/dports/biology/py-biopython/biopython-1.79/Tests/ |
H A D | test_PQR.py | 33 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():
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H A D | test_PDB_SASA.py | 55 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]
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H A D | test_PDB_MMCIFParser.py | 122 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()]
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H A D | test_PDB_PDBParser.py | 395 " ".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()),
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H A D | test_PDB_PDBIO.py | 72 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())
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H A D | test_mmtf.py | 63 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())
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/dports/science/py-gpaw/gpaw-21.6.0/gpaw/test/generic/ |
H A D | test_relax.py | 34 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()
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/dports/science/py-pymatgen/pymatgen-2022.0.15/pymatgen/io/tests/ |
H A D | test_ase.py | 21 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)
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H A D | test_jarvis.py | 18 atoms = jio.JarvisAtomsAdaptor.get_atoms(structure) 26 atoms = jio.JarvisAtomsAdaptor.get_atoms(structure)
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/dports/math/eprover/eprover-E-2.0/development_tools/ |
H A D | pylib_dimacs.py | 141 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())
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/dports/science/py-ase/ase-3.22.0/ase/test/calculator/vasp/ |
H A D | test_vasp_Al_volrelax.py | 38 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())
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/dports/science/py-OpenMC/openmc-0.12.2/tests/unit_tests/ |
H A D | test_deplete_resultslist.py | 21 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")
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H A D | test_deplete_restart.py | 90 _t, y1 = results.get_atoms("1", "1") 91 _t, y2 = results.get_atoms("1", "2")
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/dports/science/openmc/openmc-0.12.2/tests/unit_tests/ |
H A D | test_deplete_resultslist.py | 21 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")
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H A D | test_deplete_restart.py | 90 _t, y1 = results.get_atoms("1", "1") 91 _t, y2 = results.get_atoms("1", "2")
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/dports/science/py-ase/ase-3.22.0/ase/test/ |
H A D | test_pubchem.py | 8 data.get_atoms() 13 pubchem_search(cid=241, mock_test=True).get_atoms()
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/dports/lang/yap/yap-6.2.2/packages/cplint/ |
H A D | cpl.pl | 138 get_atoms(Head,Atoms), 147 get_atoms([],[]):-!. 149 get_atoms([H:_P|T],[H|TA]):- 150 get_atoms(T,TA).
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/dports/science/py-ase/ase-3.22.0/ase/vibrations/ |
H A D | data.py | 159 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()
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/dports/science/py-ase/ase-3.22.0/ase/ga/ |
H A D | data.py | 104 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)
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/dports/science/py-MDAnalysisTests/MDAnalysisTests-0.19.2/MDAnalysisTests/core/ |
H A D | test_topologyattrs.py | 103 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])),
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/dports/science/py-ase/ase-3.22.0/ase/data/ |
H A D | pubchem.py | 23 def get_atoms(self): member in PubchemData 298 return pubchem_search(*args, **kwargs).get_atoms() 315 conformers = [conformer.get_atoms() for conformer in conformers]
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/dports/science/py-ase/ase-3.22.0/ase/test/db/ |
H A D | test_db2.py | 56 a = c.get_atoms(id) 82 assert len(c.get_atoms(C=1).constraints) == 2 86 f3 = c.get_atoms(C=1).get_forces()
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/dports/science/py-MDAnalysis/MDAnalysis-0.19.2/MDAnalysis/core/ |
H A D | topologyattrs.py | 269 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 …]
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/dports/science/py-ase/ase-3.22.0/ase/gui/ |
H A D | widgets.py | 32 atoms = self.get_atoms() 48 def get_atoms(self): member in Element
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/dports/science/py-gpaw/gpaw-21.6.0/gpaw/analyse/ |
H A D | hirshfeld.py | 65 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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