def surfacePointsAndGradients(object, probe_radius=0., point_density=258):
"""
:param object: a chemical object
:type object: :class:~MMTK.Collections.GroupOfAtoms
:param probe_radius: the distance from the vdW-radii of the atoms
at which the surface is computed
:type probe_radius: float
:param point_density: the density of points that describe the surface
:type point_density: int
:returns: a dictionary that maps the surface atoms to a tuple
containing three surface-related quantities: the exposed surface
area, a list of points in the exposed surface, and a gradient
vector pointing outward from the surface.
:rtype: dict
"""
atoms = object.atomList()
smap = surfm.surface_atoms(atoms,
probe_radius,
ret_fmt=4,
point_density=point_density)
surface_data = {}
for a in atoms:
(area, volume, points1, grad) = smap[a]
if area > 0.:
# we have a surface atom
surface_data[a] = (area, map(Vector, points1), Vector(grad))
return surface_data
def surfaceAndVolume(object, probe_radius=0.):
"""
:param object: a chemical object
:type object: :class:~MMTK.Collections.GroupOfAtoms
:param probe_radius: the distance from the vdW-radii of the atoms
at which the surface is computed
:type probe_radius: float
:returns: the molecular surface and volume of object
:rtype: tuple
"""
atoms = object.atomList()
smap = surfm.surface_atoms(atoms, probe_radius, ret_fmt=2)
tot_a = 0
tot_v = 0
for a in atoms:
atom_data = smap[a]
tot_a = tot_a + atom_data[0]
tot_v = tot_v + atom_data[1]
return (tot_a, tot_v)
def surfaceAtoms(object, probe_radius=0.):
"""
:param object: a chemical object
:type object: :class:~MMTK.Collections.GroupOfAtoms
:param probe_radius: the distance from the vdW-radii of the atoms
at which the surface is computed
:type probe_radius: float
:returns: a dictionary that maps the surface atoms to their
exposed surface areas
:rtype: dict
"""
atoms = object.atomList()
smap = surfm.surface_atoms(atoms, probe_radius, ret_fmt=1)
surface_atoms = {}
for a in atoms:
area = smap[a]
if area > 0.:
# we have a surface atom
surface_atoms[a] = area
return surface_atoms
def _getSurfaceAtomIndices(self):
""" Calculates the surface atoms """
self._logger.info("Calculating surface")
surface_atoms = []
if 'surfaceArea' not in self._df.columns:
sa = np.zeros((len(self._df),), dtype=np.float)
saS = pd.Series(index=self._df.index, data=sa, name='surfaceArea')
self._df = self._df.join(saS)
# calculate surface for each peptide chain separately
for chain in self._peptideChains:
atoms = []
# indices of all atoms in peptide chains
atms = self._df.loc[(self._df.peptideChain==True) & ( self._df.chain==chain), ['vdw', 'x', 'y', 'z']]
# wrap in _Atom class for MMTK
for tpl in atms.itertuples():
row_idx, vdw, x, y, z = tpl
atoms.append(_Atom(row_idx, vdw, (x, y, z)))
# run MMTK to calculate surface
smap = surfm.surface_atoms(atoms, solvent_radius=self._solventRadius, point_density=self._pointDensity, ret_fmt=1)
for i in xrange(len(atoms)):
area = smap[atoms[i]]
self._df.loc[atoms[i].idx, 'surfaceArea'] = area
# add atoms to list if surface area is over the threshold
if area >= self._surfaceArea:
surface_atoms.append(atoms[i].idx)
self._logger.info("...Found %s surface atoms" % len(surface_atoms))
if not 'surfaceAtom' in self._df.columns:
sf = np.zeros((len(self._df),), dtype=np.bool)
sfS = pd.Series(index=self._df.index, name='surfaceAtom')
self._df = self._df.join(sfS)
self._df.loc[surface_atoms, 'surfaceAtom'] = True
return surface_atoms
