keyword stringclasses 7
values | repo_name stringlengths 8 98 | file_path stringlengths 4 244 | file_extension stringclasses 29
values | file_size int64 0 84.1M | line_count int64 0 1.6M | content stringlengths 1 84.1M ⌀ | language stringclasses 14
values |
|---|---|---|---|---|---|---|---|
3D | mcellteam/mcell | libmcell/generated/gen_molecule.h | .h | 6,553 | 188 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | Unknown |
3D | mcellteam/mcell | libmcell/generated/gen_instantiation.h | .h | 4,550 | 103 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | Unknown |
3D | mcellteam/mcell | libmcell/generated/gen_count_term.cpp | .cpp | 13,921 | 347 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | C++ |
3D | mcellteam/mcell | libmcell/generated/gen_run_utils.h | .h | 836 | 34 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | Unknown |
3D | mcellteam/mcell | libmcell/generated/gen_observables.cpp | .cpp | 8,079 | 179 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | C++ |
3D | mcellteam/mcell | libmcell/generated/gen_molecule_release_info.h | .h | 3,700 | 103 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | Unknown |
3D | mcellteam/mcell | libmcell/generated/gen_surface_property.h | .h | 4,312 | 118 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | Unknown |
3D | mcellteam/mcell | libmcell/generated/gen_molecule_release_info.cpp | .cpp | 6,397 | 175 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | C++ |
3D | mcellteam/mcell | libmcell/generated/gen_instantiation.cpp | .cpp | 10,925 | 227 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | C++ |
3D | mcellteam/mcell | libmcell/generated/gen_geometry_utils.cpp | .cpp | 2,190 | 33 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | C++ |
3D | mcellteam/mcell | libmcell/generated/gen_component.cpp | .cpp | 5,744 | 169 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | C++ |
3D | mcellteam/mcell | libmcell/generated/gen_config.h | .h | 18,852 | 439 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | Unknown |
3D | mcellteam/mcell | libmcell/generated/gen_bngl_utils.cpp | .cpp | 1,173 | 29 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | C++ |
3D | mcellteam/mcell | libmcell/generated/gen_data_utils.cpp | .cpp | 1,011 | 29 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | C++ |
3D | mcellteam/mcell | libmcell/generated/gen_surface_region.h | .h | 6,158 | 152 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | Unknown |
3D | mcellteam/mcell | libmcell/generated/gen_reaction_info.h | .h | 3,426 | 122 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | Unknown |
3D | mcellteam/mcell | libmcell/generated/gen_warnings.h | .h | 3,671 | 101 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | Unknown |
3D | mcellteam/mcell | libmcell/generated/gen_reaction_rule.h | .h | 7,557 | 188 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | Unknown |
3D | mcellteam/mcell | libmcell/generated/gen_surface_region.cpp | .cpp | 12,804 | 340 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | C++ |
3D | mcellteam/mcell | libmcell/generated/gen_rng_state.h | .h | 6,207 | 183 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | Unknown |
3D | mcellteam/mcell | libmcell/generated/gen_constants.cpp | .cpp | 12,187 | 129 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | C++ |
3D | mcellteam/mcell | libmcell/generated/gen_molecule.cpp | .cpp | 6,636 | 159 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | C++ |
3D | mcellteam/mcell | libmcell/generated/gen_count_term.h | .h | 7,843 | 202 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | Unknown |
3D | mcellteam/mcell | libmcell/generated/gen_bngl_utils.h | .h | 888 | 33 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | Unknown |
3D | mcellteam/mcell | libmcell/generated/gen_complex.cpp | .cpp | 8,882 | 183 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | C++ |
3D | mcellteam/mcell | libmcell/generated/gen_geometry_object.h | .h | 9,590 | 220 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | Unknown |
3D | mcellteam/mcell | libmcell/generated/gen_config.cpp | .cpp | 24,863 | 425 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | C++ |
3D | mcellteam/mcell | libmcell/generated/gen_run_utils.cpp | .cpp | 1,231 | 30 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | C++ |
3D | mcellteam/mcell | libmcell/generated/gen_elementary_molecule.cpp | .cpp | 7,920 | 194 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | C++ |
3D | mcellteam/mcell | libmcell/generated/gen_viz_output.h | .h | 4,969 | 135 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | Unknown |
3D | mcellteam/mcell | libmcell/generated/gen_chkpt_vol_mol.h | .h | 3,502 | 108 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | Unknown |
3D | mcellteam/mcell | libmcell/generated/gen_viz_output.cpp | .cpp | 6,918 | 180 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | C++ |
3D | mcellteam/mcell | libmcell/generated/gen_wall_wall_hit_info.h | .h | 3,281 | 97 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | Unknown |
3D | mcellteam/mcell | libmcell/generated/gen_elementary_molecule.h | .h | 4,887 | 121 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | Unknown |
3D | mcellteam/mcell | libmcell/generated/gen_rng_state.cpp | .cpp | 7,192 | 234 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | C++ |
3D | mcellteam/mcell | libmcell/generated/gen_region.cpp | .cpp | 6,362 | 193 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | C++ |
3D | mcellteam/mcell | libmcell/generated/gen_wall_wall_hit_info.cpp | .cpp | 4,383 | 145 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | C++ |
3D | mcellteam/mcell | libmcell/generated/gen_release_site.cpp | .cpp | 17,205 | 391 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | C++ |
3D | mcellteam/mcell | libmcell/generated/gen_vectors_bind.cpp | .cpp | 7,658 | 140 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | C++ |
3D | mcellteam/mcell | libmcell/generated/gen_surface_class.cpp | .cpp | 8,048 | 214 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | C++ |
3D | mcellteam/mcell | libmcell/generated/gen_warnings.cpp | .cpp | 4,852 | 131 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | C++ |
3D | mcellteam/mcell | libmcell/generated/gen_mol_wall_hit_info.cpp | .cpp | 5,381 | 127 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | C++ |
3D | mcellteam/mcell | libmcell/generated/gen_color.cpp | .cpp | 5,431 | 167 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | C++ |
3D | mcellteam/mcell | libmcell/generated/gen_count.cpp | .cpp | 9,749 | 204 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | C++ |
3D | mcellteam/mcell | libmcell/generated/gen_component_type.h | .h | 3,286 | 92 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | Unknown |
3D | mcellteam/mcell | libmcell/generated/gen_geometry_utils.h | .h | 1,179 | 37 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | Unknown |
3D | mcellteam/mcell | libmcell/generated/gen_elementary_molecule_type.h | .h | 7,126 | 173 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | Unknown |
3D | mcellteam/mcell | libmcell/generated/gen_observables.h | .h | 3,326 | 87 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | Unknown |
3D | mcellteam/mcell | libmcell/generated/gen_wall.h | .h | 5,454 | 157 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | Unknown |
3D | mcellteam/mcell | libmcell/generated/gen_initial_surface_release.h | .h | 4,261 | 118 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | Unknown |
3D | mcellteam/mcell | libmcell/generated/gen_geometry_object.cpp | .cpp | 17,578 | 441 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | C++ |
3D | mcellteam/mcell | libmcell/generated/gen_component.h | .h | 3,986 | 119 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | Unknown |
3D | mcellteam/mcell | libmcell/generated/gen_release_site.h | .h | 11,091 | 285 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | Unknown |
3D | mcellteam/mcell | libmcell/generated/gen_subsystem.cpp | .cpp | 12,723 | 272 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | C++ |
3D | mcellteam/mcell | libmcell/generated/gen_elementary_molecule_type.cpp | .cpp | 10,843 | 221 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | C++ |
3D | mcellteam/mcell | libmcell/generated/gen_region.h | .h | 4,191 | 120 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | Unknown |
3D | mcellteam/mcell | libmcell/generated/gen_initial_surface_release.cpp | .cpp | 6,024 | 168 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | C++ |
3D | mcellteam/mcell | libmcell/generated/gen_introspection.cpp | .cpp | 5,065 | 80 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | C++ |
3D | mcellteam/mcell | libmcell/generated/gen_reaction_info.cpp | .cpp | 8,115 | 160 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | C++ |
3D | mcellteam/mcell | libmcell/generated/gen_data_utils.h | .h | 792 | 33 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | Unknown |
3D | mcellteam/mcell | libmcell/generated/gen_base_chkpt_mol.cpp | .cpp | 6,779 | 208 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | C++ |
3D | mcellteam/mcell | libmcell/generated/gen_release_pattern.h | .h | 4,921 | 135 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | Unknown |
3D | mcellteam/mcell | libmcell/generated/gen_mol_wall_hit_info.h | .h | 3,053 | 105 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | Unknown |
3D | mcellteam/mcell | libmcell/generated/gen_notifications.cpp | .cpp | 7,930 | 179 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | C++ |
3D | mcellteam/mcell | libmcell/generated/gen_complex.h | .h | 4,645 | 124 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | Unknown |
3D | mcellteam/mcell | libmcell/generated/gen_surface_property.cpp | .cpp | 6,459 | 167 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | C++ |
3D | mcellteam/mcell | libmcell/generated/gen_notifications.h | .h | 6,561 | 165 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | Unknown |
3D | mcellteam/mcell | libmcell/generated/gen_species.cpp | .cpp | 12,379 | 246 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | C++ |
3D | mcellteam/mcell | libmcell/generated/gen_release_pattern.cpp | .cpp | 6,584 | 167 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | C++ |
3D | mcellteam/mcell | libmcell/generated/gen_subsystem.h | .h | 5,134 | 116 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | Unknown |
3D | mcellteam/mcell | libmcell/generated/gen_constants.h | .h | 8,439 | 294 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | Unknown |
3D | mcellteam/mcell | libmcell/generated/gen_model.cpp | .cpp | 46,902 | 564 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | C++ |
3D | mcellteam/mcell | libmcell/generated/gen_chkpt_surf_mol.cpp | .cpp | 9,755 | 291 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | C++ |
3D | mcellteam/mcell | libmcell/generated/gen_count.h | .h | 5,416 | 153 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | Unknown |
3D | mcellteam/mcell | libmcell/generated/gen_reaction_rule.cpp | .cpp | 14,487 | 275 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | C++ |
3D | mcellteam/mcell | libmcell/generated/gen_chkpt_vol_mol.cpp | .cpp | 6,655 | 215 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | C++ |
3D | mcellteam/mcell | libmcell/generated/gen_model.h | .h | 6,627 | 140 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | Unknown |
3D | mcellteam/mcell | libmcell/generated/gen_base_chkpt_mol.h | .h | 5,717 | 166 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | Unknown |
3D | mcellteam/mcell | libmcell/generated/gen_color.h | .h | 4,688 | 149 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | Unknown |
3D | mcellteam/mcell | libmcell/generated/gen_chkpt_surf_mol.h | .h | 6,163 | 173 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | Unknown |
3D | mcellteam/mcell | libmcell/generated/gen_species.h | .h | 6,693 | 167 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | Unknown |
3D | mcellteam/mcell | libmcell/generated/gen_wall.cpp | .cpp | 5,871 | 159 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | C++ |
3D | mcellteam/mcell | libmcell/generated/gen_names.h | .h | 22,427 | 411 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | Unknown |
3D | mcellteam/mcell | libmcell/generated/gen_surface_class.h | .h | 3,802 | 101 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | Unknown |
3D | mcellteam/mcell | libmcell/generated/gen_introspection.h | .h | 2,503 | 62 | /******************************************************************************
*
* Copyright (C) 2021 by
* The Salk Institute for Biological Studies
*
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
***********... | Unknown |
3D | mcellteam/mcell | libmcell/definition/gen.py | .py | 82,735 | 2,270 | #!/usr/bin/env python3
"""
Copyright (C) 2020 by
The Salk Institute for Biological Studies
Use of this source code is governed by an MIT-style
license that can be found in the LICENSE file or at
https://opensource.org/licenses/MIT.
"""
# TODO: change 'items' to 'attributes'?
# TODO: cleanup const/nonconst handling
#... | Python |
3D | mcellteam/mcell | libmcell/definition/constants.py | .py | 6,512 | 225 | """
Copyright (C) 2020 by
The Salk Institute for Biological Studies
Use of this source code is governed by an MIT-style
license that can be found in the LICENSE file or at
https://opensource.org/licenses/MIT.
"""
# categories, defines input file names and
# also ordering in documentation
CATEGORY_CONSTANTS = 'const... | Python |
3D | mcellteam/mcell | libmcell/definition/doc.py | .py | 7,463 | 213 | """
Copyright (C) 2021 by
The Salk Institute for Biological Studies
Use of this source code is governed by an MIT-style
license that can be found in the LICENSE file or at
https://opensource.org/licenses/MIT.
"""
import sys
import os
import yaml
from constants import *
from gen import indent_and_fix_rst_chars, yaml... | Python |
3D | mcellteam/mcell | docs/dynamic_geometry.md | .md | 12,643 | 262 | Dynamic Geometry
=========================================================================
Overview
-------------------------------------------------------------------------
Before we get into how the algorithm works, here is how it is used:
Mesh "snapshots" are referenced in a text file similar to how variable rate... | Markdown |
3D | jibikbam/CNN-3D-images-Tensorflow | simpleCNN_MRI.py | .py | 4,962 | 111 | # A simple CNN to predict certain characteristics of the human subject from MRI images.
# 3d convolution is used in each layer.
# Reference: https://www.tensorflow.org/get_started/mnist/pros, http://blog.naver.com/kjpark79/220783765651
# Adjust needed for your dataset e.g., max pooling, convolution parameters, training... | Python |
3D | jibikbam/CNN-3D-images-Tensorflow | input_3Dimage.py | .py | 2,281 | 75 | # A script to load images and make batch.
# Dependency: 'nibabel' to load MRI (NIFTI) images
# Reference: http://blog.naver.com/kjpark79/220783765651
import os
import tensorflow as tf
import numpy as np
import matplotlib.pyplot as plt
import random
import nibabel as nib
FLAGS = tf.app.flags.FLAGS
FLAGS.width = 256
FL... | Python |
3D | PattanaikL/ts_gen | use_trained_model.ipynb | .ipynb | 27,888 | 460 | {
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### This notebook walks you through how to use the pretrained model to generate your own transition state guesses. If using your own model and data, replace the model and data paths with your own"
]
},
{
"cell_type": "markdow... | Unknown |
3D | PattanaikL/ts_gen | train.py | .py | 11,168 | 317 | from __future__ import print_function
import os, sys, time, random
import tensorflow as tf
from tensorflow.python.client import timeline
import numpy as np
sys.path.insert(0, "model/")
from util import render_pymol
from G2C import G2C
# rdkit
from rdkit import Chem, Geometry
from optparse import OptionParser
parse... | Python |
3D | PattanaikL/ts_gen | model/GNN.py | .py | 3,817 | 92 | from __future__ import print_function
import tensorflow as tf
import numpy as np
def GNN(V_init, E_init, sizes, iterations=3, edge_layers = 2,
edge_hidden = 100, node_layers = 2, node_hidden = 100, act=tf.nn.relu):
""" Graph neural network with node & edge updates """
V, E = V_init, E_init
# Get dimen... | Python |
3D | PattanaikL/ts_gen | model/G2C.py | .py | 13,479 | 343 | from __future__ import print_function
import os, time
import numpy as np
import tensorflow as tf
import GNN
class G2C:
def __init__(self, num_gpus=1, max_size=29, build_backprop=True,
node_features=7, edge_features=3, layers=2, hidden_size=128, iterations=3, input_data=None):
""" Initialize a Gra... | Python |
3D | PattanaikL/ts_gen | model/__init__.py | .py | 2 | 2 | Python | |
3D | PattanaikL/ts_gen | model/util.py | .py | 835 | 31 | from rdkit import Chem
import pymol
import tempfile, os
import numpy as np
def render_pymol(mol, img_file, width=300, height=200):
""" Render rdkit molecule with a pymol ball & stick representation """
target = "all"
pymol.cmd.delete(target)
pymol.cmd.set("max_threads", 4)
pymol.cmd.viewport(width... | Python |
3D | marcdcfischer/PUNet | src/__init__.py | .py | 0 | 0 | null | Python |
3D | marcdcfischer/PUNet | src/main.py | .py | 5,411 | 90 | import argparse
from argparse import ArgumentParser
import pytorch_lightning as pl
from typing import Type
import pathlib as plb
from src.utils import aws
from src.data.loader_monai import BasicDataModule
from src.modules.instruction_model import InstructionModel as Model
from src.modules.instruction_model_simple impor... | Python |
3D | marcdcfischer/PUNet | src/modules/__init__.py | .py | 0 | 0 | null | Python |
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