void RotLibConvert_Dunbrack_BBInd::readDefinition( StringBuilder& sb, RotamerLibrary& _RotLib ) const
{
ASSERT( sb.size() >= 67, ParseException, "String too short to parse!!");
StringBuilder resname(3);
resname.setTo( sb, 0, 3 );
sb.TruncateLeftBy(18);
int pdbCount = sb.parseInt(0,7);
if( pdbCount == 0 )
return;
double probability = sb.parseDouble(7,8);
sb.TruncateLeftBy(37);
std::vector<double> importChis;
std::vector<std::string> parts = sb.tokenise();
ASSERT( (parts.size() % 2 == 0), ParseException, "Unexpected element count");
for( size_t i = 0; i < parts.size(); i+=2 )
{
double chi;
ASSERT( 0 == str2double( parts[i], chi ), ParseException, "Error parsing chi def");
importChis.push_back(Maths::DegToRad(chi));
}
ASSERT( importChis.size() != 0, ParseException, "No chis found!!");
_RotLib.addRotamer( resname.toString(), importChis, ConstantProbability( probability ) );
}
int main(int argc, char** argv){
if (argc != 3 ){
std::cerr << "Please provide a filename and a residue name" << std::endl;
return EXIT_FAILURE;
}
//creates one system with all atoms matching the criteria
std::string resname(argv[2]);
ESBTL::Select_by_resname selector(resname);
ESBTL::Generic_line_selector<ESBTL::Select_by_resname> sel(selector);
std::vector<ESBTL::Default_system> systems;
//declare the building that will contruct the system from the pdb file.
std::cout << sel.max_nb_systems() << std::endl;
ESBTL::All_atom_system_builder<ESBTL::Default_system> builder(systems,sel.max_nb_systems());
//read the pdb file
if (ESBTL::read_a_pdb_file(argv[1],sel,builder,Accept_none_occupancy_policy())){
if ( systems.empty() || systems[0].has_no_model() ){
std::cerr << "No atoms found" << std::endl;
return EXIT_FAILURE;
}
//consider the first model of the system
const ESBTL::Default_system::Model& model=*systems[0].models_begin();
std::cout << model.number_of_atoms() << " atoms in residue(s) named " << resname << std::endl;
}
else
return EXIT_FAILURE;
return EXIT_SUCCESS;
}
// PDBfile::pdb_Residue()
NameType PDBfile::pdb_Residue(int& current_res) {
// Res name (16-20)
char savechar = linebuffer_[20];
linebuffer_[20] = '\0';
NameType resname(linebuffer_+16);
// Replace asterisks with single quotes
resname.ReplaceAsterisk();
linebuffer_[20] = savechar;
// Res num (22-27)
savechar = linebuffer_[27];
linebuffer_[27] = '\0';
current_res = atoi( linebuffer_+22 );
linebuffer_[27] = savechar;
return resname;
}
uint16 ResMan_t7g::getRef(Common::String name, Common::String scriptname) {
// Get the name of the RL file
Common::String rlFileName(t7g_gjds[_lastGjd]);
rlFileName += ".rl";
Common::SeekableReadStream *rlFile = 0;
if (_macResFork) {
// Open the RL file from the resource fork
rlFile = _macResFork->getResource(rlFileName);
} else {
// Open the RL file
rlFile = SearchMan.createReadStreamForMember(rlFileName);
}
if (!rlFile)
error("Groovie::Resource: Couldn't open %s", rlFileName.c_str());
uint16 resNum;
bool found = false;
for (resNum = 0; !found && !rlFile->err() && !rlFile->eos(); resNum++) {
// Read the resource name
char readname[12];
rlFile->read(readname, 12);
// Test whether it's the resource we're searching
Common::String resname(readname, 12);
if (resname.hasPrefix(name.c_str())) {
debugC(2, kGroovieDebugResource | kGroovieDebugAll, "Groovie::Resource: Resource %12s matches %s", readname, name.c_str());
found = true;
}
// Skip the rest of resource information
rlFile->read(readname, 8);
}
// Close the RL file
delete rlFile;
// Verify we really found the resource
if (!found) {
error("Groovie::Resource: Couldn't find resource %s in %s", name.c_str(), rlFileName.c_str());
return (uint16)-1;
}
return (_lastGjd << 10) | (resNum - 1);
}
chain_class::chain_class(FFF* P,vector<string> lines): _P(P) {
//printf ("\nLines passed to chain_class:\n");
string last_resnum="DUMMY";
vector<string> residue_lines;
//
// Get the chain name
//
string chainid(lines[0],21,1);
//printf ("ChainID in chain_class: '%s'\n",chainid.c_str());
name=strip(chainid);
for (unsigned int ii=0;ii<lines.size();ii++) {
//
// Get the residue name and number
//
string resname(lines[ii],17,3);
string resnum(lines[ii],22,5);
if (resnum!=last_resnum) {
//
// new residue
//
if (last_resnum!="DUMMY") {
//printf ("Instantiating residue_class\n");
residue_class X(this,residue_lines);
//printf ("done resclass\n");
residues.push_back(X);
residue_lines.resize(0);
}
last_resnum=resnum;
}
residue_lines.push_back(lines[ii]);
}
//
// And the last residue...
//
if (residue_lines.size()!=0) {
residue_class X(this,residue_lines);
residues.push_back(X);
}
//printf("Chain name: %s found\n",name.c_str());
return;
}
int main(int argc,char*argv[])
{
if(argc!=2)
{
cout<<"USAGE:SIS datafile "<<endl;
exit(1);
}
//define the entry
string networkname(argv[1]); //network name
double a=1;
double alpha=0.4;
double beta=0.1;
int game_rounds=500; //MC rounds
int aver_rounds=10; //do average
double delta=1;//delta
string output_name_pre; //the network name
for(int i=0;i!=networkname.size()-4;i++)
{
output_name_pre.push_back(networkname[i]);
}
//random generator
//to initialize the random seed
igraph_rng_init(mrng,&igraph_rngtype_mt19937);
unsigned long idum; // random number seed
idum=(unsigned long)time(NULL);
igraph_rng_seed(mrng,idum);
//construct the graph
igraph_t network;
gen_graph(&network,networkname);
int nwsize=igraph_vcount(&network); //the size of the network
//to generate the name of the output file
//output file name
string resname("res.txt");
string totalname=output_name_pre+resname;
FILE *outfile;
outfile = fopen(totalname.c_str(), "w");
//construct the population
for(a=-6;a<6.1;a+=0.1 )
{
population popu(output_name_pre,&network,delta,0.01,a,2,3*nwsize,3*nwsize);
double res=0;
popu.population_dynamics(&res,alpha,beta,1000);
fprintf(outfile,"%f\t%f\n",a,res/ nwsize);
fflush(outfile);
}
fclose(outfile);
/*
igraph_t network;
int nwsize = igraph_vcount(&network); //the size of the network
igraph_watts_strogatz_game(&network, 1, 500, 4, 0.1, false, false);
string output_name_pre("small_world");
population test(output_name_pre,&network, 1, 0.01, 1, 0, 3 * nwsize, 3 * nwsize);
test.initial_state();
double res = 0;
test.population_dynamics(&res,0.3,0.1,300);
*/
//for (a=-5;a!=5;a+=0.2)
//
//{
// population test(&network,delta,0.01,a,type,3*nwsize,3*nwsize);
// vector<double> average_rres;
// for(int i=0;i!=aver_rounds;++i)
// {
// double rres=0;
// test.initial_state();
// test.population_dynamics(&rres,0.4,0.1,game_rounds);
//// printf("%f\n", rres);
// average_rres.push_back(rres);
// }
// fprintf(outfile,"%f\t%f\n",a,double (accumulate(average_rres.begin(),\
// average_rres.end(),0)/average_rres.size()));
// fflush(outfile);
//}
//fclose(outfile);
igraph_destroy(&network);
return 0;
}
std::string Condition::getName(bool tip, NameFlags::Value flags, int recursion) const
{
if (!tip) {
return (type < scen.pergame->max_condition_types) ? types[type] : "Unknown!";
} else {
std::string stype = std::string("");
std::ostringstream convert;
switch (type) {
case ConditionType::None:
// Let this act like a separator
convert << " ";
stype.append(convert.str());
break;
case ConditionType::BringObjectToArea:
convert << get_unit_full_name(object) << " " << object;
convert << " is" << areaName();
stype.append(convert.str());
break;
case ConditionType::BringObjectToObject:
convert << get_unit_full_name(object) << " " << object << " is next to unit " << get_unit_full_name(u_loc) << " " << u_loc;
stype.append(convert.str());
break;
case ConditionType::OwnObjects:
case ConditionType::OwnFewerObjects:
case ConditionType::ObjectsInArea:
{ // we define some variables in this block, therefore need scope as we are also in a case
if (valid_player()) {
convert << playerPronoun(player) << " has ";
}
switch (type) {
case ConditionType::OwnObjects:
case ConditionType::ObjectsInArea:
if (amount == 0) {
convert << "any number of";
} else {
convert << "at least " << amount;
}
break;
case ConditionType::OwnFewerObjects:
if (amount == 0) {
convert << "no";
} else {
convert << "at most " << amount;
}
break;
}
if (valid_unit_spec()) {
std::string un(wstringToString(pUnit->name()));
if (amount > 1 && !un.empty() && *un.rbegin() != 's' && !replaced(un, "man", "men")) {
convert << " " << un << "s";
} else {
convert << " " << un;
}
} else {
if (amount != 1) {
convert << " units";
} else {
convert << " unit";
}
}
convert << areaName();
stype.append(convert.str());
}
break;
case ConditionType::DestroyObject:
convert << get_unit_full_name(object) << " is killed";
stype.append(convert.str());
break;
case ConditionType::CaptureObject:
convert << playerPronoun(player) << " captured " << get_unit_full_name(object);
stype.append(convert.str());
break;
case ConditionType::AccumulateAttribute:
switch (res_type) {
case 0: // Food accumulated
convert << playerPronoun(player) << " has " << amount << " food";
break;
case 1: // Wood accumulated
convert << playerPronoun(player) << " has " << amount << " wood";
break;
case 2: // Stone accumulated
convert << playerPronoun(player) << " has " << amount << " stone";
break;
case 3: // Gold accumulated
convert << playerPronoun(player) << " has " << amount << " gold";
break;
case 20: // Units killed
if (amount == 1) {
convert << playerPronoun(player) << " kills a unit";
} else {
convert << playerPronoun(player) << " has killed " << amount << " units";
}
break;
case 44: // Kill ratio
if (amount == 0) {
convert << playerPronoun(player) << " has equal kills and deaths";
} else if (amount == 1) {
convert << playerPronoun(player) << " has killed one more than lost";
} else if (amount > 0) {
convert << playerPronoun(player) << " has " << amount << " more kills than deaths";
} else if (amount == -1) {
convert << playerPronoun(player) << " has lost one more unit than has killed";
} else {
convert << playerPronoun(player) << " has " << -amount << " more deaths than kills";
}
break;
default:
//convert << types_short[type];
if (res_type >= 0) {
const Link * list = esdata.resources.head();
for (int i=0; list; list = list->next(), i++)
{
if (i == res_type) {
std::wstring resname(list->name());
convert << playerPronoun(player) << "'s ";
convert << std::string( resname.begin(), resname.end());
convert << " >= " << amount;
break;
}
}
}
break;
}
stype.append(convert.str());
break;
case ConditionType::ResearchTehcnology:
if (valid_technology_spec()) {
convert << playerPronoun(player) << " has tech ";
std::wstring techname(pTech->name());
convert << std::string( techname.begin(), techname.end());
convert << " researched";
} else {
convert << "INVALID";
}
stype.append(convert.str());
break;
case ConditionType::ResearchingTechnology:
if (pTech && pTech->id()) {
convert << playerPronoun(player) << " is researching ";
std::wstring techname(pTech->name());
convert << std::string( techname.begin(), techname.end());
} else {
convert << "INVALID";
}
stype.append(convert.str());
break;
case ConditionType::Timer:
convert << time_string(timer) << " has passed";
stype.append(convert.str());
break;
case ConditionType::ObjectSelected:
convert << "selected unit " << object;
convert << " (" << get_unit_full_name(object) << ")";
stype.append(convert.str());
break;
case ConditionType::AISignal:
switch (ai_signal) {
case -1034:
convert << "singleplayer / cheats enabled";
break;
case -1036:
convert << "starting resources set to standard";
break;
case -1039:
convert << "regicide";
break;
case -1040:
convert << "deathmatch";
break;
case -70850:
convert << "one-click garrison";
break;
default:
if (ai_signal >= -518 && ai_signal <= -7) {
int signal = ai_signal + 518;
int taunt_player = signal / 64;
int taunt_set_id = signal % 64;
convert << "player " << taunt_player + 1 << " taunted " << taunt_set[taunt_set_id];
} else if (ai_signal >= -774 && ai_signal <= -519) {
convert << "AI goal " << ai_signal + 774 << " achieved";
} else {
convert << "AI signalled " << ai_signal;
}
}
stype.append(convert.str());
break;
case ConditionType::ObjectVisible:
convert << "unit " << object;
convert << " (" << get_unit_full_name(object) << ") is visible";
stype.append(convert.str());
break;
case ConditionType::PlayerDefeated:
if (player == 0) {
convert << "Gaia";
} else {
convert << playerPronoun(player);
}
convert << " is defeated";
stype.append(convert.str());
break;
case ConditionType::ObjectHasTarget:
convert << "unit " << object << " (" << get_unit_full_name(object) << ") is targetting";
if (null_location_unit()) {
convert << " something";
} else {
convert << " " << u_loc << " (" << get_unit_full_name(u_loc) << ")";
}
stype.append(convert.str());
break;
case ConditionType::UnitsGarrisoned:
if (amount == 1) {
convert << "unit " << object << " (" << get_unit_full_name(object) << ") has " << amount << " units garrisoned";
} else {
convert << "unit " << object << " (" << get_unit_full_name(object) << ") has one unit garrisoned";
}
stype.append(convert.str());
break;
case ConditionType::DifficultyLevel:
convert << "difficulty is ";
switch (amount) {
case DifficultyLevel::Hardest:
convert << "Hardest";
break;
case DifficultyLevel::Hard:
convert << "Hard";
break;
case DifficultyLevel::Moderate:
convert << "Moderate";
break;
case DifficultyLevel::Standard:
convert << "Standard";
break;
case DifficultyLevel::Easiest:
convert << "Easiest";
break;
}
stype.append(convert.str());
break;
case ConditionType::UnitsQueuedPastPopCap_SWGB:
if (valid_player()) {
convert << playerPronoun(player) << " has " << amount << " units queued past the pop cap";
} else {
convert << "INVALID";
}
stype.append(convert.str());
break;
case ConditionType::OwnFewerFoundations_SWGB: // Chance_HD:
switch (scen.game) {
case AOHD:
case AOF:
case AOHD4:
case AOF4:
case AOHD6:
case AOF6:
convert << amount << "% chance ";
stype.append(convert.str());
break;
case SWGB:
case SWGBCC:
if (valid_player()) {
convert << playerPronoun(player) << " has ";
}
if (amount == 0) {
convert << "no";
} else {
convert << "at most " << amount;
}
if (valid_unit_spec()) {
std::string un(wstringToString(pUnit->name()));
if (amount > 1 && !un.empty() && *un.rbegin() != 's' && !replaced(un, "man", "men")) {
convert << " " << un << " foundations";
} else {
convert << " " << un << " foundation";
}
} else {
if (amount != 1) {
convert << " foundations";
} else {
convert << " foundation";
}
}
convert << areaName();
stype.append(convert.str());
break;
default:
convert << amount << "UNKNOWN CONDITION";
stype.append(convert.str());
}
break;
default:
stype.append((type < scen.pergame->max_condition_types) ? types_short[type] : "Unknown!");
}
return flags&NameFlags::LIMITLEN?stype.substr(0,MAX_CHARS):stype;
}
}