Knows about the atoms and bonds of a chemical compounds. More...
#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 | 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 () |
| 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 136 of file compound.hh.
| enum Dialect |
Definition at line 138 of file compound.hh.
Definition at line 145 of file compound.hh.
| void AddAtom | ( | const AtomSpec & | atom | ) | [inline] |
Definition at line 225 of file compound.hh.
| void AddBond | ( | const BondSpec & | bond | ) | [inline] |
Definition at line 229 of file compound.hh.
| int GetAtomSpecIndex | ( | const String & | name | ) | const |
| const AtomSpecList& GetAtomSpecs | ( | ) | const [inline] |
Definition at line 233 of file compound.hh.
| const BondSpecList& GetBondSpecs | ( | ) | const [inline] |
Definition at line 255 of file compound.hh.
| mol::ChemClass GetChemClass | ( | ) | const [inline] |
Definition at line 201 of file compound.hh.
| mol::ChemType GetChemType | ( | ) | const [inline] |
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 213 of file compound.hh.
| const Date& GetCreationDate | ( | ) | const [inline] |
Definition at line 262 of file compound.hh.
| Dialect GetDialect | ( | ) | const [inline] |
Definition at line 166 of file compound.hh.
| String GetDialectAsString | ( | ) | const [inline] |
Definition at line 168 of file compound.hh.
| const String& GetFormula | ( | ) | [inline] |
Definition at line 245 of file compound.hh.
| const String& GetID | ( | ) | const [inline] |
three-letter code that is unique for every compound
Definition at line 163 of file compound.hh.
| const String& GetInchi | ( | ) | [inline] |
Definition at line 249 of file compound.hh.
| const String& GetInchiKey | ( | ) | [inline] |
Definition at line 253 of file compound.hh.
| const Date& GetModificationDate | ( | ) | const [inline] |
Definition at line 258 of file compound.hh.
| const String& GetName | ( | ) | [inline] |
Definition at line 239 of file compound.hh.
| char GetOneLetterCode | ( | ) | const [inline] |
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 193 of file compound.hh.
| bool IsNucleotideLinking | ( | ) | const [inline] |
Definition at line 221 of file compound.hh.
| bool IsPeptideLinking | ( | ) | const [inline] |
Definition at line 217 of file compound.hh.
| void SetChemClass | ( | mol::ChemClass | chem_class | ) | [inline] |
Definition at line 197 of file compound.hh.
| void SetChemType | ( | mol::ChemType | chem_type | ) | [inline] |
Definition at line 205 of file compound.hh.
| void SetCreationDate | ( | const Date & | creation_date | ) | [inline] |
Definition at line 272 of file compound.hh.
| void SetDialect | ( | Dialect | dialect | ) | [inline] |
Definition at line 182 of file compound.hh.
| void SetFormula | ( | const String & | formula | ) | [inline] |
Definition at line 243 of file compound.hh.
| void SetInchi | ( | const String & | inchi | ) | [inline] |
Definition at line 247 of file compound.hh.
| void SetInchiKey | ( | const String & | inchikey | ) | [inline] |
Definition at line 251 of file compound.hh.
| void SetModificationDate | ( | const Date & | mod_date | ) | [inline] |
Definition at line 267 of file compound.hh.
| void SetName | ( | const String & | name | ) | [inline] |
Definition at line 241 of file compound.hh.
| void SetOneLetterCode | ( | char | olc | ) | [inline] |
Definition at line 184 of file compound.hh.
1.6.1
