Ligand-receptor based pharmacophores can be extracted from protein-ligand complexes, using a pdb file or a file from a molecular dynamics trajectory. This was implemented via 2 classes, LigandReceptorPharmacophre and PLComplex. The former allows to store pharmacophoric points for different frames of a trajectory, handles visualization of pharmacophores and extract the pharmacophoric points from protein-ligand interactions. The PLComplex class allows us to work with a trajectory of a protein-ligand complex, it has two main functions. The first is the treatment of the receptor and ligand to for example, add hydrogens, extract the ligand and fix its bond orders of the ligand. The second is to find chemical features in the protein and the ligand that can be used to fund protein-ligand interactions.
Todos
Notable points that this PR has either accomplished or will accomplish.
[X] Ligand-receptor pharmacophores can be obtained from pdbs and MD trajectories.
[X] Visualization of pharmacophore with nglview.
[X] New classes that help to prepare the receptor and the ligand for pharmacophore extraction.
[X] Tests were split into unit tests and functional tests.
Description
Ligand-receptor based pharmacophores can be extracted from protein-ligand complexes, using a pdb file or a file from a molecular dynamics trajectory. This was implemented via 2 classes,
LigandReceptorPharmacophreandPLComplex. The former allows to store pharmacophoric points for different frames of a trajectory, handles visualization of pharmacophores and extract the pharmacophoric points from protein-ligand interactions. The PLComplex class allows us to work with a trajectory of a protein-ligand complex, it has two main functions. The first is the treatment of the receptor and ligand to for example, add hydrogens, extract the ligand and fix its bond orders of the ligand. The second is to find chemical features in the protein and the ligand that can be used to fund protein-ligand interactions.Todos
Notable points that this PR has either accomplished or will accomplish.
Status
Closes #57