| /dports/science/py-MDAnalysisTests/MDAnalysisTests-0.19.2/MDAnalysisTests/analysis/ |
| H A D | test_dihedrals.py | 39 def atomgroup(self): member in TestDihedral
45 def test_dihedral(self, atomgroup): argument
46 dihedral = Dihedral([atomgroup]).run()
53 def test_dihedral_single_frame(self, atomgroup): argument
54 dihedral = Dihedral([atomgroup]).run(start=5, stop=6)
61 def test_atomgroup_list(self, atomgroup): argument
62 dihedral = Dihedral([atomgroup, atomgroup]).run()
69 def test_enough_atoms(self, atomgroup): argument
71 dihedral = Dihedral([atomgroup[:2]]).run()
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| /dports/science/py-MDAnalysis/MDAnalysis-0.19.2/MDAnalysis/analysis/ |
| H A D | rms.py | 326 def __init__(self, atomgroup, reference=None, select='all', argument
464 super(RMSD, self).__init__(atomgroup.universe.trajectory,
466 self.atomgroup = atomgroup
467 self.reference = reference if reference is not None else self.atomgroup
478 self.mobile_atoms = self.atomgroup.select_atoms(*select['mobile'])
519 'mobile': self.atomgroup.universe.select_atoms(*s['mobile']),
685 def __init__(self, atomgroup, **kwargs): argument
801 super(RMSF, self).__init__(atomgroup.universe.trajectory, **kwargs)
802 self.atomgroup = atomgroup
805 self.sumsquares = np.zeros((self.atomgroup.n_atoms, 3))
[all …]
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| H A D | dihedrals.py | 263 def __init__(self, atomgroup, **kwargs): argument
276 super(Ramachandran, self).__init__(atomgroup.universe.trajectory, **kwargs)
277 self.atomgroup = atomgroup
278 residues = self.atomgroup.residues
279 protein = self.atomgroup.universe.select_atoms("protein").residues
382 def __init__(self, atomgroup, **kwargs): argument
399 super(Ramachandran, self).__init__(atomgroup.universe.trajectory, **kwargs)
400 self.atomgroup = atomgroup
401 residues = atomgroup.residues
402 protein = atomgroup.universe.select_atoms("protein").residues
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| H A D | pca.py | 278 def transform(self, atomgroup, n_components=None, start=None, stop=None, argument
311 if isinstance(atomgroup, Universe):
312 atomgroup = atomgroup.atoms
314 if(self._n_atoms != atomgroup.n_atoms):
318 atomgroup.n_atoms))
319 if not (self._atoms.types == atomgroup.types).all():
322 traj = atomgroup.universe.trajectory
332 xyz = atomgroup.positions.ravel() - self.mean
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| /dports/science/py-MDAnalysis/MDAnalysis-0.19.2/MDAnalysis/core/ |
| H A D | topologyattrs.py | 483 def getattr__(atomgroup, name): argument
691 def get_atoms(self, atomgroup): argument
864 atomgroup = group.atoms
874 masses = atomgroup.masses
922 atomgroup = group.atoms
924 masses = atomgroup.masses
971 atomgroup = group.atoms
973 masses = atomgroup.masses
1028 atomgroup = group.atoms
1031 masses = atomgroup.masses
[all …]
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| H A D | groups.py | 850 atomgroup = self.atoms
856 x = atomgroup.positions
888 atomgroup = self.atoms.unique
895 x = atomgroup.positions
965 atomgroup = self.atoms.unique
968 atomgroup.universe.trajectory.ts.positions[atomgroup.indices] += vector
1009 atomgroup = self.atoms.unique
1014 idx = atomgroup.indices
1017 atomgroup.translate(point)
1184 atomgroup = self.atoms.unique
[all …]
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| /dports/science/py-MDAnalysis/MDAnalysis-0.19.2/MDAnalysis/lib/ |
| H A D | _cutil.pyx | 105 def make_whole(atomgroup, reference_atom=None): argument
128 atomgroup : AtomGroup
134 Defaults to atom 0 in the atomgroup.
168 make_whole(atomgroup, reference_atom=atomgroup[10])
187 ix_view = atomgroup.ix[:]
188 natoms = atomgroup.ix.shape[0]
196 if not reference_atom in atomgroup:
200 box = atomgroup.dimensions
221 bonds = atomgroup.bonds.to_indices()
235 oldpos = atomgroup.positions
[all …]
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| /dports/science/py-MDAnalysis/MDAnalysis-0.19.2/ |
| H A D | CHANGELOG | 275 * speed up atomgroup.rotate when point = (0, 0, 0) (Issue #1707)
313 * Fixed analysis.rms.RMSD: selections are now applied to atomgroup, not to
314 atomgroup.universe
462 * Added atomgroup.center(weights, pbc) method to calculate the center
472 * Groups (atomgroup, residuegroup, and segmentgroup) have more operators,
535 * atoms.tranform/translate/rotate/rotateby return original atomgroup
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