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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< AminoAcidSetAminoAcidAlphabet
 
typedef std::vector< AtomSpecAtomSpecList
 
typedef std::vector< BondSpecBondSpecList
 
typedef boost::shared_ptr< CompoundCompoundPtr
 
typedef std::map< String, CompoundPtrCompoundMap
 
typedef boost::shared_ptr< CompoundLibCompoundLibPtr
 
typedef std::vector< CompoundPtrCompoundPtrList
 
typedef boost::shared_ptr< CompoundLibBaseCompoundLibBasePtr
 
typedef boost::shared_ptr< DiagnosticsDiagnosticsPtr
 
typedef boost::shared_ptr< HeuristicProcessorHeuristicProcessorPtr
 
typedef boost::shared_ptr< MinimalCompoundLibMinimalCompoundLibPtr
 
typedef boost::shared_ptr< ProcessorProcessorPtr
 
typedef boost::shared_ptr< RuleBasedProcessorRuleBasedProcessorPtr
 

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

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

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:
1 = (
2  'ALA', 'ARG', 'ASN',
3  'ASP', 'GLN', 'GLU',
4  'LYS', 'SER', 'CYS',
5  'MET', 'TRP', 'TYR',
6  'THR', 'VAL', 'ILE',
7  'LEU', 'GLY', 'PRO',
8  'HIS', 'PHE',
9 )

Definition at line 22 of file __init__.py.