Fixes and improvements for 'calcstate' analysis#629

Merged

drroe merged 20 commits intoAmber-MD:masterfrom

drroe:update.state

Aug 28, 2018

Commits on Aug 23, 2018

DRR - Cpptraj: Allow states to have multiple criteria
Daniel R. Roe
committed
DRR - Cpptraj: Calculate state totals.
Daniel R. Roe
committed
DRR - Cpptraj: Allow states to be defined multiple times; this effectively acts as an 'OR' operator in addition to the implicit 'AND'
Daniel R. Roe
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DRR - Cpptraj: Start adding state-specific data sets
Daniel R. Roe
committed
DRR - Cpptraj: Add more data sets for state-related data
Daniel R. Roe
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DRR - Cpptraj: Finish transitioning state-related data to data sets.
Daniel R. Roe
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DRR - Cpptraj: Correctly determine length of final lifetime when transition has not occurred.
Daniel R. Roe
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DRR - Cpptraj: Update for fixed final frame lifetime calc and new format
Daniel R. Roe
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DRR - Cpptraj: Minor version bump since 'calcstate' output format has changed slightly and certain parts are not automatically written to stdout anymore.
Daniel R. Roe
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DRR - Cpptraj: Remove old code.
Daniel R. Roe
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DRR - Cpptraj: New 'dataset' command mode: invert
Daniel R. Roe
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DRR - Cpptraj: Add keyword for specifying set containing legends.
Daniel R. Roe
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Commits on Aug 24, 2018

DRR - Cpptraj: When writing in grace format, if a single string set is present use it as data set labels.
Daniel R. Roe
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DRR - Cpptraj: Condense the state superseded warning
Daniel R. Roe
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DRR - Cpptraj: Add std data io groupbyname option
Daniel R. Roe
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DRR - Cpptraj: Update help.
Daniel R. Roe
committed

Commits on Aug 27, 2018

DRR - Cpptraj: Fix up debug output
Daniel R. Roe
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DRR - Cpptraj: Do not print definitions index to avoid confusion with state index
Daniel R. Roe
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DRR - Cpptraj: Add help and more feedback for dataset invert.
Daniel R. Roe
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DRR - Cpptraj: dataset invert test
Daniel R. Roe
committed