Loads components (Atoms, Groups, Spacer, etc.) in standard PDB format.
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| PdbLoader (istream &_input=cin, bool _permissive=false, bool _noHAtoms=false, bool _noHetAtoms=false, bool _noSecondary=false, bool _noConnection=false, bool _noWater=true, bool _verb=true, bool _allChains=false, string _NULL="", bool _onlyMetal=false, bool _noNucleotideChains=true) |
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void | checkAndSetChain () |
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void | checkModel () |
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vector< char > | getAllChains () |
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unsigned int | getMaxModels () |
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unsigned int | getMaxModelsFast () |
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virtual void | loadProtein (Protein &prot) |
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Loads components (Atoms, Groups, Spacer, etc.) in standard PDB format.
PdbLoader |
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istream & |
_input = cin , |
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bool |
_permissive = false , |
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bool |
_noHAtoms = false , |
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bool |
_noHetAtoms = false , |
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bool |
_noSecondary = false , |
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bool |
_noConnection = false , |
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bool |
_noWater = true , |
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bool |
_verb = true , |
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bool |
_allChains = false , |
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string |
_NULL = "" , |
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bool |
_onlyMetal = false , |
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bool |
_noNucleotideChains = true |
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) |
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Constructor.
- Parameters
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_input | = the PDB file object |
_permissive | = if true, allows loading residues with missing atoms |
_noHAtoms | = if true, doesn't load Hydrogens |
_noHetAtoms | = if true, doesn't load het atoms |
_noSecondary | = if true, doesn't load secondary structure (neither the one calculated from torsional angles nor the DSSP) |
_noConnection | = if true, doesn't connect residues |
_noWater | = if true, doesn't load water atoms |
_verb | = if true, verbose mode |
_allChains | = if true, loads all chains |
_NULL | = the name of the chain to be loaded, if not provided only loads the first chain |
_onlyMetal | = if true, load only metals as ligands |
_noNucleotideChains | = if true, doesn't load DNA/RNA chains |
void assignSecondary |
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Spacer & |
sp | ) |
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protected |
Try to assigns the secondary structure from the PDB header. If not present uses Spacer's setStateFromTorsionAngles().
- Parameters
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void checkAndSetChain |
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If user selected a chain, it check validity of this choice, otherwise it select first available chain.
- Parameters
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- Returns
- void
If user selected a Model, it check validity of this choice, otherwise it select first available chain.
- Parameters
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- Returns
- void
vector< char > getAllChains |
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Returns all available chain IDs for a PDB file.
- Parameters
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- Returns
- vector of chars
unsigned int getMaxModels |
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Reads in the maximum allowed number of NMR models, zero otherwise
- Parameters
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unsigned int getMaxModelsFast |
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Reads in the maximum allowed number of NMR models, zero otherwise. This is a faster version because we only need to read the line with EXPDTA
- Parameters
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- Returns
- unsigned int
Private helper function to determine if atom is backbone or sidechain.
- Parameters
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- Returns
- bool
Core function for PDB file parsing.
- Parameters
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Reimplemented from Loader.
int parsePDBline |
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string |
atomLine, |
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string |
tag, |
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Ligand * |
lig, |
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AminoAcid * |
aa |
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) |
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protected |
Parse a single line of a PDB file.
- Parameters
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atomLine | (string) the whole PDB line as it is |
tag | (string) = the first field (keyword) in a PDB line |
lig | (Ligand) pointer |
aa | (AminoAcid) pointer |
- Returns
- Residue number read from the PDB line (int)
Private helper function to set bond structure after loading the spacer.
- Parameters
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- Returns
- bool
The documentation for this class was generated from the following files:
- Biopool/Sources/PdbLoader.h
- Biopool/Sources/PdbLoader.cc