def addSolvent(universe, solvent, density, scale_factor=4.):
"""
Scales up the universe and adds as many solvent molecules
as are necessary to obtain the specified solvent density,
taking account of the solute molecules that are already present
in the universe. The molecules are placed at random positions
in the scaled-up universe, but without overlaps between
any two molecules.
:param universe: a finite universe
:type universe: :class:~MMTK.Universe.Universe
:param solvent: a molecule, or the name of a molecule in the database
:type solvent: :class:~MMTK.ChemicalObjects.Molecule or str
:param density: the density of the solvent (amu/nm**3)
:type density: float
:param scale_factor: the factor by which the initial universe is
expanded before adding the solvent molecules
:type scale_factor: float
"""
# Calculate number of solvent molecules and universe size
if isinstance(solvent, basestring):
solvent = ChemicalObjects.Molecule(solvent)
cell_volume = universe.cellVolume()
if cell_volume is None:
raise TypeError("universe volume is undefined")
solute = copy.copy(universe._objects)
solute_volume = 0.
excluded_regions = []
for o in solute:
solute_volume = solute_volume + surfaceAndVolume(o)[1]
excluded_regions.append(o.boundingSphere())
n_solvent = int(
round(density * (cell_volume - solute_volume) / solvent.mass()))
solvent_volume = n_solvent * solvent.mass() / density
cell_volume = solvent_volume + solute_volume
universe.translateBy(-solute.position())
universe.scaleSize((cell_volume / universe.cellVolume())**(1. / 3.))
# Scale up the universe and add solvent molecules at random positions
universe.scaleSize(scale_factor)
universe.scale_factor = scale_factor
for i in range(n_solvent):
m = copy.copy(solvent)
m.translateTo(universe.randomPoint())
while True:
s = m.boundingSphere()
collision = False
for region in excluded_regions:
if (s.center -
region.center).length() < s.radius + region.radius:
collision = True
break
if not collision:
break
m.translateTo(universe.randomPoint())
universe.addObject(m)
excluded_regions.append(s)
def addSolvent(universe, solvent, density, scale_factor=4.):
"""
Scales up the universe and adds as many solvent molecules
as are necessary to obtain the specified solvent density,
taking account of the solute molecules that are already present
in the universe. The molecules are placed at random positions
in the scaled-up universe, but without overlaps between
any two molecules.
:param universe: a finite universe
:type universe: :class:`~MMTK.Universe.Universe`
:param solvent: a molecule, or the name of a molecule in the database
:type solvent: :class:`~MMTK.ChemicalObjects.Molecule` or str
:param density: the density of the solvent (amu/nm**3)
:type density: float
:param scale_factor: the factor by which the initial universe is
expanded before adding the solvent molecules
:type scale_factor: float
"""
# Calculate number of solvent molecules and universe size
if isinstance(solvent, basestring):
solvent = ChemicalObjects.Molecule(solvent)
cell_volume = universe.cellVolume()
if cell_volume is None:
raise TypeError("universe volume is undefined")
solute = copy.copy(universe._objects)
solute_volume = 0.
excluded_regions = []
for o in solute:
solute_volume = solute_volume + surfaceAndVolume(o)[1]
excluded_regions.append(o.boundingSphere())
n_solvent = int(round(density*(cell_volume-solute_volume)/solvent.mass()))
solvent_volume = n_solvent*solvent.mass()/density
cell_volume = solvent_volume + solute_volume
universe.translateBy(-solute.position())
universe.scaleSize((cell_volume/universe.cellVolume())**(1./3.))
# Scale up the universe and add solvent molecules at random positions
universe.scaleSize(scale_factor)
universe.scale_factor = scale_factor
for i in range(n_solvent):
m = copy.copy(solvent)
m.translateTo(universe.randomPoint())
while True:
s = m.boundingSphere()
collision = False
for region in excluded_regions:
if (s.center-region.center).length() < s.radius+region.radius:
collision = True
break
if not collision:
break
m.translateTo(universe.randomPoint())
universe.addObject(m)
excluded_regions.append(s)
def get_sasa_mmtk(selection, state=-1, hydrogens='auto', quiet=1):
'''
DESCRIPTION
Get solvent accesible surface area using MMTK.MolecularSurface
http://dirac.cnrs-orleans.fr/MMTK/
This command is very picky with missing atoms and wrong atom naming.
SEE ALSO
stub2ala, get_sasa, get_sasa_ball
'''
try:
import MMTK
except ImportError:
print(' ImportError: please install MMTK')
raise CmdException
from MMTK.PDB import PDBConfiguration
from MMTK.Proteins import Protein
from MMTK.MolecularSurface import surfaceAndVolume
try:
from cStringIO import StringIO
except ImportError:
from io import StringIO
selection = selector.process(selection)
state, quiet = int(state), int(quiet)
radius = cmd.get_setting_float('solvent_radius')
if hydrogens == 'auto':
if cmd.count_atoms('(%s) and hydro' % selection) > 0:
hydrogens = 'all'
else:
hydrogens = 'no_hydrogens'
elif hydrogens == 'none':
hydrogens = 'no_hydrogens'
conf = PDBConfiguration(StringIO(cmd.get_pdbstr(selection)))
system = Protein(conf.createPeptideChains(hydrogens))
try:
area, volume = surfaceAndVolume(system, radius * 0.1)
except:
print(' Error: MMTK.MolecularSurface.surfaceAndVolume failed')
raise CmdException
if not quiet:
print(' get_sasa_mmtk: %.3f Angstroms^2 (volume: %.3f Angstroms^3).' %
(area * 1e2, volume * 1e3))
return area * 1e2
def get_sasa_mmtk(selection, state=-1, hydrogens='auto', quiet=1):
'''
DESCRIPTION
Get solvent accesible surface area using MMTK.MolecularSurface
http://dirac.cnrs-orleans.fr/MMTK/
This command is very picky with missing atoms and wrong atom naming.
SEE ALSO
stub2ala, get_sasa, get_sasa_ball
'''
try:
import MMTK
except ImportError:
print(' ImportError: please install MMTK')
raise CmdException
from MMTK.PDB import PDBConfiguration
from MMTK.Proteins import Protein
from MMTK.MolecularSurface import surfaceAndVolume
try:
from cStringIO import StringIO
except ImportError:
from io import StringIO
selection = selector.process(selection)
state, quiet = int(state), int(quiet)
radius = cmd.get_setting_float('solvent_radius')
if hydrogens == 'auto':
if cmd.count_atoms('(%s) and hydro' % selection) > 0:
hydrogens = 'all'
else:
hydrogens = 'no_hydrogens'
elif hydrogens == 'none':
hydrogens = 'no_hydrogens'
conf = PDBConfiguration(StringIO(cmd.get_pdbstr(selection)))
system = Protein(conf.createPeptideChains(hydrogens))
try:
area, volume = surfaceAndVolume(system, radius * 0.1)
except:
print(' Error: MMTK.MolecularSurface.surfaceAndVolume failed')
raise CmdException
if not quiet:
print(' get_sasa_mmtk: %.3f Angstroms^2 (volume: %.3f Angstroms^3).' % (area * 1e2, volume * 1e3))
return area * 1e2
def numberOfSolventMolecules(universe, solvent, density):
"""
:param universe: a finite universe
:type universe: :class:`~MMTK.Universe.Universe`
:param solvent: a molecule, or the name of a molecule in the database
:type solvent: :class:`~MMTK.ChemicalObjects.Molecule` or str
:param density: the density of the solvent (amu/nm**3)
:type density: float
:returns: the number of solvent molecules that must be added to the
universe, in addition to whatever it already contains,
to obtain the given solvent density.
:rtype: int
"""
if isinstance(solvent, basestring):
solvent = ChemicalObjects.Molecule(solvent)
cell_volume = universe.cellVolume()
if cell_volume is None:
raise TypeError("universe volume is undefined")
solute_volume = 0.
for o in universe._objects:
solute_volume = solute_volume + surfaceAndVolume(o)[1]
return int(round(density*(cell_volume-solute_volume)/solvent.mass()))
