vermouth-martinize
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marrink-lab
Describe and apply transformation on molecular structures and topologies
The pruning of edges in the tune_cys_bridge leaves the molecule as a single unconnected molecule instead of spliting the molecule into multiple connected ones.
Martinize 1 can use the -cys option to specify individual cystein bridges. Martinize 2 needs the same feature. The same code can also be used to setup arbitrary edges.
Add capped termini to martini 3. There are 3 ways a user can ask for capped termini: * the capping groups are in the PDB already as separate residues *...
Link depending on the position of two residues in a sequence rely exclusively in the resid to figure out the position in the sequence. This will surely break with branched...
It would be handy to have a flag like '-ignh' that you can use to ignore atoms by their names. For example this allows to cg atomistic pdbs with VS...
Too many things found their place directly in the martinize2 script. It means that a user of the library needs to reimplement a lot of the logic if they want...
Martinize2 (and vermouth) currently are very quiet about what they do, especially around input and DSSP. It would be valuable for the users if they became more verbose, and told...
It might be worth a try to use pynauty (https://web.cs.dal.ca/~peter/software/pynauty/html/index.html) to power the symmetry detection in our ISMAGS implementation. It would have to be an optional dependency though. Nauty is...
The problem is that some interactions (bonds, angles) are symmetric, others are sometimes (dihedrals) and others are not. And note that for angles the order of nodes matters anyway. Although,...
In case of large modifications (think of e.g. lipidation) it may be desirable to treat the modification as a separate residue in the rest of the pipeline. This is currently...
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Describe and apply transformation on molecular structures and topologies