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hbond analysis: fixed incorrect residue handling with trailing numbers (
#1339) * test for correct TIP3P resname in hbond analysis table (#801) * Fixed incorrect handling of residue names with trailing numbers in HydrogenBondAnalysis (issue #801) - fixes #801 - analysis.hbond.hbond_analysis.HydrogenBondAnalysis now correctly stores and parses donor and acceptor names and is not tripped up by resnames that end in numbers, such as TIP3 - store timeseries as _timeseries with donor and acceptor atom identifiers as tuples instead of strings (avoids the use of fragile lib.util.parse_residue()) - made timeseries a property that is generated on the fly so that old code does not break, but it is not cached (to avoid memory consumption for big trajectories) and so users should cache themselves if needed - added tests - rewrote parts of the docs and added notes on use of timeseries - updated DEPRECATION warning for 1-based indices to 0.17.0 (should have been removed in 0.16.0 but we forgot) * hbond analysis doc fixes/improvements - mostly numpy style (whenever possible): Apparently, napoleon does not like a single Notes and See Also section, need to use reST. - named the 1-based indices "idx" in the docs. - added example for analysis - describe convenience analysis functions - how to use pandas * HydrogneBondAnalysis: internal clean up Use atom.index instead of atom.index+1 internally and for debug output. * Hbond analysis: fixed docs (stated wrong defaults for updating) * hbond analysis: addressed review comments
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