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Add examples to doc #88

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sizmailov opened this issue Feb 3, 2019 · 0 comments
Open
21 of 25 tasks

Add examples to doc #88

sizmailov opened this issue Feb 3, 2019 · 0 comments
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@sizmailov
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doc Documentation related issues

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sizmailov commented Feb 3, 2019 •
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PDB I/O

  • Reading standard PDB
  • Reading non-standard PDB
  • Reading bad PDB
  • Writing standard PDB
  • Writing non-standard PDB

Basics operations

  • Degrees/Radians conversion
  • Torsional angle
  • Frame/Chain/Residue/Atom hierarchy
  • Selections inter-conversions
  • Apply filters to selections

Coordinate manipulation

  • RMSD calculation
  • RMSF calculation
  • Alter torsional angle of structure
  • Average structure calculation
  • Align trajectory frames

Frame manipulation

  • Create new Frame/Residue/Chain/Atom
  • Renumber atoms
  • Reorder atoms

Trajectory

  • Trajectory creation
  • Traverse through trajectory

Performance tips

  • Autocorrelation function for random vectors
  • Caching selections while running through trajectory

Advanced usage

  • Use of custom torsional angle
  • Build super cell
  • Remove PBC jumps
@sizmailov sizmailov self-assigned this Feb 13, 2019
@sizmailov sizmailov added the doc Documentation related issues label Feb 13, 2019
@sizmailov sizmailov mentioned this issue Feb 19, 2019
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