def saveMolecules(filebase, system, fileformat, property_map={}):
"""Save a molecular system to file.
Parameters
----------
filebase : str
The base name of the output file.
system : :class:`System <BioSimSpace._SireWrappers.System>`, \
:class:`Molecule< BioSimSpace._SireWrappers.Molecule>` \
:class:`Molecule< BioSimSpace._SireWrappers.Molecules>`
The molecular system.
fileformat : str, [str]
The file format (or formats) to save to.
property_map : dict
A dictionary that maps system "properties" to their user
defined values. This allows the user to refer to properties
with their own naming scheme, e.g. { "charge" : "my-charge" }
Returns
-------
files : [str]
The list of files that were generated.
Examples
--------
Load a molecular system from AMBER coordinate and topology files then
try to save it to all supported file formats.
>>> import BioSimSpace as BSS
>>> system = BSS.IO.readMolecules(["ala.rst7", "ala.prm7"])
>>> for format in BSS.IO.fileFormats():
... try:
... BSS.IO.saveMolecules("test", system, format)
... except:
... print("Could not convert to format: '%s'" % format)
Load a molecular system from AMBER coordinate and topology files then
try to save it to GROMACS format, mapping and un-mapping the charge
property along the way.
>>> import BioSimSpace as BSS
>>> system = BSS.IO.readMolecules(["ala.rst7", "ala.prm7"], property_map={"charge" : "my-charge"})
>>> BSS.IO.saveMolecules("test", system, ["gro87", "grotop"], property_map={"charge" : "my-charge"})
"""
global _has_gmx_warned
if _gromacs_path is None and not _has_gmx_warned:
_warn(
"BioSimSpace.IO: Please install GROMACS (http://www.gromacs.org) "
"for GROMACS topology file support.")
_has_gmx_warned = True
# Check that the filebase is a string.
if type(filebase) is not str:
raise TypeError("'filebase' must be of type 'str'")
# Check that that the system is of the correct type.
# A System object.
if type(system) is _System:
pass
# A Molecule object.
elif type(system) is _Molecule:
system = _System(system)
elif type(system) is _Molecules:
system = system.toSystem()
# A list of Molecule objects.
elif type(system) is list and all(
isinstance(x, _Molecule) for x in system):
system = _System(system)
# Invalid type.
else:
raise TypeError(
"'system' must be of type 'BioSimSpace.SireWrappers.System', "
"'BioSimSpace._SireWrappers.Molecule, 'BioSimSpace._SireWrappers.Molecules' "
"or a list of 'BiSimSpace._SireWrappers.Molecule' types.")
# Check that fileformat argument is of the correct type.
# Convert to a list if a single string is passed.
# We split on ',' since the user might pass system.fileFormats() as the argument.
if type(fileformat) is str:
fileformat = fileformat.split(",")
# Lists and tuples are okay!
elif type(fileformat) is list:
pass
elif type(fileformat) is tuple:
pass
# Invalid.
else:
raise TypeError(
"'fileformat' must be a 'str' or a 'list' of 'str' types.")
# Make sure all items in list or tuple are strings.
if not all(isinstance(x, str) for x in fileformat):
raise TypeError(
"'fileformat' must be a 'str' or a 'list' of 'str' types.")
# Make a list of the matched file formats.
formats = []
# Make sure that all of the formats are valid.
for format in fileformat:
try:
f = _formats_dict[format.replace(" ", "").upper()][0]
formats.append(f)
except KeyError:
raise ValueError("Unsupported file format '%s'. Supported formats "
"are: %s." % (format, str(_formats)))
# Validate the map.
if type(property_map) is not dict:
raise TypeError("'property_map' must be of type 'dict'")
# Copy the map.
_property_map = property_map.copy()
# Add the GROMACS topology file path.
if _gromacs_path is not None and ("GROMACS_PATH" not in _property_map):
_property_map["GROMACS_PATH"] = _gromacs_path
# Get the directory name.
dirname = _os.path.dirname(filebase)
# If the user has passed a directory, make sure that is exists.
if _os.path.basename(filebase) != filebase:
# Create the directory if it doesn't already exist.
if not _os.path.isdir(dirname):
_os.makedirs(dirname, exist_ok=True)
# Store the current working directory.
dir = _os.getcwd()
# Change to the working directory for the process.
# This avoid problems with relative paths.
if dirname != "":
_os.chdir(dirname)
# A list of the files that have been written.
files = []
# Save the system using each file format.
for format in formats:
# Add the file format to the property map.
_property_map["fileformat"] = _SireBase.wrap(format)
# Write the file.
try:
file = _SireIO.MoleculeParser.save(system._getSireObject(),
filebase, _property_map)
files += file
except Exception as e:
if dirname != "":
_os.chdir(dir)
msg = "Failed to save system to format: '%s'" % format
if _isVerbose():
raise IOError(msg) from e
else:
raise IOError(msg) from None
# Change back to the original directory.
if dirname != "":
_os.chdir(dir)
# Return the list of files.
return files
def _solvate(molecule,
box,
shell,
model,
num_point,
ion_conc,
is_neutral,
work_dir=None,
property_map={}):
"""Internal function to add solvent using 'gmx solvate'.
Parameters
----------
molecule : :class:`Molecule <BioSimSpace._SireWrappers.Molecule>`, \
:class:`System <BioSimSpace._SireWrappers.System>`
A molecule, or system of molecules.
box : [:class:`Length <BioSimSpace.Types.Length>`]
A list containing the box size in each dimension.
shell : :class:`Length` <BioSimSpace.Types.Length>`
Thickness of the water shell around the solute.
model : str
The name of the water model.
num_point : int
The number of atoms in the water model.
ion_conc : float
The ion concentration in (mol per litre).
is_neutral : bool
Whether to neutralise the system.
work_dir : str
The working directory for the process.
property_map : dict
A dictionary that maps system "properties" to their user defined
values. This allows the user to refer to properties with their
own naming scheme, e.g. { "charge" : "my-charge" }
Returns
-------
system : :class:`System <BioSimSpace._SireWrappers.System>`
The solvated system.
"""
if molecule is not None:
# Store the centre of the molecule.
center = molecule._getAABox(property_map).center()
# Work out the vector from the centre of the molecule to the centre of the
# water box, converting the distance in each direction to Angstroms.
vec = []
for x, y in zip(box, center):
vec.append(0.5 * x.angstroms().magnitude() - y)
# Translate the molecule. This allows us to create a water box
# around the molecule.
molecule.translate(vec, property_map)
if type(molecule) is _System:
# Reformat all of the water molecules so that they match the
# expected GROMACS topology template.
waters = _SireIO.setGromacsWater(
molecule._sire_object.search("water"), model)
# Convert to a BioSimSpace molecules container.
waters = _Molecules(waters.toMolecules())
# Remove the old water molecules then add those with the updated topology.
molecule.removeWaterMolecules()
molecule.addMolecules(waters)
# Create a temporary working directory and store the directory name.
if work_dir is None:
tmp_dir = _tempfile.TemporaryDirectory()
work_dir = tmp_dir.name
# Run the solvation in the working directory.
with _Utils.cd(work_dir):
# Create the gmx command.
if num_point == 3:
mod = "spc216"
else:
mod = model
command = "%s solvate -cs %s" % (_gmx_exe, mod)
if molecule is not None:
# Write the molecule/system to a GRO files.
_IO.saveMolecules("input", molecule, "gro87")
_os.rename("input.gro87", "input.gro")
# Update the command.
command += " -cp input.gro"
# Add the box information.
if box is not None:
command += " -box %f %f %f" % (box[0].nanometers().magnitude(),
box[1].nanometers().magnitude(),
box[2].nanometers().magnitude())
# Add the shell information.
if shell is not None:
command += " -shell %f" % shell.nanometers().magnitude()
# Just add box information.
else:
command += " -box %f %f %f" % (box[0].nanometers().magnitude(),
box[1].nanometers().magnitude(),
box[2].nanometers().magnitude())
# Add the output file.
command += " -o output.gro"
with open("README.txt", "w") as file:
# Write the command to file.
file.write("# gmx solvate was run with the following command:\n")
file.write("%s\n" % command)
# Create files for stdout/stderr.
stdout = open("solvate.out", "w")
stderr = open("solvate.err", "w")
# Run gmx solvate as a subprocess.
proc = _subprocess.run(command,
shell=True,
stdout=stdout,
stderr=stderr)
stdout.close()
stderr.close()
# gmx doesn't return sensible error codes, so we need to check that
# the expected output was generated.
if not _os.path.isfile("output.gro"):
raise RuntimeError("'gmx solvate failed to generate output!")
# Extract the water lines from the GRO file.
water_lines = []
with open("output.gro", "r") as file:
for line in file:
if _re.search("SOL", line):
# Store the SOL atom record.
water_lines.append(line)
# Add any box information. This is the last line in the GRO file.
water_lines.append(line)
# Write a GRO file that contains only the water atoms.
if len(water_lines) - 1 > 0:
with open("water.gro", "w") as file:
file.write("BioSimSpace %s water box\n" % model.upper())
file.write("%d\n" % (len(water_lines) - 1))
for line in water_lines:
file.write("%s" % line)
else:
raise ValueError(
"No water molecules were generated. Try increasing "
"the 'box' size or 'shell' thickness.")
# Create a TOP file for the water model. By default we use the Amber03
# force field to generate a dummy topology for the water model.
with open("water_ions.top", "w") as file:
file.write("#define FLEXIBLE 1\n\n")
file.write("; Include AmberO3 force field\n")
file.write('#include "amber03.ff/forcefield.itp"\n\n')
file.write("; Include %s water topology\n" % model.upper())
file.write('#include "amber03.ff/%s.itp"\n\n' % model)
file.write("; Include ions\n")
file.write('#include "amber03.ff/ions.itp"\n\n')
file.write("[ system ] \n")
file.write("BioSimSpace %s water box\n\n" % model.upper())
file.write("[ molecules ] \n")
file.write(";molecule name nr.\n")
file.write("SOL %d\n" %
((len(water_lines) - 1) / num_point))
# Load the water box.
water = _IO.readMolecules(["water.gro", "water_ions.top"])
# Create a new system by adding the water to the original molecule.
if molecule is not None:
# Translate the molecule and water back to the original position.
vec = [-x for x in vec]
molecule.translate(vec, property_map)
water.translate(vec)
if type(molecule) is _System:
# Extract the non-water molecules from the original system.
non_waters = _Molecules(
molecule.search("not water")._sire_object.toMolecules())
# Create a system by adding these to the water molecules from
# gmx solvate, which will include the original waters.
system = non_waters.toSystem() + water
else:
system = molecule.toSystem() + water
# Add all of the water box properties to the new system.
for prop in water._sire_object.propertyKeys():
prop = property_map.get(prop, prop)
# Add the space property from the water system.
system._sire_object.setProperty(
prop, water._sire_object.property(prop))
else:
system = water
# Now we add ions to the system and neutralise the charge.
if ion_conc > 0 or is_neutral:
# Write the molecule + water system to file.
_IO.saveMolecules("solvated", system, "gro87")
_IO.saveMolecules("solvated", system, "grotop")
_os.rename("solvated.gro87", "solvated.gro")
_os.rename("solvated.grotop", "solvated.top")
# First write an mdp file.
with open("ions.mdp", "w") as file:
file.write("; Neighbour searching\n")
file.write("cutoff-scheme = Verlet\n")
file.write("rlist = 1.1\n")
file.write("pbc = xyz\n")
file.write("verlet-buffer-tolerance = -1\n")
file.write("\n; Electrostatics\n")
file.write("coulombtype = cut-off\n")
file.write("\n; VdW\n")
file.write("rvdw = 1.0\n")
# Create the grompp command.
command = "%s grompp -f ions.mdp -po ions.out.mdp -c solvated.gro -p solvated.top -o ions.tpr" % _gmx_exe
with open("README.txt", "a") as file:
# Write the command to file.
file.write(
"\n# gmx grompp was run with the following command:\n")
file.write("%s\n" % command)
# Create files for stdout/stderr.
stdout = open("grommp.out", "w")
stderr = open("grommp.err", "w")
# Run grompp as a subprocess.
proc = _subprocess.run(command,
shell=True,
stdout=stdout,
stderr=stderr)
stdout.close()
stderr.close()
# Flag whether to break out of the ion adding stage.
is_break = False
# Check for the tpr output file.
if not _os.path.isfile("ions.tpr"):
if shell is None:
raise RuntimeError(
"'gmx grommp' failed to generate output! "
"Perhaps your box is too small?")
else:
is_break = True
_warnings.warn(
"Unable to achieve target ion concentration, try using "
"'box' option instead of 'shell'.")
# Only continue if grommp was successful. This allows us to skip the remainder
# of the code if the ion addition failed when the 'shell' option was chosen, i.e.
# because the estimated simulation box was too small.
if not is_break:
is_break = False
# The ion concentration is unset.
if ion_conc == 0:
# Get the current molecular charge.
charge = system.charge()
# Round to the nearest integer value.
charge = round(charge.magnitude())
# Create the genion command.
command = "echo SOL | %s genion -s ions.tpr -o solvated_ions.gro -p solvated.top -neutral" % _gmx_exe
# Add enough counter ions to neutralise the charge.
if charge > 0:
command += " -nn %d" % abs(charge)
else:
command += " -np %d" % abs(charge)
else:
# Create the genion command.
command = "echo SOL | %s genion -s ions.tpr -o solvated_ions.gro -p solvated.top -%s -conc %f" \
% (_gmx_exe, "neutral" if is_neutral else "noneutral", ion_conc)
with open("README.txt", "a") as file:
# Write the command to file.
file.write(
"\n# gmx genion was run with the following command:\n")
file.write("%s\n" % command)
# Create files for stdout/stderr.
stdout = open("genion.out", "w")
stderr = open("genion.err", "w")
# Run genion as a subprocess.
proc = _subprocess.run(command,
shell=True,
stdout=stdout,
stderr=stderr)
stdout.close()
stderr.close()
# Check for the output GRO file.
if not _os.path.isfile("solvated_ions.gro"):
if shell is None:
raise RuntimeError(
"'gmx genion' failed to add ions! Perhaps your box is too small?"
)
else:
is_break = True
_warnings.warn(
"Unable to achieve target ion concentration, try using "
"'box' option instead of 'shell'.")
if not is_break:
# Counters for the number of SOL, NA, and CL atoms.
num_sol = 0
num_na = 0
num_cl = 0
# We now need to loop through the GRO file to extract the lines
# corresponding to water or ion atoms.
water_ion_lines = []
with open("solvated_ions.gro", "r") as file:
for line in file:
# This is a Sodium atom.
if _re.search("NA", line):
water_ion_lines.append(line)
num_na += 1
# This is a Chlorine atom.
if _re.search("CL", line):
water_ion_lines.append(line)
num_cl += 1
# This is a water atom.
elif _re.search("SOL", line):
water_ion_lines.append(line)
num_sol += 1
# Add any box information. This is the last line in the GRO file.
water_ion_lines.append(line)
# Write a GRO file that contains only the water and ion atoms.
if len(water_ion_lines) - 1 > 0:
with open("water_ions.gro", "w") as file:
file.write("BioSimSpace %s water box\n" %
model.upper())
file.write("%d\n" % (len(water_ion_lines) - 1))
for line in water_ion_lines:
file.write("%s" % line)
# Ions have been added. Update the TOP file fo the water model
# with the new atom counts.
if num_na > 0 or num_cl > 0:
with open("water_ions.top", "w") as file:
file.write("#define FLEXIBLE 1\n\n")
file.write("; Include AmberO3 force field\n")
file.write(
'#include "amber03.ff/forcefield.itp"\n\n')
file.write("; Include %s water topology\n" %
model.upper())
file.write('#include "amber03.ff/%s.itp"\n\n' %
model)
file.write("; Include ions\n")
file.write('#include "amber03.ff/ions.itp"\n\n')
file.write("[ system ] \n")
file.write("BioSimSpace %s water box\n\n" %
model.upper())
file.write("[ molecules ] \n")
file.write(";molecule name nr.\n")
file.write("SOL %d\n" %
(num_sol / num_point))
if num_na > 0:
file.write("NA %d\n" % num_na)
if num_cl > 0:
file.write("CL %d\n" % num_cl)
# Load the water/ion box.
water_ions = _IO.readMolecules(
["water_ions.gro", "water_ions.top"])
# Create a new system by adding the water to the original molecule.
if molecule is not None:
if type(molecule) is _System:
# Extract the non-water molecules from the original system.
non_waters = _Molecules(
molecule.search(
"not water")._sire_object.toMolecules())
# Create a system by adding these to the water and ion
# molecules from gmx solvate, which will include the
# original waters.
system = non_waters.toSystem() + water_ions
else:
system = molecule.toSystem() + water_ions
# Add all of the water molecules' properties to the new system.
for prop in water_ions._sire_object.propertyKeys():
prop = property_map.get(prop, prop)
# Add the space property from the water system.
system._sire_object.setProperty(
prop, water_ions._sire_object.property(prop))
else:
system = water_ions
# Store the name of the water model as a system property.
system._sire_object.setProperty("water_model", _SireBase.wrap(model))
return system