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libcifpp
Commit fac1eb91 by Maarten L. Hekkelman
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support exporting pdb header lines

parent 3a84a8e6
Showing with 247 additions and 1 deletions
configure.ac
...@@ -15,6 +15,7 @@ AC_DEFUN([read_test], [AC_LANG_SOURCE( ...@@ -15,6 +15,7 @@ AC_DEFUN([read_test], [AC_LANG_SOURCE(
AC_PROG_INSTALL AC_PROG_INSTALL
AC_ENABLE_STATIC AC_ENABLE_STATIC
AC_DISABLE_SHARED
AC_PROG_LIBTOOL AC_PROG_LIBTOOL
AC_SUBST(LIBTOOL_DEPS) AC_SUBST(LIBTOOL_DEPS)
......
include/cif++/Cif2PDB.h
...@@ -3,3 +3,11 @@ ...@@ -3,3 +3,11 @@
#include "cif++/Cif++.h" #include "cif++/Cif++.h"
void WritePDBFile(std::ostream& pdbFile, cif::File& cifFile); void WritePDBFile(std::ostream& pdbFile, cif::File& cifFile);
/// \brief Just the HEADER, COMPND, SOURCE and AUTHOR lines
void WritePDBHeaderLines(std::ostream& os, cif::File& cifFile);
std::string GetPDBHEADERLine(cif::File& cifFile, int truncate_at = 127);
std::string GetPDBCOMPNDLine(cif::File& cifFile, int truncate_at = 127);
std::string GetPDBSOURCELine(cif::File& cifFile, int truncate_at = 127);
std::string GetPDBAUTHORLine(cif::File& cifFile, int truncate_at = 127);
src/Cif2PDB.cpp
...@@ -338,7 +338,7 @@ int WriteCitation(ostream& pdbFile, Datablock& db, Row r, int reference) ...@@ -338,7 +338,7 @@ int WriteCitation(ostream& pdbFile, Datablock& db, Row r, int reference)
return result; return result;
} }
void WriteTitle(ostream& pdbFile, Datablock& db) void WriteHeaderLines(ostream& pdbFile, Datablock& db)
{ {
// 0 1 2 3 4 5 6 7 8 // 0 1 2 3 4 5 6 7 8
// HEADER xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxDDDDDDDDD IIII // HEADER xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxDDDDDDDDD IIII
...@@ -568,6 +568,11 @@ void WriteTitle(ostream& pdbFile, Datablock& db) ...@@ -568,6 +568,11 @@ void WriteTitle(ostream& pdbFile, Datablock& db)
authors.push_back(cif2pdbAuth(r["name"].as<string>())); authors.push_back(cif2pdbAuth(r["name"].as<string>()));
if (not authors.empty()) if (not authors.empty())
WriteOneContinuedLine(pdbFile, "AUTHOR ", 2, ba::join(authors, ",")); WriteOneContinuedLine(pdbFile, "AUTHOR ", 2, ba::join(authors, ","));
}
void WriteTitle(ostream& pdbFile, Datablock& db)
{
WriteHeaderLines(pdbFile, db);
// REVDAT // REVDAT
boost::format kRevDat("REVDAT %3.3d%2.2s %9.9s %4.4s %1.1d "); boost::format kRevDat("REVDAT %3.3d%2.2s %9.9s %4.4s %1.1d ");
...@@ -3720,3 +3725,235 @@ void WritePDBFile(ostream& pdbFile, cif::File& cifFile) ...@@ -3720,3 +3725,235 @@ void WritePDBFile(ostream& pdbFile, cif::File& cifFile)
<< "END" << endl; << "END" << endl;
} }
void WritePDBHeaderLines(std::ostream& os, cif::File& cifFile)
{
io::filtering_ostream out;
out.push(FillOutLineFilter());
out.push(os);
auto filter = out.component<FillOutLineFilter>(0);
assert(filter);
auto& db = cifFile.firstDatablock();
WriteHeaderLines(os, db);
}
std::string FixStringLength(const std::string& s, int l)
{
auto result = s;
if (result.length() > l)
result = result.substr(0, l - 4) + "... ";
else if (result.length() < l)
result.append(l - result.length(), ' ');
return result;
}
std::string GetPDBHEADERLine(cif::File& cifFile, int truncate_at)
{
auto& db = cifFile.firstDatablock();
// 0 1 2 3 4 5 6 7 8
// HEADER xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxDDDDDDDDD IIII
const char kHeader[] =
"HEADER %1$-40.40s" "%2$-9.9s"" %3$-4.4s";
// HEADER
string keywords;
auto& cat1 = db["struct_keywords"];
for (auto r: cat1)
{
keywords = r["keywords"].as<string>();
if (keywords.empty())
keywords = r["pdbx_keywords"].as<string>();
if (keywords.length() > truncate_at - 40)
keywords = keywords.substr(0, truncate_at - 44) + " ...";
}
string date;
for (auto r: db["pdbx_database_status"])
{
date = r["recvd_initial_deposition_date"].as<string>();
if (date.empty())
continue;
date = cif2pdbDate(date);
break;
}
if (date.empty())
{
for (auto r: db["database_PDB_rev"])
{
date = r["date_original"].as<string>();
if (date.empty())
continue;
date = cif2pdbDate(date);
break;
}
}
return FixStringLength((boost::format(kHeader) % keywords % date % db.getName()).str(), truncate_at);
}
std::string GetPDBCOMPNDLine(cif::File& cifFile, int truncate_at)
{
auto& db = cifFile.firstDatablock();
// COMPND
using namespace std::placeholders;
int molID = 0;
vector<string> cmpnd;
for (auto r: db["entity"])
{
if (r["type"] != "polymer")
continue;
string entityId = r["id"].as<string>();
++molID;
cmpnd.push_back("MOL_ID: " + to_string(molID));
string molecule = r["pdbx_description"].as<string>();
cmpnd.push_back("MOLECULE: " + molecule);
auto poly = db["entity_poly"].find(cif::Key("entity_id") == entityId);
if (not poly.empty())
{
string chains = poly.front()["pdbx_strand_id"].as<string>();
ba::replace_all(chains, ",", ", ");
cmpnd.push_back("CHAIN: " + chains);
}
string fragment = r["pdbx_fragment"].as<string>();
if (not fragment.empty())
cmpnd.push_back("FRAGMENT: " + fragment);
for (auto sr: db["entity_name_com"].find(cif::Key("entity_id") == entityId))
{
string syn = sr["name"].as<string>();
if (not syn.empty())
cmpnd.push_back("SYNONYM: " + syn);
}
string mutation = r["pdbx_mutation"].as<string>();
if (not mutation.empty())
cmpnd.push_back("MUTATION: " + mutation);
string ec = r["pdbx_ec"].as<string>();
if (not ec.empty())
cmpnd.push_back("EC: " + ec);
if (r["src_method"] == "man" or r["src_method"] == "syn")
cmpnd.push_back("ENGINEERED: YES");
string details = r["details"].as<string>();
if (not details.empty())
cmpnd.push_back("OTHER_DETAILS: " + details);
}
return FixStringLength("COMPND " + ba::join(cmpnd, "; "), truncate_at);
}
std::string GetPDBSOURCELine(cif::File& cifFile, int truncate_at)
{
auto& db = cifFile.firstDatablock();
// SOURCE
int molID = 0;
vector<string> source;
for (auto r: db["entity"])
{
if (r["type"] != "polymer")
continue;
string entityId = r["id"].as<string>();
++molID;
source.push_back("MOL_ID: " + to_string(molID));
if (r["src_method"] == "syn")
source.push_back("SYNTHETIC: YES");
auto& gen = db["entity_src_gen"];
const pair<const char*,const char*> kGenSourceMapping[] = {
{ "gene_src_common_name", "ORGANISM_COMMON" },
{ "pdbx_gene_src_gene", "GENE" },
{ "gene_src_strain", "STRAIN" },
{ "pdbx_gene_src_cell_line", "CELL_LINE" },
{ "pdbx_gene_src_organelle", "ORGANELLE" },
{ "pdbx_gene_src_cellular_location","CELLULAR_LOCATION" },
{ "pdbx_gene_src_scientific_name", "ORGANISM_SCIENTIFIC" },
{ "pdbx_gene_src_ncbi_taxonomy_id", "ORGANISM_TAXID" },
{ "pdbx_host_org_scientific_name", "EXPRESSION_SYSTEM" },
{ "pdbx_host_org_ncbi_taxonomy_id", "EXPRESSION_SYSTEM_TAXID" },
{ "pdbx_host_org_strain", "EXPRESSION_SYSTEM_STRAIN" },
{ "pdbx_host_org_variant", "EXPRESSION_SYSTEM_VARIANT" },
{ "pdbx_host_org_cellular_location","EXPRESSION_SYSTEM_CELLULAR_LOCATION" },
{ "pdbx_host_org_vector_type", "EXPRESSION_SYSTEM_VECTOR_TYPE" },
{ "pdbx_host_org_vector", "EXPRESSION_SYSTEM_VECTOR" },
{ "pdbx_host_org_gene", "EXPRESSION_SYSTEM_GENE" },
{ "plasmid_name", "EXPRESSION_SYSTEM_PLASMID" },
{ "details", "OTHER_DETAILS" }
};
for (auto gr: gen.find(cif::Key("entity_id") == entityId))
{
for (auto m: kGenSourceMapping)
{
string cname, sname;
tie(cname, sname) = m;
string s = gr[cname].as<string>();
if (not s.empty())
source.push_back(sname + ": " + s);
}
}
auto& nat = db["entity_src_nat"];
const pair<const char*, const char*> kNatSourceMapping[] = {
{ "common_name", "ORGANISM_COMMON" },
{ "strain", "STRAIN" },
{ "pdbx_organism_scientific", "ORGANISM_SCIENTIFIC" },
{ "pdbx_ncbi_taxonomy_id", "ORGANISM_TAXID" },
{ "pdbx_cellular_location", "CELLULAR_LOCATION" },
{ "pdbx_plasmid_name", "PLASMID" },
{ "pdbx_organ", "ORGAN" },
{ "details", "OTHER_DETAILS" }
};
for (auto nr: nat.find(cif::Key("entity_id") == entityId))
{
for (auto m: kNatSourceMapping)
{
string cname, sname;
tie(cname, sname) = m;
string s = nr[cname].as<string>();
if (not s.empty())
source.push_back(sname + ": " + s);
}
}
}
return FixStringLength("SOURCE " + ba::join(source, "; "), truncate_at);
}
std::string GetPDBAUTHORLine(cif::File& cifFile, int truncate_at)
{
auto& db = cifFile.firstDatablock();
// AUTHOR
vector<string> author;
for (auto r: db["audit_author"])
author.push_back(cif2pdbAuth(r["name"].as<string>()));
return FixStringLength("AUTHOR " + ba::join(author, "; "), truncate_at);
}
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