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)
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

Typedef Documentation

typedef std::vector<AminoAcidSet> AminoAcidAlphabet

Definition at line 158 of file amino_acids.hh.

typedef std::vector<AtomSpec> AtomSpecList

Definition at line 128 of file compound.hh.

typedef std::vector<BondSpec> BondSpecList

Definition at line 129 of file compound.hh.

typedef boost::shared_ptr<CompoundLibBase> CompoundLibBasePtr

Definition at line 9 of file compound_lib_base.hh.

typedef boost::shared_ptr<CompoundLib> CompoundLibPtr

Definition at line 34 of file compound_lib.hh.

typedef std::map<String, CompoundPtr> CompoundMap

Definition at line 280 of file compound.hh.

typedef boost::shared_ptr<Compound> CompoundPtr

Definition at line 130 of file compound.hh.

typedef boost::shared_ptr<Diagnostics> DiagnosticsPtr

Definition at line 111 of file diag.hh.

typedef boost::shared_ptr<HeuristicProcessor> HeuristicProcessorPtr

Definition at line 30 of file heuristic.hh.

typedef boost::shared_ptr<MinimalCompoundLib> MinimalCompoundLibPtr

Definition at line 9 of file minimal_compound_lib.hh.

typedef boost::shared_ptr<Processor> ProcessorPtr

Definition at line 42 of file processor.hh.

typedef boost::shared_ptr<RuleBasedProcessor> RuleBasedProcessorPtr

Definition at line 33 of file rule_based.hh.

Enumeration Type Documentation

enum AminoAcid

Enumerator:

ALA
ARG
ASN
ASP
GLN
GLU
LYS
SER
CYS
MET
TRP
TYR
THR
VAL
ILE
LEU
GLY
PRO
HIS
PHE
XXX

Definition at line 35 of file amino_acids.hh.

enum ConopAction

Enumerator:

CONOP_WARN
CONOP_SILENT
CONOP_REMOVE
CONOP_REMOVE_ATOM
CONOP_REMOVE_RESIDUE
CONOP_FATAL

Definition at line 33 of file processor.hh.

enum ConopFlag

Enumerator:

NO_PEPTIDE_BONDS

Definition at line 30 of file conop.hh.

enum DiagArgType

Enumerator:

DIAG_ARG_TYPE_ATOM
DIAG_ARG_TYPE_RESIDUE
DIAG_ARG_TYPE_CHAIN
DIAG_ARG_TYPE_STRING
DIAG_ARG_TYPE_INT

Definition at line 29 of file diag.hh.

enum DiagType

Enumerator:

DIAG_UNK_ATOM
DIAG_UNK_RESIDUE
DIAG_MISSING_ATOM
DIAG_NONSTD_RESIDUE

Definition at line 37 of file diag.hh.

enum Dialect

Enumerator:

PDB_DIALECT
CHARMM_DIALECT

Definition at line 28 of file processor.hh.

Function Documentation

DLLEXPORT_OST_CONOP String ost::conop::AminoAcidToResidueName ( AminoAcid aa )

void DLLIMPORT ost::conop::AssignBackboneTorsions ( mol::ChainHandle chain )

assigns phi/psi/omega to all residues marked peptide-linking of the chain

Requires the atoms to be connected

void DLLIMPORT ost::conop::AssignBackboneTorsions ( mol::ResidueHandleList residues )

void DLLIMPORT ost::conop::AssignBackboneTorsions	(	mol::ResidueHandle	prev,
		mol::ResidueHandle	res,
		mol::ResidueHandle	next
	)

ConopAction DLLIMPORT ost::conop::ConopActionFromString ( const String & name )

bool DLLIMPORT ost::conop::CopyConserved	(	ost::mol::ResidueHandle	src_res,
		ost::mol::ResidueHandle	dst_res,
		ost::mol::XCSEditor &	edi,
		bool &	has_cbeta,
		CompoundLibPtr	lib
	)

copies atoms of src_res to dst_res, gets compound lib from builder

src_res and dst_res are thought to be conserved, e.g. the parent standard amino acid of both residues is the same. This includes cases where e.g. the src_rs is and MSE and the dst_res is a MET. This function automatically tries to do the right thing an keep as many atoms as possible from src_res

bool DLLIMPORT ost::conop::CopyConserved	(	ost::mol::ResidueHandle	src_res,
		ost::mol::ResidueHandle	dst_res,
		ost::mol::XCSEditor &	edi,
		bool &	has_cbeta
	)

copies atoms of src_res to dst_res, requires compound lib

src_res and dst_res are thought to be conserved, e.g. the parent standard amino acid of both residues is the same. This includes cases where e.g. the src_rs is and MSE and the dst_res is a MET. This function automatically tries to do the right thing an keep as many atoms as possible from src_res

bool DLLIMPORT ost::conop::CopyIdentical	(	ost::mol::ResidueHandle	src_res,
		ost::mol::ResidueHandle	dst_res,
		ost::mol::XCSEditor &	edi,
		bool &	has_cbeta
	)

copies all atom of src_res to dst_res

Parameters:

has_cbeta will be set to true if the src_res has a cbeta and the dst_residue is not a glycine

bool DLLIMPORT ost::conop::CopyModified	(	ost::mol::ResidueHandle	src_res,
		ost::mol::ResidueHandle	dst_res,
		ost::mol::XCSEditor &	edi,
		bool &	has_cbeta,
		CompoundLibPtr	lib
	)

construct a dst_res with only atoms matching the standard aminoacid from src_res when src_res is an is modified

bool DLLIMPORT ost::conop::CopyMSE	(	ost::mol::ResidueHandle	src_res,
		ost::mol::ResidueHandle	dst_res,
		ost::mol::XCSEditor &	edi,
		bool &	has_cbeta
	)

construct dst_res from src_res when src_res is an MSE

bool DLLIMPORT ost::conop::CopyNonConserved	(	ost::mol::ResidueHandle	src_res,
		ost::mol::ResidueHandle	dst_res,
		ost::mol::XCSEditor &	edi,
		bool &	has_cbeta
	)

construct dst_res in case src_res and dst_res are not conserved.

This essentially copies the backbone of src_res to dst_res. The CB atom is only copied if dst_res is not equal to glycine.

bool DLLIMPORT ost::conop::CopyResidue	(	ost::mol::ResidueHandle	src_res,
		ost::mol::ResidueHandle	dst_res,
		ost::mol::XCSEditor &	edi
	)

copies all atom of src_res to dst_res, gets compound lib from builder

Parameters:

has_cbeta will be set to true if the src_res has a cbeta and the dst_residue is not a glycine, it will be inserted if in the dst should be one and in src it was not present

bool DLLIMPORT ost::conop::CopyResidue	(	ost::mol::ResidueHandle	src_res,
		ost::mol::ResidueHandle	dst_res,
		ost::mol::XCSEditor &	edi,
		CompoundLibPtr	lib
	)

copies all atom of src_res to dst_res, requires a compound lib

Parameters:

has_cbeta will be set to true if the src_res has a cbeta and the dst_residue is not a glycine, it will be inserted if in the dst should be one and in src it was not present

def ost.conop.GetDefaultLib ( )

Definition at line 41 of file __init__.py.

mol::AtomHandleList DLLIMPORT ost::conop::GetUnknownAtoms	(	mol::ResidueHandle	res,
		CompoundPtr	compound
	)

returns all atoms not listed in the specifictaion of compound

mol::AtomHandleList DLLIMPORT ost::conop::GetUnknownAtomsOfResidue	(	mol::ResidueHandle	residue,
		CompoundPtr	compound,
		bool	strict_hydrogens = `false`
	)

String DLLIMPORT ost::conop::GuessAtomElement	(	const String &	atom_name,
		bool	hetatm,
		int	atom_count
	)

guess element of atom based on name and hetatm flag

mol::ChemClass DLLIMPORT ost::conop::GuessChemClass ( mol::ResidueHandle res )

guess chemclass based on atoms of residue

bool DLLIMPORT ost::conop::IsBondFeasible	(	const mol::AtomHandle &	,
		const mol::AtomHandle &
	)

DLLEXPORT_OST_CONOP AminoAcid ost::conop::OneLetterCodeToAminoAcid ( char olc )

DLLEXPORT_OST_CONOP String ost::conop::OneLetterCodeToResidueName ( char olc )

DLLEXPORT_OST_CONOP std::ostream& ost::conop::operator<<	(	std::ostream &	os,
		const AminoAcidSet &	aa_set
	)

char DLLEXPORT_OST_CONOP ResidueNameToOneLetterCode ( String rn )

DLLEXPORT_OST_CONOP AminoAcid ost::conop::ResidueToAminoAcid ( const mol::ResidueHandle & r )

from residue name to amino acid.

for non standard amino acids Xxx is returned.

def ost.conop.SetDefaultLib ( compound_lib )

Set the default compound library. The compound library is used by various
functions of the framework that requires knowledge of naming and 
connectivity of residues.

Definition at line 32 of file __init__.py.

String DLLIMPORT ost::conop::StringFromConopAction ( ConopAction action )

Variable Documentation

tuple STANDARD_AMINOACIDS

Initial value:

 (
  'ALA', 'ARG', 'ASN',
  'ASP', 'GLN', 'GLU',
  'LYS', 'SER', 'CYS',
  'MET', 'TRP', 'TYR',
  'THR', 'VAL', 'ILE',
  'LEU', 'GLY', 'PRO',
  'HIS', 'PHE',
 )

Definition at line 22 of file __init__.py.

Namespaces

Data Structures

Typedefs

Enumerations

Functions

Variables

Typedef Documentation

Enumeration Type Documentation

Function Documentation

Variable Documentation