diff --git a/Code/Catalogs/CatalogEntry.h b/Code/Catalogs/CatalogEntry.h index 5a7acbd82..03079f1a0 100644 --- a/Code/Catalogs/CatalogEntry.h +++ b/Code/Catalogs/CatalogEntry.h @@ -11,7 +11,6 @@ #ifndef __RD_CATALOGENTRY_H__ #define __RD_CATALOGENTRY_H__ -#include #include namespace RDCatalog { diff --git a/Code/DataManip/MetricMatrixCalc/testMatCalc.cpp b/Code/DataManip/MetricMatrixCalc/testMatCalc.cpp index 5441f0c3f..3c994bc02 100644 --- a/Code/DataManip/MetricMatrixCalc/testMatCalc.cpp +++ b/Code/DataManip/MetricMatrixCalc/testMatCalc.cpp @@ -14,6 +14,7 @@ #include #include +#include using namespace RDDataManip; int main() { diff --git a/Code/DataStructs/DiscreteDistMat.cpp b/Code/DataStructs/DiscreteDistMat.cpp index a90344d99..ff54745e5 100644 --- a/Code/DataStructs/DiscreteDistMat.cpp +++ b/Code/DataStructs/DiscreteDistMat.cpp @@ -10,7 +10,6 @@ // #include "DiscreteDistMat.h" #include "DiscreteValueVect.h" -#include #include "DatastructsException.h" namespace RDKit { diff --git a/Code/DataStructs/ExplicitBitVect.cpp b/Code/DataStructs/ExplicitBitVect.cpp index e3b5b6b5e..9786245b2 100644 --- a/Code/DataStructs/ExplicitBitVect.cpp +++ b/Code/DataStructs/ExplicitBitVect.cpp @@ -9,7 +9,6 @@ // which is included in the file license.txt, found at the root // of the RDKit source tree. // -#include #include #include "ExplicitBitVect.h" #include diff --git a/Code/DataStructs/FPBReader.h b/Code/DataStructs/FPBReader.h index 0a21fcdda..7b22c3cae 100644 --- a/Code/DataStructs/FPBReader.h +++ b/Code/DataStructs/FPBReader.h @@ -18,7 +18,6 @@ in future releases. */ -#include #include #include #include diff --git a/Code/DataStructs/Utils.cpp b/Code/DataStructs/Utils.cpp index 6d5616e79..d91bb67ce 100644 --- a/Code/DataStructs/Utils.cpp +++ b/Code/DataStructs/Utils.cpp @@ -11,7 +11,6 @@ #include "BitVects.h" #include "BitVectUtils.h" #include -#include //! Convert a SparseBitVector to an ExplicitBitVector ExplicitBitVect *convertToExplicit(const SparseBitVect *sbv) { diff --git a/Code/DataStructs/base64.cpp b/Code/DataStructs/base64.cpp index be4091126..bbd9ab3d0 100644 --- a/Code/DataStructs/base64.cpp +++ b/Code/DataStructs/base64.cpp @@ -8,7 +8,6 @@ // which is included in the file license.txt, found at the root // of the RDKit source tree. // -#include #include #include "base64.h" // Encoding table from RFC 2045 diff --git a/Code/DistGeom/BoundsMatrix.h b/Code/DistGeom/BoundsMatrix.h index e202d55eb..28ceb6edd 100644 --- a/Code/DistGeom/BoundsMatrix.h +++ b/Code/DistGeom/BoundsMatrix.h @@ -13,7 +13,6 @@ #include #include -#include #include #include diff --git a/Code/DistGeom/testDistGeom.cpp b/Code/DistGeom/testDistGeom.cpp index 379214d3a..96637533f 100644 --- a/Code/DistGeom/testDistGeom.cpp +++ b/Code/DistGeom/testDistGeom.cpp @@ -11,7 +11,6 @@ #include #include "BoundsMatrix.h" #include "TriangleSmooth.h" -#include #include #include #include diff --git a/Code/Features/testFeatures.cpp b/Code/Features/testFeatures.cpp index 4f149ec39..5d5f69512 100644 --- a/Code/Features/testFeatures.cpp +++ b/Code/Features/testFeatures.cpp @@ -8,7 +8,6 @@ // of the RDKit source tree. // #include -#include #include #include #include diff --git a/Code/ForceField/AngleConstraints.h b/Code/ForceField/AngleConstraints.h index 4f46acc92..8034613d3 100644 --- a/Code/ForceField/AngleConstraints.h +++ b/Code/ForceField/AngleConstraints.h @@ -12,7 +12,6 @@ #ifndef RD_ANGLECONSTRAINTS_H #define RD_ANGLECONSTRAINTS_H #include -#include #include "ForceField.h" #include "Contrib.h" diff --git a/Code/ForceField/DistanceConstraints.h b/Code/ForceField/DistanceConstraints.h index 3760dc0fd..64404e810 100644 --- a/Code/ForceField/DistanceConstraints.h +++ b/Code/ForceField/DistanceConstraints.h @@ -12,7 +12,6 @@ #ifndef RD_DISTANCECONSTRAINTS_H #define RD_DISTANCECONSTRAINTS_H #include -#include #include "Contrib.h" namespace ForceFields { diff --git a/Code/ForceField/MMFF/Params.cpp b/Code/ForceField/MMFF/Params.cpp index b63721a85..7a3f9706f 100644 --- a/Code/ForceField/MMFF/Params.cpp +++ b/Code/ForceField/MMFF/Params.cpp @@ -16,7 +16,6 @@ #include #include "Params.h" -#include #include #include #include diff --git a/Code/ForceField/MMFF/Params.h b/Code/ForceField/MMFF/Params.h index af75e737c..0c1b26d17 100644 --- a/Code/ForceField/MMFF/Params.h +++ b/Code/ForceField/MMFF/Params.h @@ -19,7 +19,6 @@ #include #include #include -#include #include #ifndef M_PI diff --git a/Code/ForceField/MMFF/testMMFFForceField.cpp b/Code/ForceField/MMFF/testMMFFForceField.cpp index 814c4a7fb..dba4bd7ad 100644 --- a/Code/ForceField/MMFF/testMMFFForceField.cpp +++ b/Code/ForceField/MMFF/testMMFFForceField.cpp @@ -24,7 +24,6 @@ #include #include #include -#include #include #include #include diff --git a/Code/ForceField/UFF/Params.cpp b/Code/ForceField/UFF/Params.cpp index b84968159..108b951a6 100644 --- a/Code/ForceField/UFF/Params.cpp +++ b/Code/ForceField/UFF/Params.cpp @@ -13,7 +13,6 @@ #include #include "Params.h" -#include #include #include #include diff --git a/Code/ForceField/UFF/testUFFForceField.cpp b/Code/ForceField/UFF/testUFFForceField.cpp index dbf0c00dc..03424eb9a 100644 --- a/Code/ForceField/UFF/testUFFForceField.cpp +++ b/Code/ForceField/UFF/testUFFForceField.cpp @@ -8,7 +8,6 @@ // of the RDKit source tree. // #include -#include #include #include #include diff --git a/Code/Fuzz/smiles_string_to_mol_fuzzer.cc b/Code/Fuzz/smiles_string_to_mol_fuzzer.cc index b2ae9abab..5ef5c69ec 100644 --- a/Code/Fuzz/smiles_string_to_mol_fuzzer.cc +++ b/Code/Fuzz/smiles_string_to_mol_fuzzer.cc @@ -14,8 +14,6 @@ #include -#include - #include #include diff --git a/Code/Fuzz/standalone_fuzz_target_runner.cpp b/Code/Fuzz/standalone_fuzz_target_runner.cpp index 70b1299ef..158045a4f 100644 --- a/Code/Fuzz/standalone_fuzz_target_runner.cpp +++ b/Code/Fuzz/standalone_fuzz_target_runner.cpp @@ -9,7 +9,6 @@ // e.g. the one that comes from a bug report. #include -#include #include #include diff --git a/Code/Geometry/UniformGrid3D.h b/Code/Geometry/UniformGrid3D.h index 1419477cb..c1cd3032b 100644 --- a/Code/Geometry/UniformGrid3D.h +++ b/Code/Geometry/UniformGrid3D.h @@ -14,7 +14,6 @@ #include "point.h" #include #include "Grid3D.h" -#include namespace RDGeom { class RDKIT_RDGEOMETRYLIB_EXPORT UniformGrid3D diff --git a/Code/Geometry/point.h b/Code/Geometry/point.h index ba8ad89e4..b1b39c71b 100644 --- a/Code/Geometry/point.h +++ b/Code/Geometry/point.h @@ -11,7 +11,6 @@ #include #ifndef __RD_POINT_H__ #define __RD_POINT_H__ -#include #include #include #include diff --git a/Code/Geometry/testGrid.cpp b/Code/Geometry/testGrid.cpp index 93df0426c..1d41b6166 100644 --- a/Code/Geometry/testGrid.cpp +++ b/Code/Geometry/testGrid.cpp @@ -14,7 +14,6 @@ #include #include #include "GridUtils.h" -#include #include #include #include diff --git a/Code/Geometry/testRealValueGrid.cpp b/Code/Geometry/testRealValueGrid.cpp index 6f779a89f..a62ed5347 100644 --- a/Code/Geometry/testRealValueGrid.cpp +++ b/Code/Geometry/testRealValueGrid.cpp @@ -17,7 +17,6 @@ #include #include #include -#include #include #include #include diff --git a/Code/GraphMol/Abbreviations/Abbreviations.cpp b/Code/GraphMol/Abbreviations/Abbreviations.cpp index 9e6279ed8..1b1d52f00 100644 --- a/Code/GraphMol/Abbreviations/Abbreviations.cpp +++ b/Code/GraphMol/Abbreviations/Abbreviations.cpp @@ -13,7 +13,6 @@ #include #include -#include namespace RDKit { diff --git a/Code/GraphMol/Atom.h b/Code/GraphMol/Atom.h index e853b9ed6..0a089dcd3 100644 --- a/Code/GraphMol/Atom.h +++ b/Code/GraphMol/Atom.h @@ -16,9 +16,6 @@ #ifndef _RD_ATOM_H #define _RD_ATOM_H -// Std stuff -#include - // ours #include #include diff --git a/Code/GraphMol/Basement/FeatTrees/testFeatTrees.cpp b/Code/GraphMol/Basement/FeatTrees/testFeatTrees.cpp index f0e9377ee..ff40924e0 100644 --- a/Code/GraphMol/Basement/FeatTrees/testFeatTrees.cpp +++ b/Code/GraphMol/Basement/FeatTrees/testFeatTrees.cpp @@ -13,7 +13,6 @@ #include #include #include -#include #include #include #include diff --git a/Code/GraphMol/Bond.h b/Code/GraphMol/Bond.h index 87c0833f2..ef4bbe6c3 100644 --- a/Code/GraphMol/Bond.h +++ b/Code/GraphMol/Bond.h @@ -12,7 +12,6 @@ #define RD_BOND_H // std stuff -#include #include // Ours diff --git a/Code/GraphMol/ChemReactions/ReactionParser.h b/Code/GraphMol/ChemReactions/ReactionParser.h index bd49e66db..25de3e246 100644 --- a/Code/GraphMol/ChemReactions/ReactionParser.h +++ b/Code/GraphMol/ChemReactions/ReactionParser.h @@ -37,7 +37,6 @@ #define RD_REACTIONPARSER_H_21Aug2006 #include -#include #include #include #include @@ -150,8 +149,9 @@ inline std::string ChemicalReactionToRxnSmiles(const ChemicalReaction &rxn, } //! returns the reaction SMARTS for a reaction with CX extension -RDKIT_CHEMREACTIONS_EXPORT std::string ChemicalReactionToCXRxnSmarts(const ChemicalReaction &rxn, - const SmilesWriteParams ¶ms, std::uint32_t flags = SmilesWrite::CXSmilesFields::CX_ALL); +RDKIT_CHEMREACTIONS_EXPORT std::string ChemicalReactionToCXRxnSmarts( + const ChemicalReaction &rxn, const SmilesWriteParams ¶ms, + std::uint32_t flags = SmilesWrite::CXSmilesFields::CX_ALL); //! \overload inline std::string ChemicalReactionToCXRxnSmarts(const ChemicalReaction &rxn) { SmilesWriteParams params; @@ -160,10 +160,12 @@ inline std::string ChemicalReactionToCXRxnSmarts(const ChemicalReaction &rxn) { } //! returns the reaction SMILES for a reaction with CX extension -RDKIT_CHEMREACTIONS_EXPORT std::string ChemicalReactionToCXRxnSmiles(const ChemicalReaction &rxn, - const SmilesWriteParams ¶ms, std::uint32_t flags = SmilesWrite::CXSmilesFields::CX_ALL); +RDKIT_CHEMREACTIONS_EXPORT std::string ChemicalReactionToCXRxnSmiles( + const ChemicalReaction &rxn, const SmilesWriteParams ¶ms, + std::uint32_t flags = SmilesWrite::CXSmilesFields::CX_ALL); //! \overload -inline std::string ChemicalReactionToCXRxnSmiles(const ChemicalReaction &rxn, bool canonical = true) { +inline std::string ChemicalReactionToCXRxnSmiles(const ChemicalReaction &rxn, + bool canonical = true) { SmilesWriteParams params; params.canonical = canonical; return ChemicalReactionToCXRxnSmiles(rxn, params); diff --git a/Code/GraphMol/ChemReactions/ReactionPickler.h b/Code/GraphMol/ChemReactions/ReactionPickler.h index 66c3e6890..45930332d 100644 --- a/Code/GraphMol/ChemReactions/ReactionPickler.h +++ b/Code/GraphMol/ChemReactions/ReactionPickler.h @@ -14,7 +14,6 @@ #include // Std stuff -#include #include #include #ifdef WIN32 diff --git a/Code/GraphMol/ChemReactions/testReaction.cpp b/Code/GraphMol/ChemReactions/testReaction.cpp index 27e728b38..aa66516be 100644 --- a/Code/GraphMol/ChemReactions/testReaction.cpp +++ b/Code/GraphMol/ChemReactions/testReaction.cpp @@ -36,7 +36,6 @@ #include #include #include -#include #include #include #include diff --git a/Code/GraphMol/ChemReactions/testReactionFingerprints.cpp b/Code/GraphMol/ChemReactions/testReactionFingerprints.cpp index a15e05be2..98abe5b2a 100644 --- a/Code/GraphMol/ChemReactions/testReactionFingerprints.cpp +++ b/Code/GraphMol/ChemReactions/testReactionFingerprints.cpp @@ -35,7 +35,6 @@ #include #include #include -#include #include #include #include "GraphMol/ChemReactions/ReactionFingerprints.h" diff --git a/Code/GraphMol/ChemTransforms/ChemTransforms.cpp b/Code/GraphMol/ChemTransforms/ChemTransforms.cpp index bf4b9baa9..70c6e65cb 100644 --- a/Code/GraphMol/ChemTransforms/ChemTransforms.cpp +++ b/Code/GraphMol/ChemTransforms/ChemTransforms.cpp @@ -23,7 +23,6 @@ #include #include #include -#include #include #include #include diff --git a/Code/GraphMol/ChemTransforms/ChemTransforms.h b/Code/GraphMol/ChemTransforms/ChemTransforms.h index ef03b1c36..fc29cc31e 100644 --- a/Code/GraphMol/ChemTransforms/ChemTransforms.h +++ b/Code/GraphMol/ChemTransforms/ChemTransforms.h @@ -13,7 +13,6 @@ #include #include -#include #include #include "MolFragmenter.h" diff --git a/Code/GraphMol/ChemTransforms/testChemTransforms.cpp b/Code/GraphMol/ChemTransforms/testChemTransforms.cpp index 912c46583..1f590412a 100644 --- a/Code/GraphMol/ChemTransforms/testChemTransforms.cpp +++ b/Code/GraphMol/ChemTransforms/testChemTransforms.cpp @@ -12,7 +12,6 @@ #include #include #include -#include #include #include #include diff --git a/Code/GraphMol/Depictor/Basement/depictTest.cpp b/Code/GraphMol/Depictor/Basement/depictTest.cpp index 4347da533..4f3a3a8fc 100644 --- a/Code/GraphMol/Depictor/Basement/depictTest.cpp +++ b/Code/GraphMol/Depictor/Basement/depictTest.cpp @@ -12,7 +12,6 @@ #include #include #include "Depictor.h" -#include #include #include #include diff --git a/Code/GraphMol/Depictor/DepictUtils.cpp b/Code/GraphMol/Depictor/DepictUtils.cpp index aaa15339e..9ec71c7ee 100644 --- a/Code/GraphMol/Depictor/DepictUtils.cpp +++ b/Code/GraphMol/Depictor/DepictUtils.cpp @@ -11,7 +11,6 @@ #include #include #include "DepictUtils.h" -#include #include #include #include diff --git a/Code/GraphMol/Depictor/EmbeddedFrag.cpp b/Code/GraphMol/Depictor/EmbeddedFrag.cpp index cc094b87c..25a456c4e 100644 --- a/Code/GraphMol/Depictor/EmbeddedFrag.cpp +++ b/Code/GraphMol/Depictor/EmbeddedFrag.cpp @@ -17,7 +17,6 @@ #include "EmbeddedFrag.h" #include "DepictUtils.h" #include "Templates.h" -#include #include #include #include "RDDepictor.h" diff --git a/Code/GraphMol/Depictor/RDDepictor.cpp b/Code/GraphMol/Depictor/RDDepictor.cpp index 42a8b03f0..167194fd5 100644 --- a/Code/GraphMol/Depictor/RDDepictor.cpp +++ b/Code/GraphMol/Depictor/RDDepictor.cpp @@ -31,7 +31,6 @@ #include #include "EmbeddedFrag.h" #include "DepictUtils.h" -#include #include #include diff --git a/Code/GraphMol/Depictor/Templates.h b/Code/GraphMol/Depictor/Templates.h index 28ad4d7c5..559c31abd 100644 --- a/Code/GraphMol/Depictor/Templates.h +++ b/Code/GraphMol/Depictor/Templates.h @@ -14,7 +14,6 @@ #include "TemplateSmiles.h" -#include #include #include diff --git a/Code/GraphMol/Depictor/testDepictor.cpp b/Code/GraphMol/Depictor/testDepictor.cpp index 3fc0590ea..3f3a8212b 100644 --- a/Code/GraphMol/Depictor/testDepictor.cpp +++ b/Code/GraphMol/Depictor/testDepictor.cpp @@ -12,7 +12,6 @@ #include #include #include -#include #include #include #include diff --git a/Code/GraphMol/Descriptors/AUTOCORR2D.cpp b/Code/GraphMol/Descriptors/AUTOCORR2D.cpp index 949d63b14..62021cfeb 100644 --- a/Code/GraphMol/Descriptors/AUTOCORR2D.cpp +++ b/Code/GraphMol/Descriptors/AUTOCORR2D.cpp @@ -36,7 +36,6 @@ #include "AUTOCORR2D.h" #include "MolData3Ddescriptors.h" #include -#include namespace RDKit { namespace Descriptors { diff --git a/Code/GraphMol/Descriptors/AUTOCORR3D.cpp b/Code/GraphMol/Descriptors/AUTOCORR3D.cpp index 7cc5fa196..33bfba4c0 100644 --- a/Code/GraphMol/Descriptors/AUTOCORR3D.cpp +++ b/Code/GraphMol/Descriptors/AUTOCORR3D.cpp @@ -37,7 +37,6 @@ #include "MolData3Ddescriptors.h" #include -#include #include #include diff --git a/Code/GraphMol/Descriptors/AtomFeat.cpp b/Code/GraphMol/Descriptors/AtomFeat.cpp index 80b2eb5d9..93af566c2 100644 --- a/Code/GraphMol/Descriptors/AtomFeat.cpp +++ b/Code/GraphMol/Descriptors/AtomFeat.cpp @@ -22,7 +22,6 @@ // Adding ATOM FEATURES descriptors by Guillaume Godin #include -#include #include "AtomFeat.h" diff --git a/Code/GraphMol/Descriptors/Crippen.cpp b/Code/GraphMol/Descriptors/Crippen.cpp index 1ef523cb7..4dc849785 100644 --- a/Code/GraphMol/Descriptors/Crippen.cpp +++ b/Code/GraphMol/Descriptors/Crippen.cpp @@ -15,7 +15,6 @@ #include #include "MolDescriptors.h" #include "Crippen.h" -#include #include #include #include diff --git a/Code/GraphMol/Descriptors/DCLV.cpp b/Code/GraphMol/Descriptors/DCLV.cpp index 8159ed074..19934c425 100644 --- a/Code/GraphMol/Descriptors/DCLV.cpp +++ b/Code/GraphMol/Descriptors/DCLV.cpp @@ -10,7 +10,6 @@ /*=================================================================*/ #define _USE_MATH_DEFINES -#include #include #include #include @@ -44,7 +43,7 @@ static bool checkExcludedAtoms(const Atom *atm, bool includeLigand) { switch (resName[0]) { case 'D': - if (resName == "DOD" || resName == "D20"){ + if (resName == "DOD" || resName == "D20") { return true; } break; @@ -56,7 +55,7 @@ static bool checkExcludedAtoms(const Atom *atm, bool includeLigand) { case 'S': if (resName == "SOL" || resName == "SO4" || resName == "SUL") { return true; - } + } break; case 'W': if (resName == "WAT") { @@ -78,14 +77,14 @@ static bool checkExcludedAtoms(const Atom *atm, bool includeLigand) { if (!includeLigand && static_cast(info)->getIsHeteroAtom()) { return true; - } + } } return false; } -static bool includeAsPolar(const Atom *atm, const ROMol &mol, - bool includeSandP, bool includeHs) { +static bool includeAsPolar(const Atom *atm, const ROMol &mol, bool includeSandP, + bool includeHs) { // using Peter Ertl definition, polar atoms = O, N, P, S and attached Hs switch (atm->getAtomicNum()) { @@ -105,8 +104,7 @@ static bool includeAsPolar(const Atom *atm, const ROMol &mol, case 1: { if (!includeHs) { return false; - } - else { + } else { for (const auto nbr : mol.atomNeighbors(atm)) { if (includeAsPolar(nbr, mol, includeSandP, includeHs)) { return true; @@ -130,7 +128,7 @@ struct State { double voxU = 0.0; double voxV = 0.0; double voxW = 0.0; - + std::vector grid[VOXORDER][VOXORDER][VOXORDER]; void createVoxelGrid(const Point3D &minXYZ, const Point3D &maxXYZ, @@ -205,11 +203,11 @@ struct State { for (auto idx : grid[x][y][z]) { if (idx != atm_idx) { auto dist = range + radii_[idx]; - if ((pos - positions[idx]).lengthSq() < (dist * dist)){ + if ((pos - positions[idx]).lengthSq() < (dist * dist)) { atomNeighbours.push_back(idx); } } - } + } } } } @@ -220,12 +218,9 @@ struct State { }; // constructor definition -DoubleCubicLatticeVolume::DoubleCubicLatticeVolume(const ROMol &mol, - std::vector radii, - bool isProtein, - bool includeLigand, - double probeRadius, - int confId) +DoubleCubicLatticeVolume::DoubleCubicLatticeVolume( + const ROMol &mol, std::vector radii, bool isProtein, + bool includeLigand, double probeRadius, int confId) : mol(mol), radii_(std::move(radii)), isProtein(isProtein), @@ -356,7 +351,6 @@ bool DoubleCubicLatticeVolume::testPoint( } double DoubleCubicLatticeVolume::getAtomSurfaceArea(unsigned int atomIdx) { - // surface area for single atom const auto rad = radii_[atomIdx]; @@ -420,7 +414,8 @@ double DoubleCubicLatticeVolume::getPartialSurfaceArea( return area; } -double DoubleCubicLatticeVolume::getPolarSurfaceArea(bool includeSandP, bool includeHs) { +double DoubleCubicLatticeVolume::getPolarSurfaceArea(bool includeSandP, + bool includeHs) { boost::dynamic_bitset<> polarAtoms(mol.getNumAtoms()); for (const auto atom : mol.atoms()) { if (includeAsPolar(atom, mol, includeSandP, includeHs)) { @@ -430,7 +425,8 @@ double DoubleCubicLatticeVolume::getPolarSurfaceArea(bool includeSandP, bool inc return getPartialSurfaceArea(polarAtoms); } -std::map> &DoubleCubicLatticeVolume::getSurfacePoints() { +std::map> & +DoubleCubicLatticeVolume::getSurfacePoints() { if (!surfacePoints.empty()) { return surfacePoints; } @@ -540,7 +536,8 @@ double DoubleCubicLatticeVolume::getPartialVolume( return vol; } -double DoubleCubicLatticeVolume::getPolarVolume(bool includeSandP, bool includeHs) { +double DoubleCubicLatticeVolume::getPolarVolume(bool includeSandP, + bool includeHs) { boost::dynamic_bitset<> polarAtoms(mol.getNumAtoms()); for (const auto atom : mol.atoms()) { if (includeAsPolar(atom, mol, includeSandP, includeHs)) { diff --git a/Code/GraphMol/Descriptors/DCLV.h b/Code/GraphMol/Descriptors/DCLV.h index 5a61196c3..fb8ae9d80 100644 --- a/Code/GraphMol/Descriptors/DCLV.h +++ b/Code/GraphMol/Descriptors/DCLV.h @@ -12,7 +12,6 @@ #ifndef RDKIT_DCLV_H #define RDKIT_DCLV_H -#include #include #include #include @@ -28,7 +27,7 @@ namespace RDKit { namespace Descriptors { class RDKIT_DESCRIPTORS_EXPORT DoubleCubicLatticeVolume { - public: + public: /*! \param mol: input molecule or protein @@ -51,12 +50,11 @@ class RDKIT_DESCRIPTORS_EXPORT DoubleCubicLatticeVolume { bool includeLigand = true; double probeRadius = 1.4; int confId = -1; - double maxRadius = 1.7; // treat default max radius as Carbon + double maxRadius = 1.7; // treat default max radius as Carbon - -DoubleCubicLatticeVolume(const ROMol &mol, std::vector radii, - bool isProtein = false, bool includeLigand = true, - double probeRadius = 1.4, int confId = -1); + DoubleCubicLatticeVolume(const ROMol &mol, std::vector radii, + bool isProtein = false, bool includeLigand = true, + double probeRadius = 1.4, int confId = -1); //! Class for calculation of the Shrake and Rupley surface area and volume //! using the Double Cubic Lattice Method. //! @@ -89,7 +87,7 @@ DoubleCubicLatticeVolume(const ROMol &mol, std::vector radii, /*! \return van der Waals Volume */ double getVDWVolume(); - /*! \return Polar Volume */ + /*! \return Polar Volume */ double getPolarVolume(bool includeSandP, bool includeHs); /*! \return Volume from specified atoms */ diff --git a/Code/GraphMol/Descriptors/Data3Ddescriptors.cpp b/Code/GraphMol/Descriptors/Data3Ddescriptors.cpp index 726bb001d..64dee982b 100644 --- a/Code/GraphMol/Descriptors/Data3Ddescriptors.cpp +++ b/Code/GraphMol/Descriptors/Data3Ddescriptors.cpp @@ -1,5 +1,4 @@ #include -#include #include "Data3Ddescriptors.h" using namespace std; diff --git a/Code/GraphMol/Descriptors/GETAWAY.cpp b/Code/GraphMol/Descriptors/GETAWAY.cpp index d0def4b7a..2f9091d77 100644 --- a/Code/GraphMol/Descriptors/GETAWAY.cpp +++ b/Code/GraphMol/Descriptors/GETAWAY.cpp @@ -49,7 +49,6 @@ #include #include #include -#include #include #include #include diff --git a/Code/GraphMol/Descriptors/MolData3Ddescriptors.cpp b/Code/GraphMol/Descriptors/MolData3Ddescriptors.cpp index cc1db46c4..829459bca 100644 --- a/Code/GraphMol/Descriptors/MolData3Ddescriptors.cpp +++ b/Code/GraphMol/Descriptors/MolData3Ddescriptors.cpp @@ -1,5 +1,4 @@ #include -#include #include "MolData3Ddescriptors.h" #include diff --git a/Code/GraphMol/Descriptors/test.cpp b/Code/GraphMol/Descriptors/test.cpp index 18de6fac3..d438df830 100644 --- a/Code/GraphMol/Descriptors/test.cpp +++ b/Code/GraphMol/Descriptors/test.cpp @@ -9,7 +9,6 @@ // #include -#include #include #include diff --git a/Code/GraphMol/Descriptors/test3D.cpp b/Code/GraphMol/Descriptors/test3D.cpp index 5cf3c382f..a27897678 100644 --- a/Code/GraphMol/Descriptors/test3D.cpp +++ b/Code/GraphMol/Descriptors/test3D.cpp @@ -14,7 +14,6 @@ #endif #include -#include #include #include diff --git a/Code/GraphMol/DetermineBonds/catch_tests.cpp b/Code/GraphMol/DetermineBonds/catch_tests.cpp index fa296acc4..ea8c2955b 100644 --- a/Code/GraphMol/DetermineBonds/catch_tests.cpp +++ b/Code/GraphMol/DetermineBonds/catch_tests.cpp @@ -8,7 +8,6 @@ #include #include #include -#include #include #include #include diff --git a/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp b/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp index cbffad438..de63be90a 100644 --- a/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp +++ b/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp @@ -13,14 +13,12 @@ #include #include #include -#include #include #include #include #include #include #include -#include #include "BoundsMatrixBuilder.h" #include "Embedder.h" #include diff --git a/Code/GraphMol/FMCS/DebugTrace.h b/Code/GraphMol/FMCS/DebugTrace.h index c1c7a0c3e..223179979 100644 --- a/Code/GraphMol/FMCS/DebugTrace.h +++ b/Code/GraphMol/FMCS/DebugTrace.h @@ -13,7 +13,6 @@ #include #include #include -#include #ifdef _MSC_VER #define _CRT_SECURE_NO_WARNINGS #define NOMINMAX diff --git a/Code/GraphMol/FMCS/FMCS.cpp b/Code/GraphMol/FMCS/FMCS.cpp index edc7a756e..6e9b23ecb 100644 --- a/Code/GraphMol/FMCS/FMCS.cpp +++ b/Code/GraphMol/FMCS/FMCS.cpp @@ -16,7 +16,6 @@ #include #include -#include #include #include "SubstructMatchCustom.h" #include "MaximumCommonSubgraph.h" diff --git a/Code/GraphMol/FMCS/Test/testFMCS.cpp b/Code/GraphMol/FMCS/Test/testFMCS.cpp index e9c1bc42a..cbeb6225d 100644 --- a/Code/GraphMol/FMCS/Test/testFMCS.cpp +++ b/Code/GraphMol/FMCS/Test/testFMCS.cpp @@ -43,7 +43,6 @@ #include #include #include -#include #include "../../RDKitBase.h" #include "../../FileParsers/FileParsers.h" //MOL single molecule ! #include "../../FileParsers/MolSupplier.h" //SDF @@ -1687,7 +1686,6 @@ int main(int argc, const char *argv[]) { _CrtMemCheckpoint(&_ms); #endif // while(1) // check memory leaks in TaskManager or 'top -p ...' - {} #ifdef _DEBUG // check memory leaks _CrtMemDumpAllObjectsSince(&_ms); #endif diff --git a/Code/GraphMol/FMCS/testFMCS_Unit.cpp b/Code/GraphMol/FMCS/testFMCS_Unit.cpp index fa92d5d6a..5ba70baa6 100644 --- a/Code/GraphMol/FMCS/testFMCS_Unit.cpp +++ b/Code/GraphMol/FMCS/testFMCS_Unit.cpp @@ -42,7 +42,6 @@ #include #include #include -#include #include #include #include "../RDKitBase.h" diff --git a/Code/GraphMol/FileParsers/CDXMLParser.h b/Code/GraphMol/FileParsers/CDXMLParser.h index dd2899daa..d49b75753 100644 --- a/Code/GraphMol/FileParsers/CDXMLParser.h +++ b/Code/GraphMol/FileParsers/CDXMLParser.h @@ -13,7 +13,6 @@ #include #include -#include #include namespace RDKit { @@ -35,10 +34,10 @@ struct RDKIT_FILEPARSERS_EXPORT CDXMLParserParams { bool sanitize = true; bool removeHs = true; CDXMLFormat format = CDXMLFormat::Auto; - + CDXMLParserParams() = default; - CDXMLParserParams(bool sanitize, bool removeHs, CDXMLFormat format) : - sanitize(sanitize), removeHs(removeHs), format(format) {} + CDXMLParserParams(bool sanitize, bool removeHs, CDXMLFormat format) + : sanitize(sanitize), removeHs(removeHs), format(format) {} }; //! \brief construct molecules from a CDXML file @@ -68,7 +67,8 @@ MolsFromCDXMLDataStream(std::istream &inStream, */ RDKIT_FILEPARSERS_EXPORT std::vector> MolsFromCDXMLFile( const std::string &filename, - const CDXMLParserParams ¶ms = CDXMLParserParams(true, true, CDXMLFormat::Auto)); + const CDXMLParserParams ¶ms = CDXMLParserParams(true, true, + CDXMLFormat::Auto)); //! \brief construct molecules from a CDXML block //! The RDKit is optionally built with the Revvity ChemDraw parser @@ -84,7 +84,8 @@ RDKIT_FILEPARSERS_EXPORT std::vector> MolsFromCDXMLFile( */ RDKIT_FILEPARSERS_EXPORT std::vector> MolsFromCDXML( const std::string &cdxml, - const CDXMLParserParams ¶ms = CDXMLParserParams(true, true, v2::CDXMLParser::CDXMLFormat::Auto)); + const CDXMLParserParams ¶ms = + CDXMLParserParams(true, true, v2::CDXMLParser::CDXMLFormat::Auto)); } // namespace CDXMLParser } // namespace v2 @@ -106,8 +107,8 @@ inline namespace v1 { */ inline std::vector> CDXMLDataStreamToMols( std::istream &inStream, bool sanitize = true, bool removeHs = true) { - v2::CDXMLParser::CDXMLParserParams params( - sanitize, removeHs, v2::CDXMLParser::CDXMLFormat::Auto); + v2::CDXMLParser::CDXMLParserParams params(sanitize, removeHs, + v2::CDXMLParser::CDXMLFormat::Auto); return v2::CDXMLParser::MolsFromCDXMLDataStream(inStream, params); } @@ -116,8 +117,8 @@ inline std::vector> CDXMLDataStreamToMols( //! full functionality, just the base ones required for molecule and //! reaction parsing. //! Note: If the ChemDraw extensions are available, -//! This function uses the file extension to determine the file type, .cdx or .cdxml -//! If not, it defaults to CDXML +//! This function uses the file extension to determine the file type, .cdx or +//! .cdxml If not, it defaults to CDXML /*! * \param fileName - cdxml fileName * \param sanitize - toggles sanitization and stereochemistry @@ -154,7 +155,7 @@ inline std::vector> CDXMLToMols(const std::string &cdxml, v2::CDXMLParser::CDXMLParserParams params; params.sanitize = sanitize; params.removeHs = removeHs; - params.format = v2::CDXMLParser::CDXMLFormat::Auto; + params.format = v2::CDXMLParser::CDXMLFormat::Auto; return v2::CDXMLParser::MolsFromCDXML(cdxml, params); } } // namespace v1 diff --git a/Code/GraphMol/FileParsers/FileParserUtils.h b/Code/GraphMol/FileParsers/FileParserUtils.h index 9a78d4ad8..8930fdef1 100644 --- a/Code/GraphMol/FileParsers/FileParserUtils.h +++ b/Code/GraphMol/FileParsers/FileParserUtils.h @@ -12,7 +12,6 @@ #define RD_FILEPARSERUTILS_H #include -#include #include #include #include diff --git a/Code/GraphMol/FileParsers/FileParsers.h b/Code/GraphMol/FileParsers/FileParsers.h index 750da9f82..1581b2ddc 100644 --- a/Code/GraphMol/FileParsers/FileParsers.h +++ b/Code/GraphMol/FileParsers/FileParsers.h @@ -17,7 +17,6 @@ #include "CDXMLParser.h" #include #include -#include #include #include diff --git a/Code/GraphMol/FileParsers/ForwardSDMolSupplier.cpp b/Code/GraphMol/FileParsers/ForwardSDMolSupplier.cpp index a72311c79..4d6b695d7 100644 --- a/Code/GraphMol/FileParsers/ForwardSDMolSupplier.cpp +++ b/Code/GraphMol/FileParsers/ForwardSDMolSupplier.cpp @@ -21,7 +21,6 @@ #include "FileParserUtils.h" #include -#include #include #include diff --git a/Code/GraphMol/FileParsers/GeneralFileReader.h b/Code/GraphMol/FileParsers/GeneralFileReader.h index 9a27c8003..950912fad 100644 --- a/Code/GraphMol/FileParsers/GeneralFileReader.h +++ b/Code/GraphMol/FileParsers/GeneralFileReader.h @@ -13,7 +13,6 @@ #include #include -#include #include #include #include diff --git a/Code/GraphMol/FileParsers/MaeMolSupplier.cpp b/Code/GraphMol/FileParsers/MaeMolSupplier.cpp index 92197a318..b6e75ede2 100644 --- a/Code/GraphMol/FileParsers/MaeMolSupplier.cpp +++ b/Code/GraphMol/FileParsers/MaeMolSupplier.cpp @@ -8,7 +8,6 @@ // of the RDKit source tree. // #include -#include #include #include @@ -39,7 +38,10 @@ namespace FileParsers { namespace { // Flag for parsing chirality labels -enum class [[nodiscard]] ChiralityLabelStatus{VALID, INVALID}; +enum class [[nodiscard]] ChiralityLabelStatus { + VALID, + INVALID +}; class PDBInfo { public: diff --git a/Code/GraphMol/FileParsers/MolFileWriter.cpp b/Code/GraphMol/FileParsers/MolFileWriter.cpp index dc33bce91..89d4c5b82 100644 --- a/Code/GraphMol/FileParsers/MolFileWriter.cpp +++ b/Code/GraphMol/FileParsers/MolFileWriter.cpp @@ -25,7 +25,6 @@ #include #include #include -#include #include #include @@ -586,7 +585,7 @@ void GetMolFileAtomProperties(const Atom *atom, const Conformer *conf, parityFlag = getAtomParityFlag(atom, conf); } } - + if (hasNonDefaultValence(atom)) { if (atom->getTotalDegree() == 0) { // Specify zero valence for elements/metals without neighbors @@ -609,12 +608,13 @@ const std::string GetMolFileAtomLine(const Atom *atom, const Conformer *conf, GetMolFileAtomProperties(atom, conf, totValence, atomMapNumber, parityFlag, x, y, z); - if( (x >= MAX_V2000_COORD || x <= MIN_V2000_COORD) || + if ((x >= MAX_V2000_COORD || x <= MIN_V2000_COORD) || (y >= MAX_V2000_COORD || y <= MIN_V2000_COORD) || - (z >= MAX_V2000_COORD || z <= MIN_V2000_COORD) ) { - throw ValueErrorException("MolFile coordinates must be in (-100000, 1000000)"); + (z >= MAX_V2000_COORD || z <= MIN_V2000_COORD)) { + throw ValueErrorException( + "MolFile coordinates must be in (-100000, 1000000)"); } - + int massDiff, chg, stereoCare, hCount, rxnComponentType, rxnComponentNumber, inversionFlag, exactChangeFlag; massDiff = 0; @@ -1273,24 +1273,23 @@ std::string outputMolToMolBlock(const RWMol &tmol, int confId, } bool coordMagnitudeTooLargeForV2K = false; - if(conf) { - for(auto &pos : conf->getPositions()) { - if( (pos.x >= MAX_V2000_COORD || pos.x <= MIN_V2000_COORD) || - (pos.y >= MAX_V2000_COORD || pos.y <= MIN_V2000_COORD) || - (pos.z >= MAX_V2000_COORD || pos.z <= MIN_V2000_COORD) ) { - coordMagnitudeTooLargeForV2K = true; + if (conf) { + for (auto &pos : conf->getPositions()) { + if ((pos.x >= MAX_V2000_COORD || pos.x <= MIN_V2000_COORD) || + (pos.y >= MAX_V2000_COORD || pos.y <= MIN_V2000_COORD) || + (pos.z >= MAX_V2000_COORD || pos.z <= MIN_V2000_COORD)) { + coordMagnitudeTooLargeForV2K = true; } } } if (whichFormat == MolFileFormat::V2000 && coordMagnitudeTooLargeForV2K) { throw ValueErrorException( - "V2000 format does not support atom positions <= " + - std::to_string((int)MIN_V2000_COORD) + - " or >= " + std::to_string((int)MAX_V2000_COORD) ); + "V2000 format does not support atom positions <= " + + std::to_string((int)MIN_V2000_COORD) + + " or >= " + std::to_string((int)MAX_V2000_COORD)); } - std::string text; if (tmol.getPropIfPresent(common_properties::_Name, text)) { res += text; @@ -1332,7 +1331,8 @@ std::string outputMolToMolBlock(const RWMol &tmol, int confId, if (whichFormat == MolFileFormat::V3000) { isV3000 = true; } else if (whichFormat == MolFileFormat::unspecified && - (coordMagnitudeTooLargeForV2K || hasDative || nAtoms > 999 || nBonds > 999 || nSGroups > 999 || + (coordMagnitudeTooLargeForV2K || hasDative || nAtoms > 999 || + nBonds > 999 || nSGroups > 999 || !tmol.getStereoGroups().empty())) { isV3000 = true; } diff --git a/Code/GraphMol/FileParsers/MolSupplier.h b/Code/GraphMol/FileParsers/MolSupplier.h index 8a046296d..1e3f7196c 100644 --- a/Code/GraphMol/FileParsers/MolSupplier.h +++ b/Code/GraphMol/FileParsers/MolSupplier.h @@ -18,7 +18,6 @@ #include #include #include -#include #include #include #include diff --git a/Code/GraphMol/FileParsers/MolWriters.h b/Code/GraphMol/FileParsers/MolWriters.h index 004919c06..dd11cadd6 100644 --- a/Code/GraphMol/FileParsers/MolWriters.h +++ b/Code/GraphMol/FileParsers/MolWriters.h @@ -14,7 +14,6 @@ #include -#include #include #include diff --git a/Code/GraphMol/FileParsers/PDBParser.cpp b/Code/GraphMol/FileParsers/PDBParser.cpp index 9ad74aff4..8cdf570ef 100644 --- a/Code/GraphMol/FileParsers/PDBParser.cpp +++ b/Code/GraphMol/FileParsers/PDBParser.cpp @@ -10,7 +10,6 @@ #include #include #include -#include #include #include #include diff --git a/Code/GraphMol/FileParsers/PDBWriter.cpp b/Code/GraphMol/FileParsers/PDBWriter.cpp index 1a53c172c..18cc70bef 100644 --- a/Code/GraphMol/FileParsers/PDBWriter.cpp +++ b/Code/GraphMol/FileParsers/PDBWriter.cpp @@ -9,7 +9,6 @@ // #include #include -#include #include #include #include diff --git a/Code/GraphMol/FileParsers/SDMolSupplier.cpp b/Code/GraphMol/FileParsers/SDMolSupplier.cpp index e973d1a50..bb4c21585 100644 --- a/Code/GraphMol/FileParsers/SDMolSupplier.cpp +++ b/Code/GraphMol/FileParsers/SDMolSupplier.cpp @@ -18,7 +18,6 @@ #include "FileParsers.h" #include -#include #include #include diff --git a/Code/GraphMol/FileParsers/SDWriter.cpp b/Code/GraphMol/FileParsers/SDWriter.cpp index 90ac3a8fc..2b907de5a 100644 --- a/Code/GraphMol/FileParsers/SDWriter.cpp +++ b/Code/GraphMol/FileParsers/SDWriter.cpp @@ -9,7 +9,6 @@ // #include -#include #include #include diff --git a/Code/GraphMol/FileParsers/SmilesMolSupplier.cpp b/Code/GraphMol/FileParsers/SmilesMolSupplier.cpp index 3c653ac79..4e2147e33 100644 --- a/Code/GraphMol/FileParsers/SmilesMolSupplier.cpp +++ b/Code/GraphMol/FileParsers/SmilesMolSupplier.cpp @@ -17,7 +17,6 @@ typedef boost::tokenizer> tokenizer; #include -#include #include #include #include diff --git a/Code/GraphMol/FileParsers/SmilesWriter.cpp b/Code/GraphMol/FileParsers/SmilesWriter.cpp index 5394a0379..6cc548f62 100644 --- a/Code/GraphMol/FileParsers/SmilesWriter.cpp +++ b/Code/GraphMol/FileParsers/SmilesWriter.cpp @@ -9,7 +9,6 @@ // of the RDKit source tree. // #include -#include #include #include diff --git a/Code/GraphMol/FileParsers/TDTMolSupplier.cpp b/Code/GraphMol/FileParsers/TDTMolSupplier.cpp index 4a65c09d0..f6f18f1f0 100644 --- a/Code/GraphMol/FileParsers/TDTMolSupplier.cpp +++ b/Code/GraphMol/FileParsers/TDTMolSupplier.cpp @@ -22,7 +22,6 @@ #include #include -#include #include #include diff --git a/Code/GraphMol/FileParsers/TDTWriter.cpp b/Code/GraphMol/FileParsers/TDTWriter.cpp index 032082a21..60fa8a546 100644 --- a/Code/GraphMol/FileParsers/TDTWriter.cpp +++ b/Code/GraphMol/FileParsers/TDTWriter.cpp @@ -9,7 +9,6 @@ // of the RDKit source tree. // #include -#include #include #include #include diff --git a/Code/GraphMol/FileParsers/XYZFileParser.cpp b/Code/GraphMol/FileParsers/XYZFileParser.cpp index 385856914..01575a0d8 100644 --- a/Code/GraphMol/FileParsers/XYZFileParser.cpp +++ b/Code/GraphMol/FileParsers/XYZFileParser.cpp @@ -20,7 +20,6 @@ #include #include -#include #include #include #include diff --git a/Code/GraphMol/FileParsers/testGeneralFileReader.cpp b/Code/GraphMol/FileParsers/testGeneralFileReader.cpp index 71c3f884e..bbf8e7895 100644 --- a/Code/GraphMol/FileParsers/testGeneralFileReader.cpp +++ b/Code/GraphMol/FileParsers/testGeneralFileReader.cpp @@ -16,7 +16,6 @@ #include #include #include -#include #include #include #include diff --git a/Code/GraphMol/FileParsers/testMolSupplier.cpp b/Code/GraphMol/FileParsers/testMolSupplier.cpp index e75396317..f8a557a22 100644 --- a/Code/GraphMol/FileParsers/testMolSupplier.cpp +++ b/Code/GraphMol/FileParsers/testMolSupplier.cpp @@ -11,7 +11,6 @@ #include #include #include -#include #include #include #include diff --git a/Code/GraphMol/FileParsers/testMolWriter.cpp b/Code/GraphMol/FileParsers/testMolWriter.cpp index 8fdc4bf43..515427b61 100644 --- a/Code/GraphMol/FileParsers/testMolWriter.cpp +++ b/Code/GraphMol/FileParsers/testMolWriter.cpp @@ -11,7 +11,6 @@ #include #include #include -#include #include #include diff --git a/Code/GraphMol/FilterCatalog/filtercatalogtest.cpp b/Code/GraphMol/FilterCatalog/filtercatalogtest.cpp index e8f97a72a..addf43373 100644 --- a/Code/GraphMol/FilterCatalog/filtercatalogtest.cpp +++ b/Code/GraphMol/FilterCatalog/filtercatalogtest.cpp @@ -35,7 +35,6 @@ #include #include #include -#include #include #include diff --git a/Code/GraphMol/Fingerprints/MHFP.cpp b/Code/GraphMol/Fingerprints/MHFP.cpp index 1b614234d..bace09aee 100644 --- a/Code/GraphMol/Fingerprints/MHFP.cpp +++ b/Code/GraphMol/Fingerprints/MHFP.cpp @@ -10,7 +10,6 @@ // #include -#include #include #include #include diff --git a/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp b/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp index 94961661c..3f35ad6f1 100644 --- a/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp +++ b/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp @@ -9,7 +9,6 @@ // #include -#include #include #include #include diff --git a/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.cpp b/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.cpp index ee6528f7b..a4e68cd0b 100644 --- a/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.cpp +++ b/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.cpp @@ -17,7 +17,6 @@ #include #include #include -#include #include #include diff --git a/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalFF.cpp b/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalFF.cpp index 2e3e25345..6372b8b4d 100644 --- a/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalFF.cpp +++ b/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalFF.cpp @@ -20,7 +20,6 @@ #include #include #include -#include #include #include diff --git a/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.h b/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.h index b1170d5cf..fafae6b12 100644 --- a/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.h +++ b/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.h @@ -15,7 +15,6 @@ #include #include -#include #include #include @@ -65,7 +64,10 @@ class RDKIT_FORCEFIELDHELPERS_EXPORT MMFFAtomProperties { }; typedef boost::shared_ptr MMFFAtomPropertiesPtr; -enum { CONSTANT = 1, DISTANCE = 2 }; +enum { + CONSTANT = 1, + DISTANCE = 2 +}; enum { MMFF_VERBOSITY_NONE = 0, MMFF_VERBOSITY_LOW = 1, diff --git a/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.cpp b/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.cpp index 4ccd318b2..4ac87b8fd 100644 --- a/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.cpp +++ b/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.cpp @@ -6,7 +6,6 @@ // which is included in the file license.txt, found at the root // of the RDKit source tree. // -#include #include #include diff --git a/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFHelpers.cpp b/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFHelpers.cpp index 84a13a514..e4a9db148 100644 --- a/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFHelpers.cpp +++ b/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFHelpers.cpp @@ -8,7 +8,6 @@ // #include -#include #include #include #include diff --git a/Code/GraphMol/ForceFieldHelpers/MMFF/testMultiThread.cpp b/Code/GraphMol/ForceFieldHelpers/MMFF/testMultiThread.cpp index 0418fd016..de94d15b4 100644 --- a/Code/GraphMol/ForceFieldHelpers/MMFF/testMultiThread.cpp +++ b/Code/GraphMol/ForceFieldHelpers/MMFF/testMultiThread.cpp @@ -9,7 +9,6 @@ // #include -#include #include #include #include diff --git a/Code/GraphMol/ForceFieldHelpers/UFF/AtomTyper.cpp b/Code/GraphMol/ForceFieldHelpers/UFF/AtomTyper.cpp index 97f4cece9..abdbeaa31 100644 --- a/Code/GraphMol/ForceFieldHelpers/UFF/AtomTyper.cpp +++ b/Code/GraphMol/ForceFieldHelpers/UFF/AtomTyper.cpp @@ -7,7 +7,6 @@ // which is included in the file license.txt, found at the root // of the RDKit source tree. // -#include #include #include #include diff --git a/Code/GraphMol/ForceFieldHelpers/UFF/Builder.cpp b/Code/GraphMol/ForceFieldHelpers/UFF/Builder.cpp index f491f8259..f79c9fcab 100644 --- a/Code/GraphMol/ForceFieldHelpers/UFF/Builder.cpp +++ b/Code/GraphMol/ForceFieldHelpers/UFF/Builder.cpp @@ -6,7 +6,6 @@ // which is included in the file license.txt, found at the root // of the RDKit source tree. // -#include #include #include diff --git a/Code/GraphMol/ForceFieldHelpers/UFF/testUFFHelpers.cpp b/Code/GraphMol/ForceFieldHelpers/UFF/testUFFHelpers.cpp index 6a595d4a2..b1cc84763 100644 --- a/Code/GraphMol/ForceFieldHelpers/UFF/testUFFHelpers.cpp +++ b/Code/GraphMol/ForceFieldHelpers/UFF/testUFFHelpers.cpp @@ -9,7 +9,6 @@ // #include -#include #include #include #include diff --git a/Code/GraphMol/FragCatalog/FragCatalogEntry.cpp b/Code/GraphMol/FragCatalog/FragCatalogEntry.cpp index ccd05f4e3..ba814926f 100644 --- a/Code/GraphMol/FragCatalog/FragCatalogEntry.cpp +++ b/Code/GraphMol/FragCatalog/FragCatalogEntry.cpp @@ -17,7 +17,6 @@ #include #include #include -#include #include #include #include diff --git a/Code/GraphMol/FragCatalog/FragCatalogUtils.h b/Code/GraphMol/FragCatalog/FragCatalogUtils.h index 9af89b370..635fe471c 100644 --- a/Code/GraphMol/FragCatalog/FragCatalogUtils.h +++ b/Code/GraphMol/FragCatalog/FragCatalogUtils.h @@ -15,7 +15,6 @@ #include #include #include "FragCatParams.h" -#include namespace RDKit { diff --git a/Code/GraphMol/FragCatalog/test1.cpp b/Code/GraphMol/FragCatalog/test1.cpp index bafdc5678..e71ba21bf 100644 --- a/Code/GraphMol/FragCatalog/test1.cpp +++ b/Code/GraphMol/FragCatalog/test1.cpp @@ -22,7 +22,6 @@ #include "FragCatalogUtils.h" #include "FragFPGenerator.h" #include -#include #include #include diff --git a/Code/GraphMol/MMPA/MMPA_UnitTest.cpp b/Code/GraphMol/MMPA/MMPA_UnitTest.cpp index 5606f9f4d..88218f84f 100644 --- a/Code/GraphMol/MMPA/MMPA_UnitTest.cpp +++ b/Code/GraphMol/MMPA/MMPA_UnitTest.cpp @@ -46,7 +46,6 @@ #include #include #include -#include #include #include #include diff --git a/Code/GraphMol/MarvinParse/MarvinParser.cpp b/Code/GraphMol/MarvinParse/MarvinParser.cpp index ea9e154f8..9767fbae2 100644 --- a/Code/GraphMol/MarvinParse/MarvinParser.cpp +++ b/Code/GraphMol/MarvinParse/MarvinParser.cpp @@ -12,7 +12,6 @@ #include #include -#include #include #include #include diff --git a/Code/GraphMol/MarvinParse/MarvinParser.h b/Code/GraphMol/MarvinParse/MarvinParser.h index 75cba355c..136a4cce1 100644 --- a/Code/GraphMol/MarvinParse/MarvinParser.h +++ b/Code/GraphMol/MarvinParse/MarvinParser.h @@ -17,7 +17,6 @@ #include #include -#include namespace RDKit { namespace v2 { diff --git a/Code/GraphMol/MarvinParse/MarvinWriter.cpp b/Code/GraphMol/MarvinParse/MarvinWriter.cpp index ce64558bf..1788320d1 100644 --- a/Code/GraphMol/MarvinParse/MarvinWriter.cpp +++ b/Code/GraphMol/MarvinParse/MarvinWriter.cpp @@ -12,7 +12,6 @@ #include #include -#include #include #include #include diff --git a/Code/GraphMol/MolCatalog/MolCatalogEntry.cpp b/Code/GraphMol/MolCatalog/MolCatalogEntry.cpp index 48fc486db..b4e7560e2 100644 --- a/Code/GraphMol/MolCatalog/MolCatalogEntry.cpp +++ b/Code/GraphMol/MolCatalog/MolCatalogEntry.cpp @@ -14,7 +14,6 @@ #include #include #include -#include #include #include diff --git a/Code/GraphMol/MolCatalog/MolCatalogParams.h b/Code/GraphMol/MolCatalog/MolCatalogParams.h index 2fe3f7965..edd8ded3a 100644 --- a/Code/GraphMol/MolCatalog/MolCatalogParams.h +++ b/Code/GraphMol/MolCatalog/MolCatalogParams.h @@ -7,7 +7,6 @@ #include #include -#include namespace RDKit { diff --git a/Code/GraphMol/MolCatalog/test1.cpp b/Code/GraphMol/MolCatalog/test1.cpp index e12d15359..93d0d5bdd 100644 --- a/Code/GraphMol/MolCatalog/test1.cpp +++ b/Code/GraphMol/MolCatalog/test1.cpp @@ -13,7 +13,6 @@ #include "MolCatalogParams.h" #include -#include #include #include diff --git a/Code/GraphMol/MolChemicalFeatures/FeatureParser.h b/Code/GraphMol/MolChemicalFeatures/FeatureParser.h index f65aca5b3..479b9a0ed 100644 --- a/Code/GraphMol/MolChemicalFeatures/FeatureParser.h +++ b/Code/GraphMol/MolChemicalFeatures/FeatureParser.h @@ -11,7 +11,6 @@ #ifndef __FEATUREPARSER_H_02122004_1810__ #define __FEATUREPARSER_H_02122004_1810__ -#include #include #include #include diff --git a/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.h b/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.h index e0aced301..7bd719e67 100644 --- a/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.h +++ b/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.h @@ -12,7 +12,6 @@ #define __CHEMICALFEATUREFACTORY_H_02122004_1545__ #include "MolChemicalFeatureDef.h" -#include #include namespace RDKit { diff --git a/Code/GraphMol/MolChemicalFeatures/Wrap/rdMolChemicalFeatures.cpp b/Code/GraphMol/MolChemicalFeatures/Wrap/rdMolChemicalFeatures.cpp index e7e9d5cd6..761275944 100644 --- a/Code/GraphMol/MolChemicalFeatures/Wrap/rdMolChemicalFeatures.cpp +++ b/Code/GraphMol/MolChemicalFeatures/Wrap/rdMolChemicalFeatures.cpp @@ -13,7 +13,6 @@ #include #include #include -#include #include namespace python = boost::python; using namespace RDKit; diff --git a/Code/GraphMol/MolChemicalFeatures/testFeatures.cpp b/Code/GraphMol/MolChemicalFeatures/testFeatures.cpp index e7f3860be..cc0572b63 100644 --- a/Code/GraphMol/MolChemicalFeatures/testFeatures.cpp +++ b/Code/GraphMol/MolChemicalFeatures/testFeatures.cpp @@ -10,7 +10,6 @@ // #include #include -#include #include #include #include diff --git a/Code/GraphMol/MolDraw2D/DrawMol.cpp b/Code/GraphMol/MolDraw2D/DrawMol.cpp index f58fbd357..aea718b21 100755 --- a/Code/GraphMol/MolDraw2D/DrawMol.cpp +++ b/Code/GraphMol/MolDraw2D/DrawMol.cpp @@ -11,7 +11,6 @@ // #include -#include #include #include @@ -221,7 +220,7 @@ void DrawMol::extractAll(double scale) { if (drawOptions_.addStereoAnnotation) { extractCIPCodes(drawOptions_.showAllCIPCodes); } - extractStereoGroups(); // always show StereoGroups + extractStereoGroups(); // always show StereoGroups extractBondNotes(); extractRadicals(); extractSGroupData(); @@ -469,13 +468,14 @@ void DrawMol::extractCIPCodes(bool showAllCIPCodes) { boost::dynamic_bitset<> maskedAtoms(drawMol_->getNumAtoms()); boost::dynamic_bitset<> maskedBonds(drawMol_->getNumBonds()); - if(!showAllCIPCodes) { // record atoms and bonds whose codes should be hidden + if (!showAllCIPCodes) { // record atoms and bonds whose codes should be + // hidden for (const StereoGroup &group : drawMol_->getStereoGroups()) { StereoGroupType stereoGroupType; stereoGroupType = group.getGroupType(); - if(stereoGroupType == RDKit::StereoGroupType::STEREO_OR || \ - stereoGroupType == RDKit::StereoGroupType::STEREO_AND ) { + if (stereoGroupType == RDKit::StereoGroupType::STEREO_OR || + stereoGroupType == RDKit::StereoGroupType::STEREO_AND) { for (const auto atom : group.getAtoms()) { maskedAtoms.set(atom->getIdx()); } @@ -490,8 +490,8 @@ void DrawMol::extractCIPCodes(bool showAllCIPCodes) { std::string cip; if (!maskedAtoms[atom->getIdx()] && atom->getPropIfPresent(common_properties::_CIPCode, cip)) { - cip = "(" + cip + ")"; - DrawAnnotation *annot = new DrawAnnotation( + cip = "(" + cip + ")"; + DrawAnnotation *annot = new DrawAnnotation( cip, TextAlignType::MIDDLE, "CIP_Code", drawOptions_.annotationFontScale, Point2D(0.0, 0.0), drawOptions_.atomNoteColour, textDrawer_); @@ -517,11 +517,11 @@ void DrawMol::extractCIPCodes(bool showAllCIPCodes) { if (!cip.empty()) { cip = "(" + cip + ")"; DrawAnnotation *annot = new DrawAnnotation( - cip, TextAlignType::MIDDLE, "CIP_Code", - drawOptions_.annotationFontScale, Point2D(0.0, 0.0), - drawOptions_.bondNoteColour, textDrawer_); - calcAnnotationPosition(bond, *annot); - annotations_.emplace_back(annot); + cip, TextAlignType::MIDDLE, "CIP_Code", + drawOptions_.annotationFontScale, Point2D(0.0, 0.0), + drawOptions_.bondNoteColour, textDrawer_); + calcAnnotationPosition(bond, *annot); + annotations_.emplace_back(annot); } } } diff --git a/Code/GraphMol/MolDraw2D/DrawTextFT.cpp b/Code/GraphMol/MolDraw2D/DrawTextFT.cpp index 0b6887351..007bbe358 100644 --- a/Code/GraphMol/MolDraw2D/DrawTextFT.cpp +++ b/Code/GraphMol/MolDraw2D/DrawTextFT.cpp @@ -12,7 +12,6 @@ // #include -#include #include #include diff --git a/Code/GraphMol/MolDraw2D/MolDraw2DJS.h b/Code/GraphMol/MolDraw2D/MolDraw2DJS.h index 5a0060fc9..5123bf1c0 100644 --- a/Code/GraphMol/MolDraw2D/MolDraw2DJS.h +++ b/Code/GraphMol/MolDraw2D/MolDraw2DJS.h @@ -17,7 +17,6 @@ #ifndef MOLDRAW2DJS_H #define MOLDRAW2DJS_H -#include #include #include #include diff --git a/Code/GraphMol/MolDraw2D/MolDraw2DSVG.h b/Code/GraphMol/MolDraw2D/MolDraw2DSVG.h index 5d70aafa7..dcefaea3e 100644 --- a/Code/GraphMol/MolDraw2D/MolDraw2DSVG.h +++ b/Code/GraphMol/MolDraw2D/MolDraw2DSVG.h @@ -16,7 +16,6 @@ #ifndef MOLDRAW2DSVG_H #define MOLDRAW2DSVG_H -#include #include #include diff --git a/Code/GraphMol/MolDraw2D/Qt/Demo/QT4SelectItems.cc b/Code/GraphMol/MolDraw2D/Qt/Demo/QT4SelectItems.cc index 51fc10da3..fa616c47c 100644 --- a/Code/GraphMol/MolDraw2D/Qt/Demo/QT4SelectItems.cc +++ b/Code/GraphMol/MolDraw2D/Qt/Demo/QT4SelectItems.cc @@ -18,8 +18,6 @@ #include "QT4SelectItems.H" -#include - using namespace std; namespace DACLIB { diff --git a/Code/GraphMol/MolDraw2D/Qt/Demo/RDKitSVMainWindow.cc b/Code/GraphMol/MolDraw2D/Qt/Demo/RDKitSVMainWindow.cc index cc7512425..dc99a02ef 100644 --- a/Code/GraphMol/MolDraw2D/Qt/Demo/RDKitSVMainWindow.cc +++ b/Code/GraphMol/MolDraw2D/Qt/Demo/RDKitSVMainWindow.cc @@ -34,7 +34,6 @@ #include #include -#include #include #include @@ -147,7 +146,9 @@ void RDKitSVMainWindow::parse_args(int argc, char **argv) { vector mol_files = s.mol_files(); if (!mol_files.empty()) { - BOOST_FOREACH (string mf, mol_files) { read_mols(mf); } + BOOST_FOREACH (string mf, mol_files) { + read_mols(mf); + } } string smarts_file = s.smarts_file(); @@ -357,7 +358,9 @@ void RDKitSVMainWindow::write_mols(RDKitSVPanel &panel, return; } - BOOST_FOREACH (RDKit::ROMOL_SPTR mol, mols) { mw->write(*mol); } + BOOST_FOREACH (RDKit::ROMOL_SPTR mol, mols) { + mw->write(*mol); + } delete mw; } diff --git a/Code/GraphMol/MolDraw2D/Qt/Demo/RDKitSVSettings.cc b/Code/GraphMol/MolDraw2D/Qt/Demo/RDKitSVSettings.cc index c6b1b2c8a..7cbcd7999 100644 --- a/Code/GraphMol/MolDraw2D/Qt/Demo/RDKitSVSettings.cc +++ b/Code/GraphMol/MolDraw2D/Qt/Demo/RDKitSVSettings.cc @@ -12,8 +12,6 @@ #include #include -#include - using namespace std; namespace po = boost::program_options; diff --git a/Code/GraphMol/MolDraw2D/Qt/Demo/rdkitsv_main.cc b/Code/GraphMol/MolDraw2D/Qt/Demo/rdkitsv_main.cc index 9dc70c1e6..d6fcd4383 100644 --- a/Code/GraphMol/MolDraw2D/Qt/Demo/rdkitsv_main.cc +++ b/Code/GraphMol/MolDraw2D/Qt/Demo/rdkitsv_main.cc @@ -12,8 +12,6 @@ #include -#include - #include using namespace std; diff --git a/Code/GraphMol/MolDraw2D/rxn_test1.cpp b/Code/GraphMol/MolDraw2D/rxn_test1.cpp index 8ea06119c..9a9e09659 100644 --- a/Code/GraphMol/MolDraw2D/rxn_test1.cpp +++ b/Code/GraphMol/MolDraw2D/rxn_test1.cpp @@ -28,7 +28,6 @@ #include #include -#include #include #include #include @@ -59,12 +58,12 @@ static const std::map SVG_HASHES = { }; #else static const std::map SVG_HASHES = { - {"rxn_test1_1.svg", 1119603847U}, {"rxn_test1_2.svg", 1280072916U}, + {"rxn_test1_1.svg", 1119603847U}, {"rxn_test1_2.svg", 1280072916U}, {"rxn_test1_3.svg", 2600700359U}, {"rxn_test1_4.svg", 3286429351U}, {"rxn_test1_5.svg", 2222269077U}, {"rxn_test1_6.svg", 3393541140U}, - {"rxn_test1_7.svg", 2511680934U}, {"rxn_test2_1.svg", 408938601U}, + {"rxn_test1_7.svg", 2511680934U}, {"rxn_test2_1.svg", 408938601U}, {"rxn_test2_2_1.svg", 2721276293U}, {"rxn_test2_2_2.svg", 2972357489U}, - {"rxn_test2_2_3.svg", 223414416U}, {"rxn_test2_2_4.svg", 1685655058U}, + {"rxn_test2_2_3.svg", 223414416U}, {"rxn_test2_2_4.svg", 1685655058U}, {"rxn_test3_1.svg", 3042468072U}, {"rxn_test4_1.svg", 3101203372U}, {"rxn_test4_2.svg", 2942016749U}, }; @@ -81,12 +80,12 @@ static const std::map SVG_HASHES = { // better because the floats are all output to only 1 decimal place so there // is a much smaller chance of different systems producing different files. static const std::map PNG_HASHES = { - {"rxn_test1_1.png", 801892091U}, {"rxn_test1_2.png", 507435337U}, + {"rxn_test1_1.png", 801892091U}, {"rxn_test1_2.png", 507435337U}, {"rxn_test1_3.png", 1590809137U}, {"rxn_test1_4.png", 1766700542U}, {"rxn_test1_5.png", 2552100594U}, {"rxn_test1_6.png", 3791582903U}, - {"rxn_test1_7.png", 1461397406U}, {"rxn_test2_1.png", 3551633840U}, + {"rxn_test1_7.png", 1461397406U}, {"rxn_test2_1.png", 3551633840U}, {"rxn_test2_2_1.png", 1268122583U}, {"rxn_test2_2_2.png", 82821108U}, - {"rxn_test2_2_3.png", 3828365604U}, {"rxn_test2_2_4.png", 1230108677U}, + {"rxn_test2_2_3.png", 3828365604U}, {"rxn_test2_2_4.png", 1230108677U}, {"rxn_test3_1.png", 4189980366U}, {"rxn_test4_1.png", 2745201873U}, {"rxn_test4_2.png", 3094925886U}, }; diff --git a/Code/GraphMol/MolDraw2D/test1.cpp b/Code/GraphMol/MolDraw2D/test1.cpp index 7e9cb2466..17120c3ce 100644 --- a/Code/GraphMol/MolDraw2D/test1.cpp +++ b/Code/GraphMol/MolDraw2D/test1.cpp @@ -30,7 +30,6 @@ #include #include #include -#include #include #include #include diff --git a/Code/GraphMol/MolHash/catch_tests.cpp b/Code/GraphMol/MolHash/catch_tests.cpp index 2ed9add33..15e119869 100644 --- a/Code/GraphMol/MolHash/catch_tests.cpp +++ b/Code/GraphMol/MolHash/catch_tests.cpp @@ -15,7 +15,6 @@ #include #include "MolHash.h" -#include #include using namespace RDKit; diff --git a/Code/GraphMol/MolInteractionFields/MIFDescriptors.cpp b/Code/GraphMol/MolInteractionFields/MIFDescriptors.cpp index 87facaf9d..fe99e1559 100644 --- a/Code/GraphMol/MolInteractionFields/MIFDescriptors.cpp +++ b/Code/GraphMol/MolInteractionFields/MIFDescriptors.cpp @@ -21,7 +21,6 @@ #include #include #include -#include #include #ifndef M_PI diff --git a/Code/GraphMol/MolInteractionFields/testMIF.cpp b/Code/GraphMol/MolInteractionFields/testMIF.cpp index 33da5414d..23571aa90 100644 --- a/Code/GraphMol/MolInteractionFields/testMIF.cpp +++ b/Code/GraphMol/MolInteractionFields/testMIF.cpp @@ -24,7 +24,6 @@ #include #include #include -#include #include using namespace RDGeom; diff --git a/Code/GraphMol/MolInterchange/MolInterchange.h b/Code/GraphMol/MolInterchange/MolInterchange.h index 17b173927..f2d702f0d 100644 --- a/Code/GraphMol/MolInterchange/MolInterchange.h +++ b/Code/GraphMol/MolInterchange/MolInterchange.h @@ -24,7 +24,6 @@ https://github.com/mcs07/CommonChem */ #include -#include #include #include diff --git a/Code/GraphMol/MolPickler.cpp b/Code/GraphMol/MolPickler.cpp index 3d4c254b2..e79307c3a 100644 --- a/Code/GraphMol/MolPickler.cpp +++ b/Code/GraphMol/MolPickler.cpp @@ -21,7 +21,6 @@ #include #include #include -#include #include #include diff --git a/Code/GraphMol/MolPickler.h b/Code/GraphMol/MolPickler.h index c5e5fac7f..e0ad5d063 100644 --- a/Code/GraphMol/MolPickler.h +++ b/Code/GraphMol/MolPickler.h @@ -22,7 +22,6 @@ #include // Std stuff -#include #include #include #include diff --git a/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.cpp b/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.cpp index 0906c3ec5..d3b509e28 100644 --- a/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.cpp +++ b/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.cpp @@ -13,7 +13,6 @@ #include #include #include -#include #include namespace RDKit { diff --git a/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.h b/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.h index 955b927c4..25146061c 100644 --- a/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.h +++ b/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.h @@ -16,7 +16,6 @@ #include #include #include -#include namespace RDKit { class ROMol; diff --git a/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.h b/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.h index 6b7c18b7b..f2906fadf 100644 --- a/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.h +++ b/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.h @@ -15,7 +15,6 @@ #include "AcidBaseCatalogParams.h" #include #include -#include namespace RDKit { class ROMol; diff --git a/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.cpp b/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.cpp index 9b3b595fc..0936c6aaf 100644 --- a/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.cpp +++ b/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.cpp @@ -14,7 +14,6 @@ #include #include #include -#include #include namespace RDKit { diff --git a/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.h b/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.h index f78f2a876..55baefc5e 100644 --- a/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.h +++ b/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.h @@ -16,7 +16,6 @@ #include #include #include -#include namespace RDKit { class ROMol; diff --git a/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.h b/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.h index 99420e979..272084fd5 100644 --- a/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.h +++ b/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.h @@ -14,7 +14,6 @@ #include #include "FragmentCatalogParams.h" #include -#include namespace RDKit { class ROMol; diff --git a/Code/GraphMol/MolStandardize/MolStandardize.cpp b/Code/GraphMol/MolStandardize/MolStandardize.cpp index f4f78ed9f..d98ac6f87 100644 --- a/Code/GraphMol/MolStandardize/MolStandardize.cpp +++ b/Code/GraphMol/MolStandardize/MolStandardize.cpp @@ -13,7 +13,6 @@ #include "Tautomer.h" #include "Fragment.h" #include -#include #include #include #include diff --git a/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.cpp b/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.cpp index 2315a0903..64d803fca 100644 --- a/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.cpp +++ b/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.cpp @@ -13,7 +13,6 @@ #include #include #include -#include #include namespace RDKit { diff --git a/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.h b/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.h index 911cf6eff..c7f658d93 100644 --- a/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.h +++ b/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.h @@ -15,7 +15,6 @@ #include #include #include -#include namespace RDKit { class ROMol; diff --git a/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.h b/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.h index ec48034d6..5e96ed7da 100644 --- a/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.h +++ b/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.h @@ -16,7 +16,6 @@ #include #include #include -#include #include namespace RDKit { diff --git a/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.cpp b/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.cpp index ff75af48a..fc390b426 100644 --- a/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.cpp +++ b/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.cpp @@ -14,7 +14,6 @@ #include #include #include -#include #include namespace RDKit { diff --git a/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.h b/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.h index 5f5aff6ae..30fb63d8e 100644 --- a/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.h +++ b/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.h @@ -17,7 +17,6 @@ #include #include #include -#include namespace RDKit { class ROMol; diff --git a/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.h b/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.h index c33008c29..7afec760f 100644 --- a/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.h +++ b/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.h @@ -15,7 +15,6 @@ #include "TransformCatalogParams.h" #include #include -#include namespace RDKit { class ROMol; diff --git a/Code/GraphMol/MolStandardize/Validate.cpp b/Code/GraphMol/MolStandardize/Validate.cpp index c16f174f9..2cd24cdd7 100644 --- a/Code/GraphMol/MolStandardize/Validate.cpp +++ b/Code/GraphMol/MolStandardize/Validate.cpp @@ -17,7 +17,6 @@ #include #include #include -#include #include #include #include diff --git a/Code/GraphMol/MolStandardize/Validate.h b/Code/GraphMol/MolStandardize/Validate.h index 84f99e1d6..c4e27d391 100644 --- a/Code/GraphMol/MolStandardize/Validate.h +++ b/Code/GraphMol/MolStandardize/Validate.h @@ -21,7 +21,6 @@ #include #include #include -#include #include #include #include diff --git a/Code/GraphMol/MolStandardize/catch_tests.cpp b/Code/GraphMol/MolStandardize/catch_tests.cpp index 8aef0db2c..bed9e2023 100644 --- a/Code/GraphMol/MolStandardize/catch_tests.cpp +++ b/Code/GraphMol/MolStandardize/catch_tests.cpp @@ -21,7 +21,6 @@ #include #include -#include #include using namespace RDKit; diff --git a/Code/GraphMol/MolStandardize/test1.cpp b/Code/GraphMol/MolStandardize/test1.cpp index 3e6597e38..aea1cf6f9 100644 --- a/Code/GraphMol/MolStandardize/test1.cpp +++ b/Code/GraphMol/MolStandardize/test1.cpp @@ -20,8 +20,6 @@ #include #include -#include - using namespace RDKit; void testCleanup() { diff --git a/Code/GraphMol/MolStandardize/test2.cpp b/Code/GraphMol/MolStandardize/test2.cpp index 93466e467..810900042 100644 --- a/Code/GraphMol/MolStandardize/test2.cpp +++ b/Code/GraphMol/MolStandardize/test2.cpp @@ -20,8 +20,6 @@ #include #include -#include - using namespace RDKit; using namespace MolStandardize; diff --git a/Code/GraphMol/MolStandardize/testFragment.cpp b/Code/GraphMol/MolStandardize/testFragment.cpp index e40a2ce73..367d733af 100644 --- a/Code/GraphMol/MolStandardize/testFragment.cpp +++ b/Code/GraphMol/MolStandardize/testFragment.cpp @@ -21,7 +21,6 @@ #include #include -#include #include using namespace RDKit; diff --git a/Code/GraphMol/MolStandardize/testNormalize.cpp b/Code/GraphMol/MolStandardize/testNormalize.cpp index f5416826d..1fba9e0d4 100644 --- a/Code/GraphMol/MolStandardize/testNormalize.cpp +++ b/Code/GraphMol/MolStandardize/testNormalize.cpp @@ -20,7 +20,6 @@ #include #include -#include #include #include diff --git a/Code/GraphMol/MolStandardize/testPCS.cpp b/Code/GraphMol/MolStandardize/testPCS.cpp index c8e2f35d4..dc2454624 100644 --- a/Code/GraphMol/MolStandardize/testPCS.cpp +++ b/Code/GraphMol/MolStandardize/testPCS.cpp @@ -10,7 +10,6 @@ #include #include #include -#include #include #include #include diff --git a/Code/GraphMol/MolStandardize/testValidate.cpp b/Code/GraphMol/MolStandardize/testValidate.cpp index fb16fdd3f..5c3d592e9 100644 --- a/Code/GraphMol/MolStandardize/testValidate.cpp +++ b/Code/GraphMol/MolStandardize/testValidate.cpp @@ -16,8 +16,6 @@ #include #include -#include - using namespace RDKit; using namespace std; using namespace MolStandardize; diff --git a/Code/GraphMol/MolTransforms/test1.cpp b/Code/GraphMol/MolTransforms/test1.cpp index b1bfd5414..2364f4608 100644 --- a/Code/GraphMol/MolTransforms/test1.cpp +++ b/Code/GraphMol/MolTransforms/test1.cpp @@ -18,7 +18,6 @@ #include #include #include -#include #include using namespace RDKit; diff --git a/Code/GraphMol/MonomerInfo.cpp b/Code/GraphMol/MonomerInfo.cpp index 817d5b0f6..bacc60d89 100644 --- a/Code/GraphMol/MonomerInfo.cpp +++ b/Code/GraphMol/MonomerInfo.cpp @@ -7,7 +7,7 @@ // which is included in the file license.txt, found at the root // of the RDKit source tree. // -#include +#include #include "MonomerInfo.h" using namespace RDKit; diff --git a/Code/GraphMol/PartialCharges/test1.cpp b/Code/GraphMol/PartialCharges/test1.cpp index c7ae676b1..4628b3fb1 100644 --- a/Code/GraphMol/PartialCharges/test1.cpp +++ b/Code/GraphMol/PartialCharges/test1.cpp @@ -11,7 +11,6 @@ // std bits #include -#include // RD bits #include diff --git a/Code/GraphMol/RGroupDecomposition/GaExample.cpp b/Code/GraphMol/RGroupDecomposition/GaExample.cpp index 683de747e..47b367e5f 100644 --- a/Code/GraphMol/RGroupDecomposition/GaExample.cpp +++ b/Code/GraphMol/RGroupDecomposition/GaExample.cpp @@ -9,7 +9,6 @@ // #include -#include #include #include #include diff --git a/Code/GraphMol/RGroupDecomposition/testRGroupDecomp.cpp b/Code/GraphMol/RGroupDecomposition/testRGroupDecomp.cpp index 3f6bc6c45..2dab6cb39 100644 --- a/Code/GraphMol/RGroupDecomposition/testRGroupDecomp.cpp +++ b/Code/GraphMol/RGroupDecomposition/testRGroupDecomp.cpp @@ -33,7 +33,6 @@ #include #include #include -#include #include #include #include diff --git a/Code/GraphMol/ROMol.cpp b/Code/GraphMol/ROMol.cpp index 30752e7b8..a8d63ec78 100644 --- a/Code/GraphMol/ROMol.cpp +++ b/Code/GraphMol/ROMol.cpp @@ -8,8 +8,6 @@ // of the RDKit source tree. // -#include - // our stuff #include #include diff --git a/Code/GraphMol/RascalMCES/PartitionSet.cpp b/Code/GraphMol/RascalMCES/PartitionSet.cpp index 644f8f6ef..c311b2e6c 100644 --- a/Code/GraphMol/RascalMCES/PartitionSet.cpp +++ b/Code/GraphMol/RascalMCES/PartitionSet.cpp @@ -9,7 +9,6 @@ // #include -#include #include #include #include diff --git a/Code/GraphMol/RascalMCES/RascalMCES.cpp b/Code/GraphMol/RascalMCES/RascalMCES.cpp index 3b0560454..bb8f3459d 100644 --- a/Code/GraphMol/RascalMCES/RascalMCES.cpp +++ b/Code/GraphMol/RascalMCES/RascalMCES.cpp @@ -17,7 +17,6 @@ #include #include -#include #include #include #include diff --git a/Code/GraphMol/RascalMCES/lap_a_la_scipy.cpp b/Code/GraphMol/RascalMCES/lap_a_la_scipy.cpp index 0c9986cf5..b0db6de57 100644 --- a/Code/GraphMol/RascalMCES/lap_a_la_scipy.cpp +++ b/Code/GraphMol/RascalMCES/lap_a_la_scipy.cpp @@ -49,7 +49,6 @@ Author: PM Larsen */ #include -#include #include #include #include diff --git a/Code/GraphMol/SLNParse/sln.tab.cpp.cmake b/Code/GraphMol/SLNParse/sln.tab.cpp.cmake index 87caa6eba..8905db672 100644 --- a/Code/GraphMol/SLNParse/sln.tab.cpp.cmake +++ b/Code/GraphMol/SLNParse/sln.tab.cpp.cmake @@ -105,7 +105,6 @@ #include #include -#include #include #include diff --git a/Code/GraphMol/SLNParse/sln.yy b/Code/GraphMol/SLNParse/sln.yy index ff3a44bf1..39bd8fdd9 100644 --- a/Code/GraphMol/SLNParse/sln.yy +++ b/Code/GraphMol/SLNParse/sln.yy @@ -37,7 +37,6 @@ #include #include -#include #include #include diff --git a/Code/GraphMol/SLNParse/test.cpp b/Code/GraphMol/SLNParse/test.cpp index fad9ad999..927dba767 100644 --- a/Code/GraphMol/SLNParse/test.cpp +++ b/Code/GraphMol/SLNParse/test.cpp @@ -33,7 +33,6 @@ // Created by Greg Landrum September, 2006 // #include -#include #include #include #include @@ -1264,7 +1263,6 @@ void test10() { BOOST_LOG(rdInfoLog) << "\tdone" << std::endl; } - void test12() { RDKit::RWMol *patt, *mol; std::vector mV; @@ -1883,9 +1881,9 @@ int main(int argc, char *argv[]) { (void)argv; RDLog::InitLogs(); -// FIX: need a test for handling Hs in the SLN itself. This should be done for -// both normal and query SLNs and must be done after the SLN parser handles -// that case (errr, duh) + // FIX: need a test for handling Hs in the SLN itself. This should be done for + // both normal and query SLNs and must be done after the SLN parser handles + // that case (errr, duh) test1(); test2(); test3(); diff --git a/Code/GraphMol/ScaffoldNetwork/ScaffoldNetwork.h b/Code/GraphMol/ScaffoldNetwork/ScaffoldNetwork.h index 226ac2c9e..57845fd40 100644 --- a/Code/GraphMol/ScaffoldNetwork/ScaffoldNetwork.h +++ b/Code/GraphMol/ScaffoldNetwork/ScaffoldNetwork.h @@ -16,7 +16,6 @@ #include #include #include -#include #ifdef RDK_USE_BOOST_SERIALIZATION #include diff --git a/Code/GraphMol/SmilesParse/CXSmilesOps.cpp b/Code/GraphMol/SmilesParse/CXSmilesOps.cpp index cf7a5af8b..5359680ab 100644 --- a/Code/GraphMol/SmilesParse/CXSmilesOps.cpp +++ b/Code/GraphMol/SmilesParse/CXSmilesOps.cpp @@ -18,7 +18,6 @@ #include #include -#include #include #include "SmilesWrite.h" #include "SmilesParse.h" diff --git a/Code/GraphMol/SmilesParse/cxsmiles_test.cpp b/Code/GraphMol/SmilesParse/cxsmiles_test.cpp index e605c1f86..d11fce7ab 100644 --- a/Code/GraphMol/SmilesParse/cxsmiles_test.cpp +++ b/Code/GraphMol/SmilesParse/cxsmiles_test.cpp @@ -24,7 +24,6 @@ #include "SmartsWrite.h" #include #include -#include constexpr bool GenerateExpectedFiles = false; diff --git a/Code/GraphMol/SmilesParse/nontetrahedral_tests.cpp b/Code/GraphMol/SmilesParse/nontetrahedral_tests.cpp index 546291421..ab8e87377 100644 --- a/Code/GraphMol/SmilesParse/nontetrahedral_tests.cpp +++ b/Code/GraphMol/SmilesParse/nontetrahedral_tests.cpp @@ -10,7 +10,6 @@ #include -#include #include #include diff --git a/Code/GraphMol/SmilesParse/smarts.tab.cpp.cmake b/Code/GraphMol/SmilesParse/smarts.tab.cpp.cmake index 97979f558..87a8ade00 100644 --- a/Code/GraphMol/SmilesParse/smarts.tab.cpp.cmake +++ b/Code/GraphMol/SmilesParse/smarts.tab.cpp.cmake @@ -80,7 +80,6 @@ // @@ All Rights Reserved @@ // #include -#include #include #include #include diff --git a/Code/GraphMol/SmilesParse/smarts.yy b/Code/GraphMol/SmilesParse/smarts.yy index 5e0d70c6e..e883674fc 100644 --- a/Code/GraphMol/SmilesParse/smarts.yy +++ b/Code/GraphMol/SmilesParse/smarts.yy @@ -6,7 +6,6 @@ // @@ All Rights Reserved @@ // #include -#include #include #include #include diff --git a/Code/GraphMol/SmilesParse/smatest.cpp b/Code/GraphMol/SmilesParse/smatest.cpp index 54c409886..06c9383d6 100644 --- a/Code/GraphMol/SmilesParse/smatest.cpp +++ b/Code/GraphMol/SmilesParse/smatest.cpp @@ -8,7 +8,6 @@ // of the RDKit source tree. // #include -#include #include #include "SmilesParse.h" @@ -59,8 +58,7 @@ void testPass() { "[D{1-3}]", // cactvs range queries "[D{-3}]", "[D{1-}]", "[z{1-3}]", "[Z{1-3}]", "[2H,13C]", // github #1719 - "[+{0-3}]", - "[-{0-3}]", "[-{0-3},C]", + "[+{0-3}]", "[-{0-3}]", "[-{0-3},C]", "[-{0-3},D{1-3}]", // github #2709 "C%(1000)CCC%(1000)", // github #2909 "C%(1000)CC(C%(1000))", // github #2909 @@ -474,7 +472,7 @@ void testProblems() { // nested recursion (yick!) _checkNoMatches("[O]-[!$(*=O)]", "CC(=O)O"); -// BOOST_LOG(rdInfoLog) << "-*-*-*-*-*-*-*-*-" << std::endl; + // BOOST_LOG(rdInfoLog) << "-*-*-*-*-*-*-*-*-" << std::endl; _checkNoMatches("[$([O]-[!$(*=O)])]", "CC(=O)O"); // ISSUE 78 @@ -1167,13 +1165,14 @@ void testSmartsStereochem() { _checkMatches("C/C=C/C", "C/C=C/C", 1, 4); _checkMatches("C/C=C/C", "C\\C=C\\C", 1, 4); _checkMatches("C/C=C/C", "C/C=C\\C", 1, 4); - + // directional bonds are set to be a direction \ / // and a query - SingleOrAromatic, make sure that this // is their current representation auto m1 = "C/C=C\\C"_smarts; TEST_ASSERT(m1->getBondWithIdx(0)->hasQuery()); - TEST_ASSERT(m1->getBondWithIdx(0)->getQuery()->getDescription() == "SingleOrAromaticBond"); + TEST_ASSERT(m1->getBondWithIdx(0)->getQuery()->getDescription() == + "SingleOrAromaticBond"); auto m2 = "O=c1/c(=C/c2ccccc2)sc2n1-N-C-N-N=2"_smarts; TEST_ASSERT(MolToSmarts(*m2) == "O=c1/c(=C/c2ccccc2)sc2n1-N-C-N-N=2"); diff --git a/Code/GraphMol/SmilesParse/smiles.tab.cpp.cmake b/Code/GraphMol/SmilesParse/smiles.tab.cpp.cmake index 8522734c2..8e98b9ad0 100644 --- a/Code/GraphMol/SmilesParse/smiles.tab.cpp.cmake +++ b/Code/GraphMol/SmilesParse/smiles.tab.cpp.cmake @@ -82,7 +82,6 @@ // #include -#include #include #include #include diff --git a/Code/GraphMol/SmilesParse/smiles.yy b/Code/GraphMol/SmilesParse/smiles.yy index f4afded9b..6090197ac 100644 --- a/Code/GraphMol/SmilesParse/smiles.yy +++ b/Code/GraphMol/SmilesParse/smiles.yy @@ -8,7 +8,6 @@ // #include -#include #include #include #include diff --git a/Code/GraphMol/SmilesParse/test.cpp b/Code/GraphMol/SmilesParse/test.cpp index 9c6a6983d..82925e5d6 100644 --- a/Code/GraphMol/SmilesParse/test.cpp +++ b/Code/GraphMol/SmilesParse/test.cpp @@ -8,7 +8,6 @@ // of the RDKit source tree. // #include -#include #include #include #include "SmilesParse.h" @@ -129,7 +128,7 @@ void testFail() { "[Fe@AL3]", "C", // "[Fe@TB21]", "C", // "[Fe@OH31]", "C", // - "baz", "C", // + "baz", "C", // "EOS"}; // turn off the error log temporarily: @@ -4360,34 +4359,37 @@ void testParserErrorMessage() { "c%(100000)ccccc%(100000)", "COc(c1)cccc1C#", "C)", - }; - for (const auto& smi : smis) { - // Test SMILES parsing - { - std::stringstream ss; - rdErrorLog->SetTee(ss); + }; + for (const auto &smi : smis) { + // Test SMILES parsing + { + std::stringstream ss; + rdErrorLog->SetTee(ss); - auto mol = v2::SmilesParse::MolFromSmiles(smi); - CHECK_INVARIANT(!mol, smi); + auto mol = v2::SmilesParse::MolFromSmiles(smi); + CHECK_INVARIANT(!mol, smi); - rdErrorLog->ClearTee(); - auto error_msg = ss.str(); - CHECK_INVARIANT(error_msg.find("check for mistakes around position") != std::string::npos, smi) - } + rdErrorLog->ClearTee(); + auto error_msg = ss.str(); + CHECK_INVARIANT(error_msg.find("check for mistakes around position") != + std::string::npos, + smi) + } - // Test SMARTS parsing - { - std::stringstream ss; - rdErrorLog->SetTee(ss); + // Test SMARTS parsing + { + std::stringstream ss; + rdErrorLog->SetTee(ss); - auto mol = v2::SmilesParse::MolFromSmarts(smi); - CHECK_INVARIANT(!mol, smi); - - rdErrorLog->ClearTee(); - auto error_msg = ss.str(); - CHECK_INVARIANT(error_msg.find("check for mistakes around position") != std::string::npos, smi) - } + auto mol = v2::SmilesParse::MolFromSmarts(smi); + CHECK_INVARIANT(!mol, smi); + rdErrorLog->ClearTee(); + auto error_msg = ss.str(); + CHECK_INVARIANT(error_msg.find("check for mistakes around position") != + std::string::npos, + smi) + } } } diff --git a/Code/GraphMol/SmilesParse/test2.cpp b/Code/GraphMol/SmilesParse/test2.cpp index 53423ea5f..6b1248cb5 100644 --- a/Code/GraphMol/SmilesParse/test2.cpp +++ b/Code/GraphMol/SmilesParse/test2.cpp @@ -8,7 +8,6 @@ // of the RDKit source tree. // #include -#include #include #include #include "SmilesParse.h" diff --git a/Code/GraphMol/StereoGroup.h b/Code/GraphMol/StereoGroup.h index 8f85609b3..2cdac09a2 100644 --- a/Code/GraphMol/StereoGroup.h +++ b/Code/GraphMol/StereoGroup.h @@ -18,7 +18,6 @@ #ifndef RD_StereoGroup_092018 #define RD_StereoGroup_092018 -#include #include namespace RDKit { diff --git a/Code/GraphMol/StructChecker/StructCheckerOptions.cpp b/Code/GraphMol/StructChecker/StructCheckerOptions.cpp index d350b0ae4..8be5258cb 100644 --- a/Code/GraphMol/StructChecker/StructCheckerOptions.cpp +++ b/Code/GraphMol/StructChecker/StructCheckerOptions.cpp @@ -10,7 +10,6 @@ #include #include #include -#include #include #include #include diff --git a/Code/GraphMol/Subgraphs/SubgraphUtils.cpp b/Code/GraphMol/Subgraphs/SubgraphUtils.cpp index 2cc8b3bbe..c5391e6ee 100644 --- a/Code/GraphMol/Subgraphs/SubgraphUtils.cpp +++ b/Code/GraphMol/Subgraphs/SubgraphUtils.cpp @@ -14,7 +14,6 @@ #include #include #include -#include #include #include #include diff --git a/Code/GraphMol/Subgraphs/Subgraphs.cpp b/Code/GraphMol/Subgraphs/Subgraphs.cpp index 5a835191f..d94b13db3 100644 --- a/Code/GraphMol/Subgraphs/Subgraphs.cpp +++ b/Code/GraphMol/Subgraphs/Subgraphs.cpp @@ -14,7 +14,6 @@ #include #include -#include #include #include #include diff --git a/Code/GraphMol/Subgraphs/catch_tests.cpp b/Code/GraphMol/Subgraphs/catch_tests.cpp index 67bef7d9f..1c89d9f77 100644 --- a/Code/GraphMol/Subgraphs/catch_tests.cpp +++ b/Code/GraphMol/Subgraphs/catch_tests.cpp @@ -14,7 +14,6 @@ #include #include -#include #include using namespace RDKit; diff --git a/Code/GraphMol/Subgraphs/test1.cpp b/Code/GraphMol/Subgraphs/test1.cpp index 5ffba856f..eac82c2be 100644 --- a/Code/GraphMol/Subgraphs/test1.cpp +++ b/Code/GraphMol/Subgraphs/test1.cpp @@ -13,7 +13,6 @@ #include #include -#include using namespace std; using namespace RDKit; diff --git a/Code/GraphMol/Subgraphs/test2.cpp b/Code/GraphMol/Subgraphs/test2.cpp index fb6e8bfc0..d2fc26551 100644 --- a/Code/GraphMol/Subgraphs/test2.cpp +++ b/Code/GraphMol/Subgraphs/test2.cpp @@ -15,7 +15,6 @@ #include #include -#include #include using namespace std; diff --git a/Code/GraphMol/SubstanceGroup.h b/Code/GraphMol/SubstanceGroup.h index 9f50f443c..c4fbf45a0 100644 --- a/Code/GraphMol/SubstanceGroup.h +++ b/Code/GraphMol/SubstanceGroup.h @@ -17,7 +17,6 @@ #ifndef _RD_SGROUP_H #define _RD_SGROUP_H -#include #include #include diff --git a/Code/GraphMol/Substruct/bench.cpp b/Code/GraphMol/Substruct/bench.cpp index d19385321..e07e30e78 100644 --- a/Code/GraphMol/Substruct/bench.cpp +++ b/Code/GraphMol/Substruct/bench.cpp @@ -12,9 +12,6 @@ #pragma warning(disable : 4788) // warning: long & complicated stl warning #endif -// std bits -#include - // RD bits #include #include diff --git a/Code/GraphMol/Substruct/cmd_match.cpp b/Code/GraphMol/Substruct/cmd_match.cpp index 83ef872c5..14e504d19 100644 --- a/Code/GraphMol/Substruct/cmd_match.cpp +++ b/Code/GraphMol/Substruct/cmd_match.cpp @@ -8,9 +8,6 @@ // of the RDKit source tree. // -// std bits -#include - // RD bits #include #include diff --git a/Code/GraphMol/Substruct/test1.cpp b/Code/GraphMol/Substruct/test1.cpp index 660a43191..59d45ac49 100644 --- a/Code/GraphMol/Substruct/test1.cpp +++ b/Code/GraphMol/Substruct/test1.cpp @@ -11,7 +11,6 @@ // std bits #include -#include // RD bits #include diff --git a/Code/GraphMol/SubstructLibrary/substructLibraryTest.cpp b/Code/GraphMol/SubstructLibrary/substructLibraryTest.cpp index c6dcb019a..863493d41 100644 --- a/Code/GraphMol/SubstructLibrary/substructLibraryTest.cpp +++ b/Code/GraphMol/SubstructLibrary/substructLibraryTest.cpp @@ -31,7 +31,6 @@ // std bits #include -#include // RD bits #include diff --git a/Code/GraphMol/SynthonSpaceSearch/MemoryMappedFileReader.cpp b/Code/GraphMol/SynthonSpaceSearch/MemoryMappedFileReader.cpp index 3c32f31fc..e14fb5fe5 100644 --- a/Code/GraphMol/SynthonSpaceSearch/MemoryMappedFileReader.cpp +++ b/Code/GraphMol/SynthonSpaceSearch/MemoryMappedFileReader.cpp @@ -11,7 +11,6 @@ #include #include -#include #include #include @@ -89,7 +88,7 @@ MemoryMappedFileReader::MemoryMappedFileReader(const std::string &filePath) { throw(std::runtime_error("Error reading file " + filePath + ".")); } - close(fd); // File descriptor is no longer needed + close(fd); // File descriptor is no longer needed #endif } @@ -111,7 +110,7 @@ MemoryMappedFileReader::~MemoryMappedFileReader() { } MemoryMappedFileReader &MemoryMappedFileReader::operator=( - MemoryMappedFileReader &&other) { + MemoryMappedFileReader &&other) { if (this != &other) { #ifdef _WIN32 // Windows-specific unmapping @@ -127,4 +126,4 @@ MemoryMappedFileReader &MemoryMappedFileReader::operator=( } return *this; } -}; // namespace RDKit::SynthonSpaceSearch::details +}; // namespace RDKit::SynthonSpaceSearch::details diff --git a/Code/GraphMol/SynthonSpaceSearch/SynthonSpace.cpp b/Code/GraphMol/SynthonSpaceSearch/SynthonSpace.cpp index 69a6e7c04..d24602b14 100644 --- a/Code/GraphMol/SynthonSpaceSearch/SynthonSpace.cpp +++ b/Code/GraphMol/SynthonSpaceSearch/SynthonSpace.cpp @@ -10,7 +10,6 @@ #include #include -#include #include #include #include diff --git a/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceSearch_details.cpp b/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceSearch_details.cpp index 0dedbaf64..5dfe27451 100644 --- a/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceSearch_details.cpp +++ b/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceSearch_details.cpp @@ -10,7 +10,6 @@ #include #include -#include #include #include #include diff --git a/Code/GraphMol/Wrap/seqs.hpp b/Code/GraphMol/Wrap/seqs.hpp index 5efd37be8..90f79509c 100644 --- a/Code/GraphMol/Wrap/seqs.hpp +++ b/Code/GraphMol/Wrap/seqs.hpp @@ -8,7 +8,6 @@ #include #include -#include #include namespace python = boost::python; diff --git a/Code/GraphMol/bulktest.cpp b/Code/GraphMol/bulktest.cpp index 14a86f35b..d8ff6b578 100644 --- a/Code/GraphMol/bulktest.cpp +++ b/Code/GraphMol/bulktest.cpp @@ -15,7 +15,6 @@ #include #include -#include #include using namespace RDKit; diff --git a/Code/GraphMol/cptest.cpp b/Code/GraphMol/cptest.cpp index e4c297559..e64fbdb1b 100644 --- a/Code/GraphMol/cptest.cpp +++ b/Code/GraphMol/cptest.cpp @@ -12,7 +12,6 @@ #include #include -#include using namespace std; using namespace RDKit; diff --git a/Code/GraphMol/hanoitest.cpp b/Code/GraphMol/hanoitest.cpp index b636b1634..9ef909f80 100644 --- a/Code/GraphMol/hanoitest.cpp +++ b/Code/GraphMol/hanoitest.cpp @@ -18,7 +18,6 @@ #include #include -#include #include #include #include diff --git a/Code/GraphMol/itertest.cpp b/Code/GraphMol/itertest.cpp index 6ad731c39..6f6615916 100644 --- a/Code/GraphMol/itertest.cpp +++ b/Code/GraphMol/itertest.cpp @@ -14,7 +14,6 @@ #include #include -#include #include #include diff --git a/Code/GraphMol/memtest1.cpp b/Code/GraphMol/memtest1.cpp index 1f81db30a..c964b1776 100644 --- a/Code/GraphMol/memtest1.cpp +++ b/Code/GraphMol/memtest1.cpp @@ -18,7 +18,6 @@ #include #include -#include using namespace std; using namespace RDKit; diff --git a/Code/GraphMol/molopstest.cpp b/Code/GraphMol/molopstest.cpp index 11339b8d0..3def5d561 100644 --- a/Code/GraphMol/molopstest.cpp +++ b/Code/GraphMol/molopstest.cpp @@ -9,7 +9,6 @@ // #pragma GCC diagnostic ignored "-Wdeprecated-declarations" #include -#include #include #include #include diff --git a/Code/GraphMol/new_canon.cpp b/Code/GraphMol/new_canon.cpp index 70e8c3ebd..319b69997 100644 --- a/Code/GraphMol/new_canon.cpp +++ b/Code/GraphMol/new_canon.cpp @@ -15,7 +15,6 @@ #include #include #include -#include #include // #define VERBOSE_CANON 1 diff --git a/Code/GraphMol/new_canon.h b/Code/GraphMol/new_canon.h index 9c56613eb..4ec52f2e1 100644 --- a/Code/GraphMol/new_canon.h +++ b/Code/GraphMol/new_canon.h @@ -19,7 +19,6 @@ #include #include #include -#include #include #include #include diff --git a/Code/GraphMol/querytest.cpp b/Code/GraphMol/querytest.cpp index 60956f584..7dc3b05c1 100644 --- a/Code/GraphMol/querytest.cpp +++ b/Code/GraphMol/querytest.cpp @@ -14,7 +14,6 @@ #include #include #include -#include using namespace RDKit; using namespace std; diff --git a/Code/GraphMol/resMolSupplierTest.cpp b/Code/GraphMol/resMolSupplierTest.cpp index 6d94e744a..a35ce7dd5 100644 --- a/Code/GraphMol/resMolSupplierTest.cpp +++ b/Code/GraphMol/resMolSupplierTest.cpp @@ -1,5 +1,4 @@ #include -#include #include #include #include diff --git a/Code/GraphMol/sanitTest.cpp b/Code/GraphMol/sanitTest.cpp index 27572b725..57dbf0252 100644 --- a/Code/GraphMol/sanitTest.cpp +++ b/Code/GraphMol/sanitTest.cpp @@ -16,7 +16,6 @@ #include #include -#include #include #include #include diff --git a/Code/GraphMol/test-valgrind.cpp b/Code/GraphMol/test-valgrind.cpp index fb224299c..f7216a408 100644 --- a/Code/GraphMol/test-valgrind.cpp +++ b/Code/GraphMol/test-valgrind.cpp @@ -19,7 +19,6 @@ #include #include #include -#include using namespace std; using namespace RDKit; diff --git a/Code/GraphMol/test1.cpp b/Code/GraphMol/test1.cpp index a027337fb..2e692fd63 100644 --- a/Code/GraphMol/test1.cpp +++ b/Code/GraphMol/test1.cpp @@ -22,7 +22,6 @@ #include #include #include -#include #include #include diff --git a/Code/GraphMol/testChirality.cpp b/Code/GraphMol/testChirality.cpp index 34b344e84..18dbe6db7 100644 --- a/Code/GraphMol/testChirality.cpp +++ b/Code/GraphMol/testChirality.cpp @@ -25,8 +25,6 @@ #include #include -#include - using namespace RDKit; using namespace std; diff --git a/Code/GraphMol/testMolBundle.cpp b/Code/GraphMol/testMolBundle.cpp index 0fbb8f8c3..dc97724fb 100644 --- a/Code/GraphMol/testMolBundle.cpp +++ b/Code/GraphMol/testMolBundle.cpp @@ -8,7 +8,6 @@ // of the RDKit source tree. // #include -#include #include #include #include diff --git a/Code/GraphMol/testPickler.cpp b/Code/GraphMol/testPickler.cpp index bc3a2ec8f..f56fa99b6 100644 --- a/Code/GraphMol/testPickler.cpp +++ b/Code/GraphMol/testPickler.cpp @@ -33,7 +33,6 @@ #include #include -#include #include #include diff --git a/Code/GraphMol/testPicklerGlobalSettings.cpp b/Code/GraphMol/testPicklerGlobalSettings.cpp index 47343895c..7f6f2e24d 100644 --- a/Code/GraphMol/testPicklerGlobalSettings.cpp +++ b/Code/GraphMol/testPicklerGlobalSettings.cpp @@ -46,7 +46,6 @@ #include #include -#include #include #include diff --git a/Code/ML/InfoTheory/InfoBitRanker.cpp b/Code/ML/InfoTheory/InfoBitRanker.cpp index d538d8e82..3cf1bc86d 100644 --- a/Code/ML/InfoTheory/InfoBitRanker.cpp +++ b/Code/ML/InfoTheory/InfoBitRanker.cpp @@ -11,7 +11,6 @@ #include "InfoBitRanker.h" #include "InfoGainFuncs.h" #include -#include #include #include #include diff --git a/Code/ML/InfoTheory/InfoBitRanker.h b/Code/ML/InfoTheory/InfoBitRanker.h index 18dec031f..d0ec9f86a 100644 --- a/Code/ML/InfoTheory/InfoBitRanker.h +++ b/Code/ML/InfoTheory/InfoBitRanker.h @@ -14,7 +14,6 @@ #include #include -#include /*! \brief Class used to rank bits based on a specified measure of information * diff --git a/Code/MinimalLib/cffiwrapper.cpp b/Code/MinimalLib/cffiwrapper.cpp index 13550de70..62c601587 100644 --- a/Code/MinimalLib/cffiwrapper.cpp +++ b/Code/MinimalLib/cffiwrapper.cpp @@ -10,7 +10,6 @@ #pragma GCC diagnostic ignored "-Wdeprecated-declarations" #include #include -#include #include #include diff --git a/Code/MinimalLib/minilib.cpp b/Code/MinimalLib/minilib.cpp index 96369a9cb..eee29b742 100644 --- a/Code/MinimalLib/minilib.cpp +++ b/Code/MinimalLib/minilib.cpp @@ -9,7 +9,6 @@ // of the RDKit source tree. // #include -#include #include "minilib.h" #include "common.h" diff --git a/Code/MinimalLib/testMinilib.cpp b/Code/MinimalLib/testMinilib.cpp index a381788a2..a1acbbaff 100644 --- a/Code/MinimalLib/testMinilib.cpp +++ b/Code/MinimalLib/testMinilib.cpp @@ -10,7 +10,6 @@ // #include -#include #include #include diff --git a/Code/Numerics/Matrix.h b/Code/Numerics/Matrix.h index 0a4bc55ab..603ec5287 100644 --- a/Code/Numerics/Matrix.h +++ b/Code/Numerics/Matrix.h @@ -13,7 +13,6 @@ #include #include "Vector.h" -#include #include #include #include diff --git a/Code/Numerics/Optimizer/testOptimizer.cpp b/Code/Numerics/Optimizer/testOptimizer.cpp index d39197787..8233e0a28 100644 --- a/Code/Numerics/Optimizer/testOptimizer.cpp +++ b/Code/Numerics/Optimizer/testOptimizer.cpp @@ -8,7 +8,6 @@ // of the RDKit source tree. // #include -#include #include #include #include diff --git a/Code/Numerics/Vector.h b/Code/Numerics/Vector.h index 7fb26e6c1..5d90a8d7c 100644 --- a/Code/Numerics/Vector.h +++ b/Code/Numerics/Vector.h @@ -14,7 +14,6 @@ #include #include #include -#include #include #include #include diff --git a/Code/Numerics/testConrec.cpp b/Code/Numerics/testConrec.cpp index 8eebaf85b..282b34f69 100644 --- a/Code/Numerics/testConrec.cpp +++ b/Code/Numerics/testConrec.cpp @@ -10,7 +10,6 @@ #include #include -#include #include #include "Conrec.h" #include diff --git a/Code/Numerics/testMatrices.cpp b/Code/Numerics/testMatrices.cpp index d72ba59e6..9e10d45a6 100644 --- a/Code/Numerics/testMatrices.cpp +++ b/Code/Numerics/testMatrices.cpp @@ -11,7 +11,6 @@ #include "Matrix.h" #include "SquareMatrix.h" #include "SymmMatrix.h" -#include #include #include #include diff --git a/Code/Query/test.cpp b/Code/Query/test.cpp index e4bc0ff2c..83adaffe9 100644 --- a/Code/Query/test.cpp +++ b/Code/Query/test.cpp @@ -10,7 +10,6 @@ #include #include "QueryObjects.h" -#include #include #include diff --git a/Code/RDBoost/Wrap.cpp b/Code/RDBoost/Wrap.cpp index cb2e61580..04efb9624 100644 --- a/Code/RDBoost/Wrap.cpp +++ b/Code/RDBoost/Wrap.cpp @@ -16,7 +16,6 @@ #include "pyint_api.h" #include #include -#include // A helper function for dealing with errors. Throw a Python IndexError void throw_index_error(int key) { diff --git a/Code/RDBoost/Wrap.h b/Code/RDBoost/Wrap.h index d7e1dd4ff..b77913eb7 100644 --- a/Code/RDBoost/Wrap.h +++ b/Code/RDBoost/Wrap.h @@ -30,7 +30,6 @@ #include #include -#include #include namespace python = boost::python; @@ -58,7 +57,9 @@ RDKIT_RDBOOST_EXPORT void translate_key_error(KeyErrorException const &e); \throws AttributeError if the attribute does not exist \throws Python error if assignment fails */ -RDKIT_RDBOOST_EXPORT void safeSetattr(python::object self, std::string const &name, python::object const &value); +RDKIT_RDBOOST_EXPORT void safeSetattr(python::object self, + std::string const &name, + python::object const &value); #ifdef INVARIANT_EXCEPTION_METHOD RDKIT_RDBOOST_EXPORT void throw_runtime_error( diff --git a/Code/RDBoost/Wrap/RDBase.cpp b/Code/RDBoost/Wrap/RDBase.cpp index 72132d49d..723ce3eea 100644 --- a/Code/RDBoost/Wrap/RDBase.cpp +++ b/Code/RDBoost/Wrap/RDBase.cpp @@ -8,7 +8,6 @@ // of the RDKit source tree. // #include -#include #include #include #include diff --git a/Code/RDBoost/python_streambuf.h b/Code/RDBoost/python_streambuf.h index d461c7c58..2d0f62e1c 100644 --- a/Code/RDBoost/python_streambuf.h +++ b/Code/RDBoost/python_streambuf.h @@ -28,7 +28,6 @@ #include #include -#include namespace boost_adaptbx { namespace python { diff --git a/Code/RDGeneral/Invariant.cpp b/Code/RDGeneral/Invariant.cpp index dc2e60c36..5cb61dba7 100644 --- a/Code/RDGeneral/Invariant.cpp +++ b/Code/RDGeneral/Invariant.cpp @@ -12,7 +12,6 @@ #include "Invariant.h" #include -#include #include #include "versions.h" diff --git a/Code/RDGeneral/Invariant.h b/Code/RDGeneral/Invariant.h index da140cdf9..060b541df 100644 --- a/Code/RDGeneral/Invariant.h +++ b/Code/RDGeneral/Invariant.h @@ -15,7 +15,6 @@ #include #include -#include #include #include "BoostStartInclude.h" diff --git a/Code/RDGeneral/JSONHelpers.h b/Code/RDGeneral/JSONHelpers.h index c04443270..e2bbfde59 100644 --- a/Code/RDGeneral/JSONHelpers.h +++ b/Code/RDGeneral/JSONHelpers.h @@ -1,7 +1,6 @@ #include #include #include -#include #include // Convert a JSON object with boolean keys to a bitwise enum flag set. diff --git a/Code/RDGeneral/RDAny.h b/Code/RDGeneral/RDAny.h index 569aecddf..6f24f345e 100644 --- a/Code/RDGeneral/RDAny.h +++ b/Code/RDGeneral/RDAny.h @@ -41,7 +41,6 @@ #include "RDValue.h" #include #include -#include #include namespace RDKit { diff --git a/Code/RDGeneral/RDLog.h b/Code/RDGeneral/RDLog.h index b9e4e9051..cc569c027 100644 --- a/Code/RDGeneral/RDLog.h +++ b/Code/RDGeneral/RDLog.h @@ -17,7 +17,6 @@ #include #include #include "BoostEndInclude.h" -#include #include #include #include diff --git a/Code/RDGeneral/RDValue-doublemagic.h b/Code/RDGeneral/RDValue-doublemagic.h index 7bde8d1ec..ef6495863 100644 --- a/Code/RDGeneral/RDValue-doublemagic.h +++ b/Code/RDGeneral/RDValue-doublemagic.h @@ -36,7 +36,6 @@ #include #include #include "Invariant.h" -#include #include #include #include diff --git a/Code/RDGeneral/RDValue-taggedunion.h b/Code/RDGeneral/RDValue-taggedunion.h index d6b216b0e..1180e0ba7 100644 --- a/Code/RDGeneral/RDValue-taggedunion.h +++ b/Code/RDGeneral/RDValue-taggedunion.h @@ -34,7 +34,6 @@ #include #include "Invariant.h" -#include #include #include #include diff --git a/Code/RDGeneral/StreamOps.h b/Code/RDGeneral/StreamOps.h index 0d4eb602c..e6bdc0e68 100644 --- a/Code/RDGeneral/StreamOps.h +++ b/Code/RDGeneral/StreamOps.h @@ -17,7 +17,6 @@ #include "RDProps.h" #include #include -#include #include #include #include diff --git a/Code/RDGeneral/catch_logs.cpp b/Code/RDGeneral/catch_logs.cpp index dc41601c3..62cbde6a0 100644 --- a/Code/RDGeneral/catch_logs.cpp +++ b/Code/RDGeneral/catch_logs.cpp @@ -8,7 +8,6 @@ // of the RDKit source tree. // #include -#include #include #include #include diff --git a/Code/RDGeneral/hanoiSort.h b/Code/RDGeneral/hanoiSort.h index e9d310d96..69a63d1f8 100644 --- a/Code/RDGeneral/hanoiSort.h +++ b/Code/RDGeneral/hanoiSort.h @@ -14,7 +14,6 @@ #define HANOISORT_H_ #include -#include #include #include diff --git a/Code/SimDivPickers/Wrap/LeaderPicker.cpp b/Code/SimDivPickers/Wrap/LeaderPicker.cpp index 87a12ef98..05b951272 100644 --- a/Code/SimDivPickers/Wrap/LeaderPicker.cpp +++ b/Code/SimDivPickers/Wrap/LeaderPicker.cpp @@ -22,7 +22,6 @@ #include #include #include -#include #include namespace python = boost::python; diff --git a/Code/SimDivPickers/Wrap/MaxMinPicker.cpp b/Code/SimDivPickers/Wrap/MaxMinPicker.cpp index 976a600e7..75abbe935 100644 --- a/Code/SimDivPickers/Wrap/MaxMinPicker.cpp +++ b/Code/SimDivPickers/Wrap/MaxMinPicker.cpp @@ -23,7 +23,6 @@ #include #include #include -#include #include namespace python = boost::python; diff --git a/Code/SimDivPickers/catch_tests.cpp b/Code/SimDivPickers/catch_tests.cpp index 29c96e7c8..a1ed05eb6 100644 --- a/Code/SimDivPickers/catch_tests.cpp +++ b/Code/SimDivPickers/catch_tests.cpp @@ -15,7 +15,6 @@ #include #include -#include #include template diff --git a/Code/SimDivPickers/testPickers.cpp b/Code/SimDivPickers/testPickers.cpp index 533c55b82..797398bb4 100644 --- a/Code/SimDivPickers/testPickers.cpp +++ b/Code/SimDivPickers/testPickers.cpp @@ -9,7 +9,6 @@ // #include #include "MaxMinPicker.h" -#include #include #include diff --git a/Contrib/ConformerParser/test.cpp b/Contrib/ConformerParser/test.cpp index 1a8cdb55e..e4a1586d3 100644 --- a/Contrib/ConformerParser/test.cpp +++ b/Contrib/ConformerParser/test.cpp @@ -31,7 +31,6 @@ // OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // -#include #include #include diff --git a/Contrib/PBF/PBFRDKit.h b/Contrib/PBF/PBFRDKit.h index aae0d1205..7fc06247a 100644 --- a/Contrib/PBF/PBFRDKit.h +++ b/Contrib/PBF/PBFRDKit.h @@ -46,8 +46,6 @@ #ifndef _PBFRDKit_h #define _PBFRDKit_h -#include - #include #include #include @@ -55,6 +53,6 @@ using namespace RDKit; -double PBFRD(ROMol&, int confId = -1); +double PBFRD(ROMol &, int confId = -1); #endif diff --git a/External/AvalonTools/test1.cpp b/External/AvalonTools/test1.cpp index 489316d4c..17d5180c6 100644 --- a/External/AvalonTools/test1.cpp +++ b/External/AvalonTools/test1.cpp @@ -24,7 +24,6 @@ #include #include #include -#include #include #include #include "AvalonTools.h" diff --git a/External/ChemDraw/chemdraw.cpp b/External/ChemDraw/chemdraw.cpp index 66abbfb2c..755722a4b 100644 --- a/External/ChemDraw/chemdraw.cpp +++ b/External/ChemDraw/chemdraw.cpp @@ -31,7 +31,6 @@ // #include -#include #include #include diff --git a/External/GA/util/Util.h b/External/GA/util/Util.h index c9d4a4614..42a9fa313 100644 --- a/External/GA/util/Util.h +++ b/External/GA/util/Util.h @@ -15,7 +15,6 @@ #include #include #include -#include #include #include #include diff --git a/External/pubchem_shape/PubChemShape.cpp b/External/pubchem_shape/PubChemShape.cpp index 50c078e3a..62a7ad318 100644 --- a/External/pubchem_shape/PubChemShape.cpp +++ b/External/pubchem_shape/PubChemShape.cpp @@ -1,4 +1,3 @@ -#include #include #include #include diff --git a/External/pubchem_shape/sdf_align.cpp b/External/pubchem_shape/sdf_align.cpp index 54e85aa87..3ca97aa5d 100644 --- a/External/pubchem_shape/sdf_align.cpp +++ b/External/pubchem_shape/sdf_align.cpp @@ -1,4 +1,3 @@ -#include #include #include diff --git a/External/pubchem_shape/test.cpp b/External/pubchem_shape/test.cpp index 59416f9e7..392395db2 100644 --- a/External/pubchem_shape/test.cpp +++ b/External/pubchem_shape/test.cpp @@ -1,7 +1,6 @@ #include #include -#include #include #include