Arpeggio

Outline

Arpeggio calculates interatomic contacts based on the rules defined in CREDO. The program will be freely available and require only Open Source dependencies.

Dependencies

Arpeggio is written in Python and currently has the following dependencies:

Dependencies

• Python (v2.7)
• Numpy
• BioPython (>= v1.60)
• OpenBabel (with Python bindings)

Recommended

• PyMOL (for visualising contacts)

Arpeggio may work with earlier versions of BioPython, however these haven't been tested. It is recommended that each dependency be the latest version.

Running

python arpeggio.py pdb [options]

Use python arpeggio.py -h for available options.

Arpeggio doesn't do any checking of your PDB structure, other than what BioPython does by default. Alternate locations and missing density are not explicitly accounted for and may result in anomalous results. Please use with caution.

Output Files

*.ari

Atom-aromatic ring interactions.

Column	Datatype	Description
Atom	string <chain_id>/<res_num><ins_code (stripped)>/<atom_name>	Uniquely identifies an atom
Ring ID	integer	Internal number used to identify the aromatic ring
Ring centroid	list	3D coordinates of the centre of the ring
Interaction type	list	Type(s) of interaction this atom/ring are making

*.ri

Aromatic ring-aromatic ring interactions.

Column	Datatype	Description
Ring 1 ID	integer	Internal number used to identify the first aromatic ring
Ring 1 Residue	string <chain_id>/<res_num>	Uniquely identifies the first ring's residue
Ring 1 centroid	list	3D coordinates of the centre of the first ring
Ring 2 ID	integer	Internal number used to identify the second aromatic ring
Ring 2 Residue	string <chain_id>/<res_num>	Uniquely identifies an the second ring's residue
Ring 2 centroid	list	3D coordinates of the centre of the second ring
Inter or intra residue	string from (INTER, INTRA_RESIDUE)	States whether this ring-ring interaction is within the same residue (e.g. within a small molecule ligand), or between two different residues
Interacting entities	string from (INTER, INTRA_NON_SELECTION, INTRA_SELECTION)	Distinguishes how this interacting ring pair relates to the selected atoms: see below

*.rings

Aromatic rings found in the structure

Column	Datatype	Description
Ring ID	integer	Internal number used to identify the ring
Ring Residue	string <chain_id>/<res_num>	Uniquely identifies the ring's residue
Ring centroid	list	3D coordinates of the centre of the ring

*.atomtypes

Atom types for all of the atoms for which interactions are calculated for. This includes the selected atoms, and the atoms that those atoms interact with.

Column	Datatype	Description
Atom	string <chain_id>/<res_num><ins_code (stripped)>/<atom_name>	Uniquely identifies an atom
Atom types	list	All the atom types that this atom possesses

*.contacts

Pairwise contacts between two individual atoms.

Column	Datatype	Description
Atom 1	string <chain_id>/<res_num><ins_code (stripped)>/<atom_name>	Uniquely identifies the first atom in this contact
Atom 2	string <chain_id>/<res_num><ins_code (stripped)>/<atom_name>	Uniquely identifies the second atom in this contact
Clash	boolean::integer	Denotes if the covalent radii of the two atoms are clashing, i.e. steric clash
Covalent	boolean::integer	Denotes if the two atoms appear to be covalently bonded
VdW Clash	boolean::integer	Denotes if the van der Waals radii of the two atoms are clashing
VdW	boolean::integer	Denotes if the van der Waals radii of the two atoms are interacting
Proximal	boolean::integer	Denotes the two atoms being > the VdW interaction distance, but with in 5 Angstroms of each other
Hydrogen Bond	boolean::integer	Denotes if the atoms form a hydrogen bond
Weak Hydrogen Bond	boolean::integer	Denotes if the atoms form a weak hydrogen bond
Halogen Bond	boolean::integer	Denotes if the atoms form a halogen bond
Ionic	boolean::integer	Denotes if the atoms may interact via charges
Metal Complex	boolean::integer	Denotes if the atoms are part of a metal complex
Aromatic	boolean::integer	Denotes two aromatic ring atoms interacting
Hydrophobic	boolean::integer	Denotes two hydrophobic atoms interacting
Carbonyl	boolean::integer	Denotes a carbonyl-carbon:carbonyl-carbon interaction
Polar	boolean::integer	Less strict hydrogen bonding (without angle terms)
Weak Polar	boolean::integer	Less strict weak hydrogen bonding (without angle terms)
Interacting entities	string from (INTER, INTRA_NON_SELECTION, INTRA_SELECTION, SELECTION_WATER, NON_SELECTION_WATER, WATER_WATER)	Distinguishes how this atom pair relates to the selected atoms: see below

Clash, Covalent, VdW Clash, VdW and Proximal interactions are mutually exclusive: Other interactions can occur simultaneously.

Entity interactions:

• INTER: Between an atom from the user's selection and a non-selected atom
• INTRA_SELECTION: Between two atoms both in the user's selection
• INTRA_NON_SELECTION: Between two atoms that are both not in the user's selection
• SELECTION_WATER: Between an atom in the user's selection and a water molecule
• NON_SELECTION_WATER: Between an atom that is not in the user's selection and a water molecule
• WATER_WATER: Between two water molecules

*.bs_contacts

As with *.contacts, but only including interactions in the binding site (i.e. interactions involving atoms that were selected by the user, with atoms not selected by the user, as opposed to any intra-selection interactions.

*.sift

Interaction fingerprints for individual atoms. These are binary (i.e., on/off) indications of an atom's interaction, not counts.

Column	Datatype	Description
Atom	string <chain_id>/<res_num><ins_code (stripped)>/<atom_name>	Uniquely identifies the atom
Clash	boolean::integer	Denotes if the atom is involved in a steric clash
Covalent	boolean::integer	Denotes if the atom appears to be covalently bonded
VdW Clash	boolean::integer	Denotes if the van der Waals radius of the atom is clashing with one or more other atoms
VdW	boolean::integer	Denotes if the van der Waals radius of the the atom is interacting with one or more other atoms
Proximal	boolean::integer	Denotes if the atom is > the VdW interaction distance, but with in 5 Angstroms of other atom(s)
Hydrogen Bond	boolean::integer	Denotes if the atom forms a hydrogen bond
Weak Hydrogen Bond	boolean::integer	Denotes if the atom forms a weak hydrogen bond
Halogen Bond	boolean::integer	Denotes if the atom forms a halogen bond
Ionic	boolean::integer	Denotes if the atom may interact via charges
Metal Complex	boolean::integer	Denotes if the atom is part of a metal complex
Aromatic	boolean::integer	Denotes an aromatic ring atom interacting with another aromatic ring atom
Hydrophobic	boolean::integer	Denotes hydrophobic interaction
Carbonyl	boolean::integer	Denotes a carbonyl-carbon:carbonyl-carbon interaction
Polar	boolean::integer	Less strict hydrogen bonding (without angle terms)
Weak Polar	boolean::integer	Less strict weak hydrogen bonding (without angle terms)

*.specific.sift

Interaction fingerprints for individual atoms. These are binary (i.e., on/off) indications of an atom's interaction, not counts.

The columns match the *.sift files, but the first 15 columns (after the atom identifier) denote only interactions between the selection made by the user, and non-selection atoms; the second 15 columns indicate interactions made within the selection made by the user; and the third 15 columns indicate interactions made with water only.

*.siftmatch, *.polarmatch

These files are for testing purposes.