Module fep

Functions

[hide private]

read_map(m_file)
Returns dictionary giving perturbed to original (combined) mapping.

fep_add_block(fep_handle, array_name, block)
array_name = name of block, e.g., fepio_atommaps block = [ [[ti, tj], [ai, aj]], ...

canonical_pair(p)
Construct a unique key for each pair of atoms by ordering the two atoms in ascending order.

make_pairmaps(a, b, block_name)

item_key(a)
Construct a unique item key tuple from a_{i, j, ...

make_block(a, b, block_name)
Return a list which can be turned into a fepio block.

kept_terms(map, imap, anglemaps, dihedmaps)
Assign kept (-1) and not kept (0) for angles and diheds that purely involve dummy atoms.

kept_terms_stage_2(ct1, ct2, atommaps, anglemaps, dihedmaps, map)

keep(anglemaps, i)

two_neighbors(i, neighbors, realdummy)
Return a list of 1, 2, or 3 atoms [i, j, k] such that i is bonded to j, j is bonded to k, and k is not i.

get_residue_num(atommaps, ct_a, ct_b)
Return dictionary of combined_atom_index -> residue_string

add_more_exclusions(block)

Function Details

[hide private]

fep_add_block(fep_handle, array_name, block)

array_name = name of block, e.g., fepio_atommaps block = [ [[ti, tj], [ai, aj]], ... ]

item_key(a)

Construct a unique item key tuple from a_{i, j, ... }, so that
the atom indices follow a canonical order. The canonical order is
1. for [ a_i, a_j ], we require a_i < a_j.
2. for [ a_i, a_j, a_k ], we require a_i < a_k.
3. for [ a_i, a_j, a_k, a_l ], we require a_j < a_k.

make_block(a, b, block_name)

Return a list which can be turned into a fepio block. The output list has the form [ [[ti, tj], [ai, aj]], ... ]

two_neighbors(i, neighbors, realdummy)

Return a list of 1, 2, or 3 atoms [i, j, k] such that i is bonded to j, j is bonded to k, and k is not i. Input uses 0-based indexing. Output uses 1-based indexing. (Fix this later.) Neighbors list has both directions.