Archived tutorials¶
Tutorials for releases the current workflow has moved past. Each page was run exactly as written against the release it names, and is kept unchanged as a record of that release: its commands and outputs are true for that version, and may be refused by a later one.
Use the current tutorials for the current package.
0.6.4¶
Archived because the default clustering workflow changed: t_hdbscan now enumerates the
molecule's symmetry BEFORE clustering and measures distances as the minimum over symmetry
relabellings, and frames are assigned by an absolute 18-of-20 vote. The page below clustered on the
plain torsion distance with the historical 15-neighbour margin vote and merged symmetry-related
clusters afterwards (TorsionSymmetry). Its saved outputs are those of commit 8516c12a (tag
v0.6.4), not re-executed; only the helper import path and the install link were updated. On the current package it is
reproduced with t_hdbscan(tors, symmetry=False, vote_rule="legacy-margin").
| tutorial | workflow |
|---|---|
| paracetamol clustering | the historical cluster-then-merge workflow |
0.5.3¶
Archived because 0.5.4 changed how a scaled Hamiltonian comes to exist and how a run is told which one to integrate:
- REST2 states are built once, as files, by
md-openmm build-top --rest2-scaler, with a record (scaler.yaml) and a picture of what stays unscaled. In 0.5.3 every run scaled in memory. - A stage and a ladder no longer scale anything: a hot cMD stage takes its saved state as
-s, and a REST2 ladder reads-sonly from its group file, one saved state per line. - More torsions stay unscaled in every state: aromatic ring bonds, other double bonds and every improper, as well as the ordinary amide omega.
| tutorial | method |
|---|---|
| paracetamol | cMD |
| Chinolin | cMD |
| paracetamol | REST2 -- including the 0.5.3 workaround for run.sh refusing the ladder |