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Update read and write #8

Merged
merged 31 commits into from
Oct 23, 2019
Merged

Update read and write #8

merged 31 commits into from
Oct 23, 2019

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CunliangGeng
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@CunliangGeng CunliangGeng commented Oct 9, 2019 •
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Updates:

  1. added element column
  2. update exportpdb to output properly formatted atom name and xyz values
  3. remove no_extra
  4. add read_pdb function
  5. add get_rot_axis_angle function
  6. update some functions to align with DeepRank needs
  7. update docstrings

NicoRenaud
NicoRenaud requested changes Oct 11, 2019
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It looks nice but it breaks all the tests. So we have to fix that before merging !

pdb2sql/pdb2sqlcore.py Show resolved Hide resolved
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pdb2sql/pdb2sql_base.py Show resolved Hide resolved
pdb2sql/pdb2sql_base.py
line += '\n'

f.write(line)

# close
f.close()

def _format_atomname(self, data):
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That's nice and controlled but is it needed to read the data ? But at least to write it I think it's really useful

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I assume the input PDB has strict format, so we don't it that for reading. But we do need some code to preprocess PDB files, I'll write it later.

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CunliangGeng commented Oct 21, 2019 •
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only the test_pdb2sqlAlchemy.py failed, it should be fine. I did not change anything of pdb2sqlAlchemy.py file in the PR. We can have a look at the updates together.

NicoRenaud
NicoRenaud requested changes Oct 22, 2019
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we should fix the sqlalchemy test before merging
Maybe it's as easy as using a proper pdb ...

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Actually there are two bugs in pdb2sqlAlchemy.py. Fixed.

@NicoRenaud NicoRenaud merged commit 06a67a3 into master Oct 23, 2019
@CunliangGeng CunliangGeng deleted the update_read_write branch October 23, 2019 13:11
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@CunliangGeng @NicoRenaud