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libcifpp
Commit 4732004b by Maarten L. Hekkelman
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Merge branch 'develop' into trunk

parents d4bd3faa faa9cd04
Showing with 227 additions and 130 deletions
include/cif++/Cif++.hpp
......@@ -792,7 +792,7 @@ class Row
}
void assign(const std::vector<Item> &values);
void assign(std::string_view name, const std::string &value, bool updateLinked);
void assign(std::string_view name, const std::string &value, bool updateLinked, bool validate = true);
bool operator==(const Row &rhs) const
{
......@@ -814,7 +814,7 @@ class Row
friend std::ostream &operator<<(std::ostream &os, const Row &row);
private:
void assign(size_t column, const std::string &value, bool updateLinked);
void assign(size_t column, const std::string &value, bool updateLinked, bool validate = true);
void assign(const Item &i, bool updateLinked);
static void swap(size_t column, ItemRow *a, ItemRow *b);
......@@ -2152,6 +2152,7 @@ class Category
std::vector<ItemColumn> mColumns;
ItemRow *mHead;
ItemRow *mTail;
size_t mLastUniqueNr = 0;
class CatIndex *mIndex;
std::vector<Linked> mParentLinks, mChildLinks;
......
include/cif++/Structure.hpp
......@@ -60,30 +60,101 @@ class File;
class Atom
{
private:
struct AtomImpl : public std::enable_shared_from_this<AtomImpl>
{
AtomImpl(cif::Datablock &db, const std::string &id, cif::Row row);
// constructor for a symmetry copy of an atom
AtomImpl(const AtomImpl &impl, const Point &loc, const std::string &sym_op);
AtomImpl(const AtomImpl &i) = default;
void prefetch();
int compare(const AtomImpl &b) const;
bool getAnisoU(float anisou[6]) const;
void moveTo(const Point &p);
const Compound &comp() const;
const std::string get_property(const std::string_view name) const;
void set_property(const std::string_view name, const std::string &value);
const cif::Datablock &mDb;
std::string mID;
AtomType mType;
std::string mAtomID;
std::string mCompID;
std::string mAsymID;
int mSeqID;
std::string mAltID;
std::string mAuthSeqID;
Point mLocation;
int mRefcount;
cif::Row mRow;
mutable std::vector<std::tuple<std::string,cif::detail::ItemReference>> mCachedRefs;
mutable const Compound *mCompound = nullptr;
bool mSymmetryCopy = false;
bool mClone = false;
std::string mSymmetryOperator = "1_555";
};
public:
Atom();
Atom(struct AtomImpl *impl);
Atom(const Atom &rhs);
Atom() {}
Atom(std::shared_ptr<AtomImpl> impl)
: mImpl(impl) {}
Atom(const Atom &rhs)
: mImpl(rhs.mImpl) {}
Atom(cif::Datablock &db, cif::Row &row);
// a special constructor to create symmetry copies
Atom(const Atom &rhs, const Point &symmmetry_location, const std::string &symmetry_operation);
~Atom();
explicit operator bool() const { return mImpl_ != nullptr; }
explicit operator bool() const { return (bool)mImpl; }
// return a copy of this atom, with data copied instead of referenced
Atom clone() const;
Atom clone() const
{
auto copy = std::make_shared<AtomImpl>(*mImpl);
copy->mClone = true;
return Atom(copy);
}
Atom &operator=(const Atom &rhs) = default;
Atom &operator=(const Atom &rhs);
template <typename T>
T get_property(const std::string_view name) const;
void set_property(const std::string_view name, const std::string &value)
{
mImpl->set_property(name, value);
}
template <typename T, std::enable_if_t<std::is_arithmetic_v<T>, int> = 0>
void property(const std::string_view name, const T &value)
{
set_property(name, std::to_string(value));
}
const std::string &id() const;
AtomType type() const;
const std::string &id() const { return mImpl->mID; }
AtomType type() const { return mImpl->mType; }
Point location() const;
void location(Point p);
Point location() const { return mImpl->mLocation; }
void location(Point p) { mImpl->moveTo(p); }
/// \brief Translate the position of this atom by \a t
void translate(Point t);
......@@ -91,47 +162,40 @@ class Atom
/// \brief Rotate the position of this atom by \a q
void rotate(Quaternion q);
/// \brief Translate and rotate the position of this atom by \a t and \a q
void translateAndRotate(Point t, Quaternion q);
/// \brief Translate, rotate and translate again the coordinates this atom by \a t1 , \a q and \a t2
void translateRotateAndTranslate(Point t1, Quaternion q, Point t2);
// for direct access to underlying data, be careful!
const cif::Row getRow() const;
const cif::Row getRow() const { return mImpl->mRow; }
const cif::Row getRowAniso() const;
// Atom symmetryCopy(const Point& d, const clipper::RTop_orth& rt);
bool isSymmetryCopy() const;
std::string symmetry() const;
// const clipper::RTop_orth& symop() const;
bool isSymmetryCopy() const { return mImpl->mSymmetryCopy; }
std::string symmetry() const { return mImpl->mSymmetryOperator; }
const Compound &comp() const;
bool isWater() const;
const Compound &comp() const { return mImpl->comp(); }
bool isWater() const { return mImpl->mCompID == "HOH" or mImpl->mCompID == "H2O" or mImpl->mCompID == "WAT"; }
int charge() const;
float uIso() const;
bool getAnisoU(float anisou[6]) const;
bool getAnisoU(float anisou[6]) const { return mImpl->getAnisoU(anisou); }
float occupancy() const;
template <typename T>
T property(const std::string_view name) const;
void property(const std::string_view name, const std::string &value);
template <typename T, std::enable_if_t<std::is_arithmetic_v<T>, int> = 0>
void property(const std::string_view name, const T &value)
{
property(name, std::to_string(value));
}
// specifications
const std::string& labelAtomID() const { return mAtomID; }
const std::string& labelCompID() const { return mCompID; }
const std::string& labelAsymID() const { return mAsymID; }
const std::string& labelAtomID() const { return mImpl->mAtomID; }
const std::string& labelCompID() const { return mImpl->mCompID; }
const std::string& labelAsymID() const { return mImpl->mAsymID; }
std::string labelEntityID() const;
int labelSeqID() const { return mSeqID; }
const std::string& labelAltID() const { return mAltID; }
bool isAlternate() const { return not mAltID.empty(); }
int labelSeqID() const { return mImpl->mSeqID; }
const std::string& labelAltID() const { return mImpl->mAltID; }
bool isAlternate() const { return not mImpl->mAltID.empty(); }
std::string authAtomID() const;
std::string authCompID() const;
std::string authAsymID() const;
const std::string& authSeqID() const { return mAuthSeqID; }
const std::string& authSeqID() const { return mImpl->mAuthSeqID; }
std::string pdbxAuthInsCode() const;
std::string pdbxAuthAltID() const;
......@@ -140,13 +204,6 @@ class Atom
bool operator==(const Atom &rhs) const;
// // get clipper format Atom
// clipper::Atom toClipper() const;
// Radius calculation based on integrating the density until perc of electrons is found
void calculateRadius(float resHigh, float resLow, float perc);
float radius() const;
// access data in compound for this atom
// convenience routine
......@@ -158,16 +215,10 @@ class Atom
void swap(Atom &b)
{
std::swap(mImpl_, b.mImpl_);
std::swap(mAtomID, b.mAtomID);
std::swap(mCompID, b.mCompID);
std::swap(mAsymID, b.mAsymID);
std::swap(mSeqID, b.mSeqID);
std::swap(mAltID, b.mAltID);
std::swap(mAuthSeqID, b.mAuthSeqID);
std::swap(mImpl, b.mImpl);
}
int compare(const Atom &b) const;
int compare(const Atom &b) const { return mImpl->compare(*b.mImpl); }
bool operator<(const Atom &rhs) const
{
......@@ -178,21 +229,30 @@ class Atom
private:
friend class Structure;
void setID(int id);
AtomImpl *impl();
const AtomImpl *impl() const;
std::shared_ptr<AtomImpl> mImpl;
};
template <>
inline std::string Atom::get_property<std::string>(const std::string_view name) const
{
return mImpl->get_property(name);
}
struct AtomImpl *mImpl_;
template <>
inline int Atom::get_property<int>(const std::string_view name) const
{
auto v = mImpl->get_property(name);
return v.empty() ? 0 : stoi(v);
}
// cached values
std::string mAtomID;
std::string mCompID;
std::string mAsymID;
int mSeqID;
std::string mAltID;
std::string mAuthSeqID;
};
template <>
inline float Atom::get_property<float>(const std::string_view name) const
{
return stof(mImpl->get_property(name));
}
inline void swap(mmcif::Atom &a, mmcif::Atom &b)
{
......@@ -216,19 +276,16 @@ typedef std::vector<Atom> AtomView;
class Residue
{
public:
// constructors should be private, but that's not possible for now (needed in emplace)
// constructor for waters
// constructor
Residue(const Structure &structure, const std::string &compoundID,
const std::string &asymID, const std::string &authSeqID);
// constructor for a residue without a sequence number
Residue(const Structure &structure, const std::string &compoundID,
const std::string &asymID);
// constructor for a residue with a sequence number
Residue(const Structure &structure, const std::string &compoundID,
const std::string &asymID, int seqID, const std::string &authSeqID);
const std::string &asymID, int seqID = 0, const std::string &authSeqID = {})
: mStructure(&structure)
, mCompoundID(compoundID)
, mAsymID(asymID)
, mSeqID(seqID)
, mAuthSeqID(authSeqID)
{
}
Residue(const Residue &rhs) = delete;
Residue &operator=(const Residue &rhs) = delete;
......@@ -552,6 +609,12 @@ class Structure
/// \brief Rotate the coordinates of all atoms in the structure by \a q
void rotate(Quaternion t);
/// \brief Translate and rotate the coordinates of all atoms in the structure by \a t and \a q
void translateAndRotate(Point t, Quaternion q);
/// \brief Translate, rotate and translate again the coordinates of all atoms in the structure by \a t1 , \a q and \a t2
void translateRotateAndTranslate(Point t1, Quaternion q, Point t2);
const std::vector<Residue> &getNonPolymers() const { return mNonPolymers; }
const std::vector<Residue> &getBranchResidues() const { return mBranchResidues; }
......
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/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/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/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);
}
......
test/structure-test.cpp
......@@ -179,3 +179,23 @@ _struct_asym.details ?
<< structure.getFile().data() << std::endl;
}
}
// // --------------------------------------------------------------------
// BOOST_AUTO_TEST_CASE(test_load_1)
// {
// mmcif::File cf(gTestDir / "5v3g.cif.gz");
// mmcif::Structure s(cf);
// for (auto &poly : s.polymers())
// {
// std::cout << std::string(80, '=') << std::endl;
// for (auto &res : poly)
// {
// std::cout << res << std::endl;
// for (auto &atom : res.atoms())
// std::cout << " " << atom << std::endl;
// }
// }
// }
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