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libcifpp
Commit aec60829 by Maarten L. Hekkelman
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more quiet code

parent 888c3c38
Showing with 157 additions and 127 deletions
src/BondMap.cpp
......@@ -180,7 +180,10 @@ bool CompoundBondMap::bonded(const std::string &compoundID, const std::string &a
auto compound = mmcif::CompoundFactory::instance().create(compoundID);
if (not compound)
std::cerr << "Missing compound bond info for " << compoundID << std::endl;
{
if (cif::VERBOSE >= 0)
std::cerr << "Missing compound bond info for " << compoundID << std::endl;
}
else
{
for (auto &atom : compound->bonds())
......@@ -308,7 +311,7 @@ BondMap::BondMap(const Structure &p)
{
if (c == "HOH" or c == "H2O" or c == "WAT")
{
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << "skipping water in bond map calculation" << std::endl;
continue;
}
......
src/Cif++.cpp
......@@ -1497,7 +1497,7 @@ size_t Category::getColumnIndex(std::string_view name) const
break;
}
if (VERBOSE and result == mColumns.size() and mCatValidator != nullptr) // validate the name, if it is known at all (since it was not found)
if (VERBOSE > 0 and result == mColumns.size() and mCatValidator != nullptr) // validate the name, if it is known at all (since it was not found)
{
auto iv = mCatValidator->getValidatorForItem(name);
if (iv == nullptr)
......@@ -2340,7 +2340,7 @@ void Category::validateLinks() const
if (not hasParent(r, *parentCat, *link))
++missing;
if (missing)
if (missing and VERBOSE >= 0)
{
std::cerr << "Links for " << link->mLinkGroupLabel << " are incomplete" << std::endl
<< " There are " << missing << " items in " << mName << " that don't have matching parent items in " << parentCat->mName << std::endl;
......@@ -2900,7 +2900,7 @@ void Category::update_value(RowSet &&rows, const std::string &tag, const std::st
}
// cannot update this...
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << "Cannot update child " << childCat->mName << "." << childTag << " with value " << value << std::endl;
}
......@@ -3018,7 +3018,8 @@ void Row::assign(std::string_view name, const std::string &value, bool skipUpdat
}
catch (const std::exception &ex)
{
std::cerr << "Could not assign value '" << value << "' to column _" << mData->mCategory->name() << '.' << name << std::endl;
if (cif::VERBOSE >= 0)
std::cerr << "Could not assign value '" << value << "' to column _" << mData->mCategory->name() << '.' << name << std::endl;
throw;
}
}
......@@ -3181,7 +3182,7 @@ void Row::assign(size_t column, const std::string &value, bool skipUpdateLinked)
auto rows_n = childCat->find(std::move(cond_n));
if (not rows_n.empty())
{
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << "Will not rename in child category since there are already rows that link to the parent" << std::endl;
continue;
......@@ -3387,7 +3388,7 @@ void Row::swap(size_t cix, ItemRow *a, ItemRow *b)
}
else
{
if (VERBOSE)
if (VERBOSE > 0)
std::cerr << "In " << childCat->mName << " changing " << linkChildColName << ": " << r[linkChildColName].as<std::string>() << " => " << (i ? i->mText : "") << std::endl;
r[linkChildColName] = i ? i->mText : "";
}
......@@ -3496,7 +3497,8 @@ File::File(const std::filesystem::path &path, bool validate)
}
catch (const std::exception &ex)
{
std::cerr << "Error while loading file " << path << std::endl;
if (cif::VERBOSE >= 0)
std::cerr << "Error while loading file " << path << std::endl;
throw;
}
}
......@@ -3564,7 +3566,8 @@ void File::load(const std::filesystem::path &p)
}
catch (const std::exception &ex)
{
std::cerr << "Error loading file " << path << std::endl;
if (cif::VERBOSE >= 0)
std::cerr << "Error loading file " << path << std::endl;
throw;
}
}
......@@ -3660,7 +3663,7 @@ bool File::isValid()
{
if (mValidator == nullptr)
{
if (VERBOSE)
if (VERBOSE > 0)
std::cerr << "No dictionary loaded explicitly, loading default" << std::endl;
loadDictionary();
......
src/Cif2PDB.cpp
......@@ -753,7 +753,8 @@ class Ff : public FBase
}
catch (const std::exception& ex)
{
std::cerr << "Failed to write '" << s << "' as a double, this indicates an error in the code for writing PDB files" << std::endl;
if (cif::VERBOSE >= 0)
std::cerr << "Failed to write '" << s << "' as a double, this indicates an error in the code for writing PDB files" << std::endl;
os << s;
}
}
......@@ -2329,7 +2330,8 @@ void WriteRemark200(std::ostream& pdbFile, Datablock& db)
}
catch (const std::exception& ex)
{
std::cerr << ex.what() << std::endl;
if (cif::VERBOSE >= 0)
std::cerr << ex.what() << std::endl;
}
}
......@@ -2390,7 +2392,8 @@ void WriteRemark280(std::ostream& pdbFile, Datablock& db)
}
catch (const std::exception& ex)
{
std::cerr << ex.what() << std::endl;
if (cif::VERBOSE >= 0)
std::cerr << ex.what() << std::endl;
}
}
......
src/CifParser.cpp
......@@ -288,7 +288,7 @@ SacParser::CIFToken SacParser::getNextToken()
mState = eStateTextField + 1;
else if (ch == kEOF)
error("unterminated textfield");
else if (not isAnyPrint(ch))
else if (not isAnyPrint(ch) and cif::VERBOSE >= 0)
// error("invalid character in text field '" + string({ static_cast<char>(ch) }) + "' (" + to_string((int)ch) + ")");
std::cerr << "invalid character in text field '" << std::string({static_cast<char>(ch)}) << "' (" << ch << ") line: " << mLineNr << std::endl;
break;
......@@ -1220,7 +1220,7 @@ void DictParser::linkItems()
{
for (auto &iv : cv.mItemValidators)
{
if (iv.mType == nullptr)
if (iv.mType == nullptr and cif::VERBOSE >= 0)
std::cerr << "Missing item_type for " << iv.mTag << std::endl;
}
}
......@@ -1255,7 +1255,8 @@ void DictParser::loadDictionary()
}
catch (const std::exception &)
{
std::cerr << "Error parsing dictionary" << std::endl;
if (cif::VERBOSE >= 0)
std::cerr << "Error parsing dictionary" << std::endl;
throw;
}
......
src/CifUtils.cpp
......@@ -1237,7 +1237,7 @@ std::filesystem::path gDataDir;
void addDataDirectory(std::filesystem::path dataDir)
{
if (VERBOSE and not fs::exists(dataDir))
if (VERBOSE > 0 and not fs::exists(dataDir))
std::cerr << "The specified data directory " << dataDir << " does not exist" << std::endl;
gDataDir = dataDir;
}
......
src/CifValidator.cpp
......@@ -354,7 +354,7 @@ void Validator::reportError(const std::string &msg, bool fatal) const
{
if (mStrict or fatal)
throw ValidationError(msg);
else if (VERBOSE)
else if (VERBOSE > 0)
std::cerr << msg << std::endl;
}
......
src/Compound.cpp
......@@ -193,7 +193,7 @@ Compound::Compound(cif::Datablock &db, const std::string &id, const std::string
bond.type = BondType::delo;
else
{
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << "Unimplemented chem_comp_bond.type " << btype << " in " << id << std::endl;
bond.type = BondType::sing;
}
......@@ -520,7 +520,7 @@ Compound *CCDCompoundFactoryImpl::create(const std::string &id)
}
}
if (result == nullptr and cif::VERBOSE)
if (result == nullptr and cif::VERBOSE > 0)
std::cerr << "Could not locate compound " << id << " in the CCD components file" << std::endl;
return result;
......@@ -645,13 +645,13 @@ CompoundFactory::CompoundFactory()
auto ccd = cif::loadResource("components.cif");
if (ccd)
mImpl.reset(new CCDCompoundFactoryImpl(mImpl));
else if (cif::VERBOSE)
else if (cif::VERBOSE > 0)
std::cerr << "CCD components.cif file was not found" << std::endl;
const char *clibd_mon = getenv("CLIBD_MON");
if (clibd_mon != nullptr and fs::is_directory(clibd_mon))
mImpl.reset(new CCP4CompoundFactoryImpl(clibd_mon));
else if (cif::VERBOSE)
else if (cif::VERBOSE > 0)
std::cerr << "CCP4 monomers library not found, CLIBD_MON is not defined" << std::endl;
}
......@@ -695,7 +695,8 @@ void CompoundFactory::setDefaultDictionary(const std::filesystem::path &inDictFi
}
catch (const std::exception &)
{
std::cerr << "Error loading dictionary " << inDictFile << std::endl;
if (cif::VERBOSE >= 0)
std::cerr << "Error loading dictionary " << inDictFile << std::endl;
throw;
}
}
......@@ -715,7 +716,8 @@ void CompoundFactory::pushDictionary(const std::filesystem::path &inDictFile)
}
catch (const std::exception &)
{
std::cerr << "Error loading dictionary " << inDictFile << std::endl;
if (cif::VERBOSE >= 0)
std::cerr << "Error loading dictionary " << inDictFile << std::endl;
throw;
}
}
......
src/PDB2Cif.cpp
......@@ -268,7 +268,8 @@ int PDBRecord::vI(int columnFirst, int columnLast)
}
catch (const std::exception &ex)
{
std::cerr << "Trying to parse '" << std::string(mValue + columnFirst - 7, mValue + columnLast - 7) << '\'' << std::endl;
if (cif::VERBOSE >= 0)
std::cerr << "Trying to parse '" << std::string(mValue + columnFirst - 7, mValue + columnLast - 7) << '\'' << std::endl;
throw;
}
......@@ -337,7 +338,7 @@ std::tuple<std::string, std::string> SpecificationListParser::GetNextSpecificati
}
else if (not isspace(ch))
{
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << "skipping invalid character in SOURCE ID: " << ch << std::endl;
}
break;
......@@ -354,7 +355,7 @@ std::tuple<std::string, std::string> SpecificationListParser::GetNextSpecificati
case eColon:
if (ch == ';')
{
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << "Empty value for SOURCE: " << id << std::endl;
state = eStart;
}
......@@ -418,7 +419,7 @@ std::tuple<std::string, std::string> SpecificationListParser::GetNextSpecificati
case eError:
if (ch == ';')
{
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << "Skipping invalid header line: '" << std::string(start, mP) << std::endl;
state = eStart;
}
......@@ -832,7 +833,7 @@ class PDBFileParser
if (not mChainSeq2AsymSeq.count(key))
{
ec = error::make_error_code(error::pdbErrors::residueNotFound);
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << "Residue " << chainID << resSeq << iCode << " could not be mapped" << std::endl;
}
else
......@@ -929,7 +930,7 @@ class PDBFileParser
}
catch (const std::exception &ex)
{
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << ex.what() << std::endl;
ec = error::make_error_code(error::pdbErrors::invalidDate);
}
......@@ -1160,7 +1161,8 @@ void PDBFileParser::PreParseInput(std::istream &is)
if (is.eof())
break;
std::cerr << "Line number " << lineNr << " is empty!" << std::endl;
if (cif::VERBOSE > 0)
std::cerr << "Line number " << lineNr << " is empty!" << std::endl;
getline(is, lookahead);
++lineNr;
......@@ -1278,7 +1280,8 @@ void PDBFileParser::PreParseInput(std::istream &is)
}
catch (const std::exception &ex)
{
std::cerr << "Dropping FORMUL line (" << (lineNr - 1) << ") with invalid component number '" << value.substr(1, 3) << '\'' << std::endl;
if (cif::VERBOSE >= 0)
std::cerr << "Dropping FORMUL line (" << (lineNr - 1) << ") with invalid component number '" << value.substr(1, 3) << '\'' << std::endl;
continue;
// throw_with_nested(std::runtime_error("Invalid component number '" + value.substr(1, 3) + '\''));
}
......@@ -1305,7 +1308,8 @@ void PDBFileParser::PreParseInput(std::istream &is)
}
catch (const std::exception &ex)
{
std::cerr << "Error parsing FORMUL at line " << lineNr << std::endl;
if (cif::VERBOSE >= 0)
std::cerr << "Error parsing FORMUL at line " << lineNr << std::endl;
throw;
}
}
......@@ -1412,7 +1416,8 @@ void PDBFileParser::PreParseInput(std::istream &is)
if (not dropped.empty())
{
std::cerr << "Dropped unsupported records: " << ba::join(dropped, ", ") << std::endl;
if (cif::VERBOSE >= 0)
std::cerr << "Dropped unsupported records: " << ba::join(dropped, ", ") << std::endl;
}
if (mData == nullptr)
......@@ -1440,7 +1445,7 @@ void PDBFileParser::Match(const std::string &expected, bool throwIfMissing)
{
if (throwIfMissing)
throw std::runtime_error("Expected record " + expected + " but found " + mRec->mName);
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << "Expected record " + expected + " but found " + mRec->mName << std::endl;
}
}
......@@ -1575,7 +1580,8 @@ void PDBFileParser::ParseTitle()
if (not iequals(key, "MOL_ID") and mCompounds.empty())
{
std::cerr << "Ignoring invalid COMPND record" << std::endl;
if (cif::VERBOSE >= 0)
std::cerr << "Ignoring invalid COMPND record" << std::endl;
break;
}
......@@ -1625,7 +1631,7 @@ void PDBFileParser::ParseTitle()
// auto colon = s.find(": ");
// if (colon == std::string::npos)
// {
// if (cif::VERBOSE)
// if (cif::VERBOSE > 0)
// std::cerr << "invalid source field, missing colon (" << s << ')' << std::endl;
// continue;
// }
......@@ -1713,7 +1719,7 @@ void PDBFileParser::ParseTitle()
// NUMMDL
if (mRec->is("NUMMDL"))
{
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << "skipping unimplemented NUMMDL record" << std::endl;
GetNextRecord();
}
......@@ -1816,7 +1822,7 @@ void PDBFileParser::ParseTitle()
// SPRSDE
if (mRec->is("SPRSDE"))
{
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << "skipping unimplemented SPRSDE record" << std::endl;
GetNextRecord();
}
......@@ -2265,7 +2271,7 @@ void PDBFileParser::ParseRemarks()
state = eMCP;
else if (subtopic == "CHIRAL CENTERS")
state = eChC;
else if (cif::VERBOSE)
else if (cif::VERBOSE > 0)
throw std::runtime_error("Unknown subtopic in REMARK 500: " + subtopic);
headerSeen = false;
......@@ -2342,7 +2348,7 @@ void PDBFileParser::ParseRemarks()
}
catch (const std::exception &ex)
{
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << "Dropping REMARK 500 at line " << mRec->mLineNr << " due to invalid symmetry operation" << std::endl;
continue;
}
......@@ -2675,7 +2681,7 @@ void PDBFileParser::ParseRemarks()
case sStart:
if (s == "SITE")
state = sID;
else if (cif::VERBOSE)
else if (cif::VERBOSE > 0)
throw std::runtime_error("Invalid REMARK 800 record, expected SITE");
break;
......@@ -2685,7 +2691,7 @@ void PDBFileParser::ParseRemarks()
id = m[1].str();
state = sEvidence;
}
else if (cif::VERBOSE)
else if (cif::VERBOSE > 0)
throw std::runtime_error("Invalid REMARK 800 record, expected SITE_IDENTIFIER");
break;
......@@ -2695,7 +2701,7 @@ void PDBFileParser::ParseRemarks()
evidence = m[1].str();
state = sDesc;
}
else if (cif::VERBOSE)
else if (cif::VERBOSE > 0)
throw std::runtime_error("Invalid REMARK 800 record, expected SITE_IDENTIFIER");
break;
......@@ -2906,7 +2912,7 @@ void PDBFileParser::ParseRemark200()
collectionDate = pdb2cifDate(rm200("DATE OF DATA COLLECTION", diffrnNr), ec);
if (ec)
{
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << ec.message() << " for pdbx_collection_date" << std::endl;
// The date field can become truncated when multiple values are available
......@@ -3025,7 +3031,7 @@ void PDBFileParser::ParseRemark200()
else if (inRM200({"HIGHEST RESOLUTION SHELL, RANGE LOW (A)", "COMPLETENESS FOR SHELL (%)",
"R MERGE FOR SHELL (I)", "R SYM FOR SHELL (I)", "<I/SIGMA(I)> FOR SHELL", "DATA REDUNDANCY IN SHELL"}))
{
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << "Not writing reflns_shell record since d_res_high is missing" << std::endl;
}
}
......@@ -3595,7 +3601,7 @@ void PDBFileParser::ConstructEntities()
{
auto &r = chain.mResiduesSeen[lastResidueIndex + 1];
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
{
std::cerr << "Detected residues that cannot be aligned to SEQRES" << std::endl
<< "First residue is " << chain.mDbref.chainID << ':' << r.mSeqNum << r.mIcode << std::endl;
......@@ -4005,7 +4011,7 @@ void PDBFileParser::ConstructEntities()
tie(asym, labelSeq, std::ignore) = MapResidue(seqadv.chainID, seqadv.seqNum, seqadv.iCode, ec);
if (ec)
{
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << "dropping unmatched SEQADV record" << std::endl;
continue;
}
......@@ -4319,7 +4325,7 @@ void PDBFileParser::ConstructEntities()
tie(asymID, seq, std::ignore) = MapResidue(chainID, seqNum, iCode, ec);
if (ec) // no need to write a modres if it could not be found
{
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << "dropping unmapped MODRES record" << std::endl;
continue;
}
......@@ -4415,7 +4421,7 @@ void PDBFileParser::ConstructEntities()
tie(asymID, seqNr, isPolymer) = MapResidue(unobs.chain, unobs.seq, unobs.iCode, ec);
if (ec)
{
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << "error mapping unobserved residue" << std::endl;
continue;
}
......@@ -4676,7 +4682,7 @@ void PDBFileParser::ParseSecondaryStructure()
if (ec)
{
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << "Could not map residue for HELIX " << vI(8, 10) << std::endl;
}
else
......@@ -4791,7 +4797,7 @@ void PDBFileParser::ParseSecondaryStructure()
if (ec)
{
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << "Dropping SHEET record " << vI(8, 10) << std::endl;
}
else
......@@ -4827,7 +4833,7 @@ void PDBFileParser::ParseSecondaryStructure()
if (ec)
{
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << "skipping unmatched pdbx_struct_sheet_hbond record" << std::endl;
}
else
......@@ -4927,7 +4933,7 @@ void PDBFileParser::ParseConnectivtyAnnotation()
if (ec)
{
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << "Dropping SSBOND " << vI(8, 10) << std::endl;
continue;
}
......@@ -4948,7 +4954,7 @@ void PDBFileParser::ParseConnectivtyAnnotation()
}
catch (const std::exception &ex)
{
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << "Dropping SSBOND " << vI(8, 10) << " due to invalid symmetry operation" << std::endl;
continue;
}
......@@ -4993,7 +4999,7 @@ void PDBFileParser::ParseConnectivtyAnnotation()
if (mRec->is("LINK ") or mRec->is("LINKR "))
{
if (cif::VERBOSE and mRec->is("LINKR "))
if (cif::VERBOSE > 0 and mRec->is("LINKR "))
std::cerr << "Accepting non-standard LINKR record, but ignoring extra information" << std::endl;
// 1 - 6 Record name "LINK "
......@@ -5046,7 +5052,7 @@ void PDBFileParser::ParseConnectivtyAnnotation()
if (ec)
{
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << "Dropping LINK record at line " << mRec->mLineNr << std::endl;
continue;
}
......@@ -5062,7 +5068,7 @@ void PDBFileParser::ParseConnectivtyAnnotation()
}
catch (const std::invalid_argument &)
{
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << "Distance value '" << distance << "' is not a valid float in LINK record" << std::endl;
swap(ccp4LinkID, distance); // assume this is a ccp4_link_id... oh really?
}
......@@ -5078,7 +5084,7 @@ void PDBFileParser::ParseConnectivtyAnnotation()
}
catch (const std::exception &ex)
{
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << "Dropping LINK record at line " << mRec->mLineNr << " due to invalid symmetry operation" << std::endl;
continue;
}
......@@ -5149,7 +5155,7 @@ void PDBFileParser::ParseConnectivtyAnnotation()
if (ec)
{
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << "Dropping CISPEP record at line " << mRec->mLineNr << std::endl;
continue;
}
......@@ -5215,7 +5221,7 @@ void PDBFileParser::ParseMiscellaneousFeatures()
if (ec)
{
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << "skipping struct_site_gen record" << std::endl;
}
else
......@@ -5518,7 +5524,7 @@ void PDBFileParser::ParseCoordinate(int modelNr)
{
if (groupPDB == "HETATM")
{
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << "Changing atom from HETATM to ATOM at line " << mRec->mLineNr << std::endl;
groupPDB = "ATOM";
}
......@@ -5527,7 +5533,7 @@ void PDBFileParser::ParseCoordinate(int modelNr)
{
if (groupPDB == "ATOM")
{
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << "Changing atom from ATOM to HETATM at line " << mRec->mLineNr << std::endl;
groupPDB = "HETATM";
}
......@@ -5698,7 +5704,8 @@ void PDBFileParser::Parse(std::istream &is, cif::File &result)
}
catch (const std::exception &ex)
{
std::cerr << "Error parsing REMARK 3" << std::endl;
if (cif::VERBOSE >= 0)
std::cerr << "Error parsing REMARK 3" << std::endl;
throw;
}
//
......@@ -5750,12 +5757,12 @@ void PDBFileParser::Parse(std::istream &is, cif::File &result)
if ((symm1.empty() or symm1 == "1_555") and (symm2.empty() or symm2 == "1_555"))
distance = static_cast<float>(mmcif::Distance(mmcif::Point{x1, y1, z1}, mmcif::Point{x2, y2, z2}));
else if (cif::VERBOSE)
else if (cif::VERBOSE > 0)
std::cerr << "Cannot calculate distance for link since one of the atoms is in another dimension" << std::endl;
}
catch (std::exception &ex)
{
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << "Error finding atom for LINK distance calculation: " << ex.what() << std::endl;
}
......@@ -5764,10 +5771,13 @@ void PDBFileParser::Parse(std::istream &is, cif::File &result)
}
catch (const std::exception &ex)
{
std::cerr << "Error parsing PDB";
if (mRec != nullptr)
std::cerr << " at line " << mRec->mLineNr;
std::cerr << std::endl;
if (cif::VERBOSE >= 0)
{
std::cerr << "Error parsing PDB";
if (mRec != nullptr)
std::cerr << " at line " << mRec->mLineNr;
std::cerr << std::endl;
}
throw;
}
}
......@@ -5947,7 +5957,7 @@ int PDBFileParser::PDBChain::AlignResToSeqRes()
switch (tb(x, y))
{
case -1:
// if (cif::VERBOSE)
// if (cif::VERBOSE > 0)
// std::cerr << "A residue found in the ATOM records "
// << "(" << ry[y].mMonID << " @ " << mDbref.chainID << ":" << ry[y].mSeqNum
// << ((ry[y].mIcode == ' ' or ry[y].mIcode == 0) ? "" : std::string{ ry[y].mIcode }) << ")"
......@@ -6034,7 +6044,6 @@ void ReadPDBFile(std::istream &pdbFile, cif::File &cifFile)
p.Parse(pdbFile, cifFile);
if (not cifFile.isValid())
// throw std::runtime_error("Resulting mmCIF file is invalid");
if (not cifFile.isValid() and cif::VERBOSE >= 0)
std::cerr << "Resulting mmCIF file is not valid!" << std::endl;
}
src/PDB2CifRemark3.cpp
......@@ -1320,7 +1320,7 @@ bool Remark3Parser::parse(const std::string& expMethod, PDBRecord* r, cif::Datab
if (line != "REFINEMENT.")
{
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << "Unexpected data in REMARK 3" << std::endl;
return false;
}
......@@ -1332,7 +1332,7 @@ bool Remark3Parser::parse(const std::string& expMethod, PDBRecord* r, cif::Datab
if (not std::regex_match(line, m, rxp))
{
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << "Expected valid PROGRAM line in REMARK 3" << std::endl;
return false;
}
......@@ -1367,8 +1367,9 @@ bool Remark3Parser::parse(const std::string& expMethod, PDBRecord* r, cif::Datab
}
catch(const std::exception& e)
{
std::cerr << "Error parsing REMARK 3 with " << parser->program() << std::endl
<< e.what() << '\n';
if (cif::VERBOSE >= 0)
std::cerr << "Error parsing REMARK 3 with " << parser->program() << std::endl
<< e.what() << '\n';
score = 0;
}
......@@ -1411,7 +1412,7 @@ bool Remark3Parser::parse(const std::string& expMethod, PDBRecord* r, cif::Datab
tryParser(new TNT_Remark3Parser(program, expMethod, r, db));
else if (ba::starts_with(program, "X-PLOR"))
tryParser(new XPLOR_Remark3Parser(program, expMethod, r, db));
else if (cif::VERBOSE)
else if (cif::VERBOSE > 0)
std::cerr << "Skipping unknown program (" << program << ") in REMARK 3" << std::endl;
}
......@@ -1420,7 +1421,8 @@ bool Remark3Parser::parse(const std::string& expMethod, PDBRecord* r, cif::Datab
bool guessProgram = scores.empty() or scores.front().score < 0.9f;;
if (guessProgram)
{
std::cerr << "Unknown or untrusted program in REMARK 3, trying all parsers to see if there is a match" << std::endl;
if (cif::VERBOSE >= 0)
std::cerr << "Unknown or untrusted program in REMARK 3, trying all parsers to see if there is a match" << std::endl;
tryParser(new BUSTER_TNT_Remark3Parser("BUSTER-TNT", expMethod, r, db));
tryParser(new CNS_Remark3Parser("CNS", expMethod, r, db));
......@@ -1444,7 +1446,7 @@ bool Remark3Parser::parse(const std::string& expMethod, PDBRecord* r, cif::Datab
auto& best = scores.front();
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << "Choosing " << best.parser->program() << " version '" << best.parser->version() << "' as refinement program. Score = " << best.score << std::endl;
auto& software = db["software"];
......
src/Secondary.cpp
......@@ -1240,7 +1240,7 @@ void DSSPImpl::calculateSecondaryStructure()
auto r1 = findRes(asym1, seq1);
if (r1 == mResidues.end())
{
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << "Missing (incomplete?) residue for SS bond when trying to find " << asym1 << '/' << seq1 << std::endl;
continue;
// throw std::runtime_error("Invalid file, missing residue for SS bond");
......@@ -1249,7 +1249,7 @@ void DSSPImpl::calculateSecondaryStructure()
auto r2 = findRes(asym2, seq2);
if (r2 == mResidues.end())
{
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << "Missing (incomplete?) residue for SS bond when trying to find " << asym2 << '/' << seq2 << std::endl;
continue;
// throw std::runtime_error("Invalid file, missing residue for SS bond");
......@@ -1300,7 +1300,7 @@ void DSSPImpl::calculateSecondaryStructure()
{
if (a == b)
{
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << "In the SS bonds list, the residue " << a->mM << " is bonded to itself" << std::endl;
continue;
}
......@@ -1483,7 +1483,7 @@ SecondaryStructureType DSSP::operator()(const std::string &inAsymID, int inSeqID
{ return r.mM.asymID() == inAsymID and r.mM.seqID() == inSeqID; });
if (i != mImpl->mResidues.end())
result = i->mSecondaryStructure;
else if (cif::VERBOSE)
else if (cif::VERBOSE > 0)
std::cerr << "Could not find secondary structure for " << inAsymID << ':' << inSeqID << std::endl;
return result;
}
......@@ -1501,7 +1501,7 @@ double DSSP::accessibility(const std::string &inAsymID, int inSeqID) const
{ return r.mM.asymID() == inAsymID and r.mM.seqID() == inSeqID; });
if (i != mImpl->mResidues.end())
result = i->mSecondaryStructure;
else if (cif::VERBOSE)
else if (cif::VERBOSE > 0)
std::cerr << "Could not find secondary structure for " << inAsymID << ':' << inSeqID << std::endl;
return result;
}
......@@ -1526,7 +1526,7 @@ bool DSSP::isAlphaHelixEndBeforeStart(const std::string &inAsymID, int inSeqID)
if (i != mImpl->mResidues.end() and i + 1 != mImpl->mResidues.end())
result = i->GetHelixFlag(HelixType::rh_alpha) == Helix::End and (i + 1)->GetHelixFlag(HelixType::rh_alpha) == Helix::Start;
else if (cif::VERBOSE)
else if (cif::VERBOSE > 0)
std::cerr << "Could not find secondary structure for " << inAsymID << ':' << inSeqID << std::endl;
return result;
......
src/Structure.cpp
......@@ -140,14 +140,14 @@ void FileImpl::load(const std::filesystem::path &path)
{
try
{
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << "unrecognized file extension, trying cif" << std::endl;
mData.load(in);
}
catch (const cif::CifParserError &e)
{
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << "Not cif, trying plain old PDB" << std::endl;
// pffft...
......@@ -169,7 +169,8 @@ void FileImpl::load(const std::filesystem::path &path)
}
catch (const std::exception &ex)
{
std::cerr << "Error trying to load file " << path << std::endl;
if (cif::VERBOSE >= 0)
std::cerr << "Error trying to load file " << path << std::endl;
throw;
}
......@@ -317,7 +318,7 @@ const Compound &Atom::AtomImpl::comp() const
mCompound = CompoundFactory::instance().create(compID);
if (cif::VERBOSE and mCompound == nullptr)
if (cif::VERBOSE > 0 and mCompound == nullptr)
std::cerr << "Compound not found: '" << compID << '\'' << std::endl;
}
......@@ -623,7 +624,7 @@ AtomView Residue::unique_atoms() const
firstAlt = alt;
else if (alt != firstAlt)
{
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << "skipping alternate atom " << atom << std::endl;
continue;
}
......@@ -829,7 +830,7 @@ float Monomer::phi() const
}
catch (const std::exception &ex)
{
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << ex.what() << std::endl;
}
......@@ -851,7 +852,7 @@ float Monomer::psi() const
}
catch (const std::exception &ex)
{
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << ex.what() << std::endl;
}
......@@ -875,7 +876,7 @@ float Monomer::alpha() const
}
catch (const std::exception &ex)
{
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << ex.what() << std::endl;
}
......@@ -903,7 +904,7 @@ float Monomer::kappa() const
}
catch (const std::exception &ex)
{
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << "When trying to calculate kappa for " << asymID() << ':' << seqID() << ": "
<< ex.what() << std::endl;
}
......@@ -926,7 +927,7 @@ float Monomer::tco() const
}
catch (const std::exception &ex)
{
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << "When trying to calculate tco for " << asymID() << ':' << seqID() << ": "
<< ex.what() << std::endl;
}
......@@ -945,7 +946,7 @@ float Monomer::omega() const
}
catch (const std::exception &ex)
{
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << "When trying to calculate omega for " << asymID() << ':' << seqID() << ": "
<< ex.what() << std::endl;
}
......@@ -1016,7 +1017,7 @@ float Monomer::chi(size_t nr) const
}
catch (const std::exception &e)
{
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << e.what() << std::endl;
result = 0;
}
......@@ -1182,7 +1183,7 @@ Polymer::Polymer(const Structure &s, const std::string &entityID, const std::str
ix[seqID] = index;
emplace_back(*this, index, seqID, authSeqID, compoundID);
}
else if (cif::VERBOSE)
else if (cif::VERBOSE > 0)
{
Monomer m{*this, index, seqID, authSeqID, compoundID};
std::cerr << "Dropping alternate residue " << m << std::endl;
......@@ -1327,7 +1328,7 @@ Structure::Structure(File &f, size_t modelNr, StructureOpenOptions options)
cif::tie(model_nr) = atomCat.front().get("pdbx_PDB_model_num");
if (model_nr and *model_nr != mModelNr)
{
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << "No atoms loaded for model 1, trying model " << *model_nr << std::endl;
mModelNr = *model_nr;
loadAtomsForModel(options);
......@@ -1335,7 +1336,10 @@ Structure::Structure(File &f, size_t modelNr, StructureOpenOptions options)
}
if (mAtoms.empty())
std::cerr << "Warning: no atoms loaded" << std::endl;
{
if (cif::VERBOSE >= 0)
std::cerr << "Warning: no atoms loaded" << std::endl;
}
else
loadData();
}
......@@ -1443,7 +1447,7 @@ void Structure::loadData()
if (ri == resMap.end())
{
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
std::cerr << "Missing residue for atom " << atom << std::endl;
assert(false);
......@@ -2006,7 +2010,8 @@ void Structure::changeResidue(Residue &res, const std::string &newCompound,
{ return a.labelAtomID() == a1; });
if (i == atoms.end())
{
std::cerr << "Missing atom for atom ID " << a1 << std::endl;
if (cif::VERBOSE >= 0)
std::cerr << "Missing atom for atom ID " << a1 << std::endl;
continue;
}
......
src/TlsParser.cpp
......@@ -248,7 +248,7 @@ struct TLSSelectionNot : public TLSSelection
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;
DumpSelection(residues, indentLevel);
......@@ -267,7 +267,7 @@ struct TLSSelectionAll : public TLSSelection
for (auto& r: residues)
r.selected = true;
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
{
std::cout << std::string(indentLevel * 2, ' ') << "ALL" << std::endl;
DumpSelection(residues, indentLevel);
......@@ -287,7 +287,7 @@ struct TLSSelectionChain : public TLSSelectionAll
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;
DumpSelection(residues, indentLevel);
......@@ -307,7 +307,7 @@ struct TLSSelectionResID : public TLSSelectionAll
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;
DumpSelection(residues, indentLevel);
......@@ -331,7 +331,7 @@ struct TLSSelectionRangeSeq : public TLSSelectionAll
(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;
DumpSelection(residues, indentLevel);
......@@ -374,7 +374,7 @@ struct TLSSelectionRangeID : public TLSSelectionAll
}
}
if (cif::VERBOSE)
if (cif::VERBOSE > 0)
{
std::cout << std::string(indentLevel * 2, ' ') << "Through " << m_first << ':' << m_last << std::endl;
DumpSelection(residues, indentLevel);
......@@ -407,7 +407,7 @@ struct TLSSelectionUnion : public TLSSelection
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;
DumpSelection(residues, indentLevel);
......@@ -440,7 +440,7 @@ struct TLSSelectionIntersection : public TLSSelection
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;
DumpSelection(residues, indentLevel);
......@@ -462,7 +462,7 @@ struct TLSSelectionByName : public TLSSelectionAll
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;
DumpSelection(residues, indentLevel);
......@@ -488,7 +488,7 @@ struct TLSSelectionByElement : public TLSSelectionAll
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;
DumpSelection(residues, indentLevel);
......@@ -890,7 +890,7 @@ TLSSelectionPtr TLSSelectionParserImplPhenix::Parse()
Match(pt_EOLN);
if (extraParenthesis)
if (extraParenthesis and cif::VERBOSE > 0)
std::cerr << "WARNING: too many closing parenthesis in TLS selection statement" << std::endl;
return result;
......@@ -931,7 +931,7 @@ TLSSelectionPtr TLSSelectionParserImplPhenix::ParseFactor()
case '(':
Match('(');
result = ParseAtomSelection();
if (m_lookahead == pt_EOLN)
if (m_lookahead == pt_EOLN and cif::VERBOSE > 0)
std::cerr << "WARNING: missing closing parenthesis in TLS selection statement" << std::endl;
else
Match(')');
......@@ -1033,7 +1033,7 @@ TLSSelectionPtr TLSSelectionParserImplPhenix::ParseFactor()
result.reset(new TLSSelectionRangeID(from, to, icode_from, icode_to));
else
{
if (cif::VERBOSE and (icode_from or icode_to))
if (cif::VERBOSE > 0 and (icode_from or icode_to))
std::cerr << "Warning, ignoring insertion codes" << std::endl;
result.reset(new TLSSelectionRangeSeq(from, to));
......@@ -1231,7 +1231,8 @@ TLSSelectionPtr TLSSelectionParserImplBuster::ParseGroup()
std::tie(chain2, seqNr2) = ParseAtom();
if (chain1 != chain2)
{
std::cerr << "Warning, ranges over multiple chains detected" << std::endl;
if (cif::VERBOSE > 0)
std::cerr << "Warning, ranges over multiple chains detected" << std::endl;
TLSSelectionPtr sc1(new TLSSelectionChain(chain1));
TLSSelectionPtr sr1(new TLSSelectionRangeSeq(seqNr1, kResidueNrWildcard));
......@@ -1289,7 +1290,7 @@ 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);
......@@ -1810,7 +1811,8 @@ class TLSSelectionParser
}
catch (const std::exception& ex)
{
std::cerr << "ParseError: " << ex.what() << std::endl;
if (cif::VERBOSE >= 0)
std::cerr << "ParseError: " << ex.what() << std::endl;
}
return result;
......@@ -1834,14 +1836,14 @@ TLSSelectionPtr ParseSelectionDetails(const std::string& program, const std::str
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);
}
......@@ -1852,35 +1854,35 @@ TLSSelectionPtr ParseSelectionDetails(const std::string& program, const std::str
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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