PLMD::GenericMolInfo Member List

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

Action(const ActionOptions &)PLMD::Actionexplicit
Action(const Action &a)=deletePLMD::Actionprivate
ActionAnyorder(const ActionOptions &ao)PLMD::ActionAnyorderexplicit
ActionAtomistic(const ActionOptions &ao)PLMD::ActionAtomisticexplicit
ActionPilot(const ActionOptions &)PLMD::ActionPilotexplicit
activate()PLMD::Actionvirtual
activePLMD::Actionprivate
addDependency(Action *)PLMD::Action
afterPLMD::Actionprivate
allowToAccessGlobalForces()PLMD::ActionAtomisticinline
apply() overridePLMD::GenericMolInfoinlinevirtual
applyForces()PLMD::ActionAtomistic
atomsPLMD::ActionAtomisticprotected
beforeUpdate()PLMD::Actioninlinevirtual
calculate() overridePLMD::GenericMolInfoinlinevirtual
calculateAtomicNumericalDerivatives(ActionWithValue *a, const unsigned &startnum)PLMD::ActionAtomistic
calculateFromPDB(const PDB &)PLMD::Action
PLMD::calculateNumericalDerivatives(ActionWithValue *a=NULL)PLMD::Actionvirtual
PLMD::ActionAtomistic::calculateNumericalDerivatives(ActionWithValue *a=NULL) overridePLMD::ActionAtomisticvirtual
changeBox(const Tensor &newbox)PLMD::ActionAtomistic
chargesPLMD::ActionAtomisticprivate
chargesWereSetPLMD::ActionAtomisticprivate
checkForAtom(AtomNumber a) constPLMD::GenericMolInfo
checkNeedsGradients() constPLMD::Actioninlinevirtual
checkNumericalDerivatives() constPLMD::Actioninlinevirtual
checkRead()PLMD::Action
checkUpdate() constPLMD::Action
cite(const std::string &s)PLMD::Action
clearDependencies()PLMD::Action
clearOptions()PLMD::Actionvirtual
clearOutputForces()PLMD::ActionAtomistic
commPLMD::Action
deactivate()PLMD::Actioninlinevirtual
Dependencies typedefPLMD::Action
doCheckPointPLMD::Actionprivate
doNotForce()PLMD::ActionAtomisticinline
donotforcePLMD::ActionAtomisticprivate
doNotRetrieve()PLMD::ActionAtomisticinline
donotretrievePLMD::ActionAtomisticprivate
enablePythonInterpreterPLMD::GenericMolInfoprivate
energyPLMD::ActionAtomisticprivate
error(const std::string &msg) constPLMD::Action
exit(int c=0)PLMD::Action
extraCVPLMD::ActionAtomisticprivate
fclose(FILE *fp)PLMD::Action
fflush()PLMD::Action
filesPLMD::Action
fopen(const char *path, const char *mode)PLMD::Action
forceOnEnergyPLMD::ActionAtomisticprivate
forceOnExtraCVPLMD::ActionAtomisticprivate
forcesPLMD::ActionAtomisticprivate
GenericMolInfo(const ActionOptions &ao)PLMD::GenericMolInfoexplicit
getAbsoluteIndex(int i) constPLMD::ActionAtomisticinline
getAbsoluteIndexes() constPLMD::ActionAtomisticinlinevirtual
getAtomName(AtomNumber a) constPLMD::GenericMolInfo
getBackbone(std::vector< std::string > &resstrings, const std::string &fortype, std::vector< std::vector< AtomNumber > > &backbone)PLMD::GenericMolInfo
getBox() constPLMD::ActionAtomisticinline
getChainID(AtomNumber a) constPLMD::GenericMolInfo
getCharge(int i) constPLMD::ActionAtomisticinline
getCPT() constPLMD::Action
getDependencies() constPLMD::Actioninline
getDocumentation() constPLMD::Actionvirtual
getEnergy() constPLMD::ActionAtomisticinline
getExchangeStep() constPLMD::Action
getGlobalPosition(AtomNumber) constPLMD::ActionAtomisticinline
getKeyword(const std::string &key)PLMD::Action
getLabel() constPLMD::Actioninline
getMass(int i) constPLMD::ActionAtomisticinline
getName() constPLMD::Actioninline
getNumberOfAtoms() constPLMD::ActionAtomisticinline
getPbc() constPLMD::ActionAtomisticinline
getPDBsize() constPLMD::GenericMolInfo
getPosition(AtomNumber a) constPLMD::GenericMolInfo
PLMD::ActionAtomistic::getPosition(int) constPLMD::ActionAtomisticinline
getPositions() constPLMD::ActionAtomisticinline
getResidueName(AtomNumber a) constPLMD::GenericMolInfo
getResidueNumber(AtomNumber a) constPLMD::GenericMolInfo
getRestart() constPLMD::Actioninline
getStep() constPLMD::Action
getStride() constPLMD::ActionPilot
getTime() constPLMD::Action
getTimeStep() constPLMD::Action
getTotAtoms() constPLMD::ActionAtomisticinline
getUnique() constPLMD::ActionAtomisticinline
getUniqueLocal() constPLMD::ActionAtomisticinline
indexesPLMD::ActionAtomisticprivate
interpretAtomList(std::vector< std::string > &strings, std::vector< AtomNumber > &t)PLMD::ActionAtomistic
interpretSymbol(const std::string &symbol, std::vector< AtomNumber > &atoms)PLMD::GenericMolInfo
isActive() constPLMD::Actioninline
isOptionOn(const std::string &s) constPLMD::Actioninline
isWhole() constPLMD::GenericMolInfo
iswhole_PLMD::GenericMolInfoprivate
keywordsPLMD::Action
labelPLMD::Actionprivate
linePLMD::Actionprivate
lockRequestAtomsPLMD::ActionAtomisticprivate
PLMD::lockRequests()PLMD::Actioninlinevirtual
PLMD::ActionAtomistic::lockRequests() overridePLMD::ActionAtomisticinlinevirtual
logPLMD::Action
makeWhole()PLMD::ActionAtomistic
massesPLMD::ActionAtomisticprivate
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
mytypePLMD::GenericMolInfoprivate
namePLMD::Actionprivate
onStep() constPLMD::ActionPilotvirtual
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
pbcPLMD::ActionAtomisticprivate
pbc_fwdPLMD::ActionAtomisticprivate
pbcApply(std::vector< Vector > &dlist, unsigned max_index=0) constPLMD::ActionAtomistic
pbcDistance(const Vector &, const Vector &) constPLMD::ActionAtomistic
pdbPLMD::GenericMolInfoprivate
pdb_fwdPLMD::GenericMolInfoprivate
plumedPLMD::Action
positionsPLMD::ActionAtomisticprivate
prepare() overridePLMD::GenericMolInfovirtual
pythonCmdPLMD::GenericMolInfoprivate
read_backbonePLMD::GenericMolInfoprivate
PLMD::readAtomsFromPDB(const PDB &)PLMD::Actioninlinevirtual
PLMD::ActionAtomistic::readAtomsFromPDB(const PDB &pdb) overridePLMD::ActionAtomisticvirtual
referencePLMD::GenericMolInfoprivate
registerKeywords(Keywords &keys)PLMD::GenericMolInfostatic
replica_indexPLMD::Actionprivate
requestAtoms(const std::vector< AtomNumber > &a, const bool clearDep=true)PLMD::ActionAtomistic
restartPLMD::Actionprivate
retrieveAtoms()PLMD::ActionAtomisticvirtual
runFinalJobs()PLMD::Actioninlinevirtual
selectorPLMD::GenericMolInfoprivate
setExtraCV(const std::string &name)PLMD::ActionAtomisticinlineprotected
setForcesOnAtoms(const std::vector< double > &forcesToApply, unsigned ind=0)PLMD::ActionAtomistic
setOption(const std::string &s)PLMD::Actionvirtual
setStride(const int &n)PLMD::ActionPilot
stridePLMD::ActionPilotprivate
uniquePLMD::ActionAtomisticprivate
unique_localPLMD::ActionAtomisticprivate
PLMD::unlockRequests()PLMD::Actioninlinevirtual
PLMD::ActionAtomistic::unlockRequests() overridePLMD::ActionAtomisticinlinevirtual
update()PLMD::Actioninlinevirtual
update_fromPLMD::Actionprivate
update_untilPLMD::Actionprivate
updateUniqueLocal()PLMD::ActionAtomistic
virialPLMD::ActionAtomisticprivate
warning(const std::string &msg)PLMD::Action
~Action()PLMD::Actionvirtual
~ActionAtomistic()PLMD::ActionAtomistic
~GenericMolInfo()PLMD::GenericMolInfo
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