SMArt.md.gro2gro package

Submodules

SMArt.md.gro2gro.g2g module

class SMArt.md.gro2gro.g2g.ContPref_g2g[source]

Bases: SMArt.incl.Defaults

class SMArt.md.gro2gro.g2g.FFg2g[source]

Bases: SMArt.md.gro2gro.g2g.ContPref_g2g

ff_gm2gr(**kwargs)[source]
ff_gr2gm(**kwargs)[source]
Parameters

kwargs – none

Returns

gm2gr(**kwargs)[source]
gr2gm(**kwargs)[source]
class SMArt.md.gro2gro.g2g.IntType_g2g[source]

Bases: SMArt.md.gro2gro.g2g.ContPref_g2g

generate_params_gr_gm(gr_gm_params)[source]
get_gm2gr_int_type(**kwargs)[source]
get_gr2gm_def_pref(**kwargs)[source]

gets gm_def_pref for a given class, e.g. gb_ for BondType :param kwargs:

flag_not_found

Returns

classmethod get_gr2gm_def_pref_class(**kwargs)[source]

gets gm_def_pref for a given class, e.g. gb_ for BondType :param kwargs:

flag_not_found

Returns

classmethod get_gr2gm_int_type(**kwargs)[source]
get_gr_gm_params()[source]
classmethod get_int_type(**kwargs)[source]
gm2gr(**kwargs)[source]
gr2gm(**kwargs)[source]
class SMArt.md.gro2gro.g2g.MolType_g2g[source]

Bases: object

def generate_e_p_l(self):

db = self.get_container(self.ff.PairType.find_int_container2write(), allow_not_found = True) if db:

for temp_pair in db:

at_pair = temp_pair.atoms at_pair[0].add_pair(at_pair[1], replace = -1)

self.add_exclusions_neigh(self.nrexcl) db = self.get_container(self.ff.ExclusionType.find_int_container2write(), allow_not_found = True) if db:

for temp_pair in db:

at_pair = temp_pair.atoms at_pair[0].add_excl(at_pair[1], replace = -1)

self._gr_expand_excl_pair() self._gr_reduce_excl_pair() self._gr_sort_excl_pair() self.remove_excl_from_p_l(flag_reduced=True)

def remove_excl_from_p_l(self, **kwargs):
if kwargs.get(‘flag_reduced’):

N4for = 1

else:N4for = 2 for at in self.get_atoms():

for at2 in at.p_l:

at_pair = (at, at2) for i in range(N4for):

try:

at_pair[i].e_l.remove(at_pair[(i+1)%2])

except ValueError:

pass

class SMArt.md.gro2gro.g2g.Top_g2g[source]

Bases: object

g2m (gr2gm & gm2gr) functionality for topology

generate_mol_type(atom_ids, molecule_id=None, **kwargs)[source]
generate_mol_types(*mol_ids, **kwargs)[source]
Parameters

  • mol_ids – names for each molecule type

  • kwargs – flag_add_molecule - adding molecule 1 for each molecule type num_mols - adding more than 1 molecule for each molecule type

Returns

generate_sys_atoms_from_mols_types(**kwargs)[source]
gm2gr(**kwargs)[source]
gr2gm(**kwargs)[source]
top_gm2gr(**kwargs)[source]
top_gr2gm(**kwargs)[source]
Parameters

kwargs – ff_gr2gm(**kwargs) generate_mol_types(*mol_ids, **kwargs) mol_ids - names for each molecule type flag_add_molecule - adding molecule 1 for each molecule type num_mols - adding more than 1 molecule for each molecule type

Returns

SMArt.md.gro2gro.g2g.gr_get_atom_element(a_type)[source]

Module contents