OESzmapResults

class OESzmapResults

This class represents OESzmapResults, a container for the results of OESzmap calculations with the function OECalcSzmapResults.

See also

• GetSzmapEnergies example

• SzmapBestOrientations example

Constructors

OESzmapResults()
OESzmapResults(const OESzmapResults &rhs)

Default and copy constructors. Typically an empty, default OESzmapResults is passed to OECalcSzmapResults where it is filled with the calculated results.

OESzmapResults result = new OESzmapResults();

operator=

OESzmapResults &operator=(const OESzmapResults &rhs)

Assignment operator.

operator bool

operator bool() const

True indicates that OECalcSzmapResults was called with a valid OESzmapEngine when this object was created.

Clear

void Clear()

Resets this object to an uninitialized, empty state.

GetComponent

bool GetComponent(double *compArray, unsigned int componentType) const
OESystem::OEIterBase<double> *GetComponent(unsigned int componentType) const

Returns the calculated values of a particular OEComponent, specified by componentType, for the 3D point provided to OECalcSzmapResults. Component values for each probe orientation are the low-level data used to compose OEEnsemble values (see OESzmapResults.GetEnsembleValue). The number of values in the output compArray or the iterator is OESzmapResults.NumOrientations and values are returned in the same order as the probe orientations.

System.out.println("interaction:");
OEDoubleIter coulombIter = new OEDoubleIter(result.GetComponent(OEComponent.Interaction));
while(coulombIter.hasNext()) {
    System.out.println(coulombIter.next());
}

Returns false or an empty iterator if the OEComponent type is not recognized.

GetCoords

bool GetCoords(float *xyz) const
bool GetCoords(double *xyz) const

Returns the coordinates of the 3D point where calculations were performed by OECalcSzmapResults to create this object.

The point is passed back in a float or double array of size three with coordinates in {x,y,z} order.

OEFloatArray point = new OEFloatArray(3);
result.GetCoords(point);

Returns false if this OESzmapResults is uninitialized.

GetEnsembleValue

double GetEnsembleValue(unsigned int ensembleType) const

Returns the calculated value of a particular OEEnsemble, specified by ensembleType, for the 3D point provided to OECalcSzmapResults. Ensemble values are the results of calculations over all orientations of the probe. In general, these are built by Boltzmann summation of various combinations of OEComponent values (see OESzmapResults.GetComponent).

double nddg = result.GetEnsembleValue(OEEnsemble.NeutralDiffDeltaG);

Returns 0.0 if the OEEnsemble type is not recognized or this OESzmapResults is uninitialized.

GetProbabilities

bool GetProbabilities(double *probArray) const
OESystem::OEIterBase<double> *GetProbabilities() const

Returns the statistical mechanical probabilities for each probe orientation at the 3D point provided to OECalcSzmapResults. Probability values can be used to Boltzmann weight OEComponent values and are used to select which probe orientations are returned by OESzmapResults.PlaceProbeSet. The number of values in the output probArray or the iterator is OESzmapResults.NumOrientations and values are returned in the same order as the probe orientations.

OEDoubleArray prob = new OEDoubleArray(result.NumOrientations());
result.GetProbabilities(prob);
System.out.format("greatest prob = %.3f%n", prob.getItem(order.getItem(0)));

Returns false or an empty iterator if this OESzmapResults is uninitialized.

GetProbabilityOrder

bool GetProbabilityOrder(unsigned int *orderArray) const
OESystem::OEIterBase<unsigned int> *GetProbabilityOrder() const

Returns an array or iterator of indices referring to probe orientations or associated OEComponent and probability values, sorted in the order of increasing probability (see OESzmapResults.GetProbabilities). Hence, the first (orderArray[0]) is the index of the orientation with the greatest probability (probArray[orderArray[0]]). The number of values in the output orderArray or the iterator is OESzmapResults.NumOrientations.

OEUIntArray order = new OEUIntArray(result.NumOrientations());
result.GetProbabilityOrder(order);
System.out.println("conf with greatest prob = " + order.getItem(0));

Returns false or an empty iterator if this OESzmapResults is uninitialized.

NumOrientations

unsigned int NumOrientations() const

Returns the number of orientations for the probe molecule used in the calculation. Equals the number of values returned by calls to OESzmapResults.GetComponent, OESzmapResults.GetProbabilities, or OESzmapResults.GetProbabilityOrder.

PlaceNewAtom

OEChem::OEAtomBase *PlaceNewAtom(OEChem::OEMolBase &mol,
                                 unsigned int element=OEChem::OEElemNo::O) const

Adds a new atom to the input molecule with atomic coordinates of the 3D point provided to OECalcSzmapResults when the object was created.

OEGraphMol amol = new OEGraphMol();
OEAtomBase atom = result.PlaceNewAtom(amol);
System.out.println("vdw = " + atom.GetStringData("vdw"));

The new atom has been annotated with ensemble values for this point as generic data. String versions of the data have been formatted to two decimal places for convenient display.

Generic Data Tag	Type	Value (energies in kcal/mol)
szmap_neut_diff_free_energy	double	Probe - neutral probe free energy difference
szmap_order	double	Fractional entropy loss from electrostatics
szmap_vdw	double	Van der Waals energy
free-energy	string	Formatted szmap_neut_diff_free_energy
order-param	string	Formatted szmap_order
vdw	string	Formatted szmap_vdw

The atom type can be controlled through the optional element parameter, which defaults to oxygen.

Atoms Placed at Calculation Points with Generic Data Annotation

Returns a pointer to the newly created atom to facilitate further customization.

PlaceProbeMol

bool PlaceProbeMol(OEChem::OEMolBase &outputMol, unsigned int orientation=0u,
                   bool annotate=true) const

Modifies the outputMol to be a copy of one probe orientation, placed at the 3D point provided to OECalcSzmapResults when the object was created. The probe orientation can be controlled through the optional orientation parameter (the default value of 0 refers to the first probe conformation).

OEGraphMol pmol = new OEGraphMol();
result.PlaceProbeMol(pmol, order.getItem(0));

If the optional parameter annotate is true (the default), the molecule will be annotated with OEComponent data for that orientation. See OESzmapResults.PlaceProbeSet for more information on this annotation.

Returns false if this OESzmapResults is uninitialized.

PlaceProbeSet

double PlaceProbeSet(OEChem::OEMCMolBase &probeSet, double probCutoff,
                     bool clear=true) const
double PlaceProbeSet(OEChem::OEMCMolBase &probeSet, unsigned int maxConfs=0u,
                     bool clear=true) const

Modifies the multi-conformer probeSet to contain one or more orientations of the probe, each placed at the 3D point provided to OECalcSzmapResults when the object was created. The probe set is returned in probability order (see OESzmapResults.GetProbabilityOrder).

There are three ways to select which probe orientations are placed in the probeSet:

• If just the probeSet parameter is provided, without other options, all probe orientations will be returned.

  OEMol mcmol = new OEMol();
  result.PlaceProbeSet(mcmol);
  

• If the real number parameter probCutoff is used, probe orientations will be added until the total cumulative probability is at least that amount. Cumulative probabilities are > 0.0 and <= 1.0.

  double probCutoff = 0.5;
  result.PlaceProbeSet(mcmol, probCutoff);
  System.out.println("nconf to yield 50pct = " + mcmol.NumConfs());
  

• Finally, if the integer parameter maxConfs is used, no more than number of probe orientations will be returned. A value of 0 is a special signal to return all orientations.

  boolean clear = false;
  double cumulativeProb = result.PlaceProbeSet(mcmol, 10, clear);
  System.out.println("best 10 cumulative prob = " + cumulativeProb);
  

If the optional parameter clear is set to false, any previous orientations in the probeSet will not be cleared, allowing conformers for multiple 3D points as well as multiple orientations to be stored in the probeSet. By default, previous orientations are cleared away before the new orientations are added.

Each orientation has been annotated with OEComponent data for that orientation. In addition, the total interaction + psolv + wsolv + vdw energy of each is recorded as the energy of the conformation (accessible using the GetEnergy() method of the conformer). String versions of the data have been formatted to two decimal places for convenient display. String data is also stored as SD data, so they are included in VIDA’s spreadsheet and can be saved to .sd files.

Generic/SD Data Tag	Type	SD	Value (energies in kcal/mol)
szmap_interaction	double	no	Poisson-Boltzmann probe|context interaction
szmap_psolv	double	no	(Protein) context desolvation penalty
szmap_wsolv	double	no	(Water) probe desolvation penalty
szmap_vdw	double	no	Van der Waals energy
szmap_probability	double	no	Boltzmann probability
total-energy	string	yes	szmap_interaction + psolv + wsolv + vdw
interaction	string	yes	Formatted szmap_interaction
psolv	string	yes	Formatted szmap_psolv
wsolv	string	yes	Formatted szmap_wsolv
vdw	string	yes	Formatted szmap_vdw
prob	string	yes	Formatted szmap_probability

Returns the cumulative probability of all the orientations returned, or 0.0 if this OESzmapResults is uninitialized.

SD Annotation in the VIDA Spreadsheet