Add control structures to cpptraj scripts#556

Merged

drroe merged 77 commits intoAmber-MD:masterfrom

Oct 17, 2017

Commits on Sep 27, 2017

DRR - Cpptraj: Initial attempt at adding some control structures
Daniel R. Roe
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DRR - Cpptraj: Var name change
Daniel R. Roe
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Commits on Sep 28, 2017

Merge branch 'master' into loops
Daniel R. Roe
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DRR - Cpptraj: Make for specific to atom masks initially.
Daniel R. Roe
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DRR - Cpptraj: Reorganization to allow nested control structures.
Daniel R. Roe
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DRR - Cpptraj: Detect unterminated control blocks
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DRR - Cpptraj: Add control block description, use it to provide more detailed output and error messages.
Daniel R. Roe
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DRR - Cpptraj: Add mask setup
Daniel R. Roe
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DRR - Cpptraj: Start adding logic for actually executing the control blocks.
Daniel R. Roe
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DRR - Cpptraj: Add logic for executing inner blocks recursively
Daniel R. Roe
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DRR - Cpptraj: First attempt at replacing variables.
Daniel R. Roe
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DRR - Cpptraj: Make unrecognized variable a warning
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DRR - Cpptraj: Better error handling in control structure
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Merge branch 'master' into loops
Daniel R. Roe
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DRR - Cpptraj: Come up with a way to pass variables in nested loops
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DRR - Cpptraj: for -> formask
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DRR - Cpptraj: Allow multiple masks
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DRR - Cpptraj: Add some error checking and improve output messages.
Daniel R. Roe
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DRR - Cpptraj: Make residues and molecules work as well
Daniel R. Roe
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DRR - Cpptraj: Move debug statements. Add code docs.
Daniel R. Roe
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DRR - Cpptraj: Reorganize split of Dispatch
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DRR - Cpptraj: Actually execute the commands.
Daniel R. Roe
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DRR - Cpptraj: Modify test to use new loop syntax
Daniel R. Roe
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DRR - Cpptraj: Hide debug info. Make outpout formatting a little nicer.
Daniel R. Roe
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Commits on Oct 2, 2017

DRR - Cpptraj: Switch from 'formask in' back to 'for inmask' in preparation for adding generic variables to for loop.
Daniel R. Roe
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DRR - Cpptraj: Reorganize argument parsing loop in preparation for supporting different for loop types
Daniel R. Roe
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DRR - Cpptraj: Niterations => MaxIterations
Daniel R. Roe
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DRR - Cpptraj: Generalize # iterations check
Daniel R. Roe
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DRR - Cpptraj: Initial incarnation of the generic integer for loop variable type
Daniel R. Roe
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DRR - Cpptraj: Add description
Daniel R. Roe
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DRR - Cpptraj: Enable integer for loop. Allow variable to start after beginning of argument.
Daniel R. Roe
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DRR - Cpptraj: Test using integer for variable in data set name
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DRR - Cpptraj: Add range checks. Calculate number of iterations for integer loop.
Daniel R. Roe
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DRR - Cpptraj: Allow integer loop without end condition as long as there is at least one end condition in the block
Daniel R. Roe
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DRR - Cpptraj: Update input, no longer need end condition
Daniel R. Roe
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DRR - Cpptraj: Fix up help
Daniel R. Roe
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DRR - Cpptraj: Better variable name recognition in input
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DRR - Cpptraj: Fix order of evaluations leading to small memory error. Hide debug info
Daniel R. Roe
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Commits on Oct 3, 2017

DRR - Cpptraj: Initial incarnation of the VariableArray class.
Daniel R. Roe
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DRR - Cpptraj: Change function name
Daniel R. Roe
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DRR - Cpptraj: Place current script variables in separate class. Should allow more flexibility.
Daniel R. Roe
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DRR - Cpptraj: Start() does not have to add variables since this is done during CheckDone() if needed.
Daniel R. Roe
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DRR - Cpptraj: Have ChangeArg modify ArgLine as well.
Daniel R. Roe
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DRR - Cpptraj: Have ExecuteCommand modify commands so script variables can be used outside of control blocks.
Daniel R. Roe
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DRR - Cpptraj: Script vars can be used outside of control blocks now.
Daniel R. Roe
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DRR - Cpptraj: Properly clear control blocks when an error occurs.
Daniel R. Roe
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DRR - Cpptraj: Print command when adding to control block. Hide debug info.
Daniel R. Roe
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DRR - Cpptraj: Ensure control commands inside control blocks are printed as well.
Daniel R. Roe
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DRR - Cpptraj: Add molfirstres and mollastres for mask loop types. Improve help and error messages.
Daniel R. Roe
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DRR - Cpptraj: Do not allow variables to be used as for loop start/end args yet.
Daniel R. Roe
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DRR - Cpptraj: Improve code docs and cleanup variable names.
Daniel R. Roe
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DRR - Cpptraj: Fix up code docs
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DRR - Cpptraj: Add a way to set script variables
Daniel R. Roe
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DRR - Cpptraj: Code cleanup
Daniel R. Roe
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Commits on Oct 4, 2017

DRR - Cpptraj: Allow any amount of whitespace in set.
Daniel R. Roe
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DRR - Cpptraj: Add loops test
Daniel R. Roe
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DRR - Cpptraj: Distinguish control blocks from controls.
Daniel R. Roe
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DRR - Cpptraj: Add test requirements and enable test.
Daniel R. Roe
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DRR - Cpptraj: Make Control inheritable
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DRR - Cpptraj: Add 'show' command
Daniel R. Roe
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DRR - Cpptraj: No need for separate BLOCK DispatchObject; 'for' is distinguished by its destination. This way it shows up in the CONTROL category for help.
Daniel R. Roe
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DRR - Cpptraj: Update code comments.
Daniel R. Roe
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Commits on Oct 6, 2017

Commits on Oct 10, 2017

Commits on Oct 12, 2017

DRR - Cpptraj: Replace all instances of script variables in an argument.
Daniel R. Roe
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DRR - Cpptraj: Add test of dataset as script var
Daniel R. Roe
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DRR - Cpptraj: Hide some debug info.
Daniel R. Roe
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Commits on Oct 13, 2017

Commits on Oct 16, 2017

DRR - Cpptraj: Add check for valid integer in Get12I6()
Daniel R. Roe
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