void Datagram::deserializeToDatagram(unsigned char *datagramChars,
int datagramLength) {
seqNumber = convertToInteger(datagramChars, 0);
ackNumber = convertToInteger(datagramChars, 4);
ackFlag = convertToBoolean(datagramChars, 8);
finFlag = convertToBoolean(datagramChars, 9);
length = convertToShort(datagramChars, 10);
data = getPayload(datagramChars, length);
}
/** Expect lowest replica file name to be passed in. 'remdtraj' should have
* already been parsed out of input arguments.
*/
int Trajin_Multi::SetupTrajRead(FileName const& tnameIn, ArgList& argIn, Topology *tparmIn)
{
// Set file name and topology pointer.
if (SetTraj().SetNameAndParm(tnameIn, tparmIn)) return 1;
REMDtraj_.ClearIOarray();
// Check for deprecated args
if (argIn.hasKey("remdout")) {
mprinterr("%s", TrajIOarray::DEPRECATED_remdout);
return 1;
}
// Process REMD-specific arguments
if (argIn.Contains("remdtrajidx")) {
// Looking for specific indices
ArgList indicesArg(argIn.GetStringKey("remdtrajidx"), ",");
if (indicesArg.empty()) {
mprinterr("Error: remdtrajidx expects comma-separated list of target indices in each\n"
"Error: dimension, '<dim1 idx>,<dim2 idx>,...,<dimN idx>'. Indices start\n"
"Error: from 1.\n");
return 1;
}
for (ArgList::const_iterator arg = indicesArg.begin(); // TODO: validInteger?
arg != indicesArg.end(); ++arg)
remdtrajidx_.push_back( convertToInteger( *arg ) );
targetType_ = ReplicaInfo::INDICES;
} else if (argIn.Contains("remdtrajtemp")) {
// Looking for target temperature
remdtrajtemp_ = argIn.getKeyDouble("remdtrajtemp",0.0);
targetType_ = ReplicaInfo::TEMP;
}
// Set up replica file names.
if (REMDtraj_.SetupReplicaFilenames( tnameIn, argIn )) return 1;
// Set up TrajectoryIO classes for all file names.
if (REMDtraj_.SetupIOarray(argIn, SetTraj().Counter(), cInfo_, Traj().Parm())) return 1;
// Check that replica dimension valid for desired indices.
if (targetType_ == ReplicaInfo::INDICES &&
cInfo_.ReplicaDimensions().Ndims() != (int)remdtrajidx_.size())
{
mprinterr("Error: Replica # of dim (%i) not equal to target # dim (%zu)\n",
cInfo_.ReplicaDimensions().Ndims(), remdtrajidx_.size());
return 1;
}
// If target type is temperature make sure there is temperature info.
if (targetType_ == ReplicaInfo::TEMP && !cInfo_.HasTemp()) {
mprinterr("Error: Some or all replicas are missing temperature info.\n");
return 1;
}
return 0;
}
// =============================================================================
// ----- RepName Class ---------------------------------------------------------
// RepName CONSTRUCTOR
File::RepName::RepName(FileName const& fname, int debugIn) :
extChar_('.')
{
if (debugIn > 1)
mprintf("\tREMDTRAJ: FileName=[%s]\n", fname.full());
if ( fname.Ext().empty() ) {
mprinterr("Error: Traj %s has no numerical extension, required for automatic\n"
"Error: detection of replica trajectories. Expected filename format is\n"
"Error: <Prefix>.<#> (with optional compression extension), examples:\n"
"Error: Rep.traj.nc.000, remd.x.01.gz etc.\n", fname.base());
return;
}
// Split off everything before replica extension
size_t found = fname.Full().rfind( fname.Ext() );
Prefix_.assign( fname.Full().substr(0, found) );
ReplicaExt_.assign( fname.Ext() ); // This should be the numeric extension
// Remove leading '.'
if (ReplicaExt_[0] == '.') ReplicaExt_.erase(0,1);
CompressExt_.assign( fname.Compress() );
if (debugIn > 1) {
mprintf("\tREMDTRAJ: Prefix=[%s], #Ext=[%s], CompressExt=[%s]\n",
Prefix_.c_str(), ReplicaExt_.c_str(), CompressExt_.c_str());
}
// CHARMM replica numbers are format <name>_<num>
if ( !validInteger(ReplicaExt_) ) {
size_t uscore = fname.Full().rfind('_');
if (uscore != std::string::npos) {
Prefix_.assign( fname.Full().substr(0, uscore) );
ReplicaExt_.assign( fname.Full().substr(uscore+1) );
extChar_ = '_';
if (debugIn > 0)
mprintf("\tREMDTRAJ: CHARMM style replica names detected, prefix='%s' ext='%s'\n",
Prefix_.c_str(), ReplicaExt_.c_str());
}
}
// Check that the numerical extension is valid.
if ( !validInteger(ReplicaExt_) ) {
mprinterr("Error: Replica extension [%s] is not an integer.\n", ReplicaExt_.c_str());
Prefix_.clear(); // Empty Prefix_ indicates error.
return;
}
ExtWidth_ = (int)ReplicaExt_.size();
if (debugIn > 1)
mprintf("\tREMDTRAJ: Numerical Extension width=%i\n", ExtWidth_);
// Store lowest replica number
lowestRepnum_ = convertToInteger( ReplicaExt_ );
// TODO: Do not allow negative replica numbers?
if (debugIn > 1)
mprintf("\tREMDTRAJ: index of first replica = %i\n", lowestRepnum_);
}
Action::RetType Action_MultiDihedral::Init(ArgList& actionArgs, TopologyList* PFL, FrameList* FL,
DataSetList* DSL, DataFileList* DFL, int debugIn)
{
debug_ = debugIn;
// Get keywords
outfile_ = DFL->AddDataFile( actionArgs.GetStringKey("out"), actionArgs);
range360_ = actionArgs.hasKey("range360");
std::string resrange_arg = actionArgs.GetStringKey("resrange");
if (!resrange_arg.empty())
if (resRange_.SetRange( resrange_arg )) return Action::ERR;
// Search for known dihedral keywords
dihSearch_.SearchForArgs(actionArgs);
// Get custom dihedral arguments: dihtype <name>:<a0>:<a1>:<a2>:<a3>[:<offset>]
std::string dihtype_arg = actionArgs.GetStringKey("dihtype");
while (!dihtype_arg.empty()) {
ArgList dihtype(dihtype_arg, ":");
if (dihtype.Nargs() < 5) {
mprinterr("Error: Malformed dihtype arg.\n");
return Action::ERR;
}
int offset = 0;
if (dihtype.Nargs() == 6) offset = convertToInteger(dihtype[5]);
dihSearch_.SearchForNewType(offset,dihtype[1],dihtype[2],dihtype[3],dihtype[4], dihtype[0]);
dihtype_arg = actionArgs.GetStringKey("dihtype");
}
// If no dihedral types yet selected, this will select all.
dihSearch_.SearchForAll();
// Setup DataSet(s) name
dsetname_ = actionArgs.GetStringNext();
mprintf(" MULTIDIHEDRAL: Calculating");
dihSearch_.PrintTypes();
if (!resRange_.Empty())
mprintf(" dihedrals for residues in range %s\n", resRange_.RangeArg());
else
mprintf(" dihedrals for all residues.\n");
if (!dsetname_.empty())
mprintf("\tDataSet name: %s\n", dsetname_.c_str());
if (outfile_ != 0) mprintf("\tOutput to %s\n", outfile_->DataFilename().base());
if (range360_)
mprintf("\tRange 0-360 deg.\n");
else
mprintf("\tRange -180-180 deg.\n");
masterDSL_ = DSL;
return Action::OK;
}
void TickFct_Display7Seg(void){
static unsigned char init=1;
if(init){ //initialization behavior
OUTPUT=0x3F; //displays "0" to 7-Segment Display
display_value=1; //increment
init=0;
}else if(keypad_counter){ //display Keypad Input
int temp=display_value;
display_value=convertToInteger(buffer&0x0F);
if(display_value==10)
display_value=temp;
keypad_counter=0;
}else{
display();
increment();
}
}
static inline bool IsAtomLine(ArgList& lineIn) {
for (int i = 0; i < lineIn.Nargs(); i++) {
std::string item = lineIn.GetStringNext();
if (i == 0 || i >= 5) {
try {
convertToInteger( item );
}
catch (std::runtime_error e) {
return false;
}
} else if (i >= 2 && i < 5) {
try {
convertToDouble( item );
}
catch (std::runtime_error e) {
return false;
}
}
}
return true;
}
// Parm_CIF::ReadParm()
int Parm_CIF::ReadParm(FileName const& fname, Topology &TopIn) {
CIFfile infile;
CIFfile::DataBlock::data_it line;
if (infile.Read( fname, debug_ )) return 1;
CIFfile::DataBlock const& block = infile.GetDataBlock("_atom_site");
if (block.empty()) {
mprinterr("Error: CIF data block '_atom_site' not found.\n");
return 1;
}
// Does this CIF contain multiple models?
int Nmodels = 0;
int model_col = block.ColumnIndex("pdbx_PDB_model_num");
if (model_col != -1) {
line = block.end();
--line;
Nmodels = convertToInteger( (*line)[model_col] );
if (Nmodels > 1)
mprintf("Warning: CIF '%s' contains %i models. Using first model for topology.\n",
fname.full(), Nmodels);
}
// Get essential columns
int COL[NENTRY];
for (int i = 0; i < (int)NENTRY; i++) {
COL[i] = block.ColumnIndex(Entries[i]);
if (COL[i] == -1) {
mprinterr("Error: In CIF file '%s' could not find entry '%s' in block '%s'\n",
fname.full(), Entries[i], block.Header().c_str());
return 1;
}
if (debug_>0) mprintf("DEBUG: '%s' column = %i\n", Entries[i], COL[i]);
}
// Get optional columns
int occ_col = block.ColumnIndex("occupancy");
int bfac_col = block.ColumnIndex("B_iso_or_equiv");
int icode_col = block.ColumnIndex("pdbx_PDB_ins_code");
int altloc_col = block.ColumnIndex("label_alt_id");
std::vector<AtomExtra> extra;
// Loop over all atom sites
int current_res = 0;
double XYZ[3];
double occupancy = 1.0;
double bfactor = 0.0;
char altloc = ' ';
char icode;
icode = ' ';
Frame Coords;
for (line = block.begin(); line != block.end(); ++line) {
// If more than 1 model check if we are done.
if (Nmodels > 1) {
if ( convertToInteger( (*line)[model_col] ) > 1 )
break;
}
if (occ_col != -1) occupancy = convertToDouble( (*line)[ occ_col ] );
if (bfac_col != -1) bfactor = convertToDouble( (*line)[ bfac_col ] );
if (altloc_col != -1) altloc = (*line)[ altloc_col ][0];
// '.' altloc means blank?
if (altloc == '.') altloc = ' ';
extra.push_back( AtomExtra(occupancy, bfactor, altloc) );
if (icode_col != -1) {
icode = (*line)[ icode_col ][0];
// '?' icode means blank
if (icode == '?') icode = ' ';
}
XYZ[0] = convertToDouble( (*line)[ COL[X] ] );
XYZ[1] = convertToDouble( (*line)[ COL[Y] ] );
XYZ[2] = convertToDouble( (*line)[ COL[Z] ] );
NameType currentResName( (*line)[ COL[RNAME] ] );
// It seems that in some CIF files, there doesnt have to be a residue
// number. Check if residue name has changed.
if ( (*line)[ COL[RNUM] ][0] == '.' ) {
Topology::res_iterator lastResidue = TopIn.ResEnd();
--lastResidue;
if ( currentResName != (*lastResidue).Name() )
current_res = TopIn.Nres() + 1;
} else
current_res = convertToInteger( (*line)[ COL[RNUM] ] );
TopIn.AddTopAtom( Atom((*line)[ COL[ANAME] ], " "),
Residue(currentResName, current_res, icode,
(*line)[ COL[CHAINID] ][0]) );
Coords.AddXYZ( XYZ );
}
if (TopIn.SetExtraAtomInfo( 0, extra )) return 1;
// Search for bonds // FIXME nobondsearch?
BondSearch( TopIn, Coords, Offset_, debug_ );
// Get title.
CIFfile::DataBlock const& entryblock = infile.GetDataBlock("_entry");
std::string ciftitle;
if (!entryblock.empty())
ciftitle = entryblock.Data("id");
TopIn.SetParmName( ciftitle, infile.CIFname() );
// Get unit cell parameters if present.
CIFfile::DataBlock const& cellblock = infile.GetDataBlock("_cell");
if (!cellblock.empty()) {
double cif_box[6];
cif_box[0] = convertToDouble( cellblock.Data("length_a") );
cif_box[1] = convertToDouble( cellblock.Data("length_b") );
cif_box[2] = convertToDouble( cellblock.Data("length_c") );
cif_box[3] = convertToDouble( cellblock.Data("angle_alpha") );
cif_box[4] = convertToDouble( cellblock.Data("angle_beta" ) );
cif_box[5] = convertToDouble( cellblock.Data("angle_gamma") );
mprintf("\tRead cell info from CIF: a=%g b=%g c=%g alpha=%g beta=%g gamma=%g\n",
cif_box[0], cif_box[1], cif_box[2], cif_box[3], cif_box[4], cif_box[5]);
TopIn.SetParmBox( Box(cif_box) );
}
return 0;
}
int
TransportRegistry::load_transport_configuration(const OPENDDS_STRING& file_name,
ACE_Configuration_Heap& cf)
{
const ACE_Configuration_Section_Key &root = cf.root_section();
// Create a vector to hold configuration information so we can populate
// them after the transports instances are created.
typedef std::pair<TransportConfig_rch, OPENDDS_VECTOR(OPENDDS_STRING) > ConfigInfo;
OPENDDS_VECTOR(ConfigInfo) configInfoVec;
// Record the transport instances created, so we can place them
// in the implicit transport configuration for this file.
OPENDDS_LIST(TransportInst_rch) instances;
ACE_TString sect_name;
for (int index = 0;
cf.enumerate_sections(root, index, sect_name) == 0;
++index) {
if (ACE_OS::strcmp(sect_name.c_str(), TRANSPORT_SECTION_NAME) == 0) {
// found the [transport/*] section, now iterate through subsections...
ACE_Configuration_Section_Key sect;
if (cf.open_section(root, sect_name.c_str(), 0, sect) != 0) {
ACE_ERROR_RETURN((LM_ERROR,
ACE_TEXT("(%P|%t) TransportRegistry::load_transport_configuration: ")
ACE_TEXT("failed to open section %s\n"),
sect_name.c_str()),
-1);
} else {
// Ensure there are no properties in this section
ValueMap vm;
if (pullValues(cf, sect, vm) > 0) {
// There are values inside [transport]
ACE_ERROR_RETURN((LM_ERROR,
ACE_TEXT("(%P|%t) TransportRegistry::load_transport_configuration: ")
ACE_TEXT("transport sections must have a section name\n"),
sect_name.c_str()),
-1);
}
// Process the subsections of this section (the individual transport
// impls).
KeyList keys;
if (processSections( cf, sect, keys ) != 0) {
ACE_ERROR_RETURN((LM_ERROR,
ACE_TEXT("(%P|%t) TransportRegistry::load_transport_configuration: ")
ACE_TEXT("too many nesting layers in [%s] section.\n"),
sect_name.c_str()),
-1);
}
for (KeyList::const_iterator it=keys.begin(); it != keys.end(); ++it) {
OPENDDS_STRING transport_id = (*it).first;
ACE_Configuration_Section_Key inst_sect = (*it).second;
ValueMap values;
if (pullValues( cf, (*it).second, values ) != 0) {
// Get the factory_id for the transport.
OPENDDS_STRING transport_type;
ValueMap::const_iterator vm_it = values.find("transport_type");
if (vm_it != values.end()) {
transport_type = (*vm_it).second;
} else {
ACE_ERROR_RETURN((LM_ERROR,
ACE_TEXT("(%P|%t) TransportRegistry::load_transport_configuration: ")
ACE_TEXT("missing transport_type in [transport/%C] section.\n"),
transport_id.c_str()),
-1);
}
// Create the TransportInst object and load the transport
// configuration in ACE_Configuration_Heap to the TransportInst
// object.
TransportInst_rch inst = this->create_inst(transport_id,
transport_type);
if (inst == 0) {
ACE_ERROR_RETURN((LM_ERROR,
ACE_TEXT("(%P|%t) TransportRegistry::load_transport_configuration: ")
ACE_TEXT("Unable to create transport instance in [transport/%C] section.\n"),
transport_id.c_str()),
-1);
}
instances.push_back(inst);
inst->load(cf, inst_sect);
} else {
ACE_ERROR_RETURN((LM_ERROR,
ACE_TEXT("(%P|%t) TransportRegistry::load_transport_configuration: ")
ACE_TEXT("missing transport_type in [transport/%C] section.\n"),
transport_id.c_str()),
-1);
}
}
}
} else if (ACE_OS::strcmp(sect_name.c_str(), CONFIG_SECTION_NAME) == 0) {
// found the [config/*] section, now iterate through subsections...
ACE_Configuration_Section_Key sect;
if (cf.open_section(root, sect_name.c_str(), 0, sect) != 0) {
ACE_ERROR_RETURN((LM_ERROR,
ACE_TEXT("(%P|%t) TransportRegistry::load_transport_configuration: ")
ACE_TEXT("failed to open section [%s]\n"),
sect_name.c_str()),
-1);
} else {
// Ensure there are no properties in this section
ValueMap vm;
if (pullValues(cf, sect, vm) > 0) {
// There are values inside [config]
ACE_ERROR_RETURN((LM_ERROR,
ACE_TEXT("(%P|%t) TransportRegistry::load_transport_configuration: ")
ACE_TEXT("config sections must have a section name\n"),
sect_name.c_str()),
-1);
}
// Process the subsections of this section (the individual config
// impls).
KeyList keys;
if (processSections( cf, sect, keys ) != 0) {
// Don't allow multiple layers of nesting ([config/x/y]).
ACE_ERROR_RETURN((LM_ERROR,
ACE_TEXT("(%P|%t) TransportRegistry::load_transport_configuration: ")
ACE_TEXT("too many nesting layers in [%s] section.\n"),
sect_name.c_str()),
-1);
}
for (KeyList::const_iterator it=keys.begin(); it != keys.end(); ++it) {
OPENDDS_STRING config_id = (*it).first;
// Create a TransportConfig object.
TransportConfig_rch config = this->create_config(config_id);
if (config == 0) {
ACE_ERROR_RETURN((LM_ERROR,
ACE_TEXT("(%P|%t) TransportRegistry::load_transport_configuration: ")
ACE_TEXT("Unable to create transport config in [config/%C] section.\n"),
config_id.c_str()),
-1);
}
ValueMap values;
pullValues( cf, (*it).second, values );
ConfigInfo configInfo;
configInfo.first = config;
for (ValueMap::const_iterator it=values.begin();
it != values.end(); ++it) {
OPENDDS_STRING name = (*it).first;
if (name == "transports") {
OPENDDS_STRING value = (*it).second;
char delim = ',';
size_t pos = 0;
OPENDDS_STRING token;
while ((pos = value.find(delim)) != OPENDDS_STRING::npos) {
token = value.substr(0, pos);
configInfo.second.push_back(token);
value.erase(0, pos + 1);
}
configInfo.second.push_back(value);
configInfoVec.push_back(configInfo);
} else if (name == "swap_bytes") {
OPENDDS_STRING value = (*it).second;
if ((value == "1") || (value == "true")) {
config->swap_bytes_ = true;
} else if ((value != "0") && (value != "false")) {
ACE_ERROR_RETURN((LM_ERROR,
ACE_TEXT("(%P|%t) TransportRegistry::load_transport_configuration: ")
ACE_TEXT("Illegal value for swap_bytes (%C) in [config/%C] section.\n"),
value.c_str(), config_id.c_str()),
-1);
}
} else if (name == "passive_connect_duration") {
OPENDDS_STRING value = (*it).second;
if (!convertToInteger(value,
config->passive_connect_duration_)) {
ACE_ERROR_RETURN((LM_ERROR,
ACE_TEXT("(%P|%t) TransportRegistry::load_transport_configuration: ")
ACE_TEXT("Illegal integer value for passive_connect_duration (%s) in [config/%C] section.\n"),
value.c_str(), config_id.c_str()),
-1);
}
} else {
ACE_ERROR_RETURN((LM_ERROR,
ACE_TEXT("(%P|%t) TransportRegistry::load_transport_configuration: ")
ACE_TEXT("Unexpected entry (%C) in [config/%C] section.\n"),
name.c_str(), config_id.c_str()),
-1);
}
}
if (configInfo.second.size() == 0) {
ACE_ERROR_RETURN((LM_ERROR,
ACE_TEXT("(%P|%t) TransportRegistry::load_transport_configuration: ")
ACE_TEXT("No transport instances listed in [config/%C] section.\n"),
config_id.c_str()),
-1);
}
}
}
} else if (ACE_OS::strncmp(sect_name.c_str(), OLD_TRANSPORT_PREFIX.c_str(),
OLD_TRANSPORT_PREFIX.length()) == 0) {
ACE_ERROR_RETURN((LM_ERROR,
ACE_TEXT("(%P|%t) ERROR: ")
ACE_TEXT("Obsolete transport configuration found (%s).\n"),
sect_name.c_str()),
-1);
}
}
// Populate the configurations with instances
for (unsigned int i = 0; i < configInfoVec.size(); ++i) {
TransportConfig_rch config = configInfoVec[i].first;
OPENDDS_VECTOR(OPENDDS_STRING)& insts = configInfoVec[i].second;
for (unsigned int j = 0; j < insts.size(); ++j) {
TransportInst_rch inst = this->get_inst(insts[j]);
if (inst == 0) {
ACE_ERROR_RETURN((LM_ERROR,
ACE_TEXT("(%P|%t) TransportRegistry::load_transport_configuration: ")
ACE_TEXT("The inst (%C) in [config/%C] section is undefined.\n"),
insts[j].c_str(), config->name().c_str()),
-1);
}
config->instances_.push_back(inst);
}
}
// Create and populate the default configuration for this
// file with all the instances from this file.
if (!instances.empty()) {
TransportConfig_rch config = this->create_config(file_name);
if (config == 0) {
ACE_ERROR_RETURN((LM_ERROR,
ACE_TEXT("(%P|%t) TransportRegistry::load_transport_configuration: ")
ACE_TEXT("Unable to create default transport config.\n"),
file_name.c_str()),
-1);
}
instances.sort(predicate);
for (OPENDDS_LIST(TransportInst_rch)::const_iterator it = instances.begin();
it != instances.end(); ++it) {
config->instances_.push_back(*it);
}
}
return 0;
}
int
InfoRepoDiscovery::Config::discovery_config(ACE_Configuration_Heap& cf)
{
const ACE_Configuration_Section_Key& root = cf.root_section();
ACE_Configuration_Section_Key repo_sect;
if (cf.open_section(root, REPO_SECTION_NAME, 0, repo_sect) != 0) {
if (DCPS_debug_level > 0) {
// This is not an error if the configuration file does not have
// any repository (sub)section. The code default configuration will be used.
ACE_DEBUG((LM_NOTICE,
ACE_TEXT("(%P|%t) NOTICE: InfoRepoDiscovery::Config::discovery_config ")
ACE_TEXT("failed to open [%s] section.\n"),
REPO_SECTION_NAME));
}
return 0;
} else {
// Ensure there are no properties in this section
ValueMap vm;
if (pullValues(cf, repo_sect, vm) > 0) {
// There are values inside [repo]
ACE_ERROR_RETURN((LM_ERROR,
ACE_TEXT("(%P|%t) InfoRepoDiscovery::Config::discovery_config ")
ACE_TEXT("repo sections must have a subsection name\n")),
-1);
}
// Process the subsections of this section (the individual repos)
KeyList keys;
if (processSections( cf, repo_sect, keys ) != 0) {
ACE_ERROR_RETURN((LM_ERROR,
ACE_TEXT("(%P|%t) InfoRepoDiscovery::Config::discovery_config ")
ACE_TEXT("too many nesting layers in the [repo] section.\n")),
-1);
}
// Loop through the [repo/*] sections
for (KeyList::const_iterator it=keys.begin(); it != keys.end(); ++it) {
std::string repo_name = (*it).first;
ValueMap values;
pullValues( cf, (*it).second, values );
Discovery::RepoKey repoKey = Discovery::DEFAULT_REPO;
bool repoKeySpecified = false, bitIpSpecified = false,
bitPortSpecified = false;
std::string repoIor;
int bitPort = 0;
std::string bitIp;
for (ValueMap::const_iterator it=values.begin(); it != values.end(); ++it) {
std::string name = (*it).first;
if (name == "RepositoryKey") {
repoKey = (*it).second;
repoKeySpecified = true;
if (DCPS_debug_level > 0) {
ACE_DEBUG((LM_DEBUG,
ACE_TEXT("(%P|%t) [repository/%C]: RepositoryKey == %C\n"),
repo_name.c_str(), repoKey.c_str()));
}
} else if (name == "RepositoryIor") {
repoIor = (*it).second;
if (DCPS_debug_level > 0) {
ACE_DEBUG((LM_DEBUG,
ACE_TEXT("(%P|%t) [repository/%C]: RepositoryIor == %C\n"),
repo_name.c_str(), repoIor.c_str()));
}
} else if (name == "DCPSBitTransportIPAddress") {
bitIp = (*it).second;
bitIpSpecified = true;
if (DCPS_debug_level > 0) {
ACE_DEBUG((LM_DEBUG,
ACE_TEXT("(%P|%t) [repository/%C]: DCPSBitTransportIPAddress == %C\n"),
repo_name.c_str(), bitIp.c_str()));
}
} else if (name == "DCPSBitTransportPort") {
std::string value = (*it).second;
bitPort = ACE_OS::atoi(value.c_str());
bitPortSpecified = true;
if (convertToInteger(value, bitPort)) {
} else {
ACE_ERROR_RETURN((LM_ERROR,
ACE_TEXT("(%P|%t) InfoRepoDiscovery::Config::discovery_config ")
ACE_TEXT("Illegal integer value for DCPSBitTransportPort (%C) in [repository/%C] section.\n"),
value.c_str(), repo_name.c_str()),
-1);
}
if (DCPS_debug_level > 0) {
ACE_DEBUG((LM_DEBUG,
ACE_TEXT("(%P|%t) [repository/%C]: DCPSBitTransportPort == %d\n"),
repo_name.c_str(), bitPort));
}
} else {
ACE_ERROR_RETURN((LM_ERROR,
ACE_TEXT("(%P|%t) InfoRepoDiscovery::Config::discovery_config ")
ACE_TEXT("Unexpected entry (%C) in [repository/%C] section.\n"),
name.c_str(), repo_name.c_str()),
-1);
}
}
if (values.find("RepositoryIor") == values.end()) {
ACE_ERROR_RETURN((LM_ERROR,
ACE_TEXT("(%P|%t) InfoRepoDiscovery::Config::discovery_config ")
ACE_TEXT("Repository section [repository/%C] section is missing RepositoryIor value.\n"),
repo_name.c_str()),
-1);
}
if (!repoKeySpecified) {
// If the RepositoryKey option was not specified, use the section
// name as the repo key
repoKey = repo_name;
}
InfoRepoDiscovery_rch discovery =
new InfoRepoDiscovery(repoKey, repoIor.c_str());
if (bitPortSpecified) discovery->bit_transport_port(bitPort);
if (bitIpSpecified) discovery->bit_transport_ip(bitIp);
TheServiceParticipant->add_discovery(
DCPS::static_rchandle_cast<Discovery>(discovery));
}
}
return 0;
}
Analysis::RetType Analysis_CurveFit::Internal_setup(std::string const& suffixIn, ArgList& analyzeArgs, DataSetList* datasetlist, DataFileList* DFLin, int debugIn)
{
if (dset_->Ndim() != 1) {
mprinterr("Error: Curve fitting can only be done with 1D data sets.\n");
return Analysis::ERR;
}
std::string dsoutName;
n_expected_params_ = 0;
// Determine if special equation is being used.
nexp_ = analyzeArgs.getKeyInt("nexp", -1);
bool useGauss = analyzeArgs.hasKey("gauss");
if ( useGauss || nexp_ > 0 ) {
// Multi-exponential/Gaussian specialized equation form.
dsoutName = analyzeArgs.GetStringKey("name");
if (dsoutName.empty()) {
mprinterr("Error: 'name <OutputSetName>' must be used with 'nexp <n>' or 'gauss'\n");
return Analysis::ERR;
}
equation_ = dsoutName + " = ";
if (nexp_ > 0) {
// Determine form
eqForm_ = MEXP;
std::string formStr = analyzeArgs.GetStringKey("form");
if (!formStr.empty()) {
if (formStr == "mexp") eqForm_ = MEXP;
else if (formStr == "mexpk") eqForm_ = MEXP_K;
else if (formStr == "mexpk_penalty") eqForm_ = MEXP_K_PENALTY;
else {
mprinterr("Error: Multi-exponential form '%s' not recognized.\n", formStr.c_str());
return Analysis::ERR;
}
}
// Set up equation
int nparam = 0;
if (eqForm_ != MEXP) {
equation_.append("A0 +");
nparam = 1;
}
for (int ie = 0; ie != nexp_; ie++, nparam += 2) {
if (ie > 0)
equation_.append(" + ");
equation_.append("(A" + integerToString(nparam) + " * exp(X * A" +
integerToString(nparam+1) + "))");
}
n_expected_params_ = nparam;
} else {
eqForm_ = GAUSS;
n_expected_params_ = 3;
equation_.append("A0 * exp( -((X - A1)^2) / (2 * A2^2) )");
}
} else {
// Any equation form, solve with RPNcalc.
eqForm_ = GENERAL;
// Second argument should be the equation to fit DataSet to.
equation_ = analyzeArgs.GetStringNext();
if (equation_.empty()) {
mprinterr("Error: Must specify an equation if 'nexp <n>' not specified.\n");
return Analysis::ERR;
}
Calc_.SetDebug(debugIn);
if (Calc_.ProcessExpression( equation_ )) return Analysis::ERR;
// Equation must have an assignment.
if ( Calc_.AssignStatus() != RPNcalc::YES_ASSIGN ) {
mprinterr("Error: No assignment '=' in equation '%s'.\n", equation_.c_str());
return Analysis::ERR;
}
dsoutName = Calc_.FirstTokenName();
if (dsoutName.empty()) {
mprinterr("Error: Invalid assignment in equation '%s'.\n", equation_.c_str());
return Analysis::ERR;
}
n_expected_params_ = Calc_.Nparams();
}
// Get keywords
Results_ = DFLin->AddCpptrajFile( analyzeArgs.GetStringKey("resultsout"), "Curve Fit Results",
DataFileList::TEXT, true );
DataFile* outfile = DFLin->AddDataFile( analyzeArgs.GetStringKey("out"), analyzeArgs );
tolerance_ = analyzeArgs.getKeyDouble("tol", 0.0001);
if (tolerance_ < 0.0) {
mprinterr("Error: Tolerance must be greater than or equal to 0.0\n");
return Analysis::ERR;
}
maxIt_ = analyzeArgs.getKeyInt("maxit", 50);
if (maxIt_ < 1) {
mprinterr("Error: Max iterations must be greater than or equal to 1.\n");
return Analysis::ERR;
}
outXbins_ = analyzeArgs.getKeyInt("outxbins", -1);
outXmin_ = analyzeArgs.getKeyDouble("outxmin", 0.0);
outXmax_ = analyzeArgs.getKeyDouble("outxmax", 0.0);
if (outXbins_ > 0) {
mprintf("%g %g\n", outXmin_, outXmax_);
if (outXmin_ >= outXmax_) {
mprinterr("Error: outxmin must be less than outxmax.\n");
return Analysis::ERR;
}
}
// Now get all parameters
if (n_expected_params_ < 0) return Analysis::ERR;
Params_.resize( n_expected_params_, 0.0 );
n_specified_params_ = 0;
for (int p = 0; p != n_expected_params_; p++, n_specified_params_++) {
std::string parameterArg = analyzeArgs.GetStringNext();
if (parameterArg.empty())
break;
ArgList parameter(parameterArg, " =");
if (parameter.Nargs() != 2) {
mprinterr("Error: Invalid parameter argument. Expected 'A<n>=<value>'\n");
return Analysis::ERR;
}
std::string parameterName = parameter.GetStringNext();
if (parameterName[0] != 'A') {
mprinterr("Error: Invalid parameter name (expected A<n>): %s\n", parameterName.c_str());
return Analysis::ERR;
}
int pnum = convertToInteger(parameterName.substr(1));
Params_[pnum] = parameter.getNextDouble(0.0);
}
// Check if all params specified.
if (n_specified_params_ != n_expected_params_)
mprintf("Warning: # specified params (%i) less than # expected params (%i)\n",
n_specified_params_, n_expected_params_);
// Set up output data set.
if (!suffixIn.empty()) dsoutName.append(suffixIn);
finalY_ = datasetlist->AddSet(DataSet::XYMESH, dsoutName, "FIT");
if (finalY_ == 0) return Analysis::ERR;
if (outfile != 0) outfile->AddDataSet( finalY_ );
mprintf(" CURVEFIT: Fitting set '%s' to equation '%s'\n",
dset_->legend(), equation_.c_str());
if (nexp_ > 0) {
mprintf("\tMulti-exponential form with %i exponentials.\n", nexp_);
if (eqForm_ == MEXP_K_PENALTY)
mprintf("\tMulti-exponential equation constraints: sum of prefactors = 1.0,"
" exponent parameters < 0.0\n");
} else if (eqForm_ == GAUSS)
mprintf("\tGaussian form.\n");
mprintf("\tFinal Y values will be saved in set '%s'\n", finalY_->legend());
if (outXbins_ > 0)
mprintf("\tFinal X range: %g to %g, %i points.\n", outXmin_, outXmax_, outXbins_);
mprintf("\tTolerance= %g, maximum iterations= %i\n", tolerance_, maxIt_);
mprintf("\tFinal parameters and statistics for fit will be writtent to %s\n",
Results_->Filename().full());
if (n_specified_params_ > 0) {
mprintf("\tInitial parameters:\n");
for (Darray::const_iterator ip = Params_.begin(); ip != Params_.end(); ++ip)
mprintf("\t A%u = %g\n", ip - Params_.begin(), *ip);
}
return Analysis::OK;
}
int moProperty::asInteger() {
return convertToInteger(this->type, this->val);
}
int Parm_CharmmPsf::WriteParm(FileName const& fname, Topology const& parm) {
// TODO: CMAP etc info
CpptrajFile outfile;
if (outfile.OpenWrite(fname)) return 1;
// Write PSF
outfile.Printf("PSF\n\n");
// Write title
std::string titleOut = parm.ParmName();
titleOut.resize(78);
outfile.Printf("%8i !NTITLE\n* %-78s\n\n", 1, titleOut.c_str());
// Write NATOM section
outfile.Printf("%8i !NATOM\n", parm.Natom());
unsigned int idx = 1;
// Make fake segment ids for now.
char segid[2];
segid[0] = 'A';
segid[1] = '\0';
mprintf("Warning: Assigning single letter segment IDs.\n");
int currentMol = 0;
bool inSolvent = false;
for (Topology::atom_iterator atom = parm.begin(); atom != parm.end(); ++atom, ++idx) {
int resnum = atom->ResNum();
if (atom->MolNum() != currentMol) {
if (!inSolvent) {
inSolvent = parm.Mol(atom->MolNum()).IsSolvent();
currentMol = atom->MolNum();
segid[0]++;
} else
inSolvent = parm.Mol(atom->MolNum()).IsSolvent();
}
// TODO: Print type name for xplor-like PSF
int typeindex = atom->TypeIndex() + 1;
// If type begins with digit, assume charmm numbers were read as
// type. Currently Amber types all begin with letters.
if (isdigit(atom->Type()[0]))
typeindex = convertToInteger( *(atom->Type()) );
// ATOM# SEGID RES# RES ATNAME ATTYPE CHRG MASS (REST OF COLUMNS ARE LIKELY FOR CMAP AND CHEQ)
outfile.Printf("%8i %-4s %-4i %-4s %-4s %4i %14.6G %9g %10i\n", idx, segid,
parm.Res(resnum).OriginalResNum(), parm.Res(resnum).c_str(),
atom->c_str(), typeindex, atom->Charge(),
atom->Mass(), 0);
}
outfile.Printf("\n");
// Write NBOND section
outfile.Printf("%8u !NBOND: bonds\n", parm.Bonds().size() + parm.BondsH().size());
idx = 1;
for (BondArray::const_iterator bond = parm.BondsH().begin();
bond != parm.BondsH().end(); ++bond, ++idx)
{
outfile.Printf("%8i%8i", bond->A1()+1, bond->A2()+1);
if ((idx % 4)==0) outfile.Printf("\n");
}
for (BondArray::const_iterator bond = parm.Bonds().begin();
bond != parm.Bonds().end(); ++bond, ++idx)
{
outfile.Printf("%8i%8i", bond->A1()+1, bond->A2()+1);
if ((idx % 4)==0) outfile.Printf("\n");
}
if ((idx % 4)!=0) outfile.Printf("\n");
outfile.Printf("\n");
// Write NTHETA section
outfile.Printf("%8u !NTHETA: angles\n", parm.Angles().size() + parm.AnglesH().size());
idx = 1;
for (AngleArray::const_iterator ang = parm.AnglesH().begin();
ang != parm.AnglesH().end(); ++ang, ++idx)
{
outfile.Printf("%8i%8i%8i", ang->A1()+1, ang->A2()+1, ang->A3()+1);
if ((idx % 3)==0) outfile.Printf("\n");
}
for (AngleArray::const_iterator ang = parm.Angles().begin();
ang != parm.Angles().end(); ++ang, ++idx)
{
outfile.Printf("%8i%8i%8i", ang->A1()+1, ang->A2()+1, ang->A3()+1);
if ((idx % 3)==0) outfile.Printf("\n");
}
if ((idx % 3)==0) outfile.Printf("\n");
outfile.Printf("\n");
// Write out NPHI section
outfile.Printf("%8u !NPHI: dihedrals\n", parm.Dihedrals().size() + parm.DihedralsH().size());
idx = 1;
for (DihedralArray::const_iterator dih = parm.DihedralsH().begin();
dih != parm.DihedralsH().end(); ++dih, ++idx)
{
outfile.Printf("%8i%8i%8i%8i", dih->A1()+1, dih->A2()+1, dih->A3()+1, dih->A4()+1);
if ((idx % 2)==0) outfile.Printf("\n");
}
for (DihedralArray::const_iterator dih = parm.Dihedrals().begin();
dih != parm.Dihedrals().end(); ++dih, ++idx)
{
outfile.Printf("%8i%8i%8i%8i", dih->A1()+1, dih->A2()+1, dih->A3()+1, dih->A4()+1);
if ((idx % 2)==0) outfile.Printf("\n");
}
if ((idx % 2)==0) outfile.Printf("\n");
outfile.Printf("\n");
outfile.CloseFile();
return 0;
}
/** Set up each mask/integer loop. */
int ControlBlock_For::SetupBlock(CpptrajState& State, ArgList& argIn) {
mprintf(" Setting up 'for' loop.\n");
Vars_.clear();
Topology* currentTop = 0;
static const char* TypeStr[] = { "ATOMS ", "RESIDUES ", "MOLECULES ",
"MOL_FIRST_RES ", "MOL_LAST_RES " };
static const char* OpStr[] = {"+=", "-=", "<", ">"};
description_.assign("for (");
int MaxIterations = -1;
int iarg = 0;
while (iarg < argIn.Nargs())
{
// Advance to next unmarked argument.
while (iarg < argIn.Nargs() && argIn.Marked(iarg)) iarg++;
if (iarg == argIn.Nargs()) break;
// Determine 'for' type
ForType ftype = UNKNOWN;
bool isMaskFor = true;
int argToMark = iarg;
if ( argIn[iarg] == "atoms" ) ftype = ATOMS;
else if ( argIn[iarg] == "residues" ) ftype = RESIDUES;
else if ( argIn[iarg] == "molecules" ) ftype = MOLECULES;
else if ( argIn[iarg] == "molfirstres" ) ftype = MOLFIRSTRES;
else if ( argIn[iarg] == "mollastres" ) ftype = MOLLASTRES;
else if ( argIn[iarg].find(";") != std::string::npos ) {
isMaskFor = false;
ftype = INTEGER;
}
// If type is still unknown, check for list.
if (ftype == UNKNOWN) {
if (iarg+1 < argIn.Nargs() && argIn[iarg+1] == "in") {
ftype = LIST;
isMaskFor = false;
argToMark = iarg+1;
}
}
// Exit if type could not be determined.
if (ftype == UNKNOWN) {
mprinterr("Error: for loop type not specfied.\n");
return 1;
}
argIn.MarkArg(argToMark);
Vars_.push_back( LoopVar() );
LoopVar& MH = Vars_.back();
int Niterations = -1;
// Set up for specific type
if (description_ != "for (") description_.append(", ");
// -------------------------------------------
if (isMaskFor)
{
// {atoms|residues|molecules} <var> inmask <mask> [TOP KEYWORDS]
if (argIn[iarg+2] != "inmask") {
mprinterr("Error: Expected 'inmask', got %s\n", argIn[iarg+2].c_str());
return 1;
}
AtomMask currentMask;
if (currentMask.SetMaskString( argIn.GetStringKey("inmask") )) return 1;
MH.varType_ = ftype;
Topology* top = State.DSL().GetTopByIndex( argIn );
if (top != 0) currentTop = top;
if (currentTop == 0) return 1;
MH.varname_ = argIn.GetStringNext();
if (MH.varname_.empty()) {
mprinterr("Error: 'for inmask': missing variable name.\n");
return 1;
}
MH.varname_ = "$" + MH.varname_;
// Set up mask
if (currentTop->SetupIntegerMask( currentMask )) return 1;
currentMask.MaskInfo();
if (currentMask.None()) return 1;
// Set up indices
if (MH.varType_ == ATOMS)
MH.Idxs_ = currentMask.Selected();
else if (MH.varType_ == RESIDUES) {
int curRes = -1;
for (AtomMask::const_iterator at = currentMask.begin(); at != currentMask.end(); ++at) {
int res = (*currentTop)[*at].ResNum();
if (res != curRes) {
MH.Idxs_.push_back( res );
curRes = res;
}
}
} else if (MH.varType_ == MOLECULES ||
MH.varType_ == MOLFIRSTRES ||
MH.varType_ == MOLLASTRES)
{
int curMol = -1;
for (AtomMask::const_iterator at = currentMask.begin(); at != currentMask.end(); ++at) {
int mol = (*currentTop)[*at].MolNum();
if (mol != curMol) {
if (MH.varType_ == MOLECULES)
MH.Idxs_.push_back( mol );
else {
int res;
if (MH.varType_ == MOLFIRSTRES)
res = (*currentTop)[ currentTop->Mol( mol ).BeginAtom() ].ResNum();
else // MOLLASTRES
res = (*currentTop)[ currentTop->Mol( mol ).EndAtom()-1 ].ResNum();
MH.Idxs_.push_back( res );
}
curMol = mol;
}
}
}
Niterations = (int)MH.Idxs_.size();
description_.append(std::string(TypeStr[MH.varType_]) +
MH.varname_ + " inmask " + currentMask.MaskExpression());
// -------------------------------------------
} else if (ftype == INTEGER) {
// [<var>=<start>;[<var><OP><end>;]<var><OP>[<value>]]
MH.varType_ = ftype;
ArgList varArg( argIn[iarg], ";" );
if (varArg.Nargs() < 2 || varArg.Nargs() > 3) {
mprinterr("Error: Malformed 'for' loop variable.\n"
"Error: Expected '[<var>=<start>;[<var><OP><end>;]<var><OP>[<value>]]'\n"
"Error: Got '%s'\n", argIn[iarg].c_str());
return 1;
}
// First argument: <var>=<start>
ArgList startArg( varArg[0], "=" );
if (startArg.Nargs() != 2) {
mprinterr("Error: Malformed 'start' argument.\n"
"Error: Expected <var>=<start>, got '%s'\n", varArg[0].c_str());
return 1;
}
MH.varname_ = startArg[0];
if (!validInteger(startArg[1])) {
// TODO allow variables
mprinterr("Error: Start argument must be an integer.\n");
return 1;
} else
MH.start_ = convertToInteger(startArg[1]);
// Second argument: <var><OP><end>
size_t pos0 = MH.varname_.size();
size_t pos1 = pos0 + 1;
MH.endOp_ = NO_OP;
int iargIdx = 1;
if (varArg.Nargs() == 3) {
iargIdx = 2;
if ( varArg[1][pos0] == '<' )
MH.endOp_ = LESS_THAN;
else if (varArg[1][pos0] == '>')
MH.endOp_ = GREATER_THAN;
if (MH.endOp_ == NO_OP) {
mprinterr("Error: Unrecognized end op: '%s'\n",
varArg[1].substr(pos0, pos1-pos0).c_str());
return 1;
}
std::string endStr = varArg[1].substr(pos1);
if (!validInteger(endStr)) {
// TODO allow variables
mprinterr("Error: End argument must be an integer.\n");
return 1;
} else
MH.end_ = convertToInteger(endStr);
}
// Third argument: <var><OP>[<value>]
pos1 = pos0 + 2;
MH.incOp_ = NO_OP;
bool needValue = false;
if ( varArg[iargIdx][pos0] == '+' ) {
if (varArg[iargIdx][pos0+1] == '+') {
MH.incOp_ = INCREMENT;
MH.inc_ = 1;
} else if (varArg[iargIdx][pos0+1] == '=') {
MH.incOp_ = INCREMENT;
needValue = true;
}
} else if ( varArg[iargIdx][pos0] == '-' ) {
if (varArg[iargIdx][pos0+1] == '-' ) {
MH.incOp_ = DECREMENT;
MH.inc_ = 1;
} else if (varArg[iargIdx][pos0+1] == '=') {
MH.incOp_ = DECREMENT;
needValue = true;
}
}
if (MH.incOp_ == NO_OP) {
mprinterr("Error: Unrecognized increment op: '%s'\n",
varArg[iargIdx].substr(pos0, pos1-pos0).c_str());
return 1;
}
if (needValue) {
std::string incStr = varArg[iargIdx].substr(pos1);
if (!validInteger(incStr)) {
mprinterr("Error: increment value is not a valid integer.\n");
return 1;
}
MH.inc_ = convertToInteger(incStr);
if (MH.inc_ < 1) {
mprinterr("Error: Extra '-' detected in increment.\n");
return 1;
}
}
// Description
MH.varname_ = "$" + MH.varname_;
std::string sval = integerToString(MH.start_);
description_.append("(" + MH.varname_ + "=" + sval + "; ");
std::string eval;
if (iargIdx == 2) {
// End argument present
eval = integerToString(MH.end_);
description_.append(MH.varname_ + std::string(OpStr[MH.endOp_]) + eval + "; ");
// Check end > start for increment, start > end for decrement
int maxval, minval;
if (MH.incOp_ == INCREMENT) {
if (MH.start_ >= MH.end_) {
mprinterr("Error: start must be less than end for increment.\n");
return 1;
}
minval = MH.start_;
maxval = MH.end_;
} else {
if (MH.end_ >= MH.start_) {
mprinterr("Error: end must be less than start for decrement.\n");
return 1;
}
minval = MH.end_;
maxval = MH.start_;
}
// Figure out number of iterations
Niterations = (maxval - minval) / MH.inc_;
if (((maxval-minval) % MH.inc_) > 0) Niterations++;
}
description_.append( MH.varname_ + std::string(OpStr[MH.incOp_]) +
integerToString(MH.inc_) + ")" );
// If decrementing just negate value
if (MH.incOp_ == DECREMENT)
MH.inc_ = -MH.inc_;
// DEBUG
//mprintf("DEBUG: start=%i endOp=%i end=%i incOp=%i val=%i startArg=%s endArg=%s\n",
// MH.start_, (int)MH.endOp_, MH.end_, (int)MH.incOp_, MH.inc_,
// MH.startArg_.c_str(), MH.endArg_.c_str());
// -------------------------------------------
} else if (ftype == LIST) {
// <var> in <string0>[,<string1>...]
MH.varType_ = ftype;
// Variable name
MH.varname_ = argIn.GetStringNext();
if (MH.varname_.empty()) {
mprinterr("Error: 'for in': missing variable name.\n");
return 1;
}
MH.varname_ = "$" + MH.varname_;
// Comma-separated list of strings
std::string listArg = argIn.GetStringNext();
if (listArg.empty()) {
mprinterr("Error: 'for in': missing comma-separated list of strings.\n");
return 1;
}
ArgList list(listArg, ",");
if (list.Nargs() < 1) {
mprinterr("Error: Could not parse '%s' for 'for in'\n", listArg.c_str());
return 1;
}
for (int il = 0; il != list.Nargs(); il++) {
// Check if file name expansion should occur
if (list[il].find_first_of("*?") != std::string::npos) {
File::NameArray files = File::ExpandToFilenames( list[il] );
for (File::NameArray::const_iterator fn = files.begin(); fn != files.end(); ++fn)
MH.List_.push_back( fn->Full() );
} else
MH.List_.push_back( list[il] );
}
Niterations = (int)MH.List_.size();
// Description
description_.append( MH.varname_ + " in " + listArg );
}
// Check number of values
if (MaxIterations == -1)
MaxIterations = Niterations;
else if (Niterations != -1 && Niterations != MaxIterations) {
mprintf("Warning: # iterations %i != previous # iterations %i\n",
Niterations, MaxIterations);
MaxIterations = std::min(Niterations, MaxIterations);
}
}
mprintf("\tLoop will execute for %i iterations.\n", MaxIterations);
if (MaxIterations < 1) {
mprinterr("Error: Loop has less than 1 iteration.\n");
return 1;
}
description_.append(") do");
return 0;
}
// ----- M A I N ---------------------------------------------------------------
int main(int argc, char** argv) {
SetWorldSilent(true); // No STDOUT output from cpptraj routines.
std::string topname, crdname, title, bres, pqr, sybyltype, writeconect;
std::string aatm(" pdbatom"), ter_opt(" terbyres"), box(" sg \"P 1\"");
TrajectoryFile::TrajFormatType fmt = TrajectoryFile::PDBFILE;
bool ctr_origin = false;
bool useExtendedInfo = false;
int res_offset = 0;
int debug = 0;
int numSoloArgs = 0;
for (int i = 1; i < argc; ++i) {
std::string arg( argv[i] );
if (arg == "-p" && i+1 != argc && topname.empty()) // Topology
topname = std::string( argv[++i] );
else if (arg == "-c" && i+1 != argc && crdname.empty()) // Coords
crdname = std::string( argv[++i] );
else if (arg == "-tit" && i+1 != argc && title.empty()) // Title
title = " title " + std::string( argv[++i] );
else if (arg == "-offset" && i+1 != argc) // Residue # offset
res_offset = convertToInteger( argv[++i] );
else if ((arg == "-d" || arg == "--debug") && i+1 != argc) // Debug level
debug = convertToInteger( argv[++i] );
else if (arg == "-h" || arg == "--help") { // Help
Help(argv[0], true);
return 0;
} else if (arg == "-v" || arg == "--version") { // Version info
WriteVersion();
return 0;
} else if (arg == "-aatm") // Amber atom names, include extra pts
aatm.assign(" include_ep");
else if (arg == "-sybyl") // Amber atom types to SYBYL
sybyltype.assign(" sybyltype");
else if (arg == "-conect") // Write CONECT records from bond info
writeconect.assign(" conect");
else if (arg == "-ep") // PDB atom names, include extra pts
aatm.append(" include_ep");
else if (arg == "-bres") // PDB residue names
bres.assign(" pdbres");
else if (arg == "-ext") // Use extended PDB info from Topology
useExtendedInfo = true;
else if (arg == "-ctr") // Center on origin
ctr_origin = true;
else if (arg == "-noter") // No TER cards
ter_opt.assign(" noter");
else if (arg == "-nobox") // No CRYST1 record
box.assign(" nobox");
else if (arg == "-pqr") { // Charge/Radii in occ/bfactor cols
pqr.assign(" dumpq");
++numSoloArgs;
} else if (arg == "-mol2") { // output as mol2
fmt = TrajectoryFile::MOL2FILE;
++numSoloArgs;
} else if (Unsupported(arg)) {
mprinterr("Error: Option '%s' is not yet supported.\n\n", arg.c_str());
return 1;
} else {
mprinterr("Error: Unrecognized option '%s'\n", arg.c_str());
Help(argv[0], false);
return 1;
}
}
if (debug > 0) WriteVersion();
// Check command line for errors.
if (topname.empty()) topname.assign("prmtop");
if (debug > 0 && crdname.empty())
mprinterr("| Reading Amber restart from STDIN\n");
if (numSoloArgs > 1) {
mprinterr("Error: Only one alternate output format option may be specified (found %i)\n",
numSoloArgs);
Help(argv[0], true);
return 1;
}
if (!sybyltype.empty() && fmt != TrajectoryFile::MOL2FILE) {
mprinterr("Warning: -sybyl is only valid for MOL2 file output.\n");
sybyltype.clear();
}
if (debug > 0) {
mprinterr("Warning: debug is %i; debug info will be written to STDOUT.\n", debug);
SetWorldSilent(false);
}
// Topology
ParmFile pfile;
Topology parm;
if (pfile.ReadTopology(parm, topname, debug)) {
if (topname == "prmtop") Help(argv[0], false);
return 1;
}
if (!useExtendedInfo)
parm.ResetPDBinfo();
if (res_offset != 0)
for (int r = 0; r < parm.Nres(); r++)
parm.SetRes(r).SetOriginalNum( parm.Res(r).OriginalResNum() + res_offset );
ArgList trajArgs;
// Input coords
Frame TrajFrame;
CoordinateInfo cInfo;
if (!crdname.empty()) {
Trajin_Single trajin;
if (trajin.SetupTrajRead(crdname, trajArgs, &parm)) return 1;
cInfo = trajin.TrajCoordInfo();
TrajFrame.SetupFrameV(parm.Atoms(), cInfo);
trajin.BeginTraj();
if (trajin.ReadTrajFrame(0, TrajFrame)) return 1;
trajin.EndTraj();
} else {
// Assume Amber restart from STDIN
// Check that input is from a redirect.
if ( isatty(fileno(stdin)) ) {
mprinterr("Error: No coordinates specified with '-c' and no STDIN '<'.\n");
return 1;
}
Traj_AmberRestart restartIn;
restartIn.SetDebug( debug );
//restartIn.processReadArgs( trajArgs );
int total_frames = restartIn.setupTrajin("", &parm);
if (total_frames < 1) return 1;
cInfo = restartIn.CoordInfo();
TrajFrame.SetupFrameV(parm.Atoms(), cInfo);
if (restartIn.openTrajin()) return 1;
if (restartIn.readFrame(0, TrajFrame)) return 1;
restartIn.closeTraj();
}
if (ctr_origin)
TrajFrame.CenterOnOrigin(false);
// Output coords
Trajout_Single trajout;
trajArgs.SetList( aatm + bres + pqr + title + ter_opt + box + sybyltype + writeconect, " " );
if ( trajout.PrepareStdoutTrajWrite(trajArgs, &parm, cInfo, 1, fmt) ) return 1;
trajout.WriteSingle(0, TrajFrame);
trajout.EndTraj();
return 0;
}
// Exec_DataSetCmd::Remove()
Exec::RetType Exec_DataSetCmd::Remove(CpptrajState& State, ArgList& argIn) {
std::string status;
// Get criterion type
CriterionType criterion = UNKNOWN_C;
for (int i = 1; i < (int)N_C; i++)
if (argIn.hasKey( CriterionKeys[i] )) {
criterion = (CriterionType)i;
status.assign( CriterionKeys[i] );
break;
}
if (criterion == UNKNOWN_C) {
mprinterr("Error: No criterion specified for 'remove'.\n");
return CpptrajState::ERR;
}
// Get select type
SelectType select = UNKNOWN_S;
std::string val1, val2;
for (const SelectPairType* ptr = SelectKeys; ptr->key_ != 0; ptr++)
if (argIn.Contains( ptr->key_ )) {
select = ptr->type_;
val1 = argIn.GetStringKey( ptr->key_ );
status.append( " " + std::string(ptr->key_) + " " + val1 );
// Get 'and' value for between/outside. TODO put nargs in SelectPairType?
if (select == BETWEEN || select == OUTSIDE) {
val2 = argIn.GetStringKey("and");
if (val2.empty()) {
mprinterr("Error: Missing 'and' value for selection '%s'\n", ptr->key_);
return CpptrajState::ERR;
}
status.append(" and " + val2);
}
break;
}
if (select == UNKNOWN_S || val1.empty()) {
mprinterr("Error: No selection specified for 'remove'.\n");
return CpptrajState::ERR;
}
if ( (criterion == SMODE || criterion == STYPE) &&
(select != EQUAL && select != NOT_EQUAL) )
{
mprinterr("Error: Specified select not valid for criterion '%s'\n", CriterionKeys[criterion]);
return CpptrajState::ERR;
}
mprintf("\tRemoving data sets");
std::string setSelectArg = argIn.GetStringNext();
if (setSelectArg.empty())
setSelectArg.assign("*");
else
mprintf(" within selection '%s'", setSelectArg.c_str());
mprintf(" %s\n", status.c_str());
DataSetList tempDSL = State.DSL().GetMultipleSets( setSelectArg );
if (tempDSL.empty()) {
mprinterr("Error: No data sets selected.\n");
return CpptrajState::ERR;
}
// Remove sets
unsigned int Nremoved = 0;
if ( criterion == AVERAGE ) {
if (!validDouble( val1 )) {
mprinterr("Error: '%s' is not a valid number\n", val1.c_str());
return CpptrajState::ERR;
}
double d_val1 = convertToDouble( val1 );
double d_val2 = d_val1;
if (!val2.empty()) {
if (!validDouble( val2 )) {
mprinterr("Error: '%s' is not a valid number\n", val2.c_str());
return CpptrajState::ERR;
}
d_val2 = convertToDouble( val2 );
}
for (DataSetList::const_iterator ds = tempDSL.begin(); ds != tempDSL.end(); ++ds)
{
if ( (*ds)->Group() != DataSet::SCALAR_1D )
mprintf("Warning: '%s' is not a valid data set for 'average' criterion.\n", (*ds)->legend());
else {
DataSet_1D const& ds1 = static_cast<DataSet_1D const&>( *(*ds) );
double avg = ds1.Avg();
bool remove = false;
switch (select) {
case EQUAL : remove = (avg == d_val1); break;
case NOT_EQUAL : remove = (avg != d_val1); break;
case LESS_THAN : remove = (avg < d_val1); break;
case GREATER_THAN : remove = (avg > d_val1); break;
case BETWEEN : remove = (avg > d_val1 && avg < d_val2); break;
case OUTSIDE : remove = (avg < d_val1 || avg > d_val2); break;
case UNKNOWN_S:
case N_S : return CpptrajState::ERR; // Sanity check
}
if (remove) {
mprintf("\t Removing set '%s' (avg is %g)\n", (*ds)->legend(), avg);
State.RemoveDataSet( *ds );
++Nremoved;
}
}
}
} else if ( criterion == SIZE ) {
if (!validInteger( val1 )) {
mprinterr("Error: '%s' is not a valid number\n", val1.c_str());
return CpptrajState::ERR;
}
unsigned int i_val1 = (unsigned int)convertToInteger( val1 );
unsigned int i_val2 = i_val1;
if (!val2.empty()) {
if (!validInteger( val2 )) {
mprinterr("Error: '%s' is not a valid number\n", val2.c_str());
return CpptrajState::ERR;
}
i_val2 = convertToInteger( val2 );
}
for (DataSetList::const_iterator ds = tempDSL.begin(); ds != tempDSL.end(); ++ds)
{
unsigned int size = (*ds)->Size();
bool remove = false;
switch ( select ) {
case EQUAL : remove = (size == i_val1); break;
case NOT_EQUAL : remove = (size != i_val1); break;
case LESS_THAN : remove = (size < i_val1); break;
case GREATER_THAN : remove = (size > i_val1); break;
case BETWEEN : remove = (size > i_val1 && size < i_val2); break;
case OUTSIDE : remove = (size < i_val1 || size > i_val2); break;
case UNKNOWN_S:
case N_S : return CpptrajState::ERR; // Sanity check
}
if (remove) {
mprintf("\t Removing set '%s' (size is %u)\n", (*ds)->legend(), size);
State.RemoveDataSet( *ds );
++Nremoved;
}
}
} else if ( criterion == SMODE ) {
MetaData::scalarMode mode_val = MetaData::ModeFromKeyword( val1 );
if (mode_val == MetaData::UNKNOWN_MODE) {
mprinterr("Error: '%s' is not a valid mode.\n", val1.c_str());
return CpptrajState::ERR;
}
for (DataSetList::const_iterator ds = tempDSL.begin(); ds != tempDSL.end(); ++ds)
{
bool remove = false;
MetaData::scalarMode mode = (*ds)->Meta().ScalarMode();
if (select == EQUAL ) remove = ( mode == mode_val );
else if (select == NOT_EQUAL) remove = ( mode != mode_val );
else return CpptrajState::ERR; // Sanity check
if (remove) {
mprintf("\t Removing set '%s' (mode is '%s')\n", (*ds)->legend(), MetaData::ModeString(mode));
State.RemoveDataSet( *ds );
++Nremoved;
}
}
} else if ( criterion == STYPE ) {
MetaData::scalarType type_val = MetaData::TypeFromKeyword( val1, MetaData::UNKNOWN_MODE );
if (type_val == MetaData::UNDEFINED) {
mprinterr("Error: '%s' is not a valid type.\n", val1.c_str());
return CpptrajState::ERR;
}
for (DataSetList::const_iterator ds = tempDSL.begin(); ds != tempDSL.end(); ++ds)
{
bool remove = false;
MetaData::scalarType type = (*ds)->Meta().ScalarType();
if (select == EQUAL ) remove = ( type == type_val );
else if (select == NOT_EQUAL) remove = ( type != type_val );
else return CpptrajState::ERR; // Sanity check
if (remove) {
mprintf("\t Removing set '%s' (typeis '%s')\n", (*ds)->legend(), MetaData::TypeString(type));
State.RemoveDataSet( *ds );
++Nremoved;
}
}
} else {
mprinterr("Internal Error: Criterion not yet implemented.\n");
return CpptrajState::ERR;
}
mprintf("\tRemoved %u of %zu sets.\n", Nremoved, tempDSL.size());
return CpptrajState::OK;
}
// DataIO_Mdout::ReadData()
int DataIO_Mdout::ReadData(FileName const& fname,
DataSetList& datasetlist, std::string const& dsname)
{
mprintf("\tReading from mdout file: %s\n", fname.full());
BufferedLine buffer;
if (buffer.OpenFileRead( fname )) return 1;
const char* ptr = buffer.Line();
if (ptr == 0) {
mprinterr("Error: Nothing in MDOUT file: %s\n", fname.full());
return 1;
}
// ----- PARSE THE INPUT SECTION -----
int imin = -1; // imin for this file
const char* Trigger = 0; // Trigger for storing energies, must be 8 chars long.
int frame = 0; // Frame counter for this file
double dt = 1.0; // Timestep for this file (MD)
double t0 = 0.0; // Initial time for this file (MD)
int ntpr = 1; // Value of ntpr
int irest = 0; // Value of irest
while ( ptr != 0 && strncmp(ptr, " 2. CONTROL DATA", 20) != 0 )
ptr = buffer.Line();
if (ptr == 0) return EOF_ERROR();
// Determine whether this is dynamics or minimization, get dt
ptr = buffer.Line(); // Dashes
ptr = buffer.Line(); // Blank
ptr = buffer.Line(); // title line
while ( strncmp(ptr, " 3. ATOMIC", 13) != 0 )
{
ArgList mdin_args( ptr, " ,=" ); // Remove commas, equal signs
// Scan for stuff we want
//mprintf("DEBUG:\tInput[%i] %s", mdin_args.Nargs(), mdin_args.ArgLine());
for (int col=0; col < mdin_args.Nargs(); col += 2) {
int col1 = col + 1;
if (mdin_args[col] == "imin") {
imin = convertToInteger( mdin_args[ col1 ] );
if (debug_ > 0) mprintf("\t\tMDIN: imin is %i\n", imin);
// Set a trigger for printing. For imin5 this is the word minimization.
// For imin0 or imin1 this is NSTEP.
if (imin==0) Trigger = " NSTEP =";
else if (imin==1) Trigger = " NSTEP";
else if (imin==5) Trigger = "minimiza";
// Since imin0 and imin1 first trigger has no data, set frame 1 lower.
if (imin==1 || imin==0) frame = -1;
} else if (mdin_args[col] == "dt") {
dt = convertToDouble( mdin_args[ col1 ] );
if (debug_ > 0) mprintf("\t\tMDIN: dt is %f\n", dt);
} else if (mdin_args[col] == "t") {
t0 = convertToDouble( mdin_args[ col1 ] );
if (debug_ > 0) mprintf("\t\tMDIN: t is %f\n", t0);
} else if (mdin_args[col] == "ntpr") {
ntpr = convertToInteger( mdin_args[ col1 ] );
if (debug_ > 0) mprintf("\t\tMDIN: ntpr is %i\n", ntpr);
} else if (mdin_args[col] == "irest") {
irest = convertToInteger( mdin_args[ col1 ] );
if (debug_ > 0) mprintf("\t\tMDIN: irest is %i\n", irest);
}
}
ptr = buffer.Line();
if (ptr == 0) return EOF_ERROR();
}
if (Trigger == 0) {
mprinterr("Error: Could not determine whether MDOUT is md, min, or post-process.\n");
return 1;
}
// ----- PARSE THE ATOMIC ... SECTION -----
while ( ptr != 0 && strncmp(ptr, " 4. RESULTS", 14) != 0 )
{
ptr = buffer.Line();
// If run is a restart, set the initial time value.
if (irest == 1) {
if (strncmp(ptr, " begin time", 11) == 0) {
sscanf(ptr, " begin time read from input coords = %lf", &t0);
if (debug_ > 0) mprintf("\t\tMD restart initial time= %f\n", t0);
}
}
}
if (ptr == 0) return EOF_ERROR();
// ----- PARSE THE RESULTS SECTION -----
bool finalE = false;
int nstep;
int minStep = 0; // For imin=1 only
if (irest == 0)
nstep = 0;
else
nstep = ntpr;
double Energy[N_FIELDTYPES];
std::fill( Energy, Energy+N_FIELDTYPES, 0.0 );
std::vector<bool> EnergyExists(N_FIELDTYPES, false);
DataSetList::Darray TimeVals;
DataSetList::DataListType inputSets(N_FIELDTYPES, 0);
Sarray Name(2);
double time = 0.0;
while (ptr != 0) {
// Check for end of imin 0 or 1 run; do not record Average and Stdevs
if ( (imin == 1 && (strncmp(ptr, " FINAL", 25) == 0 ||
strncmp(ptr, " 5. TIMINGS", 14) == 0 )) ||
(imin == 0 && strncmp(ptr, " A V", 9) == 0))
finalE = true;
// Check for '| TI region 2' to prevent reading duplicate energies
if ( strncmp(ptr, "| TI region 2", 14) == 0 ) {
while (ptr != 0 && !(ptr[0] == ' ' && ptr[1] == '-'))
ptr = buffer.Line();
if (ptr == 0) return EOF_ERROR();
}
// Record set for energy post-processing
if (imin == 5 && strncmp(ptr, "minimizing", 10) == 0)
nstep = atoi( ptr + 22 );
// MAIN OUTPUT ROUTINE
// If the trigger has been reached print output.
// For imin0 and imin1 the first trigger will have no data.
// If the end of the file has been reached print then exit.
if ( strncmp(ptr, Trigger, 8) == 0 || finalE ) {
if (frame > -1) {
// Store all energies present.
for (int i = 0; i < (int)N_FIELDTYPES; i++) {
if (EnergyExists[i]) {
if (inputSets[i] == 0) {
MetaData md( dsname, Enames[i] );
md.SetLegend( dsname + "_" + Enames[i] );
inputSets[i] = new DataSet_double();
inputSets[i]->SetMeta( md );
}
// Since energy terms can appear and vanish over the course of the
// mdout file, resize if necessary.
if (frame > (int)inputSets[i]->Size())
((DataSet_double*)inputSets[i])->Resize( frame );
((DataSet_double*)inputSets[i])->AddElement( Energy[i] );
}
}
TimeVals.push_back( time );
nstep += ntpr;
}
frame++;
if (finalE) break;
}
// Check for NSTEP in minimization or post-processing. Values will be
// on the next line. NOTE: NSTEP means something different for imin=5.
if ((imin == 1 || imin == 5) && strncmp(ptr, " NSTEP", 8) == 0) {
ptr = buffer.Line(); // Get next line
//sscanf(ptr, " %6lf %13lE %13lE %13lE", Energy+NSTEP, Energy+EPtot, Energy+RMS, Energy+GMAX);
sscanf(ptr, " %i %lE %lE %lE", &minStep, Energy+EPtot, Energy+RMS, Energy+GMAX);
EnergyExists[EPtot] = true;
EnergyExists[RMS] = true;
EnergyExists[GMAX] = true;
ptr = buffer.Line();
}
// Tokenize line, scan through until '=' is reached; value after is target.
int ntokens = buffer.TokenizeLine(" ");
if (ntokens > 0) {
int nidx = 0;
Name[0].clear();
Name[1].clear();
for (int tidx = 0; tidx < ntokens; tidx++) {
const char* tkn = buffer.NextToken();
if (tkn[0] == '=') {
FieldType Eindex = getEindex(Name);
tkn = buffer.NextToken();
++tidx;
if (tkn == 0)
mprintf("Warning: No numerical value, line %i column %i. Skipping.\n",
buffer.LineNumber(), tidx+1);
else if (tkn[0] == '*' || tkn[0] == 'N') // Assume if number begins with N it is NaN
mprintf("Warning: Numerical overflow detected, line %i column %i. Skipping.\n",
buffer.LineNumber(), tidx+1);
else {
if (Eindex != N_FIELDTYPES) {
Energy[Eindex] = atof( tkn );
EnergyExists[Eindex] = true;
}
}
nidx = 0;
Name[0].clear();
Name[1].clear();
} else {
if (nidx > 1) break; // Two tokens, no '=' found. Not an E line.
Name[nidx++].assign( tkn );
}
}
}
// Set time
switch (imin) {
case 5: time = (double)nstep + t0; break;
case 1: time = (double)minStep + t0; break;
case 0: time = ((double)nstep * dt) + t0; break;
}
// Read in next line
ptr = buffer.Line();
}
mprintf("\t%i frames\n", frame);
buffer.CloseFile();
std::string Xlabel;
if (imin == 5) Xlabel.assign("Set");
else if (imin == 1) Xlabel.assign("Nstep");
else Xlabel.assign("Time"); // imin == 0
if (datasetlist.AddOrAppendSets( Xlabel, TimeVals, inputSets )) return 1;
return 0;
}
/** Given an ArgList containing name,[min,max,step,bins,col,N], set up a
* coordinate with that name and parameters min, max, step, bins.
* If '*' or not specified, a default value will be set.
* \return 1 if error occurs, 0 otherwise.
*/
int Analysis_Hist::setupDimension(ArgList &arglist, DataSet_1D const& dset, size_t& offset) {
bool minArg = false;
bool maxArg = false;
bool stepArg = false;
bool binsArg = false;
if (debug_>1)
arglist.PrintList();
// Set up dimension name
// NOTE: arglist[0] should be same as dset name from CheckDimension
std::string const& dLabel = arglist[0];
// Cycle through coordinate arguments. Any argument left blank will be
// assigned a default value later.
double dMin = 0.0;
double dMax = 0.0;
double dStep = 0.0;
int dBins = -1;
for (int i = 1; i < arglist.Nargs(); i++) {
if (debug_>1) mprintf("DEBUG: setupCoord: Token %i (%s)\n", i, arglist[i].c_str());
// '*' means default explicitly requested
if (arglist[i] == "*") continue;
switch (i) {
case 1 : dMin = convertToDouble( arglist[i]); minArg = true; break;
case 2 : dMax = convertToDouble( arglist[i]); maxArg = true; break;
case 3 : dStep = convertToDouble( arglist[i]); stepArg = true; break;
case 4 : dBins = convertToInteger(arglist[i]); binsArg = true; break;
}
}
// If no min arg and no default min arg, get min from dataset
if (!minArg) {
if (!minArgSet_)
dMin = dset.Min();
else
dMin = default_min_;
}
// If no max arg and no default max arg, get max from dataset
if (!maxArg) {
if (!maxArgSet_)
dMax = dset.Max();
else
dMax = default_max_;
}
// If bins/step not specified, use default
if (!binsArg)
dBins = default_bins_;
if (!stepArg)
dStep = default_step_;
// Calculate dimension from given args.
HistBin dim;
if (dim.CalcBinsOrStep( dMin, dMax, dStep, dBins, dLabel )) {
mprinterr("Error: Could not set up histogram dimension '%s'\n", dLabel.c_str());
return 1;
}
dim.PrintHistBin();
dimensions_.push_back( dim );
// Recalculate offsets for all dimensions starting at farthest coord. This
// follows row major ordering.
size_t last_offset = 1UL; // For checking overflow.
offset = 1UL;
binOffsets_.resize( dimensions_.size() );
OffType::iterator bOff = binOffsets_.begin();
for (HdimType::const_iterator rd = dimensions_.begin();
rd != dimensions_.end(); ++rd, ++bOff)
{
if (debug_>0) mprintf("\tHistogram: %s offset is %zu\n", rd->label(), offset);
*bOff = (long int)offset;
offset *= rd->Bins();
// Check for overflow.
if ( offset < last_offset ) {
mprinterr("Error: Too many bins for histogram. Try reducing the number of bins and/or\n"
"Error: the number of dimensions.\n");
return 1;
}
last_offset = offset;
}
// offset should now be equal to the total number of bins across all dimensions
if (debug_>0) mprintf("\tHistogram: Total Bins = %zu\n",offset);
return 0;
}
// Action_MakeStructure::Init()
Action::RetType Action_MakeStructure::Init(ArgList& actionArgs, TopologyList* PFL, DataSetList* DSL, DataFileList* DFL, int debugIn)
{
debug_ = debugIn;
secstruct_.clear();
// Get all arguments
std::string ss_expr = actionArgs.GetStringNext();
while ( !ss_expr.empty() ) {
ArgList ss_arg(ss_expr, ":");
if (ss_arg.Nargs() < 2) {
mprinterr("Error: Malformed SS arg.\n");
Help();
return Action::ERR;
}
// Type is 1st arg, range is 2nd arg.
SecStructHolder ss_holder(ss_arg[1], FindSStype(ss_arg[0]));
if (ss_arg.Nargs() == 2) {
// Find SS type: <ss type>:<range>
if (ss_holder.sstype_idx == SS_EMPTY) {
mprinterr("Error: SS type %s not found.\n", ss_arg[0].c_str());
return Action::ERR;
}
ss_holder.dihSearch_.SearchFor(MetaData::PHI);
ss_holder.dihSearch_.SearchFor(MetaData::PSI);
secstruct_.push_back( ss_holder );
} else if (ss_arg[0] == "ref") {
// Use dihedrals from reference structure
if (ss_arg.Nargs() < 3) {
mprinterr("Error: Invalid 'ref' arg. Requires 'ref:<range>:<refname>[:<ref range>]'\n");
return Action::ERR;
}
ss_arg.MarkArg(0);
ss_arg.MarkArg(1);
// Sanity check: Currently only unique args of this type are allowed
if (ss_holder.sstype_idx != SS_EMPTY) {
mprinterr("Error: Ref backbone types must be unique [%s]\n", ss_arg[0].c_str());
return Action::ERR;
}
// Use backbone phi/psi from reference structure
ss_holder.dihSearch_.SearchFor(MetaData::PHI);
ss_holder.dihSearch_.SearchFor(MetaData::PSI);
// Get reference structure
DataSet_Coords_REF* REF = (DataSet_Coords_REF*)
DSL->FindSetOfType(ss_arg.GetStringNext(),
DataSet::REF_FRAME); // ss_arg[2]
if (REF == 0) {
mprinterr("Error: Could not get reference structure [%s]\n", ss_arg[2].c_str());
return Action::ERR;
}
// Get reference residue range, or use resRange
Range refRange(ss_arg.GetStringNext(), -1); // ss_arg[3]
if (!refRange.Empty()) {
if (ss_holder.resRange.Size() != refRange.Size()) {
mprinterr("Error: Reference range [%s] must match residue range [%s]\n",
refRange.RangeArg(), ss_holder.resRange.RangeArg());
return Action::ERR;
}
} else
refRange = ss_holder.resRange;
// Look for phi/psi only in reference
DihedralSearch refSearch;
refSearch.SearchFor(MetaData::PHI);
refSearch.SearchFor(MetaData::PSI);
if (refSearch.FindDihedrals( REF->Top(), refRange )) return Action::ERR;
// For each found dihedral, set theta
for (DihedralSearch::mask_it dih = refSearch.begin(); dih != refSearch.end(); ++dih)
{
double torsion = Torsion( REF->RefFrame().XYZ(dih->A0()),
REF->RefFrame().XYZ(dih->A1()),
REF->RefFrame().XYZ(dih->A2()),
REF->RefFrame().XYZ(dih->A3()) );
ss_holder.thetas_.push_back( (float)torsion );
}
secstruct_.push_back( ss_holder );
} else if (ss_arg.Nargs() == 4 && isalpha(ss_arg[2][0])) {
// Single dihedral type: <name>:<range>:<dih type>:<angle>
DihedralSearch::DihedralType dtype = DihedralSearch::GetType(ss_arg[2]);
if (ss_holder.sstype_idx == SS_EMPTY) {
// Type not yet defined. Create new type.
if (dtype == MetaData::UNDEFINED) {
mprinterr("Error: Dihedral type %s not found.\n", ss_arg[2].c_str());
return Action::ERR;
}
if (!validDouble(ss_arg[3])) {
mprinterr("Error: 4th arg (angle) is not a valid number.\n");
return Action::ERR;
}
SS.push_back( SS_TYPE(convertToDouble(ss_arg[3]), 0.0, 0.0, 0.0, 2, ss_arg[0]) );
ss_holder.sstype_idx = (int)(SS.size() - 1);
}
ss_holder.dihSearch_.SearchFor( dtype );
secstruct_.push_back( ss_holder );
} else if (ss_arg.Nargs() == 7 || ss_arg.Nargs() == 8) {
// Single custom dihedral type: <name>:<range>:<at0>:<at1>:<at2>:<at3>:<angle>[:<offset>]
if (ss_holder.sstype_idx == SS_EMPTY) {
// Type not yet defined. Create new type.
if (!validDouble(ss_arg[6])) {
mprinterr("Error: 7th arg (angle) is not a valid number.\n");
return Action::ERR;
}
SS.push_back( SS_TYPE(convertToDouble(ss_arg[6]), 0.0, 0.0, 0.0, 2, ss_arg[0]) );
ss_holder.sstype_idx = (int)(SS.size() - 1);
}
int offset = 0;
if (ss_arg.Nargs() == 8) {
if (!validInteger(ss_arg[7])) {
mprinterr("Error: 8th arg (offset) is not a valid number.\n");
return Action::ERR;
}
offset = convertToInteger(ss_arg[7]);
}
ss_holder.dihSearch_.SearchForNewType(offset,ss_arg[2],ss_arg[3],ss_arg[4],ss_arg[5],
ss_arg[0]);
secstruct_.push_back( ss_holder );
} else if (ss_arg.Nargs() == 4 || ss_arg.Nargs() == 6) {
// Custom SS/turn type: <name>:<range>:<phi1>:<psi1>[:<phi2>:<psi2>]
if (ss_holder.sstype_idx == SS_EMPTY) {
// Type not yet defined. Create new type.
if (!validDouble(ss_arg[2]) || !validDouble(ss_arg[3])) {
mprinterr("Error: 3rd or 4th arg (phi1/psi1) is not a valid number.\n");
return Action::ERR;
}
double phi1 = convertToDouble(ss_arg[2]);
double psi1 = convertToDouble(ss_arg[3]);
int isTurn = 0;
double phi2 = 0.0;
double psi2 = 0.0;
if (ss_arg.Nargs() == 6) {
isTurn = 1;
if (!validDouble(ss_arg[4]) || !validDouble(ss_arg[5])) {
mprinterr("Error: 5th or 6th arg (phi2/psi2) is not a valid number.\n");
return Action::ERR;
}
phi2 = convertToDouble(ss_arg[4]);
psi2 = convertToDouble(ss_arg[5]);
}
SS.push_back(SS_TYPE(phi1, psi1, phi2, psi2, isTurn, ss_arg[0] ));
ss_holder.sstype_idx = (int)(SS.size() - 1);
}
ss_holder.dihSearch_.SearchFor(MetaData::PHI);
ss_holder.dihSearch_.SearchFor(MetaData::PSI);
secstruct_.push_back( ss_holder );
} else {
mprinterr("Error: SS arg type [%s] not recognized.\n", ss_arg[0].c_str());
return Action::ERR;
}
ss_expr = actionArgs.GetStringNext();
} // End loop over args
if (secstruct_.empty()) {
mprinterr("Error: No SS types defined.\n");
return Action::ERR;
}
mprintf(" MAKESTRUCTURE:\n");
for (std::vector<SecStructHolder>::iterator ss = secstruct_.begin();
ss != secstruct_.end(); ++ss)
{
if (ss->sstype_idx != SS_EMPTY) {
const SS_TYPE& myType = SS[ss->sstype_idx];
switch ( myType.isTurn ) {
case 0:
mprintf("\tSS type %s will be applied to residue(s) %s\n",
myType.type_arg.c_str(), ss->resRange.RangeArg());
break;
case 1:
mprintf("\tTurn type %s will be applied to residue(s) %s\n",
myType.type_arg.c_str(), ss->resRange.RangeArg());
break;
case 2:
mprintf("\tDihedral value of %.2f will be applied to %s dihedrals in residue(s) %s\n",
myType.phi, myType.type_arg.c_str(), ss->resRange.RangeArg());
}
} else
mprintf("\tBackbone angles from reference will be applied to residue(s) %s\n",
ss->resRange.RangeArg());
}
return Action::OK;
}