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/dports/biology/emboss/EMBOSS-6.6.0/emboss/data/TAXONOMY/
H A Dnodes.dmp4 7 | 6 | species | AC | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | |
5 9 | 32199 | species | BA | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | |
7 11 | 1707 | species | CG | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | |
9 14 | 13 | species | DT | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | |
11 17 | 16 | species | MM | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | |
13 19 | 18 | species | PC | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | |
15 21 | 20 | species | PI | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | |
17 23 | 22 | species | SC | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | |
18 24 | 22 | species | SP | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | |
19 25 | 22 | species | SH | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | |
[all …]
/dports/science/py-abipy/abipy-0.9.0/abipy/test_files/
H A DSi_tdep.ssposcar9 0.05000000000000 0.05000000000000 0.05000000000000 site 1 species 1: Si
10 0.05000000000000 0.05000000000000 0.25000000000000 site 2 species 1: Si
11 0.05000000000000 0.05000000000000 0.45000000000000 site 3 species 1: Si
12 0.05000000000000 0.05000000000000 0.65000000000000 site 4 species 1: Si
13 0.05000000000000 0.05000000000000 0.85000000000000 site 5 species 1: Si
14 0.05000000000000 0.25000000000000 0.05000000000000 site 6 species 1: Si
15 0.05000000000000 0.25000000000000 0.25000000000000 site 7 species 1: Si
16 0.05000000000000 0.25000000000000 0.45000000000000 site 8 species 1: Si
17 0.05000000000000 0.25000000000000 0.65000000000000 site 9 species 1: Si
18 0.05000000000000 0.25000000000000 0.85000000000000 site 10 species 1: Si
[all …]
/dports/science/elk/elk-7.2.42/species/
H A Delk.in9 species
17 species
25 species
34 species
43 species
53 species
64 species
75 species
86 species
97 species
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/dports/science/lammps/lammps-stable_29Sep2021/src/KIM/
H A Dkim_interactions.cpp316 if (((species[ia] == words[0]) && (species[ib] == words[1])) in KIM_SET_TYPE_PARAMETERS()
317 || ((species[ib] == words[0]) && (species[ia] == words[1]))) in KIM_SET_TYPE_PARAMETERS()
323 if (species[ia] == words[0]) in KIM_SET_TYPE_PARAMETERS()
333 if (species == "H") return 1; in species_to_atomic_no()
334 else if (species == "He") return 2; in species_to_atomic_no()
335 else if (species == "Li") return 3; in species_to_atomic_no()
337 else if (species == "B") return 5; in species_to_atomic_no()
338 else if (species == "C") return 6; in species_to_atomic_no()
339 else if (species == "N") return 7; in species_to_atomic_no()
340 else if (species == "O") return 8; in species_to_atomic_no()
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/dports/biology/p5-BioPerl/BioPerl-1.7.7/t/data/taxdump/
H A Dnodes.dmp4 9606 | 9605 | species | HS | 5 | 1 | 1 | 1 | 2 | 1 | 1 | 0 | |
25 27591 | 9933 | species | GG | 2 | 1 | 1 | 1 | 2 | 1 | 1 | 0 | |
27 27596 | 9918 | species | BD | 2 | 1 | 1 | 1 | 2 | 1 | 1 | 0 | |
28 27598 | 9859 | species | CS | 2 | 1 | 1 | 1 | 2 | 1 | 1 | 0 | |
38 60720 | 44402 | species | NA | 1 | 1 | 1 | 1 | 5 | 1 | 1 | 0 | |
39 60721 | 44402 | species | NB | 1 | 1 | 1 | 1 | 5 | 1 | 1 | 0 | |
48 77110 | 4415 | species | NU | 4 | 1 | 1 | 1 | 1 | 1 | 1 | 0 | |
49 77111 | 4415 | species | NO | 4 | 1 | 1 | 1 | 1 | 1 | 1 | 0 | |
50 77112 | 4415 | species | NS | 4 | 1 | 1 | 1 | 1 | 1 | 1 | 0 | |
51 77113 | 4415 | species | NL | 4 | 1 | 1 | 1 | 1 | 1 | 1 | 0 | |
[all …]
/dports/games/nazghul/nazghul-0.7.1/src/
H A Dspecies.c59 struct species *species = (struct species *)malloc(sizeof(*species)); in species_new() local
60 assert(species); in species_new()
61 memset(species, 0, sizeof(*species)); in species_new()
99 void species_del(struct species *species) in species_del() argument
101 if (!species) in species_del()
103 if (species->tag) in species_del()
104 free(species->tag); in species_del()
105 if (species->name) in species_del()
106 free(species->name); in species_del()
107 if (species->slots) in species_del()
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/dports/games/stonesoup/crawl-0.27.1/crawl-ref/source/
H A Dspecies.cc35 namespace species namespace
144 species = in random_draconian_colour()
150 return species; in random_draconian_colour()
172 switch (species) in scale_type()
289 return species == SP_GARGOYLE || species == SP_DJINNI; in is_nonliving()
385 if (is_draconian(species) || species == SP_NAGA) in skin_name()
554 return get_species_def(species).d >= get_species_def(species).s; in has_low_str()
579 return 0 <= species && species < NUM_SPECIES; in is_valid()
595 return species[random2(species.size())]; in random_starting_species()
641 species::name(species) + " growth"); in give_level_mutations()
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H A Dspecies.h19 namespace species
35 bool is_elven(species_type species);
36 bool is_orcish(species_type species);
37 bool is_undead(species_type species);
38 bool is_draconian(species_type species);
49 bool has_hair(species_type species);
50 bool has_bones(species_type species);
53 bool has_claws(species_type species);
55 bool can_swim(species_type species);
65 int arm_count(species_type species);
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H A Dng-restr.cc22 if (species::mutation_level(species, MUT_NO_GRASPING) in _banned_combination()
31 if (species::mutation_level(species, MUT_FORLORN) in _banned_combination()
40 if (job == JOB_TRANSMUTER && species::undead_type(species) == US_UNDEAD) in _banned_combination()
62 return !_banned_combination(job, species); in character_is_allowed()
73 if (species::recommends_job(speci, job)) in job_allowed()
84 ASSERT(species::is_starting_species(ng.species)); in weapon_restriction()
89 if (species::mutation_level(ng.species, MUT_NO_GRASPING) && wpn != WPN_UNARMED) in weapon_restriction()
94 if ((ng.species == SP_NAGA || ng.species == SP_VAMPIRE) in weapon_restriction()
103 && species::mutation_level(ng.species, MUT_QUADRUMANOUS))) in weapon_restriction()
111 return species::size(ng.species) >= SIZE_MEDIUM ? CC_UNRESTRICTED in weapon_restriction()
[all …]
H A Dplayable.cc25 return string(species::get_abbrev(species)) + get_job_abbrev(job); in abbr()
51 auto species = species::get_all_species(); in playable_species() local
54 return species; in playable_species()
129 json_append_member(species, "name", json_mkstring(species::name(sp))); in _species_metadata()
130 json_append_member(species, "abbr", json_mkstring(species::get_abbrev(sp))); in _species_metadata()
140 return species; in _species_metadata()
145 JsonNode *species(json_mkarray()); in _species_metadata_array() local
152 return species; in _species_metadata_array()
157 JsonNode *species(json_mkarray()); in _job_recommended_species() local
159 json_append_element(species, json_mkstring(species::name(sp))); in _job_recommended_species()
[all …]
/dports/games/fs2open/fs2open.github.com-release_21_4_1/code/species_defs/
H A Dspecies_defs.cpp182 species = &new_species; in parse_species_tbl()
194 species = &Species_info[i]; in parse_species_tbl()
213 species->default_iff = iLoop; in parse_species_tbl()
220 species->default_iff = 0; in parse_species_tbl()
227 species->default_iff = 0; in parse_species_tbl()
243 species->fred_color.rgb.r = 0; in parse_species_tbl()
244 species->fred_color.rgb.g = 0; in parse_species_tbl()
249 species->fred_color.rgb.r = 0; in parse_species_tbl()
251 species->fred_color.rgb.b = 0; in parse_species_tbl()
256 species->fred_color.rgb.g = 0; in parse_species_tbl()
[all …]
/dports/games/diaspora/Diaspora_R1_Linux/Diaspora/fs2_open/code/species_defs/
H A Dspecies_defs.cpp193 species = &new_species; in parse_species_tbl()
207 species = &Species_info[i]; in parse_species_tbl()
229 species->default_iff = iLoop; in parse_species_tbl()
236 species->default_iff = 0; in parse_species_tbl()
243 species->default_iff = 0; in parse_species_tbl()
259 species->fred_color.rgb.r = 0; in parse_species_tbl()
260 species->fred_color.rgb.g = 0; in parse_species_tbl()
265 species->fred_color.rgb.r = 0; in parse_species_tbl()
267 species->fred_color.rgb.b = 0; in parse_species_tbl()
272 species->fred_color.rgb.g = 0; in parse_species_tbl()
[all …]
/dports/biology/py-python-libsbml/python-libsbml-5.19.0/libsbml_source/examples/csharp/fbc/
H A Dfbc_example1.cs68 species.setId("Node1"); in Main()
70 species.setConstant(false); in Main()
75 species.setId("Node2"); in Main()
84 species.setId("Node3"); in Main()
91 species.setId("Node4"); in Main()
98 species.setId("Node5"); in Main()
105 species.setId("Node6"); in Main()
112 species.setId("Node7"); in Main()
119 species.setId("Node8"); in Main()
126 species.setId("Node0"); in Main()
[all …]
/dports/biology/py-python-libsbml/python-libsbml-5.19.0/libsbml_source/examples/java/fbc/
H A Dfbc_example1.java69 species.setId("Node1"); in main()
71 species.setConstant(false); in main()
76 species.setId("Node2"); in main()
85 species.setId("Node3"); in main()
92 species.setId("Node4"); in main()
99 species.setId("Node5"); in main()
106 species.setId("Node6"); in main()
113 species.setId("Node7"); in main()
120 species.setId("Node8"); in main()
127 species.setId("Node0"); in main()
[all …]
/dports/biology/py-python-libsbml/python-libsbml-5.19.0/libsbml_source/examples/c++/dyn/
H A Ddyn_example1.cpp84 species->setId("C_EC"); in main()
87 species->setConstant(false); in main()
91 species->setId("RTR_M"); in main()
94 species->setConstant(false); in main()
98 species->setId("RCC_M"); in main()
101 species->setConstant(false); in main()
105 species->setId("A_C"); in main()
108 species->setConstant(false); in main()
112 species->setId("AA_C"); in main()
119 species->setId("T"); in main()
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/dports/biology/py-python-libsbml/python-libsbml-5.19.0/libsbml_source/examples/c++/fbc/
H A Dfbc_example1.cpp69 species->setId("Node1"); in main()
72 species->setConstant(false); in main()
76 species->setId("Node2"); in main()
83 species->setId("Node3"); in main()
90 species->setId("Node4"); in main()
97 species->setId("Node5"); in main()
104 species->setId("Node6"); in main()
111 species->setId("Node7"); in main()
118 species->setId("Node8"); in main()
125 species->setId("Node0"); in main()
[all …]
/dports/biology/py-python-libsbml/python-libsbml-5.19.0/libsbml_source/examples/perl/fbc/
H A Dexample1.pl63 $species->setId("Node1");
66 $species->setConstant(0);
70 $species->setId("Node2");
73 $species->setConstant(0);
77 $species->setId("Node3");
80 $species->setConstant(0);
84 $species->setId("Node4");
87 $species->setConstant(0);
91 $species->setId("Node5");
94 $species->setConstant(0);
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/dports/biology/py-python-libsbml/python-libsbml-5.19.0/libsbml_source/examples/ruby/fbc/
H A Dexample1.rb69 species.setId("Node1");
72 species.setConstant(false);
76 species.setId("Node2");
83 species.setId("Node3");
90 species.setId("Node4");
97 species.setId("Node5");
104 species.setId("Node6");
111 species.setId("Node7");
118 species.setId("Node8");
125 species.setId("Node0");
[all …]
/dports/biology/py-python-libsbml/python-libsbml-5.19.0/libsbml_source/examples/c/fbc/
H A Dfbc_example1.c67 Species_t * species; in main() local
109 Species_setId(species, "Node1"); in main()
112 Species_setConstant(species, 0); in main()
116 Species_setId(species, "Node2"); in main()
119 Species_setConstant(species, 0); in main()
123 Species_setId(species, "Node3"); in main()
126 Species_setConstant(species, 0); in main()
130 Species_setId(species, "Node4"); in main()
133 Species_setConstant(species, 0); in main()
137 Species_setId(species, "Node5"); in main()
[all …]
H A Dfbc_example1_v2.c67 Species_t * species; in main() local
131 Species_setId(species, "Node1"); in main()
134 Species_setConstant(species, 0); in main()
138 Species_setId(species, "Node2"); in main()
141 Species_setConstant(species, 0); in main()
145 Species_setId(species, "Node3"); in main()
148 Species_setConstant(species, 0); in main()
152 Species_setId(species, "Node4"); in main()
155 Species_setConstant(species, 0); in main()
159 Species_setId(species, "Node5"); in main()
[all …]
/dports/biology/py-python-libsbml/python-libsbml-5.19.0/libsbml_source/examples/python/fbc/
H A Dfbc_example1.py67 species.setId("Node1")
70 species.setConstant(False)
83 species.setId("Node2")
90 species.setId("Node3")
97 species.setId("Node4")
104 species.setId("Node5")
111 species.setId("Node6")
118 species.setId("Node7")
125 species.setId("Node8")
132 species.setId("Node0")
[all …]
/dports/biology/py-python-libsbml/python-libsbml-5.19.0/libsbml_source/examples/python/dyn/
H A Ddyn_example1.py77 species = model.createSpecies(); variable
78 species.setId("C_EC");
81 species.setConstant(False);
85 species.setId("RTR_M");
88 species.setConstant(False);
92 species.setId("RCC_M");
95 species.setConstant(False);
99 species.setId("A_C");
102 species.setConstant(False);
106 species.setId("AA_C");
[all …]
/dports/devel/p5-Class-AutoClass/Class-AutoClass-1.56/t/
H A Dautoclass.011.class_attributes.t18 is($parent2->species, 'human');
19 $parent1->species('canine');
21 is($parent2->species, 'canine');
27 is($child1->species, 'Dipodomys gravipes','Child declares but does not set species');
33 is($parent1->species, 'canine');
34 is($parent2->species, 'canine');
40 is($parent1->species, 'canine');
41 is($parent2->species, 'canine');
46 is($gchild1->species, 'schmoo');
48 $gchild2->species('fudd');
[all …]
/dports/biology/p5-BioPerl-Run/BioPerl-Run-1.007003/t/data/taxdump/
H A Dnodes.dmp35 9579 | 9578 | species | HA | 5 | 1 | 1 | 1 | 2 | 1 | 1 | 0 | |
36 9580 | 9578 | species | HL | 5 | 1 | 1 | 1 | 2 | 1 | 1 | 0 | |
37 9581 | 9578 | species | HS | 5 | 1 | 1 | 1 | 2 | 1 | 1 | 0 | |
39 9587 | 9578 | species | HK | 5 | 1 | 1 | 1 | 2 | 1 | 1 | 0 | |
40 9588 | 9578 | species | HM | 5 | 1 | 1 | 1 | 2 | 1 | 1 | 0 | |
41 9589 | 9578 | species | HP | 5 | 1 | 1 | 1 | 2 | 1 | 1 | 0 | |
44 9593 | 9592 | species | GG | 5 | 1 | 1 | 1 | 2 | 1 | 1 | 0 | |
48 9597 | 9596 | species | PP | 5 | 1 | 1 | 1 | 2 | 1 | 1 | 0 | |
49 9598 | 9596 | species | PT | 5 | 1 | 1 | 1 | 2 | 1 | 1 | 0 | |
51 9600 | 9599 | species | PP | 5 | 1 | 1 | 1 | 2 | 1 | 1 | 0 | |
[all …]
/dports/biology/py-biopython/biopython-1.79/Bio/Pathway/
H A D__init__.py99 t = tuple(self.species())
116 for species in all_species:
146 def species(self): member in Reaction
196 def species(self): member in System
219 species = self.species()
269 def __init__(self, species=()): argument
280 len(self.species()),
284 def add_species(self, species): argument
292 def source(self, species): argument
300 def sink(self, species): argument
[all …]

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