include/OBNbrList src/forcefields/mmff94/function.cpp src/obnbrlist.cpp src/obnbrlist.h tests/mockfunction.h tests/nbrlisttest.cpp tests/varianttest.exe tools/minimize_gaff.exe @@ -87,12 +87,9 @@ ELSE (WIN32) ENDIF(APPLE) ENDIF (WIN32) -SET( OPENCL_FOUND "NO" ) IF(OPENCL_cl_LIBRARY) - - SET( OPENCL_LIBRARIES ${OPENCL_cl_LIBRARY} ${OPENCL_LIBRARIES}) - SET( OPENCL_FOUND "YES" ) - + SET(OPENCL_LIBRARIES ${OPENCL_cl_LIBRARY} ${OPENCL_LIBRARIES}) + SET(OPENCL_FOUND True) ENDIF(OPENCL_cl_LIBRARY) # This deprecated setting is for backward compatibility with CMake1.4 cmake/modules/FindOpenCL.cmake @@ -87,7 +87,8 @@ namespace OpenBabel { { p_gaffType = (GAFFType *) GetOBFFType(); if (p_gaffType==NULL){ - p_gaffTypeRules = new GAFFTypeRules("../data/gaff.prm"); //here should be the default value to gaff.prm + std::string filename = std::string(DATADIR) + "gaff.prm"; + p_gaffTypeRules = new GAFFTypeRules(filename); //here should be the default value to gaff.prm if (p_gaffTypeRules==NULL) return false; else { @@ -102,7 +103,8 @@ namespace OpenBabel { } } else if (! (p_gaffType->IsInitialized()) ) { - p_gaffTypeRules = new GAFFTypeRules("../data/gaff.prm"); //here should be the default value to gaff.prm + std::string filename = std::string(DATADIR) + "gaff.prm"; + p_gaffTypeRules = new GAFFTypeRules(filename); //here should be the default value to gaff.prm if (p_gaffTypeRules==NULL) return false; else { @@ -112,7 +114,8 @@ namespace OpenBabel { } p_database = (GAFFParameterDB *) GetParameterDB(); if (p_database==NULL){ - p_database = new GAFFParameterDB("../data/gaff.dat");; + std::string filename = std::string(DATADIR) + "gaff.dat"; + p_database = new GAFFParameterDB(filename);; if (p_database==NULL) return false; else { src/forcefields/gaff/gafffunction.cpp @@ -19,11 +19,10 @@ GNU General Public License for more details. #include <OBFFParameterDB> namespace OpenBabel { - - class OBMol; - namespace OBFFs { - class GAFFParameterDB : public OBFFParameterDB - { +namespace OBFFs { + + class GAFFParameterDB : public OBFFParameterDB + { public: GAFFParameterDB(const std::string &filename); bool IsInitialized() const { return _initialized; } @@ -32,6 +31,7 @@ namespace OpenBabel { bool ParseParamFile(); bool _initialized; std::string _filename; - }; - } -} + }; + +} // namespace OBFFs +} // namespace OpenBabel src/forcefields/gaff/gaffparameter.h @@ -575,27 +575,28 @@ namespace OpenBabel { return valid; } - bool GAFFType::IsConnected(const unsigned int &idxA, const unsigned int &idxB) const + bool GAFFType::IsConnected(const size_t &idxA, const size_t &idxB) const { return (m_Connected.find((idxA-1)+m_numAtoms*(idxB-1))!=m_Connected.end()); } - bool GAFFType::IsOneThree(const unsigned int &idxA, const unsigned int &idxB) const + bool GAFFType::IsOneThree(const size_t &idxA, const size_t &idxB) const { return (m_OneThree.find((idxA-1)+m_numAtoms*(idxB-1))!=m_OneThree.end()); } - bool GAFFType::IsOneFour(const unsigned int &idxA, const unsigned int &idxB) const + bool GAFFType::IsOneFour(const size_t &idxA, const size_t &idxB) const { return (m_OneFour.find((idxA-1)+m_numAtoms*(idxB-1))!=m_OneFour.end()); } - const string & GAFFType::GetAtomType(const unsigned int & idx) const + const string & GAFFType::GetAtomType(const size_t & idx) const { return m_atoms[idx-1]; } + /* const vector<OBFFType::AtomIdentifier> & GAFFType::GetAtoms() const { return m_atoms; @@ -620,6 +621,7 @@ namespace OpenBabel { { return m_oops; } + */ vector<string> GAFFType::MakeAlternativeAtomNames(string aName) { src/forcefields/gaff/gafftype.cpp @@ -42,15 +42,15 @@ namespace OpenBabel { bool ValidateTypes(GAFFParameterDB * pdatabase); //Check if types are in database. If not check for default patterns. If found change name. If still not found remove interaction from list. unsigned int Idx(const size_t & i) const {return m_isIdxTrivial ? (unsigned int) i + i : m_IToIdx.at(i);} size_t I(const unsigned int & idx) const {return m_isIdxTrivial ? (size_t) idx - 1 : m_IdxToI.find(idx)->second;} - const std::string & GetAtomType(const unsigned int & idx) const; - const std::vector<AtomIdentifier> & GetAtoms() const; - const std::vector<BondIdentifier> & GetBonds() const; - const std::vector<AngleIdentifier> & GetAngles() const; - const std::vector<TorsionIdentifier> & GetTorsions() const; - const std::vector<OOPIdentifier> & GetOOPs() const; - bool IsConnected(const unsigned int & idxA, const unsigned int & idxB) const; - bool IsOneThree(const unsigned int & idxA, const unsigned int & idxB) const; - bool IsOneFour(const unsigned int & idxA, const unsigned int & idxB) const; + const std::string & GetAtomType(const size_t & idx) const; + //const std::vector<AtomIdentifier> & GetAtoms() const; + //const std::vector<BondIdentifier> & GetBonds() const; + //const std::vector<AngleIdentifier> & GetAngles() const; + //const std::vector<TorsionIdentifier> & GetTorsions() const; + //const std::vector<OOPIdentifier> & GetOOPs() const; + bool IsConnected(const size_t & idxA, const size_t & idxB) const; + bool IsOneThree(const size_t & idxA, const size_t & idxB) const; + bool IsOneFour(const size_t & idxA, const size_t & idxB) const; protected: static std::vector<std::string> MakeAlternativeAtomNames(std::string aName); static std::string MakeBondName(std::string aName, std::string bName); @@ -65,11 +65,13 @@ namespace OpenBabel { GAFFTypeRules * p_typerules; unsigned int m_numAtoms; bool m_isIdxTrivial; + /* now defined in OBFFType std::vector<AtomIdentifier> m_atoms; std::vector<BondIdentifier> m_bonds; std::vector<AngleIdentifier> m_angles; std::vector<TorsionIdentifier> m_torsions; std::vector<OOPIdentifier> m_oops; + */ std::vector<double> m_masses; std::vector<double> m_charges; std::set<unsigned long int> m_Connected; src/forcefields/gaff/gafftype.h @@ -35,13 +35,18 @@ namespace OpenBabel { const std::string AngleHarmonic::m_name = "Angle Harmonic"; AngleHarmonic::AngleHarmonic(OBFunction *function, std::string tableName) - : OBFunctionTerm(function), m_tableName(tableName), m_value(999999.99) {} + : OBFunctionTerm(function), m_tableName(tableName), m_i(0), m_calcs(0), + m_value(999999.99) + { + } AngleHarmonic::~AngleHarmonic() { - delete [] m_i; - delete [] m_calcs; + if (m_i) + delete [] m_i; + if (m_calcs) + delete [] m_calcs; } // Conventions taken from Lammps potentials @@ -109,8 +114,10 @@ namespace OpenBabel { if ( (pTable==NULL) || (pOBFFType==NULL) ) return false; m_numAngles=angles.size(); - delete [] m_i; - delete [] m_calcs; + if (m_i) + delete [] m_i; + if (m_calcs) + delete [] m_calcs; m_i = new Index [m_numAngles]; m_calcs = new Parameter [m_numAngles]; for(unsigned int i=0;i != m_numAngles;++i){ src/forceterms/angle.cpp @@ -26,17 +26,56 @@ namespace OpenBabel { class OBFFTable : public OBParameterDBTable { public: + /** + * Constructor specifying the @p tableName and @p header. + */ OBFFTable(const std::string &tableName, const std::vector<std::string> &header); + /** + * Constructor specifying the @p tableName. + */ OBFFTable(const std::string &tableName); + /** + * @return The number of rows in this table. + */ unsigned int NumRows() const; unsigned int NumColumns() const; + /** + * @return std::vector containing the column headers as std:sstring + */ std::vector<std::string> GetHeader() const; + /** + * @return std::vector containing the column types as OBVariant::Type. + */ std::vector<OBVariant::Type> GetTypes() const; + /** + * @return True if all columns types in @p values match this tables column types. + * @sa GetTypes() + */ bool VerifyTypes(const std::vector<OBVariant> &values); + /** + * Get the row with index @p row. + */ const std::vector<OBVariant>& GetRow(unsigned int row) const; + /** + * Add a row to this table containing @p values. + */ bool AddRow(const std::vector<OBVariant> &values); + /** + * Find a row that matches the specified @p query. If the query was matched in + * reverse order (e.g. 1-2-3 vs. 3-2-1), the swapped flag will be set when non-zero. + * @return A constant reference to the row. + */ const std::vector<OBVariant>& FindRow(const std::vector<Query> &query, bool *swapped = 0) const; + /** + * Find a row that matches the specified @p query. If the query was matched in + * reverse order (e.g. 1-2-3 vs. 3-2-1), the swapped flag will be set when non-zero. + * @return A copy of the row. + */ std::vector< std::vector<OBVariant> > FindRows(const std::vector<Query> &query, bool *swapped = 0) const; + /** + * Get a constant reference to all rows in this table. This function can + * be used in graphical user interfaces to quickly access all data for display. + */ const std::vector<std::vector<OBVariant> >& GetAllRows() const; private: std::string _name; @@ -51,14 +90,38 @@ namespace OpenBabel { class OBFFParameterDB : public OBParameterDB { public: + /** + * Constructor specifying the @p databaseName. + */ OBFFParameterDB(const std::string &databaseName = ""); + /** + * Destructor. + */ ~OBFFParameterDB(); + OBFFParameterDB(const OBFFParameterDB &rhs) {}; //no copying of databases allowed + /** + * @return The number of tables in this database. + */ unsigned int NumTables() const; + /** + * @return std::vector containing the table names as std::string. + */ std::vector<std::string> GetTables() const; - OBFFTable * GetTable(const std::string &tableName) const; - OBFFTable * AddTable(const std::string &tableName, const std::vector<std::string> &header); - OBFFTable * AddTable(const std::string &tableName); + /** + * Get the table with the specified @p tableName. + */ + OBFFTable* GetTable(const std::string &tableName) const; + /** + * Add a table named @p tableName and @p header. + * @return A pointer to the newly added table. + */ + OBFFTable* AddTable(const std::string &tableName, const std::vector<std::string> &header); + /** + * Add a table named @p tableName. + * @return A pointer to the newly added table. + */ + OBFFTable* AddTable(const std::string &tableName); private: std::string _name; std::vector<OBFFTable *> _tables; src/obffparameterdb.h @@ -31,42 +31,119 @@ namespace OpenBabel { public: typedef std::string AtomIdentifier; + /** + * Bond identifier + */ struct BondIdentifier { std::string name; size_t iA, iB; }; + /** + * Angle identifier. + */ struct AngleIdentifier { - std::string name; size_t iA, iB, iC; }; + /** + * Torsion identifier. + */ struct TorsionIdentifier { std::string name; size_t iA, iB, iC, iD; }; + /** + * Out-of-plane identifier. + */ struct OOPIdentifier { std::string name; size_t iA, iB, iC, iD; }; - virtual bool SetTypes(const OBMol & mol) =0; + + /** + * Find atom types and initialize atom, bond, torsion and out-of-plane + * identifiers. This function will also initialize the internal cache + * for IsConnected, IsOneThree, IsOneFour. + */ + virtual bool SetTypes(const OBMol & mol) = 0; + virtual unsigned int Idx(const size_t & i) const =0; virtual size_t I(const unsigned int & idx) const =0; virtual const std::string & GetAtomType(const size_t & i) const =0; - virtual const std::vector<AtomIdentifier> & GetAtoms() const =0; - virtual const std::vector<BondIdentifier> & GetBonds() const =0; - virtual const std::vector<AngleIdentifier> & GetAngles() const =0; - virtual const std::vector<TorsionIdentifier> & GetTorsions() const =0; - virtual const std::vector<OOPIdentifier> & GetOOPs() const =0; + /** + * Get the atoms. These are the force field atom types as std::string. + * @sa AtomIdentifier + */ + virtual const std::vector<AtomIdentifier> & GetAtoms() const + { + return m_atoms; + } + /** + * Get the bonds. These are BondIdentifier structs containing the name + * (e.g. "2-5", "C-O", "C-X") for the bond and the atom I's. + * + * @sa I() Idx() BondIdentifier + */ + virtual const std::vector<BondIdentifier> & GetBonds() const + { + return m_bonds; + } + /** + * Get the angles. These are AngleIdentifier structs containing the name + * (e.g. "2-5-2", "C-O-C", "X-C-X") for the angle and the atom I's. + * + * @sa I() Idx() AngleIdentifier + */ + virtual const std::vector<AngleIdentifier> & GetAngles() const + { + return m_angles; + } + /** + * Get the torsions. These are TorsionIdentifier structs containing the + * name (e.g. "2-5-6-2", "C-O-C-C", "X-C-C-X") for the angle and the atom I's. + * + * @sa I() Idx() TorsionIdentifier + */ + virtual const std::vector<TorsionIdentifier> & GetTorsions() const + { + return m_torsions; + } + /** + * Get the out-of-plane angles. These are OOPIdentifier structs containing the + * name (e.g. "2-5-6-2", "C-O-C-C", "X-C-C-X") for the oop angle and the atom I's. + * + * @sa I() Idx() TorsionIdentifier + */ + + virtual const std::vector<OOPIdentifier> & GetOOPs() const + { + return m_oops; + } + /** + * @return True if atoms with index iA & iB are connected. + */ virtual bool IsConnected(const size_t & iA, const size_t & iB) const =0; + /** + * @return True if atoms with index iA & iB are in a 1-3 relation. + */ virtual bool IsOneThree(const size_t & iA, const size_t & iB) const =0; + /** + * @return True if atoms with index iA & iB are in a 1-4 relation. + */ virtual bool IsOneFour(const size_t & iA, const size_t & iB) const =0; + protected: + std::vector<AtomIdentifier> m_atoms; + std::vector<BondIdentifier> m_bonds; + std::vector<AngleIdentifier> m_angles; + std::vector<TorsionIdentifier> m_torsions; + std::vector<OOPIdentifier> m_oops; }; } }// namespace OpenBabel src/obfftype.h @@ -83,7 +83,6 @@ GNU General Public License for more details. #include <openbabel/rotamer.h> #include <openbabel/rotor.h> -#include <OBCutOffGrid> #include <OBMinimize> #include <OBVectorMath> src/obforcefield.cpp @@ -21,6 +21,10 @@ GNU General Public License for more details. #include <OBMinimize> #include <openbabel/obutil.h> +#ifdef __MINGW32__ +#include <cstdio> // FIXME replace snprinf with std::stringstream +#endif + using namespace std; using namespace OpenBabel::OBFFs; src/obminimize.cpp @@ -1,3 +1,6 @@ +# define TESTDATADIR for tests that need input files +add_definitions(-DTESTDATADIR="${CMAKE_SOURCE_DIR}/tests/") + set(QT_USE_QTOPENGL true) include(${QT_USE_FILE}) @@ -25,6 +28,7 @@ link_directories( set(tests # forcefield variant + nbrlist gaffparameterdb gaffgradient gafffunction tests/CMakeLists.txt @@ -184,11 +184,16 @@ int main() OBMol mol; OBConversion conv; - conv.SetInFormat("mol"); + conv.SetInFormat("pdb"); std::ifstream ifs; //ifs.open("hexane.xyz"); - ifs.open("acetone.pdb"); + string filename = string(TESTDATADIR) + string("aceton.pdb"); + ifs.open(filename.c_str()); + if (!ifs) { + cout << "could not open aceton.pdb" << endl; + return -1; + } conv.Read(&mol, &ifs); ifs.close(); tests/gaffgradienttest.cpp @@ -495,7 +495,8 @@ void testTorsionParameters(OBParameterDB *database) int main() { - GAFFParameterDB *database = new GAFFParameterDB("d:/eajfpeters/My Documents/code/OBForceField/data/gaff.dat"); + std::cout << string(TESTDATADIR) + string("../data/gaff.dat") << std::endl; + GAFFParameterDB *database = new GAFFParameterDB(string(TESTDATADIR) + string("../data/gaff.dat")); testTables(database); testAtomProperties(database); testBondParameters(database); tests/gaffparameterdbtest.cpp include/OBCutOffGrid src/obcutoffgrid.cpp src/obcutoffgrid.h c6915bf895cee982fc8ecc3ebf2d2c758aca1baa 9f9bf7480c8e90f58dd407a70e4394cd6cdd24b5 eajfpeters e.a.j.f.peters@gmail.com http://github.com/timvdm/OBForceField/commit/cc36dec3b14a1cb6bc84958fc6448a861838f909 cc36dec3b14a1cb6bc84958fc6448a861838f909 2009-10-19T04:52:22-07:00 2009-10-19T04:52:22-07:00 Merge branch 'master' of git://github.com/timvdm/OBForceField.git Conflicts: CMakeLists.txt src/forcefields/gaff/gafffunction.cpp src/forcefields/gaff/gaffparameter.h src/forcefields/gaff/gafftype.cpp src/forcefields/gaff/gafftype.h src/forcefields/mmff94/function.cpp src/forceterms/angle.cpp src/obffparameterdb.h src/obfftype.h tests/CMakeLists.txt tests/gaffgradienttest.cpp tests/gaffparameterdbtest.cpp 575acdc58f61748e564f0bc2b5062ca0468123f8 eajfpeters e.a.j.f.peters@gmail.com