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libcifpp
Commit 42c72958 by maarten
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fix for buster-tnt parser 

git-svn-id: svn+ssh://gitlab/srv/svn-repos/pdb-redo/trunk@431 a1961a4f-ab94-4bcc-80e8-33b5a54de466
parent 13109f76
Showing with 29 additions and 21 deletions
README.md
...@@ -15,6 +15,8 @@ Other requirements are: ...@@ -15,6 +15,8 @@ Other requirements are:
- [libzeep](https://github.com/mhekkel/libzeep), a library that contains a full validating XML parser as well as a complete HTTP and SOAP server implementation. - [libzeep](https://github.com/mhekkel/libzeep), a library that contains a full validating XML parser as well as a complete HTTP and SOAP server implementation.
- [nlohmann/json](https://github.com/nlohmann/json), a header only library to parse and write JSON. This requirement will be removed in a future release (once libzeep 4 is out of beta). - [nlohmann/json](https://github.com/nlohmann/json), a header only library to parse and write JSON. This requirement will be removed in a future release (once libzeep 4 is out of beta).
Make sure you install the libraries and tools in this list first before building. You don't have to install them in system locations, paths can be set as described in the next section.
### Building ### Building
There are two makefiles, one located in the directory libcif++ and one in tools. There are two makefiles, one located in the directory libcif++ and one in tools.
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src/PDB2CifRemark3.cpp
...@@ -109,27 +109,33 @@ const TemplateLine kBusterTNT_Template[] = { ...@@ -109,27 +109,33 @@ const TemplateLine kBusterTNT_Template[] = {
/* 69 */ { R"(UTILITY TORSION :\s+(.+?);\s+(.+?);\s+(.+?))", 1, "refine_ls_restr", { "number", "weight", "pdbx_restraint_function" }, "t_utility_torsion", true }, /* 69 */ { R"(UTILITY TORSION :\s+(.+?);\s+(.+?);\s+(.+?))", 1, "refine_ls_restr", { "number", "weight", "pdbx_restraint_function" }, "t_utility_torsion", true },
/* 70 */ { R"(IDEAL-DIST CONTACT TERM :\s+(.+?);\s+(.+?);\s+(.+?))", 1, "refine_ls_restr", { "number", "weight", "pdbx_restraint_function" }, "t_ideal_dist_contact", true }, /* 70 */ { R"(IDEAL-DIST CONTACT TERM :\s+(.+?);\s+(.+?);\s+(.+?))", 1, "refine_ls_restr", { "number", "weight", "pdbx_restraint_function" }, "t_ideal_dist_contact", true },
/* 71 */ { R"(RMS DEVIATIONS FROM IDEAL VALUES\.)", 1 }, /* 71 */ { R"(RMS DEVIATIONS FROM IDEAL VALUES\.)", 1 },
/* 72 */ { R"(BOND LENGTHS \(A\) :\s+(.+?))", 1, "refine_ls_restr", { "dev_ideal" }, "t_bond_d", false }, /* 72 */ { R"(BOND LENGTHS \(A\) :\s+(.+?);\s+(.+?);\s+(.+?))", 1, "refine_ls_restr", { "dev_ideal", "weight", "number" }, "t_bond_d", false },
/* 73 */ { R"(BOND ANGLES \(DEGREES\) :\s+(.+?))", 1, "refine_ls_restr", { "dev_ideal" }, "t_angle_deg", false }, /* 73 */ { R"(BOND ANGLES \(DEGREES\) :\s+(.+?);\s+(.+?);\s+(.+?))", 1, "refine_ls_restr", { "dev_ideal", "weight", "number" }, "t_angle_deg", false },
/* 74 */ { R"(PEPTIDE OMEGA TORSION ANGLES \(DEGREES\) :\s+(.+?))", 1, "refine_ls_restr", { "dev_ideal" }, "t_omega_torsion", false }, /* 74 */ { R"(TORSION ANGLES \(DEGREES\) :\s+(.+?);\s+(.+?);\s+(.+?))", 1, "refine_ls_restr", { "dev_ideal", "weight", "number" }, "t_dihedral_angle_d", false },
/* 75 */ { R"(OTHER TORSION ANGLES \(DEGREES\) :\s+(.+?))", 1, "refine_ls_restr", { "dev_ideal" }, "t_other_torsion", false }, /* 75 */ { R"(PSEUDO ROTATION ANGLES \(DEGREES\) :\s+(.+?);\s+(.+?);\s+(.+?))", 1, "refine_ls_restr", { "dev_ideal", "weight", "number" }, "t_pseud_angle", false },
/* 76 */ { R"(TLS DETAILS\.?)", 1 }, /* 76 */ { R"(TRIGONAL CARBON PLANES \(A\) :\s+(.+?);\s+(.+?);\s+(.+?))", 1, "refine_ls_restr", { "dev_ideal", "weight", "number" }, "t_trig_c_planes", false },
/* 77 */ { R"(NUMBER OF TLS GROUPS :.+)", 1 }, /* 77 */ { R"(GENERAL PLANES \(A\) :\s+(.+?);\s+(.+?);\s+(.+?))", 1, "refine_ls_restr", { "dev_ideal", "weight", "number" }, "t_gen_planes", false },
/* 78 */ { R"(TLS GROUP :\s*(\d+))", 1, "pdbx_refine_tls", { "id" }, nullptr, true }, /* 78 */ { R"(ISOTROPIC THERMAL FACTORS \(A\*\*2\) :\s+(.+?);\s+(.+?);\s+(.+?))", 1, "refine_ls_restr", { "dev_ideal", "weight", "number" }, "t_it", false },
/* 79 */ { R"((?:SELECTION|SET) *:\s+(.+?))", 1, "pdbx_refine_tls_group", { "selection_details" }, nullptr, true }, /* 79 */ { R"(NON-BONDED CONTACTS \(A\) :\s+(.+?);\s+(.+?);\s+(.+?))", 1, "refine_ls_restr", { "dev_ideal", "weight", "number" }, "t_nbd", false },
/* 80 */ { R"(ORIGIN FOR THE GROUP \(A\):\s+(.+?)\s+(.+?)\s+(.+?))", 1, "pdbx_refine_tls", { "origin_x", "origin_y", "origin_z" } }, /* 80 */ { R"(PEPTIDE OMEGA TORSION ANGLES \(DEGREES\) :\s+(.+?);\s+(.+?);\s+(.+?))", 1, "refine_ls_restr", { "dev_ideal", "weight", "number" }, "t_omega_torsion", false },
/* 81 */ { R"(T TENSOR)", 1 }, /* 81 */ { R"(OTHER TORSION ANGLES \(DEGREES\) :\s+(.+?);\s+(.+?);\s+(.+?))", 1, "refine_ls_restr", { "dev_ideal", "weight", "number" }, "t_other_torsion", false },
/* 82 */ { R"(T11:\s+(.+?) T22:\s+(.+?))", 1, "pdbx_refine_tls", { "T[1][1]", "T[2][2]" } }, /* 82 */ { R"(TLS DETAILS\.?)", 1 },
/* 83 */ { R"(T33:\s+(.+?) T12:\s+(.+?))", 1, "pdbx_refine_tls", { "T[3][3]", "T[1][2]" } }, /* 83 */ { R"(NUMBER OF TLS GROUPS :.+)", 1 },
/* 84 */ { R"(T13:\s+(.+?) T23:\s+(.+?))", 1, "pdbx_refine_tls", { "T[1][3]", "T[2][3]" } }, /* 84 */ { R"(TLS GROUP :\s*(\d+))", 1, "pdbx_refine_tls", { "id" }, nullptr, true },
/* 85 */ { R"(L TENSOR)", 1 }, /* 85 */ { R"((?:SELECTION|SET) *:\s+(.+?))", 1, "pdbx_refine_tls_group", { "selection_details" }, nullptr, true },
/* 86 */ { R"(L11:\s+(.+?) L22:\s+(.+?))", 1, "pdbx_refine_tls", { "L[1][1]", "L[2][2]" } }, /* 86 */ { R"(ORIGIN FOR THE GROUP \(A\):\s+(.+?)\s+(.+?)\s+(.+?))", 1, "pdbx_refine_tls", { "origin_x", "origin_y", "origin_z" } },
/* 87 */ { R"(L33:\s+(.+?) L12:\s+(.+?))", 1, "pdbx_refine_tls", { "L[3][3]", "L[1][2]" } }, /* 87 */ { R"(T TENSOR)", 1 },
/* 88 */ { R"(L13:\s+(.+?) L23:\s+(.+?))", 1, "pdbx_refine_tls", { "L[1][3]", "L[2][3]" } }, /* 88 */ { R"(T11:\s+(.+?) T22:\s+(.+?))", 1, "pdbx_refine_tls", { "T[1][1]", "T[2][2]" } },
/* 89 */ { R"(S TENSOR)", 1 }, /* 89 */ { R"(T33:\s+(.+?) T12:\s+(.+?))", 1, "pdbx_refine_tls", { "T[3][3]", "T[1][2]" } },
/* 90 */ { R"(S11:\s+(.+?) S12:\s+(.+?) S13:\s+(.+?))", 1, "pdbx_refine_tls", { "S[1][1]", "S[1][2]", "S[1][3]" } }, /* 90 */ { R"(T13:\s+(.+?) T23:\s+(.+?))", 1, "pdbx_refine_tls", { "T[1][3]", "T[2][3]" } },
/* 91 */ { R"(S21:\s+(.+?) S22:\s+(.+?) S23:\s+(.+?))", 1, "pdbx_refine_tls", { "S[2][1]", "S[2][2]", "S[2][3]" } }, /* 91 */ { R"(L TENSOR)", 1 },
/* 92 */ { R"(S31:\s+(.+?) S32:\s+(.+?) S33:\s+(.+?))", 78 - 92, "pdbx_refine_tls", { "S[3][1]", "S[3][2]", "S[3][3]" } }, /* 92 */ { R"(L11:\s+(.+?) L22:\s+(.+?))", 1, "pdbx_refine_tls", { "L[1][1]", "L[2][2]" } },
/* 93 */ { R"(L33:\s+(.+?) L12:\s+(.+?))", 1, "pdbx_refine_tls", { "L[3][3]", "L[1][2]" } },
/* 94 */ { R"(L13:\s+(.+?) L23:\s+(.+?))", 1, "pdbx_refine_tls", { "L[1][3]", "L[2][3]" } },
/* 95 */ { R"(S TENSOR)", 1 },
/* 96 */ { R"(S11:\s+(.+?) S12:\s+(.+?) S13:\s+(.+?))", 1, "pdbx_refine_tls", { "S[1][1]", "S[1][2]", "S[1][3]" } },
/* 97 */ { R"(S21:\s+(.+?) S22:\s+(.+?) S23:\s+(.+?))", 1, "pdbx_refine_tls", { "S[2][1]", "S[2][2]", "S[2][3]" } },
/* 98 */ { R"(S31:\s+(.+?) S32:\s+(.+?) S33:\s+(.+?))", 84 - 98, "pdbx_refine_tls", { "S[3][1]", "S[3][2]", "S[3][3]" } },
}; };
class BUSTER_TNT_Remark3Parser : public Remark3Parser class BUSTER_TNT_Remark3Parser : public Remark3Parser
......
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