Features
Features already present in wordom are (trj stands for .dcd and .xtc files; mol stands for .pdb and .crd files):
- Manipulation
- extraction from a trj file of a single frame to a mol
- extraction from a trj file of a serie of frames to another trj
- merging of trjs into a single trj - original trjs may be listed in a file or have a common basename and a progressive numbering
- appending a trajectory to another one
- appending a mol's coordinates to a trajectory
- writing of a single mol file to a trj with a single frame
- convertion of a mol file to another mol file (different format and/or selection)
- convertion of a trj to a concatenated xyz
- showing a trj's headers
- modifying a dcd's headers
- Analysis Calculations
- Distances
- Contacts
- Angles
- Dihedral angles
- Hydrogen Bond Detection
- Radius of giration
- RMSD
- DRMS
- RMSD- and DRMS-based Clustering
- Polar and Nematic Orientational Parameters
- Principal Component Analysis
- Secondary Structure Assignment
- Elastic Network Models
- Molecular Surface
- Atomic Displacements Correlation
- Protein Structure Network
- Protein Structure Network Paths
- Kinetic Grouping Analysis
- Free Energy Profile
- General (under development)
- Python bindings
- Threading
Planned features:
- Feel free to suggest and/or contribute!