git: d63020f72bc6 - main - science/dssp: update 4.4.11 → 4.5.8
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Date: Sun, 22 Mar 2026 05:38:19 UTC
The branch main has been updated by yuri:
URL: https://cgit.FreeBSD.org/ports/commit/?id=d63020f72bc68010d0df3a0dcc4449d08a008659
commit d63020f72bc68010d0df3a0dcc4449d08a008659
Author: Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2026-03-22 05:09:32 +0000
Commit: Yuri Victorovich <yuri@FreeBSD.org>
CommitDate: 2026-03-22 05:38:13 +0000
science/dssp: update 4.4.11 → 4.5.8
---
science/dssp/Makefile | 3 +-
science/dssp/distinfo | 6 +-
science/dssp/files/patch-libdssp_src_dssp-io.cpp | 128 +++++++++++++++++++++++
science/dssp/files/patch-libdssp_src_dssp.cpp | 11 ++
science/dssp/pkg-plist | 8 --
5 files changed, 143 insertions(+), 13 deletions(-)
diff --git a/science/dssp/Makefile b/science/dssp/Makefile
index 87eaec6066d4..648a5ae9f3c2 100644
--- a/science/dssp/Makefile
+++ b/science/dssp/Makefile
@@ -1,7 +1,6 @@
PORTNAME= dssp
DISTVERSIONPREFIX= v
-DISTVERSION= 4.4.11
-PORTREVISION= 2
+DISTVERSION= 4.5.8
CATEGORIES= science
MAINTAINER= yuri@FreeBSD.org
diff --git a/science/dssp/distinfo b/science/dssp/distinfo
index 9481004e9bdd..6b8fae87332c 100644
--- a/science/dssp/distinfo
+++ b/science/dssp/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1740732635
-SHA256 (PDB-REDO-dssp-v4.4.11_GH0.tar.gz) = 49dd6560358ba65fb971e158f78a54557ab6da1c49e502704b3bb9518e17acce
-SIZE (PDB-REDO-dssp-v4.4.11_GH0.tar.gz) = 163930
+TIMESTAMP = 1774153102
+SHA256 (PDB-REDO-dssp-v4.5.8_GH0.tar.gz) = 634bf8d8dd96954bd680da90f3dcb66b87189c13b12b52b61de8af9d597b74ac
+SIZE (PDB-REDO-dssp-v4.5.8_GH0.tar.gz) = 225240
diff --git a/science/dssp/files/patch-libdssp_src_dssp-io.cpp b/science/dssp/files/patch-libdssp_src_dssp-io.cpp
new file mode 100644
index 000000000000..9c15f6050be7
--- /dev/null
+++ b/science/dssp/files/patch-libdssp_src_dssp-io.cpp
@@ -0,0 +1,128 @@
+--- libdssp/src/dssp-io.cpp.orig 2026-03-21 21:49:26.455057000 -0700
++++ libdssp/src/dssp-io.cpp 2026-03-21 21:49:47.132217000 -0700
+@@ -276,7 +276,7 @@
+ data.emplace_back("acceptor_1_auth_seq_id", acceptor.auth_seq_id());
+ data.emplace_back("acceptor_1_auth_asym_id", acceptor.auth_asym_id());
+ data.emplace_back("acceptor_1_pdbx_PDB_ins_code", acceptor.pdb_ins_code());
+- data.emplace_back("acceptor_1_energy", acceptorEnergy, 1);
++ data.emplace_back("acceptor_1_energy", cif::item_value{acceptorEnergy, 1});
+ }
+ else
+ {
+@@ -287,7 +287,7 @@
+ data.emplace_back("acceptor_2_auth_seq_id", acceptor.auth_seq_id());
+ data.emplace_back("acceptor_2_auth_asym_id", acceptor.auth_asym_id());
+ data.emplace_back("acceptor_2_pdbx_PDB_ins_code", acceptor.pdb_ins_code());
+- data.emplace_back("acceptor_2_energy", acceptorEnergy, 1);
++ data.emplace_back("acceptor_2_energy", cif::item_value{acceptorEnergy, 1});
+ }
+ }
+
+@@ -302,7 +302,7 @@
+ data.emplace_back("donor_1_auth_seq_id", donor.auth_seq_id());
+ data.emplace_back("donor_1_auth_asym_id", donor.auth_asym_id());
+ data.emplace_back("donor_1_pdbx_PDB_ins_code", donor.pdb_ins_code());
+- data.emplace_back("donor_1_energy", donorEnergy, 1);
++ data.emplace_back("donor_1_energy", cif::item_value{donorEnergy, 1});
+ }
+ else
+ {
+@@ -313,7 +313,7 @@
+ data.emplace_back("donor_2_auth_seq_id", donor.auth_seq_id());
+ data.emplace_back("donor_2_auth_asym_id", donor.auth_asym_id());
+ data.emplace_back("donor_2_pdbx_PDB_ins_code", donor.pdb_ins_code());
+- data.emplace_back("donor_2_energy", donorEnergy, 1);
++ data.emplace_back("donor_2_energy", cif::item_value{donorEnergy, 1});
+ }
+ }
+ }
+@@ -525,30 +525,30 @@
+ { "nr_of_ss_bridges_total", stats.count.SS_bridges },
+ { "nr_of_ss_bridges_intra_chain", stats.count.intra_chain_SS_bridges },
+ { "nr_of_ss_bridges_inter_chain", stats.count.SS_bridges - stats.count.intra_chain_SS_bridges },
+- { "accessible_surface_of_protein", surface_accessibility, 2 } });
++ { "accessible_surface_of_protein", cif::item_value{surface_accessibility} } });
+
+ auto &dssp_struct_hbonds = db["dssp_statistics_hbond"];
+
+ dssp_struct_hbonds.emplace({ { "entry_id", db.name() },
+ { "type", "O(I)-->H-N(J)" },
+ { "count", stats.count.H_bonds },
+- { "count_per_100", stats.count.H_bonds * 100.0 / stats.count.residues, 1 } });
++ { "count_per_100", cif::item_value{stats.count.H_bonds * 100.0 / stats.count.residues, 1} } });
+
+ dssp_struct_hbonds.emplace({ { "entry_id", db.name() },
+ { "type", "PARALLEL BRIDGES" },
+ { "count", stats.count.H_bonds_in_parallel_bridges },
+- { "count_per_100", stats.count.H_bonds_in_parallel_bridges * 100.0 / stats.count.residues, 1 } });
++ { "count_per_100", cif::item_value{stats.count.H_bonds_in_parallel_bridges * 100.0 / stats.count.residues, 1} } });
+
+ dssp_struct_hbonds.emplace({ { "entry_id", db.name() },
+ { "type", "ANTIPARALLEL BRIDGES" },
+ { "count", stats.count.H_bonds_in_antiparallel_bridges },
+- { "count_per_100", stats.count.H_bonds_in_antiparallel_bridges * 100.0 / stats.count.residues, 1 } });
++ { "count_per_100", cif::item_value{stats.count.H_bonds_in_antiparallel_bridges * 100.0 / stats.count.residues, 1} } });
+
+ for (int k = 0; k < 11; ++k)
+ dssp_struct_hbonds.emplace({ { "entry_id", db.name() },
+ { "type", "O(I)-->H-N(I"s + (k - 5 < 0 ? '-' : '+') + std::to_string(abs(k - 5)) + ")" },
+ { "count", stats.count.H_Bonds_per_distance[k] },
+- { "count_per_100", stats.count.H_Bonds_per_distance[k] * 100.0 / stats.count.residues, 1 } });
++ { "count_per_100", cif::item_value{stats.count.H_Bonds_per_distance[k] * 100.0 / stats.count.residues, 1} } });
+
+ auto &dssp_statistics_histogram = db["dssp_statistics_histogram"];
+
+@@ -701,36 +701,36 @@
+ { "ladder_1", ladders[0] },
+ { "ladder_2", ladders[1] },
+
+- { "x_ca", cax, 1 },
+- { "y_ca", cay, 1 },
+- { "z_ca", caz, 1 },
++ { "x_ca", cif::item_value{cax, 1} },
++ { "y_ca", cif::item_value{cay, 1} },
++ { "z_ca", cif::item_value{caz, 1} },
+ };
+
+ if (writeAccessibility)
+- data.emplace_back("accessibility", res.accessibility(), 1);
++ data.emplace_back("accessibility", cif::item_value{res.accessibility(), 1});
+
+ if (res.tco().has_value())
+- data.emplace_back("TCO", *res.tco(), 3);
++ data.emplace_back("TCO", cif::item_value{*res.tco(), 3});
+ else
+ data.emplace_back("TCO", ".");
+
+ if (res.kappa().has_value())
+- data.emplace_back("kappa", *res.kappa(), 1);
++ data.emplace_back("kappa", cif::item_value{*res.kappa(), 1});
+ else
+ data.emplace_back("kappa", ".");
+
+ if (res.alpha().has_value())
+- data.emplace_back("alpha", *res.alpha(), 1);
++ data.emplace_back("alpha", cif::item_value{*res.alpha(), 1});
+ else
+ data.emplace_back("alpha", ".");
+
+ if (res.phi().has_value())
+- data.emplace_back("phi", *res.phi(), 1);
++ data.emplace_back("phi", cif::item_value{*res.phi(), 1});
+ else
+ data.emplace_back("phi", ".");
+
+ if (res.psi().has_value())
+- data.emplace_back("psi", *res.psi(), 1);
++ data.emplace_back("psi", cif::item_value{*res.psi(), 1});
+ else
+ data.emplace_back("psi", ".");
+
+@@ -757,7 +757,6 @@
+
+ if (audit_conform.empty())
+ {
+- static_assert(std::is_reference_v<decltype(std::declval<cif::validator_factory>().get(""))>);
+ fill_audit_conform<cif::validator_factory>(audit_conform);
+ }
+
diff --git a/science/dssp/files/patch-libdssp_src_dssp.cpp b/science/dssp/files/patch-libdssp_src_dssp.cpp
new file mode 100644
index 000000000000..19dc7cacde12
--- /dev/null
+++ b/science/dssp/files/patch-libdssp_src_dssp.cpp
@@ -0,0 +1,11 @@
+--- libdssp/src/dssp.cpp.orig 2026-03-21 21:49:26.455914000 -0700
++++ libdssp/src/dssp.cpp 2026-03-21 21:49:52.366128000 -0700
+@@ -278,7 +278,7 @@
+ p = {};
+ }
+
+- void addAtom(cif::row_handle atom)
++ void addAtom(cif::const_row_handle atom)
+ {
+ std::string asymID, compID, atomID, type, authAsymID;
+ std::optional<std::string> altID;
diff --git a/science/dssp/pkg-plist b/science/dssp/pkg-plist
index 2647e94578a5..02428e2cde75 100644
--- a/science/dssp/pkg-plist
+++ b/science/dssp/pkg-plist
@@ -1,10 +1,2 @@
bin/mkdssp
-include/dssp.hpp
-lib/cmake/dssp/dsspConfig.cmake
-lib/cmake/dssp/dsspTargets-%%CMAKE_BUILD_TYPE%%.cmake
-lib/cmake/dssp/dsspTargets.cmake
-lib/libdssp.so
-lib/libdssp.so.4
-lib/libdssp.so.4.4.11
-share/libcifpp/dssp-extension.dic
share/man/man1/mkdssp.1.gz