propka.bonds¶
Bonds¶
PROPKA representation of bonds.
Classes
Makes bonds? |
- class propka.bonds.BondMaker[source]¶
Makes bonds?
TODO - the documentation for this class needs to be improved.
- add_pi_electron_information(molecules)[source]¶
Add pi electron information to a molecule.
- Parameters
molecules – list of molecules for adding pi electron information.
- add_pi_electron_table_info(atoms)[source]¶
Add table information on pi electrons
- Parameters
atoms – list of atoms for pi electron table information checking
- check_distance(atom1, atom2)[source]¶
Check distance between two atoms
- Parameters
atom1 – first atom for distance check
atom2 – second atom for distance check
- Returns
True if within distance, False otherwise
- check_for_cysteine_bonds(cys1, cys2)[source]¶
Looks for potential bonds between two cysteines.
- Parameters
cys1 – one of the cysteines to check
cys1 – one of the cysteines to check
- connect_backbone(residue1, residue2)[source]¶
Sets up bonds in the backbone
- Parameters
residue1 – first residue to connect
residue2 – second residue to connect
- find_bonds_for_atoms(atoms)[source]¶
Finds all bonds for a list of atoms
- Parameters
atoms – list of atoms in which to find bonds.
- find_bonds_for_atoms_disjoint(atoms1, atoms2)[source]¶
Finds all bonds between two disjoint sets of atoms.
- Parameters
atoms1 – list of atoms
atoms2 – list of atoms
- find_bonds_for_atoms_using_boxes(atoms)[source]¶
Finds all bonds for a list of atoms.
- Parameters
atoms – list of atoms for finding bonds
- find_bonds_for_ligand(ligand)[source]¶
Finds bonds for all atoms in the ligand molecule
- Parameters
ligand – ligand molecule to search for bonds
- find_bonds_for_molecules_using_boxes(molecules)[source]¶
Finds all bonds for a molecular container.
- Parameters
molecules – list of molecules for finding bonds.
- find_bonds_for_protein(protein)[source]¶
Bonds proteins based on the way atoms normally bond.
- Parameters
protein – the protein to search for bonds
- find_bonds_for_protein_by_distance(molecule)[source]¶
Finds bonds for all atoms in the molecule.
- Parameters
molecule – molecule in which to find bonds.
- Returns
list of atoms
- find_bonds_for_residue_backbone(residue)[source]¶
Find bonds for this residue’s backbone.
- Parameters
residue – reside to search for backbone bonds.
- find_bonds_for_side_chain(atoms)[source]¶
Finds bonds for a side chain.
- Parameters
atoms – list of atoms to check for bonds
- find_bonds_for_terminal_oxygen(residue)[source]¶
Look for bonds for terminal oxygen.
- Parameters
residue (residue - test) –
- generate_protein_bond_dictionary(atoms)[source]¶
Generate dictionary of protein bonds.
- Parameters
atoms – list of atoms for bonding