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another batch of warnings squashed

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This commit is contained in:
Greg Landrum
2016-03-30 13:44:21 +02:00
parent cf7ceab383
commit e04aed8ea8
8 changed files with 2020 additions and 2080 deletions
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112
Code/ForceField/MMFF/testMMFFForceField.cpp
View File

@@ -240,14 +240,14 @@ int mmffValidationSuite(int argc, char *argv[]) {
std::streampos rdkCurrent;
std::streampos refPos;
std::streampos refCurrent;
int i = 1;
int iarg = 1;
unsigned int n = 0;
bool error = false;
bool fullTest = false;
int inc = 4;
bool testFailure = false;
while (i < argc) {
arg = argv[i];
while (iarg < argc) {
arg = argv[iarg];
error = (arg.at(0) != '-');
if (error) {
break;
@@ -256,34 +256,34 @@ int mmffValidationSuite(int argc, char *argv[]) {
if (error) {
break;
} else if (arg == "-f") {
error = ((i + 1) >= argc);
error = ((iarg + 1) >= argc);
if (error) {
break;
}
ffVariant = argv[i + 1];
ffVariant = argv[iarg + 1];
error = ((ffVariant != "MMFF94") && (ffVariant != "MMFF94s"));
if (error) {
break;
}
++i;
++iarg;
} else if ((arg == "-sdf") || (arg == "-smi")) {
molType = arg.substr(1);
if ((i + 1) < argc) {
molFile = argv[i + 1];
++i;
if ((iarg + 1) < argc) {
molFile = argv[iarg + 1];
++iarg;
}
} else if (arg == "-L") {
fullTest = true;
inc = 1;
} else if (arg == "-l") {
error = ((i + 1) >= argc);
error = ((iarg + 1) >= argc);
if (error) {
break;
}
rdk = argv[i + 1];
++i;
rdk = argv[iarg + 1];
++iarg;
}
++i;
++iarg;
}
if (error) {
std::cerr << "Usage: testMMFFForceField [-L] [-f {MMFF94|MMFF94s}] "
@@ -340,14 +340,14 @@ int mmffValidationSuite(int argc, char *argv[]) {
molVec.clear();
if (*molTypeIt == "sdf") {
SDMolSupplier sdfSupplier(*molFileIt, false, false);
for (size_t i = 0; i < sdfSupplier.length(); ++i) {
molVec.push_back(sdfSupplier[i]);
for (size_t ii = 0; ii < sdfSupplier.length(); ++ii) {
molVec.push_back(sdfSupplier[ii]);
}
sdfSupplier.reset();
} else {
SmilesMolSupplier smiSupplier(*molFileIt);
for (size_t i = 0; i < smiSupplier.length(); ++i) {
molVec.push_back(smiSupplier[i]);
for (size_t ii = 0; ii < smiSupplier.length(); ++ii) {
molVec.push_back(smiSupplier[ii]);
}
smiSupplier.reset();
}
@@ -365,21 +365,19 @@ int mmffValidationSuite(int argc, char *argv[]) {
std::string computingKey = (*ffIt) + " energies for " + (*molFileIt);
std::cerr << std::endl
<< "Computing " << computingKey << "..." << std::endl;
for (size_t i = 0; i < computingKey.length(); ++i) {
for (size_t ii = 0; ii < computingKey.length(); ++ii) {
rdkFStream << "*";
}
rdkFStream << std::endl
<< computingKey << std::endl;
for (size_t i = 0; i < computingKey.length(); ++i) {
rdkFStream << std::endl << computingKey << std::endl;
for (size_t ii = 0; ii < computingKey.length(); ++ii) {
rdkFStream << "*";
}
rdkFStream << std::endl
<< std::endl;
for (size_t i = 0; i < molVec.size(); i += inc) {
rdkFStream << std::endl << std::endl;
for (size_t ii = 0; ii < molVec.size(); ii += inc) {
if (*molTypeIt == "sdf") {
mol = molVec[i];
mol = molVec[ii];
} else {
mol = MolOps::addHs(*(molVec[i]));
mol = MolOps::addHs(*(molVec[ii]));
DGeomHelpers::EmbedMolecule(*mol);
}
MMFF::sanitizeMMFFMol((RWMol &)(*mol));
@@ -433,19 +431,20 @@ int mmffValidationSuite(int argc, char *argv[]) {
double refVdWEnergy;
double refEleEnergy;
unsigned int n_failed = 0;
bool failed;
bool failed = false;
rdkFStream.seekg(0);
fgrep(rdkFStream, computingKey);
for (size_t i = 0; i < nameArray.size(); i += inc) {
size_t ii;
for (ii = 0; ii < nameArray.size(); ii += inc) {
error = false;
failed = false;
errorMsg = rdk + ": Molecule not found";
found = fgrep(rdkFStream, nameArray[i]);
found = fgrep(rdkFStream, nameArray[ii]);
if (!found) {
break;
}
errorMsg = ref + ": Molecule not found";
found = fgrep(refFStream, nameArray[i]);
found = fgrep(refFStream, nameArray[ii]);
if (!found) {
break;
}
@@ -657,9 +656,10 @@ int mmffValidationSuite(int argc, char *argv[]) {
failed = true;
std::stringstream diff;
diff << "Bond stretching: energies differ\n"
"Expected " << std::fixed << std::setprecision(4)
<< refEnergy << ", found " << std::fixed
<< std::setprecision(4) << rdkEnergy << "\n";
"Expected "
<< std::fixed << std::setprecision(4) << refEnergy
<< ", found " << std::fixed << std::setprecision(4)
<< rdkEnergy << "\n";
errorMsg += diff.str();
}
}
@@ -811,9 +811,10 @@ int mmffValidationSuite(int argc, char *argv[]) {
failed = true;
std::stringstream diff;
diff << "Angle bending: energies differ\n"
"Expected " << std::fixed << std::setprecision(4)
<< refEnergy << ", found " << std::fixed
<< std::setprecision(4) << rdkEnergy << "\n";
"Expected "
<< std::fixed << std::setprecision(4) << refEnergy
<< ", found " << std::fixed << std::setprecision(4)
<< rdkEnergy << "\n";
errorMsg += diff.str();
}
}
@@ -972,9 +973,10 @@ int mmffValidationSuite(int argc, char *argv[]) {
failed = true;
std::stringstream diff;
diff << "Stretch-bending: energies differ\n"
"Expected " << std::fixed << std::setprecision(4)
<< refEnergy << ", found " << std::fixed
<< std::setprecision(4) << rdkEnergy << "\n";
"Expected "
<< std::fixed << std::setprecision(4) << refEnergy
<< ", found " << std::fixed << std::setprecision(4)
<< rdkEnergy << "\n";
errorMsg += diff.str();
}
}
@@ -1127,9 +1129,10 @@ int mmffValidationSuite(int argc, char *argv[]) {
failed = true;
std::stringstream diff;
diff << "Out-of-plane bending: energies differ\n"
"Expected " << std::fixed << std::setprecision(4)
<< refEnergy << ", found " << std::fixed
<< std::setprecision(4) << rdkEnergy << "\n";
"Expected "
<< std::fixed << std::setprecision(4) << refEnergy
<< ", found " << std::fixed << std::setprecision(4)
<< rdkEnergy << "\n";
errorMsg += diff.str();
}
}
@@ -1293,9 +1296,10 @@ int mmffValidationSuite(int argc, char *argv[]) {
failed = true;
std::stringstream diff;
diff << "Torsional: energies differ\n"
"Expected " << std::fixed << std::setprecision(4)
<< refEnergy << ", found " << std::fixed
<< std::setprecision(4) << rdkEnergy << "\n";
"Expected "
<< std::fixed << std::setprecision(4) << refEnergy
<< ", found " << std::fixed << std::setprecision(4)
<< rdkEnergy << "\n";
errorMsg += diff.str();
}
}
@@ -1354,9 +1358,10 @@ int mmffValidationSuite(int argc, char *argv[]) {
failed = true;
std::stringstream diff;
diff << "Van der Waals: energies differ\n"
"Expected " << std::fixed << std::setprecision(4)
<< refVdWEnergy << ", found " << std::fixed
<< std::setprecision(4) << rdkEnergy << "\n";
"Expected "
<< std::fixed << std::setprecision(4) << refVdWEnergy
<< ", found " << std::fixed << std::setprecision(4)
<< rdkEnergy << "\n";
errorMsg += diff.str();
}
error = (fabs(rdkEleEnergy - refEleEnergy) > ENERGY_TOLERANCE);
@@ -1364,19 +1369,20 @@ int mmffValidationSuite(int argc, char *argv[]) {
failed = true;
std::stringstream diff;
diff << "Electrostatic: energies differ\n"
"Expected " << std::fixed << std::setprecision(4)
<< refEleEnergy << ", found " << std::fixed
<< std::setprecision(4) << rdkEnergy << "\n";
"Expected "
<< std::fixed << std::setprecision(4) << refEleEnergy
<< ", found " << std::fixed << std::setprecision(4)
<< rdkEnergy << "\n";
errorMsg += diff.str();
}
if (failed) {
std::cerr << nameArray[i] << "\n\n" << errorMsg << std::endl;
std::cerr << nameArray[ii] << "\n\n" << errorMsg << std::endl;
++n_failed;
}
}
if (!found) {
if (!failed) {
std::cerr << nameArray[i] << "\n\n";
std::cerr << nameArray[ii] << "\n\n";
}
std::cerr << errorMsg << std::endl;
} else {

7
Code/ForceField/UFF/testUFFForceField.cpp
View File

@@ -714,7 +714,7 @@ void testUFF7() {
ps.push_back(&p3);
ps.push_back(&p4);
ForceFields::UFF::AtomicParams param1, param2;
ForceFields::UFF::AtomicParams param1;
// sp3 carbon:
param1.r1 = .757;
param1.Z1 = 1.912;
@@ -724,11 +724,6 @@ void testUFF7() {
param1.V1 = 2.119;
param1.U1 = 2.0;
// H_1:
param2.r1 = 0.354;
param2.Z1 = 0.712;
param2.GMP_Xi = 4.528;
RDGeom::Point3D d, v1, v2;
double cosPhi;

2
Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalFF.cpp
View File

@@ -148,7 +148,7 @@ void testTorsionPrefs() {
TEST_ASSERT(expTorsionAngles.size() == 2);
}
int main(int argc, char *argv[]) {
int main() {
testTorsionAngleM6();
testTorsionPrefs();

6
Code/GraphMol/MMPA/MMPA_UnitTest.cpp
View File

@@ -271,7 +271,7 @@ void test1() {
strcpy(fs[8], fs1[8]);
//-----------------------------------
for (int i = 0; i < sizeof(smi) / sizeof(smi[0]); i++) {
for (unsigned int i = 0; i < sizeof(smi) / sizeof(smi[0]); i++) {
static const std::string es("NULL");
std::string id;
std::string smiles = getSmilesOnly(smi[i], &id);
@@ -376,7 +376,7 @@ void test2() {
"Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=C(NC[*:2])[*:1],"
"Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].OC[*:2]"};
for (int i = 0; i < sizeof(smi) / sizeof(smi[0]); i++) {
for (unsigned int i = 0; i < sizeof(smi) / sizeof(smi[0]); i++) {
static const std::string es("NULL");
std::string id;
std::string smiles = getSmilesOnly(smi[i], &id);
@@ -664,7 +664,7 @@ std::endl;
//====================================================================================================
//====================================================================================================
int main(int argc, const char* argv[]) {
int main() {
BOOST_LOG(rdInfoLog)
<< "*******************************************************\n";
BOOST_LOG(rdInfoLog) << "MMPA Unit Test \n";

14
Code/GraphMol/SLNParse/SLNAttribs.cpp
View File

@@ -217,7 +217,7 @@ void parseAtomAttribs(Atom *atom, AttribListType attribs, bool doingQuery) {
// a block of properties that can have "f" values, and so need special
// handling:
std::string fTag = "";
int val;
int val = 0;
if (attribVal == "f" || attribName == "f") {
fTag = "_SLN_";
atom->setProp(common_properties::_Unfinished_SLN_, 1);
@@ -352,8 +352,8 @@ void parseFinalAtomAttribs(Atom *atom, bool doingQuery) {
if (description.size() > 5 && description.substr(0, 5) == "_SLN_") {
boost::erase_head(description, 5);
query->setDescription(description);
static_cast<ATOM_EQUALS_QUERY *>(query)
->setVal((int)(query->getDataFunc()(atom)));
static_cast<ATOM_EQUALS_QUERY *>(query)->setVal(
(int)(query->getDataFunc()(atom)));
}
// now add the query's children to the queue and continue:
for (QueryAtom::QUERYATOM_QUERY::CHILD_VECT_CI cIt = query->beginChildren();
@@ -505,10 +505,10 @@ void adjustAtomChiralities(RWMol *mol) {
int nSwaps = (*atomIt)->getPerturbationOrder(bondOrdering);
if (nSwaps % 2) {
(*atomIt)
->setChiralTag((*atomIt)->getChiralTag() == Atom::CHI_TETRAHEDRAL_CW
? Atom::CHI_TETRAHEDRAL_CCW
: Atom::CHI_TETRAHEDRAL_CW);
(*atomIt)->setChiralTag((*atomIt)->getChiralTag() ==
Atom::CHI_TETRAHEDRAL_CW
? Atom::CHI_TETRAHEDRAL_CCW
: Atom::CHI_TETRAHEDRAL_CW);
}
}
}

407
External/AvalonTools/Wrap/pyAvalonTools.cpp vendored
View File

@@ -11,125 +11,121 @@
#include <AvalonTools.h>
#include <boost/cstdint.hpp>
extern "C" {
#include "struchk.h"
}
extern "C" {
#include "struchk.h"
}
namespace python = boost::python;
namespace {
RDKit::SparseIntVect<boost::uint32_t> *getAvalonCountFP(const RDKit::ROMol &mol,
unsigned int nBits,
bool isQuery,
unsigned int bitFlags) {
RDKit::SparseIntVect<boost::uint32_t> *res =
new RDKit::SparseIntVect<boost::uint32_t>(nBits);
AvalonTools::getAvalonCountFP(mol, *res, nBits, isQuery, bitFlags);
return res;
}
RDKit::SparseIntVect<boost::uint32_t> *getAvalonCountFP(const std::string &data,
bool isSmiles,
unsigned int nBits,
bool isQuery,
unsigned int bitFlags) {
RDKit::SparseIntVect<boost::uint32_t> *res =
new RDKit::SparseIntVect<boost::uint32_t>(nBits);
AvalonTools::getAvalonCountFP(data, isSmiles, *res, nBits, isQuery, bitFlags);
return res;
}
RDKit::SparseIntVect<boost::uint32_t> *getAvalonCountFP(const RDKit::ROMol &mol,
unsigned int nBits,
bool isQuery,
unsigned int bitFlags){
RDKit::SparseIntVect<boost::uint32_t> *res=new RDKit::SparseIntVect<boost::uint32_t>(nBits);
AvalonTools::getAvalonCountFP(mol,*res,nBits,isQuery,bitFlags);
return res;
}
RDKit::SparseIntVect<boost::uint32_t> *getAvalonCountFP(const std::string &data,bool isSmiles,
unsigned int nBits,
bool isQuery,
unsigned int bitFlags){
RDKit::SparseIntVect<boost::uint32_t> *res=new RDKit::SparseIntVect<boost::uint32_t>(nBits);
AvalonTools::getAvalonCountFP(data,isSmiles,*res,nBits,isQuery,bitFlags);
return res;
ExplicitBitVect *getAvalonFP(const RDKit::ROMol &mol, unsigned int nBits,
bool isQuery, bool resetVect,
unsigned int bitFlags) {
ExplicitBitVect *res = new ExplicitBitVect(nBits);
AvalonTools::getAvalonFP(mol, *res, nBits, isQuery, resetVect, bitFlags);
return res;
}
python::list getAvalonFPAsWords(const RDKit::ROMol &mol, unsigned int nBits,
bool isQuery, bool resetVect,
unsigned int bitFlags) {
std::vector<boost::uint32_t> words;
AvalonTools::getAvalonFP(mol, words, nBits, isQuery, resetVect, bitFlags);
python::list res;
for (std::vector<boost::uint32_t>::const_iterator ci = words.begin();
ci != words.end(); ++ci) {
res.append(static_cast<unsigned long>(*ci));
}
return res;
}
ExplicitBitVect *getAvalonFP(const RDKit::ROMol &mol,
unsigned int nBits,
bool isQuery,
bool resetVect,
unsigned int bitFlags){
ExplicitBitVect *res=new ExplicitBitVect(nBits);
AvalonTools::getAvalonFP(mol,*res,nBits,isQuery,resetVect,bitFlags);
return res;
}
python::list getAvalonFPAsWords(const RDKit::ROMol &mol,
unsigned int nBits,
bool isQuery,
bool resetVect,
unsigned int bitFlags){
std::vector<boost::uint32_t> words;
AvalonTools::getAvalonFP(mol,words,nBits,isQuery,resetVect,bitFlags);
python::list res;
for(std::vector<boost::uint32_t>::const_iterator ci=words.begin();
ci!=words.end();++ci){
res.append(static_cast<unsigned long>(*ci));
}
return res;
ExplicitBitVect *getAvalonFP(const std::string &data, bool isSmiles,
unsigned int nBits, bool isQuery, bool resetVect,
unsigned int bitFlags) {
ExplicitBitVect *res = new ExplicitBitVect(nBits);
AvalonTools::getAvalonFP(data, isSmiles, *res, nBits, isQuery, resetVect,
bitFlags);
return res;
}
python::list getAvalonFPAsWords(const std::string &data, bool isSmiles,
unsigned int nBits, bool isQuery,
bool resetVect, unsigned int bitFlags) {
std::vector<boost::uint32_t> words;
AvalonTools::getAvalonFP(data, isSmiles, words, nBits, isQuery, resetVect,
bitFlags);
python::list res;
for (std::vector<boost::uint32_t>::const_iterator ci = words.begin();
ci != words.end(); ++ci) {
res.append(static_cast<unsigned long>(*ci));
}
return res;
}
python::tuple CheckMolecule(const std::string &data, bool isSmiles) {
int errs = 0;
RDKit::ROMOL_SPTR rMol = AvalonTools::checkMol(errs, data, isSmiles);
return python::make_tuple(errs, rMol);
;
}
python::tuple CheckMolecule(RDKit::ROMol &mol) {
int errs = 0;
RDKit::ROMOL_SPTR rMol = AvalonTools::checkMol(errs, mol);
return python::make_tuple(errs, rMol);
;
}
python::tuple CheckMoleculeString(const std::string &data, bool isSmiles) {
std::pair<std::string, int> res = AvalonTools::checkMolString(data, isSmiles);
return python::make_tuple(res.second, res.first);
;
}
ExplicitBitVect *getAvalonFP(const std::string &data,bool isSmiles,
unsigned int nBits,
bool isQuery,
bool resetVect,
unsigned int bitFlags){
ExplicitBitVect *res=new ExplicitBitVect(nBits);
AvalonTools::getAvalonFP(data,isSmiles,*res,nBits,isQuery,resetVect,bitFlags);
return res;
}
python::list getAvalonFPAsWords(const std::string &data,bool isSmiles,
unsigned int nBits,
bool isQuery,
bool resetVect,
unsigned int bitFlags){
std::vector<boost::uint32_t> words;
AvalonTools::getAvalonFP(data,isSmiles,words,nBits,isQuery,resetVect,bitFlags);
python::list res;
for(std::vector<boost::uint32_t>::const_iterator ci=words.begin();
ci!=words.end();++ci){
res.append(static_cast<unsigned long>(*ci));
}
return res;
}
enum StruChkFlag {
bad_molecule = BAD_MOLECULE,
alias_conversion_failed = ALIAS_CONVERSION_FAILED,
transformed = TRANSFORMED,
fragments_found = FRAGMENTS_FOUND,
either_warning = EITHER_WARNING,
stereo_error = STEREO_ERROR,
dubious_stereo_removed = DUBIOUS_STEREO_REMOVED,
atom_clash = ATOM_CLASH,
atom_check_failed = ATOM_CHECK_FAILED,
size_check_failed = SIZE_CHECK_FAILED,
recharged = RECHARGED,
stereo_forced_bad = STEREO_FORCED_BAD,
stereo_transformed = STEREO_TRANSFORMED,
template_transformed = TEMPLATE_TRANSFORMED,
};
python::tuple CheckMolecule(const std::string &data, bool isSmiles) {
int errs = 0;
RDKit::ROMOL_SPTR rMol = AvalonTools::checkMol(errs, data, isSmiles);
return python::make_tuple(errs, rMol);;
}
python::tuple CheckMolecule(RDKit::ROMol &mol) {
int errs = 0;
RDKit::ROMOL_SPTR rMol = AvalonTools::checkMol(errs, mol);
return python::make_tuple(errs, rMol);;
}
python::tuple CheckMoleculeString(const std::string &data, bool isSmiles){
int errs = 0;
std::pair<std::string,int> res=AvalonTools::checkMolString(data,isSmiles);
return python::make_tuple(res.second,res.first);;
}
enum StruChkFlag {
bad_molecule=BAD_MOLECULE,
alias_conversion_failed=ALIAS_CONVERSION_FAILED,
transformed=TRANSFORMED,
fragments_found=FRAGMENTS_FOUND,
either_warning=EITHER_WARNING,
stereo_error=STEREO_ERROR,
dubious_stereo_removed=DUBIOUS_STEREO_REMOVED,
atom_clash=ATOM_CLASH,
atom_check_failed=ATOM_CHECK_FAILED,
size_check_failed=SIZE_CHECK_FAILED,
recharged=RECHARGED,
stereo_forced_bad=STEREO_FORCED_BAD,
stereo_transformed=STEREO_TRANSFORMED,
template_transformed=TEMPLATE_TRANSFORMED,
} ;
enum StruChkResult {
success=0,
bad_set=BAD_SET,
transformed_set=TRANSFORMED_SET,
} ;
enum StruChkResult {
success = 0,
bad_set = BAD_SET,
transformed_set = TRANSFORMED_SET,
};
}
BOOST_PYTHON_MODULE(pyAvalonTools) {
python::scope().attr("__doc__") =
"Module containing functionality from the Avalon toolkit.\n\
"Module containing functionality from the Avalon toolkit.\n\
\n\
The functions currently exposed are:\n\
- GetCanonSmiles() : return the canonical smiles for a molecule\n\
@@ -146,162 +142,165 @@ See the individual docstrings for more information.\n\
";
std::string docString = "returns canonical smiles for an RDKit molecule";
python::def("GetCanonSmiles", (std::string (*)(RDKit::ROMol &,int))AvalonTools::getCanonSmiles,
(python::arg("mol"), python::arg("flags")=-1),
python::def("GetCanonSmiles",
(std::string(*)(RDKit::ROMol &, int))AvalonTools::getCanonSmiles,
(python::arg("mol"), python::arg("flags") = -1),
docString.c_str());
docString = "Returns canonical smiles for some molecule data.\n\
docString =
"Returns canonical smiles for some molecule data.\n\
If the isSmiles argument is true, the data is assumed to be SMILES, otherwise\n\
MDL mol data is assumed.";
python::def("GetCanonSmiles", (std::string (*)(const std::string &,bool,int))AvalonTools::getCanonSmiles,
(python::arg("molData"), python::arg("isSmiles"), python::arg("flags")=-1),
python::def("GetCanonSmiles",
(std::string(*)(const std::string &, bool,
int))AvalonTools::getCanonSmiles,
(python::arg("molData"), python::arg("isSmiles"),
python::arg("flags") = -1),
docString.c_str());
docString = "returns the Avalon fingerprint for an RDKit molecule";
python::def("GetAvalonFP",
(ExplicitBitVect *(*)(const RDKit::ROMol &,unsigned int,bool,bool,unsigned int))getAvalonFP,
(python::arg("mol"),
python::arg("nBits")=512,
python::arg("isQuery")=false,
python::arg("resetVect")=false,
python::arg("bitFlags")=AvalonTools::avalonSimilarityBits),
(ExplicitBitVect * (*)(const RDKit::ROMol &, unsigned int, bool,
bool, unsigned int))getAvalonFP,
(python::arg("mol"), python::arg("nBits") = 512,
python::arg("isQuery") = false, python::arg("resetVect") = false,
python::arg("bitFlags") = AvalonTools::avalonSimilarityBits),
docString.c_str(),
python::return_value_policy<python::manage_new_object>());
docString = "returns the Avalon fingerprint for some molecule data.\n\
docString =
"returns the Avalon fingerprint for some molecule data.\n\
If the isSmiles argument is true, the data is assumed to be SMILES, otherwise\n\
MDL mol data is assumed.";
python::def("GetAvalonFP",
(ExplicitBitVect *(*)(const std::string&,bool,unsigned int,bool,bool,unsigned int))getAvalonFP,
(python::arg("molData"),python::arg("isSmiles"),
python::arg("nBits")=512,
python::arg("isQuery")=false,
python::arg("resetVect")=false,
python::arg("bitFlags")=AvalonTools::avalonSimilarityBits),
(ExplicitBitVect * (*)(const std::string &, bool, unsigned int,
bool, bool, unsigned int))getAvalonFP,
(python::arg("molData"), python::arg("isSmiles"),
python::arg("nBits") = 512, python::arg("isQuery") = false,
python::arg("resetVect") = false,
python::arg("bitFlags") = AvalonTools::avalonSimilarityBits),
docString.c_str(),
python::return_value_policy<python::manage_new_object>());
docString = "Generates 2d coordinates for an RDKit molecule";
python::def("Generate2DCoords", (unsigned int (*)(RDKit::ROMol &,bool))AvalonTools::set2DCoords,
(python::arg("mol"),python::arg("clearConfs")=true),
python::def("Generate2DCoords",
(unsigned int (*)(RDKit::ROMol &, bool))AvalonTools::set2DCoords,
(python::arg("mol"), python::arg("clearConfs") = true),
docString.c_str());
docString = "returns an MDL mol block with 2D coordinates for some molecule data.\n\
docString =
"returns an MDL mol block with 2D coordinates for some molecule data.\n\
If the isSmiles argument is true, the data is assumed to be SMILES, otherwise\n\
MDL mol data is assumed.";
python::def("Generate2DCoords", (std::string (*)(const std::string &,bool))AvalonTools::set2DCoords,
(python::arg("molData"),python::arg("isSmiles")),
docString.c_str());
python::def(
"Generate2DCoords",
(std::string(*)(const std::string &, bool))AvalonTools::set2DCoords,
(python::arg("molData"), python::arg("isSmiles")), docString.c_str());
docString = "returns the Avalon fingerprint for an RDKit molecule as a list of ints";
docString =
"returns the Avalon fingerprint for an RDKit molecule as a list of ints";
python::def("GetAvalonFPAsWords",
(python::list (*)(const RDKit::ROMol &,unsigned int,bool,bool,unsigned int))getAvalonFPAsWords,
(python::arg("mol"),
python::arg("nBits")=512,
python::arg("isQuery")=false,
python::arg("resetVect")=false,
python::arg("bitFlags")=AvalonTools::avalonSimilarityBits),
(python::list(*)(const RDKit::ROMol &, unsigned int, bool, bool,
unsigned int))getAvalonFPAsWords,
(python::arg("mol"), python::arg("nBits") = 512,
python::arg("isQuery") = false, python::arg("resetVect") = false,
python::arg("bitFlags") = AvalonTools::avalonSimilarityBits),
docString.c_str());
docString = "returns the Avalon count fingerprint for an RDKit molecule";
python::def("GetAvalonCountFP",
(RDKit::SparseIntVect<boost::uint32_t> *(*)(const RDKit::ROMol &,unsigned int,bool,unsigned int))getAvalonCountFP,
(python::arg("mol"),
python::arg("nBits")=512,
python::arg("isQuery")=false,
python::arg("bitFlags")=AvalonTools::avalonSimilarityBits),
python::def("GetAvalonCountFP", (RDKit::SparseIntVect<boost::uint32_t> *
(*)(const RDKit::ROMol &, unsigned int, bool,
unsigned int))getAvalonCountFP,
(python::arg("mol"), python::arg("nBits") = 512,
python::arg("isQuery") = false,
python::arg("bitFlags") = AvalonTools::avalonSimilarityBits),
docString.c_str(),
python::return_value_policy<python::manage_new_object>());
docString = "returns the Avalon count fingerprint for some molecule data.\n\
docString =
"returns the Avalon count fingerprint for some molecule data.\n\
If the isSmiles argument is true, the data is assumed to be SMILES, otherwise\n\
MDL mol data is assumed.";
python::def("GetAvalonCountFP",
(RDKit::SparseIntVect<boost::uint32_t> *(*)(const std::string&,bool,unsigned int,bool,unsigned int))getAvalonCountFP,
(python::arg("molData"),python::arg("isSmiles"),
python::arg("nBits")=512,
python::arg("isQuery")=false,
python::arg("bitFlags")=AvalonTools::avalonSimilarityBits),
python::def("GetAvalonCountFP", (RDKit::SparseIntVect<boost::uint32_t> *
(*)(const std::string &, bool, unsigned int,
bool, unsigned int))getAvalonCountFP,
(python::arg("molData"), python::arg("isSmiles"),
python::arg("nBits") = 512, python::arg("isQuery") = false,
python::arg("bitFlags") = AvalonTools::avalonSimilarityBits),
docString.c_str(),
python::return_value_policy<python::manage_new_object>());
docString = "returns the Avalon fingerprint for some molecule data as a list of ints.\n\
docString =
"returns the Avalon fingerprint for some molecule data as a list of ints.\n\
If the isSmiles argument is true, the data is assumed to be SMILES, otherwise\n\
MDL mol data is assumed.";
python::def("GetAvalonFPAsWords",
(python::list (*)(const std::string&,bool,unsigned int,bool,bool,unsigned int))getAvalonFPAsWords,
(python::arg("molData"),python::arg("isSmiles"),
python::arg("nBits")=512,
python::arg("isQuery")=false,
python::arg("resetVect")=false,
python::arg("bitFlags")=AvalonTools::avalonSimilarityBits),
(python::list(*)(const std::string &, bool, unsigned int, bool,
bool, unsigned int))getAvalonFPAsWords,
(python::arg("molData"), python::arg("isSmiles"),
python::arg("nBits") = 512, python::arg("isQuery") = false,
python::arg("resetVect") = false,
python::arg("bitFlags") = AvalonTools::avalonSimilarityBits),
docString.c_str());
docString = "initializes the structure checker.\n\
docString =
"initializes the structure checker.\n\
The argument should contain option lines separated by embedded newlines.\
An empty string will be used if the argument is omitted.\
An non-zero error code is returned in case of failure.";
python::def("InitializeCheckMol",
(int(*)(const std::string&)) AvalonTools::initCheckMol,
(python::arg("options") = ""),
docString.c_str());
docString = "close open files used by molecule-checking functions.";
python::def("CloseCheckMolFiles",
AvalonTools::closeCheckMolFiles,
docString.c_str());
python::def("InitializeCheckMol",
(int (*)(const std::string &))AvalonTools::initCheckMol,
(python::arg("options") = ""), docString.c_str());
docString = "close open files used by molecule-checking functions.";
python::def("CloseCheckMolFiles", AvalonTools::closeCheckMolFiles,
docString.c_str());
docString = "check a molecule passed in as a string.\n\
docString =
"check a molecule passed in as a string.\n\
If the isSmiles argument is true, the string should represent the SMILES encoding\n\
of the molecule, otherwise it should be encoded as an MDL molfile.\n\
The first member of the return tuple contains the bit-encoded corrections made to the molecule.\n\
If possible, the molecule (corrected when appropriate) is returned as the second member of \n\
the return tuple. Otherwise, None is returned.";
python::def("CheckMolecule",
(python::tuple(*)(const std::string&, bool)) CheckMolecule,
(python::arg("molstring"), python::arg("isSmiles")),
docString.c_str());
python::def("CheckMolecule",
(python::tuple(*)(const std::string &, bool))CheckMolecule,
(python::arg("molstring"), python::arg("isSmiles")),
docString.c_str());
docString = "check a molecule passed in as an RDKit molecule.\n\
docString =
"check a molecule passed in as an RDKit molecule.\n\
The first member of the return tuple contains the bit-encoded corrections made to the molecule.\n\
If possible, the molecule (corrected when appropriate) is returned as the second member of \n\
the return tuple. Otherwise, None is returned.";
python::def("CheckMolecule",
(python::tuple(*)(RDKit::ROMol&)) CheckMolecule,
(python::arg("mol")),
docString.c_str());
python::def("CheckMolecule", (python::tuple(*)(RDKit::ROMol &))CheckMolecule,
(python::arg("mol")), docString.c_str());
docString = "check a molecule passed in as a string and returns the result as a string.\n\
docString =
"check a molecule passed in as a string and returns the result as a string.\n\
If the isSmiles argument is true, the string should represent the SMILES encoding\n\
of the molecule, otherwise it should be encoded as an MDL molfile.\n\
The first member of the return tuple contains the bit-encoded corrections made to the molecule.\n\
If possible, a corrected CTAB for the molecule is returned as the second member of \n\
the return tuple.";
python::def("CheckMoleculeString",
CheckMoleculeString,
(python::arg("molstring"), python::arg("isSmiles")),
docString.c_str());
python::def("CheckMoleculeString", CheckMoleculeString,
(python::arg("molstring"), python::arg("isSmiles")),
docString.c_str());
python::scope().attr("avalonSSSBits")=AvalonTools::avalonSSSBits;
python::scope().attr("avalonSimilarityBits")=AvalonTools::avalonSimilarityBits;
python::scope().attr("avalonSSSBits") = AvalonTools::avalonSSSBits;
python::scope().attr("avalonSimilarityBits") =
AvalonTools::avalonSimilarityBits;
python::enum_<StruChkFlag>("StruChkFlag")
.value("bad_molecule",bad_molecule)
.value("alias_conversion_failed",alias_conversion_failed)
.value("transformed",transformed)
.value("fragments_found",fragments_found)
.value("either_warning",either_warning)
.value("stereo_error",stereo_error)
.value("dubious_stereo_removed",dubious_stereo_removed)
.value("atom_clash",atom_clash)
.value("atom_check_failed",atom_check_failed)
.value("size_check_failed",size_check_failed)
.value("recharged",recharged)
.value("stereo_forced_bad",stereo_forced_bad)
.value("stereo_transformed",stereo_transformed)
.value("template_transformed",template_transformed)
;
.value("bad_molecule", bad_molecule)
.value("alias_conversion_failed", alias_conversion_failed)
.value("transformed", transformed)
.value("fragments_found", fragments_found)
.value("either_warning", either_warning)
.value("stereo_error", stereo_error)
.value("dubious_stereo_removed", dubious_stereo_removed)
.value("atom_clash", atom_clash)
.value("atom_check_failed", atom_check_failed)
.value("size_check_failed", size_check_failed)
.value("recharged", recharged)
.value("stereo_forced_bad", stereo_forced_bad)
.value("stereo_transformed", stereo_transformed)
.value("template_transformed", template_transformed);
python::enum_<StruChkResult>("StruChkResult")
.value("success",success)
.value("bad_set",bad_set)
.value("transformed_set",transformed_set)
;
.value("success", success)
.value("bad_set", bad_set)
.value("transformed_set", transformed_set);
}

10
External/AvalonTools/test1.cpp vendored
View File

@@ -276,7 +276,8 @@ void testSmilesSegFault() {
void testGithub336() {
BOOST_LOG(rdInfoLog) << "testing github issue 336: bad canonical smiles for "
"conjugated double bonds" << std::endl;
"conjugated double bonds"
<< std::endl;
// some tests around dealing with bad mol blocks
{
std::string pathName = getenv("RDBASE");
@@ -386,7 +387,6 @@ void testCountFps() {
void testInitStruChk() {
BOOST_LOG(rdInfoLog) << "testing init struchk " << std::endl;
{
std::string pathName = getenv("RDBASE");
pathName += "/Data/struchk/";
std::string struchk_init =
@@ -402,9 +402,9 @@ void testInitStruChk() {
"-cs\n"
"-cn 999\n"
"-l " +
#ifdef _WIN32
#ifdef _WIN32
std::getenv("TEMP") +
#endif
#endif
std::string(std::tmpnam(NULL)) + std::string("\n");
int errs = AvalonTools::initCheckMol(struchk_init);
TEST_ASSERT(!errs);
@@ -414,7 +414,7 @@ void testInitStruChk() {
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
int main(int argc, char *argv[]) {
int main() {
RDLog::InitLogs();
#if 1
test1();

3542
External/INCHI-API/inchi.cpp vendored
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