Namespaces |
namespace | cleanup |
Data Structures |
class | AminoAcidSetIterator |
class | AminoAcidSet |
| Amino acid bit set. More...
|
struct | Date |
struct | AtomSpec |
struct | BondSpec |
class | Compound |
| Knows about the atoms and bonds of a chemical compounds. More...
|
class | CompoundLib |
class | CompoundLibBase |
class | Conopology |
class | Diag |
class | DiagError |
class | Diagnostics |
class | HeuristicProcessor |
class | MinimalCompoundLib |
class | Checker |
class | Processor |
class | RingFinder |
| Class for finding rings in an entity. More...
|
class | RuleBasedProcessor |
Typedefs |
typedef std::vector< AminoAcidSet > | AminoAcidAlphabet |
typedef std::vector< AtomSpec > | AtomSpecList |
typedef std::vector< BondSpec > | BondSpecList |
typedef boost::shared_ptr
< Compound > | CompoundPtr |
typedef std::map< String,
CompoundPtr > | CompoundMap |
typedef boost::shared_ptr
< CompoundLib > | CompoundLibPtr |
typedef boost::shared_ptr
< CompoundLibBase > | CompoundLibBasePtr |
typedef boost::shared_ptr
< Diagnostics > | DiagnosticsPtr |
typedef boost::shared_ptr
< HeuristicProcessor > | HeuristicProcessorPtr |
typedef boost::shared_ptr
< MinimalCompoundLib > | MinimalCompoundLibPtr |
typedef boost::shared_ptr
< Processor > | ProcessorPtr |
typedef boost::shared_ptr
< RuleBasedProcessor > | RuleBasedProcessorPtr |
Enumerations |
enum | AminoAcid {
ALA,
ARG,
ASN,
ASP,
GLN,
GLU,
LYS,
SER,
CYS,
MET,
TRP,
TYR,
THR,
VAL,
ILE,
LEU,
GLY,
PRO,
HIS,
PHE,
XXX
} |
enum | ConopFlag { NO_PEPTIDE_BONDS = 1
} |
enum | DiagArgType {
DIAG_ARG_TYPE_ATOM,
DIAG_ARG_TYPE_RESIDUE,
DIAG_ARG_TYPE_CHAIN,
DIAG_ARG_TYPE_STRING,
DIAG_ARG_TYPE_INT
} |
enum | DiagType { DIAG_UNK_ATOM,
DIAG_UNK_RESIDUE,
DIAG_MISSING_ATOM,
DIAG_NONSTD_RESIDUE
} |
enum | Dialect { PDB_DIALECT,
CHARMM_DIALECT
} |
enum | ConopAction {
CONOP_WARN = 0,
CONOP_SILENT,
CONOP_REMOVE,
CONOP_REMOVE_ATOM,
CONOP_REMOVE_RESIDUE,
CONOP_FATAL
} |
Functions |
DLLEXPORT_OST_CONOP AminoAcid | ResidueToAminoAcid (const mol::ResidueHandle &r) |
DLLEXPORT_OST_CONOP String | AminoAcidToResidueName (AminoAcid aa) |
DLLEXPORT_OST_CONOP String | OneLetterCodeToResidueName (char olc) |
DLLEXPORT_OST_CONOP AminoAcid | OneLetterCodeToAminoAcid (char olc) |
char DLLEXPORT_OST_CONOP | ResidueNameToOneLetterCode (String rn) |
AminoAcid DLLEXPORT_OST_CONOP | ResidueNameToAminoAcid (String rn) |
DLLEXPORT_OST_CONOP std::ostream & | operator<< (std::ostream &os, const AminoAcidSet &aa_set) |
bool DLLIMPORT | CopyResidue (ost::mol::ResidueHandle src_res, ost::mol::ResidueHandle dst_res, ost::mol::XCSEditor &edi) |
bool DLLIMPORT | CopyResidue (ost::mol::ResidueHandle src_res, ost::mol::ResidueHandle dst_res, ost::mol::XCSEditor &edi, CompoundLibPtr lib) |
bool DLLIMPORT | CopyIdentical (ost::mol::ResidueHandle src_res, ost::mol::ResidueHandle dst_res, ost::mol::XCSEditor &edi, bool &has_cbeta) |
bool DLLIMPORT | CopyConserved (ost::mol::ResidueHandle src_res, ost::mol::ResidueHandle dst_res, ost::mol::XCSEditor &edi, bool &has_cbeta, CompoundLibPtr lib) |
bool DLLIMPORT | CopyConserved (ost::mol::ResidueHandle src_res, ost::mol::ResidueHandle dst_res, ost::mol::XCSEditor &edi, bool &has_cbeta) |
bool DLLIMPORT | CopyNonConserved (ost::mol::ResidueHandle src_res, ost::mol::ResidueHandle dst_res, ost::mol::XCSEditor &edi, bool &has_cbeta) |
bool DLLIMPORT | CopyMSE (ost::mol::ResidueHandle src_res, ost::mol::ResidueHandle dst_res, ost::mol::XCSEditor &edi, bool &has_cbeta) |
bool DLLIMPORT | CopyModified (ost::mol::ResidueHandle src_res, ost::mol::ResidueHandle dst_res, ost::mol::XCSEditor &edi, bool &has_cbeta, CompoundLibPtr lib) |
ConopAction DLLIMPORT | ConopActionFromString (const String &name) |
String DLLIMPORT | StringFromConopAction (ConopAction action) |
String DLLIMPORT | GuessAtomElement (const String &atom_name, bool hetatm, int atom_count) |
mol::ChemClass DLLIMPORT | GuessChemClass (mol::ResidueHandle res) |
void DLLIMPORT | AssignBackboneTorsions (mol::ChainHandle chain) |
void DLLIMPORT | AssignBackboneTorsions (mol::ResidueHandleList residues) |
void DLLIMPORT | AssignBackboneTorsions (mol::ResidueHandle prev, mol::ResidueHandle res, mol::ResidueHandle next) |
bool DLLIMPORT | IsBondFeasible (const mol::AtomHandle &, const mol::AtomHandle &) |
mol::AtomHandleList DLLIMPORT | GetUnknownAtomsOfResidue (mol::ResidueHandle residue, CompoundPtr compound, bool strict_hydrogens=false) |
mol::AtomHandleList DLLIMPORT | GetUnknownAtoms (mol::ResidueHandle res, CompoundPtr compound) |
def | SetDefaultLib |
def | GetDefaultLib |
Variables |
tuple | STANDARD_AMINOACIDS |