to get properties of a residue from pdb file

Question

I have a pdb file and I want to parse the pdb using python and I want to find the following for residues in pdb:

1. hydrophobicity
2. interface topology
3. solvent accessible surface area

I have tried using pybel

file_name = "4hhb.pdb"
allmols = [mol for mol in pybel.readfile("pdb", file_name)]
for mol in allmols:
    dir(mols)

but, I am only able to see few properties.

'addh', 'atoms', 'calcdesc', 'calcfp', 'charge', 'conformers', 'data', 'dim', 'draw', 'energy', 'exactmass', 'formula', 'localopt', 'make3D', 'molwt', 'removeh', 'spin', 'sssr', 'title', 'unitcell', 'write

How can I find these 3 properties from pdb? I can use any module available in python to get these properties.

Answer 1

As mentioned in this1 answer, BioPython2 provides support for parsing .pdb files

Answer 2

Hidrophobicity (for each AA) can be found in:

Bio.SeqUtils.ProtParamData.kd

kd = {'A': 1.8, 'R':-4.5, 'N':-3.5, 'D':-3.5, 'C': 2.5, 
      'Q':-3.5, 'E':-3.5, 'G':-0.4, 'H':-3.2, 'I': 4.5, 
      'L': 3.8, 'K':-3.9, 'M': 1.9, 'F': 2.8, 'P':-1.6, 
      'S':-0.8, 'T':-0.7, 'W':-0.9, 'Y':-1.3, 'V': 4.2 }

I guess you have to add all the aminoacid values and get the overall hidrophobicity.

http://biopython.org/DIST/docs/api/Bio.SeqUtils.ProtParamData-pysrc.html

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You can use GROMACs (http://manual.gromacs.org/programs/gmx-sasa.html) to get the other two parameters. Viewing the C source code (https://github.com/gromacs/gromacs/blob/master/src/gromacs/trajectoryanalysis/modules/sasa.cpp), those parameters are far from obvious calculations.

I would wrap gmx_sasa with a subprocess.Popen() and get the results.