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replace code with pdb2sql package #111
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Pull Request Test Coverage Report for Build 639
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@NicoRenaud All checks failed because the current |
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Finally freesasa can be installed using pip, but only version 2.0.3.post7. |
NicoRenaud
approved these changes
Nov 25, 2019
| @@ -81,7 +81,7 @@ def __init__(self, pdbfile, param_charge=None, param_vdw=None, | |||
| self.atom_key = 'chainID, resSeq, resName, name' | |||
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| # read the pdb as an sql | |||
| self.sqldb = pdb2sql(self.pdbfile) | |||
| self.sqldb = pdb2sql.pdb2sql(self.pdbfile) | |||
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that's from pdb2sql_core right ?
| if ds: | ||
| ds = np.array(ds).astype('|S' + str(len(ds[0]))) | ||
| else: | ||
| ds = np.array(ds) |
deeprank/generate/DataGenerator.py
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| @@ -411,11 +413,11 @@ def create_database( | |||
| self.f5.copy(mol_name + '/features/', molgrp) | |||
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| # rotate the feature | |||
| self._rotate_feature(molgrp, axis, angle, mol_center) | |||
| DataGenerator._rotate_feature(molgrp, axis, angle, mol_center) | |||
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I misunderstood static method before. self is better here.
deeprank/generate/DataGenerator.py
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| @@ -577,7 +579,7 @@ def add_feature(self, remove_error=True, prog_bar=True): | |||
| aug_molgrp.create_dataset("features/" + k, data=data) | |||
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| # rotate | |||
| self._rotate_feature( | |||
| DataGenerator._rotate_feature( | |||
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same here, why DataGenerator. and not self._rotate_feature ?
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| # get the pdb-format data | ||
| data = sqldb.sql2pdb() |
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nice little function here :)
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To solve issues: #100 #102.
Note: please first merge RP #103 and #107 and then this RP.