Loader for proteins from PDB files using ESBTL Loader for proteins from PDB files using ESBTL.
More...
#include <Protein_representation_loader.hpp>
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bool | load (unsigned verbose=0, std::ostream &out=std::cout) |
| Loads the data. More...
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std::string | get_output_prefix (void) const |
| Returns a prefix that concatains the input line options used when running the module. More...
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std::string | get_name (void) const |
| Return the name of the class itself. More...
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bool | check_options (std::string &message) const |
| Checks that the input options' values are coherent. More...
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template<class ProteinRepresentation, class MolecularCovalentStructureBuilder = SBL::CSB::T_Molecular_covalent_structure_builder_for_proteins<typename ProteinRepresentation::Polypeptide_chain::Molecular_covalent_structure>, class PDBLineFormat = ESBTL::PDB::Line_format<>>
class SBL::IO::T_Protein_representation_loader< ProteinRepresentation, MolecularCovalentStructureBuilder, PDBLineFormat >
Loader for proteins from PDB files using ESBTL Loader for proteins from PDB files using ESBTL.
- Template Parameters
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ProteinRepresentation | A model of SBL::CSB::T_Protein_representation |
MolecularCovalentStructureBuilder | Builder of the covalent structure. |
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<>) |
◆ Base
Base loader from which any loader should inherit.
Requirements are...
◆ FT
typedef ESBTL::CGAL::EPIC_kernel_with_atom::FT FT |
Representation of the number type.
◆ Polypeptide_chain
Reprenstation of a single polypeptidic chain within a protein representation.
- Template Parameters
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ParticleTraits | Traits class providing the particle type, see package ParticleTraits |
MolecularCovalentStructure | Graph representation of a covalent structure. |
ConformationType | Representation of a conformation as a point in dimension D, where D is three times the number of particles in the conformation. |
◆ Protein_representation
Representaiton of a protein with its polypeptide chains.
Representaiton of a protein with its polypeptide chains.
- Template Parameters
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◆ Self
◆ add_input_pdb_file()
void add_input_pdb_file |
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const std::string & |
file_name | ) |
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inlinestatic |
Add manually the name of an input PDB file for loading a covalent structure.
- Parameters
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file_name | Path to the PDB file to add |
◆ add_options()
boost::program_options::options_description add_options |
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void |
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const |
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inlinevirtual |
◆ check_options()
bool check_options |
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std::string & |
message | ) |
const |
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inlinevirtual |
◆ delete_options()
static void delete_options |
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void |
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inlinestaticinherited |
◆ get_input_file_name() [1/2]
const std::string & get_input_file_name |
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unsigned |
i | ) |
const |
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inline |
Return the name of the ith input file.
- Parameters
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i | Number of the input PDB file |
- Returns
- The name of the ith input PDB file.
◆ get_input_file_name() [2/2]
const std::string & get_input_file_name |
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void |
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const |
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inline |
Return the name of the input file when only one is given.
- Returns
- The name of the input PDB file.
◆ get_loaded_chains() [1/2]
std::string get_loaded_chains |
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unsigned |
i | ) |
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inlinestatic |
◆ get_loaded_chains() [2/2]
std::string get_loaded_chains |
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void |
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inlinestatic |
◆ get_loader_instance_name()
const std::string& get_loader_instance_name |
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void |
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const |
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inlineinherited |
◆ get_model_number()
unsigned get_model_number |
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void |
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inlinestatic |
Return the number of the selected model for the input PDB files.
- Returns
- Number of the model.
◆ get_name()
std::string get_name |
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void |
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const |
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inlinevirtual |
Return the name of the class itself.
Reimplemented from Loader_base.
◆ get_number_of_loaded_proteins()
unsigned get_number_of_loaded_proteins |
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void |
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const |
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inline |
Return the number of successfuly loaded PDB files.
- Returns
- Number of loaded proteins
◆ get_occupancy_factor()
unsigned get_occupancy_factor |
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void |
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inlinestatic |
◆ get_options()
static boost::program_options::options_description*& get_options |
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void |
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inlinestaticinherited |
Access to the options' description of the module.
◆ get_output_prefix()
std::string get_output_prefix |
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void |
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const |
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inlinevirtual |
◆ get_protein() [1/2]
ProteinRepresentation & get_protein |
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unsigned |
i | ) |
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inline |
◆ get_protein() [2/2]
const ProteinRepresentation & get_protein |
( |
unsigned |
i | ) |
const |
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inline |
◆ has_options()
static bool has_options |
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void |
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inlinestaticinherited |
◆ initialize_options()
static void initialize_options |
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const std::string & |
caption | ) |
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inlinestaticinherited |
◆ is_loaded_hetatoms()
bool is_loaded_hetatoms |
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void |
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inlinestatic |
◆ is_loaded_water()
bool is_loaded_water |
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void |
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inlinestatic |
◆ load()
bool load |
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unsigned |
verbose = 0 , |
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std::ostream & |
out = std::cout |
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) |
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inlinevirtual |
◆ set_allow_incomplete_chains()
void set_allow_incomplete_chains |
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bool |
with_incomplete_chains | ) |
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inlinestatic |
Set the load incomplete residues tag.
◆ set_alternate_coordinate()
void set_alternate_coordinate |
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char |
altc | ) |
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inlinestatic |
Alternate coordinates: alternative to be used.
- Parameters
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altc | Alternate coordinate value |
◆ set_coarse_level()
void set_coarse_level |
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unsigned |
coarse_level | ) |
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inlinestatic |
Configure the loader to build the covalent structure at different levels.
- Parameters
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coarse_level | Building level of the covalent structure (0 : all atoms, 1 : heavy atoms only, 2 : c-alpha only) |
◆ set_loaded_chains() [1/2]
void set_loaded_chains |
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const std::string & |
chains | ) |
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inlinestatic |
Subset of chains to be loaded : do it for all input PDB files.
- Parameters
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chains | Concatenated list of chains |
◆ set_loaded_chains() [2/2]
void set_loaded_chains |
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unsigned |
i, |
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const std::string & |
chains |
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) |
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inlinestatic |
Subset of chains to be loaded : do it for the ith input PDB file.
- Parameters
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i | Number of the PDB file for which chains are specified |
chains | Concatenated list of chains |
◆ set_loaded_hetatoms()
void set_loaded_hetatoms |
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bool |
with_hetatoms | ) |
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inlinestatic |
Configure the loader to load or not the hetero-atoms.
- Parameters
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with_hetatoms | Tag to set with or without hetero-atoms |
◆ set_loaded_water()
void set_loaded_water |
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bool |
with_water | ) |
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inlinestatic |
Configure the loader to load or not the water molecules.
- Parameters
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with_water | Tag to set with or without water |
◆ set_loader_instance_name()
void set_loader_instance_name |
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const std::string & |
loader_instance_name | ) |
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inlineinherited |
◆ set_max_bond_distance()
void set_max_bond_distance |
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double |
max_bond_distance | ) |
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inlinestatic |
Set the maximal bond distance between the C of a residue and the N of its next residue.
◆ set_occupancy_factor()
void set_occupancy_factor |
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unsigned |
i | ) |
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inlinestatic |
Selection policy for atoms in the input PDB files with no alternate location and occupancy not equal to 1.
- Parameters
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i | Occupancy value. Allowed values are: 1 (all), 2 (forbbiden, default), 3 (none), 4 (max), 5 (min) |
◆ set_PDB_model_number()
void set_PDB_model_number |
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unsigned |
n | ) |
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inlinestatic |
ID of the model to be loaded frome the PDB file (default is 1)
- Parameters
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◆ set_without_disulfide_bonds()
void set_without_disulfide_bonds |
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bool |
without_ss | ) |
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inlinestatic |
Configure the loader not to build disulfide bonds.
- Parameters
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without_ss | Tag to set with or without disulfide bonds |