/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() [all …]
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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() [all …]
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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); [all …]
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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) { [all …]
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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; [all …]
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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; [all …]
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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, [all …]
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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, [all …]
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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; [all …]
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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() [all …]
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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() [all …]
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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() [all …]
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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) [all …]
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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() [all …]
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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() [all …]
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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() [all …]
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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() [all …]
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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 [all …]
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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() [all …]
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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() [all …]
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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> [all …]
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