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Resolve cyclic import issues #50

Merged
merged 6 commits into from Jun 4, 2020
Merged

Resolve cyclic import issues #50

merged 6 commits into from Jun 4, 2020

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sobolevnrm
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@sobolevnrm sobolevnrm commented May 30, 2020 •
edited

Fixes #49

@sobolevnrm
Break propka.calculations into parts.
461edda 
Broken into three files to simplify import analysis:

* `calculations.py` - distance calculations and simple math
* `energy.py` - energy calculations
* `hydrogens.py` - hydrogen geometry calculations

Working towards addressing jensengroup#49
@sobolevnrm
Remove cyclic import based on atom.py
397d5e1 
Partially addresses jensengroup#49
@sobolevnrm
Remove cyclic import based on I/O in pdb.py.
b597a6f 
Partially addresses jensengroup#49
@sobolevnrm
Resolve cyclic import problem.
84846aa 
Fixes jensengroup#49

Moved I/O into higher level of of code; should make
issue jensengroup#51
easier to resolve
@sobolevnrm
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@speleo3 and @orbeckst - can you please take a look at this?

Note that I had to refactor some modules and create new ones to fix the problem We're now definitely in the realm of PROPKA 3.2.

@sobolevnrm sobolevnrm mentioned this pull request May 31, 2020
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speleo3
speleo3 reviewed Jun 3, 2020
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speleo3 approved these changes Jun 3, 2020
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Pretty large patch, but looks good from what I could see.

@sobolevnrm sobolevnrm merged commit df028e4 into jensengroup:master Jun 4, 2020
@sobolevnrm sobolevnrm deleted the nathan/import branch June 4, 2020 00:50
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@speleo3 speleo3 speleo3 approved these changes

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Fix cyclic import in PROPKA
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@sobolevnrm @speleo3