EasyTrajH5

Trajectory management for mdtraj H5 files

• EasyH5File wrapper for h5py
  • methods-based interface for dataset/attr management
  • string, json, file import/export methods
  • useful schema dictionary
• select_mask with new atom selection language for MD
  • proper set operations using 'not', 'diff', 'merge', 'intersect'
  • allows both amber and mdtraj style selections
  • proper 0-based indexing using flexible numbering list and ranges
  • user defined residue classes
• EasyTrajH5File
  • drop-in replacement for mdtraj.H5TrajecotryFile
  • subclasses EasyH5File with all above methods
  • allows simple override to h5pyd
  • efficient streaming of mdtraj.Trajectory from file using fancy indexing and atom masks with select_mask
• conveient transforms between mdtraj, parmed and openmm
• cli for interrogating h5 files

Selection Language

Selects atom based on a selection string which is based on a combination atom selection langauge.There are several different types of selection modes strings, where the first word is often used a mode selector.

• keywords
  • If more than one keyword is specified, it is assumed they are joined with "or" operation (i.e. 'ligand protein' will return both ligand and protein atom indices).
  • accepts (in any order): 'ligand', 'protein', 'water', 'lipid', 'salt', 'solvent', 'lipid', 'nucleic', 'resname', 'resid', 'atom'
  • 'ligand' will find the residue 'LIG', 'UNL', 'UNK', or whatever is in 'ligand' in the h5 'easytrajh5/data/select.yaml'
  • 'pocket' will find the closest 6 residues to the 'ligand' group.
  • 'near' will require a following resname, with an optional integer, e.g.: 'near ATP' 'near ATP 5'
  • 'resname' identifies a single residue type (usually a ligand): 'resname LEU'
  • 'resi' for residue 0-indexed selections "resi 0 10-13" - selects atoms in the first and 11th, 12th and 13th residues
  • 'atom' atom 0-indexed selections "atom 0 55 43 101-105" - selects the first, 56th, 44th, 101 to 105th atom
• AMBER-style atom selection https://parmed.github.io/ParmEd/html/amber.html#amber-mask-syntax "amber :ALA,LYS" - selects all alanine and lysine residues
• MDTraj-style atom selection - https://mdtraj.org/1.9.4/atom_selection.html "mdtraj protein and water" - selects protein and water
• furthermore, selections can be combined with set operators ("not", "intersect", "merge", "diff"), "intersect {not {amber :ALA}} {protein}" "diff {protein} {not {amber :ALA}}" "not {resname LEU}" "merge {near BSM 8} {amber :ALA}"
• some useful masks:
  • no solvent "not {solvent}"
  • just the protein "protein"
  • heavy protein atoms "diff {protein} {amber @/H}"
  • no hydrogens "not {amber @/H}"
  • pocket and ligand "pocket ligand"
  • specified ligand with 10 closest neighbours "resname UNL near UNL 10"