Change default PDB chain ID from blank to 'Z'#747

Merged

drroe merged 25 commits intoAmber-MD:masterfrom

drroe:pdbchainid

Aug 22, 2019

Commits on Aug 15, 2019

DRR - Cpptraj: Make a blank chain ID null, and make the default chain ID when null 'Z'.
Daniel R. Roe
committed
DRR - Cpptraj: Ensure a blank character can be used as a chain ID if necessary
Daniel R. Roe
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DRR - Cpptraj: Set blank chain IDs for backwards compat. Add default chain ID test.
Daniel R. Roe
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DRR - Cpptraj: Changes related to default chainID now being Z
Daniel R. Roe
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DRR - Cpptraj: Set blank chain ID
Daniel R. Roe
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DRR - Cpptraj: Set blank chain IDs
Daniel R. Roe
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DRR - Cpptraj: Add 'trajargs' keyword to 'mask' command for passing in additional output trajectory options.
Daniel R. Roe
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DRR - Cpptraj: Set chainID to ' '
Daniel R. Roe
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DRR - Cpptraj: Update 'mask' command doc and PDB trajectory out doc.
Daniel R. Roe
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DRR - Cpptraj: Use blank chain id
Daniel R. Roe
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DRR - Cpptraj: Blank chain ID
Daniel R. Roe
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DRR - Cpptraj: Fix documentation for residue selection by chain ID.
Daniel R. Roe
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DRR - Cpptraj: Ensure blank chain ID
Daniel R. Roe
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DRR - Cpptraj: Make the internal default chain id still a space; only use the default chain id when writing. This makes it so that e.g. selection by chainid wont return a false positive when specif…
Daniel R. Roe
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DRR - Cpptraj: Since the PQR format breaks the PDB standard anyway, do not bother with a default chain ID
Daniel R. Roe
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DRR - Cpptraj: Minor version bump; default PDB chain ID set to 'Z'
Daniel R. Roe
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DRR - Cpptraj: Fix text going off the page in output pdf
Daniel R. Roe
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DRR - Cpptraj: Update manual
Daniel R. Roe
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Commits on Aug 17, 2019

DRR - Cpptraj: Slight rework of default and blank chain IDs.
drroe
committed

Commits on Aug 22, 2019

DRR - Cpptraj: Set CPPTRAJ_ERROR to an actual file on windows since windows doesnt know about /dev/stderr
Daniel R. Roe
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DRR - Do not replace valgrind.out on windows
Daniel R. Roe
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DRR - Cpptraj: No /dev/stdout on windows
Daniel R. Roe
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DRR - Cpptraj: Do not explicitly redirect test header to stdout
Daniel R. Roe
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DRR - Cpptraj: Remove reference to /dev/stdout in ParseValgrindOut
Daniel R. Roe
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DRR - Cpptraj: All error messages wrapped in ErrMsg
Daniel R. Roe
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