class chemcoord.xyz_functions.Cartesian(init)[source]

The main class for dealing with cartesian Coordinates.

Chemical Methods

get_bonds([modified_properties, ...]) Returns a dictionary representing the bonds.
to_zmat([buildlist, fragment_list, ...]) Transform to internal coordinates.
location([indexlist]) Returns the location of an atom.
bond_lengths(buildlist[, start_row]) Return the distances between given atoms.
angle_degrees(buildlist[, start_row]) Return the angles between given atoms.
dihedral_degrees(buildlist[, start_row]) Return the angles between given atoms.
move([vector, matrix, indices, copy]) Move a Cartesian.
basistransform(new_basis[, old_basis, ...]) Transforms the frame to a new basis.
add_data([list_of_columns, inplace]) Adds a column with the requested data.
total_mass() Returns the total mass in g/mol.
barycenter() Returns the mass weighted average location.
inertia() Calculates the inertia tensor and transforms along rotation axes.
topologic_center() Returns the average location.
cutcuboid([a, b, c, origin, outside_sliced, ...]) Cuts a cuboid specified by edge and radius.
cutsphere([radius, origin, outside_sliced, ...]) Cuts a sphere specified by origin and radius.
connected_to(index_of_atom[, exclude, ...]) Returns a Cartesian of atoms connected to the specified one.
distance_to([origin, ...]) Returns a Cartesian with a column for the distance from origin.
get_fragment(list_of_indextuples[, ...]) Get the indices of the atoms in a fragment.
fragmentate([give_only_index]) Get the indices of non bonded parts in the molecule.
make_similar(Cartesian2[, follow_bonds, ...]) Similarizes two Cartesians.
align(Cartesian2[, ignore_hydrogens]) Aligns two Cartesians.
change_numbering(rename_dict[, inplace]) Returns the reindexed version of Cartesian.
move_to(Cartesian2[, step, extrapolate]) Returns list of Cartesians for the movement from self to Cartesian2.
partition_chem_env([follow_bonds]) This function partitions the molecule into subsets of the same chemical environment.

Technical Methods

__init__(init) How to initialize a Cartesian instance.
index Returns the index.
columns Returns the columns.
replace([to_replace, value, inplace, limit, ...]) Replace values given in ‘to_replace’ with ‘value’.
sort_index([axis, level, ascending, ...]) Sort object by labels (along an axis)
set_index(keys[, drop, append, inplace, ...]) Set the DataFrame index (row labels) using one or more existing columns.
append(other[, ignore_index, verify_integrity]) Append rows of other to the end of this frame, returning a new object.
insert(loc, column, value[, ...]) Insert column into DataFrame at specified location.
sort_values(by[, axis, ascending, inplace, ...]) Sort by the values along either axis
write(outputfile[, sort_index]) Writes the Cartesian into a file.
read_xyz(inputfile[, pythonic_index, get_bonds]) Reads a xyz file.
read_molden(inputfile[, pythonic_index, ...]) Reads a molden file.

Advanced methods

_divide_et_impera([maximum_edge_length, ...]) Returns a molecule split into cuboids.
_preserve_bonds(sliced_cartesian) Is called after cutting geometric shapes.
_get_buildlist([fixed_buildlist]) Create a buildlist for a Zmatrix.
_clean_dihedral(buildlist_to_check) Reindexes the dihedral defining atom if colinear.
_build_zmat(buildlist) Creates the zmatrix from a buildlist.