDS(filename, filename_y)[source]
Load data from .ds file.
Possible graph formats include:
‘.ct’: see function loadCT for detail.
‘.gxl’: see dunction loadGXL for detail.
Note these graph formats are checked automatically by the extensions of graph files.
- loadMAT(filename, extra_params)[source]
Load graph data from a MATLAB (up to version 7.1) .mat file.
Notes
A MAT file contains a struct array containing graphs, and a column vector lx containing a class label for each graph. Check README in downloadable file for detailed structure.
- loadSDF(filename)[source]
load data from structured data file (.sdf file).
Notes
A SDF file contains a group of molecules, represented in the similar way as in MOL format. Check here for detailed structure.
- loadTXT(filename)[source]
Load graph data from a .txt file.
Notes
The graph data is loaded from separate files. Check README in downloadable file, 2018 for detailed structure.