Module viparr_residue

Functions

[hide private]

dfs(G, marked, start_vert, ordering)

templates_reorder_atoms(templates)
Reorder the atoms in the template to be more suitable for the isomorphism test.

get_hill_order(elm)
Given a list of elements, return the list in hill order ( C 1st, H 2nd, others in alpha order.

residue_formula(nlist)
Given a list of atomic numbers, return a string which is its chemical formula (elements given in hill order).

get_formula_dict(templates)
Dictionary for mapping formulas to a list of template residue names.

residue_structure_mae(neighbors, res)
Return structure of mae residue.

residue_structure_template(template)
Return structure of template residue.

res_add_externals(res, template, neighbors)
Add external atoms to res.atoms dict (Does not depend on $dollar sign.)

compare_lists(gl, hl)
Given two lists, check that they contain the same elements (which may be repeated).

get_residue_list(atoms, neighbors, templates)
Top-level function for constructing the residue list.

Variables

[hide private]

__package__ = 'schrodinger.application.desmond.packages.viparr...

Function Details

[hide private]

templates_reorder_atoms(templates)

Reorder the atoms in the template to be more suitable for the isomorphism test. Input is a raw template (not internal format). This function must be called before converting the template to internal format.

get_hill_order(elm)

Given a list of elements, return the list in hill order ( C 1st, H 2nd, others in alpha order. If no C, use alpha order).

get_residue_list(atoms, neighbors, templates)

Top-level function for constructing the residue list. In this new version, each residue knows about the immediate atoms that connect to it from outside the residue. Note that in this new version, it is not important that the residues be ordered linearly in a chain; i.e., the list data structure can be replaced by a dict.

Variables Details

[hide private]

package

Value:

'schrodinger.application.desmond.packages.viparr1.viparr'