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onehot encoding for residue type and polarity #21
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NicoRenaud
reviewed
Dec 3, 2020
graphprot/Graph.py
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| if self.score['irmsd'] < 1.0 : | ||
| _class = 1 | ||
| elif self.score['irmsd'] < 2.0 : | ||
| _class = 2 | ||
| elif self.score['irmsd'] < 4.0 : | ||
| _class = 3 | ||
| elif self.score['irmsd'] < 6.0 : | ||
| _class = 4 | ||
| else : | ||
| _class = 5 | ||
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| self.score['class'] = _class |
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do you need the _class variable ? why not
if self.score['irmsd'] < 1.0:
self.score['class'] = 1I also find 'class' a bit generic. Maybe 'capri_class' ?
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you could also shorten the code
self.score['class'] = 5
for thr, val in zip([6.0, 4.0, 2.0, 1.0],[4,3,2,1]):
if self.score['irmsd'] <= thr:
self.score['class'] = valbut of course it's a bit less readable ... so up to you :) (plus I don't know if what I propose here works :D)
graphprot/GraphGen.py
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| pssmA = os.path.join(pssm_path, mol_name+'.A.pssm') | ||
| pssmB = os.path.join(pssm_path, mol_name+'.B.pssm') |
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we should rename the files we give in example then Or at least check that the example still work
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| #self.nx.edges[node1, node2]['polarity'] = self._get_edge_polarity( | ||
| # node1, node2) |
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so we don't have any edge features ? no polarity and no distance ? (sorry I forgot a bit about the inner workings of the code)
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