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Modifications to ITPParser #2408

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Merged
richardjgowers merged 15 commits into from
Jan 27, 2020
Merged

Modifications to ITPParser #2408

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52a9f47
fixed itp impropers, type parsing
lilyminium Nov 20, 2019
edac256
rearranged impropers to central atom first
lilyminium Nov 20, 2019
b396919
updated changelog
lilyminium Nov 20, 2019
dddafa0
changed tests
lilyminium Nov 21, 2019
0a00ec5
removed map
lilyminium Nov 21, 2019
345df0a
added if/else to itpparser
lilyminium Dec 18, 2019
76cc152
renamed and documented reduce_singular
lilyminium Jan 7, 2020
82991f6
fixed indent
lilyminium Jan 13, 2020
dbf2c7d
added section explaining keyword preprocessor flags
lilyminium Jan 14, 2020
8032830
generalised ITPParser to ITP and TOP files, so it now reads #include,…
lilyminium Jan 16, 2020
0dac71e
switched pathlib for os.path
lilyminium Jan 16, 2020
478a35e
removed split keywords and updated docs
lilyminium Jan 16, 2020
6bab7a4
added test for sequential values
lilyminium Jan 16, 2020
2c858bf
switched FileNotFoundError to IOError
lilyminium Jan 16, 2020
ce13299
removed if_stack in favour if nested skipping
lilyminium Jan 17, 2020
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4 changes: 4 additions & 0 deletions package/CHANGELOG
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Original file line number Diff line number Diff line change
Expand Up @@ -33,6 +33,10 @@ Fixes
* The expected frames are made available when a trajectory slice is sliced itself
with an incomplete slice and/or with a negative step (Issue #2413)
* TXYZ parser uses strings for the atom types like other parsers (Issue #2435)
* ITPParser now parses ITP *and* TOP files from GROMACS, reads #include files, and
substitutes #define variables both from the file and when passed in as a keyword
argument. The directives parsed into bonds, angles, impropers, and dihedrals now
match TPRParser. (PR #2408)

Enhancements
* Enhanges exception message when trajectory output file has no extension assigned.
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