OEPlaceHydrogensDetails

class OEPlaceHydrogensDetails

The read-only container OEPlaceHydrogensDetails holds information about the results of applying the function OEPlaceHydrogens to a particular molecule. Details objects can provide insight into the conformational states and how they were chosen.

Information is broken down into clusters (including singletons) of “movers” or moving functional groups and their associated “background” of non-moving groups. Information about each mover is collected in a corresponding OEPlaceHydrogensMoverNote.

See also

Constructors

OEPlaceHydrogensDetails()
OEPlaceHydrogensDetails(const OEPlaceHydrogensDetails &rhs)

Default and copy constructor.

operator=

OEPlaceHydrogensDetails &operator=(const OEPlaceHydrogensDetails &rhs)

Assignment operator.

ClusterHasBadClash

bool ClusterHasBadClash(unsigned clusterIdx) const

Returns true if the cluster referred to by clusterIdx is in a conformation that generates a “bad” atom-atom clash.

See also

Describe

std::string Describe(bool showBackground=false) const

Returns a multi-line description of the conformation and score of movers in each cluster processed by the OEPlaceHydrogens function.

OEBio 2.1.1: score system MMFF-NIE: flip bias 2.000
87 clusters : 5 flips
cluster 0  : score -53.935!
             CG  ASN44(A)   :      amide:   -6.084  (o=-53.93!,f=-8.42!)
             NZ  LYS47(A)   : NH3 150deg:  -14.865
             CG  HIS80(A)   :    +bothHN:   -5.628  (o=-53.93!,f=-15.89!)
             OG1 THR81(A)   : OH   65deg:    1.255
             CD  GLN87(A)   :FLIP  amide:   -4.976  (o=-26.48!,f=-53.93!)
             CG  ASN126(A)  :      amide:   -5.193  (o=-53.93!,f=-35.33!)
             CG  ASN169(A)  :      amide:   -2.230  (o=-53.93!,f=-33.02!)
             CD  GLN203(A)  :      amide:   -1.400  (o=-53.93!,f=-15.53!)
             CG  HIS205(A)  :    +bothHN:   -8.693! (o=-53.93!,f=-6.89!)
             OG1 THR232(A)  : OH  179deg:    9.120
             O3B XYP601(A)  : OH  280deg:   -5.020
             O2B XYP601(A)  : OH  173deg:    3.917
             O4B XYP601(A)  : OH   50deg:    1.236
             O3  XIF602(A)  : OH   29deg:   -3.688
cluster 1  : score -85.724!
             CG  HIS85(A)   :    +bothHN:   -7.737! (o=-85.72!,f=-84.85!)
             OG  SER86(A)   : OH  241deg:    2.116
             OG  SER139(A)  : OH  185deg:    3.367!
             OH  TYR171(A)  : OH   25deg:   -3.384
             CG  ASN172(A)  :      amide:    1.153  (o=-85.72!,f=-68.75!)
             NZ  LYS179(A)  : NH3 188deg:  -39.497
...
single  13 : OG1 THR2(A)    : OH  151deg:    1.545
single  14 : OG  SER25(A)   : OH  292deg:    2.046
single  15 : OH  TYR29(A)   : OH  199deg:   -1.262
single  16 : OG  SER35(A)   : OH  254deg:    1.935
...

Key elements in the description output:

  • The score system is MMFF-NIE which stands for “MMFF Neighbor Interaction Energies”. This is is a physics based score where the Coulombic and Van der Waals terms are from MMFF94 (including MMFF partial charges), with a weighting factor of 1:3 Coulomb to VDW. There are biases against ionization and “flipping” a group. Interactions are scored between movers and between movers and non-moving background atoms. Background atoms are neighboring atoms that form a “dipole cluster”, the sum of the partial charges of these clusters are the same as the sum of the formal charges.

  • The count 87 clusters includes both groups of interacting movers and singletons, movers that interact only with non-moving atoms or waters.

  • 5 flips indicates that five movers were “flipped” by 180 degrees to improve hydrogen bonding or avoid clashes. Groups such as the asparagine sidechain CD  GLN87(A)   :FLIP  amide: are occasionally modeled with certain heavy atoms in the wrong orientation. Any free amide or imidazole group will be considered for flipping.

  • The score in OG  SER139(A)  : OH  185deg:    3.367! is from score system MMFF-NIE for this mover in the specified conformation. Lower numbers represent better scores. The exclamation point (!) indicates a clash between this group and another group or non-moving background atom.

  • The score in cluster 0  : score -53.935! is the sum of both the mover scores, and the background scores (not shown here, but displayable if the showBackground parameter is set to true). The exclamation point (!) indicates that at least one mover had a clash.

  • The pair of scores for flippable groups (o=-53.93!,f=-8.42!) are the best cluster scores for both the original (o) and the flipped (f) state. After the basic optimization, each flippable mover in a cluster is fixed in the opposite flip state and the optimization is re-run. A group is flipped only if the flipped cluster score is lower than the original score by more than flip bias 2.000.

  • Imidazoles have both flipped states and three protonation states for each flip state. The description indicates whether the group is flipped and where protons are with respect to the two ring nitrogens: :     no HE2: neutral with HD1 but no HE2 or :FLIP no HD1: flipped neutral with HE2 but no HD1 or :    +bothHN: + charged with two NH protons.

  • Other groups have descriptions of their state. O3B XYP601(A)  : OH  280deg: shows the orientation of one of the hydroxyl rotors in the residue XYP.

  • Waters (not shown above) are processed after other movers, progressively in shells away from the protein.

See also

GetClusterScore

double GetClusterScore(unsigned clusterIdx) const

Returns the combined score of all the movers (plus non-moving background) of the cluster referred to by clusterIdx.

See also

GetFlipBias

double GetFlipBias() const

Returns the score bias against flipping functional groups (e.g. imidazole, amide) used by OEPlaceHydrogens when this details object was produced.

See also

GetMoverNotes

OESystem::OEIterBase<OEPlaceHydrogensMoverNote> *
  GetMoverNotes(unsigned clusterIdx) const

Returns an iterator of all the mover notes describing the state of movers in the cluster referred to by clusterIdx.

See also

GetNumClusters

unsigned GetNumClusters() const

Returns the number of mover clusters processed by OEPlaceHydrogens when this details object was produced.

GetNumFlips

unsigned GetNumFlips() const

Returns the number movers OEPlaceHydrogens decided to flip when this details object was produced.

See also

GetNumHydrogensStandardized

unsigned GetNumHydrogensStandardized() const

Returns the number of bonds between a hydrogen and a heavy atom whose length was adjusted by OEPlaceHydrogens when this details object was produced.

See also

GetNumMovers

unsigned GetNumMovers(unsigned clusterIdx) const

Returns the number of movers in the cluster referred to by clusterIdx (including all non-moving background “movers”).

See also

IsSingleton

bool IsSingleton(unsigned clusterIdx) const

Returns true if the cluster referred to by clusterIdx only contains a single mover (not counting the corresponding non-moving background).

See also

IsValid

bool IsValid() const

Returns true if this details object contains valid information. Returns false if OEPlaceHydrogens failed.