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src/m/d/MDAnalysis-0.8.1/MDAnalysis/analysis/hbonds.py   MDAnalysis(Download)
            self.logger_debug("Size of selection 2 before filtering: %d atoms" % len(self._s2))
            ns_selection_2 = NS.AtomNeighborSearch(self._s2)
            self._s2 = ns_selection_2.search_list(self._s1, 3.*self.distance)
        self.logger_debug("Size of selection 2: %d atoms" % len(self._s2))
 
                    d = self._s1_donors[i]
                    for h in donor_h_set:
                        res = ns_acceptors.search_list(AtomGroup([h]), self.distance)
                        for a in res:
                            angle = self.calc_angle(d,h,a)
                    d = self._s2_donors[i]
                    for h in donor_h_set:
                        res = ns_acceptors.search_list(AtomGroup([h]), self.distance)
                        for a in res:
                            if remove_duplicates and \

src/m/d/MDAnalysis-0.8.1/MDAnalysis/analysis/distances.py   MDAnalysis(Download)
  from MDAnalysis.core.AtomGroup import AtomGroup
  ns_group = AtomNeighborSearch(group)
  resA = set(ns_group.search_list(A, distance))
  resB = set(ns_group.search_list(B, distance))
  return AtomGroup(resB.intersection(resA))

src/m/d/MDAnalysis-0.8.1/MDAnalysis/analysis/density.py   MDAnalysis(Download)
            def notwithin_coordinates(cutoff=cutoff):
                # must update every time step
                ns_w = NS.AtomNeighborSearch(solvent)  # build kd-tree on solvent (N_w > N_protein)
                solvation_shell = ns_w.search_list(protein,cutoff)  # solvent within CUTOFF of protein
                group = MDAnalysis.core.AtomGroup.AtomGroup(set_solvent - set(solvation_shell)) # bulk
            def notwithin_coordinates(cutoff=cutoff):
                # acts as '<solvent> WITHIN <cutoff> OF <protein>'
                # must update every time step
                ns_w = NS.AtomNeighborSearch(solvent)  # build kd-tree on solvent (N_w > N_protein)
                group = ns_w.search_list(protein,cutoff)  # solvent within CUTOFF of protein

src/m/d/MDAnalysisTests-0.8.1/MDAnalysisTests/test_pdbqt.py   MDAnalysisTests(Download)
        ns_protein = kdNS.AtomNeighborSearch(protein)
        query_atoms = self.query_universe.atoms
        residue_neighbors = ns_protein.search_list(query_atoms, 4.0)
        assert_equal(len(residue_neighbors), 80)