def sesExposurePercent():
"""Compute the percentage of solvent exposed surface for each amino acide.
After running this macro, each residue has the 2 following members:
ses_area: total surface area for this residue
ses_ratio: percentage of residue surface exposed to solvent
The ratio is the percentage of SES area exposed to the solvent in each
residue, where 100 is the surface of that particular residue when all other
atoms are ignored
"""
import mslib
import numpy.oldnumeric as Numeric
from Pmv.guiTools import MoleculeChooser
mol = MoleculeChooser(self).go(modal=0, blocking=1)
allrads = mol.defaultRadii()
allResidues = mol.chains.residues
allAtoms = mol.allAtoms
# compute the surface
srf = mslib.MSMS(coords=allAtoms.coords, radii=allrads)
srf.compute()
srf.compute_ses_area()
# get surface areas per atom
import swig
ses_areas = []
for i in xrange(srf.nbat):
atm = srf.get_atm(i)
ses_areas.append(swig.getdoublearray(atm.ses_area, (1,))[0])
# get surface areas to each atom
allAtoms.ses_area = ses_areas
# sum up ses areas over resdiues
for r in allResidues:
r.ses_area = Numeric.sum(r.atoms.ses_area)
# compute the surface for each residue independantly
# compute the % of ses
srfList = []
for r in allResidues:
coords = r.atoms.coords
rad = map(lambda x: x.radius, r.atoms)
m = mslib.MSMS(coords=coords, radii=rad)
m.compute()
m.compute_ses_area()
srfList.append(m)
if r.ses_area > 0.0:
r.ses_ratio = (r.ses_area * 100) / m.sesr.fst.a_ses_area
else:
r.ses_ratio = 0.0
def sesExposurePercent():
"""Compute the percentage of solvent exposed surface for each amino acide.
After running this macro, each residue has the 2 following members:
ses_area: total surface area for this residue
ses_ratio: percentage of residue surface exposed to solvent
The ratio is the percentage of SES area exposed to the solvent in each
residue, where 100 is the surface of that particular residue when all other
atoms are ignored
"""
import mslib
import numpy.oldnumeric as Numeric
from Pmv.guiTools import MoleculeChooser
mol = MoleculeChooser(self).go(modal=0, blocking=1)
allrads = mol.defaultRadii()
allResidues = mol.chains.residues
allAtoms = mol.allAtoms
# compute the surface
srf = mslib.MSMS(coords=allAtoms.coords, radii=allrads)
srf.compute()
srf.compute_ses_area()
# get surface areas per atom
ses_areas = []
for i in xrange(srf.nbat):
atm = srf.get_atm(i)
ses_areas.append(atm.get_ses_area(0))
# get surface areas to each atom
allAtoms.ses_area = ses_areas
# sum up ses areas over resdiues
for r in allResidues:
r.ses_area = Numeric.sum(r.atoms.ses_area)
# compute the surface for each residue independantly
# compute the % of ses
srfList = []
for r in allResidues:
coords = r.atoms.coords
rad = map(lambda x: x.radius, r.atoms)
m = mslib.MSMS(coords=coords, radii=rad)
m.compute()
m.compute_ses_area()
srfList.append(m)
if r.ses_area > 0.0:
r.ses_ratio = (r.ses_area * 100) / m.sesr.fst.a_ses_area
else:
r.ses_ratio = 0.0
