PLMD::secondarystructure::SecondaryStructureRMSD Member List

This is the complete list of members for PLMD::secondarystructure::SecondaryStructureRMSD, including all inherited members.

Action(const ActionOptions &)PLMD::Actionexplicit
Action(const Action &a)=deletePLMD::Actionprivate
ActionAtomistic(const ActionOptions &ao)PLMD::ActionAtomisticexplicit
actionIsBridgedPLMD::vesselbase::ActionWithVesselprivate
ActionWithValue(const ActionOptions &ao)PLMD::ActionWithValueexplicit
ActionWithVessel(const ActionOptions &ao)PLMD::vesselbase::ActionWithVesselexplicit
activate()PLMD::Actionvirtual
activePLMD::Actionprivate
addBridgingVessel(ActionWithVessel *tome)PLMD::vesselbase::ActionWithVesselprotected
addColvar(const std::vector< unsigned > &newatoms)PLMD::secondarystructure::SecondaryStructureRMSDprotected
addComponent(const std::string &name)PLMD::ActionWithValue
addComponentWithDerivatives(const std::string &name)PLMD::ActionWithValue
addDependency(Action *)PLMD::Action
addTaskToList(const unsigned &taskCode)PLMD::vesselbase::ActionWithVesselprotected
addValue()PLMD::ActionWithValue
addValueWithDerivatives()PLMD::ActionWithValue
addVessel(const std::string &name, const std::string &input, const int numlab=0)PLMD::vesselbase::ActionWithVesselprotected
addVessel(std::unique_ptr< Vessel > vv)PLMD::vesselbase::ActionWithVesselprotected
afterPLMD::Actionprivate
align_atom_1PLMD::secondarystructure::SecondaryStructureRMSDprivate
align_atom_2PLMD::secondarystructure::SecondaryStructureRMSDprivate
align_strandsPLMD::secondarystructure::SecondaryStructureRMSDprivate
alignTypePLMD::secondarystructure::SecondaryStructureRMSDprivate
all_atomsPLMD::secondarystructure::SecondaryStructureRMSDprivate
allowToAccessGlobalForces()PLMD::ActionAtomisticinline
apply() overridePLMD::secondarystructure::SecondaryStructureRMSDvirtual
applyBridgeForces(const std::vector< double > &bb)PLMD::vesselbase::ActionWithVesselinlinevirtual
applyForces()PLMD::ActionAtomistic
atomsPLMD::ActionAtomisticprotected
beforeUpdate()PLMD::Actioninlinevirtual
bridgeVariablePLMD::vesselbase::ActionWithVesselprotected
bufferPLMD::vesselbase::ActionWithVesselprivate
buildDataStashes(ActionWithVessel *actionThatUses)PLMD::vesselbase::ActionWithVessel
calculate() overridePLMD::secondarystructure::SecondaryStructureRMSDvirtual
calculateAllVessels(const unsigned &taskCode, MultiValue &myvals, MultiValue &bvals, std::vector< double > &buffer, std::vector< unsigned > &der_list)PLMD::vesselbase::ActionWithVesselprotected
calculateAtomicNumericalDerivatives(ActionWithValue *a, const unsigned &startnum)PLMD::ActionAtomistic
calculateFromPDB(const PDB &)PLMD::Action
calculateNumericalDerivatives(ActionWithValue *a=NULL) overridePLMD::ActionAtomisticvirtual
changeBox(const Tensor &newbox)PLMD::ActionAtomistic
chargesPLMD::ActionAtomisticprivate
chargesWereSetPLMD::ActionAtomisticprivate
checkFieldsAllowed()PLMD::ActionWithValueinlinevirtual
checkNeedsGradients() constPLMD::Actioninlinevirtual
PLMD::checkNumericalDerivatives() constPLMD::Actioninlinevirtual
PLMD::ActionWithValue::checkNumericalDerivatives() const overridePLMD::ActionWithValueinlinevirtual
checkRead()PLMD::Action
checkUpdate() constPLMD::Action
cite(const std::string &s)PLMD::Action
clearDependencies()PLMD::Action
clearDerivatives()PLMD::ActionWithValuevirtual
clearInputForces()PLMD::ActionWithValue
clearOptions()PLMD::Actionvirtual
clearOutputForces()PLMD::ActionAtomistic
colvar_atomsPLMD::secondarystructure::SecondaryStructureRMSDprivate
commPLMD::Action
componentIsNotPeriodic(const std::string &name)PLMD::ActionWithValue
componentIsPeriodic(const std::string &name, const std::string &min, const std::string &max)PLMD::ActionWithValue
componentsAreNotOptional(Keywords &keys)PLMD::ActionWithValuestatic
contributorsAreUnlockedPLMD::vesselbase::ActionWithVesselprotected
copyOutput(const std::string &name) constPLMD::ActionWithValue
copyOutput(const unsigned &n) constPLMD::ActionWithValue
deactivate()PLMD::Actioninlinevirtual
deactivateAllTasks()PLMD::vesselbase::ActionWithVesselprotected
Dependencies typedefPLMD::Action
der_listPLMD::vesselbase::ActionWithVesselprivate
derivativesAreRequired() constPLMD::vesselbase::ActionWithVesselinline
dertimePLMD::vesselbase::ActionWithVesselprotected
dertime_can_be_offPLMD::vesselbase::ActionWithVesselprivate
doCheckPointPLMD::Actionprivate
doJobsRequiredBeforeTaskList()PLMD::vesselbase::ActionWithVesselvirtual
doNotCalculateDerivatives() constPLMD::ActionWithValueinlinevirtual
doNotForce()PLMD::ActionAtomisticinline
donotforcePLMD::ActionAtomisticprivate
doNotRetrieve()PLMD::ActionAtomisticinline
donotretrievePLMD::ActionAtomisticprivate
energyPLMD::ActionAtomisticprivate
error(const std::string &msg) constPLMD::Action
exists(const std::string &name) constPLMD::ActionWithValue
exit(int c=0)PLMD::Action
extraCVPLMD::ActionAtomisticprivate
fclose(FILE *fp)PLMD::Action
fflush()PLMD::Action
filesPLMD::Action
finishComputations(const std::vector< double > &buffer)PLMD::vesselbase::ActionWithVesselvirtual
fopen(const char *path, const char *mode)PLMD::Action
forceOnEnergyPLMD::ActionAtomisticprivate
forceOnExtraCVPLMD::ActionAtomisticprivate
forcesPLMD::ActionAtomisticprivate
forcesToApplyPLMD::secondarystructure::SecondaryStructureRMSDprivate
fullTaskListPLMD::vesselbase::ActionWithVesselprivate
functionsPLMD::vesselbase::ActionWithVesselprivate
getAbsoluteIndex(int i) constPLMD::ActionAtomisticinline
getAbsoluteIndexes() constPLMD::ActionAtomisticinlinevirtual
getActiveTask(const unsigned &ii) constPLMD::vesselbase::ActionWithVesselinline
getAtomIndex(const unsigned &current, const unsigned &iatom) constPLMD::secondarystructure::SecondaryStructureRMSDinlineprivate
getBox() constPLMD::ActionAtomisticinline
getCharge(int i) constPLMD::ActionAtomisticinline
getComponent(const std::string &name) constPLMD::ActionWithValueprivate
getComponentsList() constPLMD::ActionWithValue
getComponentsVector() constPLMD::ActionWithValue
getCPT() constPLMD::Action
getCurrentNumberOfActiveTasks() constPLMD::vesselbase::ActionWithVesselinline
getDependencies() constPLMD::Actioninline
getDocumentation() constPLMD::Actionvirtual
getEnergy() constPLMD::ActionAtomisticinline
getExchangeStep() constPLMD::Action
getForcesFromVessels(std::vector< double > &forcesToApply)PLMD::vesselbase::ActionWithVesselprotected
getFullNumberOfTasks() constPLMD::vesselbase::ActionWithVesselinline
getGlobalPosition(AtomNumber) constPLMD::ActionAtomisticinline
getKeyword(const std::string &key)PLMD::Action
getLabel() constPLMD::Actioninline
getMass(int i) constPLMD::ActionAtomisticinline
getName() constPLMD::Actioninline
getNLTolerance() constPLMD::vesselbase::ActionWithVesselinlineprotected
getNumberOfAtoms() constPLMD::ActionAtomisticinline
getNumberOfComponents() constPLMD::ActionWithValueinline
getNumberOfDerivatives() overridePLMD::secondarystructure::SecondaryStructureRMSDinlinevirtual
getNumberOfFunctionsInAction()PLMD::secondarystructure::SecondaryStructureRMSDinline
getNumberOfQuantities() const overridePLMD::secondarystructure::SecondaryStructureRMSDinlinevirtual
getNumberOfVessels() constPLMD::vesselbase::ActionWithVesselinline
getOutputQuantity(const unsigned j) constPLMD::ActionWithValueinline
getOutputQuantity(const std::string &name) constPLMD::ActionWithValueinline
getPbc() constPLMD::ActionAtomisticinline
getPntrToComponent(int i)PLMD::ActionWithValueprotected
getPntrToComponent(const std::string &name)PLMD::ActionWithValueprotected
getPntrToValue()PLMD::ActionWithValueprotected
getPntrToVessel(const unsigned &i)PLMD::vesselbase::ActionWithVesselinline
getPosition(int) constPLMD::ActionAtomisticinline
getPositionInCurrentTaskList(const unsigned &myind) constPLMD::vesselbase::ActionWithVesselinline
getPositionInFullTaskList(const unsigned &ii) constPLMD::vesselbase::ActionWithVesselinline
getPositions() constPLMD::ActionAtomisticinline
getRestart() constPLMD::Actioninline
getSizeOfBuffer(unsigned &bufsize)PLMD::vesselbase::ActionWithVesselprotected
getStep() constPLMD::Action
getTaskCode(const unsigned &ii) constPLMD::vesselbase::ActionWithVesselinline
getTime() constPLMD::Action
getTimeStep() constPLMD::Action
getTolerance() constPLMD::vesselbase::ActionWithVesselinlineprotected
getTotAtoms() constPLMD::ActionAtomisticinline
getUnique() constPLMD::ActionAtomisticinline
getUniqueLocal() constPLMD::ActionAtomisticinline
getVesselWithName(const std::string &mynam)PLMD::vesselbase::ActionWithVessel
indexesPLMD::ActionAtomisticprivate
indexOfTaskInFullListPLMD::vesselbase::ActionWithVesselprivate
interpretAtomList(std::vector< std::string > &strings, std::vector< AtomNumber > &t)PLMD::ActionAtomistic
isActive() constPLMD::Actioninline
isOptionOn(const std::string &s) constPLMD::Actioninline
isPeriodic() overridePLMD::secondarystructure::SecondaryStructureRMSDinlinevirtual
keywordsPLMD::Action
labelPLMD::Actionprivate
linePLMD::Actionprivate
lockContributors()PLMD::vesselbase::ActionWithVessel
lockRequestAtomsPLMD::ActionAtomisticprivate
lockRequests() overridePLMD::ActionAtomisticinlinevirtual
logPLMD::Action
lowmemPLMD::vesselbase::ActionWithVesselprivate
makeWhole()PLMD::ActionAtomistic
massesPLMD::ActionAtomisticprivate
maxderivativesPLMD::vesselbase::ActionWithVesselprivate
modifyForceOnEnergy()PLMD::ActionAtomisticinline
modifyForceOnExtraCV()PLMD::ActionAtomisticinline
modifyForces()PLMD::ActionAtomisticinline
modifyGlobalForce(AtomNumber)PLMD::ActionAtomisticinline
modifyGlobalPbc()PLMD::ActionAtomisticinline
modifyGlobalPosition(AtomNumber)PLMD::ActionAtomisticinline
modifyGlobalVirial()PLMD::ActionAtomisticinline
modifyVirial()PLMD::ActionAtomisticinline
multi_sim_commPLMD::Action
mydataPLMD::vesselbase::ActionWithVesselprotected
nactive_tasksPLMD::vesselbase::ActionWithVesselprivate
namePLMD::Actionprivate
needsDerivatives()PLMD::vesselbase::ActionWithVesselprotected
nl_tolerancePLMD::vesselbase::ActionWithVesselprivate
noAnalyticalDerivatives(Keywords &keys)PLMD::ActionWithValuestatic
PLMD::noderivPLMD::ActionWithValueprivate
nopbcPLMD::secondarystructure::SecondaryStructureRMSDprivate
normalizeVector(std::vector< double > &vals) constPLMD::vesselbase::ActionWithVesselinlinevirtual
normalizeVectorDerivatives(MultiValue &myvals) constPLMD::vesselbase::ActionWithVesselinlinevirtual
numericalDerivativesPLMD::ActionWithValueprivate
operator=(const Action &a)=deletePLMD::Actionprivate
optionsPLMD::Actionprivate
parse(const std::string &key, T &t)PLMD::Action
parseAtomList(const std::string &key, std::vector< AtomNumber > &t)PLMD::ActionAtomistic
parseAtomList(const std::string &key, const int num, std::vector< AtomNumber > &t)PLMD::ActionAtomistic
parseFlag(const std::string &key, bool &t)PLMD::Action
parseNumbered(const std::string &key, const int no, T &t)PLMD::Action
parseNumberedVector(const std::string &key, const int no, std::vector< T > &t)PLMD::Action
parseVector(const std::string &key, std::vector< T > &t)PLMD::Action
partialTaskListPLMD::vesselbase::ActionWithVesselprivate
pbcPLMD::ActionAtomisticprivate
pbc_fwdPLMD::ActionAtomisticprivate
pbcApply(std::vector< Vector > &dlist, unsigned max_index=0) constPLMD::ActionAtomistic
pbcDistance(const Vector &, const Vector &) constPLMD::ActionAtomistic
performTask(const unsigned &, const unsigned &, MultiValue &) const overridePLMD::secondarystructure::SecondaryStructureRMSDvirtual
plumedPLMD::Action
positionsPLMD::ActionAtomisticprivate
prepare()PLMD::Actionvirtual
readAtomsFromPDB(const PDB &pdb) overridePLMD::ActionAtomisticvirtual
readBackboneAtoms(const std::string &backnames, std::vector< unsigned > &chain_lengths)PLMD::secondarystructure::SecondaryStructureRMSDprotected
readVesselKeywords()PLMD::vesselbase::ActionWithVesselprotected
referencesPLMD::secondarystructure::SecondaryStructureRMSDprivate
registerKeywords(Keywords &keys)PLMD::secondarystructure::SecondaryStructureRMSDstatic
replica_indexPLMD::Actionprivate
requestAtoms(const std::vector< AtomNumber > &a, const bool clearDep=true)PLMD::ActionAtomistic
resizeFunctions()PLMD::vesselbase::ActionWithVesselprotected
restartPLMD::Actionprivate
retrieveAtoms()PLMD::ActionAtomisticvirtual
retrieveDomain(std::string &min, std::string &max)PLMD::vesselbase::ActionWithVesselvirtual
runAllTasks()PLMD::vesselbase::ActionWithVesselprotected
runFinalJobs()PLMD::Actioninlinevirtual
s_cutoff2PLMD::secondarystructure::SecondaryStructureRMSDprivate
SecondaryStructureRMSD(const ActionOptions &)PLMD::secondarystructure::SecondaryStructureRMSDexplicit
serialPLMD::vesselbase::ActionWithVesselprivate
serialCalculation() constPLMD::vesselbase::ActionWithVesselinlineprotected
setAtomsFromStrands(const unsigned &atom1, const unsigned &atom2)PLMD::secondarystructure::SecondaryStructureRMSDprotected
setExtraCV(const std::string &name)PLMD::ActionAtomisticinlineprotected
setForcesOnAtoms(const std::vector< double > &forcesToApply, unsigned ind=0)PLMD::ActionAtomistic
setGradientsIfNeeded()PLMD::ActionWithValue
setLowMemOption(const bool &)PLMD::vesselbase::ActionWithVesselinlineprotected
setNotPeriodic()PLMD::ActionWithValue
setOption(const std::string &s)PLMD::Actionvirtual
setPeriodic(const std::string &min, const std::string &max)PLMD::ActionWithValue
setSecondaryStructure(std::vector< Vector > &structure, double bondlength, double units)PLMD::secondarystructure::SecondaryStructureRMSDprotected
setValue(const double &d)PLMD::ActionWithValueinlineprotected
setValue(Value *, double)PLMD::ActionWithValue
stopwatchPLMD::vesselbase::ActionWithVesselprivate
stopwatch_fwdPLMD::vesselbase::ActionWithVesselprivate
taskFlagsPLMD::vesselbase::ActionWithVesselprotected
taskIsCurrentlyActive(const unsigned &index) constPLMD::vesselbase::ActionWithVessel
threadSafe() constPLMD::vesselbase::ActionWithVesselinlinevirtual
timersPLMD::vesselbase::ActionWithVesselprivate
tmpforcesPLMD::vesselbase::ActionWithVesselprivate
tolerancePLMD::vesselbase::ActionWithVesselprivate
transformBridgedDerivatives(const unsigned &current, MultiValue &invals, MultiValue &outvals) constPLMD::vesselbase::ActionWithVesselvirtual
turnOnDerivatives() overridePLMD::secondarystructure::SecondaryStructureRMSDvirtual
uniquePLMD::ActionAtomisticprivate
unique_localPLMD::ActionAtomisticprivate
unlockRequests() overridePLMD::ActionAtomisticinlinevirtual
update()PLMD::Actioninlinevirtual
update_fromPLMD::Actionprivate
update_untilPLMD::Actionprivate
updateUniqueLocal()PLMD::ActionAtomistic
useCustomisableComponents(Keywords &keys)PLMD::ActionWithValuestatic
useNumericalDerivatives()PLMD::ActionWithValueinline
usingLowMem() constPLMD::vesselbase::ActionWithVesselinlineprotected
valuesPLMD::ActionWithValueprivate
verbose_outputPLMD::secondarystructure::SecondaryStructureRMSDprivate
virialPLMD::ActionAtomisticprivate
warning(const std::string &msg)PLMD::Action
weightHasDerivativesPLMD::vesselbase::ActionWithVesselprotected
weightWithDerivatives() constPLMD::vesselbase::ActionWithVesselinline
~Action()PLMD::Actionvirtual
~ActionAtomistic()PLMD::ActionAtomistic
~ActionWithValue()PLMD::ActionWithValue
~ActionWithVessel()PLMD::vesselbase::ActionWithVessel
~SecondaryStructureRMSD()PLMD::secondarystructure::SecondaryStructureRMSDvirtual