ost::conop Namespace Reference

Namespaces
	cleanup

Data Structures
class	AminoAcidSetIterator
class	AminoAcidSet
struct	Date
struct	AtomSpec
struct	BondSpec
class	Compound
class	CompoundLib
class	CompoundLibBase
class	Conopology
class	Diag
class	DiagError
class	Diagnostics
class	HeuristicProcessor
class	MinimalCompoundLib
class	Checker
class	Processor
class	RingFinder
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 std::vector< CompoundPtr >	CompoundPtrList
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)
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 (compound_lib)
def	GetDefaultLib ()

Variables
tuple	STANDARD_AMINOACIDS

Typedef Documentation

AminoAcidAlphabet

typedef std::vector<AminoAcidSet> AminoAcidAlphabet

Definition at line 163 of file amino_acids.hh.

AtomSpecList

typedef std::vector<AtomSpec> AtomSpecList

Definition at line 132 of file compound.hh.

BondSpecList

typedef std::vector<BondSpec> BondSpecList

Definition at line 133 of file compound.hh.

CompoundLibBasePtr

typedef boost::shared_ptr<CompoundLibBase> CompoundLibBasePtr

Definition at line 10 of file compound_lib_base.hh.

CompoundLibPtr

typedef boost::shared_ptr<CompoundLib> CompoundLibPtr

Definition at line 34 of file compound_lib.hh.

CompoundMap

typedef std::map<String, CompoundPtr> CompoundMap

Definition at line 322 of file compound.hh.

CompoundPtr

typedef boost::shared_ptr<Compound> CompoundPtr

Definition at line 135 of file compound.hh.

CompoundPtrList

typedef std::vector<CompoundPtr> CompoundPtrList

Definition at line 35 of file compound_lib.hh.

DiagnosticsPtr

typedef boost::shared_ptr<Diagnostics> DiagnosticsPtr

Definition at line 113 of file diag.hh.

HeuristicProcessorPtr

typedef boost::shared_ptr<HeuristicProcessor> HeuristicProcessorPtr

Definition at line 32 of file heuristic.hh.

MinimalCompoundLibPtr

typedef boost::shared_ptr<MinimalCompoundLib> MinimalCompoundLibPtr

Definition at line 10 of file minimal_compound_lib.hh.

ProcessorPtr

typedef boost::shared_ptr<Processor> ProcessorPtr

Definition at line 43 of file processor.hh.

RuleBasedProcessorPtr

typedef boost::shared_ptr<RuleBasedProcessor> RuleBasedProcessorPtr

Definition at line 35 of file rule_based.hh.

Enumeration Type Documentation

AminoAcid

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.

ConopAction

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.

ConopFlag

enum ConopFlag

Enumerator
NO_PEPTIDE_BONDS

Definition at line 30 of file conop.hh.

DiagArgType

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.

DiagType

enum DiagType

Enumerator
DIAG_UNK_ATOM
DIAG_UNK_RESIDUE
DIAG_MISSING_ATOM
DIAG_NONSTD_RESIDUE

Definition at line 37 of file diag.hh.

Dialect

enum Dialect

Enumerator
PDB_DIALECT
CHARMM_DIALECT

Definition at line 28 of file processor.hh.

Function Documentation

AminoAcidToResidueName()

DLLEXPORT_OST_CONOP String ost::conop::AminoAcidToResidueName

(

AminoAcid

aa

)

AssignBackboneTorsions() [1/3]

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

AssignBackboneTorsions() [2/3]

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

AssignBackboneTorsions() [3/3]

void DLLIMPORT ost::conop::AssignBackboneTorsions

(

mol::ResidueHandleList

residues

)

ConopActionFromString()

ConopAction DLLIMPORT ost::conop::ConopActionFromString

(

const String &

name

)

GetDefaultLib()

def ost.conop.GetDefaultLib

(

)

Definition at line 41 of file __init__.py.

GetUnknownAtoms()

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

returns all atoms not listed in the specifictaion of compound

GetUnknownAtomsOfResidue()

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

GuessAtomElement()

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

guess element of atom based on name and hetatm flag

GuessChemClass()

mol::ChemClass DLLIMPORT ost::conop::GuessChemClass

(

mol::ResidueHandle

res

)

guess chemclass based on atoms of residue

IsBondFeasible()

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

OneLetterCodeToAminoAcid()

DLLEXPORT_OST_CONOP AminoAcid ost::conop::OneLetterCodeToAminoAcid

(

char

olc

)

OneLetterCodeToResidueName()

DLLEXPORT_OST_CONOP String ost::conop::OneLetterCodeToResidueName

(

char

olc

)

operator<<()

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

ResidueNameToAminoAcid()

AminoAcid DLLEXPORT_OST_CONOP ost::conop::ResidueNameToAminoAcid

(

String

rn

)

ResidueNameToOneLetterCode()

char DLLEXPORT_OST_CONOP ost::conop::ResidueNameToOneLetterCode

(

String

rn

)

ResidueToAminoAcid()

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.

SetDefaultLib()

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.

StringFromConopAction()

String DLLIMPORT ost::conop::StringFromConopAction

(

ConopAction

action

)

Variable Documentation

STANDARD_AMINOACIDS

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.