Commit d6f10bd9 authored by pjropp's avatar pjropp

Updated `get_distance...` and `steric_clash...`

parent 9d47bce4
......@@ -1768,7 +1768,7 @@ class Molecule: # here's the actual Molecule class
Requires the :any:`numpy` and :any:`scipy<scipy.spatial>` libraries.
Wrapper function for :meth:`~scoria.OtherMolecules.OtherMolecules.get_distance_to_another_molecules`
Wrapper function for :meth:`~scoria.OtherMolecules.OtherMolecules.get_distance_to_another_molecule`
:param scoria.Molecule other_molecules: a scoria.Molecule, the other molecular
model.
......@@ -1844,12 +1844,13 @@ class Molecule: # here's the actual Molecule class
def steric_clash_with_another_molecules(self, other_mol, cutoff,
pairwise_comparison = True):
"""
DEPRECATION WARNING: Please use :meth:`~scoria.Molecule.Molecule.steric_clash_with_another_molecule`
Detects steric clashes between the scoria.Molecule (self) and
another scoria.Molecule.
Requires the :any:`numpy` and :any:`scipy<scipy.spatial>` libraries.
Wrapper function for :meth:`~scoria.OtherMolecules.OtherMolecules.steric_clash_with_another_molecules`
Wrapper function for :meth:`~scoria.OtherMolecules.OtherMolecules.steric_clash_with_another_molecule`
:param scoria.Molecule other_mol: The scoria.Molecule object that will be
evaluated for steric clashes.
......@@ -1864,15 +1865,58 @@ class Molecule: # here's the actual Molecule class
are not.
"""
return self.other_molecules.steric_clash_with_another_molecules(
return self.other_molecules.steric_clash_with_another_molecule(
other_mol, cutoff, pairwise_comparison
)
def steric_clash_with_another_molecule(self, other_mol, cutoff,
pairwise_comparison = True):
"""
Detects steric clashes between the scoria.Molecule (self) and
another scoria.Molecule.
Requires the :any:`numpy` and :any:`scipy<scipy.spatial>` libraries.
Wrapper function for :meth:`~scoria.OtherMolecules.OtherMolecules.steric_clash_with_another_molecule`
:param scoria.Molecule other_mol: The scoria.Molecule object that will be
evaluated for steric clashes.
:param float cutoff: A float, the user-defined distance cutoff in
Angstroms.
:param bool pairwise_comparison: An optional boolean, whether or not to
perform a simple pairwise distance comparison (if True) or
to use a more sophisitcated method (if False). True by
default.
:returns: A boolean. True if steric clashes are present, False if they
are not.
"""
return self.other_molecules.steric_clash_with_another_molecule(
other_mol, cutoff, pairwise_comparison
)
def merge_with_another_molecules(self, other_molecules):
"""
DEPRECATION WARNING: Please use :meth:`~scoria.Molecule.Molecule.merge_with_another_molecule`
Merges two molecular models into a single model.
Wrapper function for :meth:`~scoria.OtherMolecules.OtherMolecules.merge_with_another_molecule`
:param scoria.Molecule other_molecules: A molecular model (scoria.Molecule
object).
:returns: A single scoria.Molecule object containing the atoms of
this model combined with the atoms of other_molecules.
"""
return self.other_molecules.merge_with_another_molecule(other_molecules)
def merge_with_another_molecule(self, other_molecules):
"""
Merges two molecular models into a single model.
Wrapper function for :meth:`~scoria.OtherMolecules.OtherMolecules.merge_with_another_molecules`
Wrapper function for :meth:`~scoria.OtherMolecules.OtherMolecules.merge_with_another_molecule`
:param scoria.Molecule other_molecules: A molecular model (scoria.Molecule
object).
......@@ -1881,7 +1925,7 @@ class Molecule: # here's the actual Molecule class
this model combined with the atoms of other_molecules.
"""
return self.other_molecules.merge_with_another_molecules(other_molecules)
return self.other_molecules.merge_with_another_molecule(other_molecules)
######## Supporting functions ########
......
......@@ -146,7 +146,7 @@ class OtherMolecules():
return new_mol
def steric_clash_with_another_molecules(self, other_mol, cutoff,
def steric_clash_with_another_molecule(self, other_mol, cutoff,
pairwise_comparison = True):
"""
Detects steric clashes between the scoria.Molecule (self) and
......@@ -154,7 +154,7 @@ class OtherMolecules():
Requires the :any:`numpy` and :any:`scipy<scipy.spatial>` libraries.
Wrapper function for :meth:`~scoria.Molecule.Molecule.steric_clash_with_another_molecules`
Wrapper function for :meth:`~scoria.Molecule.Molecule.steric_clash_with_another_molecule`
:param scoria.Molecule other_mol: The scoria.Molecule object that will be
evaluated for steric clashes.
......@@ -195,11 +195,11 @@ class OtherMolecules():
else:
return True
def merge_with_another_molecules(self, other_molecules):
def merge_with_another_molecule(self, other_molecules):
"""
Merges two molecular models into a single model.
Wrapper function for :meth:`~scoria.Molecule.Molecule.merge_with_another_molecules`
Wrapper function for :meth:`~scoria.Molecule.Molecule.merge_with_another_molecule`
:param scoria.Molecule other_molecules: A molecular model (scoria.Molecule
object).
......@@ -274,7 +274,7 @@ class OtherMolecules():
Requires the :any:`numpy` and :any:`scipy<scipy.spatial>` libraries.
Wrapper function for :meth:`~scoria.Molecule.Molecule.get_distance_to_another_molecules`
Wrapper function for :meth:`~scoria.Molecule.Molecule.get_distance_to_another_molecule`
:param scoria.Molecule other_molecules: a scoria.Molecule, the other molecular
model.
......
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