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/dports/biology/py-biopython/biopython-1.79/Tests/
H A Dtest_PQR.py33 atom = next(struct.get_atoms())
68 atom = next(structure.get_atoms())
76 atom = next(structure.get_atoms())
101 atom = next(structure.get_atoms())
109 atom = next(structure.get_atoms())
117 atom = next(structure.get_atoms())
178 original_atoms = self.example_structure.get_atoms()
179 for atom in output_struct.get_atoms():
H A Dtest_PDB_SASA.py55 result = [a.sasa for a in m.get_atoms()][:5]
67 result = [a.sasa for a in m.get_atoms()][:5]
79 result = [a.sasa for a in m.get_atoms()][:5]
104 atom_sum = sum(a.sasa for a in c.get_atoms())
126 atom = list(self.model.get_atoms())[0]
H A Dtest_PDB_MMCIFParser.py122 s_atoms = list(structure.get_atoms())
123 f_atoms = list(f_structure.get_atoms())
152 s_atoms = list(structure.get_atoms())
153 f_atoms = list(f_structure.get_atoms())
358 pdb_atom_names = [a.name for a in pdb_struct.get_atoms()]
359 cif_atom_names = [a.name for a in cif_struct.get_atoms()]
362 pdb_atom_elems = [a.element for a in pdb_struct.get_atoms()]
363 cif_atom_elems = [a.element for a in cif_struct.get_atoms()]
H A Dtest_PDB_PDBParser.py395 " ".join(atom.name for atom in chain.get_atoms()),
399 " ".join(atom.element for atom in chain.get_atoms()), "N C C C D O C O CA"
423 " ".join(atom.name for atom in chain.get_atoms()),
460 " ".join(atom.element for atom in chain.get_atoms()),
549 " ".join(atom.name for atom in chain.get_atoms()),
588 " ".join(atom.element for atom in chain.get_atoms()),
H A Dtest_PDB_PDBIO.py72 serials = [a.serial_number for a in struct.get_atoms()]
89 serials = [a.serial_number for a in struct.get_atoms()]
90 og_serials = [a.serial_number for a in self.structure.get_atoms()]
184 latoms = list(struct2.get_atoms())
310 atom = next(struct1.get_atoms())
327 atom = next(struct1.get_atoms())
H A Dtest_mmtf.py63 self.mmcif_atoms = list(mmcif_r.get_atoms())
64 self.mmtf_atoms = list(mmtf_r.get_atoms())
74 self.mmcif_atoms = list(mmcif_struct.get_atoms())
75 self.mmtf_atoms = list(mmtf_struct.get_atoms())
/dports/science/py-gpaw/gpaw-21.6.0/gpaw/test/generic/
H A Dtest_relax.py34 molecule = GPAW('H2.gpw', txt=None).get_atoms()
36 molecule = GPAW('H2a.gpw', txt=None).get_atoms()
38 molecule = GPAW('H2f.gpw', txt=None).get_atoms()
40 molecule = GPAW('H2fa.gpw', txt=None).get_atoms()
82 molecule = GPAW('H2fa.gpw', txt='H2.txt').get_atoms()
/dports/science/py-pymatgen/pymatgen-2022.0.15/pymatgen/io/tests/
H A Dtest_ase.py21 atoms = aio.AseAtomsAdaptor.get_atoms(structure)
30 atoms = aio.AseAtomsAdaptor.get_atoms(m)
39 atoms = aio.AseAtomsAdaptor.get_atoms(p.structure)
45 atoms = aio.AseAtomsAdaptor.get_atoms(m)
H A Dtest_jarvis.py18 atoms = jio.JarvisAtomsAdaptor.get_atoms(structure)
26 atoms = jio.JarvisAtomsAdaptor.get_atoms(structure)
/dports/math/eprover/eprover-E-2.0/development_tools/
H A Dpylib_dimacs.py141 def get_atoms(self): member in prop_clause
173 def get_atoms(self): member in prop_formula
176 res.extend(i.get_atoms())
180 a = self.get_atoms()
211 atoms = map(dimacs_to_mathsat_lit, self.get_atoms())
/dports/science/py-ase/ase-3.22.0/ase/test/calculator/vasp/
H A Dtest_vasp_Al_volrelax.py38 calc.get_atoms().get_cell())
43 assert (calc.get_atoms().get_cell() == CONTCAR_Al.get_cell()).all()
60 print('Al post ASE volume relaxation\n', calc.get_atoms().get_cell())
/dports/science/py-OpenMC/openmc-0.12.2/tests/unit_tests/
H A Dtest_deplete_resultslist.py21 t, n = res.get_atoms("1", "Xe135")
33 t_days, n_cm3 = res.get_atoms("1", "Xe135", nuc_units="atom/cm3", time_units="d")
38 t_min, n_bcm = res.get_atoms("1", "Xe135", nuc_units="atom/b-cm", time_units="min")
42 t_hour, _n = res.get_atoms("1", "Xe135", time_units="h")
H A Dtest_deplete_restart.py90 _t, y1 = results.get_atoms("1", "1")
91 _t, y2 = results.get_atoms("1", "2")
/dports/science/openmc/openmc-0.12.2/tests/unit_tests/
H A Dtest_deplete_resultslist.py21 t, n = res.get_atoms("1", "Xe135")
33 t_days, n_cm3 = res.get_atoms("1", "Xe135", nuc_units="atom/cm3", time_units="d")
38 t_min, n_bcm = res.get_atoms("1", "Xe135", nuc_units="atom/b-cm", time_units="min")
42 t_hour, _n = res.get_atoms("1", "Xe135", time_units="h")
H A Dtest_deplete_restart.py90 _t, y1 = results.get_atoms("1", "1")
91 _t, y2 = results.get_atoms("1", "2")
/dports/science/py-ase/ase-3.22.0/ase/test/
H A Dtest_pubchem.py8 data.get_atoms()
13 pubchem_search(cid=241, mock_test=True).get_atoms()
/dports/lang/yap/yap-6.2.2/packages/cplint/
H A Dcpl.pl138 get_atoms(Head,Atoms),
147 get_atoms([],[]):-!.
149 get_atoms([H:_P|T],[H|TA]):-
150 get_atoms(T,TA).
/dports/science/py-ase/ase-3.22.0/ase/vibrations/
H A Ddata.py159 def get_atoms(self) -> Atoms: member in VibrationsData
232 return {'atoms': self.get_atoms(),
443 atoms = self.get_atoms()
465 atoms = self.get_atoms()
491 all_images = list(self._get_jmol_images(atoms=self.get_atoms(),
586 new_atoms = self.get_atoms()
/dports/science/py-ase/ase-3.22.0/ase/ga/
H A Ddata.py104 return self.get_atoms(allcands[-1].id)
270 return self.c.get_atoms(simulation_cell=True)
317 t = self.get_atoms(id=v.id)
333 t = self.get_atoms(id=v.id)
382 def get_atoms(self, id, add_info=True): member in DataConnection
384 a = self.c.get_atoms(id, add_additional_information=add_info)
/dports/science/py-MDAnalysisTests/MDAnalysisTests-0.19.2/MDAnalysisTests/core/
H A Dtest_topologyattrs.py103 result = attr.get_atoms(DummyGroup([2, 1]))
113 assert_equal(attr.get_atoms(dg), np.array([567, 567]))
119 assert_equal(attr.get_atoms(dg), np.array([23, 504]))
216 assert_equal(attr.get_atoms(DummyGroup([7, 3, 9])),
265 assert_equal(attr.get_atoms(DummyGroup([3, 7])), np.array([11, 20]))
342 assert_equal(attr.get_atoms(DummyGroup([2, 4, 1])),
/dports/science/py-ase/ase-3.22.0/ase/data/
H A Dpubchem.py23 def get_atoms(self): member in PubchemData
298 return pubchem_search(*args, **kwargs).get_atoms()
315 conformers = [conformer.get_atoms() for conformer in conformers]
/dports/science/py-ase/ase-3.22.0/ase/test/db/
H A Dtest_db2.py56 a = c.get_atoms(id)
82 assert len(c.get_atoms(C=1).constraints) == 2
86 f3 = c.get_atoms(C=1).get_forces()
/dports/science/py-MDAnalysis/MDAnalysis-0.19.2/MDAnalysis/core/
H A Dtopologyattrs.py269 return self.get_atoms(group)
288 def get_atoms(self, ag): member in TopologyAttr
337 def get_atoms(self, ag): member in Atomindices
366 def get_atoms(self, ag): member in Resindices
400 def get_atoms(self, ag): member in Segindices
423 def get_atoms(self, ag): member in AtomAttr
691 def get_atoms(self, atomgroup): member in RecordTypes
699 return [self.get_atoms(r.atoms) for r in rg]
1222 def get_atoms(self, ag): member in ResidueAttr
1480 def get_atoms(self, ag): member in SegmentAttr
[all …]
/dports/science/py-ase/ase-3.22.0/ase/gui/
H A Dwidgets.py32 atoms = self.get_atoms()
48 def get_atoms(self): member in Element
/dports/science/py-gpaw/gpaw-21.6.0/gpaw/analyse/
H A Dhirshfeld.py65 all_atoms = self.calculator.get_atoms()
70 atoms = self.calculator.get_atoms()[atom_indices]
109 self.atoms = self.calculator.get_atoms()

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