void cESBTL::pdbReadAtom (const std::string& fileIn, cSetPoint3<double>& atomList, const std::string& atomName)
{
checkExtension(fileIn);
ESBTL::PDB_line_selector pdbSelector;
std::vector<ESBTL::Default_system> pdbSystems;
ESBTL::All_atom_system_builder<ESBTL::Default_system> pdbBuilder(pdbSystems, pdbSelector.max_nb_systems());
require(ESBTL::read_a_pdb_file(fileIn, pdbSelector, pdbBuilder, Occupancy_policy_all()), "cannot read PDB file");
require(!pdbSystems.empty(), "No PDB system");
require( pdbSystems.size() == 1, "More than one PDB system: pdbSystems.size() = " + num2str(pdbSystems.size()));
require(!pdbSystems[0].has_no_model(), "No model in 1st PDB system");
require( pdbSystems[0].number_of_models() == 1, "More than one model in PDB system: pdbSystems[0].number_of_models() = "
+ num2str(pdbSystems[0].number_of_models()));
for (ESBTL::Default_system::Models_iterator iterModel = pdbSystems[0].models_begin();
iterModel != pdbSystems[0].models_end();
iterModel++) {
const ESBTL::Default_system::Model& model = *iterModel;
for (ESBTL::Default_system::Model::Atoms_const_iterator iterAtom = model.atoms_begin();
iterAtom != model.atoms_end();
iterAtom++) {
if ((atomName != "" && iterAtom->atom_name() == atomName) || atomName == "") {
atomList.push_back(cVector3<double>(iterAtom->x(),iterAtom->y(),iterAtom->z()));
}
}
}
}
void cESBTL::pdbTransRotTrans(const std::string& fileIn, const std::string& fileOut, const cVector3<double>& offset1, const cVector3<double>& angle, const cVector3<double>& offset2)
{
checkExtension(fileIn);
checkExtension(fileOut);
// input
ESBTL::PDB_line_selector pdbSelector;
std::vector<ESBTL::Default_system> pdbSystems;
ESBTL::All_atom_system_builder<ESBTL::Default_system> pdbBuilder(pdbSystems, pdbSelector.max_nb_systems());
require(ESBTL::read_a_pdb_file(fileIn, pdbSelector, pdbBuilder, Occupancy_policy_all()), "cannot read PDB file");
require(!pdbSystems.empty(), "No PDB system");
require( pdbSystems.size() == 1, "More than one PDB system: pdbSystems.size() = " + num2str(pdbSystems.size()));
require(!pdbSystems[0].has_no_model(), "No model in 1st PDB system");
require( pdbSystems[0].number_of_models() == 1, "More than one model in 1st PDB system: pdbSystems[0].number_of_models() = "
+ num2str(pdbSystems[0].number_of_models()));
// output
std::ofstream output(fileOut.c_str());
assure(output);
// translate - rotate - translate
cVector3<double> pointRot;
cMatrix33<double> matRot;
transform_rotmat(angle[0], angle[1], angle[2],
matRot[0][0], matRot[0][1], matRot[0][2],
matRot[1][0], matRot[1][1], matRot[1][2],
matRot[2][0], matRot[2][1], matRot[2][2],
ROT3D_RIGHT_ZYZ);
for (ESBTL::Default_system::Models_iterator iterModel = pdbSystems[0].models_begin();
iterModel != pdbSystems[0].models_end();
iterModel++) {
const ESBTL::Default_system::Model& model = *iterModel;
for (ESBTL::Default_system::Model::Atoms_const_iterator iterAtom = model.atoms_begin();
iterAtom != model.atoms_end();
iterAtom++) {
ESBTL::Default_system::Atom atom(*iterAtom);
pointRot = matRot * cVector3<double>(atom.x() + offset1[0],
atom.y() + offset1[1],
atom.z() + offset1[2]);
atom.x() = pointRot[0] + offset2[0];
atom.y() = pointRot[1] + offset2[1];
atom.z() = pointRot[2] + offset2[2];
output << ESBTL::PDB::get_atom_pdb_format(atom) << "\n";
}
}
}
void cESBTL::pdbTranslate(const std::string& fileIn, const std::string& fileOut, const cVector3<double>& offset)
{
checkExtension(fileIn);
checkExtension(fileOut);
// input
ESBTL::PDB_line_selector pdbSelector;
std::vector<ESBTL::Default_system> pdbSystems;
ESBTL::All_atom_system_builder<ESBTL::Default_system> pdbBuilder(pdbSystems, pdbSelector.max_nb_systems());
require(ESBTL::read_a_pdb_file(fileIn, pdbSelector, pdbBuilder, Occupancy_policy_all()), "cannot read PDB file");
require(!pdbSystems.empty(), "No PDB system");
require( pdbSystems.size() == 1, "More than one PDB system: pdbSystems.size() = " + num2str(pdbSystems.size()));
require(!pdbSystems[0].has_no_model(), "No model in 1st PDB system");
require( pdbSystems[0].number_of_models() == 1, "More than one model in 1st PDB system: pdbSystems[0].number_of_models() = "
+ num2str(pdbSystems[0].number_of_models()));
// output
std::ofstream output(fileOut.c_str());
assure(output);
// translate
for (ESBTL::Default_system::Models_iterator iterModel = pdbSystems[0].models_begin();
iterModel != pdbSystems[0].models_end();
iterModel++) {
const ESBTL::Default_system::Model& model = *iterModel;
for (ESBTL::Default_system::Model::Atoms_const_iterator iterAtom = model.atoms_begin();
iterAtom != model.atoms_end();
iterAtom++) {
ESBTL::Default_system::Atom atom(*iterAtom);
atom.x() += offset[0];
atom.y() += offset[1];
atom.z() += offset[2];
output << ESBTL::PDB::get_atom_pdb_format(atom) << "\n";
}
}
}
void cESBTL::pdbExtractChain(const std::string& fileIn, const std::string& fileOut, const std::string& chainIDs)
{
checkExtension(fileIn);
checkExtension(fileOut);
// input
ESBTL::PDB_line_selector pdbSelector;
std::vector<ESBTL::Default_system> pdbSystems;
ESBTL::All_atom_system_builder<ESBTL::Default_system> pdbBuilder(pdbSystems, pdbSelector.max_nb_systems());
require(ESBTL::read_a_pdb_file(fileIn, pdbSelector, pdbBuilder, Occupancy_policy_all()), "cannot read PDB file");
require(!pdbSystems.empty(), "No PDB system");
require( pdbSystems.size() == 1, "More than one PDB system: pdbSystems.size() = " + num2str(pdbSystems.size()));
require(!pdbSystems[0].has_no_model(), "No model in 1st PDB system");
require( pdbSystems[0].number_of_models() == 1, "More than one model in 1st PDB system: pdbSystems[0].number_of_models() = "
+ num2str(pdbSystems[0].number_of_models()));
// output
std::ofstream output(fileOut.c_str());
assure(output);
// selection
ESBTL::Select_by_chainids pdbSelectorChainIDs(chainIDs);
for (ESBTL::Default_system::Models_iterator iterModel = pdbSystems[0].models_begin();
iterModel != pdbSystems[0].models_end();
iterModel++) {
const ESBTL::Default_system::Model& model = *iterModel;
for (Restrict_iterator iterAtom = ESBTL::make_selected_atom_iterator(model.atoms_begin(),pdbSelectorChainIDs);
iterAtom != ESBTL::make_selected_atom_iterator<ESBTL::Select_by_chainids>(model.atoms_end());
iterAtom++) {
output << ESBTL::PDB::get_atom_pdb_format(*iterAtom) << "\n";
}
output.close();
}
}
bool extract_balls_from_pdb(const char *filename,
std::list<Weighted_point> &weighted_points)
{
typedef ESBTL::CGAL::EPIC_kernel_with_atom ESBTL_K;
typedef ESBTL::CGAL::Default_system ESBTL_System;
typedef ESBTL::Generic_classifier<ESBTL::Radius_of_atom<double,ESBTL_System::Atom> > T_Atom_classifier;
typedef ESBTL::PDB::Line_format<Mandatory_fields_for_skin_surface> Line_format;
typedef ESBTL::Accept_none_occupancy_policy< Line_format > Accept_none_occupancy_policy;
typedef ESBTL::Weighted_atom_iterator<ESBTL_System::Model,
CGAL::Weighted_point<ESBTL_K::Point_3, double>,
ESBTL::Weight_of_atoms<T_Atom_classifier> > Weighted_atom_iterator;
//Container for molecular system
std::vector<ESBTL_System> systems;
ESBTL::PDB_line_selector sel;
ESBTL::All_atom_system_builder<ESBTL_System> builder(systems,sel.max_nb_systems());
T_Atom_classifier atom_classifier;
ESBTL::Line_reader<
Line_format,
ESBTL::PDB_line_selector,
ESBTL::All_atom_system_builder<ESBTL_System> >(sel,builder).read<ESBTL::ASCII>(filename,Accept_none_occupancy_policy(),' ');
//ESBTL::read_a_pdb_file(filename,sel,builder,Accept_none_occupancy_policy());
if ( systems.empty() || systems[0].has_no_model() ){
return false;
}
const ESBTL_System::Model& model= *systems[0].models_begin();
Weighted_atom_iterator atom_begin(model.atoms_begin(),&atom_classifier);
Weighted_atom_iterator atom_end(model.atoms_end(),&atom_classifier);
for (Weighted_atom_iterator it = atom_begin; it != atom_end; ++it) {
weighted_points.push_back(Weighted_point(Bare_point(it->x(), it->y(), it->z()), it->weight()));
}
return true;
}
void cESBTL::pdbPrintAtom(const std::string& fileIn, const std::string& atomName)
{
checkExtension(fileIn);
ESBTL::PDB_line_selector pdbSelector;
std::vector<ESBTL::Default_system> pdbSystems;
ESBTL::All_atom_system_builder<ESBTL::Default_system> pdbBuilder(pdbSystems, pdbSelector.max_nb_systems());
require(ESBTL::read_a_pdb_file(fileIn, pdbSelector, pdbBuilder, Occupancy_policy_all()), "cannot read PDB file");
require(!pdbSystems.empty(), "No PDB system");
require( pdbSystems.size() == 1, "More than one PDB system: pdbSystems.size() = " + num2str(pdbSystems.size()));
require(!pdbSystems[0].has_no_model(), "No model in 1st PDB system");
require( pdbSystems[0].number_of_models() == 1, "More than one model in 1st PDB system: pdbSystems[0].number_of_models() = "
+ num2str(pdbSystems[0].number_of_models()));
// iterate over all models
for (ESBTL::Default_system::Models_iterator iterModel = pdbSystems[0].models_begin();
iterModel != pdbSystems[0].models_end();
iterModel++) {
const ESBTL::Default_system::Model& model = *iterModel;
//std::cout << "Model " << model.model_number() << std::endl;
for (ESBTL::Default_system::Model::Chains_const_iterator iterChain = model.chains_begin();
iterChain != model.chains_end();
iterChain++) {
const ESBTL::Default_system::Chain& chain = *iterChain;
//std::cout << "Model " << model.model_number()
// << ", chain " << chain.chain_identifier() << std::endl;
for (ESBTL::Default_system::Chain::Residues_const_iterator iterResidue = chain.residues_begin();
iterResidue != chain.residues_end();
iterResidue++) {
const ESBTL::Default_system::Residue& residue = *iterResidue;
//std::cout << "Model " << model.model_number()
// << ", chain " << chain.chain_identifier()
// << ", residue " << residue.residue_name() << std::endl;
for (ESBTL::Default_system::Residue::Atoms_const_iterator iterAtom = residue.atoms_begin();
iterAtom != residue.atoms_end();
iterAtom++) {
if (atomName == "" || iterAtom->atom_name() == atomName) {
std::cout << "Model " << model.model_number()
<< ", chain " << chain.chain_identifier()
<< ", residue " << residue.residue_name()
<< ", atom " << iterAtom->atom_name();
std::cout << std::setprecision(4) << std::fixed
<< std::setw(7) << iterAtom->atom_serial_number()
<< std::setw(5) << iterAtom->charge()
<< std::setw(4) << iterAtom->element()
<< std::setw(11) << iterAtom->x()
<< std::setw(11) << iterAtom->y()
<< std::setw(11) << iterAtom->z();
std::cout << std::endl;
}
}
}
}
}
}