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fix for buster-tnt parser

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git-svn-id: svn+ssh://gitlab/srv/svn-repos/pdb-redo/trunk@431 a1961a4f-ab94-4bcc-80e8-33b5a54de466
This commit is contained in:
maarten
2019-07-09 13:09:35 +00:00
parent 13109f767a
commit 42c72958a8
2 changed files with 29 additions and 21 deletions
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2
README.md
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@@ -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.
- [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
There are two makefiles, one located in the directory libcif++ and one in tools.

48
src/PDB2CifRemark3.cpp
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@@ -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 },
/* 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 },
/* 72 */ { R"(BOND LENGTHS \(A\) :\s+(.+?))", 1, "refine_ls_restr", { "dev_ideal" }, "t_bond_d", false },
/* 73 */ { R"(BOND ANGLES \(DEGREES\) :\s+(.+?))", 1, "refine_ls_restr", { "dev_ideal" }, "t_angle_deg", false },
/* 74 */ { R"(PEPTIDE OMEGA TORSION ANGLES \(DEGREES\) :\s+(.+?))", 1, "refine_ls_restr", { "dev_ideal" }, "t_omega_torsion", false },
/* 75 */ { R"(OTHER TORSION ANGLES \(DEGREES\) :\s+(.+?))", 1, "refine_ls_restr", { "dev_ideal" }, "t_other_torsion", false },
/* 76 */ { R"(TLS DETAILS\.?)", 1 },
/* 77 */ { R"(NUMBER OF TLS GROUPS :.+)", 1 },
/* 78 */ { R"(TLS GROUP :\s*(\d+))", 1, "pdbx_refine_tls", { "id" }, nullptr, true },
/* 79 */ { R"((?:SELECTION|SET) *:\s+(.+?))", 1, "pdbx_refine_tls_group", { "selection_details" }, nullptr, true },
/* 80 */ { R"(ORIGIN FOR THE GROUP \(A\):\s+(.+?)\s+(.+?)\s+(.+?))", 1, "pdbx_refine_tls", { "origin_x", "origin_y", "origin_z" } },
/* 81 */ { R"(T TENSOR)", 1 },
/* 82 */ { R"(T11:\s+(.+?) T22:\s+(.+?))", 1, "pdbx_refine_tls", { "T[1][1]", "T[2][2]" } },
/* 83 */ { R"(T33:\s+(.+?) T12:\s+(.+?))", 1, "pdbx_refine_tls", { "T[3][3]", "T[1][2]" } },
/* 84 */ { R"(T13:\s+(.+?) T23:\s+(.+?))", 1, "pdbx_refine_tls", { "T[1][3]", "T[2][3]" } },
/* 85 */ { R"(L TENSOR)", 1 },
/* 86 */ { R"(L11:\s+(.+?) L22:\s+(.+?))", 1, "pdbx_refine_tls", { "L[1][1]", "L[2][2]" } },
/* 87 */ { R"(L33:\s+(.+?) L12:\s+(.+?))", 1, "pdbx_refine_tls", { "L[3][3]", "L[1][2]" } },
/* 88 */ { R"(L13:\s+(.+?) L23:\s+(.+?))", 1, "pdbx_refine_tls", { "L[1][3]", "L[2][3]" } },
/* 89 */ { R"(S TENSOR)", 1 },
/* 90 */ { R"(S11:\s+(.+?) S12:\s+(.+?) S13:\s+(.+?))", 1, "pdbx_refine_tls", { "S[1][1]", "S[1][2]", "S[1][3]" } },
/* 91 */ { R"(S21:\s+(.+?) S22:\s+(.+?) S23:\s+(.+?))", 1, "pdbx_refine_tls", { "S[2][1]", "S[2][2]", "S[2][3]" } },
/* 92 */ { R"(S31:\s+(.+?) S32:\s+(.+?) S33:\s+(.+?))", 78 - 92, "pdbx_refine_tls", { "S[3][1]", "S[3][2]", "S[3][3]" } },
/* 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+(.+?);\s+(.+?);\s+(.+?))", 1, "refine_ls_restr", { "dev_ideal", "weight", "number" }, "t_angle_deg", false },
/* 74 */ { R"(TORSION ANGLES \(DEGREES\) :\s+(.+?);\s+(.+?);\s+(.+?))", 1, "refine_ls_restr", { "dev_ideal", "weight", "number" }, "t_dihedral_angle_d", false },
/* 75 */ { R"(PSEUDO ROTATION ANGLES \(DEGREES\) :\s+(.+?);\s+(.+?);\s+(.+?))", 1, "refine_ls_restr", { "dev_ideal", "weight", "number" }, "t_pseud_angle", false },
/* 76 */ { R"(TRIGONAL CARBON PLANES \(A\) :\s+(.+?);\s+(.+?);\s+(.+?))", 1, "refine_ls_restr", { "dev_ideal", "weight", "number" }, "t_trig_c_planes", false },
/* 77 */ { R"(GENERAL PLANES \(A\) :\s+(.+?);\s+(.+?);\s+(.+?))", 1, "refine_ls_restr", { "dev_ideal", "weight", "number" }, "t_gen_planes", false },
/* 78 */ { R"(ISOTROPIC THERMAL FACTORS \(A\*\*2\) :\s+(.+?);\s+(.+?);\s+(.+?))", 1, "refine_ls_restr", { "dev_ideal", "weight", "number" }, "t_it", false },
/* 79 */ { R"(NON-BONDED CONTACTS \(A\) :\s+(.+?);\s+(.+?);\s+(.+?))", 1, "refine_ls_restr", { "dev_ideal", "weight", "number" }, "t_nbd", false },
/* 80 */ { R"(PEPTIDE OMEGA TORSION ANGLES \(DEGREES\) :\s+(.+?);\s+(.+?);\s+(.+?))", 1, "refine_ls_restr", { "dev_ideal", "weight", "number" }, "t_omega_torsion", false },
/* 81 */ { R"(OTHER TORSION ANGLES \(DEGREES\) :\s+(.+?);\s+(.+?);\s+(.+?))", 1, "refine_ls_restr", { "dev_ideal", "weight", "number" }, "t_other_torsion", false },
/* 82 */ { R"(TLS DETAILS\.?)", 1 },
/* 83 */ { R"(NUMBER OF TLS GROUPS :.+)", 1 },
/* 84 */ { R"(TLS GROUP :\s*(\d+))", 1, "pdbx_refine_tls", { "id" }, nullptr, true },
/* 85 */ { R"((?:SELECTION|SET) *:\s+(.+?))", 1, "pdbx_refine_tls_group", { "selection_details" }, nullptr, true },
/* 86 */ { R"(ORIGIN FOR THE GROUP \(A\):\s+(.+?)\s+(.+?)\s+(.+?))", 1, "pdbx_refine_tls", { "origin_x", "origin_y", "origin_z" } },
/* 87 */ { R"(T TENSOR)", 1 },
/* 88 */ { R"(T11:\s+(.+?) T22:\s+(.+?))", 1, "pdbx_refine_tls", { "T[1][1]", "T[2][2]" } },
/* 89 */ { R"(T33:\s+(.+?) T12:\s+(.+?))", 1, "pdbx_refine_tls", { "T[3][3]", "T[1][2]" } },
/* 90 */ { R"(T13:\s+(.+?) T23:\s+(.+?))", 1, "pdbx_refine_tls", { "T[1][3]", "T[2][3]" } },
/* 91 */ { R"(L TENSOR)", 1 },
/* 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