Other
OtherMolecules(parent_molecule_object)
¶
A class for characterizing the relationships between multiple pymolecule.
Initializes the pymolecule.OtherMolecules class.
| PARAMETER | DESCRIPTION |
|---|---|
parent_molecule_object
|
The pymolecule.Molecule object associated with this class.
|
parent_molecule = parent_molecule_object
instance-attribute
¶
align_other_molecule_to_this(other_mol, tethers)
¶
Aligns a molecule to self (this pymolecule.Molecule object) using a quaternion RMSD alignment.
| PARAMETER | DESCRIPTION |
|---|---|
other_mol
|
A pymolecule.Molecule that is to be aligned to this one.
|
tethers
|
A tuple of two np.array objects, where each array contains the indices of self and other_mol, respectively, such that equivalent atoms are listed in the same order. So, for example, if (atom 1, self = atom 3, other) and (atom2, self = atom6, other) than the tethers would be (np.array([1,2]), np.array([3,6])).
|
distance_to_another_molecule(other_molecule, pairwise_comparison=True)
¶
Computes the minimum distance between any of the atoms of this molecular model and any of the atoms of a second specified model.
| PARAMETER | DESCRIPTION |
|---|---|
other_molecule
|
a pymolecule.Molecule, the other molecular model.
|
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.
DEFAULT:
|
| RETURNS | DESCRIPTION |
|---|---|
|
A float, the minimum distance between any two atoms of the two specified molecular models (self and other_molecule). |
merge_with_another_molecule(other_molecule)
¶
Merges two molecular models into a single model.
| PARAMETER | DESCRIPTION |
|---|---|
other_molecule
|
A molecular model (pymolecule.Molecule object).
|
| RETURNS | DESCRIPTION |
|---|---|
|
A single pymolecule.Molecule object containing the atoms of this model combined with the atoms of other_molecule. |
rmsd_equivalent_atoms_specified(other_mol, tethers)
¶
Calculates the RMSD between this pymolecule.Molecle object and another, where equivalent atoms are explicitly specified.
| PARAMETER | DESCRIPTION |
|---|---|
other_mol
|
The other pymolecule.Molecule object.
|
tethers
|
A tuple of two np.array objects, where each array contains the indices of self and other_mol, respectively, such that equivalent atoms are listed in the same order. So, for example, if (atom 1, self = atom 3, other) and (atom2, self = atom6, other) than the tethers would be (np.array([1,2]), np.array([3,6])).
|
| RETURNS | DESCRIPTION |
|---|---|
|
A float, the RMSD between self and other_mol. |
rmsd_order_dependent(other_mol)
¶
Calculates the RMSD between two structures, where equivalent atoms are listed in the same order.
| PARAMETER | DESCRIPTION |
|---|---|
other_mol
|
The other pymolecule.Molecule object.
|
| RETURNS | DESCRIPTION |
|---|---|
|
A float, the RMSD between self and other_mol. |
steric_clash_with_another_molecule(other_mol, cutoff, pairwise_comparison=True)
¶
Detects steric clashes between the pymolecule.Molecule (self) and another pymolecule.Molecule.
| PARAMETER | DESCRIPTION |
|---|---|
other_mol
|
The pymolecule.Molecule object that will be evaluated for steric clashes.
|
cutoff
|
A float, the user-defined distance cutoff in Angstroms.
|
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.
DEFAULT:
|
| RETURNS | DESCRIPTION |
|---|---|
|
A boolean. True if steric clashes are present, False if they are not. |