def download(pdb_id=None,
output_filename=None,
tempfile=False,
wwPDB_Partner='RCSB PDB'):
from molsysmt._private.files_and_directories import temp_filename
from urllib.request import urlretrieve
output = None
if tempfile:
output_filename = temp_filename(extension="pdb")
if wwPDB_Partner == 'RCSB PDB':
filename = pdb_id + '.pdb'
fullurl = 'https://files.rcsb.org/download/' + filename
if output_filename is None:
output_filename = filename
urlretrieve(fullurl, output_filename)
output = output_filename
else:
raise NotImplementedError()
return output
def extract(item, atom_indices='all', structure_indices='all', output_filename=None):
if output_filename is None:
output_filename = temp_filename(extension='dcd')
if (atom_indices is 'all') and (structure_indices is 'all'):
raise NotImplementedError()
else:
raise NotImplementedError()
return tmp_item
def to_pdbfixer_PDBFixer(item, molecular_system=None, atom_indices='all', structure_indices='all'):
from molsysmt._private.files_and_directories import temp_filename
from molsysmt.api_forms.api_file_pdb import to_pdbfixer_PDBFixer as file_pdb_to_pdbfixer_PDBFixer
from os import remove
tmp_file = temp_filename(extension='pdb')
tmp_item, tmp_molecular_system = to_file_pdb(item, molecular_system=molecular_system, output_filename=tmp_file, atom_indices=atom_indices, structure_indices=structure_indices)
tmp_item, tmp_molecular_system = file_pdb_to_pdbfixer_PDBFixer(tmp_file, molecular_system=tmp_molecular_system)
remove(tmp_pdbfile)
return tmp_item, tmp_molecular_system
def extract(item,
atom_indices='all',
structure_indices='all',
output_filename=None):
if output_filename is None:
output_filename = temp_filename(extension='crd')
if (atom_indices is 'all') and (structure_indices is 'all'):
from shutil import copy as copy_file
from molsysmt._private.files_and_directories import temp_filename
copy_file(item, output_filename)
tmp_item = output_filename
else:
raise NotImplementedError()
return tmp_item
def to_file_pdb(item, atom_indices='all', structure_indices='all', output_filename=None, check=True):
if check:
digest_item(item, 'string:pdb_text')
atom_indices = digest_atom_indices(atom_indices)
structure_indices = digest_structure_indices(structure_indices)
from . import extract
from molsysmt._private.files_and_directories import temp_filename
if output_filename is None:
output_filename = temp_filename(extension='pdb')
tmp_item = extract(item, atom_indices=atom_indices, structure_indices=structure_indices, copy_if_all=False, check=False)
with open(output_filename, 'w') as fff:
fff.write(tmp_item)
tmp_item = output_filename
return tmp_item
def extract(item,
atom_indices='all',
structure_indices='all',
output_filename=None):
if output_filename is None:
output_filename = temp_filename(extension='top')
if (atom_indices is 'all') and (structure_indices is 'all'):
raise NotImplementedError()
else:
tmp_item, _ = to_openmm_GromacsTopologyFile(
item,
atom_indices=atom_indices,
structure_indices=structure_indices)
tmp_item.save(output_filename)
del (tmp_item)
tmp_item = output_filename
return tmp_item
def build_peptide(molecular_system,
box_geometry='cubic',
clearance='10.0 Å',
to_form='molsysmt.MolSys',
engine='LEaP',
logfile=False,
verbose=False,
check=True):
# box_geometry: "cubic" or "truncated octahedral"
engine = digest_engine(engine)
if engine == "LEaP":
from molsysmt.basic import convert
from os import getcwd, chdir
from molsysmt.thirds.tleap import TLeap
from molsysmt._private.files_and_directories import temp_directory, temp_filename
from shutil import rmtree, copyfile
sequence = convert(molecular_system, to_form='string:aminoacids3')
sequence = sequence.upper()
sequence = ' '.join(
[sequence[ii:ii + 3] for ii in range(0, len(sequence), 3)])
molecular_mechanics = convert(molecular_system,
to_form='molsysmt.MolecularMechanics')
mm_parameters = molecular_mechanics.get_leap_parameters()
forcefield = mm_parameters['forcefield']
water_model = mm_parameters['water_model']
implicit_solvent = mm_parameters['implicit_solvent']
if water_model is not None:
if water_model == 'SPC':
solvent_model = 'SPCBOX'
elif water_model == 'TIP3P':
solvent_model = 'TIP3PBOX'
else:
raise NotImplementedError
current_directory = getcwd()
working_directory = temp_directory()
temp_prmtop = temp_filename(dir=working_directory, extension='prmtop')
temp_inpcrd = temp_prmtop.replace('prmtop', 'inpcrd')
temp_logfile = temp_prmtop.replace('prmtop', 'leap.log')
if verbose:
print('Working directory:', working_directory)
tleap = TLeap()
tleap.load_parameters(*forcefield)
if implicit_solvent == 'OBC1':
tleap.set_global_parameter(PBRadii='mbondi2')
tleap.make_sequence('peptide', sequence)
tleap.check_unit('peptide')
tleap.get_total_charge('peptide')
if water_model is not None:
tleap.solvate('peptide', solvent_model, clearance, box_geometry)
tleap.save_unit('peptide', temp_prmtop)
errors = tleap.run(working_directory=working_directory,
verbose=verbose)
del (tleap)
if logfile:
copyfile(temp_logfile, current_directory + '/build_peptide.log')
temp_item = convert([temp_prmtop, temp_inpcrd], to_form=to_form)
rmtree(working_directory)
else:
raise NotImplementedError
return temp_item
def solvate(molecular_system,
box_geometry="truncated octahedral",
clearance='14.0 angstroms',
anion='Cl-',
num_anions="neutralize",
cation='Na+',
num_cations="neutralize",
ionic_strength='0.0 molar',
engine="LEaP",
to_form=None,
logfile=False,
verbose=False):
"""solvate(item, geometry=None, water=None, engine=None)
Methods and wrappers to create and solvate boxes
Parameters
----------
anion: 'Cl-', 'Br-', 'F-', and 'I-'
num_anions: number of cations to add. integer or "neutralize"
cation: "NA" 'Cs+', 'K+', 'Li+', 'Na+', and 'Rb+'
num_cations: number of cations to add. integer or "neutralize"
box_geometry: "cubic", "truncated_octahedral" or "rhombic_dodecahedron" (Default: "truncated_octahedral")
Returns
-------
item : bla bla
bla bla
Examples
--------
See Also
--------
Notes
-----
"""
from molsysmt.basic import get_form, convert
engine = digest_engine(engine)
to_form = digest_to_form(to_form)
if to_form is None:
to_form = get_form(molecular_system)
if engine == "OpenMM":
from openmm import Vec3
clearance = puw.convert(clearance, to_form='openmm.unit')
ionic_strength = puw.convert(ionic_strength, to_form='openmm.unit')
modeller = convert(molecular_system, to_form='openmm.Modeller')
molecular_mechanics = convert(molecular_system,
to_form='molsysmt.MolecularMechanics')
parameters = molecular_mechanics.get_openmm_System_parameters()
forcefield = molecular_mechanics.to_openmm_ForceField()
solvent_model = None
if molecular_mechanics.water_model == 'SPC':
solvent_model = 'tip3p'
elif molecular_mechanics.water_model in [
'TIP3P', 'TIP3PFB', 'SPCE', 'TIP4PEW', 'TIP4PFB', 'TIP5P'
]:
solvent_model = molecular_mechanics.water_model.lower()
else:
raise NotImplementedError()
if box_geometry == "truncated octahedral":
max_size = max(
max((pos[i] for pos in modeller.positions)) -
min((pos[i] for pos in modeller.positions)) for i in range(3))
vectors = Vec3(1.0, 0,
0), Vec3(1.0 / 3.0, 2.0 * np.sqrt(2.0) / 3.0,
0.0), Vec3(-1.0 / 3.0,
np.sqrt(2.0) / 3.0,
np.sqrt(6.0) / 3.0)
box_vectors = [(max_size + clearance) * v for v in vectors]
modeller.addSolvent(forcefield,
model=solvent_model,
boxVectors=box_vectors,
ionicStrength=ionic_strength,
positiveIon=cation,
negativeIon=anion)
elif box_geometry == "rhombic dodecahedral":
max_size = max(
max((pos[i] for pos in modeller.positions)) -
min((pos[i] for pos in modeller.positions)) for i in range(3))
vectors = Vec3(1.0, 0.0,
0.0), Vec3(0.0, 1.0,
0.0), Vec3(0.5, 0.5,
np.sqrt(2) / 2)
box_vectors = [(max_size + clearance) * v for v in vectors]
modeller.addSolvent(forcefield,
model=solvent_model,
boxVectors=box_vectors,
ionicStrength=ionic_strength,
positiveIon=cation,
negativeIon=anion)
else:
modeller.addSolvent(forcefield,
model=solvent_model,
padding=clearance,
ionicStrength=ionic_strength,
positiveIon=cation,
negativeIon=anion)
tmp_item = convert(modeller, to_form=to_form)
del (modeller)
return tmp_item
elif engine == "PDBFixer":
from openmm import Vec3
clearance = puw.convert(clearance, to_form='openmm.unit')
ionic_strength = puw.convert(ionic_strength, to_form='openmm.unit')
pdbfixer = convert(molecular_system, to_form='pdbfixer.PDBFixer')
max_size = max(
max((pos[i] for pos in pdbfixer.positions)) -
min((pos[i] for pos in pdbfixer.positions)) for i in range(3))
box_size = None
box_vectors = None
if box_geometry == "truncated octahedral":
vectors = Vec3(1.0, 0,
0), Vec3(1.0 / 3.0, 2.0 * np.sqrt(2.0) / 3.0,
0.0), Vec3(-1.0 / 3.0,
np.sqrt(2.0) / 3.0,
np.sqrt(6.0) / 3.0)
elif box_geometry == "rhombic dodecahedral":
vectors = Vec3(1.0, 0.0,
0.0), Vec3(0.0, 1.0,
0.0), Vec3(0.5, 0.5,
np.sqrt(2) / 2)
elif box_geometry == "cubic":
vectors = Vec3(1.0, 0.0, 0.0), Vec3(0.0, 1.0,
0.0), Vec3(0.0, 0.0, 1.0)
box_vectors = [(max_size + clearance) * v for v in vectors]
pdbfixer.addSolvent(boxVectors=box_vectors,
ionicStrength=ionic_strength,
positiveIon=cation,
negativeIon=anion)
tmp_item = convert(pdbfixer, to_form=to_form)
del (pdbfixer)
return tmp_item
elif engine == "LEaP":
from molsysmt.thirds.tleap import TLeap
from molsysmt._private.files_and_directories import temp_directory, temp_filename
from molsysmt.tools.file_pdb import replace_HETATM_by_ATOM_in_terminal_cappings
from shutil import rmtree, copyfile
from os import getcwd, chdir
from molsysmt.basic import set as _set, select
from molsysmt.build import has_hydrogens, remove_hydrogens
if has_hydrogens(molecular_system):
raise ValueError(
"A molecular system without hydrogen atoms is needed.")
#molecular_system = remove_hydrogens(molecular_system)
#if verbose:
# print("All Hydrogen atoms were removed to be added by LEaP\n\n")
indices_NME_C = select(
molecular_system,
target='atom',
selection='group_name=="NME" and atom_name=="C"')
with_NME_C = (len(indices_NME_C) > 0)
if with_NME_C:
_set(molecular_system,
target='atom',
selection='group_name=="NME" and atom_name=="C"',
atom_name='CH3')
current_directory = getcwd()
working_directory = temp_directory()
pdbfile_in = temp_filename(dir=working_directory, extension='pdb')
_ = convert(molecular_system, to_form=pdbfile_in)
#replace_HETATM_from_capping_atoms(pdbfile_in)
tmp_prmtop = temp_filename(dir=working_directory, extension='prmtop')
tmp_inpcrd = tmp_prmtop.replace('prmtop', 'inpcrd')
tmp_logfile = tmp_prmtop.replace('prmtop', 'leap.log')
molecular_mechanics = convert(molecular_system,
to_form='molsysmt.MolecularMechanics')
parameters = molecular_mechanics.get_leap_parameters()
forcefield = parameters['forcefield']
water = parameters['water_model']
solvent_model = None
if water == 'SPC':
solvent_model = 'SPCBOX'
elif water == 'TIP3P':
solvent_model = 'TIP3PBOX'
elif water == 'TIP4P':
solvent_model = 'TIP4PBOX'
if verbose:
print('Working directory:', working_directory)
tleap = TLeap()
tleap.load_parameters(*forcefield)
tleap.load_unit('MolecularSystem', pdbfile_in)
tleap.check_unit('MolecularSystem')
tleap.get_total_charge('MolecularSystem')
tleap.solvate('MolecularSystem',
solvent_model,
clearance,
box_geometry=box_geometry)
if num_anions != 0:
if num_anions == 'neutralize':
num_anions = 0
tleap.add_ions('MolecularSystem',
anion,
num_ions=num_anions,
replace_solvent=True)
if num_cations != 0:
if num_cations == 'neutralize':
num_cations = 0
tleap.add_ions('MolecularSystem',
cation,
num_ions=num_cations,
replace_solvent=True)
tleap.save_unit('MolecularSystem', tmp_prmtop)
errors = tleap.run(working_directory=working_directory,
verbose=verbose)
del (tleap)
if logfile:
copyfile(tmp_logfile, current_directory + '/build_peptide.log')
tmp_item = convert([tmp_prmtop, tmp_inpcrd], to_form=to_form)
if with_NME_C:
_set(tmp_item,
target='atom',
selection='group_name=="NME" and atom_name=="CH3"',
atom_name='C')
rmtree(working_directory)
return tmp_item
else:
raise NotImplementedError
