Cartesian

class chemcoord.xyz_functions.Cartesian(init)

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.