Module iviparr

Functions

[hide private]

atom_types_simple(ct)
Return dictionary of atom index to type name.

neighbor_list(ct)
Return neighbor list.

check_dihedral(dih, nlist)
Return true for proper and false for improper dihedral.

improper_residue(dih, nlist)
Return name of template that should be associated with the improper.

remove_duplicate_templates(templates)
Given a templates dict, return a new templates dict that only contains unique templates.

Function Details

[hide private]

atom_types_simple(ct)

Return dictionary of atom index to type name. Each atom index has its own type name.

neighbor_list(ct)

Return neighbor list. 0-based indexing, but entries are 1-based. Use m_bond structure. Compare to CtBonds function in viparr_util.py.

remove_duplicate_templates(templates)

Given a templates dict, return a new templates dict that only contains unique templates. The algorithm is to construct the new templates dict one entry at a time. For each entry considered, we loop over the new templates to see if the entry is already included.