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