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another clang-format run

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This commit is contained in:
Greg Landrum
2017-10-12 06:42:15 +02:00
parent f94e277856
commit 1efa8e696e
72 changed files with 1439 additions and 1386 deletions
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256
Code/GraphMol/SubstructLibrary/SubstructLibrary.h
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@@ -53,7 +53,7 @@ class MolHolderBase {
//! Add a new molecule to the substructure search library
//! Returns the molecules index in the library
virtual unsigned int addMol( const ROMol &m ) = 0;
virtual unsigned int addMol(const ROMol &m) = 0;
// implementations should throw IndexError on out of range
virtual boost::shared_ptr<ROMol> getMol(unsigned int) const = 0;
@@ -68,7 +68,7 @@ class MolHolderBase {
However it is very memory intensive.
*/
class MolHolder : public MolHolderBase {
std::vector<boost::shared_ptr<ROMol> > mols;
std::vector<boost::shared_ptr<ROMol>> mols;
public:
MolHolder() : MolHolderBase(), mols() {}
@@ -79,8 +79,7 @@ class MolHolder : public MolHolderBase {
}
virtual boost::shared_ptr<ROMol> getMol(unsigned int idx) const {
if(idx >= mols.size())
throw IndexErrorException(idx);
if (idx >= mols.size()) throw IndexErrorException(idx);
return mols[idx];
}
@@ -112,13 +111,12 @@ class CachedMolHolder : public MolHolderBase {
//! Adds a pickled binary molecule, no validity checking of the input
//! is done.
unsigned int addBinary(const std::string &pickle) {
mols.push_back( pickle );
return size()-1;
mols.push_back(pickle);
return size() - 1;
}
virtual boost::shared_ptr<ROMol> getMol(unsigned int idx) const {
if(idx >= mols.size())
throw IndexErrorException(idx);
if (idx >= mols.size()) throw IndexErrorException(idx);
boost::shared_ptr<ROMol> mol(new ROMol);
MolPickler::molFromPickle(mols[idx], mol.get());
return mol;
@@ -152,15 +150,14 @@ class CachedSmilesMolHolder : public MolHolderBase {
//! Add a smiles to the dataset, no validation is done
//! to the inputs.
unsigned int addSmiles( const std::string &smiles ) {
unsigned int addSmiles(const std::string &smiles) {
mols.push_back(smiles);
return size() - 1;
}
virtual boost::shared_ptr<ROMol> getMol(unsigned int idx) const {
if(idx >= mols.size())
throw IndexErrorException(idx);
if (idx >= mols.size()) throw IndexErrorException(idx);
boost::shared_ptr<ROMol> mol(SmilesToMol(mols[idx]));
return mol;
}
@@ -176,7 +173,7 @@ class CachedSmilesMolHolder : public MolHolderBase {
RDKit has generated. This indicates that fewer
sanitization steps are required. See
http://rdkit.blogspot.com/2016/09/avoiding-unnecessary-work-and.html
This implementation uses quite a bit less memory than the
cached binary or uncached implementation. However, due to the
reduced speed it should be used in conjunction with a pattern
@@ -198,14 +195,13 @@ class CachedTrustedSmilesMolHolder : public MolHolderBase {
//! Add a smiles to the dataset, no validation is done
//! to the inputs.
unsigned int addSmiles( const std::string &smiles ) {
unsigned int addSmiles(const std::string &smiles) {
mols.push_back(smiles);
return size() - 1;
}
virtual boost::shared_ptr<ROMol> getMol(unsigned int idx) const {
if(idx >= mols.size())
throw IndexErrorException(idx);
if (idx >= mols.size()) throw IndexErrorException(idx);
RWMol *m = SmilesToMol(mols[idx], 0, false);
m->updatePropertyCache();
@@ -224,44 +220,42 @@ class FPHolderBase {
public:
virtual ~FPHolderBase() {
for (size_t i = 0; i < fps.size(); ++i) delete fps[i];
}
}
//! Adds a molecule to the fingerprinter
unsigned int addMol( const ROMol &m) {
fps.push_back(makeFingerprint(m));
return rdcast<unsigned int>(fps.size() - 1);
}
//! Adds a molecule to the fingerprinter
unsigned int addMol(const ROMol &m) {
fps.push_back(makeFingerprint(m));
return rdcast<unsigned int>(fps.size() - 1);
}
//! Adds a raw bit vector to the fingerprinter
unsigned int addFingerprint( const ExplicitBitVect &v ) {
fps.push_back( new ExplicitBitVect(v) );
return rdcast<unsigned int>(fps.size() - 1);
}
//! Adds a raw bit vector to the fingerprinter
unsigned int addFingerprint(const ExplicitBitVect &v) {
fps.push_back(new ExplicitBitVect(v));
return rdcast<unsigned int>(fps.size() - 1);
}
//! Return false if a substructure search can never match the molecule
bool passesFilter(unsigned int idx, const ExplicitBitVect &query) const {
if(idx >= fps.size())
throw IndexErrorException(idx);
//! Return false if a substructure search can never match the molecule
bool passesFilter(unsigned int idx, const ExplicitBitVect &query) const {
if (idx >= fps.size()) throw IndexErrorException(idx);
return AllProbeBitsMatch(query, *fps[idx]);
}
return AllProbeBitsMatch(query, *fps[idx]);
}
//! Get the bit vector at the specified index (throws IndexError if out of range)
const ExplicitBitVect &getFingerprint(unsigned int idx) const {
if(idx >= fps.size())
throw IndexErrorException(idx);
return *fps[idx];
}
//! make the query vector
//! Caller owns the vector!
virtual ExplicitBitVect *makeFingerprint(const ROMol &m) const = 0;
//! Get the bit vector at the specified index (throws IndexError if out of
//! range)
const ExplicitBitVect &getFingerprint(unsigned int idx) const {
if (idx >= fps.size()) throw IndexErrorException(idx);
return *fps[idx];
}
//! make the query vector
//! Caller owns the vector!
virtual ExplicitBitVect *makeFingerprint(const ROMol &m) const = 0;
};
//! Uses the pattern fingerprinter to rule out matches
class PatternHolder : public FPHolderBase {
public:
public:
//! Caller owns the vector!
virtual ExplicitBitVect *makeFingerprint(const ROMol &m) const {
return PatternFingerprintMol(m, 2048);
@@ -287,7 +281,7 @@ class SubstructLibrary {
: molholder(new MolHolder),
fpholder(),
mols(molholder.get()),
fps(NULL) {}
fps(NULL) {}
SubstructLibrary(boost::shared_ptr<MolHolderBase> molecules)
: molholder(molecules), fpholder(), mols(molholder.get()), fps(0) {}
@@ -299,26 +293,26 @@ class SubstructLibrary {
mols(molholder.get()),
fps(fpholder.get()) {}
//!Get the underlying molecule holder implementation
MolHolderBase & getMolHolder() {
//! Get the underlying molecule holder implementation
MolHolderBase &getMolHolder() {
PRECONDITION(mols, "Molecule holder NULL in SubstructLibrary");
return *mols;
}
const MolHolderBase & getMolecules() const {
const MolHolderBase &getMolecules() const {
PRECONDITION(mols, "Molecule holder NULL in SubstructLibrary");
return *mols;
}
//!Get the underlying fingerprint implementation.
//! Get the underlying fingerprint implementation.
/*! Throws a value error if no fingerprints have been set */
FPHolderBase & getFingerprints() {
FPHolderBase &getFingerprints() {
if (!fps)
throw ValueErrorException("Substruct Library does not have fingerprints");
return *fps;
}
const FPHolderBase & getFingerprints() const {
const FPHolderBase &getFingerprints() const {
if (!fps)
throw ValueErrorException("Substruct Library does not have fingerprints");
return *fps;
@@ -335,111 +329,121 @@ class SubstructLibrary {
//! Get the matching indices for the query
/*!
\param query Query to match against molecules
\param recursionPossible flags whether or not recursive matches are allowed [ default true ]
\param useChirality use atomic CIP codes as part of the comparison [ default true ]
\param useQueryQueryMatches if set, the contents of atom and bond queries [ default false ]
will be used as part of the matching
\param recursionPossible flags whether or not recursive matches are allowed
[ default true ]
\param useChirality use atomic CIP codes as part of the comparison [
default true ]
\param useQueryQueryMatches if set, the contents of atom and bond queries [
default false ]
will be used as part of the matching
\param numThreads If -1 use all available processors [default -1]
\param maxResults Maximum results to return, -1 means return all [default
-1]
*/
std::vector<unsigned int> getMatches(const ROMol &query,
bool recursionPossible=true,
bool useChirality=true,
bool useQueryQueryMatches=false,
int numThreads=-1,
int maxResults=-1);
//!Get the matching indices for the query between the given indices
bool recursionPossible = true,
bool useChirality = true,
bool useQueryQueryMatches = false,
int numThreads = -1,
int maxResults = -1);
//! Get the matching indices for the query between the given indices
/*!
\param query Query to match against molecules
\param startIdx Start index of the search
\param endIdx Ending idx (non-inclusive) of the search.
\param recursionPossible flags whether or not recursive matches are allowed [ default true ]
\param useChirality use atomic CIP codes as part of the comparison [ default true ]
\param useQueryQueryMatches if set, the contents of atom and bond queries [ default false ]
will be used as part of the matching
\param recursionPossible flags whether or not recursive matches are allowed
[ default true ]
\param useChirality use atomic CIP codes as part of the comparison [
default true ]
\param useQueryQueryMatches if set, the contents of atom and bond queries [
default false ]
will be used as part of the matching
\param numThreads If -1 use all available processors [default -1]
\param maxResults Maximum results to return, -1 means return all [default
-1]
*/
std::vector<unsigned int> getMatches(const ROMol &query,
unsigned int startIdx, unsigned int endIdx,
bool recursionPossible=true,
bool useChirality=true,
bool useQueryQueryMatches=false,
int numThreads=-1,
int maxResults=-1);
std::vector<unsigned int> getMatches(
const ROMol &query, unsigned int startIdx, unsigned int endIdx,
bool recursionPossible = true, bool useChirality = true,
bool useQueryQueryMatches = false, int numThreads = -1,
int maxResults = -1);
//! Return the number of matches for the query
/*!
\param query Query to match against molecules
\param recursionPossible flags whether or not recursive matches are allowed [ default true ]
\param useChirality use atomic CIP codes as part of the comparison [ default true ]
\param useQueryQueryMatches if set, the contents of atom and bond queries [ default false ]
will be used as part of the matching
\param recursionPossible flags whether or not recursive matches are allowed
[ default true ]
\param useChirality use atomic CIP codes as part of the comparison [
default true ]
\param useQueryQueryMatches if set, the contents of atom and bond queries [
default false ]
will be used as part of the matching
\param numThreads If -1 use all available processors [default -1]
*/
unsigned int countMatches(const ROMol &query,
bool recursionPossible=true,
bool useChirality=true,
bool useQueryQueryMatches=false,
int numThreads=-1);
//!Return the number of matches for the query between the given indices
*/
unsigned int countMatches(const ROMol &query, bool recursionPossible = true,
bool useChirality = true,
bool useQueryQueryMatches = false,
int numThreads = -1);
//! Return the number of matches for the query between the given indices
/*!
\param query Query to match against molecules
\param startIdx Start index of the search
\param endIdx Ending idx (non-inclusive) of the search.
\param recursionPossible flags whether or not recursive matches are allowed [ default true ]
\param useChirality use atomic CIP codes as part of the comparison [ default true ]
\param useQueryQueryMatches if set, the contents of atom and bond queries [ default false ]
will be used as part of the matching
\param recursionPossible flags whether or not recursive matches are allowed
[ default true ]
\param useChirality use atomic CIP codes as part of the comparison [
default true ]
\param useQueryQueryMatches if set, the contents of atom and bond queries [
default false ]
will be used as part of the matching
\param numThreads If -1 use all available processors [default -1]
*/
unsigned int countMatches(const ROMol &query,
unsigned int startIdx, unsigned int endIdx,
bool recursionPossible=true,
bool useChirality=true,
bool useQueryQueryMatches=false,
int numThreads=-1);
*/
unsigned int countMatches(const ROMol &query, unsigned int startIdx,
unsigned int endIdx, bool recursionPossible = true,
bool useChirality = true,
bool useQueryQueryMatches = false,
int numThreads = -1);
//! Returns true if any match exists for the query
/*!
\param query Query to match against molecules
\param recursionPossible flags whether or not recursive matches are allowed [ default true ]
\param useChirality use atomic CIP codes as part of the comparison [ default true ]
\param useQueryQueryMatches if set, the contents of atom and bond queries [ default false ]
will be used as part of the matching
\param recursionPossible flags whether or not recursive matches are allowed
[ default true ]
\param useChirality use atomic CIP codes as part of the comparison [
default true ]
\param useQueryQueryMatches if set, the contents of atom and bond queries [
default false ]
will be used as part of the matching
\param numThreads If -1 use all available processors [default -1]
*/
bool hasMatch(const ROMol &query,
bool recursionPossible=true,
bool useChirality=true,
bool useQueryQueryMatches=false,
int numThreads=-1);
//! Returns true if any match exists for the query between the specified indices
*/
bool hasMatch(const ROMol &query, bool recursionPossible = true,
bool useChirality = true, bool useQueryQueryMatches = false,
int numThreads = -1);
//! Returns true if any match exists for the query between the specified
//! indices
/*!
\param query Query to match against molecules
\param startIdx Start index of the search
\param endIdx Ending idx (inclusive) of the search.
\param recursionPossible flags whether or not recursive matches are allowed [ default true ]
\param useChirality use atomic CIP codes as part of the comparison [ default true ]
\param useQueryQueryMatches if set, the contents of atom and bond queries [ default false ]
will be used as part of the matching
\param recursionPossible flags whether or not recursive matches are allowed
[ default true ]
\param useChirality use atomic CIP codes as part of the comparison [
default true ]
\param useQueryQueryMatches if set, the contents of atom and bond queries [
default false ]
will be used as part of the matching
\param numThreads If -1 use all available processors [default -1]
*/
bool hasMatch(const ROMol &query,
unsigned int startIdx, unsigned int endIdx,
bool recursionPossible=true,
bool useChirality=true,
bool useQueryQueryMatches=false,
int numThreads=-1);
*/
bool hasMatch(const ROMol &query, unsigned int startIdx, unsigned int endIdx,
bool recursionPossible = true, bool useChirality = true,
bool useQueryQueryMatches = false, int numThreads = -1);
//! Returns the molecule at the given index
/*!
\param idx Index of the molecule in the library
*/
boost::shared_ptr<ROMol> getMol(unsigned int idx) const {
// expects implementation to throw IndexError if out of range
// expects implementation to throw IndexError if out of range
PRECONDITION(mols, "molholder is null in SubstructLibrary");
return mols->getMol(idx);
}
@@ -447,8 +451,8 @@ class SubstructLibrary {
//! Returns the molecule at the given index
/*!
\param idx Index of the molecule in the library
*/
boost::shared_ptr<ROMol> operator[] (unsigned int idx) {
*/
boost::shared_ptr<ROMol> operator[](unsigned int idx) {
// expects implementation to throw IndexError if out of range
PRECONDITION(mols, "molholder is null in SubstructLibrary");
return mols->getMol(idx);