molecular

Module that provides molecular visualization tools.

Molecule([atomic_numbers, coords, ...])	Your molecule class.
PTable	A class to obtain properties of elements (eg: Covalent Radius, Van Der Waals Radius, Symbol etc.).
add_atom(molecule, atomic_num, x_coord, ...)	Add atomic data to our molecule.
add_bond(molecule, atom1_index, atom2_index)	Add bonding data to our molecule.
get_atomic_number(molecule, atom_index)	Get the atomic number of an atom for a specified index.
set_atomic_number(molecule, atom_index, ...)	Set the atomic number of an atom for a specified index.
get_atomic_position(molecule, atom_index)	Get the atomic coordinates of an atom for a specified index.
set_atomic_position(molecule, atom_index, ...)	Set the atomic coordinates of an atom for a specified index.
get_bond_order(molecule, bond_index)	Get the order of bond for a specified index.
set_bond_order(molecule, bond_index, bond_order)	Set the bond order of a bond for a specified index.
get_all_atomic_numbers(molecule)	Return an array of atomic numbers corresponding to the atoms present in a given molecule.
get_all_bond_orders(molecule)	Return an array of integers containing the bond orders (single/double/ triple) corresponding to the bonds present in the molecule.
get_all_atomic_positions(molecule)	Return an array of atomic coordinates corresponding to the atoms present in the molecule.
deep_copy_molecule(molecule1, molecule2)	Deep copies the atomic information (atoms and bonds) from molecule2 into molecule1.
compute_bonding(molecule)	Uses vtkSimpleBondPerceiver to generate bonding information for a molecule.
sphere_cpk(molecule[, colormode])	Create an actor for sphere molecular representation.
ball_stick(molecule[, colormode, ...])	Create an actor for ball and stick molecular representation.
stick(molecule[, colormode, bond_thickness])	Create an actor for stick molecular representation.
ribbon(molecule)	Create an actor for ribbon molecular representation.
bounding_box(molecule[, colors, linewidth])	Create a bounding box for a molecule.

Molecule

class fury.molecular.Molecule(atomic_numbers=None, coords=None, atom_names=None, model=None, residue_seq=None, chain=None, sheet=None, helix=None, is_hetatm=None)

Bases: vtkMolecule

Your molecule class.

An object that is used to create molecules and store molecular data (e.g. coordinate and bonding data). This is a more pythonic version of Molecule.

__init__(atomic_numbers=None, coords=None, atom_names=None, model=None, residue_seq=None, chain=None, sheet=None, helix=None, is_hetatm=None)

Send the atomic data to the molecule.

Parameters:

• atomic_numbers (ndarray of integers, optional) – The shape of the array must be (N, ) where N is the total number of atoms present in the molecule. Array having atomic number corresponding to each atom of the molecule.

• coords (ndarray of floats, optional) – The shape of the array must be (N, 3) where N is the total number of atoms present in the molecule. Array having coordinates corresponding to each atom of the molecule.

• atom_names (ndarray of strings, optional) – The shape of the array must be (N, ) where N is the total number of atoms present in the molecule. Array having the names of atoms.

• model (ndarray of integers, optional) – The shape of the array must be (N, ) where N is the total number of atoms present in the molecule. Array having the model number corresponding to each atom.

• residue_seq (ndarray of integers, optional) – The shape of the array must be (N, ) where N is the total number of atoms present in the molecule. Array having the residue sequence number corresponding to each atom of the molecule.

• chain (ndarray of integers, optional) – The shape of the array must be (N, ) where N is the total number of atoms present in the molecule. Array having the chain number corresponding to each atom.

• sheet (ndarray of integers, optional) – The shape of the array must be (S, 4) where S is the total number of sheets present in the molecule. Array containing information about sheets present in the molecule.

• helix (ndarray of integers, optional) – The shape of the array must be (H, 4) where H is the total number of helices present in the molecule. Array containing information about helices present in the molecule.

• is_hetatm (ndarray of bools, optional) – The shape of the array must be (N, ) where N is the total number of atoms present in the molecule. Array containing a bool value to indicate if an atom is a heteroatom.

property total_num_atoms

Return the total number of atoms in a given molecule.

property total_num_bonds

Return the total number of bonds in a given molecule.

PTable

class fury.molecular.PTable

Bases: vtkPeriodicTable

A class to obtain properties of elements (eg: Covalent Radius, Van Der Waals Radius, Symbol etc.).

This is a more pythonic version of vtkPeriodicTable providing simple methods to access atomic properties. It provides access to essential functionality available in vtkPeriodicTable. An object of this class provides access to atomic information sourced from Blue Obelisk Data Repository.

__init__()

atom_color(atomic_number)

Given an atomic number, return the RGB tuple associated with that element (CPK coloring convention) provided by the Blue Obelisk Data Repository.

Parameters:

atomicNumber (int) – Atomic number of the element whose RGB tuple is to be obtained.

atomic_number(element_name)

Given a case-insensitive string that contains the symbol or name of an element, return the corresponding atomic number.

Parameters:

element_name (string) – Name of the element whose atomic number is to be obtained.

atomic_radius(atomic_number, radius_type='VDW')

Given an atomic number, return either the covalent radius of the atom (in Å) or return the Van Der Waals radius (in Å) of the atom depending on radius_type.

Parameters:

• atomic_number (int) – Atomic number of the element whose atomic radius is to be obtained.

• radius_type (string) –

  Type of atomic radius to be obtained. Two valid choices:

  • ’VDW’ : for Van der Waals radius of the atom

  • ’Covalent’ : for covalent radius of the atom

  Default: ‘VDW’

atomic_symbol(atomic_number)

Given an atomic number, returns the symbol associated with the element.

Parameters:

atomic_number (int) – Atomic number of the element whose symbol is to be obtained.

element_name(atomic_number)

Given an atomic number, returns the name of the element.

Parameters:

atomic_number (int) – Atomic number of the element whose name is to be obtained.

add_atom

fury.molecular.add_atom(molecule, atomic_num, x_coord, y_coord, z_coord)

Add atomic data to our molecule.

Parameters:

• molecule (Molecule) – The molecule to which the atom is to be added.

• atomic_num (int) – Atomic number of the atom.

• x_coord (float) – x-coordinate of the atom.

• y_coord (float) – y-coordinate of the atom.

• z_coord (float) – z-coordinate of the atom.

add_bond

fury.molecular.add_bond(molecule, atom1_index, atom2_index, bond_order=1)

Add bonding data to our molecule. Establish a bond of type bond_order between the atom at atom1_index and the atom at atom2_index.

Parameters:

• molecule (Molecule) – The molecule to which the bond is to be added.

• atom1_index (int) – Index of the first atom.

• atom2_index (int) – Index of the second atom.

• bond_order (int (optional)) – Bond order (whether it’s a single/double/triple bond). Default: 1

Notes

Ensure that the total number of bonds between two atoms doesn’t exceed 3. Calling add_bond to add bonds between atoms that already have a triple bond between them leads to erratic behavior and must be avoided.

get_atomic_number

fury.molecular.get_atomic_number(molecule, atom_index)

Get the atomic number of an atom for a specified index.

Returns the atomic number of the atom present at index atom_index.

Parameters:

• molecule (Molecule) – The molecule to which the atom belongs.

• atom_index (int) – Index of the atom whose atomic number is to be obtained.

set_atomic_number

fury.molecular.set_atomic_number(molecule, atom_index, atomic_num)

Set the atomic number of an atom for a specified index.

Assign atomic_num as the atomic number of the atom present at atom_index.

Parameters:

• molecule (Molecule) – The molecule to which the atom belongs.

• atom_index (int) – Index of the atom to whom the atomic number is to be assigned.

• atom_num (int) – Atomic number to be assigned to the atom.

get_atomic_position

fury.molecular.get_atomic_position(molecule, atom_index)

Get the atomic coordinates of an atom for a specified index.

Returns the atomic coordinates of the atom present at index atom_index.

Parameters:

• molecule (Molecule) – The molecule to which the atom belongs.

• atom_index (int) – Index of the atom whose atomic coordinates are to be obtained.

set_atomic_position

fury.molecular.set_atomic_position(molecule, atom_index, x_coord, y_coord, z_coord)

Set the atomic coordinates of an atom for a specified index.

Assign atom_coordinate to the coordinates of the atom present at atom_index.

Parameters:

• molecule (Molecule) – The molecule to which the atom belongs.

• atom_index (int) – Index of the atom to which the coordinates are to be assigned.

• x_coord (float) – x-coordinate of the atom.

• y_coord (float) – y-coordinate of the atom.

• z_coord (float) – z-coordinate of the atom.

get_bond_order

fury.molecular.get_bond_order(molecule, bond_index)

Get the order of bond for a specified index.

Returns the order of bond (whether it’s a single/double/triple bond) present at bond_index.

Parameters:

• molecule (Molecule) – The molecule to which the bond belongs.

• bond_index (int) – Index of the bond whose order is to be obtained.

set_bond_order

fury.molecular.set_bond_order(molecule, bond_index, bond_order)

Set the bond order of a bond for a specified index.

Assign bond_order (whether it’s a single/double/triple bond) to the bond present at the bond_index.

Parameters:

• molecule (Molecule) – The molecule to which the bond belongs.

• bond_index (int) – Index of the bond whose order is to be assigned.

• bond_order (int) – Bond order (whether it’s a single/double/triple bond).

get_all_atomic_numbers

fury.molecular.get_all_atomic_numbers(molecule)

Return an array of atomic numbers corresponding to the atoms present in a given molecule.

Parameters:

molecule (Molecule) – The molecule whose atomic number array is to be obtained.

get_all_bond_orders

fury.molecular.get_all_bond_orders(molecule)

Return an array of integers containing the bond orders (single/double/ triple) corresponding to the bonds present in the molecule.

Parameters:

molecule (Molecule) – The molecule whose bond types array is to be obtained.

get_all_atomic_positions

fury.molecular.get_all_atomic_positions(molecule)

Return an array of atomic coordinates corresponding to the atoms present in the molecule.

Parameters:

molecule (Molecule) – The molecule whose atomic position array is to be obtained.

deep_copy_molecule

fury.molecular.deep_copy_molecule(molecule1, molecule2)

Deep copies the atomic information (atoms and bonds) from molecule2 into molecule1.

Parameters:

• molecule1 (Molecule) – The molecule to which the atomic information is copied.

• molecule2 (Molecule) – The molecule from which the atomic information is copied.

compute_bonding

fury.molecular.compute_bonding(molecule)

Uses vtkSimpleBondPerceiver to generate bonding information for a molecule. vtkSimpleBondPerceiver performs a simple check of all interatomic distances and adds a single bond between atoms that are reasonably close. If the interatomic distance is less than the sum of the two atom’s covalent radii plus a tolerance, a single bond is added.

Parameters:

molecule (Molecule) – The molecule for which bonding information is to be generated.

Notes

This algorithm does not consider valences, hybridization, aromaticity, or anything other than atomic separations. It will not produce anything other than single bonds.

sphere_cpk

fury.molecular.sphere_cpk(molecule, colormode='discrete')

Create an actor for sphere molecular representation. It’s also referred to as CPK model and space-filling model.

Parameters:

• molecule (Molecule) – The molecule to be rendered.

• colormode (string, optional) –

  Set the colormode for coloring the atoms. Two valid color modes:

  • ’discrete’: Atoms are colored using CPK coloring convention.

  • ’single’: All atoms are colored with same color (grey). RGB tuple used for coloring the atoms when ‘single’ colormode is selected: (150, 150, 150).

  Default: ‘discrete’

Returns:

molecule_actor – Actor created to render the space filling representation of the molecule to be visualized.

Return type:

vtkActor

References

Corey R.B.; Pauling L. Molecular Models of Amino Acids, Peptides, and Proteins Review of Scientific Instruments 1953, 24 (8), 621-627.

ball_stick

fury.molecular.ball_stick(molecule, colormode='discrete', atom_scale_factor=0.3, bond_thickness=0.1, multiple_bonds=True)

Create an actor for ball and stick molecular representation.

Parameters:

• molecule (Molecule) – The molecule to be rendered.

• colormode (string, optional) –

  Set the colormode for coloring the atoms. Two valid color modes:

  • ’discrete’: Atoms and bonds are colored using CPK coloring convention.

  • ’single’: All atoms are colored with same color (grey) and all bonds are colored with same color (dark grey). RGB tuple used for coloring the atoms when ‘single’ colormode is selected: (150, 150, 150). RGB tuple used for coloring the bonds when ‘single’ colormode is selected: (50, 50, 50)

  Default: ‘discrete’

• atom_scale_factor (float, optional) – Scaling factor. Default: 0.3

• bond_thickness (float, optional) – Used to manipulate the thickness of bonds (i.e. thickness of tubes which are used to render bonds) Default: 0.1 (Optimal range: 0.1 - 0.5).

• multiple_bonds (bool, optional) – Set whether multiple tubes will be used to represent multiple bonds. If True, multiple bonds (double, triple) will be shown by using multiple tubes. If False, all bonds (single, double, triple) will be shown as single bonds (i.e. shown using one tube each). Default is True.

Returns:

molecule_actor – Actor created to render the ball and stick representation of the molecule to be visualized.

Return type:

vtkActor

References

Turner, M. Ball and stick models for organic chemistry J. Chem. Educ. 1971, 48, 6, 407.

stick

fury.molecular.stick(molecule, colormode='discrete', bond_thickness=0.1)

Create an actor for stick molecular representation.

Parameters:

• molecule (Molecule) – The molecule to be rendered.

• colormode (string, optional) –

  Set the colormode for coloring the bonds. Two valid color modes:

  • ’discrete’: Bonds are colored using CPK coloring convention.

  • ’single’: All bonds are colored with the same color (dark grey) RGB tuple used for coloring the bonds when ‘single’ colormode is selected: (50, 50, 50)

  Default: ‘discrete’

• bond_thickness (float, optional) – Used to manipulate the thickness of bonds (i.e. thickness of tubes which are used to render bonds). Default: 0.1 (Optimal range: 0.1 - 0.5).

Returns:

molecule_actor – Actor created to render the stick representation of the molecule to be visualized.

Return type:

vtkActor

ribbon

fury.molecular.ribbon(molecule)

Create an actor for ribbon molecular representation.

Parameters:

molecule (Molecule) – The molecule to be rendered.

Returns:

molecule_actor – Actor created to render the rubbon representation of the molecule to be visualized.

Return type:

vtkActor

References

Richardson, J.S. The anatomy and taxonomy of protein structure Advances in Protein Chemistry, 1981, 34, 167-339.

bounding_box

fury.molecular.bounding_box(molecule, colors=(1, 1, 1), linewidth=0.3)

Create a bounding box for a molecule.

Parameters:

• molecule (Molecule) – The molecule around which the bounding box is to be created.

• colors (tuple (3,) or ndarray of shape (3,), optional) – Color of the bounding box. Default: (1, 1, 1)

• linewidth (float, optional) – Thickness of tubes used to compose bounding box. Default: 0.3

Returns:

bbox_actor – Actor created to serve as a bounding box for a given molecule.

Return type:

vtkActor