| /dports/biology/dsr-pdb/dsr-pdb-1.0.3/lib/ |
| H A D | Residue_data.cc | 204 …TOMS( Residue::AL_CB, Residue::AL_1HB, Residue::AL_2HB, Residue::AL_CG, Residue::AL_CD1, Residue::… in get_residue_initialization_data()
230 …TOMS( Residue::AL_CB, Residue::AL_1HB, Residue::AL_2HB, Residue::AL_CG, Residue::AL_CD1, Residue::… in get_residue_initialization_data()
231 …Residue::AL_CE3, Residue::AL_1HE, Residue::AL_3HE, Residue::AL_CZ2, Residue::AL_CZ3, Residue::AL_2… in get_residue_initialization_data()
288 …Residue::AL_CB, Residue::AL_1HB, Residue::AL_2HB, Residue::AL_CG, Residue::AL_1HG, Residue::AL_2HG… in get_residue_initialization_data()
305 …TOMS( Residue::AL_CB, Residue::AL_1HB, Residue::AL_2HB, Residue::AL_CG, Residue::AL_CD1, Residue::… in get_residue_initialization_data()
354 …ATOMS(Residue::AL_CB, Residue::AL_1HB, Residue::AL_2HB, Residue::AL_CG, Residue::AL_1HG, Residue::… in get_residue_initialization_data()
355 …Residue::AL_CE, Residue::AL_1HE, Residue::AL_2HE, Residue::AL_NZ, Residue::AL_1HZ, Residue::AL_2HZ… in get_residue_initialization_data()
398 …TOMS(Residue::AL_CB, Residue::AL_HB, Residue::AL_CG1, Residue::AL_CG2, Residue::AL_1HG1, Residue::… in get_residue_initialization_data()
419 …ATOMS(Residue::AL_CB, Residue::AL_1HB, Residue::AL_2HB, Residue::AL_CG, Residue::AL_ND1, Residue::… in get_residue_initialization_data()
445 …Residue::AL_CB, Residue::AL_1HB, Residue::AL_2HB, Residue::AL_CG, Residue::AL_1HG, Residue::AL_2HG… in get_residue_initialization_data()
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| H A D | Residue.cc | 57 bool Residue::has_atom(Residue::Atom_label ial) const { in has_atom()
71 bool Residue::can_have_atom(Residue::Atom_label ial) const { in can_have_atom()
88 const Atom &Residue::atom(Residue::Atom_label al) const { in atom()
102 void Residue::set_atom(Residue::Atom_label ial, const Atom &a) { in set_atom()
135 Residue::Type Residue::type() const { in type()
204 void Residue::set_index(Residue::Index i) { in set_index()
221 Atom::Index Residue::index(Residue::Atom_label al) const { in index()
245 Residue::Residue(Type al): atoms_(20), label_(al){ in Residue() function in dsrpdb::Residue
280 Residue::Atom_label Residue::atom_label(const char *nm) { in atom_label()
333 Residue::Type Residue::type(const std::string &s){ in type()
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| H A D | Residue_data.h | 14 typedef std::pair<Residue::Atom_label, Residue::Atom_label> Possible_bond;
21 std::vector<Residue::Atom_label> atoms;
23 std::vector<Residue::Atom_label> extremes;
34 Residue::Atom_label l;
44 Residue::Atom_label* atms_;
45 Residue::Atom_label* bnds_;
46 Residue::Atom_label* extr_;
55 Residue::Atom_label l;
56 Residue::Atom_label lr;
71 Residue_init_data get_residue_initialization_data(Residue::Type rl);
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| H A D | Protein.cc | 27 static Residue dummy_residue_;
44 std::vector<Residue::Type> Protein::sequence() const{ in sequence()
45 std::vector<Residue::Type> ret(residues_.size()); in sequence()
76 void Protein::new_residue(const Residue &res){ in new_residue()
83 if (!residues_.back().has_atom(Residue::AL_C)) { in new_residue()
89 if (!residues_.back().has_atom(Residue::AL_N)) { in new_residue()
112 const Residue &r= residues_[i];
133 const Residue &r= residues_[i];
145 const Residue &aa= *it;
148 if (it->first == Residue::AL_C || it->first== Residue::AL_CA || it->first== Residue::AL_N) {
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| /dports/math/cado-nfs/cado-nfs-f4284e2391121b2bfb97bc4880b6273c7250dc2f/utils/ |
| H A D | mod64.hpp | 31 Residue(const Residue &&s) : r(s.r) {} in Residue() function in Modulus64::Residue
73 Residue *ptr = static_cast<Residue *>(t); in newArray()
120 void sub (Residue &r, const Residue &a, const Residue &b) const { in sub()
129 void mul (Residue &r, const Residue &a, const Residue &b) const { in mul()
183 void V_dadd (Residue &r, const Residue &a, const Residue &b, in V_dadd()
193 void V_dbl (Residue &r, const Residue &a, const Residue &two) const { in V_dbl()
200 bool div3 (Residue &, const Residue &) const;
201 bool div5 (Residue &, const Residue &) const;
216 void V (Residue &r, Residue *rp1, const Residue &b,
221 bool inv (Residue &, const Residue &) const;
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| H A D | modredc64.hpp | 35 Residue(const Residue &&s) : r(s.r) {} in Residue() function in ModulusREDC64::Residue
115 Residue *ptr = static_cast<Residue *>(t); in newArray()
181 void sub (Residue &r, const Residue &a, const Residue &b) const { in sub()
193 void mul (Residue &r, const Residue &a, const Residue &b) const { in mul()
232 void V_dadd (Residue &r, const Residue &a, const Residue &b, in V_dadd()
242 void V_dbl (Residue &r, const Residue &a, const Residue &two) const { in V_dbl()
251 bool div3 (Residue &, const Residue &) const;
252 bool div5 (Residue &, const Residue &) const;
264 void V (Residue &r, Residue *rp1, const Residue &b,
269 bool inv (Residue &, const Residue &) const;
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| H A D | mod_mpz_new.hpp | 36 Residue(const Modulus &m, const Residue &s) { in Residue() function in ModulusMPZ::Residue
43 Residue(Residue &&s) : r(s.r) { in Residue() function in ModulusMPZ::Residue
46 Residue(Residue const & s) = delete;
47 Residue& operator=(Residue &&s) { in operator =()
272 void add (Residue &r, const Residue &a, const Residue &b) const { in add()
311 void sub (Residue &r, const Residue &a, const Residue &b) const { in sub()
350 void mul (Residue &r, const Residue &a, const Residue &b) const { in mul()
416 void V_dadd (Residue &r, const Residue &a, const Residue &b, in V_dadd()
426 void V_dbl (Residue &r, const Residue &a, const Residue &two) const { in V_dbl()
451 void V (Residue &r, Residue *rp1, const Residue &b,
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| H A D | modredc126.hpp | 116 void redc1 (Residue &r, const Residue &s) const in redc1()
146 Residue *ptr = static_cast<Residue *>(t); in newArray()
188 void swap (Residue &a, Residue &b) const { in swap()
214 void add (Residue &r, const Residue &a, const Residue &b) const { in add()
221 void sub (Residue &r, const Residue &a, const Residue &b) const { in sub()
305 void mul (Residue &r, const Residue &a, const Residue &b) const { in mul()
562 bool divn (Residue &r, const Residue &a, in divn()
623 void V_dadd (Residue &r, const Residue &a, const Residue &b, in V_dadd()
633 void V_dbl (Residue &r, const Residue &a, const Residue &two) const { in V_dbl()
656 void V (Residue &r, Residue *rp1, const Residue &b,
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| H A D | modredc126.cpp | 14 ModulusREDC126::div3 (Residue &r, const Residue &a) const in div3()
16 Residue t(*this); in div3()
74 ModulusREDC126::div5 (Residue &r, const Residue &a) const in div5()
87 ModulusREDC126::div7 (Residue &r, const Residue &a) const in div7()
99 ModulusREDC126::div11 (Residue &r, const Residue &a) const in div11()
111 ModulusREDC126::div13 (Residue &r, const Residue &a) const in div13()
225 simple_mul (ModulusREDC126::Residue &r, const ModulusREDC126::Residue &a,
567 ModulusREDC126::inv (Residue &r, const Residue &A) const in inv()
699 Residue R(*this); in batchinv()
800 Residue *tr;
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| H A D | mod_mpz_new.cpp | 15 void ModulusMPZ::pow (Residue &r, const Residue &b, const uint64_t e) const in pow()
28 void ModulusMPZ::pow (Residue &r, const Residue &b, const Integer &e) const in pow()
37 void ModulusMPZ::pow (Residue &r, const Residue &b, const uint64_t *e, const size_t nrWords) const in pow()
73 ModulusMPZ::div3(ModulusMPZ::Residue &r, ModulusMPZ::Residue const &a) const { in div3()
74 Residue t(*this); in div3()
98 ModulusMPZ::divn (Residue &r, const Residue &a, const unsigned long b, in divn()
177 ModulusMPZ::div5 (Residue &r, const Residue &a) const in div5()
190 ModulusMPZ::div7 (Residue &r, const Residue &a) const in div7()
202 ModulusMPZ::div11 (Residue &r, const Residue &a) const in div11()
214 ModulusMPZ::div13 (Residue &r, const Residue &a) const in div13()
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| H A D | mod_common.cpp | 10 Modulus::pow (Residue &r, const Residue &b, const uint64_t e) const in pow()
13 Residue t(*this); in pow()
44 Modulus::pow (Residue &r, const Residue &b, const uint64_t *e, in pow()
48 Residue t(*this); in pow()
84 Modulus::pow (Residue &r, const Residue &b, const Integer &e) const in pow()
90 Residue t(*this); in pow()
127 Modulus::find_minus1 (Residue &r1, const Residue &minusone, const int po2) const in find_minus1()
147 Modulus::V (Residue &r, Residue *rp1, const Residue &b, in V()
246 Modulus::batchinv (Residue *r, const Residue *a, const size_t n, in batchinv()
247 const Residue *c) const in batchinv()
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| H A D | mod64_common.cpp | 16 Modulus::div3 (Residue &r, const Residue &a) const in div3()
20 Residue t(*this); in div3()
44 Residue c(*this); in div3()
58 Modulus::div5 (Residue &r, const Residue &a) const in div5()
61 Residue t(*this); in div5()
88 Residue c(*this); in div5()
103 Modulus::div7 (Residue &r, const Residue &a) const in div7()
106 Residue t(*this); in div7()
133 Residue c(*this); in div7()
149 Modulus::div11 (Residue &r, const Residue &a) const in div11()
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| /dports/math/cgal/CGAL-5.3/include/CGAL/Modular_arithmetic/ |
| H A D | Residue_type.h | 30 class Residue; variable
32 Residue operator + (const Residue&);
33 Residue operator - (const Residue&);
49 class Residue:
54 typedef Residue Self;
55 typedef Residue NT;
277 inline Residue operator + (const Residue& p1)
280 inline Residue operator - (const Residue& p1){
282 Residue r;
287 inline bool operator == (const Residue& p1, const Residue& p2)
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| /dports/science/gchemutils/gnome-chemistry-utils-0.14.16/libs/gcp/ |
| H A D | residue.cc | 39 void (*Residue::m_AddCb) (Residue *res) = NULL;
41 Residue::Residue (): gcu::Residue () in Residue() function in gcp::Residue
48 Residue::Residue (char const *name): gcu::Residue (name) in Residue() function in gcp::Residue
55 Residue::Residue (char const *name, char const *symbol, Molecule *mol, Document *doc): gcu::Residue… in Residue() function in gcp::Residue
69 Residue::~Residue () in ~Residue()
73 void Residue::Load (xmlNodePtr node, bool ro, gcu::Application *app) in Load()
94 gcu::Residue::Load (node, app); in Load()
97 bool Residue::operator== (gcu::Molecule const &mol) const in operator ==()
102 void Residue::Register () in Register()
109 void Residue::Ref () in Ref()
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| H A D | fragment-residue.cc | 44 m_Residue = dynamic_cast <Residue const *> (Residue::GetResidue (symbol, NULL)); in FragmentResidue()
45 const_cast <Residue *> (m_Residue)->Ref (); in FragmentResidue()
52 const_cast <Residue *> (m_Residue)->Unref (); in ~FragmentResidue()
55 void FragmentResidue::SetResidue (Residue const *res, char const *symbol) in SetResidue()
58 const_cast <Residue *> (m_Residue)->Unref (); in SetResidue()
64 const_cast <Residue *> (m_Residue)->Ref (); in SetResidue()
96 Residue *residue = (Residue*) Residue::GetResidue (buf, NULL); in Load()
101 Residue *res0 = new Residue (NULL, NULL, NULL, doc); in Load()
110 residue = new Residue (); in Load()
118 const_cast <Residue *> (m_Residue)->Ref (); in Load()
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| H A D | residue.h | 44 class Residue: public gcu::Residue
50 Residue ();
56 Residue (char const *name);
65 Residue (char const *name, char const *symbol, Molecule *mol, Document *doc);
69 virtual ~Residue ();
107 static void SetPostAddCallback (void (*cb) (Residue *res)) {m_AddCb = cb;} in SetPostAddCallback()
110 static void (*m_AddCb) (Residue *res);
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| /dports/science/avogadrolibs/avogadrolibs-1.94.0/avogadro/core/ |
| H A D | residue.cpp | 24 Residue::Residue() {} in Residue() function in Avogadro::Core::Residue
26 Residue::Residue(std::string& name) : m_residueName(name) {} in Residue() function in Avogadro::Core::Residue
28 Residue::Residue(std::string& name, Index& number) in Residue() function in Avogadro::Core::Residue
32 Residue::Residue(std::string& name, Index& number, char& id) in Residue() function in Avogadro::Core::Residue
36 Residue::Residue(const Residue& other) in Residue() function in Avogadro::Core::Residue
41 Residue& Residue::operator=(Residue other) in operator =()
49 Residue::~Residue() {} in ~Residue()
51 void Residue::addResidueAtom(std::string& name, Atom& atom) in addResidueAtom()
56 std::vector<Atom> Residue::residueAtoms() in residueAtoms()
66 void Residue::resolveResidueBonds(Molecule& mol) in resolveResidueBonds()
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| H A D | residue.h | 40 class AVOGADROCORE_EXPORT Residue
47 Residue();
48 Residue(std::string& name);
49 Residue(std::string& name, Index& number);
50 Residue(std::string& name, Index& number, char& id);
52 Residue(const Residue& other);
54 Residue& operator=(Residue other);
56 virtual ~Residue();
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| /dports/science/py-avogadrolibs/avogadrolibs-1.94.0/avogadro/core/ |
| H A D | residue.cpp | 24 Residue::Residue() {} in Residue() function in Avogadro::Core::Residue
26 Residue::Residue(std::string& name) : m_residueName(name) {} in Residue() function in Avogadro::Core::Residue
28 Residue::Residue(std::string& name, Index& number) in Residue() function in Avogadro::Core::Residue
32 Residue::Residue(std::string& name, Index& number, char& id) in Residue() function in Avogadro::Core::Residue
36 Residue::Residue(const Residue& other) in Residue() function in Avogadro::Core::Residue
41 Residue& Residue::operator=(Residue other) in operator =()
49 Residue::~Residue() {} in ~Residue()
51 void Residue::addResidueAtom(std::string& name, Atom& atom) in addResidueAtom()
56 std::vector<Atom> Residue::residueAtoms() in residueAtoms()
66 void Residue::resolveResidueBonds(Molecule& mol) in resolveResidueBonds()
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| H A D | residue.h | 40 class AVOGADROCORE_EXPORT Residue
47 Residue();
48 Residue(std::string& name);
49 Residue(std::string& name, Index& number);
50 Residue(std::string& name, Index& number, char& id);
52 Residue(const Residue& other);
54 Residue& operator=(Residue other);
56 virtual ~Residue();
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| /dports/biology/dsr-pdb/dsr-pdb-1.0.3/include/dsrpdb/ |
| H A D | Protein.h | 94 void new_residue(const Residue &res);
145 std::vector<Residue::Type> sequence() const;
163 const Residue& residue(Residue::Index i) const;
166 bool has_residue(Residue::Index i) const;
207 std::vector<Residue> residues_;
266 std::vector<Residue>::iterator rit_, rend_;
267 Residue::Atoms_iterator ait_, aend_;
325 Residue::Const_atoms_iterator ait_, aend_;
356 && orit->has_atom(Residue::AL_C) && rit_->has_atom(Residue::AL_N)){
395 rit_->atom(Residue::AL_N).index()); in cur_bond()
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| /dports/science/quantum-espresso/q-e-qe-6.7.0/TDDFPT/examples/example09/reference/ |
| H A D | C6H6.tddfpt.out | 116 Residue(Squared modulus): 1 0.0010057 0.0000000
117 Residue(Squared modulus): 2 0.0007810 0.0000003
118 Residue(Squared modulus): 3 0.0002946 0.0000003
119 Residue(Squared modulus): 4 0.0122273 0.0000007
120 Residue(Squared modulus): 5 0.0122294 0.0000007
134 Residue(Squared modulus): 1 0.0000396 0.0000295
135 Residue(Squared modulus): 2 0.0001581 0.0001234
136 Residue(Squared modulus): 3 0.0000675 0.0000719
137 Residue(Squared modulus): 4 0.0011085 0.0002343
138 Residue(Squared modulus): 5 0.0011057 0.0002330
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| /dports/science/gchemutils/gnome-chemistry-utils-0.14.16/libs/gcu/ |
| H A D | residue.cc | 49 map<string, Residue*> rtbn; // indexed by name
64 Residue::Residue (): in Residue() function in gcu::Residue
73 Residue::Residue (char const *name, Document *doc): in Residue() function in gcu::Residue
87 Residue::~Residue () in ~Residue()
101 unsigned Residue::MaxSymbolLength = 0;
103 void Residue::SetName (char const *name) in SetName()
113 void Residue::AddSymbol (char const *symbol) in AddSymbol()
126 void Residue::RemoveSymbol (char const *symbol) in RemoveSymbol()
133 void Residue::Load (xmlNodePtr node, Application *app) in Load()
229 Residue const *Residue::GetResidue (char const *symbol, bool *ambiguous) in GetResidue()
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| /dports/math/cado-nfs/cado-nfs-f4284e2391121b2bfb97bc4880b6273c7250dc2f/sieve/ecm/ |
| H A D | ec_arith_Weierstrass_new.hpp | 25 typedef typename Modulus::Residue Residue; typedef in ECWeierstrass
29 Residue a;
55 typedef typename Modulus::Residue Residue; typedef in ECWeierstrass::AffinePoint
59 Residue x, y;
66 AffinePoint(const ECurve &c, const Residue &_x, const Residue &_y) in AffinePoint()
128 void set(const Residue &_x, const Residue &_y) { in set()
198 typedef typename Modulus::Residue Residue; typedef in ECWeierstrass::ProjectivePoint
202 Residue x, y, z;
205 ProjectivePoint(const ECurve &c, const Residue &_x, const Residue &_y, const Residue &_z) in ProjectivePoint()
277 void set(const Residue &_x, const Residue &_y, const Residue &_z) { in set()
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| /dports/math/givaro/givaro-4.1.1/src/library/poly1/ |
| H A D | givpoly1factor.h | 205 template<class Residue>
206 bool find_irred_binomial(Element &R, Degree n, Residue MOD) const;
208 template<class Residue>
211 template<class Residue>
215 template<class Residue>
216 bool find_irred_trinomial(Element &R, Degree n, Residue MOD) const;
218 template<class Residue>
221 template<class Residue>
225 template<class Residue>
228 template<class Residue>
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