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Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
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Application allowing to load conformations from a list of PDB files using ESBTL, or from a plain txt file listing the conformations as Point_d. More...
#include <XTC_file_loader.hpp>
Classes | |
struct | Is_loaded_atom |
Public Types | |
typedef T_XTC_file_loader< ConformationType, ConformationBuilder, ESBTLMolecularSystem, PDBLineFormat > | Self |
typedef SBL::IO::Loader_base | Base |
typedef ESBTL::CGAL::EPIC_kernel_with_atom::FT | FT |
typedef ConformationType | Molecular_geometric_model |
typedef std::vector< Molecular_geometric_model > | Molecular_geometric_model_ensemble |
Static Public Member Functions | |
static boost::program_options::options_description *& | get_options (void) |
Access to the options' description of the module. More... | |
static bool | has_options (void) |
static void | delete_options (void) |
static void | initialize_options (const std::string &caption) |
Constructors | |
T_XTC_file_loader (void) | |
Default Constructor. More... | |
Parameters | |
boost::program_options::options_description | add_options (void) const |
Virtual method for adding options to the module. More... | |
const std::string & | get_input_file_name (void) const |
Return the name of the input file when only one is given. More... | |
const std::string & | get_input_file_name (unsigned i) const |
Return the name of the ith input file. More... | |
unsigned | get_model_number (void) const |
Return the number of the model used in the PDB files. More... | |
bool | is_loaded_water (void) const |
Check that water molecules are loaded. More... | |
bool | is_loaded_hydrogen (void) const |
Check that hydrogen are loaded. More... | |
void | set_loaded_chains (const std::string &loaded_chains) |
Access | |
unsigned | get_number_of_loaded_geometric_model_ensembles (void) const |
Number of loaded XTC ensembles. More... | |
const Molecular_geometric_model_ensemble & | get_geometric_model_ensemble (unsigned i) const |
ith XTC ensemble (const). More... | |
Molecular_geometric_model_ensemble & | get_geometric_model_ensemble (unsigned i) |
ith XTC ensemble. More... | |
const Molecular_geometric_model_ensemble & | get_geometric_model_ensemble (void) const |
XTC ensemble. (use only if one input file was provided) (const). More... | |
Molecular_geometric_model_ensemble & | get_geometric_model_ensemble (void) |
onformations ensemble. (use only if one input file was provided). More... | |
Requirements | |
bool | load (unsigned verbose=false, std::ostream &out=std::cout) |
Loads the data. More... | |
std::string | get_output_prefix (void) const |
Returns a prefix that concatains the input line options used when running the module. More... | |
std::string | get_name (void) const |
Return the name of the class itself. More... | |
bool | check_options (std::string &message) const |
Checks that the input options' values are coherent. More... | |
Management | |
void | set_loader_instance_name (const std::string &loader_instance_name) |
const std::string & | get_loader_instance_name (void) const |
Application allowing to load conformations from a list of PDB files using ESBTL, or from a plain txt file listing the conformations as Point_d.
It combines the options from the SBL::Models::T_PDB_file_loader and the SBL::Models::T_Points_d_file_loader
ConformationType | Representation of a conformation as a point in dimension D, where D is three times the number of particles in the conformation. |
ConformationBuilder | Functor building a conformation from a dD point or a molecular model from the ESBTL. |
ESBTLMolecularSystem | Representation of a molecular system in ESBTL (default is ESBTL::Default_system) |
PDBLineFormat | Format of a line in a PDB file, determining wether a field of a line is mandatory or not (default is ESBTL::Line_format<>) |
typedef SBL::IO::Loader_base Base |
typedef ESBTL::CGAL::EPIC_kernel_with_atom::FT FT |
typedef ConformationType Molecular_geometric_model |
typedef std::vector<Molecular_geometric_model> Molecular_geometric_model_ensemble |
typedef T_XTC_file_loader<ConformationType, ConformationBuilder, ESBTLMolecularSystem, PDBLineFormat> Self |
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Default Constructor.
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inlinevirtual |
Virtual method for adding options to the module.
Reimplemented from T_Module_option_description< Dummy >.
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inlinevirtual |
Checks that the input options' values are coherent.
Reimplemented from T_Module_option_description< Dummy >.
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inlinestaticinherited |
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inline |
ith XTC ensemble.
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inline |
ith XTC ensemble (const).
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inline |
onformations ensemble. (use only if one input file was provided).
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inline |
XTC ensemble. (use only if one input file was provided) (const).
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inline |
Return the name of the ith input file.
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inline |
Return the name of the input file when only one is given.
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inlineinherited |
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inline |
Return the number of the model used in the PDB files.
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inlinevirtual |
Return the name of the class itself.
Reimplemented from Loader_base.
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inline |
Number of loaded XTC ensembles.
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inlinestaticinherited |
Access to the options' description of the module.
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inlinevirtual |
Returns a prefix that concatains the input line options used when running the module.
Reimplemented from T_Module_option_description< Dummy >.
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inlinestaticinherited |
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inlinestaticinherited |
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inline |
Check that hydrogen are loaded.
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inline |
Check that water molecules are loaded.
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inlinevirtual |
Loads the data.
Reimplemented from Loader_base.
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inline |
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inlineinherited |