pub_soft/rdkit
3
0
Fork 0
mirror of https://github.com/rdkit/rdkit.git synced 2026-06-03 21:44:30 +08:00
Code Issues Packages Projects Releases Wiki Activity

Modernization: use nullptr (#3143)

Browse Source
This commit is contained in:
Eisuke Kawashima
2020-05-25 16:40:01 +09:00
committed by GitHub
parent 29ad06f099
commit e86e2c1d5d
88 changed files with 411 additions and 402 deletions
Download Patch File Download Diff File Expand all files Collapse all files

4
Code/Catalogs/Catalog.h
View File

@@ -43,7 +43,7 @@ class Catalog {
typedef paramType paramType_t;
//------------------------------------
Catalog() : d_fpLength(0), dp_cParams(0){};
Catalog() : d_fpLength(0), dp_cParams(nullptr){};
//------------------------------------
virtual ~Catalog() { delete dp_cParams; }
@@ -371,7 +371,7 @@ class HierarchCatalog : public Catalog<entryType, paramType> {
URANGE_CHECK(idx, this->getFPLength());
typename boost::property_map<CatalogGraph, vertex_entry_t>::const_type
pMap = boost::get(vertex_entry_t(), d_graph);
const entryType *res = NULL;
const entryType *res = nullptr;
for (unsigned int i = idx; i < this->getNumEntries(); i++) {
const entryType *e = pMap[i];
if (e->getBitId() == static_cast<int>(idx)) {

4
Code/DataStructs/ExplicitBitVect.h
View File

@@ -28,10 +28,10 @@
*/
class RDKIT_DATASTRUCTS_EXPORT ExplicitBitVect : public BitVect {
public:
ExplicitBitVect() : dp_bits(0), d_size(0), d_numOnBits(0){};
ExplicitBitVect() : dp_bits(nullptr), d_size(0), d_numOnBits(0){};
//! initialize with a particular size;
explicit ExplicitBitVect(unsigned int size)
: dp_bits(0), d_size(0), d_numOnBits(0) {
: dp_bits(nullptr), d_size(0), d_numOnBits(0) {
_initForSize(size);
};
//! initialize with a particular size and all bits set

10
Code/DataStructs/FPBReader.h
View File

@@ -58,8 +58,8 @@ struct FPBReader_impl;
class RDKIT_DATASTRUCTS_EXPORT FPBReader {
public:
FPBReader()
: dp_istrm(NULL),
dp_impl(NULL),
: dp_istrm(nullptr),
dp_impl(nullptr),
df_owner(false),
df_init(false),
df_lazyRead(false){};
@@ -91,14 +91,14 @@ class RDKIT_DATASTRUCTS_EXPORT FPBReader {
FPBReader(std::istream *inStream, bool takeOwnership = true,
bool lazyRead = false)
: dp_istrm(inStream),
dp_impl(NULL),
dp_impl(nullptr),
df_owner(takeOwnership),
df_init(false),
df_lazyRead(lazyRead){};
~FPBReader() {
destroy();
if (df_owner) delete dp_istrm;
dp_istrm = NULL;
dp_istrm = nullptr;
df_init = false;
};
@@ -271,7 +271,7 @@ class RDKIT_DATASTRUCTS_EXPORT FPBReader {
throw BadFileException(errout.str());
}
dp_istrm = tmpStream;
dp_impl = NULL;
dp_impl = nullptr;
df_owner = true;
df_init = false;
df_lazyRead = lazyRead;

6
Code/DataStructs/SparseBitVect.h
View File

@@ -33,16 +33,16 @@ typedef IntSet::const_iterator IntSetConstIter;
*/
class RDKIT_DATASTRUCTS_EXPORT SparseBitVect : public BitVect {
public:
SparseBitVect() : dp_bits(0), d_size(0){};
SparseBitVect() : dp_bits(nullptr), d_size(0){};
//! initialize with a particular size;
explicit SparseBitVect(unsigned int size) : dp_bits(0), d_size(0) {
explicit SparseBitVect(unsigned int size) : dp_bits(nullptr), d_size(0) {
_initForSize(size);
};
//! copy constructor
SparseBitVect(const SparseBitVect &other) : BitVect(other) {
d_size = 0;
dp_bits = 0;
dp_bits = nullptr;
_initForSize(other.getNumBits());
IntSet *bv = other.dp_bits;
std::copy(bv->begin(), bv->end(), std::inserter(*dp_bits, dp_bits->end()));

2
Code/DistGeom/DistGeomUtils.h
View File

@@ -119,7 +119,7 @@ RDKIT_DISTGEOMETRY_EXPORT ForceFields::ForceField *constructForceField(
const BoundsMatrix &mmat, RDGeom::PointPtrVect &positions,
const VECT_CHIRALSET &csets, double weightChiral = 1.0,
double weightFourthDim = 0.1,
std::map<std::pair<int, int>, double> *extraWeights = 0,
std::map<std::pair<int, int>, double> *extraWeights = nullptr,
double basinSizeTol = 5.0, boost::dynamic_bitset<> *fixedPts = nullptr);
//! Force field with experimental torsion angle preferences and 1-2/1-3 distance

2
Code/ForceField/Contrib.h
View File

@@ -19,7 +19,7 @@ class RDKIT_FORCEFIELD_EXPORT ForceFieldContrib {
public:
friend class ForceField;
ForceFieldContrib() : dp_forceField(0){};
ForceFieldContrib() : dp_forceField(nullptr){};
ForceFieldContrib(ForceFields::ForceField *owner) : dp_forceField(owner){};
virtual ~ForceFieldContrib(){};

48
Code/ForceField/ForceField.h
View File

@@ -19,24 +19,25 @@
namespace RDKit {
namespace ForceFieldsHelper {
void RDKIT_FORCEFIELD_EXPORT normalizeAngleDeg(double &angleDeg);
void RDKIT_FORCEFIELD_EXPORT computeDihedral(const RDGeom::PointPtrVect &pos, unsigned int idx1,
unsigned int idx2, unsigned int idx3, unsigned int idx4,
double *dihedral = NULL, double *cosPhi = NULL,
RDGeom::Point3D r[4] = NULL, RDGeom::Point3D t[2] = NULL,
double d[2] = NULL);
void RDKIT_FORCEFIELD_EXPORT computeDihedral(const double *pos, unsigned int idx1,
unsigned int idx2, unsigned int idx3, unsigned int idx4,
double *dihedral = NULL, double *cosPhi = NULL,
RDGeom::Point3D r[4] = NULL, RDGeom::Point3D t[2] = NULL,
double d[2] = NULL);
void RDKIT_FORCEFIELD_EXPORT computeDihedral(const RDGeom::Point3D *p1, const RDGeom::Point3D *p2,
const RDGeom::Point3D *p3, const RDGeom::Point3D *p4,
double *dihedral = NULL, double *cosPhi = NULL,
RDGeom::Point3D r[4] = NULL, RDGeom::Point3D t[2] = NULL,
double d[2] = NULL);
}
}
void RDKIT_FORCEFIELD_EXPORT normalizeAngleDeg(double &angleDeg);
void RDKIT_FORCEFIELD_EXPORT computeDihedral(
const RDGeom::PointPtrVect &pos, unsigned int idx1, unsigned int idx2,
unsigned int idx3, unsigned int idx4, double *dihedral = nullptr,
double *cosPhi = nullptr, RDGeom::Point3D r[4] = nullptr,
RDGeom::Point3D t[2] = nullptr, double d[2] = nullptr);
void RDKIT_FORCEFIELD_EXPORT computeDihedral(
const double *pos, unsigned int idx1, unsigned int idx2, unsigned int idx3,
unsigned int idx4, double *dihedral = nullptr, double *cosPhi = nullptr,
RDGeom::Point3D r[4] = nullptr, RDGeom::Point3D t[2] = nullptr,
double d[2] = nullptr);
void RDKIT_FORCEFIELD_EXPORT
computeDihedral(const RDGeom::Point3D *p1, const RDGeom::Point3D *p2,
const RDGeom::Point3D *p3, const RDGeom::Point3D *p4,
double *dihedral = nullptr, double *cosPhi = nullptr,
RDGeom::Point3D r[4] = nullptr, RDGeom::Point3D t[2] = nullptr,
double d[2] = nullptr);
} // namespace ForceFieldsHelper
} // namespace RDKit
namespace ForceFields {
class ForceFieldContrib;
@@ -80,7 +81,10 @@ class RDKIT_FORCEFIELD_EXPORT ForceField {
public:
//! construct with a dimension
ForceField(unsigned int dimension = 3)
: d_dimension(dimension), df_init(false), d_numPoints(0), dp_distMat(0){};
: d_dimension(dimension),
df_init(false),
d_numPoints(0),
dp_distMat(nullptr){};
~ForceField();
@@ -101,7 +105,7 @@ class RDKIT_FORCEFIELD_EXPORT ForceField {
double *
the positions need to be converted to double * here
*/
double calcEnergy(std::vector<double> *contribs = NULL) const;
double calcEnergy(std::vector<double> *contribs = nullptr) const;
// these next two aren't const because they may update our
// distance matrix
@@ -200,7 +204,7 @@ class RDKIT_FORCEFIELD_EXPORT ForceField {
- if the distance between i and j has not previously been calculated,
our internal distance matrix will be updated.
*/
double distance(unsigned int i, unsigned int j, double *pos = 0);
double distance(unsigned int i, unsigned int j, double *pos = nullptr);
//! returns the distance between two points
/*!
@@ -215,7 +219,7 @@ class RDKIT_FORCEFIELD_EXPORT ForceField {
<b>Note:</b>
The internal distance matrix is not updated in this case
*/
double distance(unsigned int i, unsigned int j, double *pos = 0) const;
double distance(unsigned int i, unsigned int j, double *pos = nullptr) const;
//! returns the dimension of the forcefield
unsigned int dimension() const { return d_dimension; }

30
Code/ForceField/MMFF/Params.h
View File

@@ -168,7 +168,7 @@ class RDKIT_FORCEFIELD_EXPORT MMFFAromCollection {
: false);
}
MMFFAromCollection(const std::uint8_t mmffArom[]=nullptr);
MMFFAromCollection(const std::uint8_t mmffArom[] = nullptr);
std::vector<std::uint8_t> d_params; //!< the aromatic type vector
};
@@ -187,7 +187,7 @@ class RDKIT_FORCEFIELD_EXPORT MMFFDefCollection {
#else
return ((atomType && (atomType <= d_params.size()))
? &d_params[atomType - 1]
: NULL);
: nullptr);
#endif
}
@@ -220,7 +220,7 @@ class RDKIT_FORCEFIELD_EXPORT MMFFPropCollection {
return ((bounds.first != bounds.second)
? &d_params[bounds.first - d_iAtomType.begin()]
: NULL);
: nullptr);
#endif
}
@@ -248,7 +248,7 @@ class RDKIT_FORCEFIELD_EXPORT MMFFPBCICollection {
#else
return ((atomType && (atomType <= d_params.size()))
? &d_params[atomType - 1]
: NULL);
: nullptr);
#endif
}
@@ -271,7 +271,7 @@ class RDKIT_FORCEFIELD_EXPORT MMFFChgCollection {
const unsigned int bondType, const unsigned int iAtomType,
const unsigned int jAtomType) const {
int sign = -1;
const MMFFChg *mmffChgParams = NULL;
const MMFFChg *mmffChgParams = nullptr;
unsigned int canIAtomType = iAtomType;
unsigned int canJAtomType = jAtomType;
if (iAtomType > jAtomType) {
@@ -341,7 +341,7 @@ class RDKIT_FORCEFIELD_EXPORT MMFFBondCollection {
const MMFFBond *operator()(const unsigned int bondType,
const unsigned int atomType,
const unsigned int nbrAtomType) const {
const MMFFBond *mmffBondParams = NULL;
const MMFFBond *mmffBondParams = nullptr;
unsigned int canAtomType = atomType;
unsigned int canNbrAtomType = nbrAtomType;
if (atomType > nbrAtomType) {
@@ -412,7 +412,7 @@ class RDKIT_FORCEFIELD_EXPORT MMFFBndkCollection {
\return a pointer to the MMFFBndk object, NULL on failure.
*/
const MMFFBond *operator()(const int atomicNum, const int nbrAtomicNum) const {
const MMFFBond *mmffBndkParams = NULL;
const MMFFBond *mmffBndkParams = nullptr;
unsigned int canAtomicNum = atomicNum;
unsigned int canNbrAtomicNum = nbrAtomicNum;
if (atomicNum > nbrAtomicNum) {
@@ -468,7 +468,7 @@ class RDKIT_FORCEFIELD_EXPORT MMFFHerschbachLaurieCollection {
\return a pointer to the MMFFHerschbachLaurie object, NULL on failure.
*/
const MMFFHerschbachLaurie *operator()(const int iRow, const int jRow) const {
const MMFFHerschbachLaurie *mmffHerschbachLaurieParams = NULL;
const MMFFHerschbachLaurie *mmffHerschbachLaurieParams = nullptr;
unsigned int canIRow = iRow;
unsigned int canJRow = jRow;
if (iRow > jRow) {
@@ -538,7 +538,7 @@ class RDKIT_FORCEFIELD_EXPORT MMFFCovRadPauEleCollection {
return ((bounds.first != bounds.second)
? &d_params[bounds.first - d_atomicNum.begin()]
: NULL);
: nullptr);
#endif
}
@@ -563,7 +563,7 @@ class RDKIT_FORCEFIELD_EXPORT MMFFAngleCollection {
const unsigned int iAtomType,
const unsigned int jAtomType,
const unsigned int kAtomType) const {
const MMFFAngle *mmffAngleParams = NULL;
const MMFFAngle *mmffAngleParams = nullptr;
unsigned int iter = 0;
// For bending of the i-j-k angle, a five-stage process based
@@ -676,7 +676,7 @@ class RDKIT_FORCEFIELD_EXPORT MMFFStbnCollection {
const unsigned int stretchBendType, const unsigned int bondType1,
const unsigned int bondType2, const unsigned int iAtomType,
const unsigned int jAtomType, const unsigned int kAtomType) const {
const MMFFStbn *mmffStbnParams = NULL;
const MMFFStbn *mmffStbnParams = nullptr;
bool swap = false;
unsigned int canIAtomType = iAtomType;
unsigned int canKAtomType = kAtomType;
@@ -783,7 +783,7 @@ class RDKIT_FORCEFIELD_EXPORT MMFFDfsbCollection {
std::map<const unsigned int,
std::map<const unsigned int, MMFFStbn>>::const_iterator res2;
std::map<const unsigned int, MMFFStbn>::const_iterator res3;
const MMFFStbn *mmffDfsbParams = NULL;
const MMFFStbn *mmffDfsbParams = nullptr;
bool swap = false;
unsigned int canPeriodicTableRow1 = periodicTableRow1;
unsigned int canPeriodicTableRow3 = periodicTableRow3;
@@ -823,7 +823,7 @@ class RDKIT_FORCEFIELD_EXPORT MMFFOopCollection {
const unsigned int jAtomType,
const unsigned int kAtomType,
const unsigned int lAtomType) const {
const MMFFOop *mmffOopParams = NULL;
const MMFFOop *mmffOopParams = nullptr;
unsigned int iter = 0;
std::vector<unsigned int> canIKLAtomType(3);
// For out-of-plane bending ijk; I , where j is the central
@@ -933,7 +933,7 @@ class RDKIT_FORCEFIELD_EXPORT MMFFTorCollection {
const std::pair<unsigned int, unsigned int> torType,
const unsigned int iAtomType, const unsigned int jAtomType,
const unsigned int kAtomType, const unsigned int lAtomType) const {
const MMFFTor *mmffTorParams = NULL;
const MMFFTor *mmffTorParams = nullptr;
unsigned int iter = 0;
unsigned int iWildCard = 0;
unsigned int lWildCard = 0;
@@ -1117,7 +1117,7 @@ class RDKIT_FORCEFIELD_EXPORT MMFFVdWCollection {
return ((bounds.first != bounds.second)
? &d_params[bounds.first - d_atomType.begin()]
: NULL);
: nullptr);
#endif
}

2
Code/ForceField/UFF/Params.h
View File

@@ -140,7 +140,7 @@ class RDKIT_FORCEFIELD_EXPORT ParamCollection {
if (res != d_params.end()) {
return &((*res).second);
}
return 0;
return nullptr;
}
private:

6
Code/Geometry/UniformGrid3D.h
View File

@@ -38,8 +38,8 @@ class RDKIT_RDGEOMETRYLIB_EXPORT UniformGrid3D : public Grid3D {
UniformGrid3D(double dimX, double dimY, double dimZ, double spacing = 0.5,
RDKit::DiscreteValueVect::DiscreteValueType valType =
RDKit::DiscreteValueVect::TWOBITVALUE,
const RDGeom::Point3D *offset = 0) {
if (offset == 0) {
const RDGeom::Point3D *offset = nullptr) {
if (offset == nullptr) {
initGrid(dimX, dimY, dimZ, spacing, valType,
Point3D(-0.5 * dimX, -0.5 * dimY, -0.5 * dimZ));
} else {
@@ -187,7 +187,7 @@ class RDKIT_RDGEOMETRYLIB_EXPORT UniformGrid3D : public Grid3D {
void initGrid(double dimX, double dimY, double dimZ, double spacing,
RDKit::DiscreteValueVect::DiscreteValueType valType,
const RDGeom::Point3D &offSet,
RDKit::DiscreteValueVect *data = 0);
RDKit::DiscreteValueVect *data = nullptr);
unsigned int d_numX, d_numY,
d_numZ; //! number of grid points along x, y, z axes
double d_spacing; //! grid spacing

4
Code/GraphMol/BondIterators.h
View File

@@ -28,7 +28,7 @@ class RDKIT_GRAPHMOL_EXPORT BondIterator_ {
// FIX: I'm not pleased with the lack of internal testing code
// (PREs and the like) in here
public:
BondIterator_() : _mol(NULL){};
BondIterator_() : _mol(nullptr){};
BondIterator_(ROMol *mol);
BondIterator_(ROMol *mol, ROMol::EDGE_ITER pos);
BondIterator_(const BondIterator_ &other);
@@ -51,7 +51,7 @@ class RDKIT_GRAPHMOL_EXPORT BondIterator_ {
//! but it theoretically ought to be RandomAccess.
class RDKIT_GRAPHMOL_EXPORT ConstBondIterator_ {
public:
ConstBondIterator_() : _mol(NULL){};
ConstBondIterator_() : _mol(nullptr){};
ConstBondIterator_(ROMol const *mol);
ConstBondIterator_(ROMol const *mol, ROMol::EDGE_ITER pos);
ConstBondIterator_(const ConstBondIterator_ &other);

4
Code/GraphMol/Canon.h
View File

@@ -114,8 +114,8 @@ typedef boost::tuple<int, int, Bond *> PossibleType;
RDKIT_GRAPHMOL_EXPORT void canonicalizeFragment(
ROMol &mol, int atomIdx, std::vector<AtomColors> &colors,
const std::vector<unsigned int> &ranks, MolStack &molStack,
const boost::dynamic_bitset<> *bondsInPlay = 0,
const std::vector<std::string> *bondSymbols = 0,
const boost::dynamic_bitset<> *bondsInPlay = nullptr,
const std::vector<std::string> *bondSymbols = nullptr,
bool doIsomericSmiles = false, bool doRandom = false);
//! Check if a chiral atom needs to have its tag flipped after reading or before

4
Code/GraphMol/ChemReactions/Enumerate/EnumerateBase.h
View File

@@ -72,7 +72,7 @@ class RDKIT_CHEMREACTIONS_EXPORT EnumerateLibraryBase {
//! construct with a chemical reaction and an enumeration strategy
EnumerateLibraryBase(const ChemicalReaction &rxn,
EnumerationStrategyBase *enumerator = 0)
EnumerationStrategyBase *enumerator = nullptr)
: m_rxn(rxn),
m_enumerator(enumerator ? enumerator : new CartesianProductStrategy),
m_initialEnumerator(m_enumerator->copy()) {
@@ -82,7 +82,7 @@ class RDKIT_CHEMREACTIONS_EXPORT EnumerateLibraryBase {
//! Copy constructor
EnumerateLibraryBase(const EnumerateLibraryBase &rhs)
: m_rxn(rhs.m_rxn),
m_enumerator(rhs.m_enumerator ? rhs.m_enumerator->copy() : 0),
m_enumerator(rhs.m_enumerator ? rhs.m_enumerator->copy() : nullptr),
m_initialEnumerator(m_enumerator->copy()) {}
virtual ~EnumerateLibraryBase() {}

8
Code/GraphMol/ChemReactions/Reaction.h
View File

@@ -185,7 +185,7 @@ class RDKIT_CHEMREACTIONS_EXPORT ChemicalReaction : public RDProps {
*/
void removeUnmappedReactantTemplates(double thresholdUnmappedAtoms = 0.2,
bool moveToAgentTemplates = true,
MOL_SPTR_VECT *targetVector = NULL);
MOL_SPTR_VECT *targetVector = nullptr);
//! Removes the product templates from a reaction if its atom mapping ratio is
// below a given threshold
@@ -196,11 +196,11 @@ class RDKIT_CHEMREACTIONS_EXPORT ChemicalReaction : public RDProps {
*/
void removeUnmappedProductTemplates(double thresholdUnmappedAtoms = 0.2,
bool moveToAgentTemplates = true,
MOL_SPTR_VECT *targetVector = NULL);
MOL_SPTR_VECT *targetVector = nullptr);
/*! Removes the agent templates from a reaction if a pointer to a
molecule vector is provided the agents are stored therein.*/
void removeAgentTemplates(MOL_SPTR_VECT *targetVector = NULL);
void removeAgentTemplates(MOL_SPTR_VECT *targetVector = nullptr);
//! Runs the reaction on a set of reactants
/*!
@@ -437,7 +437,7 @@ RDKIT_CHEMREACTIONS_EXPORT void addRecursiveQueriesToReaction(
ChemicalReaction &rxn, const std::map<std::string, ROMOL_SPTR> &queries,
const std::string &propName,
std::vector<std::vector<std::pair<unsigned int, std::string>>>
*reactantLabels = NULL);
*reactantLabels = nullptr);
} // namespace RDKit

2
Code/GraphMol/ChemReactions/ReactionParser.h
View File

@@ -82,7 +82,7 @@ RDKIT_CHEMREACTIONS_EXPORT ChemicalReaction *RxnDataStreamToChemicalReaction(
*/
RDKIT_CHEMREACTIONS_EXPORT ChemicalReaction *RxnSmartsToChemicalReaction(
const std::string &text,
std::map<std::string, std::string> *replacements = 0,
std::map<std::string, std::string> *replacements = nullptr,
bool useSmiles = false);
//! Parse a ROMol into a ChemicalReaction, RXN role must be set before

3
Code/GraphMol/ChemTransforms/ChemTransforms.h
View File

@@ -230,7 +230,8 @@ RDKIT_CHEMTRANSFORMS_EXPORT ROMol *combineMols(
RDKIT_CHEMTRANSFORMS_EXPORT void addRecursiveQueries(
ROMol &mol, const std::map<std::string, ROMOL_SPTR> &queries,
const std::string &propName,
std::vector<std::pair<unsigned int, std::string>> *reactantLabels = NULL);
std::vector<std::pair<unsigned int, std::string>> *reactantLabels =
nullptr);
//! \brief parses a query definition file and sets up a set of definitions
//! suitable for use by addRecursiveQueries()

24
Code/GraphMol/ChemTransforms/MolFragmenter.h
View File

@@ -50,21 +50,23 @@ struct RDKIT_CHEMTRANSFORMS_EXPORT FragmenterBondType {
RDKIT_CHEMTRANSFORMS_EXPORT ROMol *fragmentOnBonds(
const ROMol &mol, const std::vector<unsigned int> &bondIndices,
bool addDummies = true,
const std::vector<std::pair<unsigned int, unsigned int>> *dummyLabels = 0,
const std::vector<Bond::BondType> *bondTypes = 0,
std::vector<unsigned int> *nCutsPerAtom = 0);
const std::vector<std::pair<unsigned int, unsigned int>> *dummyLabels =
nullptr,
const std::vector<Bond::BondType> *bondTypes = nullptr,
std::vector<unsigned int> *nCutsPerAtom = nullptr);
//! \overload
RDKIT_CHEMTRANSFORMS_EXPORT ROMol *fragmentOnBonds(
const ROMol &mol, const std::vector<FragmenterBondType> &bondPatterns,
const std::map<unsigned int, ROMOL_SPTR> *atomEnvirons = 0,
std::vector<unsigned int> *nCutsPerAtom = 0);
const std::map<unsigned int, ROMOL_SPTR> *atomEnvirons = nullptr,
std::vector<unsigned int> *nCutsPerAtom = nullptr);
RDKIT_CHEMTRANSFORMS_EXPORT void fragmentOnSomeBonds(
const ROMol &mol, const std::vector<unsigned int> &bondIndices,
std::vector<ROMOL_SPTR> &resMols, unsigned int maxToCut = 1,
bool addDummies = true,
const std::vector<std::pair<unsigned int, unsigned int>> *dummyLabels = 0,
const std::vector<Bond::BondType> *bondTypes = 0,
std::vector<std::vector<unsigned int>> *nCutsPerAtom = 0);
const std::vector<std::pair<unsigned int, unsigned int>> *dummyLabels =
nullptr,
const std::vector<Bond::BondType> *bondTypes = nullptr,
std::vector<std::vector<unsigned int>> *nCutsPerAtom = nullptr);
//! \brief Fragments a molecule by breaking all BRICS bonds
/*!
@@ -77,14 +79,14 @@ RDKIT_CHEMTRANSFORMS_EXPORT ROMol *fragmentOnBRICSBonds(const ROMol &mol);
RDKIT_CHEMTRANSFORMS_EXPORT void constructFragmenterAtomTypes(
std::istream *inStream, std::map<unsigned int, std::string> &defs,
const std::string &comment = "//", bool validate = true,
std::map<unsigned int, ROMOL_SPTR> *environs = 0);
std::map<unsigned int, ROMOL_SPTR> *environs = nullptr);
RDKIT_CHEMTRANSFORMS_EXPORT void constructFragmenterAtomTypes(
const std::string &str, std::map<unsigned int, std::string> &defs,
const std::string &comment = "//", bool validate = true,
std::map<unsigned int, ROMOL_SPTR> *environs = 0);
std::map<unsigned int, ROMOL_SPTR> *environs = nullptr);
RDKIT_CHEMTRANSFORMS_EXPORT void constructBRICSAtomTypes(
std::map<unsigned int, std::string> &defs,
std::map<unsigned int, ROMOL_SPTR> *environs = 0);
std::map<unsigned int, ROMOL_SPTR> *environs = nullptr);
RDKIT_CHEMTRANSFORMS_EXPORT void constructFragmenterBondTypes(
std::istream *inStream,
const std::map<unsigned int, std::string> &atomTypes,

6
Code/GraphMol/Conformer.h
View File

@@ -45,10 +45,12 @@ class RDKIT_GRAPHMOL_EXPORT Conformer : public RDProps {
friend class ROMol;
//! Constructor
Conformer() : df_is3D(true), d_id(0), dp_mol(NULL) { d_positions.clear(); };
Conformer() : df_is3D(true), d_id(0), dp_mol(nullptr) {
d_positions.clear();
};
//! Constructor with number of atoms specified ID specification
Conformer(unsigned int numAtoms) : df_is3D(true), d_id(0), dp_mol(NULL) {
Conformer(unsigned int numAtoms) : df_is3D(true), d_id(0), dp_mol(nullptr) {
if (numAtoms) {
d_positions.resize(numAtoms, RDGeom::Point3D(0.0, 0.0, 0.0));
} else {

2
Code/GraphMol/Depictor/EmbeddedFrag.h
View File

@@ -350,7 +350,7 @@ class RDKIT_DEPICTOR_EXPORT EmbeddedFrag {
void randomSampleFlipsAndPermutations(unsigned int nBondsPerSample = 3,
unsigned int nSamples = 100,
int seed = 100,
const DOUBLE_SMART_PTR *dmat = 0,
const DOUBLE_SMART_PTR *dmat = nullptr,
double mimicDmatWt = 0.0,
bool permuteDeg4Nodes = false);

8
Code/GraphMol/Depictor/RDDepictor.h
View File

@@ -71,7 +71,7 @@ class RDKIT_DEPICTOR_EXPORT DepictException : public std::exception {
*/
RDKIT_DEPICTOR_EXPORT unsigned int compute2DCoords(
RDKit::ROMol &mol, const RDGeom::INT_POINT2D_MAP *coordMap = 0,
RDKit::ROMol &mol, const RDGeom::INT_POINT2D_MAP *coordMap = nullptr,
bool canonOrient = false, bool clearConfs = true,
unsigned int nFlipsPerSample = 0, unsigned int nSamples = 0,
int sampleSeed = 0, bool permuteDeg4Nodes = false, bool forceRDKit = false);
@@ -126,7 +126,7 @@ RDKIT_DEPICTOR_EXPORT unsigned int compute2DCoords(
*/
RDKIT_DEPICTOR_EXPORT unsigned int compute2DCoordsMimicDistMat(
RDKit::ROMol &mol, const DOUBLE_SMART_PTR *dmat = 0,
RDKit::ROMol &mol, const DOUBLE_SMART_PTR *dmat = nullptr,
bool canonOrient = true, bool clearConfs = true, double weightDistMat = 0.5,
unsigned int nFlipsPerSample = 3, unsigned int nSamples = 100,
int sampleSeed = 25, bool permuteDeg4Nodes = true, bool forceRDKit = false);
@@ -159,7 +159,7 @@ RDKIT_DEPICTOR_EXPORT unsigned int compute2DCoordsMimicDistMat(
*/
RDKIT_DEPICTOR_EXPORT void generateDepictionMatching2DStructure(
RDKit::ROMol &mol, const RDKit::ROMol &reference, int confId = -1,
RDKit::ROMol *referencePattern = static_cast<RDKit::ROMol *>(0),
RDKit::ROMol *referencePattern = static_cast<RDKit::ROMol *>(nullptr),
bool acceptFailure = false, bool forceRDKit = false);
//! \brief Generate a 2D depiction for a molecule where all or part of
@@ -186,7 +186,7 @@ RDKIT_DEPICTOR_EXPORT void generateDepictionMatching2DStructure(
*/
RDKIT_DEPICTOR_EXPORT void generateDepictionMatching3DStructure(
RDKit::ROMol &mol, const RDKit::ROMol &reference, int confId = -1,
RDKit::ROMol *referencePattern = 0, bool acceptFailure = false,
RDKit::ROMol *referencePattern = nullptr, bool acceptFailure = false,
bool forceRDKit = false);
}; // namespace RDDepict

2
Code/GraphMol/Descriptors/ConnectivityDescriptors.h
View File

@@ -144,7 +144,7 @@ const std::string chiNnVersion = "1.2.0";
Note: this can be a time-consuming calculation.
*/
RDKIT_DESCRIPTORS_EXPORT double calcHallKierAlpha(
const ROMol &mol, std::vector<double> *atomContribs = 0);
const ROMol &mol, std::vector<double> *atomContribs = nullptr);
const std::string hallKierAlphaVersion = "1.2.0";
//! calculate the Hall-Kier kappa1 value for a molecule

4
Code/GraphMol/Descriptors/Crippen.h
View File

@@ -50,8 +50,8 @@ const std::string crippenVersion = "1.2.0";
RDKIT_DESCRIPTORS_EXPORT void getCrippenAtomContribs(
const ROMol &mol, std::vector<double> &logpContribs,
std::vector<double> &mrContribs, bool force = false,
std::vector<unsigned int> *atomTypes = 0,
std::vector<std::string> *atomTypeLabels = 0);
std::vector<unsigned int> *atomTypes = nullptr,
std::vector<std::string> *atomTypeLabels = nullptr);
//! generate Wildman-Crippen LogP and MR estimates for a molecule
/*!

4
Code/GraphMol/Descriptors/Lipinski.h
View File

@@ -143,13 +143,13 @@ RDKIT_DESCRIPTORS_EXPORT extern const std::string NumSpiroAtomsVersion;
//! calculates the number of spiro atoms (atoms shared between rings that share
// exactly one atom)
RDKIT_DESCRIPTORS_EXPORT unsigned int calcNumSpiroAtoms(
const ROMol &mol, std::vector<unsigned int> *atoms = NULL);
const ROMol &mol, std::vector<unsigned int> *atoms = nullptr);
RDKIT_DESCRIPTORS_EXPORT extern const std::string NumBridgeheadAtomsVersion;
//! calculates the number of bridgehead atoms (atoms shared between rings that
// share at least two bonds)
RDKIT_DESCRIPTORS_EXPORT unsigned int calcNumBridgeheadAtoms(
const ROMol &mol, std::vector<unsigned int> *atoms = NULL);
const ROMol &mol, std::vector<unsigned int> *atoms = nullptr);
RDKIT_DESCRIPTORS_EXPORT extern const std::string NumAtomStereoCentersVersion;
//! calculates the total number of atom stereo centers

6
Code/GraphMol/Descriptors/MolSurf.h
View File

@@ -105,11 +105,11 @@ RDKIT_DESCRIPTORS_EXPORT double calcTPSA(const ROMol &mol, bool force = false,
bool includeSandP = false);
RDKIT_DESCRIPTORS_EXPORT std::vector<double> calcSlogP_VSA(
const ROMol &mol, std::vector<double> *bins = 0, bool force = false);
const ROMol &mol, std::vector<double> *bins = nullptr, bool force = false);
RDKIT_DESCRIPTORS_EXPORT std::vector<double> calcSMR_VSA(
const ROMol &mol, std::vector<double> *bins = 0, bool force = false);
const ROMol &mol, std::vector<double> *bins = nullptr, bool force = false);
RDKIT_DESCRIPTORS_EXPORT std::vector<double> calcPEOE_VSA(
const ROMol &mol, std::vector<double> *bins = 0, bool force = false);
const ROMol &mol, std::vector<double> *bins = nullptr, bool force = false);
RDKIT_DESCRIPTORS_EXPORT std::vector<double> calcCustomProp_VSA(
const ROMol &mol, const std::string &customPropName,
const std::vector<double> &bins, bool force = false);

2
Code/GraphMol/Descriptors/Property.h
View File

@@ -51,7 +51,7 @@ struct RDKIT_DESCRIPTORS_EXPORT PropertyFunctor {
double (*d_dataFunc)(const ROMol &);
PropertyFunctor(const std::string &name, const std::string &version,
double (*func)(const ROMol &) = NULL)
double (*func)(const ROMol &) = nullptr)
: propName(name), propVersion(version), d_dataFunc(func) {}
virtual ~PropertyFunctor(){};

8
Code/GraphMol/DistGeomHelpers/Embedder.h
View File

@@ -124,7 +124,7 @@ struct RDKIT_DISTGEOMHELPERS_EXPORT EmbedParameters {
boxSizeMult(2.0),
randNegEig(true),
numZeroFail(1),
coordMap(NULL),
coordMap(nullptr),
optimizerForceTol(1e-3),
ignoreSmoothingFailures(false),
enforceChirality(true),
@@ -282,7 +282,7 @@ inline int EmbedMolecule(
bool clearConfs = true, bool useRandomCoords = false,
double boxSizeMult = 2.0, bool randNegEig = true,
unsigned int numZeroFail = 1,
const std::map<int, RDGeom::Point3D> *coordMap = 0,
const std::map<int, RDGeom::Point3D> *coordMap = nullptr,
double optimizerForceTol = 1e-3, bool ignoreSmoothingFailures = false,
bool enforceChirality = true, bool useExpTorsionAnglePrefs = false,
bool useBasicKnowledge = false, bool verbose = false,
@@ -381,7 +381,7 @@ inline void EmbedMultipleConfs(
bool useRandomCoords = false, double boxSizeMult = 2.0,
bool randNegEig = true, unsigned int numZeroFail = 1,
double pruneRmsThresh = -1.0,
const std::map<int, RDGeom::Point3D> *coordMap = 0,
const std::map<int, RDGeom::Point3D> *coordMap = nullptr,
double optimizerForceTol = 1e-3, bool ignoreSmoothingFailures = false,
bool enforceChirality = true, bool useExpTorsionAnglePrefs = false,
bool useBasicKnowledge = false, bool verbose = false,
@@ -403,7 +403,7 @@ inline INT_VECT EmbedMultipleConfs(
int seed = -1, bool clearConfs = true, bool useRandomCoords = false,
double boxSizeMult = 2.0, bool randNegEig = true,
unsigned int numZeroFail = 1, double pruneRmsThresh = -1.0,
const std::map<int, RDGeom::Point3D> *coordMap = 0,
const std::map<int, RDGeom::Point3D> *coordMap = nullptr,
double optimizerForceTol = 1e-3, bool ignoreSmoothingFailures = false,
bool enforceChirality = true, bool useExpTorsionAnglePrefs = false,
bool useBasicKnowledge = false, bool verbose = false,

6
Code/GraphMol/FMCS/DebugTrace.h
View File

@@ -67,7 +67,7 @@ static inline int gettimeofday(struct timeval *tv, struct timezone *tz) {
unsigned __int64 tmpres = 0;
static int tzflag;
if (NULL != tv) {
if (nullptr != tv) {
GetSystemTimeAsFileTime(&ft);
tmpres |= ft.dwHighDateTime;
@@ -81,7 +81,7 @@ static inline int gettimeofday(struct timeval *tv, struct timezone *tz) {
tv->tv_usec = (long)(tmpres % 1000000UL);
}
if (NULL != tz) {
if (nullptr != tz) {
if (!tzflag) {
_tzset();
tzflag++;
@@ -96,7 +96,7 @@ static inline int gettimeofday(struct timeval *tv, struct timezone *tz) {
static inline unsigned long long nanoClock(
void) { // actually returns microseconds
struct timeval t;
gettimeofday(&t, (struct timezone *)0);
gettimeofday(&t, (struct timezone *)nullptr);
return t.tv_usec + t.tv_sec * 1000000ULL;
}

2
Code/GraphMol/FMCS/FMCS.h
View File

@@ -167,7 +167,7 @@ RDKIT_FMCS_EXPORT void parseMCSParametersJSON(const char* json,
MCSParameters* params);
RDKIT_FMCS_EXPORT MCSResult findMCS(const std::vector<ROMOL_SPTR>& mols,
const MCSParameters* params = 0);
const MCSParameters* params = nullptr);
RDKIT_FMCS_EXPORT MCSResult findMCS_P(const std::vector<ROMOL_SPTR>& mols,
const char* params_json);

4
Code/GraphMol/FMCS/RingMatchTableSet.h
View File

@@ -63,7 +63,7 @@ class RDKIT_FMCS_EXPORT RingMatchTableSet {
std::map<const INT_VECT*, unsigned> QueryRingIndex;
public:
RingMatchTableSet() : QueryBondRingsIndeces(0) {}
RingMatchTableSet() : QueryBondRingsIndeces(nullptr) {}
inline void clear() {
if (QueryBondRingsIndeces) QueryBondRingsIndeces->clear();
@@ -170,7 +170,7 @@ class RDKIT_FMCS_EXPORT RingMatchTableSet {
#else // noticeable slowly:
FMCS::SubstructMatchCustom(
graph2, *targetMolecule, graph1, *query, parameters.AtomTyper,
parameters.BondTyper, NULL, parameters.AtomCompareParameters,
parameters.BondTyper, nullptr, parameters.AtomCompareParameters,
bp, parameters.CompareFunctionsUserData);
#endif
if (match) m.setMatch(i, &*r2);

2
Code/GraphMol/FMCS/Seed.h
View File

@@ -47,7 +47,7 @@ struct RDKIT_FMCS_EXPORT NewBond {
: SourceAtomIdx(-1),
BondIdx(-1),
NewAtomIdx(-1),
NewAtom(0),
NewAtom(nullptr),
EndAtomIdx(-1) {}
NewBond(unsigned from_atom, unsigned bond_idx, unsigned new_atom,

6
Code/GraphMol/FMCS/SubstructMatchCustom.h
View File

@@ -27,9 +27,9 @@ RDKIT_FMCS_EXPORT bool SubstructMatchCustomTable(
const ROMol& querySrc // seed and full source query molecules
,
const MatchTable& atomMatchTable, const MatchTable& bondMatchTable,
const MCSParameters* parameters = 0 // for final checker (CHIRALITY)
const MCSParameters* parameters = nullptr // for final checker (CHIRALITY)
,
match_V_t* match = 0);
match_V_t* match = nullptr);
RDKIT_FMCS_EXPORT bool SubstructMatchCustom(
const FMCS::Graph& target, const ROMol& mol, const FMCS::Graph& query,
@@ -38,6 +38,6 @@ RDKIT_FMCS_EXPORT bool SubstructMatchCustom(
MCSAtomCompareFunction atomCompare, MCSBondCompareFunction bondCompare,
MCSFinalMatchCheckFunction finalCompare,
const MCSAtomCompareParameters& acp, const MCSBondCompareParameters& bcp,
void* user_data, match_V_t* match = 0);
void* user_data, match_V_t* match = nullptr);
} // namespace FMCS
} // namespace RDKit

2
Code/GraphMol/FMCS/SubstructureCache.h
View File

@@ -125,7 +125,7 @@ class RDKIT_FMCS_EXPORT SubstructureCache {
std::map<KeyNumericMetrics::TValue, size_t>::const_iterator entryit =
NumericIndex.find(key.NumericMetrics.Value);
if (NumericIndex.end() != entryit) return &ValueStorage[entryit->second];
return NULL; // not found
return nullptr; // not found
}
// if find() did not found any entry for this key of seed a new entry will be

2
Code/GraphMol/FileParsers/MolSupplier.h
View File

@@ -126,7 +126,7 @@ class RDKIT_FILEPARSERS_EXPORT ForwardSDMolSupplier : public MolSupplier {
if (df_owner && dp_inStream) {
delete dp_inStream;
df_owner = false;
dp_inStream = NULL;
dp_inStream = nullptr;
}
};

2
Code/GraphMol/FileParsers/MolWriters.h
View File

@@ -145,7 +145,7 @@ class RDKIT_FILEPARSERS_EXPORT SDWriter : public MolWriter {
//! \brief return the text that would be written to the file
static std::string getText(const ROMol &mol, int confId = defaultConfId,
bool kekulize = true, bool force_V3000 = false,
int molid = -1, STR_VECT *propNames = NULL);
int molid = -1, STR_VECT *propNames = nullptr);
//! \brief write a new molecule to the file
void write(const ROMol &mol, int confId = defaultConfId);

12
Code/GraphMol/FilterCatalog/FilterMatchers.h
View File

@@ -546,12 +546,12 @@ class RDKIT_FILTERCATALOG_EXPORT FilterHierarchyMatcher
// Register all known filter matcher types for serialization
template <class Archive>
void registerFilterMatcherTypes(Archive &ar) {
ar.register_type(static_cast<FilterMatchOps::And *>(NULL));
ar.register_type(static_cast<FilterMatchOps::Or *>(NULL));
ar.register_type(static_cast<FilterMatchOps::Not *>(NULL));
ar.register_type(static_cast<SmartsMatcher *>(NULL));
ar.register_type(static_cast<ExclusionList *>(NULL));
ar.register_type(static_cast<FilterHierarchyMatcher *>(NULL));
ar.register_type(static_cast<FilterMatchOps::And *>(nullptr));
ar.register_type(static_cast<FilterMatchOps::Or *>(nullptr));
ar.register_type(static_cast<FilterMatchOps::Not *>(nullptr));
ar.register_type(static_cast<SmartsMatcher *>(nullptr));
ar.register_type(static_cast<ExclusionList *>(nullptr));
ar.register_type(static_cast<FilterHierarchyMatcher *>(nullptr));
}
#endif
} // namespace RDKit

6
Code/GraphMol/FilterCatalog/Filters.h
View File

@@ -55,9 +55,9 @@ unsigned int GetNumPropertyEntries(FilterCatalogParams::FilterCatalogs catalog);
const FilterProperty_t *GetFilterProperties(
FilterCatalogParams::FilterCatalogs catalog);
FilterCatalogEntry *MakeFilterCatalogEntry(const FilterData_t &,
unsigned int num_props = 0,
const FilterProperty_t *props = 0);
FilterCatalogEntry *MakeFilterCatalogEntry(
const FilterData_t &, unsigned int num_props = 0,
const FilterProperty_t *props = nullptr);
} // namespace RDKit
#endif

42
Code/GraphMol/Fingerprints/AtomPairs.h
View File

@@ -79,15 +79,15 @@ const std::string atomPairsVersion = "1.1.0";
*/
RDKIT_FINGERPRINTS_EXPORT SparseIntVect<std::int32_t> *getAtomPairFingerprint(
const ROMol &mol, unsigned int minLength, unsigned int maxLength,
const std::vector<std::uint32_t> *fromAtoms = 0,
const std::vector<std::uint32_t> *ignoreAtoms = 0,
const std::vector<std::uint32_t> *atomInvariants = 0,
const std::vector<std::uint32_t> *fromAtoms = nullptr,
const std::vector<std::uint32_t> *ignoreAtoms = nullptr,
const std::vector<std::uint32_t> *atomInvariants = nullptr,
bool includeChirality = false, bool use2D = true, int confId = -1);
//! \overload
RDKIT_FINGERPRINTS_EXPORT SparseIntVect<std::int32_t> *getAtomPairFingerprint(
const ROMol &mol, const std::vector<std::uint32_t> *fromAtoms = 0,
const std::vector<std::uint32_t> *ignoreAtoms = 0,
const std::vector<std::uint32_t> *atomInvariants = 0,
const ROMol &mol, const std::vector<std::uint32_t> *fromAtoms = nullptr,
const std::vector<std::uint32_t> *ignoreAtoms = nullptr,
const std::vector<std::uint32_t> *atomInvariants = nullptr,
bool includeChirality = false, bool use2D = true, int confId = -1);
//! returns the hashed atom-pair fingerprint for a molecule
@@ -121,9 +121,9 @@ RDKIT_FINGERPRINTS_EXPORT SparseIntVect<std::int32_t>
*getHashedAtomPairFingerprint(
const ROMol &mol, unsigned int nBits = 2048, unsigned int minLength = 1,
unsigned int maxLength = maxPathLen - 1,
const std::vector<std::uint32_t> *fromAtoms = 0,
const std::vector<std::uint32_t> *ignoreAtoms = 0,
const std::vector<std::uint32_t> *atomInvariants = 0,
const std::vector<std::uint32_t> *fromAtoms = nullptr,
const std::vector<std::uint32_t> *ignoreAtoms = nullptr,
const std::vector<std::uint32_t> *atomInvariants = nullptr,
bool includeChirality = false, bool use2D = true, int confId = -1);
//! returns the hashed atom-pair fingerprint for a molecule as a bit vector
/*!
@@ -158,9 +158,9 @@ RDKIT_FINGERPRINTS_EXPORT ExplicitBitVect *
getHashedAtomPairFingerprintAsBitVect(
const ROMol &mol, unsigned int nBits = 2048, unsigned int minLength = 1,
unsigned int maxLength = maxPathLen - 1,
const std::vector<std::uint32_t> *fromAtoms = 0,
const std::vector<std::uint32_t> *ignoreAtoms = 0,
const std::vector<std::uint32_t> *atomInvariants = 0,
const std::vector<std::uint32_t> *fromAtoms = nullptr,
const std::vector<std::uint32_t> *ignoreAtoms = nullptr,
const std::vector<std::uint32_t> *atomInvariants = nullptr,
unsigned int nBitsPerEntry = 4, bool includeChirality = false,
bool use2D = true, int confId = -1);
@@ -193,9 +193,9 @@ getHashedAtomPairFingerprintAsBitVect(
RDKIT_FINGERPRINTS_EXPORT SparseIntVect<boost::int64_t>
*getTopologicalTorsionFingerprint(
const ROMol &mol, unsigned int targetSize = 4,
const std::vector<std::uint32_t> *fromAtoms = 0,
const std::vector<std::uint32_t> *ignoreAtoms = 0,
const std::vector<std::uint32_t> *atomInvariants = 0,
const std::vector<std::uint32_t> *fromAtoms = nullptr,
const std::vector<std::uint32_t> *ignoreAtoms = nullptr,
const std::vector<std::uint32_t> *atomInvariants = nullptr,
bool includeChirality = false);
//! returns a hashed topological-torsion fingerprint for a molecule
/*!
@@ -227,9 +227,9 @@ RDKIT_FINGERPRINTS_EXPORT SparseIntVect<boost::int64_t>
RDKIT_FINGERPRINTS_EXPORT SparseIntVect<boost::int64_t> *
getHashedTopologicalTorsionFingerprint(
const ROMol &mol, unsigned int nBits = 2048, unsigned int targetSize = 4,
const std::vector<std::uint32_t> *fromAtoms = 0,
const std::vector<std::uint32_t> *ignoreAtoms = 0,
const std::vector<std::uint32_t> *atomInvariants = 0,
const std::vector<std::uint32_t> *fromAtoms = nullptr,
const std::vector<std::uint32_t> *ignoreAtoms = nullptr,
const std::vector<std::uint32_t> *atomInvariants = nullptr,
bool includeChirality = false);
//! returns a hashed topological-torsion fingerprint for a molecule as a bit
// vector
@@ -258,9 +258,9 @@ getHashedTopologicalTorsionFingerprint(
RDKIT_FINGERPRINTS_EXPORT ExplicitBitVect *
getHashedTopologicalTorsionFingerprintAsBitVect(
const ROMol &mol, unsigned int nBits = 2048, unsigned int targetSize = 4,
const std::vector<std::uint32_t> *fromAtoms = 0,
const std::vector<std::uint32_t> *ignoreAtoms = 0,
const std::vector<std::uint32_t> *atomInvariants = 0,
const std::vector<std::uint32_t> *fromAtoms = nullptr,
const std::vector<std::uint32_t> *ignoreAtoms = nullptr,
const std::vector<std::uint32_t> *atomInvariants = nullptr,
unsigned int nBitsPerEntry = 4, bool includeChirality = false);
} // namespace AtomPairs
} // namespace RDKit

2
Code/GraphMol/Fingerprints/FingerprintUtil.h
View File

@@ -128,7 +128,7 @@ const std::string morganConnectivityInvariantVersion = "1.0.0";
*/
RDKIT_FINGERPRINTS_EXPORT void getFeatureInvariants(
const ROMol &mol, std::vector<std::uint32_t> &invars,
std::vector<const ROMol *> *patterns = 0);
std::vector<const ROMol *> *patterns = nullptr);
const std::string morganFeatureInvariantVersion = "0.1.0";
} // namespace MorganFingerprints

27
Code/GraphMol/Fingerprints/Fingerprints.h
View File

@@ -55,10 +55,10 @@ RDKIT_FINGERPRINTS_EXPORT ExplicitBitVect *RDKFingerprintMol(
unsigned int fpSize = 2048, unsigned int nBitsPerHash = 2,
bool useHs = true, double tgtDensity = 0.0, unsigned int minSize = 128,
bool branchedPaths = true, bool useBondOrder = true,
std::vector<std::uint32_t> *atomInvariants = 0,
const std::vector<std::uint32_t> *fromAtoms = 0,
std::vector<std::vector<std::uint32_t>> *atomBits = 0,
std::map<std::uint32_t, std::vector<std::vector<int>>> *bitInfo = 0);
std::vector<std::uint32_t> *atomInvariants = nullptr,
const std::vector<std::uint32_t> *fromAtoms = nullptr,
std::vector<std::vector<std::uint32_t>> *atomBits = nullptr,
std::map<std::uint32_t, std::vector<std::vector<int>>> *bitInfo = nullptr);
const std::string RDKFingerprintMolVersion = "2.0.0";
//! \brief Generates a topological (Daylight like) fingerprint for a molecule
@@ -105,9 +105,9 @@ const std::string RDKFingerprintMolVersion = "2.0.0";
RDKIT_FINGERPRINTS_EXPORT ExplicitBitVect *LayeredFingerprintMol(
const ROMol &mol, unsigned int layerFlags = 0xFFFFFFFF,
unsigned int minPath = 1, unsigned int maxPath = 7,
unsigned int fpSize = 2048, std::vector<unsigned int> *atomCounts = 0,
ExplicitBitVect *setOnlyBits = 0, bool branchedPaths = true,
const std::vector<std::uint32_t> *fromAtoms = 0);
unsigned int fpSize = 2048, std::vector<unsigned int> *atomCounts = nullptr,
ExplicitBitVect *setOnlyBits = nullptr, bool branchedPaths = true,
const std::vector<std::uint32_t> *fromAtoms = nullptr);
const unsigned int maxFingerprintLayers = 10;
const std::string LayeredFingerprintMolVersion = "0.7.0";
const unsigned int substructLayers = 0x07;
@@ -143,17 +143,18 @@ const unsigned int substructLayers = 0x07;
*/
RDKIT_FINGERPRINTS_EXPORT ExplicitBitVect *PatternFingerprintMol(
const ROMol &mol, unsigned int fpSize = 2048,
std::vector<unsigned int> *atomCounts = 0,
ExplicitBitVect *setOnlyBits = 0);
std::vector<unsigned int> *atomCounts = nullptr,
ExplicitBitVect *setOnlyBits = nullptr);
RDKIT_FINGERPRINTS_EXPORT SparseIntVect<boost::uint64_t>
*getUnfoldedRDKFingerprintMol(
const ROMol &mol, unsigned int minPath = 1, unsigned int maxPath = 7,
bool useHs = true, bool branchedPaths = true, bool useBondOrder = true,
std::vector<std::uint32_t> *atomInvariants = 0,
const std::vector<std::uint32_t> *fromAtoms = 0,
std::vector<std::vector<boost::uint64_t>> *atomBits = 0,
std::map<boost::uint64_t, std::vector<std::vector<int>>> *bitInfo = 0);
std::vector<std::uint32_t> *atomInvariants = nullptr,
const std::vector<std::uint32_t> *fromAtoms = nullptr,
std::vector<std::vector<boost::uint64_t>> *atomBits = nullptr,
std::map<boost::uint64_t, std::vector<std::vector<int>>> *bitInfo =
nullptr);
} // namespace RDKit

20
Code/GraphMol/Fingerprints/MorganFingerprints.h
View File

@@ -104,10 +104,10 @@ const std::string morganFingerprintVersion = "1.0.0";
*/
RDKIT_FINGERPRINTS_EXPORT SparseIntVect<std::uint32_t> *getFingerprint(
const ROMol &mol, unsigned int radius,
std::vector<boost::uint32_t> *invariants = 0,
const std::vector<boost::uint32_t> *fromAtoms = 0,
std::vector<boost::uint32_t> *invariants = nullptr,
const std::vector<boost::uint32_t> *fromAtoms = nullptr,
bool useChirality = false, bool useBondTypes = true, bool useCounts = true,
bool onlyNonzeroInvariants = false, BitInfoMap *atomsSettingBits = 0,
bool onlyNonzeroInvariants = false, BitInfoMap *atomsSettingBits = nullptr,
bool includeRedundantEnvironments = false);
//! returns the Morgan fingerprint for a molecule
@@ -156,10 +156,10 @@ RDKIT_FINGERPRINTS_EXPORT SparseIntVect<std::uint32_t> *getFingerprint(
*/
RDKIT_FINGERPRINTS_EXPORT SparseIntVect<std::uint32_t> *getHashedFingerprint(
const ROMol &mol, unsigned int radius, unsigned int nBits = 2048,
std::vector<boost::uint32_t> *invariants = 0,
const std::vector<boost::uint32_t> *fromAtoms = 0,
std::vector<boost::uint32_t> *invariants = nullptr,
const std::vector<boost::uint32_t> *fromAtoms = nullptr,
bool useChirality = false, bool useBondTypes = true,
bool onlyNonzeroInvariants = false, BitInfoMap *atomsSettingBits = 0,
bool onlyNonzeroInvariants = false, BitInfoMap *atomsSettingBits = nullptr,
bool includeRedundantEnvironments = false);
//! returns the Morgan fingerprint for a molecule as a bit vector
@@ -198,10 +198,10 @@ RDKIT_FINGERPRINTS_EXPORT SparseIntVect<std::uint32_t> *getHashedFingerprint(
*/
RDKIT_FINGERPRINTS_EXPORT ExplicitBitVect *getFingerprintAsBitVect(
const ROMol &mol, unsigned int radius, unsigned int nBits,
std::vector<std::uint32_t> *invariants = 0,
const std::vector<std::uint32_t> *fromAtoms = 0, bool useChirality = false,
bool useBondTypes = true, bool onlyNonzeroInvariants = false,
BitInfoMap *atomsSettingBits = 0,
std::vector<std::uint32_t> *invariants = nullptr,
const std::vector<std::uint32_t> *fromAtoms = nullptr,
bool useChirality = false, bool useBondTypes = true,
bool onlyNonzeroInvariants = false, BitInfoMap *atomsSettingBits = nullptr,
bool includeRedundantEnvironments = false);
} // end of namespace MorganFingerprints

6
Code/GraphMol/FragCatalog/FragCatalogEntry.h
View File

@@ -27,7 +27,7 @@ namespace RDKit {
class RDKIT_FRAGCATALOG_EXPORT FragCatalogEntry
: public RDCatalog::CatalogEntry {
public:
FragCatalogEntry() : dp_mol(0), d_descrip(""), d_order(0) {
FragCatalogEntry() : dp_mol(nullptr), d_descrip(""), d_order(0) {
dp_props = new Dict();
setBitId(-1);
}
@@ -38,10 +38,10 @@ class RDKIT_FRAGCATALOG_EXPORT FragCatalogEntry
~FragCatalogEntry() {
delete dp_mol;
dp_mol = 0;
dp_mol = nullptr;
if (dp_props) {
delete dp_props;
dp_props = 0;
dp_props = nullptr;
}
}

4
Code/GraphMol/MMPA/MMPA_UnitTest.cpp
View File

@@ -78,7 +78,7 @@ static inline int gettimeofday(struct timeval* tv, struct timezone* tz) {
unsigned __int64 tmpres = 0;
static int tzflag;
if (NULL != tv) {
if (nullptr != tv) {
GetSystemTimeAsFileTime(&ft);
tmpres |= ft.dwHighDateTime;
@@ -92,7 +92,7 @@ static inline int gettimeofday(struct timeval* tv, struct timezone* tz) {
tv->tv_usec = (long)(tmpres % 1000000UL);
}
if (NULL != tz) {
if (nullptr != tz) {
if (!tzflag) {
_tzset();
tzflag++;

16
Code/GraphMol/MolAlign/AlignMolecules.h
View File

@@ -65,8 +65,8 @@ class RDKIT_MOLALIGN_EXPORT MolAlignException : public std::exception {
*/
RDKIT_MOLALIGN_EXPORT double getAlignmentTransform(
const ROMol &prbMol, const ROMol &refMol, RDGeom::Transform3D &trans,
int prbCid = -1, int refCid = -1, const MatchVectType *atomMap = 0,
const RDNumeric::DoubleVector *weights = 0, bool reflect = false,
int prbCid = -1, int refCid = -1, const MatchVectType *atomMap = nullptr,
const RDNumeric::DoubleVector *weights = nullptr, bool reflect = false,
unsigned int maxIters = 50);
//! Optimally (minimum RMSD) align a molecule to another molecule
@@ -98,8 +98,8 @@ RDKIT_MOLALIGN_EXPORT double getAlignmentTransform(
*/
RDKIT_MOLALIGN_EXPORT double alignMol(
ROMol &prbMol, const ROMol &refMol, int prbCid = -1, int refCid = -1,
const MatchVectType *atomMap = 0,
const RDNumeric::DoubleVector *weights = 0, bool reflect = false,
const MatchVectType *atomMap = nullptr,
const RDNumeric::DoubleVector *weights = nullptr, bool reflect = false,
unsigned int maxIters = 50);
//! Returns the optimal RMS for aligning two molecules, taking
@@ -148,10 +148,10 @@ RDKIT_MOLALIGN_EXPORT double getBestRMS(
conformations
*/
RDKIT_MOLALIGN_EXPORT void alignMolConformers(
ROMol &mol, const std::vector<unsigned int> *atomIds = 0,
const std::vector<unsigned int> *confIds = 0,
const RDNumeric::DoubleVector *weights = 0, bool reflect = false,
unsigned int maxIters = 50, std::vector<double> *RMSlist = 0);
ROMol &mol, const std::vector<unsigned int> *atomIds = nullptr,
const std::vector<unsigned int> *confIds = nullptr,
const RDNumeric::DoubleVector *weights = nullptr, bool reflect = false,
unsigned int maxIters = 50, std::vector<double> *RMSlist = nullptr);
} // namespace MolAlign
} // namespace RDKit
#endif

22
Code/GraphMol/MolAlign/O3AAlignMolecules.h
View File

@@ -188,8 +188,8 @@ class RDKIT_MOLALIGN_EXPORT LAP {
class RDKIT_MOLALIGN_EXPORT SDM {
public:
// constructor
SDM(const Conformer *prbConf = NULL, const Conformer *refConf = NULL,
O3AConstraintVect *o3aConstraintVect = NULL)
SDM(const Conformer *prbConf = nullptr, const Conformer *refConf = nullptr,
O3AConstraintVect *o3aConstraintVect = nullptr)
: d_prbConf(prbConf),
d_refConf(refConf),
d_o3aConstraintVect(o3aConstraintVect){};
@@ -278,10 +278,10 @@ class RDKIT_MOLALIGN_EXPORT O3A {
AtomTypeScheme atomTypes = MMFF94, const int prbCid = -1,
const int refCid = -1, const bool reflect = false,
const unsigned int maxIters = 50, unsigned int options = 0,
const MatchVectType *constraintMap = NULL,
const RDNumeric::DoubleVector *constraintWeights = NULL,
LAP *extLAP = NULL, MolHistogram *extPrbHist = NULL,
MolHistogram *extRefHist = NULL);
const MatchVectType *constraintMap = nullptr,
const RDNumeric::DoubleVector *constraintWeights = nullptr,
LAP *extLAP = nullptr, MolHistogram *extPrbHist = nullptr,
MolHistogram *extRefHist = nullptr);
O3A(int (*costFunc)(const unsigned int, const unsigned int, double, void *),
double (*weightFunc)(const unsigned int, const unsigned int, void *),
double (*scoringFunc)(const unsigned int, const unsigned int, void *),
@@ -289,9 +289,9 @@ class RDKIT_MOLALIGN_EXPORT O3A {
const int refCid, const boost::dynamic_bitset<> &prbHvyAtoms,
const boost::dynamic_bitset<> &refHvyAtoms, const bool reflect = false,
const unsigned int maxIters = 50, unsigned int options = 0,
O3AConstraintVect *o3aConstraintVect = NULL, ROMol *extWorkPrbMol = NULL,
LAP *extLAP = NULL, MolHistogram *extPrbHist = NULL,
MolHistogram *extRefHist = NULL);
O3AConstraintVect *o3aConstraintVect = nullptr,
ROMol *extWorkPrbMol = nullptr, LAP *extLAP = nullptr,
MolHistogram *extPrbHist = nullptr, MolHistogram *extRefHist = nullptr);
~O3A() {
if (d_o3aMatchVect) {
delete d_o3aMatchVect;
@@ -346,8 +346,8 @@ RDKIT_MOLALIGN_EXPORT void getO3AForProbeConfs(
std::vector<boost::shared_ptr<O3A>> &res, int numThreads = 1,
O3A::AtomTypeScheme atomTypes = O3A::MMFF94, const int refCid = -1,
const bool reflect = false, const unsigned int maxIters = 50,
unsigned int options = 0, const MatchVectType *constraintMap = NULL,
const RDNumeric::DoubleVector *constraintWeights = NULL);
unsigned int options = 0, const MatchVectType *constraintMap = nullptr,
const RDNumeric::DoubleVector *constraintWeights = nullptr);
} // namespace MolAlign
} // namespace RDKit
#endif

2
Code/GraphMol/MolCatalog/MolCatalogEntry.h
View File

@@ -16,7 +16,7 @@ class ROMol;
//! This class is used to store ROMol objects in a MolCatalog
class RDKIT_MOLCATALOG_EXPORT MolCatalogEntry : public RDCatalog::CatalogEntry {
public:
MolCatalogEntry() : dp_mol(0), d_order(0), d_descrip("") {
MolCatalogEntry() : dp_mol(nullptr), d_order(0), d_descrip("") {
dp_props = new Dict();
setBitId(-1);
}

2
Code/GraphMol/MolDraw2D/MolDraw2DCairo.h
View File

@@ -46,7 +46,7 @@ class RDKIT_MOLDRAW2D_EXPORT MolDraw2DCairo : public MolDraw2D {
if (cairo_get_reference_count(dp_cr) > 0) {
cairo_destroy(dp_cr);
}
dp_cr = NULL;
dp_cr = nullptr;
}
}

20
Code/GraphMol/MolDraw2D/MultiMolDraw2D.cpp
View File

@@ -61,7 +61,7 @@ void MolDraw2D::drawMolecule(const ROMol &mol, const std::string &legend,
}
}
drawMolecule(mol, legend, highlight_atoms, &highlight_bonds,
highlight_atom_map, NULL, highlight_radii, confId);
highlight_atom_map, nullptr, highlight_radii, confId);
}
void MolDraw2D::doContinuousHighlighting(
@@ -143,13 +143,13 @@ void MolDraw2D::doContinuousHighlighting(
void drawMolecules(
const std::vector<ROMOL_SPTR> &mols,
const std::vector<std::string> *legends = NULL,
const std::vector<std::vector<int> > *highlight_atoms = NULL,
const std::vector<std::vector<int> > *highlight_bonds = NULL,
const std::vector<std::map<int, DrawColour> > *highlight_atom_maps = NULL,
const std::vector<std::map<int, DrawColour> > *highlight_bond_maps = NULL,
const std::vector<std::map<int, double> > *highlight_radii = NULL,
const std::vector<int> *confIds = NULL){};
const std::vector<std::string> *legends = nullptr,
const std::vector<std::vector<int>> *highlight_atoms = nullptr,
const std::vector<std::vector<int>> *highlight_bonds = nullptr,
const std::vector<std::map<int, DrawColour>> *highlight_atom_maps = nullptr,
const std::vector<std::map<int, DrawColour>> *highlight_bond_maps = nullptr,
const std::vector<std::map<int, double>> *highlight_radii = nullptr,
const std::vector<int> *confIds = nullptr){};
void MolDraw2D::drawMolecule(const ROMol &mol,
const vector<int> *highlight_atoms,
@@ -206,8 +206,8 @@ void MolDraw2D::drawMolecule(const ROMol &mol,
highlight_radii);
// at this point we shouldn't be doing any more highlighting, so blow out
// those variables:
highlight_bonds = NULL;
highlight_atoms = NULL;
highlight_bonds = nullptr;
highlight_atoms = nullptr;
} else if (drawOptions().circleAtoms && highlight_atoms) {
ROMol::VERTEX_ITER this_at, end_at;
boost::tie(this_at, end_at) = mol.getVertices();

16
Code/GraphMol/MolDraw2D/MultiMolDraw2D.h
View File

@@ -26,13 +26,15 @@ class RDKIT_MOLDRAW2D_EXPORT MultiMolDraw2D {
virtual ~MultiMolDraw2D() {}
virtual void drawMolecules(
const std::vector<ROMOL_SPTR> &mols,
const std::vector<std::string> *legends = NULL,
const std::vector<std::vector<int>> *highlight_atoms = NULL,
const std::vector<std::vector<int>> *highlight_bonds = NULL,
const std::vector<std::map<int, DrawColour>> *highlight_atom_maps = NULL,
const std::vector<std::map<int, DrawColour>> *highlight_bond_maps = NULL,
const std::vector<std::map<int, double>> *highlight_radii = NULL,
const std::vector<int> *confIds = NULL);
const std::vector<std::string> *legends = nullptr,
const std::vector<std::vector<int>> *highlight_atoms = nullptr,
const std::vector<std::vector<int>> *highlight_bonds = nullptr,
const std::vector<std::map<int, DrawColour>> *highlight_atom_maps =
nullptr,
const std::vector<std::map<int, DrawColour>> *highlight_bond_maps =
nullptr,
const std::vector<std::map<int, double>> *highlight_radii = nullptr,
const std::vector<int> *confIds = nullptr);
virtual int width() const { return width_; }
virtual int height() const { return height_; }

43
Code/GraphMol/MolOps.h
View File

@@ -102,8 +102,9 @@ RDKIT_GRAPHMOL_EXPORT unsigned int getMolFrags(
*/
RDKIT_GRAPHMOL_EXPORT std::vector<boost::shared_ptr<ROMol>> getMolFrags(
const ROMol &mol, bool sanitizeFrags = true, std::vector<int> *frags = 0,
std::vector<std::vector<int>> *fragsMolAtomMapping = 0,
const ROMol &mol, bool sanitizeFrags = true,
std::vector<int> *frags = nullptr,
std::vector<std::vector<int>> *fragsMolAtomMapping = nullptr,
bool copyConformers = true);
//! splits a molecule into pieces based on labels assigned using a query
@@ -124,7 +125,7 @@ template <typename T>
RDKIT_GRAPHMOL_EXPORT std::map<T, boost::shared_ptr<ROMol>>
getMolFragsWithQuery(const ROMol &mol, T (*query)(const ROMol &, const Atom *),
bool sanitizeFrags = true,
const std::vector<T> *whiteList = 0,
const std::vector<T> *whiteList = nullptr,
bool negateList = false);
#if 0
@@ -151,7 +152,7 @@ getMolFragsWithQuery(const ROMol &mol, T (*query)(const ROMol &, const Atom *),
*/
RDKIT_GRAPHMOL_EXPORT double computeBalabanJ(
const ROMol &mol, bool useBO = true, bool force = false,
const std::vector<int> *bondPath = 0, bool cacheIt = true);
const std::vector<int> *bondPath = nullptr, bool cacheIt = true);
//! \overload
RDKIT_GRAPHMOL_EXPORT double computeBalabanJ(double *distMat, int nb, int nAts);
@@ -182,13 +183,13 @@ RDKIT_GRAPHMOL_EXPORT double computeBalabanJ(double *distMat, int nb, int nAts);
*/
RDKIT_GRAPHMOL_EXPORT ROMol *addHs(const ROMol &mol, bool explicitOnly = false,
bool addCoords = false,
const UINT_VECT *onlyOnAtoms = NULL,
const UINT_VECT *onlyOnAtoms = nullptr,
bool addResidueInfo = false);
//! \overload
// modifies the molecule in place
RDKIT_GRAPHMOL_EXPORT void addHs(RWMol &mol, bool explicitOnly = false,
bool addCoords = false,
const UINT_VECT *onlyOnAtoms = NULL,
const UINT_VECT *onlyOnAtoms = nullptr,
bool addResidueInfo = false);
//! returns a copy of a molecule with hydrogens removed
@@ -359,11 +360,11 @@ RDKIT_GRAPHMOL_EXPORT void parseAdjustQueryParametersFromJSON(
\return the new molecule
*/
RDKIT_GRAPHMOL_EXPORT ROMol *adjustQueryProperties(
const ROMol &mol, const AdjustQueryParameters *params = NULL);
const ROMol &mol, const AdjustQueryParameters *params = nullptr);
//! \overload
// modifies the molecule in place
RDKIT_GRAPHMOL_EXPORT void adjustQueryProperties(
RWMol &mol, const AdjustQueryParameters *params = NULL);
RWMol &mol, const AdjustQueryParameters *params = nullptr);
//! returns a copy of a molecule with the atoms renumbered
/*!
@@ -518,7 +519,7 @@ typedef enum {
*/
RDKIT_GRAPHMOL_EXPORT int setAromaticity(
RWMol &mol, AromaticityModel model = AROMATICITY_DEFAULT,
int (*func)(RWMol &) = NULL);
int (*func)(RWMol &) = nullptr);
//! Designed to be called by the sanitizer to handle special cases before
// anything is done.
@@ -643,8 +644,8 @@ RDKIT_GRAPHMOL_EXPORT void setHybridization(ROMol &mol);
RDKIT_GRAPHMOL_EXPORT int findSSSR(const ROMol &mol,
std::vector<std::vector<int>> &res);
//! \overload
RDKIT_GRAPHMOL_EXPORT int findSSSR(const ROMol &mol,
std::vector<std::vector<int>> *res = 0);
RDKIT_GRAPHMOL_EXPORT int findSSSR(
const ROMol &mol, std::vector<std::vector<int>> *res = nullptr);
//! use a DFS algorithm to identify ring bonds and atoms in a molecule
/*!
@@ -710,8 +711,8 @@ RDKIT_GRAPHMOL_EXPORT int symmetrizeSSSR(ROMol &mol);
*/
RDKIT_GRAPHMOL_EXPORT double *getAdjacencyMatrix(
const ROMol &mol, bool useBO = false, int emptyVal = 0, bool force = false,
const char *propNamePrefix = 0,
const boost::dynamic_bitset<> *bondsToUse = 0);
const char *propNamePrefix = nullptr,
const boost::dynamic_bitset<> *bondsToUse = nullptr);
//! Computes the molecule's topological distance matrix
/*!
@@ -735,11 +736,9 @@ RDKIT_GRAPHMOL_EXPORT double *getAdjacencyMatrix(
*/
RDKIT_GRAPHMOL_EXPORT double *getDistanceMat(const ROMol &mol,
bool useBO = false,
bool useAtomWts = false,
bool force = false,
const char *propNamePrefix = 0);
RDKIT_GRAPHMOL_EXPORT double *getDistanceMat(
const ROMol &mol, bool useBO = false, bool useAtomWts = false,
bool force = false, const char *propNamePrefix = nullptr);
//! Computes the molecule's topological distance matrix
/*!
@@ -790,11 +789,9 @@ RDKIT_GRAPHMOL_EXPORT double *getDistanceMat(
In other cases the caller is responsible for freeing the memory.
*/
RDKIT_GRAPHMOL_EXPORT double *get3DDistanceMat(const ROMol &mol,
int confId = -1,
bool useAtomWts = false,
bool force = false,
const char *propNamePrefix = 0);
RDKIT_GRAPHMOL_EXPORT double *get3DDistanceMat(
const ROMol &mol, int confId = -1, bool useAtomWts = false,
bool force = false, const char *propNamePrefix = nullptr);
//! Find the shortest path between two atoms
/*!
Uses the Bellman-Ford algorithm

8
Code/GraphMol/MolTransforms/MolTransforms.h
View File

@@ -67,7 +67,7 @@ RDKIT_MOLTRANSFORMS_EXPORT RDGeom::Point3D computeCentroid(
RDKIT_MOLTRANSFORMS_EXPORT bool computePrincipalAxesAndMoments(
const RDKit::Conformer &conf, Eigen::Matrix3d &axes,
Eigen::Vector3d &moments, bool ignoreHs = false, bool force = false,
const std::vector<double> *weights = NULL);
const std::vector<double> *weights = nullptr);
//! Compute principal axes and moments from the gyration matrix of a conformer
/*!
@@ -90,7 +90,7 @@ RDKIT_MOLTRANSFORMS_EXPORT bool
computePrincipalAxesAndMomentsFromGyrationMatrix(
const RDKit::Conformer &conf, Eigen::Matrix3d &axes,
Eigen::Vector3d &moments, bool ignoreHs = false, bool force = false,
const std::vector<double> *weights = NULL);
const std::vector<double> *weights = nullptr);
#endif
//! Compute the transformation require to orient the conformation
@@ -110,7 +110,7 @@ computePrincipalAxesAndMomentsFromGyrationMatrix(
\param ignoreHs Optionally ignore hydrogens
*/
RDKIT_MOLTRANSFORMS_EXPORT RDGeom::Transform3D *computeCanonicalTransform(
const RDKit::Conformer &conf, const RDGeom::Point3D *center = 0,
const RDKit::Conformer &conf, const RDGeom::Point3D *center = nullptr,
bool normalizeCovar = false, bool ignoreHs = true);
//! Transform the conformation using the specified transformation
@@ -131,7 +131,7 @@ RDKIT_MOLTRANSFORMS_EXPORT void transformConformer(
*/
RDKIT_MOLTRANSFORMS_EXPORT void canonicalizeConformer(
RDKit::Conformer &conf, const RDGeom::Point3D *center = 0,
RDKit::Conformer &conf, const RDGeom::Point3D *center = nullptr,
bool normalizeCovar = false, bool ignoreHs = true);
//! Canonicalize all the conformations in a molecule

4
Code/GraphMol/QueryAtom.h
View File

@@ -28,7 +28,7 @@ class RDKIT_GRAPHMOL_EXPORT QueryAtom : public Atom {
public:
typedef Queries::Query<int, Atom const *, true> QUERYATOM_QUERY;
QueryAtom() : Atom(), dp_query(NULL){};
QueryAtom() : Atom(), dp_query(nullptr){};
explicit QueryAtom(int num) : Atom(num), dp_query(makeAtomNumQuery(num)){};
explicit QueryAtom(const Atom &other)
: Atom(other), dp_query(makeAtomNumQuery(other.getAtomicNum())){};
@@ -48,7 +48,7 @@ class RDKIT_GRAPHMOL_EXPORT QueryAtom : public Atom {
Atom *copy() const;
// This method can be used to distinguish query atoms from standard atoms:
bool hasQuery() const { return dp_query != 0; };
bool hasQuery() const { return dp_query != nullptr; };
//! replaces our current query with the value passed in
void setQuery(QUERYATOM_QUERY *what) {

4
Code/GraphMol/QueryBond.h
View File

@@ -29,7 +29,7 @@ class RDKIT_GRAPHMOL_EXPORT QueryBond : public Bond {
public:
typedef Queries::Query<int, Bond const *, true> QUERYBOND_QUERY;
QueryBond() : Bond(), dp_query(NULL){};
QueryBond() : Bond(), dp_query(nullptr){};
//! initialize with a particular bond order
explicit QueryBond(BondType bT);
//! initialize from a bond
@@ -57,7 +57,7 @@ class RDKIT_GRAPHMOL_EXPORT QueryBond : public Bond {
bool QueryMatch(QueryBond const *what) const;
// This method can be used to distinguish query bonds from standard bonds
bool hasQuery() const { return dp_query != 0; };
bool hasQuery() const { return dp_query != nullptr; };
//! returns our current query
QUERYBOND_QUERY *getQuery() const { return dp_query; };

8
Code/GraphMol/QueryOps.h
View File

@@ -775,7 +775,7 @@ class HasPropQuery : public Queries::EqualityQuery<int, TargetPtr, true> {
: Queries::EqualityQuery<int, TargetPtr, true>(), propname(v) {
// default is to just do a number of rings query:
this->setDescription("AtomHasProp");
this->setDataFunc(0);
this->setDataFunc(nullptr);
};
virtual bool Match(const TargetPtr what) const {
@@ -828,7 +828,7 @@ class HasPropWithValueQuery
tolerance(tol) {
// default is to just do a number of rings query:
this->setDescription("HasPropWithValue");
this->setDataFunc(0);
this->setDataFunc(nullptr);
};
virtual bool Match(const TargetPtr what) const {
@@ -892,7 +892,7 @@ class HasPropWithValueQuery<TargetPtr, std::string>
RDUNUSED_PARAM(tol);
// default is to just do a number of rings query:
this->setDescription("HasPropWithValue");
this->setDataFunc(0);
this->setDataFunc(nullptr);
};
virtual bool Match(const TargetPtr what) const {
@@ -962,7 +962,7 @@ class HasPropWithValueQuery<TargetPtr, ExplicitBitVect>
val(v),
tol(tol) {
this->setDescription("HasPropWithValue");
this->setDataFunc(0);
this->setDataFunc(nullptr);
};
virtual bool Match(const TargetPtr what) const {

2
Code/GraphMol/ROMol.h
View File

@@ -282,7 +282,7 @@ class RDKIT_GRAPHMOL_EXPORT ROMol : public RDProps {
*/
ROMol(const ROMol &other, bool quickCopy = false, int confId = -1)
: RDProps() {
dp_ringInfo = 0;
dp_ringInfo = nullptr;
initFromOther(other, quickCopy, confId);
numBonds = rdcast<unsigned int>(boost::num_edges(d_graph));
};

7
Code/GraphMol/ReducedGraphs/ReducedGraphs.h
View File

@@ -32,7 +32,8 @@ namespace ReducedGraphs {
*/
RDKIT_REDUCEDGRAPHS_EXPORT ROMol *generateMolExtendedReducedGraph(
const ROMol &mol, std::vector<boost::dynamic_bitset<>> *atomTypes = 0);
const ROMol &mol,
std::vector<boost::dynamic_bitset<>> *atomTypes = nullptr);
//! \brief Generates a ErG fingerprint vector for a molecule that's already a
// reduced graph
/*!
@@ -53,7 +54,7 @@ RDKIT_REDUCEDGRAPHS_EXPORT ROMol *generateMolExtendedReducedGraph(
*/
RDKIT_REDUCEDGRAPHS_EXPORT RDNumeric::DoubleVector *
generateErGFingerprintForReducedGraph(
const ROMol &mol, std::vector<boost::dynamic_bitset<>> *atomTypes = 0,
const ROMol &mol, std::vector<boost::dynamic_bitset<>> *atomTypes = nullptr,
double fuzzIncrement = 0.3, unsigned int minPath = 1,
unsigned int maxPath = 15);
@@ -75,7 +76,7 @@ generateErGFingerprintForReducedGraph(
*/
RDKIT_REDUCEDGRAPHS_EXPORT RDNumeric::DoubleVector *getErGFingerprint(
const ROMol &mol, std::vector<boost::dynamic_bitset<>> *atomTypes = 0,
const ROMol &mol, std::vector<boost::dynamic_bitset<>> *atomTypes = nullptr,
double fuzzIncrement = 0.3, unsigned int minPath = 1,
unsigned int maxPath = 15);
} // namespace ReducedGraphs

2
Code/GraphMol/RingInfo.h
View File

@@ -198,7 +198,7 @@ class RDKIT_GRAPHMOL_EXPORT RingInfo {
const VECT_INT_VECT &bondRingFamilies() const { return d_bondRingFamilies; };
//! check if the ring families have been initialized
bool areRingFamiliesInitialized() const { return dp_urfData != NULL; }
bool areRingFamiliesInitialized() const { return dp_urfData != nullptr; }
#endif
//@}

2
Code/GraphMol/SLNParse/SLNAttribs.h
View File

@@ -54,7 +54,7 @@ typedef enum {
class RDKIT_SLNPARSE_EXPORT AttribType {
public:
AttribType()
: first(""), second(""), op(""), negated(false), structQuery(0){};
: first(""), second(""), op(""), negated(false), structQuery(nullptr){};
std::string first;
std::string second;
std::string op;

2
Code/GraphMol/SLNParse/SLNParseOps.h
View File

@@ -275,7 +275,7 @@ int addBranchToMol(std::vector<RWMol *> &molList, unsigned int molIdx,
} else {
delete bond;
}
bond = 0;
bond = nullptr;
delete branch;
unsigned int sz = molList.size();

40
Code/GraphMol/SLNParse/lex.yysln.cpp.cmake
View File

@@ -1951,7 +1951,7 @@ static int yy_get_next_buffer (yyscan_t yyscanner)
}
else
/* Can't grow it, we don't own it. */
b->yy_ch_buf = 0;
b->yy_ch_buf = nullptr;
if ( ! b->yy_ch_buf )
YY_FATAL_ERROR(
@@ -2288,7 +2288,7 @@ static void yysln__load_buffer_state (yyscan_t yyscanner)
return;
if ( b == YY_CURRENT_BUFFER ) /* Not sure if we should pop here. */
YY_CURRENT_BUFFER_LVALUE = (YY_BUFFER_STATE) 0;
YY_CURRENT_BUFFER_LVALUE = (YY_BUFFER_STATE) nullptr;
if ( b->yy_is_our_buffer )
yysln_free((void *) b->yy_ch_buf ,yyscanner );
@@ -2366,7 +2366,7 @@ extern int isatty (int );
void yysln_push_buffer_state (YY_BUFFER_STATE new_buffer , yyscan_t yyscanner)
{
struct yyguts_t * yyg = (struct yyguts_t*)yyscanner;
if (new_buffer == NULL)
if (new_buffer == nullptr)
return;
yysln_ensure_buffer_stack(yyscanner);
@@ -2401,7 +2401,7 @@ void yysln_pop_buffer_state (yyscan_t yyscanner)
return;
yysln__delete_buffer(YY_CURRENT_BUFFER ,yyscanner);
YY_CURRENT_BUFFER_LVALUE = NULL;
YY_CURRENT_BUFFER_LVALUE = nullptr;
if (yyg->yy_buffer_stack_top > 0)
--yyg->yy_buffer_stack_top;
@@ -2472,7 +2472,7 @@ YY_BUFFER_STATE yysln__scan_buffer (char * base, yy_size_t size , yyscan_t yys
base[size-2] != YY_END_OF_BUFFER_CHAR ||
base[size-1] != YY_END_OF_BUFFER_CHAR )
/* They forgot to leave room for the EOB's. */
return 0;
return nullptr;
b = (YY_BUFFER_STATE) yysln_alloc(sizeof( struct yy_buffer_state ) ,yyscanner );
if ( ! b )
@@ -2481,7 +2481,7 @@ YY_BUFFER_STATE yysln__scan_buffer (char * base, yy_size_t size , yyscan_t yys
b->yy_buf_size = size - 2; /* "- 2" to take care of EOB's */
b->yy_buf_pos = b->yy_ch_buf = base;
b->yy_is_our_buffer = 0;
b->yy_input_file = 0;
b->yy_input_file = nullptr;
b->yy_n_chars = b->yy_buf_size;
b->yy_is_interactive = 0;
b->yy_at_bol = 1;
@@ -2779,14 +2779,14 @@ void yysln_set_lval (YYSTYPE * yylval_param , yyscan_t yyscanner)
int yysln_lex_init(yyscan_t* ptr_yy_globals)
{
if (ptr_yy_globals == NULL){
if (ptr_yy_globals == nullptr){
errno = EINVAL;
return 1;
}
*ptr_yy_globals = (yyscan_t) yysln_alloc ( sizeof( struct yyguts_t ), NULL );
*ptr_yy_globals = (yyscan_t) yysln_alloc ( sizeof( struct yyguts_t ), nullptr );
if (*ptr_yy_globals == NULL){
if (*ptr_yy_globals == nullptr){
errno = ENOMEM;
return 1;
}
@@ -2812,14 +2812,14 @@ int yysln_lex_init_extra(YY_EXTRA_TYPE yy_user_defined,yyscan_t* ptr_yy_globals
yysln_set_extra (yy_user_defined, &dummy_yyguts);
if (ptr_yy_globals == NULL){
if (ptr_yy_globals == nullptr){
errno = EINVAL;
return 1;
}
*ptr_yy_globals = (yyscan_t) yysln_alloc ( sizeof( struct yyguts_t ), &dummy_yyguts );
if (*ptr_yy_globals == NULL){
if (*ptr_yy_globals == nullptr){
errno = ENOMEM;
return 1;
}
@@ -2840,24 +2840,24 @@ static int yy_init_globals (yyscan_t yyscanner)
* This function is called from yysln_lex_destroy(), so don't allocate here.
*/
yyg->yy_buffer_stack = 0;
yyg->yy_buffer_stack = nullptr;
yyg->yy_buffer_stack_top = 0;
yyg->yy_buffer_stack_max = 0;
yyg->yy_c_buf_p = (char *) 0;
yyg->yy_c_buf_p = (char *) nullptr;
yyg->yy_init = 0;
yyg->yy_start = 0;
yyg->yy_start_stack_ptr = 0;
yyg->yy_start_stack_depth = 0;
yyg->yy_start_stack = NULL;
yyg->yy_start_stack = nullptr;
/* Defined in main.c */
#ifdef YY_STDINIT
yyin = stdin;
yyout = stdout;
#else
yyin = (FILE *) 0;
yyout = (FILE *) 0;
yyin = (FILE *) nullptr;
yyout = (FILE *) nullptr;
#endif
/* For future reference: Set errno on error, since we are called by
@@ -2874,17 +2874,17 @@ int yysln_lex_destroy (yyscan_t yyscanner)
/* Pop the buffer stack, destroying each element. */
while(YY_CURRENT_BUFFER){
yysln__delete_buffer(YY_CURRENT_BUFFER ,yyscanner );
YY_CURRENT_BUFFER_LVALUE = NULL;
YY_CURRENT_BUFFER_LVALUE = nullptr;
yysln_pop_buffer_state(yyscanner);
}
/* Destroy the stack itself. */
yysln_free(yyg->yy_buffer_stack ,yyscanner);
yyg->yy_buffer_stack = NULL;
yyg->yy_buffer_stack = nullptr;
/* Destroy the start condition stack. */
yysln_free(yyg->yy_start_stack ,yyscanner );
yyg->yy_start_stack = NULL;
yyg->yy_start_stack = nullptr;
/* Reset the globals. This is important in a non-reentrant scanner so the next time
* yysln_lex() is called, initialization will occur. */
@@ -2892,7 +2892,7 @@ int yysln_lex_destroy (yyscan_t yyscanner)
/* Destroy the main struct (reentrant only). */
yysln_free ( yyscanner , yyscanner );
yyscanner = NULL;
yyscanner = nullptr;
return 0;
}

2
Code/GraphMol/SLNParse/sln.tab.cpp.cmake
View File

@@ -1953,7 +1953,7 @@ yyreduce:
#line 404 "sln.yy" /* yacc.c:1651 */
{
if(!doQueries){
yysln_error(input,molList,doQueries,0,"sequential bonds not allowed in non-queries");
yysln_error(input,molList,doQueries,nullptr,"sequential bonds not allowed in non-queries");
YYABORT;
} else {
RDKit::QueryBond *b1=static_cast<RDKit::QueryBond *>((yyvsp[-1].bond_T));

2
Code/GraphMol/ScaffoldNetwork/Wrap/rdScaffoldNetwork.cpp
View File

@@ -73,7 +73,7 @@ BOOST_PYTHON_MODULE(rdScaffoldNetwork) {
boost::python::type_id<std::vector<ScaffoldNetwork::NetworkEdge>>();
const boost::python::converter::registration *reg =
boost::python::converter::registry::query(info);
if (reg == NULL || (*reg).m_to_python == NULL) {
if (reg == nullptr || (*reg).m_to_python == nullptr) {
python::class_<std::vector<ScaffoldNetwork::NetworkEdge>>(
"NetworkEdge_VECT")
.def(python::vector_indexing_suite<

4
Code/GraphMol/ShapeHelpers/ShapeEncoder.h
View File

@@ -42,7 +42,7 @@ namespace MolShapes {
*/
RDKIT_SHAPEHELPERS_EXPORT void EncodeShape(
const ROMol &mol, RDGeom::UniformGrid3D &grid, int confId = -1,
const RDGeom::Transform3D *trans = 0, double vdwScale = 0.8,
const RDGeom::Transform3D *trans = nullptr, double vdwScale = 0.8,
double stepSize = 0.25, int maxLayers = -1, bool ignoreHs = true);
//! Emcode the shape of a conformer on to a grid
@@ -66,7 +66,7 @@ RDKIT_SHAPEHELPERS_EXPORT void EncodeShape(
*/
RDKIT_SHAPEHELPERS_EXPORT void EncodeShape(
const Conformer &conf, RDGeom::UniformGrid3D &grid,
const RDGeom::Transform3D *trans = 0, double vdwScale = 0.8,
const RDGeom::Transform3D *trans = nullptr, double vdwScale = 0.8,
double stepSize = 0.25, int maxLayers = -1, bool ignoreHs = true);
} // namespace MolShapes
} // namespace RDKit

6
Code/GraphMol/ShapeHelpers/ShapeUtils.h
View File

@@ -29,7 +29,7 @@ namespace MolShapes {
//! from the origin
RDKIT_SHAPEHELPERS_EXPORT void computeConfDimsAndOffset(
const Conformer &conf, RDGeom::Point3D &dims, RDGeom::Point3D &offSet,
const RDGeom::Transform3D *trans = 0, double padding = 2.5);
const RDGeom::Transform3D *trans = nullptr, double padding = 2.5);
//! Compute the box that will fit the conformer
/*!
@@ -42,7 +42,7 @@ RDKIT_SHAPEHELPERS_EXPORT void computeConfDimsAndOffset(
*/
RDKIT_SHAPEHELPERS_EXPORT void computeConfBox(
const Conformer &conf, RDGeom::Point3D &leftBottom,
RDGeom::Point3D &rightTop, const RDGeom::Transform3D *trans = 0,
RDGeom::Point3D &rightTop, const RDGeom::Transform3D *trans = nullptr,
double padding = 2.5);
//! Compute the union of two boxes
@@ -60,7 +60,7 @@ RDKIT_SHAPEHELPERS_EXPORT void computeUnionBox(
*/
RDKIT_SHAPEHELPERS_EXPORT std::vector<double> getConfDimensions(
const Conformer &conf, double padding = 2.5,
const RDGeom::Point3D *center = 0, bool ignoreHs = true);
const RDGeom::Point3D *center = nullptr, bool ignoreHs = true);
//! Compute the shape tversky index between two molecule based on a
// predefined alignment

4
Code/GraphMol/SmilesParse/SmilesParse.h
View File

@@ -65,7 +65,7 @@ RDKIT_SMILESPARSE_EXPORT Bond *SmilesToBond(const std::string &smi);
*/
inline RWMol *SmilesToMol(
const std::string &smi, int debugParse = 0, bool sanitize = true,
std::map<std::string, std::string> *replacements = 0) {
std::map<std::string, std::string> *replacements = nullptr) {
SmilesParserParams params;
params.debugParse = debugParse;
params.replacements = replacements;
@@ -93,7 +93,7 @@ inline RWMol *SmilesToMol(
*/
RDKIT_SMILESPARSE_EXPORT RWMol *SmartsToMol(
const std::string &sma, int debugParse = 0, bool mergeHs = false,
std::map<std::string, std::string> *replacements = 0);
std::map<std::string, std::string> *replacements = nullptr);
RDKIT_SMILESPARSE_EXPORT Atom *SmartsToAtom(const std::string &sma);
RDKIT_SMILESPARSE_EXPORT Bond *SmartsToBond(const std::string &sma);

14
Code/GraphMol/SmilesParse/SmilesWrite.h
View File

@@ -39,7 +39,7 @@ RDKIT_SMILESPARSE_EXPORT bool inOrganicSubset(int atomicNumber);
*/
RDKIT_SMILESPARSE_EXPORT std::string GetAtomSmiles(const Atom *atom,
bool doKekule = false,
const Bond *bondIn = 0,
const Bond *bondIn = nullptr,
bool allHsExplicit = false,
bool isomericSmiles = true);
@@ -121,9 +121,9 @@ RDKIT_SMILESPARSE_EXPORT std::vector<std::string> MolToRandomSmilesVect(
*/
RDKIT_SMILESPARSE_EXPORT std::string MolFragmentToSmiles(
const ROMol &mol, const std::vector<int> &atomsToUse,
const std::vector<int> *bondsToUse = 0,
const std::vector<std::string> *atomSymbols = 0,
const std::vector<std::string> *bondSymbols = 0,
const std::vector<int> *bondsToUse = nullptr,
const std::vector<std::string> *atomSymbols = nullptr,
const std::vector<std::string> *bondSymbols = nullptr,
bool doIsomericSmiles = true, bool doKekule = false, int rootedAtAtom = -1,
bool canonical = true, bool allBondsExplicit = false,
bool allHsExplicit = false);
@@ -174,9 +174,9 @@ RDKIT_SMILESPARSE_EXPORT std::string MolToCXSmiles(
*/
RDKIT_SMILESPARSE_EXPORT std::string MolFragmentToCXSmiles(
const ROMol &mol, const std::vector<int> &atomsToUse,
const std::vector<int> *bondsToUse = 0,
const std::vector<std::string> *atomSymbols = 0,
const std::vector<std::string> *bondSymbols = 0,
const std::vector<int> *bondsToUse = nullptr,
const std::vector<std::string> *atomSymbols = nullptr,
const std::vector<std::string> *bondSymbols = nullptr,
bool doIsomericSmiles = true, bool doKekule = false, int rootedAtAtom = -1,
bool canonical = true, bool allBondsExplicit = false,
bool allHsExplicit = false);

40
Code/GraphMol/SmilesParse/lex.yysmarts.cpp.cmake
View File

@@ -2132,7 +2132,7 @@ static int yy_get_next_buffer (yyscan_t yyscanner)
}
else
/* Can't grow it, we don't own it. */
b->yy_ch_buf = NULL;
b->yy_ch_buf = nullptr;
if ( ! b->yy_ch_buf )
YY_FATAL_ERROR(
@@ -2477,7 +2477,7 @@ static void yy_load_buffer_state (yyscan_t yyscanner)
return;
if ( b == YY_CURRENT_BUFFER ) /* Not sure if we should pop here. */
YY_CURRENT_BUFFER_LVALUE = (YY_BUFFER_STATE) 0;
YY_CURRENT_BUFFER_LVALUE = (YY_BUFFER_STATE) nullptr;
if ( b->yy_is_our_buffer )
yyfree( (void *) b->yy_ch_buf , yyscanner );
@@ -2551,7 +2551,7 @@ static void yy_load_buffer_state (yyscan_t yyscanner)
void yypush_buffer_state (YY_BUFFER_STATE new_buffer , yyscan_t yyscanner)
{
struct yyguts_t * yyg = (struct yyguts_t*)yyscanner;
if (new_buffer == NULL)
if (new_buffer == nullptr)
return;
yyensure_buffer_stack(yyscanner);
@@ -2586,7 +2586,7 @@ void yypop_buffer_state (yyscan_t yyscanner)
return;
yy_delete_buffer(YY_CURRENT_BUFFER , yyscanner);
YY_CURRENT_BUFFER_LVALUE = NULL;
YY_CURRENT_BUFFER_LVALUE = nullptr;
if (yyg->yy_buffer_stack_top > 0)
--yyg->yy_buffer_stack_top;
@@ -2657,7 +2657,7 @@ YY_BUFFER_STATE yy_scan_buffer (char * base, yy_size_t size , yyscan_t yyscann
base[size-2] != YY_END_OF_BUFFER_CHAR ||
base[size-1] != YY_END_OF_BUFFER_CHAR )
/* They forgot to leave room for the EOB's. */
return NULL;
return nullptr;
b = (YY_BUFFER_STATE) yyalloc( sizeof( struct yy_buffer_state ) , yyscanner );
if ( ! b )
@@ -2666,7 +2666,7 @@ YY_BUFFER_STATE yy_scan_buffer (char * base, yy_size_t size , yyscan_t yyscann
b->yy_buf_size = (int) (size - 2); /* "- 2" to take care of EOB's */
b->yy_buf_pos = b->yy_ch_buf = base;
b->yy_is_our_buffer = 0;
b->yy_input_file = NULL;
b->yy_input_file = nullptr;
b->yy_n_chars = b->yy_buf_size;
b->yy_is_interactive = 0;
b->yy_at_bol = 1;
@@ -2965,14 +2965,14 @@ void yyset_lval (YYSTYPE * yylval_param , yyscan_t yyscanner)
*/
int yylex_init(yyscan_t* ptr_yy_globals)
{
if (ptr_yy_globals == NULL){
if (ptr_yy_globals == nullptr){
errno = EINVAL;
return 1;
}
*ptr_yy_globals = (yyscan_t) yyalloc ( sizeof( struct yyguts_t ), NULL );
*ptr_yy_globals = (yyscan_t) yyalloc ( sizeof( struct yyguts_t ), nullptr );
if (*ptr_yy_globals == NULL){
if (*ptr_yy_globals == nullptr){
errno = ENOMEM;
return 1;
}
@@ -2996,14 +2996,14 @@ int yylex_init_extra( YY_EXTRA_TYPE yy_user_defined, yyscan_t* ptr_yy_globals )
yyset_extra (yy_user_defined, &dummy_yyguts);
if (ptr_yy_globals == NULL){
if (ptr_yy_globals == nullptr){
errno = EINVAL;
return 1;
}
*ptr_yy_globals = (yyscan_t) yyalloc ( sizeof( struct yyguts_t ), &dummy_yyguts );
if (*ptr_yy_globals == NULL){
if (*ptr_yy_globals == nullptr){
errno = ENOMEM;
return 1;
}
@@ -3024,24 +3024,24 @@ static int yy_init_globals (yyscan_t yyscanner)
* This function is called from yylex_destroy(), so don't allocate here.
*/
yyg->yy_buffer_stack = NULL;
yyg->yy_buffer_stack = nullptr;
yyg->yy_buffer_stack_top = 0;
yyg->yy_buffer_stack_max = 0;
yyg->yy_c_buf_p = NULL;
yyg->yy_c_buf_p = nullptr;
yyg->yy_init = 0;
yyg->yy_start = 0;
yyg->yy_start_stack_ptr = 0;
yyg->yy_start_stack_depth = 0;
yyg->yy_start_stack = NULL;
yyg->yy_start_stack = nullptr;
/* Defined in main.c */
#ifdef YY_STDINIT
yyin = stdin;
yyout = stdout;
#else
yyin = NULL;
yyout = NULL;
yyin = nullptr;
yyout = nullptr;
#endif
/* For future reference: Set errno on error, since we are called by
@@ -3058,17 +3058,17 @@ int yylex_destroy (yyscan_t yyscanner)
/* Pop the buffer stack, destroying each element. */
while(YY_CURRENT_BUFFER){
yy_delete_buffer( YY_CURRENT_BUFFER , yyscanner );
YY_CURRENT_BUFFER_LVALUE = NULL;
YY_CURRENT_BUFFER_LVALUE = nullptr;
yypop_buffer_state(yyscanner);
}
/* Destroy the stack itself. */
yyfree(yyg->yy_buffer_stack , yyscanner);
yyg->yy_buffer_stack = NULL;
yyg->yy_buffer_stack = nullptr;
/* Destroy the start condition stack. */
yyfree( yyg->yy_start_stack , yyscanner );
yyg->yy_start_stack = NULL;
yyg->yy_start_stack = nullptr;
/* Reset the globals. This is important in a non-reentrant scanner so the next time
* yylex() is called, initialization will occur. */
@@ -3076,7 +3076,7 @@ int yylex_destroy (yyscan_t yyscanner)
/* Destroy the main struct (reentrant only). */
yyfree ( yyscanner , yyscanner );
yyscanner = NULL;
yyscanner = nullptr;
return 0;
}

40
Code/GraphMol/SmilesParse/lex.yysmiles.cpp.cmake
View File

@@ -2409,7 +2409,7 @@ static int yy_get_next_buffer (yyscan_t yyscanner)
}
else
/* Can't grow it, we don't own it. */
b->yy_ch_buf = NULL;
b->yy_ch_buf = nullptr;
if ( ! b->yy_ch_buf )
YY_FATAL_ERROR(
@@ -2754,7 +2754,7 @@ static void yy_load_buffer_state (yyscan_t yyscanner)
return;
if ( b == YY_CURRENT_BUFFER ) /* Not sure if we should pop here. */
YY_CURRENT_BUFFER_LVALUE = (YY_BUFFER_STATE) 0;
YY_CURRENT_BUFFER_LVALUE = (YY_BUFFER_STATE) nullptr;
if ( b->yy_is_our_buffer )
yyfree( (void *) b->yy_ch_buf , yyscanner );
@@ -2828,7 +2828,7 @@ static void yy_load_buffer_state (yyscan_t yyscanner)
void yypush_buffer_state (YY_BUFFER_STATE new_buffer , yyscan_t yyscanner)
{
struct yyguts_t * yyg = (struct yyguts_t*)yyscanner;
if (new_buffer == NULL)
if (new_buffer == nullptr)
return;
yyensure_buffer_stack(yyscanner);
@@ -2863,7 +2863,7 @@ void yypop_buffer_state (yyscan_t yyscanner)
return;
yy_delete_buffer(YY_CURRENT_BUFFER , yyscanner);
YY_CURRENT_BUFFER_LVALUE = NULL;
YY_CURRENT_BUFFER_LVALUE = nullptr;
if (yyg->yy_buffer_stack_top > 0)
--yyg->yy_buffer_stack_top;
@@ -2934,7 +2934,7 @@ YY_BUFFER_STATE yy_scan_buffer (char * base, yy_size_t size , yyscan_t yyscann
base[size-2] != YY_END_OF_BUFFER_CHAR ||
base[size-1] != YY_END_OF_BUFFER_CHAR )
/* They forgot to leave room for the EOB's. */
return NULL;
return nullptr;
b = (YY_BUFFER_STATE) yyalloc( sizeof( struct yy_buffer_state ) , yyscanner );
if ( ! b )
@@ -2943,7 +2943,7 @@ YY_BUFFER_STATE yy_scan_buffer (char * base, yy_size_t size , yyscan_t yyscann
b->yy_buf_size = (int) (size - 2); /* "- 2" to take care of EOB's */
b->yy_buf_pos = b->yy_ch_buf = base;
b->yy_is_our_buffer = 0;
b->yy_input_file = NULL;
b->yy_input_file = nullptr;
b->yy_n_chars = b->yy_buf_size;
b->yy_is_interactive = 0;
b->yy_at_bol = 1;
@@ -3201,14 +3201,14 @@ void yyset_lval (YYSTYPE * yylval_param , yyscan_t yyscanner)
*/
int yylex_init(yyscan_t* ptr_yy_globals)
{
if (ptr_yy_globals == NULL){
if (ptr_yy_globals == nullptr){
errno = EINVAL;
return 1;
}
*ptr_yy_globals = (yyscan_t) yyalloc ( sizeof( struct yyguts_t ), NULL );
*ptr_yy_globals = (yyscan_t) yyalloc ( sizeof( struct yyguts_t ), nullptr );
if (*ptr_yy_globals == NULL){
if (*ptr_yy_globals == nullptr){
errno = ENOMEM;
return 1;
}
@@ -3232,14 +3232,14 @@ int yylex_init_extra( YY_EXTRA_TYPE yy_user_defined, yyscan_t* ptr_yy_globals )
yyset_extra (yy_user_defined, &dummy_yyguts);
if (ptr_yy_globals == NULL){
if (ptr_yy_globals == nullptr){
errno = EINVAL;
return 1;
}
*ptr_yy_globals = (yyscan_t) yyalloc ( sizeof( struct yyguts_t ), &dummy_yyguts );
if (*ptr_yy_globals == NULL){
if (*ptr_yy_globals == nullptr){
errno = ENOMEM;
return 1;
}
@@ -3260,24 +3260,24 @@ static int yy_init_globals (yyscan_t yyscanner)
* This function is called from yylex_destroy(), so don't allocate here.
*/
yyg->yy_buffer_stack = NULL;
yyg->yy_buffer_stack = nullptr;
yyg->yy_buffer_stack_top = 0;
yyg->yy_buffer_stack_max = 0;
yyg->yy_c_buf_p = NULL;
yyg->yy_c_buf_p = nullptr;
yyg->yy_init = 0;
yyg->yy_start = 0;
yyg->yy_start_stack_ptr = 0;
yyg->yy_start_stack_depth = 0;
yyg->yy_start_stack = NULL;
yyg->yy_start_stack = nullptr;
/* Defined in main.c */
#ifdef YY_STDINIT
yyin = stdin;
yyout = stdout;
#else
yyin = NULL;
yyout = NULL;
yyin = nullptr;
yyout = nullptr;
#endif
/* For future reference: Set errno on error, since we are called by
@@ -3294,17 +3294,17 @@ int yylex_destroy (yyscan_t yyscanner)
/* Pop the buffer stack, destroying each element. */
while(YY_CURRENT_BUFFER){
yy_delete_buffer( YY_CURRENT_BUFFER , yyscanner );
YY_CURRENT_BUFFER_LVALUE = NULL;
YY_CURRENT_BUFFER_LVALUE = nullptr;
yypop_buffer_state(yyscanner);
}
/* Destroy the stack itself. */
yyfree(yyg->yy_buffer_stack , yyscanner);
yyg->yy_buffer_stack = NULL;
yyg->yy_buffer_stack = nullptr;
/* Destroy the start condition stack. */
yyfree( yyg->yy_start_stack , yyscanner );
yyg->yy_start_stack = NULL;
yyg->yy_start_stack = nullptr;
/* Reset the globals. This is important in a non-reentrant scanner so the next time
* yylex() is called, initialization will occur. */
@@ -3312,7 +3312,7 @@ int yylex_destroy (yyscan_t yyscanner)
/* Destroy the main struct (reentrant only). */
yyfree ( yyscanner , yyscanner );
yyscanner = NULL;
yyscanner = nullptr;
return 0;
}

2
Code/GraphMol/Subgraphs/SubgraphUtils.h
View File

@@ -25,7 +25,7 @@ typedef boost::tuples::tuple<std::uint32_t, std::uint32_t, std::uint32_t>
RDKIT_SUBGRAPHS_EXPORT DiscrimTuple calcPathDiscriminators(
const ROMol &mol, const PATH_TYPE &path, bool useBO = true,
std::vector<std::uint32_t> *extraInvars = 0);
std::vector<std::uint32_t> *extraInvars = nullptr);
RDKIT_SUBGRAPHS_EXPORT PATH_LIST uniquifyPaths(const ROMol &mol,
const PATH_LIST &allPathsb,
bool useBO = true);

6
Code/GraphMol/Substruct/vf2.hpp
View File

@@ -163,7 +163,7 @@ class VF2SubState {
if (sortNodes) {
order = SortNodesByFrequency(ag1);
} else {
order = NULL;
order = nullptr;
}
core_len = 0;
@@ -184,7 +184,7 @@ class VF2SubState {
core_2[i] = NULL_NODE;
term_2[i] = 0;
}
vs_compared = 0;
vs_compared = nullptr;
// vs_compared = new int[n1*n2];
// memset((void *)vs_compared,0,n1*n2*sizeof(int));
@@ -287,7 +287,7 @@ class VF2SubState {
boost::adjacent_vertices(core_1[*n1iter_beg], *g2);
pair.hasiter = true;
}
} else if (pair.n1 == 0 && order != NULL) {
} else if (pair.n1 == 0 && order != nullptr) {
// Optimisation: if the order vector is laid out in a DFS/BFS then this
// loop can be replaced with:
// pair.n1=order[core_len];

2
Code/GraphMol/SubstructLibrary/SubstructLibrary.h
View File

@@ -378,7 +378,7 @@ class RDKIT_SUBSTRUCTLIBRARY_EXPORT SubstructLibrary {
fps(nullptr) {}
SubstructLibrary(boost::shared_ptr<MolHolderBase> molecules)
: molholder(molecules), fpholder(), mols(molholder.get()), fps(0) {}
: molholder(molecules), fpholder(), mols(molholder.get()), fps(nullptr) {}
SubstructLibrary(boost::shared_ptr<MolHolderBase> molecules,
boost::shared_ptr<FPHolderBase> fingerprints)

10
Code/GraphMol/SubstructLibrary/SubstructLibrarySerialization.h
View File

@@ -150,11 +150,11 @@ void serialize(Archive &ar, RDKit::PatternHolder &pattern_holder,
template <class Archive>
void registerSubstructLibraryTypes(Archive &ar) {
ar.register_type(static_cast<RDKit::MolHolder *>(NULL));
ar.register_type(static_cast<RDKit::CachedMolHolder *>(NULL));
ar.register_type(static_cast<RDKit::CachedSmilesMolHolder *>(NULL));
ar.register_type(static_cast<RDKit::CachedTrustedSmilesMolHolder *>(NULL));
ar.register_type(static_cast<RDKit::PatternHolder *>(NULL));
ar.register_type(static_cast<RDKit::MolHolder *>(nullptr));
ar.register_type(static_cast<RDKit::CachedMolHolder *>(nullptr));
ar.register_type(static_cast<RDKit::CachedSmilesMolHolder *>(nullptr));
ar.register_type(static_cast<RDKit::CachedTrustedSmilesMolHolder *>(nullptr));
ar.register_type(static_cast<RDKit::PatternHolder *>(nullptr));
}
template <class Archive>

2
Code/GraphMol/Trajectory/Snapshot.h
View File

@@ -33,7 +33,7 @@ class RDKIT_TRAJECTORY_EXPORT Snapshot {
\param energy is the energy associated with this set of coordinates
*/
Snapshot(boost::shared_array<double> pos, double energy = 0.0)
: d_trajectory(NULL), d_energy(energy), d_pos(pos) {}
: d_trajectory(nullptr), d_energy(energy), d_pos(pos) {}
/*! \return a const pointer to the parent Trajectory
*/
const Trajectory *trajectory() const { return d_trajectory; }

2
Code/GraphMol/Trajectory/Trajectory.h
View File

@@ -29,7 +29,7 @@ class RDKIT_TRAJECTORY_EXPORT Trajectory {
the Trajectory takes ownership of the SnapshotVect
*/
Trajectory(unsigned int dimension, unsigned int numPoints,
SnapshotVect *snapshotVect = NULL);
SnapshotVect *snapshotVect = nullptr);
/*! \brief Copy constructor
*/
Trajectory(const Trajectory &other);

16
Code/GraphMol/Wrap/MolSupplier.h
View File

@@ -27,14 +27,14 @@ T *MolSupplIter(T *suppl) {
template <typename T>
ROMol *MolForwardSupplNext(T *suppl) {
ROMol *res = 0;
ROMol *res = nullptr;
if (!suppl->atEnd()) {
try {
res = suppl->next();
} catch (const FileParseException&) {
throw;
} catch (...) {
res = 0;
res = nullptr;
}
} else {
PyErr_SetString(PyExc_StopIteration, "End of supplier hit");
@@ -49,14 +49,14 @@ ROMol *MolForwardSupplNext(T *suppl) {
template <typename T>
ROMol *MolSupplNext(T *suppl) {
ROMol *res = 0;
ROMol *res = nullptr;
if (!suppl->atEnd()) {
try {
res = suppl->next();
} catch (const FileParseException&) {
throw;
} catch (...) {
res = 0;
res = nullptr;
}
} else {
PyErr_SetString(PyExc_StopIteration, "End of supplier hit");
@@ -68,14 +68,14 @@ ROMol *MolSupplNext(T *suppl) {
template <typename T>
ROMol *MolSupplNextAcceptNullLastMolecule(T *suppl) {
ROMol *res = 0;
ROMol *res = nullptr;
if (!suppl->atEnd()) {
try {
res = suppl->next();
} catch (const FileParseException&) {
throw;
} catch (...) {
res = 0;
res = nullptr;
}
} else {
PyErr_SetString(PyExc_StopIteration, "End of supplier hit");
@@ -86,7 +86,7 @@ ROMol *MolSupplNextAcceptNullLastMolecule(T *suppl) {
template <typename T>
ROMol *MolSupplGetItem(T *suppl, int idx) {
ROMol *res = 0;
ROMol *res = nullptr;
if (idx < 0) {
idx = suppl->length() + idx;
}
@@ -102,7 +102,7 @@ ROMol *MolSupplGetItem(T *suppl, int idx) {
PyErr_SetString(PyExc_IndexError, "invalid index");
throw boost::python::error_already_set();
} else {
res = 0;
res = nullptr;
}
}
return res;

49
Code/GraphMol/new_canon.h
View File

@@ -89,14 +89,14 @@ class RDKIT_GRAPHMOL_EXPORT canon_atom {
std::vector<bondholder> bonds;
canon_atom()
: atom(NULL),
: atom(nullptr),
index(-1),
degree(0),
totalNumHs(0),
hasRingNbr(false),
isRingStereoAtom(false),
nbrIds(NULL),
p_symbol(NULL){};
nbrIds(nullptr),
p_symbol(nullptr){};
~canon_atom() { free(nbrIds); }
};
@@ -126,14 +126,14 @@ class RDKIT_GRAPHMOL_EXPORT SpecialChiralityAtomCompareFunctor {
const boost::dynamic_bitset<> *dp_atomsInPlay, *dp_bondsInPlay;
SpecialChiralityAtomCompareFunctor()
: dp_atoms(NULL),
dp_mol(NULL),
dp_atomsInPlay(NULL),
dp_bondsInPlay(NULL){};
: dp_atoms(nullptr),
dp_mol(nullptr),
dp_atomsInPlay(nullptr),
dp_bondsInPlay(nullptr){};
SpecialChiralityAtomCompareFunctor(
Canon::canon_atom *atoms, const ROMol &m,
const boost::dynamic_bitset<> *atomsInPlay = NULL,
const boost::dynamic_bitset<> *bondsInPlay = NULL)
const boost::dynamic_bitset<> *atomsInPlay = nullptr,
const boost::dynamic_bitset<> *bondsInPlay = nullptr)
: dp_atoms(atoms),
dp_mol(&m),
dp_atomsInPlay(atomsInPlay),
@@ -182,14 +182,14 @@ class RDKIT_GRAPHMOL_EXPORT SpecialSymmetryAtomCompareFunctor {
const boost::dynamic_bitset<> *dp_atomsInPlay, *dp_bondsInPlay;
SpecialSymmetryAtomCompareFunctor()
: dp_atoms(NULL),
dp_mol(NULL),
dp_atomsInPlay(NULL),
dp_bondsInPlay(NULL){};
: dp_atoms(nullptr),
dp_mol(nullptr),
dp_atomsInPlay(nullptr),
dp_bondsInPlay(nullptr){};
SpecialSymmetryAtomCompareFunctor(
Canon::canon_atom *atoms, const ROMol &m,
const boost::dynamic_bitset<> *atomsInPlay = NULL,
const boost::dynamic_bitset<> *bondsInPlay = NULL)
const boost::dynamic_bitset<> *atomsInPlay = nullptr,
const boost::dynamic_bitset<> *bondsInPlay = nullptr)
: dp_atoms(atoms),
dp_mol(&m),
dp_atomsInPlay(atomsInPlay),
@@ -380,17 +380,17 @@ class RDKIT_GRAPHMOL_EXPORT AtomCompareFunctor {
bool df_useChiralityRings;
AtomCompareFunctor()
: dp_atoms(NULL),
dp_mol(NULL),
dp_atomsInPlay(NULL),
dp_bondsInPlay(NULL),
: dp_atoms(nullptr),
dp_mol(nullptr),
dp_atomsInPlay(nullptr),
dp_bondsInPlay(nullptr),
df_useNbrs(false),
df_useIsotopes(true),
df_useChirality(true),
df_useChiralityRings(true){};
AtomCompareFunctor(Canon::canon_atom *atoms, const ROMol &m,
const boost::dynamic_bitset<> *atomsInPlay = NULL,
const boost::dynamic_bitset<> *bondsInPlay = NULL)
const boost::dynamic_bitset<> *atomsInPlay = nullptr,
const boost::dynamic_bitset<> *bondsInPlay = nullptr)
: dp_atoms(atoms),
dp_mol(&m),
dp_atomsInPlay(atomsInPlay),
@@ -514,7 +514,7 @@ class RDKIT_GRAPHMOL_EXPORT ChiralAtomCompareFunctor {
const ROMol *dp_mol;
bool df_useNbrs;
ChiralAtomCompareFunctor()
: dp_atoms(NULL), dp_mol(NULL), df_useNbrs(false){};
: dp_atoms(nullptr), dp_mol(nullptr), df_useNbrs(false){};
ChiralAtomCompareFunctor(Canon::canon_atom *atoms, const ROMol &m)
: dp_atoms(atoms), dp_mol(&m), df_useNbrs(false){};
int operator()(int i, int j) const {
@@ -725,8 +725,9 @@ RDKIT_GRAPHMOL_EXPORT void rankFragmentAtoms(
const ROMol &mol, std::vector<unsigned int> &res,
const boost::dynamic_bitset<> &atomsInPlay,
const boost::dynamic_bitset<> &bondsInPlay,
const std::vector<std::string> *atomSymbols = NULL, bool breakTies = true,
bool includeChirality = true, bool includeIsotopes = true);
const std::vector<std::string> *atomSymbols = nullptr,
bool breakTies = true, bool includeChirality = true,
bool includeIsotopes = true);
RDKIT_GRAPHMOL_EXPORT void chiralRankMolAtoms(const ROMol &mol,
std::vector<unsigned int> &res);

2
Code/ML/InfoTheory/CorrMatGenerator.h
View File

@@ -44,7 +44,7 @@ class BitCorrMatGenerator {
~BitCorrMatGenerator() { delete[] dp_corrMat; }
void initGenerator() {
dp_corrMat = 0;
dp_corrMat = nullptr;
d_descs.resize(0);
d_nExamples = 0;
};

4
Code/ML/InfoTheory/InfoBitRanker.h
View File

@@ -120,9 +120,9 @@ class RDKIT_INFOTHEORY_EXPORT InfoBitRanker {
d_clsCount.resize(d_classes, 0);
d_nInst = 0;
d_top = 0;
dp_topBits = 0;
dp_topBits = nullptr;
d_biasList.resize(0);
dp_maskBits = 0;
dp_maskBits = nullptr;
}
~InfoBitRanker() {

2
Code/Numerics/Alignment/AlignPoints.h
View File

@@ -41,7 +41,7 @@ namespace Alignments {
double RDKIT_ALIGNMENT_EXPORT
AlignPoints(const RDGeom::Point3DConstPtrVect &refPoints,
const RDGeom::Point3DConstPtrVect &probePoints,
RDGeom::Transform3D &trans, const DoubleVector *weights = 0,
RDGeom::Transform3D &trans, const DoubleVector *weights = nullptr,
bool reflect = false, unsigned int maxIterations = 50);
} // namespace Alignments
} // namespace RDNumeric

8
Code/Numerics/EigenSolvers/PowerEigenSolver.h
View File

@@ -53,11 +53,9 @@ We use the iterative power method, which works like this:
*/
bool RDKIT_EIGENSOLVERS_EXPORT powerEigenSolver(unsigned int numEig,
DoubleSymmMatrix &mat,
DoubleVector &eigenValues,
DoubleMatrix *eigenVectors = 0,
int seed = -1);
bool RDKIT_EIGENSOLVERS_EXPORT powerEigenSolver(
unsigned int numEig, DoubleSymmMatrix &mat, DoubleVector &eigenValues,
DoubleMatrix *eigenVectors = nullptr, int seed = -1);
//! \overload
static inline bool powerEigenSolver(unsigned int numEig, DoubleSymmMatrix &mat,
DoubleVector &eigenValues,

8
Code/Numerics/Optimizer/BFGSOpt.h
View File

@@ -251,7 +251,7 @@ int minimize(unsigned int dim, double *pos, double gradTol,
if (snapshotVect && snapshotFreq) {
RDKit::Snapshot s(boost::shared_array<double>(newPos), fp);
snapshotVect->push_back(s);
newPos = NULL;
newPos = nullptr;
}
CLEANUP();
return 0;
@@ -275,7 +275,7 @@ int minimize(unsigned int dim, double *pos, double gradTol,
if (snapshotVect && snapshotFreq) {
RDKit::Snapshot s(boost::shared_array<double>(newPos), fp);
snapshotVect->push_back(s);
newPos = NULL;
newPos = nullptr;
}
CLEANUP();
return 0;
@@ -382,8 +382,8 @@ int minimize(unsigned int dim, double *pos, double gradTol,
unsigned int &numIters, double &funcVal, EnergyFunctor func,
GradientFunctor gradFunc, double funcTol = TOLX,
unsigned int maxIts = MAXITS) {
return minimize(dim, pos, gradTol, numIters, funcVal, func, gradFunc, 0, NULL,
funcTol, maxIts);
return minimize(dim, pos, gradTol, numIters, funcVal, func, gradFunc, 0,
nullptr, funcTol, maxIts);
}
} // namespace BFGSOpt

6
Code/Query/Query.h
View File

@@ -55,8 +55,8 @@ class Query {
Query()
: d_description(""),
df_negate(false),
d_matchFunc(NULL),
d_dataFunc(NULL){};
d_matchFunc(nullptr),
d_dataFunc(nullptr){};
virtual ~Query() { this->d_children.clear(); };
//! sets whether or not we are negated
@@ -163,7 +163,7 @@ class Query {
MatchFuncArgType TypeConvert(MatchFuncArgType what,
Int2Type<false> /*d*/) const {
MatchFuncArgType mfArg;
if (this->d_dataFuncSameType != NULL &&
if (this->d_dataFuncSameType != nullptr &&
std::is_same<MatchFuncArgType, DataFuncArgType>::value) {
mfArg = this->d_dataFuncSameType(what);
} else {

2
Code/RDBoost/Wrap.h
View File

@@ -165,7 +165,7 @@ class RDKIT_RDBOOST_EXPORT RDUNUSED NOGIL {
inline ~NOGIL() {
PyEval_RestoreThread(m_thread_state);
m_thread_state = NULL;
m_thread_state = nullptr;
}
private:

2
Code/RDBoost/import_array.h
View File

@@ -18,7 +18,7 @@ void rdkit_import_array()
// returns void)
import_array();
#if PY_MAJOR_VERSION >= 3
return NULL;
return nullptr;
#endif
}

8
Code/RDBoost/python_streambuf.h
View File

@@ -142,10 +142,10 @@ class streambuf : public std::basic_streambuf<char> {
py_seek(getattr(python_file_obj, "seek", bp::object())),
py_tell(getattr(python_file_obj, "tell", bp::object())),
buffer_size(buffer_size_ != 0 ? buffer_size_ : default_buffer_size),
write_buffer(0),
write_buffer(nullptr),
pos_of_read_buffer_end_in_py_file(0),
pos_of_write_buffer_end_in_py_file(buffer_size),
farthest_pptr(0) {
farthest_pptr(nullptr) {
TEST_ASSERT(buffer_size != 0);
/* Some Python file objects (e.g. sys.stdout and sys.stdin)
have non-functional seek and tell. If so, assign None to
@@ -179,7 +179,7 @@ class streambuf : public std::basic_streambuf<char> {
farthest_pptr = pptr();
} else {
// The first attempt at output will result in a call to overflow
setp(0, 0);
setp(nullptr, nullptr);
}
if (py_tell != bp::object()) {
@@ -259,7 +259,7 @@ class streambuf : public std::basic_streambuf<char> {
bp::ssize_t py_n_read;
if (PyBytes_AsStringAndSize(read_buffer.ptr(), &read_buffer_data,
&py_n_read) == -1) {
setg(0, 0, 0);
setg(nullptr, nullptr, nullptr);
throw std::invalid_argument(
"The method 'read' of the Python file object "
"did not return a string.");

2
Code/RDGeneral/Dict.h
View File

@@ -71,7 +71,7 @@ class RDKIT_RDGENERAL_EXPORT Dict {
if (other._hasNonPodData) _hasNonPodData = true;
for (size_t i = 0; i < other._data.size(); ++i) {
const Pair &pair = other._data[i];
Pair *target = 0;
Pair *target = nullptr;
for (size_t i = 0; i < _data.size(); ++i) {
if (_data[i].key == pair.key) {
target = &_data[i];

14
Code/RDGeneral/RDLog.h
View File

@@ -36,8 +36,8 @@ class RDKIT_RDGENERAL_EXPORT rdLogger {
: dp_dest(dest),
df_owner(owner),
df_enabled(true),
tee(NULL),
teestream(NULL){};
tee(nullptr),
teestream(nullptr){};
//! Sets a stream to tee the output to.
void SetTee(std::ostream &stream) {
@@ -53,8 +53,8 @@ class RDKIT_RDGENERAL_EXPORT rdLogger {
if (dp_dest) {
delete teestream;
delete tee;
tee = NULL;
teestream = NULL;
tee = nullptr;
teestream = nullptr;
}
}
~rdLogger() {
@@ -63,12 +63,12 @@ class RDKIT_RDGENERAL_EXPORT rdLogger {
if (df_owner) {
delete dp_dest;
}
dp_dest = NULL;
dp_dest = nullptr;
}
delete teestream;
teestream = NULL;
teestream = nullptr;
delete tee;
tee = NULL;
tee = nullptr;
}
private:

2
Code/RDGeneral/types.h
View File

@@ -367,7 +367,7 @@ RDKIT_RDGENERAL_EXPORT void Intersect(const INT_VECT &r1, const INT_VECT &r2,
from the union.
*/
RDKIT_RDGENERAL_EXPORT void Union(const VECT_INT_VECT &rings, INT_VECT &res,
const INT_VECT *exclude = NULL);
const INT_VECT *exclude = nullptr);
//! given a current combination of numbers change it to the next possible
// combination

2
Code/SimDivPickers/MaxMinPicker.h
View File

@@ -225,7 +225,7 @@ RDKit::INT_VECT MaxMinPicker::lazyPick(T &func, unsigned int poolSize,
double maxOFmin = -1.0;
double tmpThreshold = -1.0;
while (picked < pickSize) {
unsigned int *pick_prev = 0;
unsigned int *pick_prev = nullptr;
maxOFmin = -1.0;
prev = &pool_list;
do {