OETorLib¶
class OETorLib
This class represents OETorLib.
See also
OETorDriveOptions class
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
. Method returns
True
if the library is added successfully.
AddTorsionRule¶
bool AddTorsionRule(const std::string &)
Add a single torsion rule as a string. The format for
rules is a SMARTS pattern followed by the torsion angles. Method returns
True
if the rule 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
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
rule = "[O:1]=[C:2]-[O:3][CH3:4] 90"
if not torlib.AddTorsionRule(rule):
oechem.OEThrow.Fatal("Failed to add torsion rule: %s" % rule)
omegaOpts.SetTorLib(torlib)
omega.SetOptions(omegaOpts)
if omega(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> °rees)
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
qmol = oechem.OEQMol()
oechem.OEParseSmarts(qmol, "[O:1]=[C:2]-[O:3][CH3:4]")
degrees = oechem.OEIntVector([45])
if not torlib.AddTorsionRule(qmol, degrees):
oechem.OEThrow.Fatal("Failed to add torsion rule")
omegaOpts.SetTorLib(torlib)
omega.SetOptions(omegaOpts)
if omega(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
OEGetTorValues
function.
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.