OETorLib

class OETorLib

This class represents OETorLib.

See also

Constructors

OETorLib()
OETorLib(unsigned int type)

Default and copy constructors. The constructor with the type parameter allows the user to set the torsion library type from values in the OETorLibType namespace.

operator bool

operator bool() const

Returns false if the OETorLib object is empty, otherwise returns true.

AddTorsionLibrary

bool AddTorsionLibrary(const std::string &)
bool AddTorsionLibrary(OEPlatform::oeistream &)

Takes a string or an oeistream object to add a torsion library. This will put the new torsion library above the current torsion library, which means that they will be checked first for a match. To replace the torsion library, call OETorLib.SetTorsionLibrary. The format for rules is a SMARTS pattern followed by the torsion angles. Method returns True if the library is added successfully. The following is an example of a general rule:

[*:1][CH2:2][a:3][a:4] 0 180 90 -90 45 -45 135 -135

AddTorsionRule

bool AddTorsionRule(const std::string &)

Add a single torsion rule as a string. The string should be in the same format as a single line from a torsion library file. The following code demonstrates how to add a new torsion rule to an existing OEOmega object named omega.

Example of adding a new torsion rule

// Adding the torsion rule "[O:1]=[C:2]-[O:3][CH3:4] 90" as a string
// This takes precedent over previous rule
final String rule = "[O:1]=[C:2]-[O:3][CH3:4] 90";
if(!torlib.AddTorsionRule(rule))
    oechem.OEThrow.Fatal("Failed to add torsion rule: " + rule);

omegaOpts.SetTorLib(torlib);
omega.SetOptions(omegaOpts);
if(omega.call(mol))
    oechem.OEWriteMolecule(ofs, mol);

The new rule will take precedence over all rules previously added to this object either from a file or calling this method.

bool AddTorsionRule(OEChem::OEQMolBase &qmol, std::vector<int> &degrees)

The next signature of AddTorsionRule takes a generic OEQMolBase with a corresponding std::vector<int> containing the angles. The pattern represented by OEQMolBase should have map indices set on the atoms considered the torsion. In SMARTS this means the atoms should have map indices numbered from 1-4. This can theoretically allow torsion rules to be written in other query file formats provided there is a method for setting the appropriate map indices. The following code demonstrates how to initialize an OEQMolBase and use it to define a new torsion rule.

Example of adding a new torsion rule from a query molecule

// Adding torsion rule "[O:1]=[C:2]-[O:3][CH3:4] 45" as a query
// molecule. This takes precedent over default rule
OEQMol qmol = new OEQMol();
oechem.OEParseSmarts(qmol, "[O:1]=[C:2]-[O:3][CH3:4]");
ArrayList<Integer> degrees = new ArrayList<Integer>();
degrees.add(45);

if (!torlib.AddTorsionRule(qmol, degrees))
    oechem.OEThrow.Fatal("Failed to add torsion rule");

omegaOpts.SetTorLib(torlib);
omega.SetOptions(omegaOpts);
if (omega.call(mol))
    oechem.OEWriteMolecule(ofs, mol);

ClearTorsionLibrary

void ClearTorsionLibrary()

Clears the current torsion library. Omega cannot operate with an empty torsion library, so a new torsion library must be set before running Omega.

GetTorRule

const OEChem::OESubSearch* GetTorRule(const OEChem::OEMolBase&,
      const OEChem::OEBondBase&) const

Returns the torsion rule associated with the specified bond of the specified molecule. Method returns a null pointer if a torsion rule is not found. The rules are stored as OESubSearch objects.

See also

GetTorRules

OESystem::OEIterBase<OEChem::OESubSearch> *GetTorRules()

Returns an iterator over the torsion rules. The rules are stored as OESubSearch objects.

HasTorRule

bool HasTorRule(const OEChem::OEMolBase&, const OEChem::OEBondBase&) const

Checks if a torsion rule exists with the specified bond of the specified molecule. Returns true if a rule exists.

ResetTorsionLibrary

bool ResetTorsionLibrary()

Resets the torsion library stored internally by Omega. Method returns True if the library is reset successfully.

SetTorsionLibrary

bool SetTorsionLibrary(const std::string &)
bool SetTorsionLibrary(OEPlatform::oeistream &)
bool SetTorsionLibrary(unsigned int type)

Replaces the current torsion library with the one passed in as an argument. If the argument is a type, it is expected to be a value in the OETorLibType namespace. Method returns True if the library is set successfully.