Calculate statistics from a set of structures¶
SOAP statistical table
- class statsTable.rawsp(pdbset='', features='', genmethod='', tlib=None, decoy=False, routine='calc_sp_all', model={})[source]¶
Statistics from a set of structures
- Parameters:
pdbset (str) – the name of the set of PDB or decoy structures
genmethod (str) – the filters used for generating the table, see
utility.decode_genmethod()
for more detail.decoy (str) – True if the
rawsp.pdbset
represent decoysmodel (dict) – the parameters for this class can also be passed by a dict
- Example genmethod:
bs2dsp: bond separation 2 with disulfide bond taken into consideration
cs1: chain separation >=1
ss1: sequence separation >=1
- class statsTable.scaledsp(pm='', rspo=[], model=[], previouspm='')[source]¶
Processed statistics table from a set of structures
- Parameters:
pm definition:
pm => [pp[0-9]+,+] ,[(gps|ks)\number,+] ,npend|npsum pp[0-9]+ : add number to raw table (gps|ks)\number : gaussian process or kernel smoothing with strength \number. npend|npsum : normalize the count by the last bin or by the sum of the distribution (results in a proper discrete probabilistic distribution).