def import_restraints(self, verbose: bool = False) -> t.List[dict]:
"""
This function reads in a gromos distance restraint file. TODO: Read
in additional Settings (r0, w0, etc...)
TODO: WE could try to read thefile in get_args to get the Error there already.
IDEA: READ THE WHOLE TEXT IN GET ARGS AND ONLY CONVERT IT HERE. OS ALLERRORS HAPPEN IN GET ARGS
Parameters
----------
verbose
Returns
-------
t.List[dict]
returns a dict containing the atom ids for each disres. (has to be
translated in interface_Pymol
"""
restraint_objects = [
] # Define before try_block, so we can return the empty list in case of errors
try:
# readFiles
disres_file = Files.Gromos_files.disres(self.in_path)
if verbose: print(disres_file)
if verbose: print("READ: " + "".join(disres_file["TITLE"]))
# Analogous new version
for restraint in disres_file.distance_res_spec_block.RESTRAINTS:
if verbose: print(restraint)
atom1 = u.find_atom_by_property(self.all_atoms,
restraint.atom1i)
atom2 = u.find_atom_by_property(self.all_atoms,
restraint.atom2i)
new_restraint = Restraints.DistanceRestraint(atomA=atom1,
atomB=atom2)
restraint_objects.append(new_restraint)
# PRINT RESULTS
for i_r, r in enumerate(restraint_objects):
print('PairRestraint', str(i_r), ': Atom1_ID:',
str(r.atoms[0].id), 'Atom2_ID:', str(r.atoms[1].id))
except FileNotFoundError:
print("Error: Could not find the file: \'" + self.in_path + "\'",
mv=4)
except KeyError:
print("Error: Could not read the file: " + self.in_path, mv=4)
except ImportError:
print(
"BAD ERROR: FAILED TO IMPORT THE MODULES NECESSARY FOR IMPORTING AND EXPORTING GROMOS FILES!",
mv=4)
if (len(restraint_objects) == 0):
warnings.warn("Could not find any Restraint in file: " +
str(self.in_path))
return restraint_objects
def import_restraints(self, verbose: bool = False) -> t.List[dict]:
"""
This function reads in a gromos distance restraint file. TODO: Read
in additional Settings (r0, w0, etc...)
TODO: WE could try to read thefile in get_args to get the Error there already.
IDEA: READ THE WHOLE TEXT IN GET ARGS AND ONLY CONVERT IT HERE. OS ALLERRORS HAPPEN IN GET ARGS
Parameters
----------
verbose
Returns
-------
t.List[dict]
returns a dict containing the atom ids for each disres. (has to be
translated in interface_Pymol
"""
restraint_objects = [
] # Define before try_block, so we can return the empty list in case of errors
try:
tmp_file_content = json.load(open(self.in_path, "r"))
# Analogous new version
for i, restraint in tmp_file_content.items():
if verbose: print(restraint)
atom1 = u.find_atom_by_property(self.all_atoms,
restraint['a1']['id'])
atomRef = u.find_atom_by_property(self.all_atoms,
restraint['aR']['id'])
new_restraint = Restraints.PositionRestraint(
atomA=atom1, reference_atom=atomRef)
restraint_objects.append(new_restraint)
# PRINT RESULTS
for i_r, r in enumerate(restraint_objects):
print('PositionRestraint', str(i_r), ': Atom1_ID:',
str(r.atoms[0].id), 'AtomR_ID:',
str(r.reference_atom.id))
except FileNotFoundError:
print("Error: Could not find the file: \'" + self.in_path + "\'",
mv=4)
except KeyError:
print("Error: Could not read the file: " + self.in_path, mv=4)
except ImportError:
print(
"BAD ERROR: FAILED TO IMPORT THE MODULES NECESSARY FOR IMPORTING AND EXPORTING JSON FILES!",
mv=4)
if (len(restraint_objects) == 0):
warnings.warn("Could not find any Restraint in file: " +
str(self.in_path))
return restraint_objects
