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Refactor align#1136

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kain88-de wants to merge 14 commits intoMDAnalysis:developMDAnalysis/mdanalysis:developfrom kain88-de:refactor-alignkain88-de/mdanalysis:refactor-alignCopy head branch name to clipboard

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Commits on Jan 27, 2017

• refactor rms.py:rmsd

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• Add weights kwarg to alignto

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• introduce weights kwargs also for AlignTrj

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• RMSD uses new weights kwarg, fixes bug as well

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• correct test results!

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• convert RMSF to AnalysisBase

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• fix docs from using deprecated method

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• add deprecation warnings

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• update CHANGELOG

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• add deprecation tests

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• Change encore function expect conf distance

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• fix docs and default parameters

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Commits on Feb 4, 2017

• update confdistmatrix.py to new weights

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• update tests to new kwargs

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