def modifications():
"""
Provides modifications
"""
mods = {}
mod_a = Link(force_field=FF_UNIVERSAL, name='mA')
mod_a.add_node('mA', atomname='mA', PTM_atom=True)
mods['mA'] = mod_a
mod_c = Link(force_field=FF_UNIVERSAL, name='mC')
mod_c.add_node('mC', atomname='mC', PTM_atom=True)
mods['mC'] = mod_c
mod_d = Link(force_field=FF_UNIVERSAL, name='mD')
mod_d.add_node('mD', atomname='mD', PTM_atom=True)
mods['mD'] = mod_d
mod_fg = Link(force_field=FF_UNIVERSAL, name='mFG')
mod_fg.add_node('mF', atomname='mF', PTM_atom=True)
mod_fg.add_node('mG', atomname='mG', PTM_atom=True)
mod_fg.add_edge('mF', 'mG')
mod_fg.add_interaction('bond', ['mF', 'mG'], (3, 4))
mods['mFG'] = mod_fg
mod_i = Link(force_field=FF_UNIVERSAL, name='mI')
mod_i.add_node('mI', atomname='mI', PTM_atom=True)
mods['mI'] = mod_i
mod_i2 = Link(force_field=FF_UNIVERSAL, name='mI2')
mod_i2.add_node('mI2', atomname='mI2', PTM_atom=True)
mods['mI2'] = mod_i2
mod_j = Link(force_field=FF_UNIVERSAL, name='mJ')
mod_j.add_node('mJ', atomname='mJ', PTM_atom=True)
mods['mJ'] = mod_j
mod_j2 = Link(force_field=FF_UNIVERSAL, name='mJ2')
mod_j2.add_node('mJ2', atomname='mJ2', PTM_atom=True)
mods['mJ2'] = mod_j2
mod = Link(name=('mJ', 'mJ2'), force_field=FF_UNIVERSAL)
mod.add_nodes_from((['mJ', {'atomname': 'mJ', 'PTM_atom': True}],
['mJ2', {'atomname': 'mJ2', 'PTM_atom': True}],
['J', {'atomname': 'J', 'PTM_atom': False}]))
mod.add_edges_from([('J', 'mJ'), ('J', 'mJ2')])
mods[('mJ', 'mJ2')] = mod
return mods
def build_forcefield_with_mods():
"""
Build a force field that describe some modifications.
Returns
-------
vermouth.ForceField
"""
nter = Link(name='N-ter')
nter.add_nodes_from((
(0, {'atomname': 'CA', 'PTM_atom': False, 'element': 'C'}),
(1, {'atomname': 'N', 'PTM_atom': False, 'element': 'N'}),
(2, {'atomname': 'HN', 'PTM_atom': False, 'element': 'H'}),
(3, {'atomname': 'H', 'PTM_atom': True, 'element': 'H'}),
))
nter.add_edges_from([[0, 1], [1, 2], [1, 3]])
cter = Link(name='C-ter')
cter.add_nodes_from((
(0, {'atomname': 'C', 'PTM_atom': False, 'element': 'C'}),
(1, {'atomname': 'O', 'PTM_atom': False, 'element': 'O'}),
(2, {'atomname': 'OXT', 'PTM_atom': True, 'element': 'O'}),
))
cter.add_edges_from([[0, 1], [0, 2]])
gluh = Link(name='GLU-H')
gluh.add_nodes_from((
(0, {'atomname': 'CD', 'PTM_atom': False, 'element': 'C'}),
(1, {'atomname': 'OE1', 'PTM_atom': False, 'element': 'O'}),
(2, {'atomname': 'OE2', 'PTM_atom': False, 'element': 'O'}),
(3, {'atomname': 'HE1', 'PTM_atom': True, 'element': 'H'}),
))
gluh.add_edges_from([[0, 1], [0, 2], [1, 3]])
forcefield = copy.copy(vermouth.forcefield.get_native_force_field('universal'))
forcefield.modifications = {}
for mod in [nter, gluh, cter]:
forcefield.modifications[mod.name] = mod
forcefield.renamed_residues[('GLU', ('GLU-H', 'N-ter'))] = 'GLU0'
return forcefield
def make_link(mol_nodes, mol_edges=[]):
mol = Link()
mol.add_nodes_from(mol_nodes)
mol.add_edges_from(mol_edges)
return mol