Detailed Guides#
Here are some detailed guides that (we hope) will make it easier to use and understand various parts of sire.
- Searching
- Views
- Identifiers
- Numbers
- Strings
- Comparisons
- Logical operators
- Returned View Types
- Expansive (with) and Contractive (in) Searches
- Match All Atoms, Residues, Chains etc.
- Advanced
withandinSearches - Searching for Bonds using
in,with,fromandto - Searching by Chemical Element
- Searching by Count (i.e. Number of Atoms)
- Searching by Charge or Mass
- Searching by Charge using Approximate Comparisons
- Searching by Property
- Finding the Nth View that Matches
- Searching by Distance
- Searching by Closest and Furthest
- Searching using Smiles or Smarts Strings
- Searching for Water or Protein Molecules
- Creating Custom Search Tokens
- Trajectories
- Supported file formats
- Loading trajectories
- Loading and joining multiple trajectories
- Saving trajectories
- Saving trajectory for subsets of molecules
- Saving to multiple files in parallel
- Saving to file trajectories
- Visualising trajectories
- Smoothing and aligning frames
- Aligning to molecules outside the trajectory
- Calculating energies across frames
- Viewing Molecules
- 2D Views
- 3D Views
- Choosing the 3D representation
- Choosing colors and opacities
- Centering the view
- Viewing trajectories
- Wrapping molecules into the current box
- Trajectory Alignment
- Trajectory Smoothing
- Integration with trajectories
- Setting the background color
- Closer integration with NGLView
- Saving 3D views to files
- OpenMM Integration
- Units