Hp::Hp(FILE * resultsFile, FILE * reporter, vector<Soup *> A, vector<Soup *> B):Method(reporter)
{
/*** write out to out file **/
writeDescription(reporter);
set_parameters();
if(A.size() != B.size())
{
cout << "WARNING: An equal amount of protein and ligand structures must be given to the HP function!\n";
return;
}
float result;
for(unsigned int i=0; i<A.size(); i++)
{
result = calculate(A[i],B[i]);
string decoy_number;
if(B[i]->name.find_last_of("_")== string::npos)
decoy_number = "-1";
else
decoy_number = B[i]->name.substr(B[i]->name.find_last_of("_")+1);
fprintf(resultsFile,"%-4s %-4s %8f\n",
A[i]->name.substr(0,4).c_str(),
decoy_number.c_str(),
result);
}
}
Matrix_IO::Matrix_IO(FILE * reporter):Method(reporter)
{
/*** write out to out file **/
writeDescription(reporter);
//lista = fopen("A.txt","a");
//listb = fopen("b.txt","a");
}
Bfactor::Bfactor(FILE * reporter, vector<Soup*> proteins, vector<Soup*> ligands):Method(reporter)
{
/*** write out to out file **/
writeDescription(reporter);
calculate(proteins,ligands);
}
Hp::Hp(FILE * reporter):Method(reporter)
{
/*** write out to out file **/
writeDescription(reporter);
set_parameters();
}
Pdbwriter::Pdbwriter(FILE * reporter, string fn, Soup * A):Method(reporter)
{
/*** write out to out file **/
writeDescription(reporter);
write(fn, A);
}
NN_DISCRIMINATION_PREPARATION::NN_DISCRIMINATION_PREPARATION(FILE * resultsFile,FILE * reporter)
{
/*** write out to out file **/
writeDescription(reporter,resultsFile);
go();
}
NN_VDW::NN_VDW(FILE * reporter):Nnmodel()
{
/*** write out to out file **/
writeDescription(reporter);
printf("Using the NN_VDW network!\n");
set_parameters();
}
void StateManagerWindow::saveAction() {
QList<QTreeWidgetItem*> items = list->selectedItems();
if(items.count() > 0) {
QTreeWidgetItem *item = items[0];
unsigned n = item->data(0, Qt::UserRole).toUInt();
saveState(n);
writeDescription();
synchronize();
descriptionText->setFocus();
}
}
ElementsNN::ElementsNN(FILE * reporter):Nnmodel()
{
/*** write out to out file **/
writeDescription(reporter);
printf("Using the elements network!\n");
threshold = 10;
}
ProteinEntropy::ProteinEntropy(FILE * reporter):Method(reporter)
{
/*** set parameters ***/
set_parameters();
/*** write out to out file **/
writeDescription(reporter);
}
Complementarity::Complementarity(FILE * resultsFile, FILE * reporter, vector<Soup*> A, vector<Soup*> B):Method(reporter)
{
set_parameters();
double result =0;
bool include = true;
/*** write out to out file **/
writeDescription(reporter);
Distances calc(reporter);
for(unsigned int i=0; i< A.size(); i++ )
{
calc.calculate(A[i], B[i], false);
vector<vector<float> > d =calc.getResult();
vector<Atom *> Aatoms = A[i]->getAtoms();
vector<Atom *> Batoms = B[i]->getAtoms();
for(unsigned int x=0; x<d.size(); x++)
for(unsigned int y=0; y<d[0].size(); y++)
{
include = true;
if(ignore_h == 1 && Aatoms[x]->element =="H")
include = false;
if(ignore_h == 1 && Batoms[y]->element =="H")
include = false;
// cout<<"A:"<<Aatoms[x]->element<<" B:"<<Batoms[y]->element<<" Dist:"<<sqrt(d[x][y]);
if(d[x][y] < tsq && include)
{
result += complEnergy;
// cout<<" INCLUDED";
}
// cout<<endl;
}
string decoy_number;
if(B[i]->name.find_last_of("_")== string::npos)
decoy_number = "-1";
else
decoy_number = B[i]->name.substr(B[i]->name.find_last_of("_")+1);
fprintf(resultsFile,"%-4s %-4s %8f\n",
A[i]->name.substr(0,4).c_str(),
decoy_number.c_str(),
result);
}
// fprintf(reporter,"The result is: %f kcal/mol\n", result);
// fprintf(resultsFile,"%-10s %5.3f\n",A[0]->identify().substr(0,4).c_str(),result);
}
void Energy::initiate()
{
FILE * reporter = fopen("out.txt","w");
// write out to out file
writeDescription(reporter);
are_coefficients_set = false;
// read parameters from file
read_parameters();
return;
}
Energy::Energy(FILE * reporter, vector<Soup *> proteins_in, vector<Soup *> ligands_in):Method(reporter)
{
/*** write out to out file **/
writeDescription(reporter);
/*** do A and B have equal lengths? ***/
if(proteins.size() != ligands.size())
{
cout << "WARNING: An equal amount of protein and ligand structures must be given to the energy function!\n";
return;
}
are_coefficients_set = false;
/*** copy structures and read in setup ***/
proteins = proteins_in;ligands = ligands_in;
read_parameters();
/*** set parameters ***/
// Generalparameters prepA(rep,proteins);
// Generalparameters prepB(rep,ligands);
simple_parameters.prepare(proteins);
simple_parameters.prepare(ligands);
/*** set targets ***/
generate_target_vector();
test();
if(mode == "train")
train();
/*** write out matrices for octave ***/
Matrix_IO M(rep);
M.open("binding.m");
M.write_matrix("A", A);
M.write_vector("b",b);
M.update_lists(names,A,b);
M.write_string_vector("Names",names);
M.close();
if(are_coefficients_set)
stream_results();
}
void MSC::initiate()
{
FILE * reporter = fopen("out.txt","w");
//resultsFile = fopen(res.c_str(),"w");
// write out to out file
writeDescription(reporter);
coefficients_are_set = 0;
// read parameters from file
read_parameters();
}
Hp::Hp(FILE * resultsFile, FILE * reporter, vector<Soup *> A):Method(reporter)
{
/*** write out to out file **/
writeDescription(reporter);
set_parameters();
float result;
for(unsigned int i=0; i<A.size(); i++)
{
result = calculate(A[i]);
fprintf(resultsFile,"%-4s %8f\n",
A[i]->name.substr(0,4).c_str(),
result);
}
}
status CAFFile::writeInit(AFfilesetup setup)
{
if (initFromSetup(setup) == AF_FAIL)
return AF_FAIL;
initCompressionParams();
Tag caff("caff");
if (!writeTag(&caff)) return AF_FAIL;
const uint8_t versionAndFlags[4] = { 0, 1, 0, 0 };
if (m_fh->write(versionAndFlags, 4) != 4) return AF_FAIL;
if (writeDescription() == AF_FAIL)
return AF_FAIL;
if (writeData(false) == AF_FAIL)
return AF_FAIL;
return AF_SUCCEED;
}
Targets::Targets(FILE * reporter, string dataset):Method(reporter)
{
/*** write out to out file **/
writeDescription(reporter);
T = 300;// K
//R = 1.9872 / 1000;// kcal/(K mol)
R = 8.314472/1000; // kJ/(K mol)
log_conversion = 2.302585093;
if (dataset == "wang")
read_file_wang("/home/people/chresten/run/docksets/wang/all_original_dockset/complex_list_all");
else if(dataset == "pdbbind")
read_file_pdbbind("/home/people/chresten/run/docksets/pdbbind/original/INDEX.2004.refined.pkd");
else if(dataset == "pdbbind2007")
read_file_pdbbind("/rnase_local/chresten/run/docksets/pdbbind2007//INDEX.2007.refined.data");
else if(dataset == "fictive")
read_file_fictive("targets.txt");
}
ProteinEntropy::ProteinEntropy(FILE * resultsFile, FILE * reporter, vector<Soup*> A, vector<Soup*> B):Method(reporter)
{
/*** set parameters ***/
set_parameters();
/*** write out to out file **/
writeDescription(reporter);
if(A.size() != B.size())
{
cout << "WARNING: An equal amount of protein and ligand structures must be given to the ProteinEntropy function!\n";
return;
}
vector<vector<float> > distances;
for(unsigned int i=0; i<A.size(); i++)
{
float result = calculate(A[i],B[i]);
string decoy_number;
if(B[i]->name.find_last_of("_")== string::npos)
decoy_number = "-1";
else
decoy_number = B[i]->name.substr(B[i]->name.find_last_of("_")+1);
fprintf(resultsFile,"%-4s %-4s %8f\n",
A[i]->name.substr(0,4).c_str(),
decoy_number.c_str(),
result);
// fprintf(resultsFile,"%-10s %f\n",convert_soup_to_objects(A[i])[0]->identify().substr(0,4).c_str(),result);
}
}
Bfactor::Bfactor(FILE * reporter):Method(reporter)
{
/*** write out to out file **/
writeDescription(reporter);
}
PrepinReader::PrepinReader(FILE * reporter):Method(reporter)
{
/*** write out to out file **/
writeDescription(reporter);
}
PrepinReader::PrepinReader(FILE * reporter, vector<Soup *> A):Method(reporter)
{
/*** write out to out file **/
writeDescription(reporter);
go(A);
}
MSC::MSC(FILE * reporter, FILE * results, vector<Soup *> wts_in, vector<Soup *> mutants_in):Method(reporter)
{
/**********************************************************************
Mutant stability change
Input: Proberly protonated wild type and mutant structures
**********************************************************************/
wts = wts_in;
mts = mutants_in;
// write out to out file
writeDescription(reporter);
coefficients_are_set = 0;
// does wts and mutants have equal lengths?
if(wts.size() != mts.size())
{
cout << "ERROR: An equal amount of wild type and mutant structures must be given!\n";
return;
}
// read parameters from file
read_parameters();
// set parameters
if(include_ff_components)
{
//correct_names.go(wts);
//correct_names.go(mts);
//prepin.go(wts);
//prepin.go(mts);
simple_parameters.prepare(wts);
simple_parameters.prepare(mts);
}
test();
if(mode == "train")
train();
/*** write out matrices for octave ***/
Matrix_IO M(rep);
M.open("stability.m");
M.write_matrix("Astability", A);
M.write_vector("bstability",b);
M.write_string_vector("Names",names);
M.close();
cout<<"Done writting to octave file"<<endl;
if(coefficients_are_set)
stream_results();
}
