OpenStructure
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#include <compound.hh>
Public Types | |
enum | Dialect { PDB ='P', CHARMM ='C', OPLS ='O', AMBER ='A' } |
Public Member Functions | |
Compound (const String &id) | |
const String & | GetID () const |
Dialect | GetDialect () const |
String | GetDialectAsString () const |
void | SetDialect (Dialect dialect) |
void | SetOneLetterCode (char olc) |
char | GetOneLetterCode () const |
void | SetChemClass (mol::ChemClass chem_class) |
mol::ChemClass | GetChemClass () const |
void | SetObsolete (bool obsolete) |
bool | GetObsolete () const |
void | SetReplacedBy (const String &replaced_by) |
const String & | GetReplacedBy () const |
void | SetChemType (mol::ChemType chem_type) |
mol::ChemType | GetChemType () const |
bool | IsPeptideLinking () const |
bool | IsNucleotideLinking () const |
void | AddAtom (const AtomSpec &atom) |
void | AddBond (const BondSpec &bond) |
const AtomSpecList & | GetAtomSpecs () const |
int | GetAtomSpecIndex (const String &name) const |
const String & | GetName () |
void | SetName (const String &name) |
void | SetFormula (const String &formula) |
const String & | GetFormula () |
void | SetInchi (const String &inchi) |
const String & | GetInchi () |
void | SetInchiKey (const String &inchikey) |
const String & | GetInchiKey () |
void | SetSMILES (const String &smiles) |
const String & | GetSMILES () |
const BondSpecList & | GetBondSpecs () const |
const Date & | GetModificationDate () const |
const Date & | GetCreationDate () const |
void | SetModificationDate (const Date &mod_date) |
void | SetCreationDate (const Date &creation_date) |
Knows about the atoms and bonds of a chemical compounds.
Definition at line 139 of file compound.hh.
enum Dialect |
Enumerator | |
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PDB | |
CHARMM | |
OPLS | |
AMBER |
Definition at line 141 of file compound.hh.
Definition at line 148 of file compound.hh.
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Definition at line 247 of file compound.hh.
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Definition at line 251 of file compound.hh.
int GetAtomSpecIndex | ( | const String & | name | ) | const |
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Definition at line 255 of file compound.hh.
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Definition at line 281 of file compound.hh.
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Definition at line 207 of file compound.hh.
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PDB ligand classification from component dictionary.
The PDB classifies all compounds into 7 categories. This classification is extracted from the PDB component dictionary (field: pdbx_type)
Definition at line 235 of file compound.hh.
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Definition at line 288 of file compound.hh.
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Definition at line 172 of file compound.hh.
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Definition at line 174 of file compound.hh.
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Definition at line 267 of file compound.hh.
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three-letter code that is unique for every compound
Definition at line 169 of file compound.hh.
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Definition at line 271 of file compound.hh.
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Definition at line 275 of file compound.hh.
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Definition at line 284 of file compound.hh.
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Definition at line 261 of file compound.hh.
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Definition at line 215 of file compound.hh.
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one letter code, if available.
For compounds without a defined one-letter code, the code is set to "?". One letter codes are ambigous. For instance, both glycine and guanosine have G as their one-letter code.
Definition at line 199 of file compound.hh.
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Definition at line 223 of file compound.hh.
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Definition at line 279 of file compound.hh.
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Definition at line 243 of file compound.hh.
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Definition at line 239 of file compound.hh.
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Definition at line 203 of file compound.hh.
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Definition at line 227 of file compound.hh.
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Definition at line 298 of file compound.hh.
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Definition at line 188 of file compound.hh.
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Definition at line 265 of file compound.hh.
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Definition at line 269 of file compound.hh.
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Definition at line 273 of file compound.hh.
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Definition at line 293 of file compound.hh.
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Definition at line 263 of file compound.hh.
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Definition at line 211 of file compound.hh.
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Definition at line 190 of file compound.hh.
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Definition at line 219 of file compound.hh.
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Definition at line 277 of file compound.hh.