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src/b/i/biopython-1.63/Bio/PDB/NeighborSearch.py   biopython(Download)
import numpy
 
from Bio.KDTree import KDTree
 
from Bio.PDB.PDBExceptions import PDBException
        assert(bucket_size>1)
        assert(self.coords.shape[1]==3)
        self.kdt=KDTree(3, bucket_size)
        self.kdt.set_coords(self.coords)
 

src/b/i/biopython-HEAD/Bio/PDB/NeighborSearch.py   biopython(Download)
import numpy
 
from Bio.KDTree import KDTree
 
from Bio.PDB.PDBExceptions import PDBException
        assert(bucket_size>1)
        assert(self.coords.shape[1]==3)
        self.kdt=KDTree(3, bucket_size)
        self.kdt.set_coords(self.coords)
 

src/p/y/pygnm-0.1/pygnm/GNM.py   pygnm(Download)
import time
 
from Bio.KDTree import KDTree
from Bio.PDB import PDBParser
 
                    self.n_atoms += count
        self.coordinates = np.array(self.coordinates, 'd')
        self._kdtree = KDTree(3)
        self._kdtree.set_coords(self.coordinates)
        self.bfactors = np.array(self.bfactors)