def create_sol(o, struct, top, posres, box=None):
# make a top if we don't have one
# topology returns:
# {'top': '/home/andy/tmp/Au/top/system.top',
# 'dirname': 'top',
# 'posres': 'protein_posres.itp',
# 'struct': '/home/andy/tmp/Au/top/protein.pdb'}
# convert Angstrom to Nm, GROMACS works in Nm, and
# we use MDAnalysis which uses Angstroms
print("attempting auto solvation...")
if box is None:
universe = MDAnalysis.Universe(struct)
box=universe.trajectory.ts.dimensions[:3]
else:
# box could be anything, fine as long as we can convert to an array
box = array(box)
print("user specified periodic boundary conditions: {}".format(box))
sol = md.solvate(dirname=o,struct=struct,top=top,box=box/10.0)
# solvate returns
# {'ndx': '/home/andy/tmp/Au/solvate/main.ndx',
# 'mainselection': '"Protein"',
# 'struct': '/home/andy/tmp/Au/solvate/solvated.pdb',
# 'qtot': 0})
print("auto solvation successfull")
print(sol)
def create_sol(o, struct, top, posres, box=None):
# make a top if we don't have one
# topology returns:
# {'top': '/home/andy/tmp/Au/top/system.top',
# 'dirname': 'top',
# 'posres': 'protein_posres.itp',
# 'struct': '/home/andy/tmp/Au/top/protein.pdb'}
# convert Angstrom to Nm, GROMACS works in Nm, and
# we use MDAnalysis which uses Angstroms
print("attempting auto solvation...")
if box is None:
universe = MDAnalysis.Universe(struct)
box = universe.trajectory.ts.dimensions[:3]
else:
# box could be anything, fine as long as we can convert to an array
box = array(box)
print("user specified periodic boundary conditions: {}".format(box))
sol = md.solvate(dirname=o, struct=struct, top=top, box=box / 10.0)
# solvate returns
# {'ndx': '/home/andy/tmp/Au/solvate/main.ndx',
# 'mainselection': '"Protein"',
# 'struct': '/home/andy/tmp/Au/solvate/solvated.pdb',
# 'qtot': 0})
print("auto solvation successfull")
print(sol)
def solvate(self):
"""
Solvate the current structure (self.universe)
Neither the universe, nor the contents of the universe are harmed by this operation.
@return: A MDManager context manager which contains the solvated structure and
topology files, as well as a 'sub' index which will be used to later
pick out the original unsolvated atoms.
"""
return md.solvate(struct=self.universe, top=self.top, top_includes = self.top_includes,
mainselection=self.mainselection)
def solvate(self):
"""
Solvate the current structure (self.universe)
Neither the universe, nor the contents of the universe are harmed by this operation.
@return: A MDManager context manager which contains the solvated structure and
topology files, as well as a 'sub' index which will be used to later
pick out the original unsolvated atoms.
"""
return md.solvate(struct=self.universe,
top=self.top,
top_includes=self.top_includes,
mainselection=self.mainselection)
print("succesfully auto-generated topology")
print('pwd', os.getcwd())
print('top', top)
filedata_fromfile(TOPOL_TOP, top["top"])
filedata_fromfile(STRUCT_PDB, top["struct"])
include_dirs = [os.path.abspath(top.dirname)]
read_includes(top["top"])
# check to see if solvation is possible
if should_solvate:
# convert Angstrom to Nm, GROMACS works in Nm, and
# we use MDAnalysis which uses Angstroms
print("attempting auto solvation...")
with md.solvate(top_includes=top_includes.values(), box=box/10.0, **top):
# solvate returns
# {'ndx': '/home/andy/tmp/Au/solvate/main.ndx',
# 'mainselection': '"Protein"',
# 'struct': '/home/andy/tmp/Au/solvate/solvated.pdb',
# 'qtot': 0})
print("auto solvation successfull")
else:
# use user specified top
print("using user specified topology file {}".format(top))
filedata_fromfile(TOPOL_TOP, top)
filedata_fromfile(STRUCT_PDB, struct)
read_includes(top)
print('pwd', os.getcwd())
print('top', top)
filedata_fromfile(TOPOL_TOP, top["top"])
filedata_fromfile(STRUCT_PDB, top["struct"])
include_dirs = [os.path.abspath(top.dirname)]
read_includes(top["top"])
# check to see if solvation is possible
if should_solvate:
# convert Angstrom to Nm, GROMACS works in Nm, and
# we use MDAnalysis which uses Angstroms
print("attempting auto solvation...")
with md.solvate(top_includes=top_includes.values(),
box=box / 10.0,
**top):
# solvate returns
# {'ndx': '/home/andy/tmp/Au/solvate/main.ndx',
# 'mainselection': '"Protein"',
# 'struct': '/home/andy/tmp/Au/solvate/solvated.pdb',
# 'qtot': 0})
print("auto solvation successfull")
else:
# use user specified top
print("using user specified topology file {}".format(top))
filedata_fromfile(TOPOL_TOP, top)
filedata_fromfile(STRUCT_PDB, struct)
read_includes(top)
