コード例 #1
0
ファイル: FragmentMapper.py プロジェクト: cbirdlab/sap
    def __sub__(self, other):
        """
        Return rmsd between two fragments.

        Example:
            >>> rmsd=fragment1-fragment2

        @return: rmsd between fragments
        @rtype: float
        """
        sup = SVDSuperimposer()
        sup.set(self.coords_ca, other.coords_ca)
        sup.run()
        return sup.get_rms()
コード例 #2
0
ファイル: FragmentMapper.py プロジェクト: kaspermunch/sap
    def __sub__(self, other):
        """
        Return rmsd between two fragments.

        Example:
            >>> rmsd=fragment1-fragment2

        @return: rmsd between fragments
        @rtype: float
        """
        sup=SVDSuperimposer()
        sup.set(self.coords_ca, other.coords_ca)
        sup.run()
        return sup.get_rms()
コード例 #3
0
ファイル: Superimposer.py プロジェクト: cbirdlab/sap
    def set_atoms(self, fixed, moving):
        """
        Put (translate/rotate) the atoms in fixed on the atoms in
        moving, in such a way that the RMSD is minimized.

        @param fixed: list of (fixed) atoms
        @param moving: list of (moving) atoms
        @type fixed,moving: [L{Atom}, L{Atom},...]
        """
        if not (len(fixed) == len(moving)):
            raise PDBException("Fixed and moving atom lists differ in size")
        l = len(fixed)
        fixed_coord = numpy.zeros((l, 3))
        moving_coord = numpy.zeros((l, 3))
        for i in range(0, len(fixed)):
            fixed_coord[i] = fixed[i].get_coord()
            moving_coord[i] = moving[i].get_coord()
        sup = SVDSuperimposer()
        sup.set(fixed_coord, moving_coord)
        sup.run()
        self.rms = sup.get_rms()
        self.rotran = sup.get_rotran()
コード例 #4
0
ファイル: Superimposer.py プロジェクト: kaspermunch/sap
    def set_atoms(self, fixed, moving):
        """
        Put (translate/rotate) the atoms in fixed on the atoms in
        moving, in such a way that the RMSD is minimized.

        @param fixed: list of (fixed) atoms
        @param moving: list of (moving) atoms
        @type fixed,moving: [L{Atom}, L{Atom},...]
        """
        if not (len(fixed)==len(moving)):
            raise PDBException("Fixed and moving atom lists differ in size")
        l=len(fixed)
        fixed_coord=numpy.zeros((l, 3))
        moving_coord=numpy.zeros((l, 3))
        for i in range(0, len(fixed)):
            fixed_coord[i]=fixed[i].get_coord()
            moving_coord[i]=moving[i].get_coord()
        sup=SVDSuperimposer()
        sup.set(fixed_coord, moving_coord)
        sup.run()
        self.rms=sup.get_rms()
        self.rotran=sup.get_rotran()