def perform_bilayer_removing(atoms, ref_lipid_atom, ref_water_atom, verbose):
""" Remove the water molecules inside a bilayer"""
if verbose:
print()
print("Checking the reference atom...")
if not find_ref_atom(atoms, ref_lipid_atom):
raise RefObjectError(
("The reference atom {0} for the bilayer was not find. "
"Exiting...").format(ref_lipid_atom))
if not find_ref_atom(atoms, ref_water_atom):
raise RefObjectError(
("The reference atom {0} for the water was not find. "
"Exiting...").format(ref_water_atom))
# Get Z mean for the upper and lower leaflet
z_lower, z_upper = z_mean_values(atoms, ref_lipid_atom)
if verbose:
print("Removing water inside the bilayer...")
# Remove water molecules inside the bilayer
temp_atoms, nb_water_removed = remove_water(atoms, z_upper, z_lower,
ref_water_atom)
if verbose:
print("Renumber residues and atoms...")
output = groIO.renumber(temp_atoms)
return (output, nb_water_removed)
def perform_bilayer_removing(atoms, ref_lipid_atom, ref_water_atom, verbose):
""" Remove the water molecules inside a bilayer"""
if verbose:
print()
print("Checking the reference atom...")
if not find_ref_atom(atoms, ref_lipid_atom):
raise RefObjectError(("The reference atom {0} for the bilayer was not find. "
"Exiting...").format(ref_lipid_atom))
if not find_ref_atom(atoms, ref_water_atom):
raise RefObjectError(("The reference atom {0} for the water was not find. "
"Exiting...").format(ref_water_atom))
# Get Z mean for the upper and lower leaflet
z_lower, z_upper = z_mean_values(atoms, ref_lipid_atom)
if verbose:
print("Removing water inside the bilayer...")
# Remove water molecules inside the bilayer
temp_atoms, nb_water_removed = remove_water(atoms, z_upper, z_lower, ref_water_atom)
if verbose:
print("Renumber residues and atoms...")
output = groIO.renumber(temp_atoms)
return (output, nb_water_removed)
def perform_sphere_removing(atoms, sphere_residus, sphere_radius,
ref_water_residue, verbose):
"""
Remove the water molecules inside a sphere centered on the
geometrical center of the atom with a given set of residue name
"""
if verbose:
print()
print("The reference residue for the sphere is {0}".format(
", ".join(sphere_residus)))
print("The reference residue for the water is {0}".format(
ref_water_residue))
for residue in sphere_residus:
if not find_ref_residue(atoms, residue):
raise RefObjectError(
("The reference residue {0} for the sphere was not find. "
"Exiting...").format(residue))
if not find_ref_residue(atoms, ref_water_residue):
raise RefObjectError(
("The reference residue {0} for water was not find. "
"Exiting...").format(ref_water_residue))
resids = get_resids(atoms, sphere_residus)
dic_center = geometric_center(atoms, resids)
if not verbose:
print("Removing water molecules...")
output_atoms = atoms
sum_water_removed = 0
for resid, center in dic_center.items():
if verbose:
print(
"Removing water inside the sphere centered ({x:.1f} {y:.1f} {z:.1f})"
" on residue {res}".format(res=resid, **center))
tmp_atoms, nb_water_removed = remove_sphere(output_atoms,
ref_water_residue, center,
sphere_radius)
sum_water_removed += nb_water_removed
output_atoms = groIO.renumber(tmp_atoms)
return (output_atoms, sum_water_removed)
def _create_runumbered(atoms, removed_res):
"""
Remove residues from a structure and renumber the atoms and residues.
:Parameters:
- atoms: the list of dictionnary for atoms
- remove_res: a list of resid to remove from the structure
:Returns:
- the new list renumbered
"""
# Remove some residues
keep = [atom for atom in atoms if not atom['resid'] in removed_res]
# Renumber residues and atoms
renumbered = groIO.renumber(keep)
return renumbered
def perform_sphere_removing(atoms, sphere_residus, sphere_radius,
ref_water_residue, verbose):
"""
Remove the water molecules inside a sphere centered on the
geometrical center of the atom with a given set of residue name
"""
if verbose:
print()
print("The reference residue for the sphere is {0}".format(", ".join(sphere_residus)))
print("The reference residue for the water is {0}".format(ref_water_residue))
for residue in sphere_residus:
if not find_ref_residue(atoms, residue):
raise RefObjectError(("The reference residue {0} for the sphere was not find. "
"Exiting...").format(residue))
if not find_ref_residue(atoms, ref_water_residue):
raise RefObjectError(("The reference residue {0} for water was not find. "
"Exiting...").format(ref_water_residue))
resids = get_resids(atoms, sphere_residus)
dic_center = geometric_center(atoms, resids)
if not verbose:
print("Removing water molecules...")
output_atoms = atoms
sum_water_removed = 0
for resid, center in dic_center.items():
if verbose:
print("Removing water inside the sphere centered ({x:.1f} {y:.1f} {z:.1f})"
" on residue {res}".format(res=resid, **center))
tmp_atoms, nb_water_removed = remove_sphere(output_atoms, ref_water_residue,
center, sphere_radius)
sum_water_removed += nb_water_removed
output_atoms = groIO.renumber(tmp_atoms)
return (output_atoms, sum_water_removed)