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Commit 958d1fb3 by maarten
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round trip fidelity 

git-svn-id: svn+ssh://gitlab/srv/svn-repos/pdb-redo/trunk@365 a1961a4f-ab94-4bcc-80e8-33b5a54de466
parent 28620841
Showing with 38 additions and 11 deletions
src/Cif2PDB.cpp
...@@ -1883,7 +1883,7 @@ void WriteRemark3NuclSQ(ostream& pdbFile, Datablock& db) ...@@ -1883,7 +1883,7 @@ void WriteRemark3NuclSQ(ostream& pdbFile, Datablock& db)
<< RM3("") << endl << RM3("") << endl
<< RM3(" FIT/AGREEMENT OF MODEL WITH ALL DATA.") << endl << RM3(" FIT/AGREEMENT OF MODEL WITH ALL DATA.") << endl
<< RM3(" R VALUE (WORKING + TEST SET, NO CUTOFF) : ") << Fs(pdbx_refine, "R_factor_all_no_cutoff") << endl << RM3(" R VALUE (WORKING + TEST SET, NO CUTOFF) : ") << Fs(refine, "ls_R_factor_all") << endl
<< RM3(" R VALUE (WORKING SET, NO CUTOFF) : ") << Fs(pdbx_refine, "R_factor_obs_no_cutoff") << endl << RM3(" R VALUE (WORKING SET, NO CUTOFF) : ") << Fs(pdbx_refine, "R_factor_obs_no_cutoff") << endl
<< RM3(" FREE R VALUE (NO CUTOFF) : ") << Fs(pdbx_refine, "free_R_factor_no_cutoff") << endl << RM3(" FREE R VALUE (NO CUTOFF) : ") << Fs(pdbx_refine, "free_R_factor_no_cutoff") << endl
...@@ -1901,7 +1901,7 @@ void WriteRemark3NuclSQ(ostream& pdbFile, Datablock& db) ...@@ -1901,7 +1901,7 @@ void WriteRemark3NuclSQ(ostream& pdbFile, Datablock& db)
<< RM3("") << endl << RM3("") << endl
<< RM3(" B VALUES.") << endl << RM3(" B VALUES.") << endl
<< RM3(" B VALUE TYPE : ", 7, 2) << Fs(refine, "pdbx_TLS_residual_ADP_flag") << endl // << RM3(" B VALUE TYPE : ", 7, 2) << Fs(refine, "pdbx_TLS_residual_ADP_flag") << endl
<< RM3(" FROM WILSON PLOT (A**2) : ", 7, 2) << Ff(reflns, "B_iso_Wilson_estimate") << endl << RM3(" FROM WILSON PLOT (A**2) : ", 7, 2) << Ff(reflns, "B_iso_Wilson_estimate") << endl
<< RM3(" MEAN B VALUE (OVERALL, A**2) : ", 7, 2) << Ff(refine, "B_iso_mean") << endl << RM3(" MEAN B VALUE (OVERALL, A**2) : ", 7, 2) << Ff(refine, "B_iso_mean") << endl
<< RM3(" OVERALL ANISOTROPIC B VALUE.") << endl << RM3(" OVERALL ANISOTROPIC B VALUE.") << endl
...@@ -1987,7 +1987,7 @@ void WriteRemark3ProlSQ(ostream& pdbFile, Datablock& db) ...@@ -1987,7 +1987,7 @@ void WriteRemark3ProlSQ(ostream& pdbFile, Datablock& db)
<< RM3("") << endl << RM3("") << endl
<< RM3(" FIT/AGREEMENT OF MODEL WITH ALL DATA.") << endl << RM3(" FIT/AGREEMENT OF MODEL WITH ALL DATA.") << endl
<< RM3(" R VALUE (WORKING + TEST SET, NO CUTOFF) : ") << Fs(pdbx_refine, "R_factor_all_no_cutoff") << endl << RM3(" R VALUE (WORKING + TEST SET, NO CUTOFF) : ") << Fs(refine, "ls_R_factor_all") << endl
<< RM3(" R VALUE (WORKING SET, NO CUTOFF) : ") << Fs(pdbx_refine, "R_factor_obs_no_cutoff") << endl << RM3(" R VALUE (WORKING SET, NO CUTOFF) : ") << Fs(pdbx_refine, "R_factor_obs_no_cutoff") << endl
<< RM3(" FREE R VALUE (NO CUTOFF) : ") << Fs(pdbx_refine, "free_R_factor_no_cutoff") << endl << RM3(" FREE R VALUE (NO CUTOFF) : ") << Fs(pdbx_refine, "free_R_factor_no_cutoff") << endl
...@@ -2005,7 +2005,7 @@ void WriteRemark3ProlSQ(ostream& pdbFile, Datablock& db) ...@@ -2005,7 +2005,7 @@ void WriteRemark3ProlSQ(ostream& pdbFile, Datablock& db)
<< RM3("") << endl << RM3("") << endl
<< RM3(" B VALUES.") << endl << RM3(" B VALUES.") << endl
<< RM3(" B VALUE TYPE : ", 7, 2) << Fs(refine, "pdbx_TLS_residual_ADP_flag") << endl // << RM3(" B VALUE TYPE : ", 7, 2) << Fs(refine, "pdbx_TLS_residual_ADP_flag") << endl
<< RM3(" FROM WILSON PLOT (A**2) : ", 7, 2) << Ff(reflns, "B_iso_Wilson_estimate") << endl << RM3(" FROM WILSON PLOT (A**2) : ", 7, 2) << Ff(reflns, "B_iso_Wilson_estimate") << endl
<< RM3(" MEAN B VALUE (OVERALL, A**2) : ", 7, 2) << Ff(refine, "B_iso_mean") << endl << RM3(" MEAN B VALUE (OVERALL, A**2) : ", 7, 2) << Ff(refine, "B_iso_mean") << endl
<< RM3(" OVERALL ANISOTROPIC B VALUE.") << endl << RM3(" OVERALL ANISOTROPIC B VALUE.") << endl
......
src/PDB2Cif.cpp
...@@ -750,8 +750,7 @@ class PDBFileParser ...@@ -750,8 +750,7 @@ class PDBFileParser
string pdb2cifDate(string s) string pdb2cifDate(string s)
{ {
boost::system::error_code ec; boost::system::error_code ec;
pdb2cifDate(s, ec); return pdb2cifDate(s, ec);
return s;
} }
string pdb2cifAuth(string author) string pdb2cifAuth(string author)
...@@ -1564,8 +1563,8 @@ void PDBFileParser::ParseTitle() ...@@ -1564,8 +1563,8 @@ void PDBFileParser::ParseTitle()
} }
/* /*
This is internal stuff for PDB, don't write it This is internal stuff for PDB, don't write it ???
*/
sort(revdats.begin(), revdats.end()); sort(revdats.begin(), revdats.end());
for (auto& revdat: revdats) for (auto& revdat: revdats)
{ {
...@@ -1587,7 +1586,7 @@ void PDBFileParser::ParseTitle() ...@@ -1587,7 +1586,7 @@ void PDBFileParser::ParseTitle()
}); });
} }
} }
*/ //*/
// SPRSDE // SPRSDE
if (mRec->is("SPRSDE")) if (mRec->is("SPRSDE"))
......
src/PDB2CifRemark3.cpp
...@@ -343,7 +343,7 @@ const TemplateLine kNUCLSQ_Template[] = { ...@@ -343,7 +343,7 @@ const TemplateLine kNUCLSQ_Template[] = {
/* 12 */ { R"(FREE R VALUE TEST SET SIZE \(%\)\s*:\s*(.+))", 1, "refine", { "ls_percent_reflns_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" } }, /* 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 }, /* 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" } }, /* 15 */ { R"(R VALUE \(WORKING \+ TEST SET, NO CUTOFF\)\s*:\s*(.+))", 1, "refine", { "ls_R_factor_all" } },
/* 16 */ { R"(R VALUE \(WORKING SET, NO CUTOFF\)\s*:\s*(.+))", 1, "pdbx_refine", { "R_factor_obs_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" } }, /* 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" } }, /* 18 */ { R"(FREE R VALUE TEST SET SIZE \(%, NO CUTOFF\)\s*:\s*(.+))", 1, "pdbx_refine", { "free_R_val_test_set_size_perc_no_cutoff" } },
...@@ -393,6 +393,20 @@ class NUCLSQ_Remark3Parser : public Remark3Parser ...@@ -393,6 +393,20 @@ class NUCLSQ_Remark3Parser : public Remark3Parser
NUCLSQ_Remark3Parser(const string& name, const string& expMethod, PDBRecord* r, cif::Datablock& db) 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), : Remark3Parser(name, expMethod, r, db, kNUCLSQ_Template, sizeof(kNUCLSQ_Template) / sizeof(TemplateLine),
regex(R"((NUCLSQ)(?: (\d+(?:\.\d+)?))?)")) {} regex(R"((NUCLSQ)(?: (\d+(?:\.\d+)?))?)")) {}
virtual void fixup()
{
for (auto r: mDb["refine_hist"])
{
try
{
int p, n, h, s;
cif::tie(p, n, h, s) = r.get("pdbx_number_atoms_protein", "pdbx_number_atoms_nucleic_acid", "pdbx_number_atoms_ligand", "number_atoms_solvent");
r["number_atoms_total"] = p + n + h + s;
}
catch (...) {}
}
}
}; };
const TemplateLine kPROLSQ_Template[] = { const TemplateLine kPROLSQ_Template[] = {
...@@ -411,7 +425,7 @@ const TemplateLine kPROLSQ_Template[] = { ...@@ -411,7 +425,7 @@ const TemplateLine kPROLSQ_Template[] = {
/* 12 */ { R"(FREE R VALUE TEST SET SIZE \(%\)\s*:\s*(.+))", 1, "refine", { "ls_percent_reflns_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" } }, /* 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 }, /* 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" } }, /* 15 */ { R"(R VALUE \(WORKING \+ TEST SET, NO CUTOFF\)\s*:\s*(.+))", 1, "refine", { "ls_R_factor_all" } },
/* 16 */ { R"(R VALUE \(WORKING SET, NO CUTOFF\)\s*:\s*(.+))", 1, "pdbx_refine", { "R_factor_obs_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" } }, /* 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" } }, /* 18 */ { R"(FREE R VALUE TEST SET SIZE \(%, NO CUTOFF\)\s*:\s*(.+))", 1, "pdbx_refine", { "free_R_val_test_set_size_perc_no_cutoff" } },
...@@ -468,6 +482,20 @@ class PROLSQ_Remark3Parser : public Remark3Parser ...@@ -468,6 +482,20 @@ class PROLSQ_Remark3Parser : public Remark3Parser
PROLSQ_Remark3Parser(const string& name, const string& expMethod, PDBRecord* r, cif::Datablock& db) 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), : Remark3Parser(name, expMethod, r, db, kPROLSQ_Template, sizeof(kPROLSQ_Template) / sizeof(TemplateLine),
regex(R"((PROLSQ)(?: (\d+(?:\.\d+)?))?)")) {} regex(R"((PROLSQ)(?: (\d+(?:\.\d+)?))?)")) {}
virtual void fixup()
{
for (auto r: mDb["refine_hist"])
{
try
{
int p, n, h, s;
cif::tie(p, n, h, s) = r.get("pdbx_number_atoms_protein", "pdbx_number_atoms_nucleic_acid", "pdbx_number_atoms_ligand", "number_atoms_solvent");
r["number_atoms_total"] = p + n + h + s;
}
catch (...) {}
}
}
}; };
const TemplateLine kREFMAC_Template[] = { const TemplateLine kREFMAC_Template[] = {
......
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