pin.py 文件源码

def add_delaunay_triangulation_(self):
        """
        Computes the Delaunay triangulation of the protein structure.

        This has been used in prior work. References:
        - Harrison, R. W., Yu, X. & Weber, I. T. Using triangulation to include
          target structure improves drug resistance prediction accuracy. in 1–1
          (IEEE, 2013). doi:10.1109/ICCABS.2013.6629236
        - Yu, X., Weber, I. T. & Harrison, R. W. Prediction of HIV drug
          resistance from genotype with encoded three-dimensional protein
          structure. BMC Genomics 15 Suppl 5, S1 (2014).

        Notes:
        1. We do not use the add_interacting_resis function, because this
           interaction is computed on the CA atoms. Therefore, there is code
           duplication. For now, I have chosen to leave this code duplication
           in.
        """
        ca_coords = self.dataframe[self.dataframe['atom'] == 'CA']

        tri = Delaunay(ca_coords[['x', 'y', 'z']])  # this is the triangulation
        for simplex in tri.simplices:
            nodes = ca_coords.reset_index().ix[simplex]['node_id']

            for n1, n2 in combinations(nodes, 2):
                if self.has_edge(n1, n2):
                    self.edge[n1][n2]['kind'].add('delaunay')
                else:
                    self.add_edge(n1, n2, kind={'delaunay'})