stko.molecule_analysis.DitopicThreeSiteAnalyser
- class stko.molecule_analysis.DitopicThreeSiteAnalyser[source]
Bases:
objectAnalyses geometry of functional groups in ditopic molecules.
Warning
This code is only present in the latest versions of stko that require Python 3.11!
Methods
Get the position of centroids of atoms adjacent to binder atoms.
Get the torsion (-180, 180) between binders and their adjacents.
Get the binder-adjacent-binder angles.
Get the angle between binders-adjacent vectors.
Get the angle between binders and molecule centroid.
Get the distance between binder atoms in Angstrom.
Get the half-bite angles defined by the binders.
- get_adjacent_centroids(molecule)[source]
Get the position of centroids of atoms adjacent to binder atoms.
- get_binder_adjacent_torsion(molecule)[source]
Get the torsion (-180, 180) between binders and their adjacents.
- Parameters:
molecule (BuildingBlock) – Molecule to analyse.
- Raises:
NotDitopicThreeSiteError – if does not have two ThreeSiteFG.
- Return type:
- get_binder_angles(molecule)[source]
Get the binder-adjacent-binder angles.
Represents the two reaction angles of the ligand, or the internal angles from DOI: 10.1039/D3SC03991A.
Caution with the direction of the vectors!
- get_binder_binder_angle(molecule)[source]
Get the angle between binders-adjacent vectors.
- Parameters:
molecule (BuildingBlock) – Molecule to analyse.
- Raises:
NotDitopicThreeSiteError – if does not have two ThreeSiteFG.
- Return type:
- get_binder_centroid_angle(molecule)[source]
Get the angle between binders and molecule centroid.
- Parameters:
molecule (BuildingBlock) – Molecule to analyse.
- Raises:
NotDitopicThreeSiteError – if does not have two ThreeSiteFG.
- Return type:
- get_binder_distance(molecule)[source]
Get the distance between binder atoms in Angstrom.
- Parameters:
molecule (BuildingBlock) – Molecule to analyse.
- Raises:
NotDitopicThreeSiteError – if does not have two ThreeSiteFG.
- Return type:
- get_halfbite_angles(molecule)[source]
Get the half-bite angles defined by the binders.
The bite angle is a common measure used in metal-organic cages that represents the angle between the two reaction angles of the ligand as if the molecule was symmetric and the torsion between binders is 0 degrees. Caution using this for many molecules that are flexible!
Here the bite angle is defined
visuallyas in:Technically, the measure of interest is the sum of the two floats output by this method, which should be two times either one. (They should be similar!)