Split (1)

train · ~2.21M rows (showing the first 156k)

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	src/mcell_react_out.h	.h	2,624	65	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	Unknown
3D	mcellteam/mcell	src/util.c	.c	68,351	2,267	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	C
3D	mcellteam/mcell	src/edge_util.h	.h	1,651	48	/****************************************************************************** * * Copyright (C) 2006-2017,2020 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in...	Unknown
3D	mcellteam/mcell	src/pymcell_helpers.py	.py	48,110	1,298	"""pyMCell helper functions. Currently, this contains a mix of the original pyMCell functions and classes and a set of more refined intuitive functions and classes. Future versions will provide a cleaner separation between these two with the aim of eventually deprecating or removing the original ones. """ import pym...	Python
3D	mcellteam/mcell	src/bng_util.h	.h	540	16	/****************************************************************************** * * 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. * ***********...	Unknown
3D	mcellteam/mcell	src/mcell_structs_shared.h	.h	2,252	74	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	Unknown
3D	mcellteam/mcell	src/argparse.c	.c	14,499	420	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	C
3D	mcellteam/mcell	src/test_api.c	.c	10,649	245	#include "config.h" #include <stdlib.h> #include "mcell_misc.h" #include "mcell_objects.h" #include "mcell_react_out.h" #include "mcell_reactions.h" #include "mcell_release.h" #include "mcell_species.h" #include "mcell_viz.h" #include "mcell_surfclass.h" #define CHECKED_CALL_EXIT(function, error_message) ...	C
3D	mcellteam/mcell	src/strfunc.c	.c	2,766	101	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	C
3D	mcellteam/mcell	src/react_util_nfsim.c	.c	2,931	90	#include "react.h" #include "mcell_reactions.h" #include "react_nfsim.h" #include <stdlib.h> #include <string.h> void calculate_reactant_orientation(struct abstract_molecule reac, struct abstract_molecule reac2, bool *orientation_flag1, ...	C
3D	mcellteam/mcell	src/init.h	.h	5,040	116	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	Unknown
3D	mcellteam/mcell	src/dyngeom_parse_extras.c	.c	13,761	406	#include <stdlib.h> #include <string.h> #include "dyngeom_parse_extras.h" #include "mcell_structs.h" #include "sym_table.h" #include "logging.h" /*************************************************************************** setup_root_obj_inst: This needs to be called before reading every new DG file. In: dg_pars...	C
3D	mcellteam/mcell	src/util.h	.h	10,201	301	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	Unknown
3D	mcellteam/mcell	src/triangle_overlap.c	.c	6,430	201	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	C
3D	mcellteam/mcell	src/minrng.c	.c	857	33	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	C
3D	mcellteam/mcell	src/wall_util.c	.c	98,572	2,961	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	C
3D	mcellteam/mcell	src/mdlparse_aux.h	.h	5,486	199	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	Unknown
3D	mcellteam/mcell	src/minrng.h	.h	833	33	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	Unknown
3D	mcellteam/mcell	src/diffuse_util.c	.c	8,714	285	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	C
3D	mcellteam/mcell	src/mdlparse_util.c	.c	303,068	8,656	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * This program is free software; you can redistribute it and/or * modify it under the ter...	C
3D	mcellteam/mcell	src/logging.h	.h	4,762	143	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	Unknown
3D	mcellteam/mcell	src/diffuse.h	.h	5,439	122	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	Unknown
3D	mcellteam/mcell	src/bng_util.cpp	.cpp	5,120	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. * ***********...	C++
3D	mcellteam/mcell	src/rng.h	.h	1,570	55	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	Unknown
3D	mcellteam/mcell	src/chkpt.c	.c	53,194	1,395	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	C
3D	mcellteam/mcell	src/dyngeom.h	.h	7,408	199	/****************************************************************************** * * Copyright (C) 2006-2014 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	Unknown
3D	mcellteam/mcell	src/argparse.h	.h	629	22	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	Unknown
3D	mcellteam/mcell	src/sym_table.c	.c	12,685	517	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	C
3D	mcellteam/mcell	src/react_nfsim.h	.h	1,547	39	/****************************************************************************** * * Copyright (C) 2006-2015 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	Unknown
3D	mcellteam/mcell	src/map_c.h	.h	1,535	56	/****************************************************************************** * * Copyright (C) 2019 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the LICEN...	Unknown
3D	mcellteam/mcell	src/mcell_react_out.c	.c	24,823	710	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	C
3D	mcellteam/mcell	src/volume_output.h	.h	718	20	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	Unknown
3D	mcellteam/mcell	src/react_output.h	.h	1,886	48	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	Unknown
3D	mcellteam/mcell	src/nfsim_func.h	.h	1,173	39	#ifndef NFSIM_FUNC #define NFSIM_FUNC #include "mcell_structs.h" // typedef double (get_reactant_diffusion)(int a, int b); void initialize_diffusion_function(struct abstract_molecule mol_ptr); void initialize_rxn_diffusion_functions(struct rxn mol_ptr); double get_standard_diffusion(void self); double get_nfsim...	Unknown
3D	mcellteam/mcell	src/mem_util.c	.c	19,418	621	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	C
3D	mcellteam/mcell	src/viz_output.c	.c	101,714	2,583	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	C
3D	mcellteam/mcell	src/data_model_import.py	.py	9,605	249	import pymcell as m import json import pickle import logging from typing import List, Dict, Tuple, Any def read_json_data_model(file_name: str) -> Dict[str, Any]: """ Read a CellBlender data model in JSON format """ with open(file_name, 'r') as f: json_model = f.read() data_model = json.loads(...	Python
3D	mcellteam/mcell	src/triangle_overlap.h	.h	565	18	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	Unknown
3D	mcellteam/mcell	src/mcell_species.h	.h	1,813	61	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	Unknown
3D	mcellteam/mcell	src/dyngeom_parse_extras.h	.h	2,521	71	#ifndef DYNGEOM_PARSE_EXTRAS_H #define DYNGEOM_PARSE_EXTRAS_H #include "mcell_structs.h" #define MAX_INCLUDE_DEPTH 16 struct dyngeom_parse_vars * create_dg_parse(struct volume state); struct dyngeom_parse_vars { struct sym_table_head reg_sym_table; struct sym_table_head obj_sym_table; struct geom_object r...	Unknown
3D	mcellteam/mcell	src/vector.c	.c	18,751	760	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	C
3D	mcellteam/mcell	src/mcell_dyngeom.c	.c	7,248	190	/****************************************************************************** * * Copyright (C) 2006-2014 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	C
3D	mcellteam/mcell	src/test_api.h	.h	236	12	#pragma once #include "mcell_misc.h" #include "mcell_objects.h" #include "mcell_react_out.h" #include "mcell_reactions.h" #include "mcell_release.h" #include "mcell_species.h" #include "mcell_viz.h" void test_api(MCELL_STATE *state);	Unknown
3D	mcellteam/mcell	src/chkpt.h	.h	1,008	32	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	Unknown
3D	mcellteam/mcell	src/dyngeom_yacc.h	.h	3,363	125	/* A Bison parser, made by GNU Bison 3.0.4. / / Bison interface for Yacc-like parsers in C Copyright (C) 1984, 1989-1990, 2000-2015 Free Software Foundation, Inc. This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by t...	Unknown
3D	mcellteam/mcell	src/mcell_run.c	.c	29,264	827	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	C
3D	mcellteam/mcell	src/mcell_surfclass.c	.c	6,043	179	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	C
3D	mcellteam/mcell	src/grid_util.c	.c	112,822	3,068	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	C
3D	mcellteam/mcell	src/react_outc.c	.c	72,235	1,838	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	C
3D	mcellteam/mcell	src/diffuse_util.h	.h	736	20	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	Unknown
3D	mcellteam/mcell	src/dump_state.cpp	.cpp	109,945	2,339	/****************************************************************************** * * Copyright (C) 2019 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the LICEN...	C++
3D	mcellteam/mcell	src/wall_util.h	.h	6,775	161	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	Unknown
3D	mcellteam/mcell	src/dyngeom.c	.c	84,145	2,261	/****************************************************************************** * * Copyright (C) 2006-2014 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	C
3D	mcellteam/mcell	src/mcell_reactions.h	.h	5,696	159	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	Unknown
3D	mcellteam/mcell	src/sym_table.h	.h	1,197	33	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	Unknown
3D	mcellteam/mcell	src/count_util.c	.c	76,361	2,063	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	C
3D	mcellteam/mcell	src/mcell_misc.h	.h	1,480	46	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	Unknown
3D	mcellteam/mcell	src/c_vector.cpp	.cpp	1,351	57	/****************************************************************************** * * Copyright (C) 2019 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the LICEN...	C++
3D	mcellteam/mcell	src/mdlparse_util.h	.h	42,706	943	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	Unknown
3D	mcellteam/mcell	src/react.h	.h	11,259	252	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	Unknown
3D	mcellteam/mcell	src/mcell_dyngeom.h	.h	900	29	/****************************************************************************** * * Copyright (C) 2006-2014 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	Unknown
3D	mcellteam/mcell	src/rng.c	.c	11,797	239	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	C
3D	mcellteam/mcell	src/vol_util.h	.h	5,676	131	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	Unknown
3D	mcellteam/mcell	src/isaac64.c	.c	5,846	156	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	C
3D	mcellteam/mcell	src/pymcell_unittests.py	.py	1,080	34	import unittest import pymcell as m class SimpleSpeciesTestCase(unittest.TestCase): def setUp(self): self.vm1 = m.Species("vm1", 1e-6) self.vm1_down = m.OrientedSpecies(self.vm1, m.Orient.down) self.sm1 = m.Species("sm1", 1e-6, surface=True) self.sm1_up = m.OrientedSpecies(self.sm1,...	Python
3D	mcellteam/mcell	src/sched_util.h	.h	3,264	79	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	Unknown
3D	mcellteam/mcell	src/isaac64.h	.h	3,891	93	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	Unknown
3D	mcellteam/mcell	src/react_trig.c	.c	43,059	1,153	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	C
3D	mcellteam/mcell	src/react_util.h	.h	1,377	35	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	Unknown
3D	mcellteam/mcell	src/vol_util.c	.c	94,050	2,689	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	C
3D	mcellteam/mcell	src/c_vector.h	.h	1,010	41	/****************************************************************************** * * Copyright (C) 2019 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the LICEN...	Unknown
3D	mcellteam/mcell	src/mcell_run.h	.h	1,382	38	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	Unknown
3D	mcellteam/mcell	src/react_outc_nfsim.c	.c	28,885	817	#include "config.h" #include <assert.h> #include <math.h> #include <stdlib.h> #include <string.h> #include "count_util.h" #include "grid_util.h" #include "logging.h" #include "mcell_reactions.h" #include "nfsim_func.h" #include "react.h" #include "react_nfsim.h" #include "react_util.h" #include "rng.h" #include "util...	C
3D	mcellteam/mcell	src/edge_util.c	.c	7,068	224	/****************************************************************************** * * Copyright (C) 2006-2017,2020 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in...	C
3D	mcellteam/mcell	src/mcell_reactions.c	.c	138,355	3,961	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	C
3D	mcellteam/mcell	src/mcell_surfclass.h	.h	1,229	45	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	Unknown
3D	mcellteam/mcell	src/config-nix.h	.h	1,670	45	/****************************************************************************** * * Copyright (C) 2006-2025 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	Unknown
3D	mcellteam/mcell	src/version_info.c	.c	4,037	117	/****************************************************************************** * * Copyright (C) 2006-2025 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	C
3D	mcellteam/mcell	src/mcell_structs.h	.h	86,736	2,049	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	Unknown
3D	mcellteam/mcell	src/viz_output.h	.h	872	27	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	Unknown
3D	mcellteam/mcell	src/vector.h	.h	2,737	70	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	Unknown
3D	mcellteam/mcell	src/sched_util.c	.c	21,046	728	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	C
3D	mcellteam/mcell	src/react_outc_trimol.c	.c	82,041	1,985	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	C
3D	mcellteam/mcell	src/grid_util.h	.h	7,428	168	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	Unknown
3D	mcellteam/mcell	src/mcell_species.c	.c	12,051	355	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	C
3D	mcellteam/mcell	src/rules_py/mcell3r.py	.py	5,071	119	#!/usr/bin/env python3 import os import sys import subprocess import argparse from pathlib import Path def define_console(): parser = argparse.ArgumentParser(description='MCellR runner/postprocessor') parser.add_argument('-v', '--version', action='store_true', help='print program versio...	Python
3D	mcellteam/mcell	src/rules_py/nfsim_python.py	.py	4,194	112	from ctypes import Structure, c_int, c_char_p, c_void_p, cdll, POINTER class NFSim: def __init__(self, libnfsim_c_path, libNFsim_path=None): if libNFsim_path!=None: libNFsim = cdll.LoadLibrary(libNFsim_path) self.lib = cdll.LoadLibrary(libnfsim_c_path) self.lib.setupNFSim_c.argt...	Python
3D	mcellteam/mcell	src/rules_py/write_bngxmle.py	.py	2,628	53	from lxml import etree def create_property_node(parentNode, key, value): if value.startswith('"'): propertyNode = etree.SubElement(parentNode, "Property", id=key, value=value.strip('"'), type="str") else: propertyNode = etree.SubElement(parentNode, "Property", id=key, value=value, type="num") ...	Python
3D	mcellteam/mcell	src/rules_py/write_mdl.py	.py	17,848	453	import json import grammar_definition as gd import argparse import read_mdl try: from StringIO import StringIO except ImportError: from io import StringIO def read_bngljson(bngljson): with open(bngljson, 'r') as f: json_dict = json.load(f) return json_dict def write_raw_section(original_mdl,...	Python
3D	mcellteam/mcell	src/rules_py/small_structures.py	.py	30,264	801	# -- coding: utf-8 -- """ Created on Wed May 30 11:44:17 2012 @author: proto """ from copy import deepcopy import re from random import randint from pyparsing import Word, Suppress, Optional, alphanums, Group, ZeroOrMore from collections import Counter, defaultdict try: from StringIO import StringIO except Impo...	Python
3D	mcellteam/mcell	src/rules_py/postprocess_mcell3r.py	.py	2,253	71	#!/usr/bin/env python import os import sys import shutil def postprocess(mcellr_react_filename, run_seed): print('') print ( ' Postprocessing: %s' % (mcellr_react_filename) ) mcellr_react_dir = './' react_dir = os.path.join(mcellr_react_dir, 'react_data') # if os.path.exists(react_dir): # shutil.rmtr...	Python
3D	mcellteam/mcell	src/rules_py/grammar_definition.py	.py	9,831	178	from pyparsing import Word, Suppress, Optional, alphanums, Group, ZeroOrMore, \ Keyword, Literal, CaselessLiteral, nums, Combine, alphas, nestedExpr, \ cppStyleComment, OneOrMore, quotedString, restOfLine, delimitedList, \ dictOf, Forward, Dict lbrace = Suppress("{") rbrace = Suppress("}") lbracket = Supp...	Python
3D	mcellteam/mcell	src/rules_py/mdlr2mdl.py	.py	11,374	267	#!/usr/bin/env python3 import argparse import read_mdl import write_mdl from subprocess import call import split_bngxml import re from nfsim_python import NFSim import os import read_bngxml import write_bngxmle as writeBXe import sys # set by argument FAIL_ON_ERROR = False def define_console(): parser = argpars...	Python
3D	mcellteam/mcell	src/rules_py/read_mdl.py	.py	14,763	375	from __future__ import print_function from grammar_definition import statementGrammar, grammar, species_definition import sys try: from StringIO import StringIO except ImportError: from io import StringIO import small_structures as st from subprocess import call from collections import defaultdict import write...	Python
3D	mcellteam/mcell	src/rules_py/split_bngxml.py	.py	864	33	import argparse def defineConsole(): """ input console options """ parser = argparse.ArgumentParser(description='SBML to BNGL translator') parser.add_argument('-i', '--input', type=str, help='input MDLr file', required=True) return parser def extractSeedBNG(xmlname): with open(xmlname, '...	Python
3D	mcellteam/mcell	src/rules_py/read_bngxml.py	.py	13,302	374	# -- coding: utf-8 -- """ Created on Mon Nov 19 14:28:16 2012 @author: proto """ from lxml import etree import small_structures as st try: from cStringIO import StringIO except ImportError: from io import StringIO # http://igraph.sourceforge.net/documentation.html # ------------------------------------------...	Python
3D	mcellteam/mcell	appveyor_windows/mdlparse.c	.c	301,064	6,571	/* A Bison parser, made by GNU Bison 3.0.4. / / Bison implementation for Yacc-like parsers in C Copyright (C) 1984, 1989-1990, 2000-2015 Free Software Foundation, Inc. This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by...	C
3D	mcellteam/mcell	appveyor_windows/mdlparse.h	.h	10,323	392	/* A Bison parser, made by GNU Bison 3.0.4. / / Bison interface for Yacc-like parsers in C Copyright (C) 1984, 1989-1990, 2000-2015 Free Software Foundation, Inc. This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by t...	Unknown
3D	mcellteam/mcell	appveyor_windows/config.h	.h	22,216	713	/****************************************************************************** * * Copyright (C) 2006-2017 by * The Salk Institute for Biological Studies and * Pittsburgh Supercomputing Center, Carnegie Mellon University * * Use of this source code is governed by an MIT-style * license that can be found in the ...	Unknown
3D	mcellteam/mcell	appveyor_windows/version.h	.h	1,949	42	/**************************************************************** * This file is automatically generated. Do not edit it. * version.h updated at Wed Feb 5 12:46:27 PM PST 2025 on huxley by bkaynak ***************************************************************/ / Program version info */ #define MCELL_VERSION "4....	Unknown

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