[BioPython] HSE (half-sphere exposure)

[Thomas Hamelryck]

On Tue, March 7, 2006 10:38 pm, ziemys at ecr6.ohio-state.edu wrote:
> Hi
>
>
> Can anybody give more details about how to use HSE in BioPython ?
>
>
> (BioPython is very nice, but at the same it suffers from the lack of
> documentations...)
>
> With best
> Arturas
>

Hi Arturas,

Below is an example.
Note that HSE-alpha is undefined for the first and last
residues of a polypeptide.

Best regards,

-Thomas

----

from Bio.PDB import *
import sys

p=PDBParser()
s=p.get_structure('X', sys.argv[1])
model=s[0]

RADIUS=12.0

hse=HSExposureCA(model, radius=RADIUS)
hse=HSExposureCB(model, radius=RADIUS)
hse=ExposureCN(model, radius=RADIUS)

for r in model.get_residues():
    if is_aa(r):
        print r
        try:
            # Contact number
            print r.xtra["EXP_CN"]
            # HSE alpha up
            print r.xtra["EXP_HSE_A_U"]
            # HSE alpha down
            print r.xtra["EXP_HSE_A_D"]
            # HSE beta up
            print r.xtra["EXP_HSE_B_U"]
            # HSE beta down
            print r.xtra["EXP_HSE_B_D"]
            print
        except:
            pass