def rmsd_to_me(self, other_conf):
"""Calculate the rms distance between this conformer and another one.
:param other_conf: The other conformer to align.
:type other_conf: MyConformer
:return: The rmsd, a float.
:rtype: float
"""
# Make a new molecule.
amol = Chem.MolFromSmiles(self.smiles, sanitize=False)
amol = MOH.check_sanitization(amol)
amol = MOH.try_reprotanation(amol)
# Add the conformer of the other MyConformer object.
amol.AddConformer(self.conformer(), assignId=True)
amol.AddConformer(other_conf.conformer(), assignId=True)
# Get the two confs.
first_conf = amol.GetConformers()[0]
last_conf = amol.GetConformers()[-1]
# Return the RMSD.
amol = MOH.try_deprotanation(amol)
rmsd = AllChem.GetConformerRMS(amol,
first_conf.GetId(),
last_conf.GetId(),
prealigned=True)
return rmsd
def smiles(self, noh=False):
"""Get the desalted, canonical smiles string associated with this
object. (Not the input smiles!)
:param noh: Whether or not hydrogen atoms should be included in the
canonical smiles string., defaults to False
:param noh: bool, optional
:return: The canonical smiles string, or None if it cannot be
determined.
:rtype: str or None
"""
# See if it's already been calculated.
if noh == False:
# They want the hydrogen atoms.
if self.can_smi != "":
# Return previously determined canonical SMILES.
return self.can_smi
else:
# Need to determine canonical SMILES.
try:
can_smi = Chem.MolToSmiles(self.rdkit_mol,
isomericSmiles=True,
canonical=True)
except:
# Sometimes this conversion just can't happen. Happened
# once with this beast, for example:
# CC(=O)NC1=CC(=C=[N+]([O-])O)C=C1O
Utils.log("Warning: Couldn't put " + self.orig_smi + " (" +
self.name +
") in canonical form. Got this error: " +
str(sys.exc_info()[0]) +
". This molecule will be " + "discarded.")
self.can_smi = None
return None
self.can_smi = can_smi
return can_smi
else:
# They don't want the hydrogen atoms.
if self.can_smi_noh != "":
# Return previously determined string.
return self.can_smi_noh
# So remove hydrogens. Note that this assumes you will have called
# this function previously with noh = False
amol = copy.copy(self.rdkit_mol)
amol = MOH.try_deprotanation(amol)
self.can_smi_noh = Chem.MolToSmiles(amol,
isomericSmiles=True,
canonical=True)
return self.can_smi_noh