From d81953f8a51f6c2281a0863cd7900cbcfe089175 Mon Sep 17 00:00:00 2001 From: okkevaneck Date: Sun, 13 Aug 2023 13:18:42 +0200 Subject: [PATCH] Removed allow violations option as it is not needed anymore --- archives/prospr_core.tar.gz | Bin 8485 -> 8437 bytes archives/prospr_core.zip | Bin 14090 -> 14035 bytes prospr/core/core_module.cpp | 4 ++-- prospr/core/src/protein.cpp | 7 ++----- prospr/core/src/protein.hpp | 3 +-- 5 files changed, 5 insertions(+), 9 deletions(-) diff --git a/archives/prospr_core.tar.gz b/archives/prospr_core.tar.gz index c966fcd1728836cf129eb32acdb879e3320571a6..5cce9ea9572ea105dbf060bc50b86463bed0c28d 100644 GIT binary patch delta 8322 zcmV-|AbsDZLiIs^ABzY80000000ZqkX>S`xviYoE(b3{LltL-gVH>b40gmIW4R{?P z&OR)jArK>SB+Z(f;m!;#YaQ)xe|7XxeejShc{g4Tf|#1=v%2oCuFl3qS@p9)G29+Z zCg0r4(}U;Hqka5$=kddy{1>0SM-Lx=v$May_i%5oxAz!-%I)m#?d^Y~diOIN|Cu&z zRx9;Q_5OW6uiT>Vf6(WLP4#mz%AY9lWFAhesZI4$-VEwu(iT<8CEr%ldXTF#sH)DY zT4g2IQdmn>r+?1}t-37Qi=tHRMXp{RZ;h*AKHA3CUKfMBY($^GT@($s1^rhS0 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zk+nhbUcMDqMTB~`>-P;O@|;|-h?Y&++)4~>!yauWogy;nG$cR2KCK^L-`^6^ zo{kW_SUS^u1cv@}YlJ1DX}=9!O(?`zzC)9+T#1I$iPOY)g0020?FDv zWvRT-87-zW7WqVa$WWx4i?M+JP;A{K&R-X9B8Avm8pagSX-`3A6pKax`W2<^RhoQ|oP1)qycM}e>-p#N;|_=tL5k890(2L zWjvO_0f(2Ai(*~}Q1V%hUvUf;w504!=&a_V)?MSE-`D2YK1#gwHc>EJV&neb;4(Ry z?>*vUYZ5;d-~Tt_Wd9600D$nXprOzIn*Yr=|6|Kh07&qEd!h(h$zuGv2o=fS_;nFc cIFb+ebr5WmMFk8H;K?Zh!l)&@|9#}Y01hu|A^-pY diff --git a/prospr/core/core_module.cpp b/prospr/core/core_module.cpp index 438b46c..96d1613 100644 --- a/prospr/core/core_module.cpp +++ b/prospr/core/core_module.cpp @@ -36,10 +36,10 @@ PYBIND11_MODULE(prospr_core, m) { /* Protein class definition. */ py::class_(m, "Protein") .def(py::init, bool, bool &>(), + std::map, bool &>(), "Protein constructor", py::arg("sequence"), py::arg("dim") = 2, py::arg("model") = "HP", py::arg("bond_values") = bond_values, - py::arg("bond_symmetry") = true, py::arg("allow_violations") = false) + py::arg("bond_symmetry") = true) .def_property_readonly("solutions_checked", &Protein::get_solutions_checked) .def_property_readonly("aminos_placed", &Protein::get_aminos_placed) diff --git a/prospr/core/src/protein.cpp b/prospr/core/src/protein.cpp index a163c99..62eb2a3 100644 --- a/prospr/core/src/protein.cpp +++ b/prospr/core/src/protein.cpp @@ -33,7 +33,6 @@ Protein::Protein(const Protein &other) { this->bond_values = other.bond_values; this->weighted_amino_acids = other.weighted_amino_acids; this->max_weights = other.max_weights; - this->allow_violations = other.allow_violations; /* Create new AminoAcid objects for all amino acids. */ AminoAcid *new_aa; @@ -61,8 +60,7 @@ Protein::Protein(const Protein &other) { /* Construct a new Protein. */ Protein::Protein(std::string sequence, int dim, std::string model, - std::map bond_values, bool bond_symmetry, - bool allow_violations) { + std::map bond_values, bool bond_symmetry) { this->sequence = sequence; space = {}; cur_len = 0; @@ -72,7 +70,6 @@ Protein::Protein(std::string sequence, int dim, std::string model, score = 0; solutions_checked = 0; aminos_placed = 0; - this->allow_violations = allow_violations; /* Deduct what model to use, or apply custom one. */ if (model == "HP") { @@ -301,7 +298,7 @@ void Protein::place_amino(int move, bool track) { last_pos[abs(move) - 1] += move / abs(move); /* Check for illegal folds. */ - if (!allow_violations && space.count(last_pos) > 0) + if (space.count(last_pos) > 0) throw std::runtime_error("Protein folded onto itself.."); /* Place amino acid on new (valid) position. */ diff --git a/prospr/core/src/protein.hpp b/prospr/core/src/protein.hpp index 1a84e18..93f3513 100644 --- a/prospr/core/src/protein.hpp +++ b/prospr/core/src/protein.hpp @@ -29,7 +29,7 @@ class Protein { /* Construct a new Protein. */ Protein(std::string sequence, int dim = 2, std::string model = "HP", std::map bond_values = {}, - bool bond_symmetry = true, bool allow_violations = false); + bool bond_symmetry = true); /* Overload assignment operator for assignments. */ Protein &operator=(const Protein &other); @@ -113,7 +113,6 @@ class Protein { std::uint64_t aminos_placed; std::uint64_t solutions_checked; std::vector amino_acids; - bool allow_violations; /* Change score according to the already performed addition or removal * of the given move.