PLMD::SetupMolInfo Member List

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

Action(const ActionOptions &)PLMD::Actionexplicit
ActionAtomistic(const ActionOptions &ao)PLMD::ActionAtomisticexplicit
ActionSetup(const ActionOptions &ao)PLMD::ActionSetupexplicit
activate()PLMD::Actionvirtual
addDependency(Action *)PLMD::Action
allowToAccessGlobalForces()PLMD::ActionAtomisticinline
apply()PLMD::ActionSetupinlinevirtual
applyForces()PLMD::ActionAtomistic
atomsPLMD::ActionAtomisticprotected
beforeUpdate()PLMD::Actioninlinevirtual
calculate()PLMD::ActionSetupinlinevirtual
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)PLMD::ActionAtomisticvirtual
changeBox(const Tensor &newbox)PLMD::ActionAtomistic
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
doNotForce()PLMD::ActionAtomisticinline
doNotRetrieve()PLMD::ActionAtomisticinline
error(const std::string &msg) constPLMD::Action
exit(int c=0)PLMD::Action
fclose(FILE *fp)PLMD::Action
fflush()PLMD::Action
filesPLMD::Action
fopen(const char *path, const char *mode)PLMD::Action
getAbsoluteIndex(int i) constPLMD::ActionAtomisticinline
getAbsoluteIndexes() constPLMD::ActionAtomisticinlinevirtual
getAtomName(AtomNumber a) constPLMD::SetupMolInfo
getBackbone(std::vector< std::string > &resstrings, const std::string &fortype, std::vector< std::vector< AtomNumber > > &backbone)PLMD::SetupMolInfo
getBox() constPLMD::ActionAtomisticinline
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
getPosition(int) constPLMD::ActionAtomisticinline
getPositions() constPLMD::ActionAtomisticinline
getResidueName(AtomNumber a) constPLMD::SetupMolInfo
getResidueNumber(AtomNumber a) constPLMD::SetupMolInfo
getRestart() constPLMD::Actioninline
getStep() constPLMD::Action
getTime() constPLMD::Action
getTimeStep() constPLMD::Action
getTotAtoms() constPLMD::ActionAtomisticinline
getUnique() constPLMD::ActionAtomisticinline
getUniqueLocal() constPLMD::ActionAtomisticinline
interpretAtomList(std::vector< std::string > &strings, std::vector< AtomNumber > &t)PLMD::ActionAtomistic
interpretSymbol(const std::string &symbol, std::vector< AtomNumber > &atoms) constPLMD::SetupMolInfo
isActive() constPLMD::Actioninline
isOptionOn(const std::string &s) constPLMD::Actioninline
keywordsPLMD::Action
PLMD::lockRequests()PLMD::Actioninlinevirtual
PLMD::ActionAtomistic::lockRequests()PLMD::ActionAtomisticinlinevirtual
logPLMD::Action
makeWhole()PLMD::ActionAtomistic
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::SetupMolInfoprivate
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
pbcApply(std::vector< Vector > &dlist, unsigned max_index=0) constPLMD::ActionAtomistic
pbcDistance(const Vector &, const Vector &) constPLMD::ActionAtomistic
pdbPLMD::SetupMolInfoprivate
pdb_fwdPLMD::SetupMolInfoprivate
plumedPLMD::Action
prepare()PLMD::Actionvirtual
read_backbonePLMD::SetupMolInfoprivate
PLMD::readAtomsFromPDB(const PDB &)PLMD::Actioninlinevirtual
PLMD::ActionAtomistic::readAtomsFromPDB(const PDB &pdb)PLMD::ActionAtomisticvirtual
registerKeywords(Keywords &keys)PLMD::SetupMolInfostatic
requestAtoms(const std::vector< AtomNumber > &a, const bool clearDep=true)PLMD::ActionAtomistic
retrieveAtoms()PLMD::ActionAtomisticvirtual
runFinalJobs()PLMD::Actioninlinevirtual
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
SetupMolInfo(const ActionOptions &ao)PLMD::SetupMolInfoexplicit
PLMD::unlockRequests()PLMD::Actioninlinevirtual
PLMD::ActionAtomistic::unlockRequests()PLMD::ActionAtomisticinlinevirtual
update()PLMD::Actioninlinevirtual
updateUniqueLocal()PLMD::ActionAtomistic
warning(const std::string &msg)PLMD::Action
~Action()PLMD::Actionvirtual
~ActionAtomistic()PLMD::ActionAtomistic
~SetupMolInfo()PLMD::SetupMolInfo
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