molecupy.structures.molecules (Atomic Structures)

Contains classes for simple structures made of atoms.

class molecupy.structures.molecules.AtomicStructure(*atoms)

The base class for all structures which are composed of atoms.

Parameters:atoms – A sequence of Atom objects.

atoms(atom_type='localised')

Returns the atoms in this structure as a set.

Parameters:atom_type (str) – The kind of atom to return. "all" will return all atoms, "localised" just standard Atoms and "ghost" will just return generic GhostAtom atoms. Return type:set

add_atom(atom)

Adds an atom to the structure.

Parameters:atom (Atom) – The atom to add.

remove_atom(atom)

Removes an atom from the structure.

Parameters:atom (Atom) – The atom to add.

mass(atom_type='localised')

Returns the mass of the structure by summing the mass of all its atoms.

Parameters:atom_type (str) – The kind of atom to use. "all" will use all atoms, "localised" just standard Atoms and "ghost" will just return generic GhostAtom atoms. Return type:float

formula(atom_type='localised', include_hydrogens=False)

Retrurns the formula (count of each atom) of the structure.

Parameters:

• atom_type (str) – The kind of atom to use. "all" will use all atoms, "localised" just standard Atoms and "ghost" will just return generic GhostAtom atoms.
• include_hydrogens (bool) – determines whether hydrogen atoms should be included.

Return type:

Counter

contacts_with(other_atomic_structure, distance=4, include_hydrogens=True)

Returns the set of all ‘contacts’ with another atomic structure, where a contact is defined as any atom-atom pair with an inter-atomic distance less than or equal to some number of Angstroms.

If the other atomic structure has atoms which are also in this atomic structure, those atoms will not be counted as part of the other structure.

Parameters:

• other_structure (AtomicStructure) – The other atomic structure to compare to.
• distance – The distance to use (default is 4).
• include_hydrogens (bool) – determines whether hydrogen atoms should be included.

Return type:

set of frozenset contacts.

internal_contacts(distance=4, include_hydrogens=True)

Returns the set of all atomic contacts within the atoms of an atomic structure, where a contact is defined as any atom-atom pair with an inter-atomic distance less than or equal to four Angstroms.

Contacts between atoms covalently bonded to each other will be ignored, as will contacts between atoms separated by just two covalent bonds.

Parameters:

• distance – The distance to use (default is 4).
• include_hydrogens (bool) – determines whether hydrogen atoms should be included.

Return type:

set of frozenset contacts.

predict_bind_site(distance=5, include_hydrogens=True)

Attempts to predict the residues that might make up the atomic structure’s binding site by using atomic distances.

Parameters:

• distance – The distance to use (default is 5s).
• include_hydrogens (bool) – determines whether hydrogen atoms should be included.

Return type:

BindSite or None

translate(x, y, z)

Translates the structure in space.

Parameters:

• x – The distance in Angstroms to move in the x-direction.
• y – The distance in Angstroms to move in the y-direction.
• z – The distance in Angstroms to move in the z-direction.

rotate(axis, angle)

Rotates the structure around an axis.

Parameters:

• axis (str) – The axis to rotate around - must be "x", "y" or "z".
• angle – The angle, in degrees, to rotate by. Rotation is clockwise.

center_of_mass()

Returns the location of the structure’s center of mass.

Return type:tuple

radius_of_gyration()

The radius of gyration of an atomic structure is a measure of how extended it is. It is the root mean square deviation of the atoms from the structure’s center of mass.

Return type:float

get_atom_by_id(atom_id)

Retrurns the first atom that matches a given atom ID.

Parameters:atom_id (int) – The atom ID to search by. Return type:Atom or None

get_atoms_by_element(element, atom_type='localised')

Retruns all the atoms a given element.

Parameters:

• element (str) – The element to search by.
• atom_type (str) – The kind of atom to use. "all" will use all atoms, "localised" just standard Atoms and "ghost" will just return generic GhostAtom atoms.
• include_hydrogens (bool) – determines whether hydrogen atoms should be included.

Return type:

set of Atom objects.

get_atom_by_element(element, atom_type='localised')

Retrurns the first atom that matches a given element.

Parameters:

• element (str) – The element to search by.
• atom_type (str) – The kind of atom to use. "all" will use all atoms, "localised" just standard Atoms and "ghost" will just return generic GhostAtom atoms.
• include_hydrogens (bool) – determines whether hydrogen atoms should be included.

Return type:

Atom or None

get_atoms_by_name(atom_name, atom_type='localised')

Retruns all the atoms a given name.

Parameters:

• atom_name (str) – The name to search by.
• atom_type (str) – The kind of atom to use. "all" will use all atoms, "localised" just standard Atoms and "ghost" will just return generic GhostAtom atoms.
• include_hydrogens (bool) – determines whether hydrogen atoms should be included.

Return type:

set of Atom objects.

get_atom_by_name(atom_name, atom_type='localised')

Retrurns the first atom that matches a given name.

Parameters:

• atom_name (str) – The name to search by.
• atom_type (str) – The kind of atom to use. "all" will use all atoms, "localised" just standard Atoms and "ghost" will just return generic GhostAtom atoms.
• include_hydrogens (bool) – determines whether hydrogen atoms should be included.

Return type:

Atom or None

class molecupy.structures.molecules.SmallMolecule(molecule_id, molecule_name, *atoms)

Base class: AtomicStructure

Represents the ligands, solvent molecules, and other non-polymeric molecules in a structure.

Parameters:

• molecule_id (str) – The molecule’s ID.
• molecule_name (str) – The molecule’s name.
• atoms – The molecule’s atoms.

molecule_id()

Returns the molecule’s ID.

Return type:str

molecule_name(molecule_name=None)

Returns or sets the molecule’s name.

Parameters:name (str) – If given, the molecule’s name will be set to this. Return type:str

bind_site(bind_site=None)

Returns or sets the molecule’s BindSite.

Parameters:bind_site (BindSite) – If given, the atom’s bindsite will be set to this. Return type:BindSite

model()

Returns the Model that the molecule inhabits.

Return type:Model

class molecupy.structures.molecules.Residue(residue_id, residue_name, *atoms)

Base class: AtomicStructure

A Residue on a chain.

Parameters:

• residue_id (str) – The residue’s ID.
• residue_name (str) – The residue’s name.
• atoms – The residue’s atoms.

residue_id()

Returns the residue’s ID.

Return type:str

residue_name(residue_name=None)

Returns or sets the residue’s name.

Parameters:name (str) – If given, the residue’s name will be set to this. Return type:str

chain()

Returns the Chain that the residue is within.

Return type:Chain

is_missing()

Returns True if the residue was not observed in the experiment (and is therefore made up entirely of atoms with no coordinates).

Return type:bool

downstream_residue()

Returns the residue connected to this residue’s carboxy end.

Return type:Residue

upstream_residue()

Returns the residue connected to this residue’s amino end.

Return type:Residue

connect_to(downstream_residue)

Connects this residue to a downstream residue.

Parameters:downstream_residue (Residue) – The other residue.

disconnect_from(other_residue)

Breaks a connection with another residue.

Parameters:other_residue (Residue) – The other residue.

alpha_carbon()

Attempts to retrieve the alpha carbon of the residue.

Return type:Atom