bool SLICKEnergy::setup()
{
setName("SLICKEnergy");
options_.set(NonpolarSolvation::Option::NONPOLAR_METHOD, NonpolarSolvation::CALCULATION__PCM);
options_.setInteger(PolarSolvation::Option::POLAR_METHOD, PolarSolvation::CALCULATION__FULL_CYCLE_FOCUSED);
options_.setInteger(VanDerWaalsSlick::Option::VDW_METHOD, VanDerWaalsSlick::CALCULATION__SOFTENED_LJ_POTENTIAL_LOG);
options_.setReal(VanDerWaalsSlick::Option::VDW_SOFTENING_LIMIT, 5.0f);
float CONST = options_.setDefaultReal(SLICKEnergy::Option::CONST, SLICKEnergy::Default::CONST);
setIntercept(CONST);
// register all components of the force field
registerComponents_();
// check whether we know which molecule is the protein and which is the
// ligand in this complex. In case we don't know, we have to guess.
// This can be wrong if we got two PDB files which will both be tagged
// as protein.
if ((getReceptor() == 0) || (getLigand() == 0))
{
Log.error() << "I don't know what the protein and the ligand is."
<< std::endl;
return false;
}
return true ;
}
bool SLICKScore::setup()
{
setName("SLICKScore");
// Set VDW to use a cut repulsive potential with a limit of 5 kJ/mol per interaction
options_.setInteger(VanDerWaalsSlick::Option::VDW_METHOD, VanDerWaalsSlick::CALCULATION__SOFTENED_LJ_POTENTIAL_LOG);
options_.setReal(VanDerWaalsSlick::Option::VDW_SOFTENING_LIMIT, 5.0f);
// Use simple (and fast) Coulomb interactions for the scoring
options_.setInteger(PolarSolvation::Option::POLAR_METHOD, PolarSolvation::CALCULATION__COULOMB);
// Now extract options_ from options table and set the coefficients of
// the components accordingly.
float CONST = options_.setDefaultReal(SLICKScore::Option::CONST, SLICKScore::Default::CONST);
setIntercept(CONST);
// register all components of the force field
registerComponents_();
// check whether we know which molecule is the protein and which is the
// ligand in this complex. In case we don't know, we have to guess.
// This can be wrong if we got two PDB files which will both be tagged
// as protein.
if ((getReceptor() == 0) || (getLigand() == 0))
{
Log.error() << "I don't know what the protein and the ligand is."
<< std::endl;
return false;
}
return true;
}
void
StopAndWaitRC::doOnData(const CompoundPtr& compound, Port<Ack>)
{
StopAndWaitRCCommand *command = getCommand(compound->getCommandPool());
assure(command->peer.type == StopAndWaitRCCommand::RR,
"Received I frame via 'Data' port");
MESSAGE_BEGIN(NORMAL, logger, m, getFUN()->getName());
m << " processIncoming(compound), Received RR frame "
<< " expected (this->NS) " << NS
<< " received (command->peer.NS) " << command->peer.NS;
MESSAGE_END();
if(!(command->peer.NS == NS || command->peer.NS == NS-1))
{
// this can not happen.
wns::Exception e;
e << "StopAndWait-ARQ received an ACK that with neither (NS) nor (NS-1). "
<< "This cannot happen and is most probably an implementation error";
// stop here
throw e;
}
// only compounds with NS == NS or NS == NS-1 are left
if(command->peer.NS == NS-1)
{
// duplicate ACK (must be due to duplicate I)
MESSAGE_BEGIN(NORMAL, logger, m, getFUN()->getName());
m << " Unexpected RR frame (due to duplicate I frame).";
m << "\nHINT: Check your resend timeout. This indicates it is too short.";
MESSAGE_END();
}
else
{
// this is the ACK we've been waiting for -> we can stop
// the timeout
MESSAGE_SINGLE(NORMAL, logger, getFUN()->getName()
<< " This is the RR frame (ACK) for the last sent I frame (compound)");
// statusCollector->onSuccessfullTransmission(activeCompound);
activeCompound = CompoundPtr();
if (hasTimeoutSet() == true)
{
MESSAGE_SINGLE(VERBOSE, logger, getFUN()->getName() << "Stopping timeout.");
cancelTimeout();
}
MESSAGE_SINGLE(VERBOSE, logger, getFUN()->getName()
<< " Ready for next compound from higher FU.");
getReceptor()->wakeup();
}
}
void
StopAndWaitRC::doWakeup(Port<Data>)
{
if (sendNowData &&
getPortConnector< Port<Data> >()->hasAcceptor(activeCompound))
{
setTimeout(resendTimeout);
getPortConnector< Port<Data> >()->getAcceptor(activeCompound)->sendData(activeCompound->copy());
sendNowData = false;
}
getReceptor()->wakeup();
}
virtual void
doWakeup()
{
getReceptor()->wakeup();
} // wakeup
