Splicer Processor Task

The Splicer Processor Task, also known as ProcessPDBTask accepts a PDB file and processes it into PGD Protein Models.

Running From the command line

Like all splicer components ProcessPDBTask can be run from the commandline to simplify debugging the task. It requires the follow arguments:
  • PDB Code - 4 character alphanumeric code for a protein.
  • Threshold - Float
  • Resolution - Float
  • Rfactor - Float
  • Rfree - Float

When debugging only the PDB code need be a real value. The other values are required, but not validated.


  • BioPython - A library that can parse PDB files and contains various functions within its PDB API for extracting data from them.
  • DSSP - A program for calculating secondary structure. BioPython has bindings for this program.

Parsing PDBs

Some properties are available as simple properties using the Residue class within BioPython. Most others require calculations involving individual Atoms within a Residue

Parsing Geometric Properties

Geometric properties must be calculated from raw atom data. BioPython supplies several functions for calculating functions between atom vectors.
  • calc_length(vector, vector) - Calculates distance between atoms in 3D space (supplied by PGD)
  • calc_angle - Calculates the angle between 3 atoms.
  • calc_dihedral - Calculates the dihedral (torsion) angle between 4 atoms

These functions require vectors which can be retrieved using Atom.get_vector()

Example a3


N = residue[‘N’].get_vector() CA = residue[‘CA’].get_vector() C = residue[‘C’].get_vector()

a3 = calc_angle(N,CA,C)

Example: Ome


oldCA = prev_residue[‘CA’].get_vector() oldC = prev_residue[‘C’].get_vector() N = residue[‘N’].get_vector() CA = residue[‘CA’].get_vector()

ome = calc_dihedral(oldCA,oldC,N,CA)

Parsing Averaged Properties

Several properties are presented as averages across the Main-Chain, *Side-Chain, and Carbon Gamma atoms.

  • Main-Chain - atoms N, C-alpha, C, O, OXT
  • Side-Chain - all other atoms excluding Main-Chain, C-gamma, and HETs (water)
  • Carbon-gamma - also known as C-gamma or Cg. A single atom.

This properties are calculated as the average of an atom level property across the atoms in this group.

Example B-factor: Bm, Bs, Bg

Other B Averages
    Bm - Average of bfactors in main chain.
    Bm - Average of bfactors in side chain.
main_chain = []
side_chain = []
for a in res.child_list:
    if a.name in ('N', 'CA', 'C', 'O','OXT'):
    elif a.name in ('H'):

if main_chain != []:
    res_dict['bm'] = sum(main_chain)/len(main_chain)

if side_chain != []:
    res_dict['bs'] = sum(side_chain)/len(side_chain)

Parsing Side Chain Properties

Side chains are different for each type of atom. They require a map of connections to determine which atoms require angles, lengths, and dihedral angles calculated.

Currently Chi1, Chi2, Chi3, and Chi4*are calculated using a map in *chi.py. Sidechain lengths and angles will be added later, requiring an additional map of connections between atoms.

Update Checking

PDB Processor checks for updates when processing proteins. The Protein Model contains a timestamp which corresponds to the update timestamp on the PDB file it was imported from. A protein will only be processed if the PDB file is newer.