nomodeco_classes

class nomodeco_classes.Molecule(iterable=(), /)

Nomodeco molecule class

Attributes:

a list of of atoms

class Atom(symbol, coordinates)

The atom class in nomodeco

Attributes:

symbol:
Enumerated atomic symbol of the molecule

coordinates:
3D coordinates of a atom in a tuple

is_donor() → bool

Checks if a given atom is a donor molecule

Attributes:: self: a object of the Atom class
Returns:: True if a atom is a donor atom

is_hydrogen() → bool

Checks if a given atom is a hydrogen atom

Attributes:: self: a object of the Atom class
Returns:: True if the atom is hydrogen

swap_deuterium() → self

Swaps a given hydrogen atom with a deuterium atom

Attributes:: self: a object of the Atom class
Returns:: a object of the atom class with H swapped to D

actual_length(symbol1, symbol2) → float

Calculates the actual bond length between two atoms

Attributes:

self:: a object of the Molecule Class
symbol1: str: a string of the first atom in question
symbol2: str: a string of the second atom in question

Returns:

a floating point number with the actual bond length

append(value)

Appends a given atom to the Molecule Class

Attributes:: self: a object of the Molecule Class value: a object of the Atom Class

bond_angle(symbol1, symbol2, symbol3) → float

Calculates the bond angle between three atoms in the Molecule object

Attributes:

self:: a object of the Molecule class
symbol1: str: a string of the atom
symbol2: str: a string of the atom
symbol3: str: a string of the atom

Returns:

The angle between the three atoms (ABC) in radiant

bond_dict(bonds) → dict

Created a dictionary where for each atom the corresponding “bonded” atoms are stored

Attributes:

self:: a object of the Molecule class
bonds:: a list of tuples containing the bonds which are used for the dict creation

Returns:

A dictionary containing the bonded atom for each atom e.q {H1: [O1,O2]}

static count_connected_components(graph) → int

Using the dfs algorithm counts the fully covalently connected components inside a molecule

Attributes:

graph:: a molecular graph created by Molecule.graph_rep()

Returns:

a integer which represents the total count of connected components ranges from 1..N

covalent_bonds(degofc_table) → list

Searches for covalent bonds between two atoms. A covalent bond is found when the degree of covalence is greater than 0.75

Attributes:

self:: a object of the Molecule class
degofc_table: dict: a dictionary containing the degrees of covalence

Returns:

a list of possible bonds e.q [(O1,H2), …]

degree_of_covalance() → dict

Calculates the degree of covalance between all the combinations of two atoms

Reference https://doi.org/10.1002/qua.21049

Returns:: a python dictionary with the two atoms as a tuple and the value of the degree of covalance

detect_submolecules()

A graph theory oriented function to detect the covalent submolecules

Attributes:

self:: a object of the molecule class

Returns:

connected_components: more information see networkx.connected_components submolecules: a dictionary containing the subgraphs of the molecule submolecule_symbols: a list of the atomic symbols of the submolecules

static dfs(graph, start, visited)

A static method that applies dfs algorithm on a given graph

Attributes:

graph:: a molecular graph created by Molecule.graph_rep()
start:: start node for the dfs algorithm
visitied:: visited list for the dfs algorithm

get_atom_coords_by_symbol(symbol)

Retries a atom by specifying a atomic symbol

Attributes:

self:: a object of the Molecule class
symbol:: a atomic symbol as a string

get_donor_atoms() → list: Returns the class variable donor_atom of the Atom class

graph_rep()

Generates the covalent bonds and using the covalent bonds a graph representation of a molecule

Attributes:

self:: a object of the Molecule class

Returns:

a dictionary where the graph representation of the molecule is stored

idof_general() → int: Returns the degrees of freedom in the general case 3N-6

idof_linear() → int: Returns the degrees of freedom in the linear case 3N-5

static is_connected(graph)

Uses the dfs method and a molecular graph to check if a graph is connected

Attributes:

graph:: a molecular graph created by Molecule.graph_rep()

Returns:

True if the length of the visited list is equal in length of the total graph

list_of_atom_symbols() → list: Returns a list of just the symbols in the given Molecule

e.q [‘H1’,’O2’,’H2’]

list_of_atom_symbols_xyz() → list

Special function that is used for printing of B and D matrix

Returns a list of Symbols, xyz

num_atoms() → int: Returns the number of atoms given of the given Molecule

theoretical_length(symbol1, symbol2) → float

Returns the theoretical covalent bond length between two atoms

Attributes:

self:: a object of the Molecule Class
symbol1: str: a string of the first atom in question
symbol2: str: a string of the second atom in question

Returns:

a floating point number with the covalent bond length

theoretical_length_vdw(symbol1, symbol2) → float

Returns the theoretical vdw length between two atoms

Attributes:

self:: a object of the Molecule Class
symbol1: str: a string of the first atom in question
symbol2: str: a string of the second atom in question

Returns:

a floating point number with the vdw bond length