proteindf_bridge.atomgroup module

class proteindf_bridge.atomgroup.AtomGroup(*args, **kwargs)

Bases: object

>>> group1 = AtomGroup()
>>> atom1 = Atom(symbol='C')
>>> atom2 = Atom(symbol='H')
>>> atom3 = Atom(symbol='N')
>>> subgrp = AtomGroup()
>>> subgrp.set_atom('C1', atom1)
>>> subgrp.set_atom('H1', atom2)
>>> subgrp.set_atom('N1', atom3)
>>> group1.set_group('grp', subgrp)
>>> group1['grp']['C1'].symbol
'C'
>>> group1.get_number_of_atoms()
0
>>> group1.get_number_of_groups()
1
>>> group1.get_number_of_all_atoms()
3
>>> group1.sum_of_atomic_number()
14.0

>>> group2 = AtomGroup()
>>> atom_with_path1 = Atom(symbol='C')
>>> atom_with_path2 = Atom(symbol='N')
>>> group2.set_atom('/group1/subgroup1/C1', atom_with_path1)
>>> group2.set_atom('/group1/subgroup2/N2', atom_with_path2)
>>> print(group2)
# group key= name=
  # group key=group1 name=   parent=
    # group key=subgroup1 name=     parent=
    C ()        0.000    0.000    0.000,  0.00,    0.000    0.000    0.000 /group1/subgroup1/C1
    # group key=subgroup2 name=     parent=
    N ()        0.000    0.000    0.000,  0.00,    0.000    0.000    0.000 /group1/subgroup2/N2

>>> group2['group1']['subgroup1'].has_atom('C1')
True

add_bond(atom1, atom2, order=1)

Add bond information. order = bond order

assign_charges(charges)

atoms()

Return the list of atoms.

Return type:

Iterator[Tuple[str, Atom]]

box()

center()

return Position value of the center

property charge

static divide_path(path)

erase_atom(key)

remove atom

Deprecated since version use: remove_atom() instead.

erase_group(key)

remove group

Deprecated since version use: remove_group() instead.

Return type:

None

formula()

get_atom(key_or_name)

Return the atom if one matching the given key or name is contained; otherwise return None.

Return type:

Optional[Atom]

get_atom_keys()

Return type:

List[str]

get_atom_kinds()

Return the list of atomic species (symbols).

get_atom_kinds_count()

Return a dict mapping atomic species (symbols) to their counts.

get_atom_list()

Collect the atoms within the subgroups into a list and return it.

get_bond_list(bond_list=None)

Return a list of tuples (‘atom1 path’, ‘atom2 path’, bond order).

get_family(query_path)

get_formula()

Return the molecular formula (composition formula).

get_group(key_or_name)

Return the group if one matching the given key or name is contained; otherwise return None.

Return type:

Optional[AtomGroup]

get_group_list()

Return type:

List[str]

get_number_of_all_atoms()

get_number_of_atoms()

get_number_of_bonds()

get_number_of_groups()

get_path_list()

Return the list of paths of the atoms within the group.

get_raw_data()

get_xyz()

Return the XYZ-format string.

groups()

Return the list of molecular groups.

Return type:

Iterator[Tuple[str, AtomGroup]]

has_atom(key_or_name)

Return True if an atom matching the given key or name is contained; otherwise return False.

has_atomkey(key)

Return True if an atom with the given key is contained; otherwise return False.

has_atomname(name)

Return True if an atom with the given name is contained; otherwise return False.

has_group(key_or_name)

Return True if a group matching the given key or name is contained; otherwise return False.

Return type:

bool

has_groupkey(key)

Return True if a group with the given key is contained; otherwise return False.

Return type:

bool

has_groupname(name)

Return True if a group with the given name is contained; otherwise return False.

Return type:

bool

merge(rhs)

Merge in another molecular group.

property name

property nuclei_charge

property parent

property path

pickup_atoms(key_or_name)

Return the array of atoms whose key or name matches.

property real_nuclei_charge

remove_atom(key)

remove atom

remove_group(key)

remove group

Return type:

None

restructure(reference, range=1e-05)

Rebuild the data structure by referring to the structure of reference.

Useful when building up a flat list of atoms into a PDB-like data structure.

rotate(rotmat)

save_csv(path)

select(selector)

Pass a Selector object as selector to get back the corresponding molecular group.

set_atom(key, value)

Return type:

None

set_by_dict_data(data)

set_group(key, value)

Return type:

None

shift_by(direction)

property sort_atoms

property sort_groups

sum_of_atomic_number()

Return the sum of atomic numbers.

property weight