chemcoord.AsymmetricUnitCartesian
- class chemcoord.AsymmetricUnitCartesian(frame=None, atoms=None, coords=None, index=None, metadata=None, _metadata=None)[source]
Manipulate cartesian coordinates while preserving the point group.
This class has all the methods of a
Cartesian
, with one additionalget_cartesian()
method and contains only one member of each symmetry equivalence class.- __init__(frame=None, atoms=None, coords=None, index=None, metadata=None, _metadata=None)
How to initialize a Cartesian instance.
- Parameters:
frame (pd.DataFrame) – A Dataframe with at least the columns
['atom', 'x', 'y', 'z']
. Where'atom'
is a string for the elementsymbol.atoms (sequence) – A list of strings. (Elementsymbols)
coords (sequence) – A
n_atoms * 3
array containg the positions of the atoms. Note that atoms and coords are mutually exclusive to frame. Besides atoms and coords have to be both either None or not None.
- Returns:
A new cartesian instance.
- Return type:
Methods
__init__
([frame, atoms, coords, index, ...])How to initialize a Cartesian instance.
add_data
([new_cols])Adds a column with the requested data.
align
(other[, mass_weight])Align two Cartesians.
apply
(*args, **kwargs)Applies function along input axis of DataFrame.
applymap
(*args, **kwargs)Applies function elementwise
basistransform
(new_basis[, old_basis, ...])Transform the frame to a new basis.
change_numbering
(rename_dict[, inplace])Return the reindexed version of Cartesian.
check_absolute_refs
(construction_table)Checks first three rows of
construction_table
for linear referencescheck_dihedral
(construction_table)Checks, if the dihedral defining atom is colinear.
copy
()correct_absolute_refs
(construction_table)Reindexe construction_table if linear reference in first three rows present.
correct_dihedral
(construction_table[, ...])Reindexe the dihedral defining atom if linear reference is used.
cut_cuboid
([a, b, c, origin, ...])Cut a cuboid specified by edge and radius.
cut_sphere
([radius, origin, outside_sliced, ...])Cut a sphere specified by origin and radius.
fragmentate
([give_only_index, use_lookup])Get the indices of non bonded parts in the molecule.
from_ase_atoms
(atoms)Create an instance of the own class from an ase molecule
from_pymatgen_molecule
(molecule)Create an instance of the own class from a pymatgen molecule
get_align_transf
(other[, mass_weight, centered])Return the rotation matrix that aligns other onto self.
get_angle_degrees
(indices)Return the angles between given atoms.
get_ase_atoms
()Create an Atoms instance of the ase library
get_asymmetric_unit
([eq])get_barycenter
()Return the mass weighted average location.
get_bond_lengths
(indices)Return the distances between given atoms.
get_bonds
([self_bonding_allowed, offset, ...])Return a dictionary representing the bonds.
Return a
Cartesian
where all members of a symmetry equivalence class are inserted back in.get_centroid
()Return the average location.
get_construction_table
([fragment_list, ...])Create a construction table for a Zmatrix.
get_coordination_sphere
(index_of_atom[, ...])Return a Cartesian of atoms in the n-th coordination sphere.
get_dihedral_degrees
(indices[, start_row])Return the dihedrals between given atoms.
get_distance_to
([origin, other_atoms, sort])Return a Cartesian with a column for the distance from origin.
get_electron_number
([charge])Return the number of electrons.
get_equivalent_atoms
([tolerance])Returns sets of equivalent atoms with symmetry operations
get_fragment
(list_of_indextuples[, ...])Get the indices of the atoms in a fragment.
get_grad_zmat
(construction_table[, as_function])Return the gradient for the transformation to a Zmatrix.
get_inertia
()Calculate the inertia tensor and transforms along rotation axes.
get_pointgroup
([tolerance])Returns a PointGroup object for the molecule.
get_pymatgen_molecule
()Create a Molecule instance of the pymatgen library
get_shortest_distance
(other)Calculate the shortest distance between self and other
get_total_mass
()Returns the total mass in g/mol.
get_without
(fragments[, use_lookup])Return self without the specified fragments.
get_zmat
([construction_table, use_lookup])Transform to internal coordinates.
has_same_sumformula
(other)Determines if
other
has the same sumformulainsert
(loc, column, value[, ...])Insert column into molecule at specified location.
partition_chem_env
([n_sphere, use_lookup])This function partitions the molecule into subsets of the same chemical environment.
read_cjson
(buf)Read a cjson file or a dictionary.
read_xyz
(buf[, start_index, get_bonds, ...])Read a file of coordinate information.
reindex_similar
(other[, n_sphere])Reindex
other
to be similarly indexed asself
.replace
([to_replace, value, inplace, limit, ...])Replace values given in 'to_replace' with 'value'.
reset_index
()Resets the index to 0...n
restrict_bond_dict
(bond_dict)Restrict a bond dictionary to self.
set_index
(keys[, drop, append, inplace, ...])Set the DataFrame index (row labels) using one or more existing columns.
sort_index
([axis, level, ascending, ...])Sort object by labels (along an axis)
sort_values
(by[, axis, ascending, inplace, ...])Sort by the values along either axis
subs
(*args)Substitute a symbolic expression in
['x', 'y', 'z']
symmetrize
([max_n, tolerance, epsilon])Returns a symmetrized molecule
to_cjson
([buf])Write a cjson file or return dictionary.
to_latex
([buf, columns, col_space, header, ...])Render a DataFrame to a tabular environment table.
to_string
([buf, columns, col_space, header, ...])Render a DataFrame to a console-friendly tabular output.
to_xyz
([buf, sort_index, index, header, ...])Write xyz-file
to_zmat
(*args, **kwargs)Deprecated, use
get_zmat()
view
([viewer, use_curr_dir])View your molecule.
write_xyz
(*args, **kwargs)Deprecated, use
to_xyz()
Attributes
columns
Returns the columns.
dtypes
empty
iloc
Label based indexing
index
Returns the index.
loc
Label based indexing
shape