Structure

structure.Atom

A class containing atomic information.

read_pdb_line(Line, default_chain_id='A')

Reads atomic information from a string formatted according to the PDB standard.

PARAMETER	DESCRIPTION
Line	A string formatted according to the PDB standard. TYPE: str
default_chain_id	If the chain ID is missing, replace it with this. TYPE: str DEFAULT: 'A'

structure.Molecule

Loads, saves, and manipulates molecular models.

get_center_of_mass_from_selection_by_atom_indices(indices_selection)

Gets the center of mass of a set of atoms

PARAMETER	DESCRIPTION
indices_selection	a numpy array containing the indices of the atoms to consider

Returns a numpy array containing the 3D coordinates of the center of mass of those atoms

get_indices_of_atoms_in_a_residue_by_atom_name(residue_identifier, atom_names_list, not_selection=False)

Gets the indices of atoms in a specified residue

PARAMETER	DESCRIPTION
residue_identifier	a string (chain_resname_resid) specifying the residue
atom_names_list	a list of strings containing the names of the atoms to keep
not_selection	a optional boolean. if False, match the atom_names_list items. if True, match the items not in atom_names_list DEFAULT: False

RETURNS	DESCRIPTION
	a numpy array containing the indices of the atoms to keep

get_mass(element_name)

A library to provide the mass of a given element

PARAMETER	DESCRIPTION
element_name	a string that specifies the element

RETURNS	DESCRIPTION
	a float, the mass of the specified element. If the element is not in the
	library, returns None.

load_pdb_from_list(alist)

Loads a list of PDB ATOM/HETATM lines into the current Molecule object.

PARAMETER	DESCRIPTION
alist	the list of PDB lines

map_atoms_to_residues()

Sets up self.residue_identifier_to_atom_indices, which matches chain_resname_resid to associated atom indices

map_nodes_to_residues(node_definition)

For each residue in the molecule, define the node

PARAMETER	DESCRIPTION
node_definition	a string describing the definition of the node: CA, RESIDUE_COM, BACKBONE_COM, or SIDECHAIN_COM

save_pdb(filename)

Saves a pdb file

PARAMETER	DESCRIPTION
filename	a string specifying the file name