Namespaces
namespace	cleanup
namespace	detail

Data Structures
class	AminoAcidSetIterator
class	AminoAcidSet
	Amino acid bit set. More...
class	Builder
	abstract builder interface More...
struct	Date
struct	AtomSpec
struct	BondSpec
class	Compound
	Knows about the atoms and bonds of a chemical compounds. More...
class	CompoundLib
class	Conopology
class	HeuristicBuilder
class	RingFinder
	Class for finding rings in an entity. More...
class	RuleBasedBuilder
	Use library of chemical compounds to derive bonds and clean-up structural problems. More...

Typedefs
typedef std::vector< AminoAcidSet >	AminoAcidAlphabet
typedef boost::shared_ptr < Builder >	BuilderP
typedef std::vector< AtomSpec >	AtomSpecList
typedef std::vector< BondSpec >	BondSpecList
typedef boost::shared_ptr < Compound >	CompoundPtr
typedef boost::shared_ptr < CompoundLib >	CompoundLibPtr
typedef std::map< String, CompoundPtr >	CompoundMap
typedef boost::shared_ptr < RuleBasedBuilder >	RuleBasedBuilderPtr

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	Dialect { PDB_DIALECT, CHARMM_DIALECT }
enum	ConopFlag { NO_PEPTIDE_BONDS = 1 }

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	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)
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)
def	ConnectAll
def	GetBuilder
def	RegisterBuilder
def	SetDefaultBuilder

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 109 of file compound.hh.

typedef std::vector<BondSpec> BondSpecList

Definition at line 110 of file compound.hh.

typedef boost::shared_ptr<Builder> BuilderP

Definition at line 26 of file builder_fw.hh.

typedef boost::shared_ptr<CompoundLib> CompoundLibPtr

Definition at line 33 of file compound_lib.hh.

typedef std::map<String, CompoundPtr> CompoundMap

Definition at line 36 of file compound_lib.hh.

typedef boost::shared_ptr<Compound> CompoundPtr

Definition at line 111 of file compound.hh.

typedef boost::shared_ptr<RuleBasedBuilder> RuleBasedBuilderPtr

Definition at line 145 of file rule_based_builder.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 ConopFlag

Enumerator:

NO_PEPTIDE_BONDS

Definition at line 30 of file conop.hh.

enum Dialect

Enumerator:

PDB_DIALECT
CHARMM_DIALECT

Definition at line 32 of file builder.hh.

Function Documentation

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

def ost.conop.ConnectAll ( ent )

Uses the current default builder to connect the atoms of the entity, assign 
torsions, and fill in missing or correct erroneous information such as the 
chemical class of the residues and the atom's element.

:param ent: A valid entity
:type ent: :class:`~ost.mol.EntityHandle`

Definition at line 32 of file __init__.py.

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

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
	)

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

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.GetBuilder ( name = 'DEFAULT' )

Get registered builder by name

:param name: The name of the builder

:returns: The builder or None, if the builder doesn't exist

Definition at line 44 of file __init__.py.

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
	)

def ost.conop.RegisterBuilder	(	builder,
		name
	)

Register builder to OpenStructure

:param builder: A instance of :class:`Builder`

:param name: The name of the builder

Definition at line 54 of file __init__.py.

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.SetDefaultBuilder ( builder_name )

Set the builder with the given name as the default. You will have to register
a builder with :func:`RegisterBuilder` before you will be able to set it as
the default.

:raises: :exc:`RuntimeError` when trying to set a builder as the default that
  has not been registered yet.

Definition at line 65 of file __init__.py.

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