babel.cpp File Reference Detailed DescriptionImplementation of the minimalistic Cuik-OpenBabel interface.
Definition in file babel.cpp.
Function Documentation
Initializes the molecule information from a file. This function also sets up the force field to be used for energy computations. For small molecules (less than 100 atoms) we use the MMFF94 force field. For larger ones we use the Generalized Amber Force Field (GAFF). The idea is that larger molecules correspond to proteins where the GAFF is more accurate.
Definition at line 46 of file babel.cpp. References TMolInfo::ff, and TMolInfo::mol. Referenced by InitBioWorld().
Stores the molecule information into a file (eg. a pdb).
Definition at line 79 of file babel.cpp. References Error(), and TMolInfo::mol. Referenced by SaveBioWorldBioInfo().
Number of atoms in a molecule.
Definition at line 100 of file babel.cpp. References TMolInfo::mol. Referenced by GetMoleculeBasicInfo().
Returns the atomic number of a given atom.
Definition at line 109 of file babel.cpp. References TMolInfo::mol. Referenced by AdjustBioWorldGeometry(), Atoms2Transforms(), DetectLinksAndJointsFromResidues(), and InitWorldFromMolecule().
Returns the number of the residue including the given atom.
Definition at line 121 of file babel.cpp. References TMolInfo::mol, and NO_UINT. Referenced by Atoms2Transforms(), and DetectLinksAndJointsFromResidues().
Returns a char identifying the chain of the atom (A B C...). Only works for atoms in residues.
Definition at line 138 of file babel.cpp. References TMolInfo::mol. Referenced by DetectLinksAndJointsFromResidues(). Identifies atoms in proline residues.
Definition at line 155 of file babel.cpp. References FALSE, and TMolInfo::mol. Referenced by DetectLinksAndJointsFromResidues().
Returns the Van der Waals radius for a given atom. This is used for representation purposes. The returned value is the standard VdW radius, that can be different from the VdW parameters used in the force field. Thus, this parameter can be adjusted (scaled down) if you want use this radius to radpidly discard high-energy conformations.
Definition at line 172 of file babel.cpp. References TMolInfo::mol. Referenced by GetMoleculeBasicInfo(), and InitWorldFromMolecule(). Determines if a bond between a given pair of atoms exists.
Definition at line 184 of file babel.cpp. References FALSE, TMolInfo::mol, and TRUE. Referenced by Atoms2Transforms(), and ReadRigidsAndHinges().
Adds a simple bond between the two given atoms. If the bond already exists it is re-added (probably OpenBabel takes care of removing duplicates). To ensure no duplicates are introduced use HasBond before adding it.
Definition at line 209 of file babel.cpp. References TMolInfo::mol. Referenced by ReadRigidsAndHinges().
Removes a bond between the two given atoms. No check is done on whether the bond actually exists.
Definition at line 218 of file babel.cpp. References TMolInfo::mol. Referenced by InitBioWorld().
Gets the identifier of the first neighbour of a given atom in the molecule.
Definition at line 244 of file babel.cpp. References FALSE, TMolInfo::mol, and NO_UINT. Referenced by AdjustBioWorldGeometry(), Atoms2Transforms(), DetectLinksAndJoints(), DetectLinksAndJointsFromResidues(), DetectLinksAndJointsFromRigidsAndHinges(), GetMoleculeBasicInfo(), and InitWorldFromMolecule().
Gets the identifier of the next neighbour of a given atom in the molecule.
Definition at line 271 of file babel.cpp. References FALSE, TMolInfo::mol, and NO_UINT. Referenced by AdjustBioWorldGeometry(), Atoms2Transforms(), DetectLinksAndJoints(), DetectLinksAndJointsFromResidues(), DetectLinksAndJointsFromRigidsAndHinges(), GetMoleculeBasicInfo(), and InitWorldFromMolecule().
Deletes the iterator defined in GetFirstNeighbour.
Definition at line 299 of file babel.cpp. Referenced by AdjustBioWorldGeometry(), Atoms2Transforms(), DetectLinksAndJoints(), DetectLinksAndJointsFromResidues(), DetectLinksAndJointsFromRigidsAndHinges(), GetMoleculeBasicInfo(), and InitWorldFromMolecule().
Gets the 3D positions of the atoms in the molecule. The space for the buffer must be allocated externally before using this function. This is typically used only once, after reading the molecule from file to have access to the "default" atom positions. After this we typically call SetAtomCoordinates so that the molecule and our system share the same vector of atom position.
Definition at line 308 of file babel.cpp. References TMolInfo::mol. Referenced by GetAtomPositions().
Sets the 3D positions of the atoms in the molecule. Note that this only need to be done once. The molecule store a pointer to the given array of positions that can be latter on modified externally.
Definition at line 325 of file babel.cpp. References TMolInfo::mol. Referenced by BioWordSetAtomPositionsFromConformation(), and InitBioWorld().
Computes the potential energy of a molecule according the the MMFF94 force field. The different conformations are defined by directly editing the vector of 3D positions of atoms given to the molecule using SetAtomCoordinates.
Definition at line 334 of file babel.cpp. References Error(), TMolInfo::ff, and TMolInfo::mol. Referenced by BioWorldEnergy().
Molecule information destructor.
Definition at line 353 of file babel.cpp. Referenced by DeleteBioWorld(). |
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