Skip to content

L
libcifpp
Commit 28620841 by maarten
Options

prolsq/nuclsq 

git-svn-id: svn+ssh://gitlab/srv/svn-repos/pdb-redo/trunk@364 a1961a4f-ab94-4bcc-80e8-33b5a54de466
parent e0d2c132
Showing with 73 additions and 2 deletions
src/PDB2CifRemark3.cpp
......@@ -327,6 +327,74 @@ void PHENIX_Remark3Parser::fixup()
}
}
const TemplateLine kNUCLSQ_Template[] = {
/* 0 */ { R"(DATA USED IN REFINEMENT\.)", 1 },
/* 1 */ { R"(RESOLUTION RANGE HIGH \(ANGSTROMS\)\s*:\s*(.+))", 1, "refine", { "ls_d_res_high" } },
/* 2 */ { R"(RESOLUTION RANGE LOW \(ANGSTROMS\)\s*:\s*(.+))", 1, "refine", { "ls_d_res_low" } },
/* 3 */ { R"(DATA CUTOFF \(SIGMA\(F\)\)\s*:\s*(.+))", 1, "refine", { "pdbx_ls_sigma_F" } },
/* 4 */ { R"(COMPLETENESS FOR RANGE \(%\)\s*:\s*(.+))", 1, "refine", { "ls_percent_reflns_obs" } },
/* 5 */ { R"(NUMBER OF REFLECTIONS\s*:\s*(.+))", 1, "refine", { "ls_number_reflns_obs" } },
/* 6 */ { R"(FIT TO DATA USED IN REFINEMENT\.)", 1 },
/* 7 */ { R"(CROSS-VALIDATION METHOD\s*:\s*(.+))", 1, "refine", { "pdbx_ls_cross_valid_method" } },
/* 8 */ { R"(FREE R VALUE TEST SET SELECTION\s*:\s*(.+))", 1, "refine", { "pdbx_R_Free_selection_details" } },
/* 9 */ { R"(R VALUE \(WORKING \+ TEST SET\)\s*:\s*(.+))", 1, "refine", { "ls_R_factor_obs" } },
/* 10 */ { R"(R VALUE \(WORKING SET\)\s*:\s*(.+))", 1, "refine", { "ls_R_factor_R_work" } },
/* 11 */ { R"(FREE R VALUE\s*:\s*(.+))", 1, "refine", { "ls_R_factor_R_free" } },
/* 12 */ { R"(FREE R VALUE TEST SET SIZE \(%\)\s*:\s*(.+))", 1, "refine", { "ls_percent_reflns_R_free" } },
/* 13 */ { R"(FREE R VALUE TEST SET COUNT\s*:\s*(.+))", 1, "refine", { "ls_number_reflns_R_free" } },
/* 14 */ { R"(FIT/AGREEMENT OF MODEL WITH ALL DATA\.)", 1 },
/* 15 */ { R"(R VALUE \(WORKING \+ TEST SET, NO CUTOFF\)\s*:\s*(.+))", 1, "pdbx_refine", { "R_factor_all_no_cutoff" } },
/* 16 */ { R"(R VALUE \(WORKING SET, NO CUTOFF\)\s*:\s*(.+))", 1, "pdbx_refine", { "R_factor_obs_no_cutoff" } },
/* 17 */ { R"(FREE R VALUE \(NO CUTOFF\)\s*:\s*(.+))", 1, "pdbx_refine", { "free_R_factor_no_cutoff" } },
/* 18 */ { R"(FREE R VALUE TEST SET SIZE \(%, NO CUTOFF\)\s*:\s*(.+))", 1, "pdbx_refine", { "free_R_val_test_set_size_perc_no_cutoff" } },
/* 19 */ { R"(FREE R VALUE TEST SET COUNT \(NO CUTOFF\)\s*:\s*(.+))", 1, "pdbx_refine", { "free_R_val_test_set_ct_no_cutoff" } },
/* 20 */ { R"(TOTAL NUMBER OF REFLECTIONS \(NO CUTOFF\)\s*:\s*(.+))", 1, "refine", { "ls_number_reflns_all" } },
/* 21 */ { R"(NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT\.)", 1 },
/* 22 */ { R"(PROTEIN ATOMS\s*:\s*(.+))", 1, "refine_hist", { "pdbx_number_atoms_protein" } },
/* 23 */ { R"(NUCLEIC ACID ATOMS\s*:\s*(.+))", 1, "refine_hist", { "pdbx_number_atoms_nucleic_acid" } },
/* 24 */ { R"(HETEROGEN ATOMS\s*:\s*(.+))", 1, "refine_hist", { "pdbx_number_atoms_ligand" } },
/* 25 */ { R"(SOLVENT ATOMS\s*:\s*(.+))", 1, "refine_hist", { "number_atoms_solvent" } },
/* 26 */ { R"(B VALUES\.)", 1 },
/* 27 */ { R"(B VALUE TYPE\s*:\s*(.+))", 1, "refine", { "pdbx_TLS_residual_ADP_flag" } },
/* 28 */ { R"(FROM WILSON PLOT \(A\*\*2\)\s*:\s*(.+))", 1, "reflns", { "B_iso_Wilson_estimate" } },
/* 29 */ { R"(MEAN B VALUE \(OVERALL, A\*\*2\)\s*:\s*(.+))", 1, "refine", { "B_iso_mean" } },
/* 30 */ { R"(OVERALL ANISOTROPIC B VALUE\.)", 1 },
/* 31 */ { R"(B11 \(A\*\*2\)\s*:\s*(.+))", 1, "refine", { "aniso_B[1][1]" } },
/* 32 */ { R"(B22 \(A\*\*2\)\s*:\s*(.+))", 1, "refine", { "aniso_B[2][2]" } },
/* 33 */ { R"(B33 \(A\*\*2\)\s*:\s*(.+))", 1, "refine", { "aniso_B[3][3]" } },
/* 34 */ { R"(B12 \(A\*\*2\)\s*:\s*(.+))", 1, "refine", { "aniso_B[1][2]" } },
/* 35 */ { R"(B13 \(A\*\*2\)\s*:\s*(.+))", 1, "refine", { "aniso_B[1][3]" } },
/* 36 */ { R"(B23 \(A\*\*2\)\s*:\s*(.+))", 1, "refine", { "aniso_B[2][3]" } },
/* 37 */ { R"(ESTIMATED COORDINATE ERROR\.)", 1 },
/* 38 */ { R"(ESD FROM LUZZATI PLOT \(A\)\s*:\s*(.+))", 1, "refine_analyze", { "Luzzati_coordinate_error_obs" } },
/* 39 */ { R"(ESD FROM SIGMAA \(A\)\s*:\s*(.+))", 1, "refine_analyze", { "Luzzati_sigma_a_obs" } },
/* 40 */ { R"(LOW RESOLUTION CUTOFF \(A\)\s*:\s*(.+))", 1, "refine_analyze", { "Luzzati_d_res_low_obs" } },
/* 41 */ { R"(RMS DEVIATIONS FROM IDEAL VALUES\.)", 1 },
/* 42 */ { R"(DISTANCE RESTRAINTS\. RMS SIGMA)", 1 },
/* 43 */ { R"(SUGAR-BASE BOND DISTANCE \(A\)\s*:\s*(.+)\s*;\s*(.+))", 1, "refine_ls_restr", { "dev_ideal", "dev_ideal_target" }, "n_sugar_bond_d", false },
/* 44 */ { R"(SUGAR-BASE BOND ANGLE DISTANCE \(A\)\s*:\s*(.+)\s*;\s*(.+))", 1, "refine_ls_restr", { "dev_ideal", "dev_ideal_target" }, "n_sugar_bond_angle_d", false },
/* 45 */ { R"(PHOSPHATE BONDS DISTANCE \(A\)\s*:\s*(.+)\s*;\s*(.+))", 1, "refine_ls_restr", { "dev_ideal", "dev_ideal_target" }, "n_phos_bond_d", false },
/* 46 */ { R"(PHOSPHATE BOND ANGLE, H-BOND \(A\)\s*:\s*(.+)\s*;\s*(.+))", 1, "refine_ls_restr", { "dev_ideal", "dev_ideal_target" }, "n_phos_bond_angle_d", false },
/* 47 */ { R"(PLANE RESTRAINT \(A\)\s*:\s*(.+)\s*;\s*(.+))", 1, "refine_ls_restr", { "dev_ideal", "dev_ideal_target" }, "n_plane_restr", false },
/* 48 */ { R"(CHIRAL-CENTER RESTRAINT \(A\*\*3\)\s*:\s*(.+)\s*;\s*(.+))", 1, "refine_ls_restr", { "dev_ideal", "dev_ideal_target" }, "n_chiral_restr", false },
/* 49 */ { R"(NON-BONDED CONTACT RESTRAINTS\.)", 1 },
/* 50 */ { R"(SINGLE TORSION \(A\)\s*:\s*(.+)\s*;\s*(.+))", 1, "refine_ls_restr", { "dev_ideal", "dev_ideal_target" }, "n_singtor_nbd", false },
/* 51 */ { R"(MULTIPLE TORSION \(A\)\s*:\s*(.+)\s*;\s*(.+))", 1, "refine_ls_restr", { "dev_ideal", "dev_ideal_target" }, "n_multtor_nbd", false },
/* 59 */ { R"(ISOTROPIC THERMAL FACTOR RESTRAINTS\. RMS SIGMA)", 1 },
/* 60 */ { R"(SUGAR-BASE BONDS \(A\*\*2\)\s*:\s*(.+)\s*;\s*(.+))", 1, "refine_ls_restr", { "dev_ideal", "dev_ideal_target" }, "n_sugar_bond_it", false },
/* 61 */ { R"(SUGAR-BASE ANGLES \(A\*\*2\)\s*:\s*(.+)\s*;\s*(.+))", 1, "refine_ls_restr", { "dev_ideal", "dev_ideal_target" }, "n_sugar_angle_it", false },
/* 62 */ { R"(PHOSPHATE BONDS \(A\*\*2\)\s*:\s*(.+)\s*;\s*(.+))", 1, "refine_ls_restr", { "dev_ideal", "dev_ideal_target" }, "n_phos_bond_it", false },
/* 63 */ { R"(PHOSPHATE BOND ANGLE, H-BOND \(A\*\*2\)\s*:\s*(.+)\s*;\s*(.+))", 1, "refine_ls_restr", { "dev_ideal", "dev_ideal_target" }, "n_phos_angle_it", false },
};
class NUCLSQ_Remark3Parser : public Remark3Parser
{
public:
NUCLSQ_Remark3Parser(const string& name, const string& expMethod, PDBRecord* r, cif::Datablock& db)
: Remark3Parser(name, expMethod, r, db, kNUCLSQ_Template, sizeof(kNUCLSQ_Template) / sizeof(TemplateLine),
regex(R"((NUCLSQ)(?: (\d+(?:\.\d+)?))?)")) {}
};
const TemplateLine kPROLSQ_Template[] = {
/* 0 */ { R"(DATA USED IN REFINEMENT\.)", 1 },
/* 1 */ { R"(RESOLUTION RANGE HIGH \(ANGSTROMS\)\s*:\s*(.+))", 1, "refine", { "ls_d_res_high" } },
......@@ -399,7 +467,7 @@ class PROLSQ_Remark3Parser : public Remark3Parser
public:
PROLSQ_Remark3Parser(const string& name, const string& expMethod, PDBRecord* r, cif::Datablock& db)
: Remark3Parser(name, expMethod, r, db, kPROLSQ_Template, sizeof(kPROLSQ_Template) / sizeof(TemplateLine),
regex(R"((PROLSQ|NUCLSQ)(?: (\d+(?:\.\d+)?))?)")) {}
regex(R"((PROLSQ)(?: (\d+(?:\.\d+)?))?)")) {}
};
const TemplateLine kREFMAC_Template[] = {
......@@ -1257,7 +1325,9 @@ bool Remark3Parser::parse(const string& expMethod, PDBRecord* r, cif::Datablock&
tryParser(new CNS_Remark3Parser(program, expMethod, r, db));
else if (ba::starts_with(program, "PHENIX"))
tryParser(new PHENIX_Remark3Parser(program, expMethod, r, db));
else if (ba::starts_with(program, "PROLSQ") or ba::starts_with(program, "NUCLSQ"))
else if (ba::starts_with(program, "NUCLSQ"))
tryParser(new NUCLSQ_Remark3Parser(program, expMethod, r, db));
else if (ba::starts_with(program, "PROLSQ"))
tryParser(new PROLSQ_Remark3Parser(program, expMethod, r, db));
else if (ba::starts_with(program, "REFMAC"))
{
......
src/Point.cpp
// Lib for working with structures as contained in mmCIF and PDB files
#include <random>
#include <valarray>
#include "cif++/Point.h"
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment