Default PDB chain ID back to blank. Add option to write anisotropic displacement factors to PDB file.#767

Merged

drroe merged 30 commits intomasterfrom

pdbchainid

Oct 16, 2019

Commits on Oct 15, 2019

DRR - Cpptraj: Make the default chain ID blank again unless user requests compliance with pdb residue naming via pdbres; always writing a default of Z can break things like mmpbsa.py
Daniel R. Roe
committed
DRR - Add the 'pdbres' option to the test so that the deault chain ID of Z gets written. Also triggers HETATM and CONECT print, so update the test.
Daniel R. Roe
committed
DRR - Cpptraj: Store ANISOU in AtomExtra
Daniel R. Roe
committed
DRR - Start adding symmetric tensor data set
Daniel R. Roe
committed
DRR - Finish the tensor DataSet type
Daniel R. Roe
committed
DRR - Revert these files; will store calculated anisotropic factors in a data set instead of topology
Daniel R. Roe
committed
DRR - Add tensor DataSet to DataSetList
Daniel R. Roe
committed
DRR - Use tensor data set in atomicfluct
Daniel R. Roe
committed
DRR - Use space, not blank chain ID
Daniel R. Roe
committed
DRR - Default chain id for adpout is blank
Daniel R. Roe
committed
DRR - Set a default legend
Daniel R. Roe
committed
DRR - Update help text and manual.
Daniel R. Roe
committed
DRR - Protect again potential segfault, set correct dimension label.
Daniel R. Roe
committed
DRR - Pass in anisou as pointer; convert to integer inside PDBfile.
Daniel R. Roe
committed
DRR - Add 'adpdata' option
Daniel R. Roe
committed
DRR - Add some debug info
Daniel R. Roe
committed
DRR - Rename test data set; add test for writing a PDB with adpdata.
Daniel R. Roe
committed
DRR - Fix accidental shut off of adpdata after first frame written
Daniel R. Roe
committed
DRR - Add test save for write out of tensor data
Daniel R. Roe
committed

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Default PDB chain ID back to blank. Add option to write anisotropic displacement factors to PDB file.#767

Default PDB chain ID back to blank. Add option to write anisotropic displacement factors to PDB file.#767
drroe merged 30 commits intomasterfrom
pdbchainid

Commits on Oct 15, 2019

DRR - Cpptraj: Make the default chain ID blank again unless user requests compliance with pdb residue naming via pdbres; always writing a default of Z can break things like mmpbsa.py

DRR - Add the 'pdbres' option to the test so that the deault chain ID of Z gets written. Also triggers HETATM and CONECT print, so update the test.

DRR - Cpptraj: Store ANISOU in AtomExtra

DRR - Start adding symmetric tensor data set

DRR - Finish the tensor DataSet type

DRR - Revert these files; will store calculated anisotropic factors in a data set instead of topology

DRR - Add tensor DataSet to DataSetList

DRR - Use tensor data set in atomicfluct

DRR - Use space, not blank chain ID

DRR - Default chain id for adpout is blank

DRR - Set a default legend

DRR - Update help text and manual.

DRR - Protect again potential segfault, set correct dimension label.

DRR - Pass in anisou as pointer; convert to integer inside PDBfile.

DRR - Add 'adpdata' option

DRR - Add some debug info

DRR - Rename test data set; add test for writing a PDB with adpdata.

DRR - Fix accidental shut off of adpdata after first frame written

DRR - Add test save for write out of tensor data

Commits on Oct 16, 2019

DRR - Write bfactors to output PDB

DRR - Add test on subset

DRR - Minor version bump; reverting default PDB chain ID behavior

DRR - Instead of first hairpin, do heavy atoms; better test of selection since multiple non-contiguous segments, and is a useful example.

DRR - Add utility for actually writing formal charge string

DRR - Charge of 0 not printed for ANISOU anymore

DRR - Fix segfault when calc_adp specified but not adpout. Change second adp test so its only calc_a

DRR - Cross reference atomicfluct command for output pdb adpdata; add an example of calculating an averaged pdb with anisotropic and isotropic b factors to the atomicfluct command.

DRR - Fix up manual entry about default chain ID behavior for PDB write. Update manual PDF.

DRR - Add 'gcc' to brew install to try to get 'gfortran' installed (now getting a gfortran not found error on OSX suddenly...)

DRR - Add 'brew update' to try to fix failing homebrew on Travis