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libcifpp
Commit d5a71b0b by Maarten L. Hekkelman
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Fix verbose checking 

faster aniso_row retrieval
report missing header line for pdb
parent d95b7be2
Showing with 30 additions and 21 deletions
include/cif++/model.hpp
......@@ -101,13 +101,13 @@ class atom
row_handle row_aniso()
{
auto cat = m_db.get("atom_site_anisotrop");
return cat ? cat->find1(key("id") == m_id) : row_handle{};
return cat ? cat->operator[]({ {"id", m_id} }) : row_handle{};
}
const row_handle row_aniso() const
{
auto cat = m_db.get("atom_site_anisotrop");
return cat ? cat->find1(key("id") == m_id) : row_handle{};
return cat ? cat->operator[]({ {"id", m_id} }) : row_handle{};
}
const datablock &m_db;
......
src/pdb/pdb2cif.cpp
......@@ -6211,7 +6211,16 @@ file read(std::istream &is)
if (ch == 'h' or ch == 'H')
ReadPDBFile(is, result);
else
result.load(is);
{
try
{
result.load(is);
}
catch (const std::exception &ex)
{
std::throw_with_nested(std::runtime_error("Since the file did not start with a valid PDB HEADER line mmCIF was assumed, but that failed."));
}
}
}
// Must be a PDB like file, right?
......
src/pdb/tls.cpp
......@@ -320,7 +320,7 @@ struct tls_selection_not : public tls_selection
for (auto &r : residues)
r.selected = not r.selected;
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
{
std::cout << std::string(indentLevel * 2, ' ') << "NOT" << std::endl;
dump_selection(residues, indentLevel);
......@@ -339,7 +339,7 @@ struct tls_selection_all : public tls_selection
for (auto &r : residues)
r.selected = true;
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
{
std::cout << std::string(indentLevel * 2, ' ') << "ALL" << std::endl;
dump_selection(residues, indentLevel);
......@@ -361,7 +361,7 @@ struct tls_selection_chain : public tls_selection_all
for (auto &r : residues)
r.selected = allChains or r.chainID == m_chain;
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
{
std::cout << std::string(indentLevel * 2, ' ') << "CHAIN " << m_chain << std::endl;
dump_selection(residues, indentLevel);
......@@ -384,7 +384,7 @@ struct tls_selection_res_id : public tls_selection_all
for (auto &r : residues)
r.selected = r.seqNr == m_seq_nr and r.iCode == m_icode;
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
{
std::cout << std::string(indentLevel * 2, ' ') << "ResID " << m_seq_nr << (m_icode ? std::string{ m_icode } : "") << std::endl;
dump_selection(residues, indentLevel);
......@@ -411,7 +411,7 @@ struct tls_selection_range_seq : public tls_selection_all
(r.seqNr <= m_last or m_last == kResidueNrWildcard));
}
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
{
std::cout << std::string(indentLevel * 2, ' ') << "Range " << m_first << ':' << m_last << std::endl;
dump_selection(residues, indentLevel);
......@@ -461,7 +461,7 @@ struct tls_selection_range_id : public tls_selection_all
}
}
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
{
std::cout << std::string(indentLevel * 2, ' ') << "Through " << m_first << ':' << m_last << std::endl;
dump_selection(residues, indentLevel);
......@@ -502,7 +502,7 @@ struct tls_selection_union : public tls_selection
for (auto ai = a.begin(), bi = b.begin(), ri = residues.begin(); ri != residues.end(); ++ai, ++bi, ++ri)
ri->selected = ai->selected or bi->selected;
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
{
std::cout << std::string(indentLevel * 2, ' ') << "Union" << std::endl;
dump_selection(residues, indentLevel);
......@@ -543,7 +543,7 @@ struct tls_selection_intersection : public tls_selection
for (auto ai = a.begin(), bi = b.begin(), ri = residues.begin(); ri != residues.end(); ++ai, ++bi, ++ri)
ri->selected = ai->selected and bi->selected;
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
{
std::cout << std::string(indentLevel * 2, ' ') << "Intersection" << std::endl;
dump_selection(residues, indentLevel);
......@@ -567,7 +567,7 @@ struct tls_selection_by_name : public tls_selection_all
for (auto &r : residues)
r.selected = r.name == m_name;
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
{
std::cout << std::string(indentLevel * 2, ' ') << "Name " << m_name << std::endl;
dump_selection(residues, indentLevel);
......@@ -595,7 +595,7 @@ struct tls_selection_by_element : public tls_selection_all
for (auto &r : residues)
r.selected = iequals(r.name, m_element);
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
{
std::cout << std::string(indentLevel * 2, ' ') << "Element " << m_element << std::endl;
dump_selection(residues, indentLevel);
......@@ -1404,7 +1404,7 @@ std::tuple<std::string, int> TLSSelectionParserImplBuster::ParseAtom()
match(':');
std::string atom = m_value_s;
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << "Warning: ignoring atom ID '" << atom << "' in TLS selection" << std::endl;
match(bt_IDENT);
......@@ -1958,14 +1958,14 @@ std::unique_ptr<tls_selection> parse_tls_selection_details(const std::string &pr
if (not result)
{
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << "Falling back to old BUSTER" << std::endl;
result = busterOld.Parse(selection);
}
if (not result)
{
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << "Falling back to PHENIX" << std::endl;
result = phenix.Parse(selection);
}
......@@ -1976,35 +1976,35 @@ std::unique_ptr<tls_selection> parse_tls_selection_details(const std::string &pr
if (not result)
{
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << "Falling back to BUSTER" << std::endl;
result = buster.Parse(selection);
}
if (not result)
{
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << "Falling back to old BUSTER" << std::endl;
result = busterOld.Parse(selection);
}
}
else
{
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << "No known program specified, trying PHENIX" << std::endl;
result = phenix.Parse(selection);
if (not result)
{
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << "Falling back to BUSTER" << std::endl;
result = buster.Parse(selection);
}
if (not result)
{
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << "Falling back to old BUSTER" << std::endl;
result = busterOld.Parse(selection);
}
......
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