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/dports/science/py-pymatgen/pymatgen-2022.0.15/pymatgen/optimization/tests/
H A Dtest_neighbors.py36 all_coords=np.array(points),
46 all_coords=np.array(points),
55 all_coords=np.array(points),
/dports/science/py-pymatgen/pymatgen-2022.0.15/pymatgen/io/
H A Datat.py120 all_coords = []
126 all_coords.append(scaled_coords)
153 return Structure(lattice, all_species, all_coords)
/dports/science/py-dipy/dipy-1.4.1/dipy/tracking/
H A Dlife.py295 all_coords = np.concatenate(transformed_streamline)
296 unique_idx = unique_rows(np.round(all_coords))
357 all_coords = np.concatenate(streamline)
358 vox_coords = unique_rows(np.round(all_coords).astype(np.intp))
359 del all_coords
/dports/games/freeorion/freeorion-0.4.10.2/default/python/universe_generation/
H A Dstarnames.py62 all_coords = [(pos[0], pos[1]) for pos in positions]
64 clusters[0] = assign_clusters(all_coords, centers) # assign clusters based on init centers
68 recalc_centers(centers, all_coords, clusters[old_c]) # get new centers
69 … clusters[1 - old_c] = assign_clusters(all_coords, centers) # assign clusters based on new centers
/dports/science/berkeleygw/BGW-2.0.0/Common/qhull/
H A Dlibtile_qhull_find.c252 coordT *all_coords; in init_barycentric_transforms() local
270 all_coords = qh first_point; /* (npts,ndim) */ in init_barycentric_transforms()
285 last_coord = all_coords + last_vertex*(ndim+1); in init_barycentric_transforms()
291 T[i*ndim + j] = all_coords[jvertex*(ndim+1) + i] - (*last_coord); in init_barycentric_transforms()
304 printf(" %11.6f",all_coords[jvertex*(ndim+1) + ii]); in init_barycentric_transforms()
/dports/science/openbabel/openbabel-3.1.1/src/
H A Dconfsearch.cpp113 std::vector<vector3> GetHeavyAtomCoords(const std::vector<vector3> &all_coords);
265 std::vector<vector3> OBDiversePoses::GetHeavyAtomCoords(const std::vector<vector3> &all_coords) { in GetHeavyAtomCoords() argument
269 v_hvyatoms.push_back(all_coords[a]); in GetHeavyAtomCoords()
280 std::vector<vector3> GetHeavyAtomCoords(const OBMol* mol, const std::vector<vector3> &all_coords) { in GetHeavyAtomCoords() argument
284 v_hvyatoms.push_back(all_coords[a]); in GetHeavyAtomCoords()
/dports/science/py-MDAnalysisTests/MDAnalysisTests-0.19.2/MDAnalysisTests/lib/
H A Dtest_nsgrid.py171 all_coords = np.concatenate([points, query])
172 lmax = all_coords.max(axis=0)
173 lmin = all_coords.min(axis=0)
/dports/graphics/R-cran-pROC/pROC/R/
H A Dcoords.R333 …all_coords <- roc.utils.calc.coords(roc, rep(NA, length(roc$sensitivities)), roc$sensitivities, ro… functionVar
334 input_values <- all_coords[, input]
335 se <- all_coords[, "sensitivity"]
336 sp <- all_coords[, "specificity"]
337 thr <- all_coords[, "threshold"]
/dports/devel/py-xarray/xarray-0.20.1/xarray/core/
H A Dalignment.py282 all_coords = defaultdict(list)
287 all_coords[dim].append(obj.coords[dim])
327 index = maybe_coerce_to_str(index.to_pandas_index(), all_coords[dim])
330 index = all_coords[dim][0]
/dports/science/py-MDAnalysis/MDAnalysis-0.19.2/MDAnalysis/lib/
H A Dpkdtree.py148 self.all_coords = np.concatenate([self.coords, self.aug])
149 self.ckdt = cKDTree(self.all_coords, leafsize=self.leafsize)
H A Ddistances.py693 all_coords = np.concatenate([reference, configuration])
694 lmax = all_coords.max(axis=0)
695 lmin = all_coords.min(axis=0)
H A Dnsgrid.pyx762 lmax = all_coords.max(axis=0)
763 lmin = all_coords.min(axis=0)
766 shift = all_coords.copy()
/dports/math/R-cran-igraph/igraph/R/
H A Dlayout.R97 all_coords <- merge_coords( functionVar
102 all_coords[ unlist(sapply(comps, vertex_attr, "id")), ] <- all_coords[]
103 result <- all_coords
/dports/science/py-pymatgen/pymatgen-2022.0.15/pymatgen/core/
H A Dlattice.py1494 all_coords=cart_coords,
1560 all_coords=cart_coords,
1881 all_coords: np.ndarray,
1929 image_offsets = lattice.get_fractional_coords(all_coords)
1950 ind = np.arange(len(all_coords))
1961 valid_coords = all_coords # type: ignore
H A Dstructure.py852 all_coords = [] # type: List[List[float]]
857 all_coords.extend(cc)
861 return cls(latt, all_sp, all_coords, site_properties=all_site_properties)
953 all_coords = [] # type: List[List[float]]
959 all_coords.extend(cc)
967 return cls(latt, all_sp, all_coords, site_properties=all_site_properties)
2945 all_coords: List[ArrayLike] = []
2968 if len(all_coords) == 0:
2972 lattice.get_fractional_coords(all_coords),
2984 all_coords.extend(new_coords)
[all …]
H A Dsurface.py968 all_coords = []
972 all_coords.extend(fcoords)
974 slab = Structure(new_lattice, species * nlayers_slab, all_coords, site_properties=props)
/dports/x11/xscreensaver/xscreensaver-5.44/hacks/
H A Dpetri.c620 static const XPoint all_coords[] = {{-1, -1}, {-1, 1}, {1, -1}, {1, 1}, in update() local
631 coords = all_coords; in update()
635 coords = &all_coords[4]; in update()
/dports/science/py-pymatgen/pymatgen-2022.0.15/pymatgen/core/tests/
H A Dtest_lattice.py535 all_coords=np.array(points),
545 all_coords=np.array(points),
556 all_coords=np.array(points),
/dports/science/dalton/dalton-66052b3af5ea7225e31178bf9a8b031913c72190/external/pelib/src/
H A Dpelib_options.F90214 real(rp), dimension(:,:), allocatable, save :: all_coords variable
H A Dpelib.F902056 allocate(all_coords(3,nnucs+nsites))
2059 all_coords(1:3,1:nnucs) = Rm(1:3,1:nnucs)
2062 all_coords(1:3,nnucs+1:nnucs+nsites) = Rs(1:3,1:nsites)
2066 call fixtes(all_coords, all_charges)
/dports/science/py-pymatgen/pymatgen-2022.0.15/pymatgen/analysis/
H A Dphase_diagram.py1142 all_coords = []
1151 for di in all_coords:
1161 all_coords.append(res)
1162 return all_coords
1197 all_coords = []
1200 all_coords.append(v)
2022 all_coords = labels.keys()
2023 miny = min([c[1] for c in all_coords])
/dports/x11/xlockmore/xlockmore-5.67/modes/
H A Dpetri.c978 static XPoint all_coords[] = {{-1, -1}, {-1, 1}, {1, -1}, {1, 1}, in draw_petri() local
989 coords = all_coords; in draw_petri()
993 coords = &all_coords[4]; in draw_petri()
/dports/graphics/R-cran-pROC/pROC/man/
H A Droc.Rd23 ret = c("roc", "coords", "all_coords"), ...)
30 roc_(data, response, predictor, ret = c("roc", "coords", "all_coords"), ...)
114 all the coordinates at all thresholds (\dQuote{all_coords}) or the
/dports/science/py-pymatgen/pymatgen-2022.0.15/pymatgen/analysis/tests/
H A Dtest_local_env.py189 all_coords = np.sort([x["site"].coords for x in site.values()], axis=0)
192 self.assertArrayAlmostEqual(all_coords, by_one_coords)
/dports/science/py-pymatgen/pymatgen-2022.0.15/pymatgen/analysis/defects/
H A Dutils.py878 def __init__(self, lattice, frac_coords, polyhedron_indices, all_coords, name=None): argument
889 self.polyhedron_coords = np.array(all_coords)[list(polyhedron_indices), :]

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