vermouth.rcsu.go_vs_includes module¶
- class vermouth.rcsu.go_vs_includes.VirtualSiteCreator(go_anchor_bead='BB', go_atomname='CA')[source]¶
Bases:
Processor
Create virtual-sites for the Martini Go model implementation or the specific water biasing options.
See
vermouth.rcsu
for more details.Every molecule must have a moltype name under the “moltype” key of the molecule meta.
- add_virtual_sites(molecule, prefix, backbone, atomname, charge=0)[source]¶
Add the virtual sites for GoMartini in the molecule.
One virtual site is added per backbone bead of the Martini protein. Each virtual site copies the resid, resname, and chain of the backbone bead. It also copies the reference to the position array, so the virtual site position follows if the backbone bead is translated. The virtual sites are added after all the other atoms of the molecule, each in its own charge group, with “CA” as atomname, and a charge of 0. The atomname and charge can be set with the atomname and charge argument, respectively.
The bead type of the virtual sites is names “<prefix>_<resid>”. Where prefix is provided as an argument of the function, and is expected to be the molecule type name.
- Parameters:
molecule (vermouth.molecule.Molecule) – The molecule to augment with virtual sites.
prefix (str) – The prefix to use for bead type names. Usually the molecule type name.
backbone (str) – The atomname of the backbone beads.
atomname (str) – The atomname of the virtual sites.