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ost::conop Namespace Reference

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< AminoAcidSetAminoAcidAlphabet
typedef std::vector< AtomSpecAtomSpecList
typedef std::vector< BondSpecBondSpecList
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.

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.

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_cbetawill 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_cbetawill 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_cbetawill 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:
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.