Expand mask syntax#548

Merged

drroe merged 27 commits intoAmber-MD:masterfrom

drroe:expand_mask

Sep 27, 2017

Commits on Sep 26, 2017

DRR - Cpptraj: Start adding code for selection of molecules by mask. Modify ArgList::ArgIsMask so that it looks for characters which are valid to start masks, not just mask characters in a string.
Daniel R. Roe
committed
DRR - Cpptraj: Add some notes on new ArgIsMask behavior
Daniel R. Roe
committed
DRR - Cpptraj: Finish adding code to select atoms by molecule number. Update dependencies.
Daniel R. Roe
committed
DRR - Cpptraj: Hide debug info
Daniel R. Roe
committed
DRR - Cpptraj: Add molecule selection syntax test
Daniel R. Roe
committed
DRR - Cpptraj: Add molecule AND atom shorthand
Daniel R. Roe
committed
DRR - Cpptraj: Add molecule AND residue shorthand
Daniel R. Roe
committed
DRR - Cpptraj: Record all input in history, even if it doesnt work. Will add option to return to original behavior later.
Daniel R. Roe
committed
DRR - Cpptraj: Add beginnings of ResChain for ChainID
Daniel R. Roe
committed
DRR - Cpptraj: Finish selection by chain ID
Daniel R. Roe
committed
DRR - Cpptraj: Add selection by chain ID test
Daniel R. Roe
committed
DRR - Cpptraj: Remove terminal underscores from passed in variable names
Daniel R. Roe
committed
DRR - Cpptraj: Use typedefs
Daniel R. Roe
committed
DRR - Cpptraj: Slight reconfig of MaskToken in preparation for adding distance selection by molecule
Daniel R. Roe
committed
DRR - Cpptraj: Add molecule selection by distance
Daniel R. Roe
committed
DRR - Cpptraj: Add molecule selection by distance test
Daniel R. Roe
committed
DRR - Cpptraj: Add distance based mask outside molecule selection test
Daniel R. Roe
committed
DRR - Cpptraj: Add function to select by original residue number
Daniel R. Roe
committed
DRR - Cpptraj: Clean up function names.
Daniel R. Roe
committed
DRR - Cpptraj: Enable original residue number selection.
Daniel R. Roe
committed
DRR - Cpptraj: Add original residue number selection test
Daniel R. Roe
committed
DRR - Cpptraj: Some cleanup.
Daniel R. Roe
committed
DRR - Cpptraj: resX_ -> idxX_; more descriptive.
Daniel R. Roe
committed

Commits on Sep 27, 2017

DRR - Cpptraj: Add mol+res+atom selection test
Daniel R. Roe
committed
DRR - Cpptraj: Add missing flag set.
Daniel R. Roe
committed
DRR - Cpptraj: Test modifying the tokenizer to recognize '::' as a legit operator.
Daniel R. Roe
committed
DRR - Cpptraj: Use '::' instead of ':/' for chain ID selection.
Daniel R. Roe
committed

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Expand mask syntax#548

Expand mask syntax#548
drroe merged 27 commits intoAmber-MD:masterfrom
drroe:expand_mask

Commits on Sep 26, 2017

DRR - Cpptraj: Start adding code for selection of molecules by mask. Modify ArgList::ArgIsMask so that it looks for characters which are valid to start masks, not just mask characters in a string.

DRR - Cpptraj: Add some notes on new ArgIsMask behavior

DRR - Cpptraj: Finish adding code to select atoms by molecule number. Update dependencies.

DRR - Cpptraj: Hide debug info

DRR - Cpptraj: Add molecule selection syntax test

DRR - Cpptraj: Add molecule AND atom shorthand

DRR - Cpptraj: Add molecule AND residue shorthand

DRR - Cpptraj: Record all input in history, even if it doesnt work. Will add option to return to original behavior later.

DRR - Cpptraj: Add beginnings of ResChain for ChainID

DRR - Cpptraj: Finish selection by chain ID

DRR - Cpptraj: Add selection by chain ID test

DRR - Cpptraj: Remove terminal underscores from passed in variable names

DRR - Cpptraj: Use typedefs

DRR - Cpptraj: Slight reconfig of MaskToken in preparation for adding distance selection by molecule

DRR - Cpptraj: Add molecule selection by distance

DRR - Cpptraj: Add molecule selection by distance test

DRR - Cpptraj: Add distance based mask outside molecule selection test

DRR - Cpptraj: Add function to select by original residue number

DRR - Cpptraj: Clean up function names.

DRR - Cpptraj: Enable original residue number selection.

DRR - Cpptraj: Add original residue number selection test

DRR - Cpptraj: Some cleanup.

DRR - Cpptraj: resX_ -> idxX_; more descriptive.

Commits on Sep 27, 2017

DRR - Cpptraj: Add mol+res+atom selection test

DRR - Cpptraj: Add missing flag set.

DRR - Cpptraj: Test modifying the tokenizer to recognize '::' as a legit operator.

DRR - Cpptraj: Use '::' instead of ':/' for chain ID selection.