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Merged
merged 37 commits into from
Dec 7, 2020
Merged

Implement Alternative Inputs #15

merged 37 commits into from
Dec 7, 2020

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jackgisby
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@jackgisby jackgisby commented Dec 7, 2020 •
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  • Main metaboblend functions spread across more .py files
  • Implement functions for parsing of MSP files (MoNa and MassBank style)
  • Add integer substructure keys to substructure database
  • Test isomorphism database on linux only

jackgisby and others added 30 commits September 19, 2020 12:24
@jackgisby
Return metabolite ID with msn annotation results
ae0bf23
@jackgisby
Rewrite MSn method for limiting connectivity to fragment edges only
de6eab2
@jackgisby
Add option for use of smiles without non-structural isomeric information
cf2378e
@jackgisby
Update tests
4726b3a
@jackgisby
Correct return type hints
dd2013b
@jackgisby
Implement SQLITE3 annotate_msn results database
071e9a2
@jackgisby
Add msn option to ResultsDb
4d52c40
@jackgisby
Re-structure results db tables
918b7b0
@jackgisby
Update add_ms to add ms information to the queries table
030083b
@jackgisby
Add function to insert entries into the results and substructures tables
b91c1ae
@jackgisby
Add function to get structure frequencies and/or SMILEs
4125307
@jackgisby
Update user-facing functions for compatibility with ResultsDb
6017bda
@jackgisby
Remove text-based output and return substructure smiles from build fu…
b7f405b 
…nctions in addition to final structures
@jackgisby
Update build unit tests for ResultsDb
3c04cf0
@jackgisby
Add CSV output for build functions
8a9dd0e
@jackgisby
Check if ResultsDb output matches reference files
c75ac38
@jackgisby
Check ResultsDb CSV files line by line vs reference
94e31cd
@jackgisby
Implement simple bond dissociation energy calculations
38c8ee0
@jackgisby
Add integer MS integer IDs and implement calculate_frequencies to mor…
be844fc 
…e efficiently calculate structure frequencies
@jackgisby
Re-format get_bond_enthalpies
a5d7dcb
@jackgisby
Use integer IDs for results DB
f36e174
@jackgisby
Add retain_substructures option
580219d
@jackgisby
Make filter_hmdbid_substructures a filtered version of the hmdbid_sub…
a9b2cfd 
…structures table
@jackgisby
Implement the substructure network generation algorithm in SQLite ins…
26e2c89 
…tead of networkx
@jackgisby
Add get_substructure_network function to convert SQLite3 substructure…
9eaea12 
… network to a networkx graph
@jackgisby
Implement get_single_edge to get substructure edge weights without th…
8a19a0e 
…e generation of a substructure network
@jackgisby
Add integer substructure key
3e43432
@jackgisby
Update unit tests
151a189
@jackgisby
Add parse_ms_data function to convert user provided raw data into a l…
d9f1607 
…ist required for building
@jackgisby
Implement msp parsing, update existing tests and spread functions acr…
a10ca66 
…oss additional files
@jackgisby jackgisby requested a review from RJMW December 7, 2020 20:08
@jackgisby jackgisby merged commit 1ea6ed4 into dev Dec 7, 2020
@jackgisby jackgisby deleted the feat-alternate_inputs branch December 7, 2020 20:52
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@RJMW RJMW RJMW approved these changes

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@jackgisby @RJMW