ost::mol::alg Namespace Reference

Namespaces

namespace  hbond
namespace  helix_kinks
namespace  qsscoring
namespace  structure_analysis
namespace  superpose
namespace  trajectory_analysis
namespace  views

Data Structures

class  NACCESSAccessibilityParam
class  DSSPAccessibilityParam
struct  OverlapResult
class  AdjacencyBitmap
struct  Contact
struct  LDT
class  DistanceMatrix
class  UniqueAtomIdentifier
 Contains the infomation needed to uniquely identify an atom in a structure. More...
struct  Domain
class  Domains
class  BondLengthInfo
class  ClashEvent
class  ClashingInfo
class  StereoChemicalBondViolation
class  StereoChemicalAngleViolation
class  StereoChemistryInfo
class  ClashingDistances
 List of reference atom-atom distances to detect clashes between non-bonded atoms. More...
class  StereoChemicalParams
 List of stereo chemical parameters (Bonds and angles). More...
class  PDBize
struct  SecStructureSegment
 a consecutive secondary structure element More...
class  SimilarityMatrix
struct  SuperpositionResult
 stores the number of cycles and the two final EntityViews (in case IterativeSuperposition was applied), the root mean square deviation of the two superposed objects and the transformation matrix (geom::Mat4) to superpose input1 onto input2. More...
class  MeanSquareMinimizer

Typedefs

typedef std::vector< ContactContactList
typedef boost::shared_ptr
< DistanceMatrix
DistanceMatrixPtr
typedef std::pair
< UniqueAtomIdentifier,
UniqueAtomIdentifier
UAtomIdentifiers
typedef std::map< std::pair
< UniqueAtomIdentifier,
UniqueAtomIdentifier >
, std::pair< Real, Real > > 
ResidueRDMap
typedef std::map
< ost::mol::ResNum,
ResidueRDMap
GlobalRDMap
typedef std::map
< UniqueAtomIdentifier, int > 
ExistenceMap
typedef boost::shared_ptr
< Domains
DomainsPtr
typedef std::map< int, DomainDomainsMap
typedef std::vector
< SecStructureSegment
SecStructureSegments

Enumerations

enum  AccessibilityAlgorithm { NACCESS, DSSP }
enum  OverlapMode { OM_RELATIVE, OM_ABSOLUTE }
enum  DensityType { HIGH_RESOLUTION, LOW_RESOLUTION }

Functions

Real Accessibility (ost::mol::EntityView &ent, Real probe_radius=1.4, bool include_hydrogens=false, bool include_hetatm=false, bool include_water=false, bool oligo_mode=false, const String &selection="", const String &asa_abs="asaAbs", const String &asa_rel="asaRel", const String &asa_atom="asaAtom", AccessibilityAlgorithm algorithm=NACCESS)
Real Accessibility (ost::mol::EntityHandle &ent, Real probe_radius=1.4, bool include_hydrogens=false, bool include_hetatm=false, bool include_water=false, bool oligo_mode=false, const String &selection="", const String &asa_abs="asaAbs", const String &asa_rel="asaRel", const String &asa_atom="asaAtom", AccessibilityAlgorithm algorithm=NACCESS)
Real DLLEXPORT_OST_MOL_ALG ClashScore (const mol::EntityView &ent_a, const mol::EntityView &ent_b)
Real DLLEXPORT_OST_MOL_ALG ClashScore (const mol::EntityHandle &ent_a, const mol::EntityView &ent_b)
Real DLLEXPORT_OST_MOL_ALG ClashScore (const mol::AtomHandle &atom, const mol::EntityView &ent_b)
Real DLLEXPORT_OST_MOL_ALG StericEnergy (const geom::Vec3 &pos1, Real r1, const geom::Vec3 &pos2, Real r2)
bool DLLEXPORT_OST_MOL_ALG ResidueNamesMatch (const EntityView &probe, const EntityView &reference, bool log_as_error=false)
geom::Vec3 DLLEXPORT_OST_MOL_ALG CBetaPosition (const ResidueHandle &residue, Real bond_length=1.5)
geom::Vec3 DLLEXPORT_OST_MOL_ALG CBetaPosition (const geom::Vec3 &n_pos, const geom::Vec3 &ca_pos, const geom::Vec3 &c_pos, Real bond_length=1.5)
void DLLEXPORT_OST_MOL_ALG ConstructCBetas (EntityHandle &entity_handle, bool include_gly=false)
ContactList DLLEXPORT_OST_MOL_ALG Contacts (const ost::mol::EntityView &ent, Real min_dist, Real max_dist)
void DLLEXPORT_OST_MOL_ALG CalcContactNodeDegree (const ContactList &contacts)
Real DLLEXPORT_OST_MOL_ALG ContactOverlap (const DistanceMatrixPtr &lhs, const DistanceMatrixPtr &rhs, Real tolerance, OverlapMode mode=OM_RELATIVE, Real dist_limit=1e6)
Real DLLEXPORT_OST_MOL_ALG LocalDistanceTest (const ost::mol::EntityView &mdl, const ost::mol::EntityView &ref, Real max_dist, Real tolerance=0.02, bool only_complete=false)
SimilarityMatrix
DLLEXPORT_OST_MOL_ALG 
ContactOverlapMap (const ost::seq::AlignmentHandle &target_tpl_aln, Real tolerance, int idx_a, int idx_b)
SimilarityMatrix
DLLEXPORT_OST_MOL_ALG 
ContactOverlapMap (const ost::seq::AlignmentHandle &target_tpl_aln, Real tolerance, OverlapMode mode=OM_RELATIVE, Real max_dist=1e6)
SimilarityMatrix
DLLEXPORT_OST_MOL_ALG 
ContactOverlapMap (const DistanceMatrix &dmat1, const DistanceMatrix &dmat2, Real tolerance, OverlapMode mode=OM_RELATIVE, Real max_dist=1e6)
void DLLEXPORT_OST_MOL_ALG DomainsFromCOM (const SimilarityMatrix &sim, ost::seq::AlignmentHandle aln, Real tolerance, int idx_a=-1, int idx_b=-1)
std::pair< Real, long int >
DLLEXPORT_OST_MOL_ALG 
DistanceRMSDTest (const EntityView &mdl, const GlobalRDMap &glob_dist_list, Real cap_distance, int sequence_separation=0, const String &local_drmsdt_property_string="")
Real DLLEXPORT_OST_MOL_ALG DRMSD (const EntityView &v, const GlobalRDMap &global_dist_list, Real cap_distance, int sequence_separation=0)
String DLLEXPORT_OST_MOL_ALG SwappedName (const String &name)
bool DLLEXPORT_OST_MOL_ALG Swappable (const String &rname, const String &aname)
void DLLEXPORT_OST_MOL_ALG EntityToDensityScattering (const mol::EntityView &entity_view, img::MapHandle &map, Real falloff_start, Real falloff_end, bool clear_map_flag=false, Real source_wavelength=1.5418)
void DLLEXPORT_OST_MOL_ALG EntityToDensityRosetta (const mol::EntityView &entity_view, img::MapHandle &map, const DensityType &density_type, Real resolution, bool clear_map_flag=false, Real source_wavelength=1.5418)
ClashingDistances
DLLEXPORT_OST_MOL_ALG 
FillClashingDistances (std::vector< String > &stereo_chemical_props_file)
StereoChemicalParams
DLLEXPORT_OST_MOL_ALG 
FillStereoChemicalParams (const String &header, std::vector< String > &stereo_chemical_props_file)
std::pair< EntityView,
ClashingInfo >
DLLEXPORT_OST_MOL_ALG 
FilterClashes (const EntityView &ent, const ClashingDistances &min_distances, bool always_remove_bb=false)
std::pair< EntityView,
ClashingInfo >
DLLEXPORT_OST_MOL_ALG 
FilterClashes (const EntityHandle &ent, const ClashingDistances &min_distances, bool always_remove_bb=false)
std::pair< EntityView,
StereoChemistryInfo >
DLLEXPORT_OST_MOL_ALG 
CheckStereoChemistry (const EntityView &ent, const StereoChemicalParams &bond_table, const StereoChemicalParams &angle_table, Real bond_tolerance, Real angle_tolerance, bool always_remove_bb=false)
std::pair< EntityView,
StereoChemistryInfo >
DLLEXPORT_OST_MOL_ALG 
CheckStereoChemistry (const EntityHandle &ent, const StereoChemicalParams &bond_table, const StereoChemicalParams &angle_table, Real bond_tolerance, Real angle_tolerance, bool always_remove_bb=false)
std::pair< long int, long int >
DLLEXPORT_OST_MOL_ALG 
LocalDistDiffTest (const EntityView &mdl, const GlobalRDMap &dist_list, std::vector< Real > cutoff_list, int sequence_separation=0, const String &local_ldt_property_string="")
Real DLLEXPORT_OST_MOL_ALG LocalDistDiffTest (const EntityView &mdl, const EntityView &target, Real cutoff, Real max_dist, const String &local_ldt_property_string="")
Real DLLEXPORT_OST_MOL_ALG LocalDistDiffTest (const ost::seq::AlignmentHandle &aln, Real cutoff, Real max_dist, int ref_index=0, int mdl_index=1)
Real DLLEXPORT_OST_MOL_ALG LDDTHA (EntityView &v, const GlobalRDMap &global_dist_list, int sequence_separation=0)
GlobalRDMap DLLEXPORT_OST_MOL_ALG CreateDistanceList (const EntityView &ref, Real max_dist)
GlobalRDMap DLLEXPORT_OST_MOL_ALG CreateDistanceListFromMultipleReferences (const std::vector< EntityView > &ref_list, std::vector< Real > &cutoff_list, int sequence_separation, Real max_dist)
void DLLEXPORT_OST_MOL_ALG PrintGlobalRDMap (const GlobalRDMap &glob_dist_list)
void DLLEXPORT_OST_MOL_ALG PrintResidueRDMap (const ResidueRDMap &res_dist_list)
bool DLLEXPORT_OST_MOL_ALG IsStandardResidue (String rn)
Real DSSPHBondEnergy (const geom::Vec3 &h_pos, const geom::Vec3 &n_pos, const geom::Vec3 &c_pos, const geom::Vec3 &o_pos)
String RawEstimateSS (const std::vector< geom::Vec3 > &ca_positions, int start_idx, int size, const std::vector< int > &donor_for_one, const std::vector< int > &donor_for_two, const std::vector< int > &connected_to_next)
void PrepareSSData (const ost::mol::ResidueViewList &res_list, std::vector< int > &res_indices, std::vector< geom::Vec3 > &ca_positions, std::vector< int > &donor_for_one, std::vector< int > &donor_for_two, std::vector< int > &connected_to_next)
void AssignSecStruct (ost::mol::EntityView &ent)
void AssignSecStruct (ost::mol::EntityHandle &ent)
geom::Vec3List DLLIMPORT GetPosListFromView (const EntityView &view)
std::vector< Real > DLLIMPORT CalculateAgreementWithDensityMap (const geom::Vec3List &vl, img::MapHandle &density_map)
Real DLLIMPORT CalculateAverageAgreementWithDensityMap (const geom::Vec3List &vl, img::MapHandle &density_map)
void DLLIMPORT WrapEntityInPeriodicCell (EntityHandle eh, const geom::Vec3 cell_center, const geom::Vec3 ucell_size, const geom::Vec3 ucell_angles=geom::Vec3(), bool group_res=true, bool follow_bond=true)
std::vector< std::vector< Real >
> DLLIMPORT 
PariwiseDistanceMatrix (const EntityView &view1, const EntityView &view2)
std::vector< std::vector< Real >
> DLLIMPORT 
PariwiseDistanceMatrix (const EntityView &view)
CoordGroupHandle DLLIMPORT SuperposeFrames (CoordGroupHandle &cg, EntityView &sel, int begin=0, int end=-1, int ref=-1)
CoordGroupHandle DLLIMPORT SuperposeFrames (CoordGroupHandle &cg, EntityView &sel, EntityView &ref_view, int begin=0, int end=-1)
SuperpositionResult DLLIMPORT SuperposeAtoms (const mol::AtomViewList &atoms1, const mol::AtomViewList &atoms2, bool apply_transform)
SuperpositionResult DLLIMPORT SuperposeSVD (const mol::EntityView &ev1, const mol::EntityView &ev2, bool apply_transform)
SuperpositionResult DLLIMPORT SuperposeSVD (const geom::Vec3List &pl1, const geom::Vec3List &pl2)
SuperpositionResult DLLIMPORT IterativeSuperposeSVD (const mol::EntityView &ev1, const mol::EntityView &ev2, int max_cycles, Real distance_threshold, bool apply_transform)
SuperpositionResult DLLIMPORT IterativeSuperposeSVD (const geom::Vec3List &pl1, const geom::Vec3List &pl2, int max_cycles, Real distance_threshold)
Real DLLIMPORT CalculateRMSD (const mol::EntityView &ev1, const mol::EntityView &ev2, const geom::Mat4 &transformation)
geom::Vec3List DLLIMPORT AnalyzeAtomPos (const CoordGroupHandle &traj, const AtomHandle &a1, unsigned int stride=1)
geom::Vec3List DLLIMPORT AnalyzeCenterOfMassPos (const CoordGroupHandle &traj, const EntityView &sele, unsigned int stride=1)
std::vector< Real > DLLIMPORT AnalyzeDistanceBetwAtoms (const CoordGroupHandle &traj, const AtomHandle &a1, const AtomHandle &a2, unsigned int stride=1)
std::vector< Real > DLLIMPORT AnalyzeAngle (const CoordGroupHandle &traj, const AtomHandle &a1, const AtomHandle &a2, const AtomHandle &a3, unsigned int stride=1)
std::vector< Real > DLLIMPORT AnalyzeDistanceBetwCenterOfMass (const CoordGroupHandle &traj, const EntityView &sele1, const EntityView &sele2, unsigned int stride=1)
std::vector< Real > DLLIMPORT AnalyzeDihedralAngle (const CoordGroupHandle &traj, const AtomHandle &a1, const AtomHandle &a2, const AtomHandle &a3, const AtomHandle &a4, unsigned int stride=1)
std::vector< Real > DLLIMPORT AnalyzeRMSD (const CoordGroupHandle &traj, const EntityView &reference_view, const EntityView &sele, unsigned int stride=1)
Real DLLIMPORT AnalyzeRMSF (const CoordGroupHandle &traj, const EntityView &selection, int from=0, int to=-1, unsigned int stride=1)
std::vector< Real > DLLIMPORT AnalyzeMinDistance (const CoordGroupHandle &traj, const EntityView &view1, const EntityView &view2, unsigned int stride=1)
std::vector< Real > DLLIMPORT AnalyzeMinDistanceBetwCenterOfMassAndView (const CoordGroupHandle &traj, const EntityView &view_cm, const EntityView &view_atoms, unsigned int stride=1)
std::vector< Real > DLLIMPORT AnalyzeAromaticRingInteraction (const CoordGroupHandle &traj, const EntityView &view_ring1, const EntityView &view_ring2, unsigned int stride=1)
void DLLIMPORT AnalyzeAlphaHelixAxis (const CoordGroupHandle &traj, const EntityView &prot_seg, geom::Vec3List &directions, geom::Vec3List &centers, unsigned int stride=1)
void DLLIMPORT AnalyzeBestFitLine (const CoordGroupHandle &traj, const EntityView &prot_seg, geom::Vec3List &directions, geom::Vec3List &centers, unsigned int stride=1)
void DLLIMPORT AnalyzeBestFitPlane (const CoordGroupHandle &traj, const EntityView &prot_seg, geom::Vec3List &normals, geom::Vec3List &origins, unsigned int stride=1)
EntityHandle DLLIMPORT CreateMeanStructure (const CoordGroupHandle &traj, const EntityView &selection, int from=0, int to=-1, unsigned int stride=1)
std::vector< Real > DLLIMPORT AnalyzeHelicity (const CoordGroupHandle &traj, const EntityView &prot_seg, unsigned int stride=1)
def FillClashingDistancesFromFile
def FillBondStereoChemicalParamsFromFile
def FillAngleStereoChemicalParamsFromFile
def DefaultClashingDistances
def DefaultBondStereoChemicalParams
def DefaultAngleStereoChemicalParams

Variables

const char * POLYPEPTIDE_CHAIN_NAMES
const char * LIGAND_CHAIN_NAME
const char * WATER_CHAIN_NAME

Typedef Documentation

typedef std::vector<Contact> ContactList

Definition at line 35 of file contact_overlap.hh.

typedef boost::shared_ptr<DistanceMatrix> DistanceMatrixPtr

Definition at line 56 of file contact_overlap.hh.

typedef std::map<int, Domain> DomainsMap

Definition at line 77 of file domain_find.hh.

typedef boost::shared_ptr<Domains> DomainsPtr

Definition at line 30 of file domain_find.hh.

typedef std::map<UniqueAtomIdentifier,int> ExistenceMap

Definition at line 98 of file distance_test_common.hh.

Global distance list.

Container for all the residue-based interatomic distance lists that are checked in a Local Distance Difference Test and belong to the same structure

Definition at line 95 of file distance_test_common.hh.

typedef std::map<std::pair<UniqueAtomIdentifier,UniqueAtomIdentifier>,std::pair<Real,Real> > ResidueRDMap

Residue distance list.

Container for all the interatomic distances that are checked in a Local Distance Difference Test and are originating from a single specific residue

Definition at line 89 of file distance_test_common.hh.

Definition at line 46 of file sec_structure_segments.hh.

Definition at line 83 of file distance_test_common.hh.


Enumeration Type Documentation

Enumerator:
NACCESS 
DSSP 

Definition at line 28 of file accessibility.hh.

type of density being created by the EntityToDensity function

Enumerator:
HIGH_RESOLUTION 
LOW_RESOLUTION 

Definition at line 13 of file entity_to_density.hh.

Enumerator:
OM_RELATIVE 
OM_ABSOLUTE 

Definition at line 42 of file contact_overlap.hh.


Function Documentation

Real ost::mol::alg::Accessibility ( ost::mol::EntityHandle ent,
Real  probe_radius = 1.4,
bool  include_hydrogens = false,
bool  include_hetatm = false,
bool  include_water = false,
bool  oligo_mode = false,
const String selection = "",
const String asa_abs = "asaAbs",
const String asa_rel = "asaRel",
const String asa_atom = "asaAtom",
AccessibilityAlgorithm  algorithm = NACCESS 
)
Real ost::mol::alg::Accessibility ( ost::mol::EntityView ent,
Real  probe_radius = 1.4,
bool  include_hydrogens = false,
bool  include_hetatm = false,
bool  include_water = false,
bool  oligo_mode = false,
const String selection = "",
const String asa_abs = "asaAbs",
const String asa_rel = "asaRel",
const String asa_atom = "asaAtom",
AccessibilityAlgorithm  algorithm = NACCESS 
)
void DLLIMPORT ost::mol::alg::AnalyzeAlphaHelixAxis ( const CoordGroupHandle &  traj,
const EntityView &  prot_seg,
geom::Vec3List directions,
geom::Vec3List centers,
unsigned int  stride = 1 
)
std::vector<Real> DLLIMPORT ost::mol::alg::AnalyzeAngle ( const CoordGroupHandle &  traj,
const AtomHandle &  a1,
const AtomHandle &  a2,
const AtomHandle &  a3,
unsigned int  stride = 1 
)
std::vector<Real> DLLIMPORT ost::mol::alg::AnalyzeAromaticRingInteraction ( const CoordGroupHandle &  traj,
const EntityView &  view_ring1,
const EntityView &  view_ring2,
unsigned int  stride = 1 
)
geom::Vec3List DLLIMPORT ost::mol::alg::AnalyzeAtomPos ( const CoordGroupHandle &  traj,
const AtomHandle &  a1,
unsigned int  stride = 1 
)
void DLLIMPORT ost::mol::alg::AnalyzeBestFitLine ( const CoordGroupHandle &  traj,
const EntityView &  prot_seg,
geom::Vec3List directions,
geom::Vec3List centers,
unsigned int  stride = 1 
)
void DLLIMPORT ost::mol::alg::AnalyzeBestFitPlane ( const CoordGroupHandle &  traj,
const EntityView &  prot_seg,
geom::Vec3List normals,
geom::Vec3List origins,
unsigned int  stride = 1 
)
geom::Vec3List DLLIMPORT ost::mol::alg::AnalyzeCenterOfMassPos ( const CoordGroupHandle &  traj,
const EntityView &  sele,
unsigned int  stride = 1 
)
std::vector<Real> DLLIMPORT ost::mol::alg::AnalyzeDihedralAngle ( const CoordGroupHandle &  traj,
const AtomHandle &  a1,
const AtomHandle &  a2,
const AtomHandle &  a3,
const AtomHandle &  a4,
unsigned int  stride = 1 
)
std::vector<Real> DLLIMPORT ost::mol::alg::AnalyzeDistanceBetwAtoms ( const CoordGroupHandle &  traj,
const AtomHandle &  a1,
const AtomHandle &  a2,
unsigned int  stride = 1 
)
std::vector<Real> DLLIMPORT ost::mol::alg::AnalyzeDistanceBetwCenterOfMass ( const CoordGroupHandle &  traj,
const EntityView &  sele1,
const EntityView &  sele2,
unsigned int  stride = 1 
)
std::vector<Real> DLLIMPORT ost::mol::alg::AnalyzeHelicity ( const CoordGroupHandle &  traj,
const EntityView &  prot_seg,
unsigned int  stride = 1 
)
std::vector<Real> DLLIMPORT ost::mol::alg::AnalyzeMinDistance ( const CoordGroupHandle &  traj,
const EntityView &  view1,
const EntityView &  view2,
unsigned int  stride = 1 
)
std::vector<Real> DLLIMPORT ost::mol::alg::AnalyzeMinDistanceBetwCenterOfMassAndView ( const CoordGroupHandle &  traj,
const EntityView &  view_cm,
const EntityView &  view_atoms,
unsigned int  stride = 1 
)
std::vector<Real> DLLIMPORT ost::mol::alg::AnalyzeRMSD ( const CoordGroupHandle &  traj,
const EntityView &  reference_view,
const EntityView &  sele,
unsigned int  stride = 1 
)
Real DLLIMPORT ost::mol::alg::AnalyzeRMSF ( const CoordGroupHandle &  traj,
const EntityView &  selection,
int  from = 0,
int  to = -1,
unsigned int  stride = 1 
)
void ost::mol::alg::AssignSecStruct ( ost::mol::EntityHandle ent  ) 
void ost::mol::alg::AssignSecStruct ( ost::mol::EntityView ent  ) 
void DLLEXPORT_OST_MOL_ALG ost::mol::alg::CalcContactNodeDegree ( const ContactList &  contacts  ) 

calculates and assigns the contact node degree as the int property 'degree' for each atom

std::vector<Real> DLLIMPORT ost::mol::alg::CalculateAgreementWithDensityMap ( const geom::Vec3List vl,
img::MapHandle &  density_map 
)
Real DLLIMPORT ost::mol::alg::CalculateAverageAgreementWithDensityMap ( const geom::Vec3List vl,
img::MapHandle &  density_map 
)
Real DLLIMPORT ost::mol::alg::CalculateRMSD ( const mol::EntityView &  ev1,
const mol::EntityView &  ev2,
const geom::Mat4 transformation 
)

calculates RMSD for two entity view

geom::Vec3 DLLEXPORT_OST_MOL_ALG ost::mol::alg::CBetaPosition ( const geom::Vec3 n_pos,
const geom::Vec3 ca_pos,
const geom::Vec3 c_pos,
Real  bond_length = 1.5 
)
geom::Vec3 DLLEXPORT_OST_MOL_ALG ost::mol::alg::CBetaPosition ( const ResidueHandle &  residue,
Real  bond_length = 1.5 
)
std::pair<EntityView,StereoChemistryInfo> DLLEXPORT_OST_MOL_ALG ost::mol::alg::CheckStereoChemistry ( const EntityHandle &  ent,
const StereoChemicalParams &  bond_table,
const StereoChemicalParams &  angle_table,
Real  bond_tolerance,
Real  angle_tolerance,
bool  always_remove_bb = false 
)

Filters a structure based on detected stereo-chemical violations. Handle version.

If a stereo-chemical violation (i.e., a bond or an angle with a value outside the range defined by the mean value, the standard deviation and the tolerance parameter) is detected in a residue's side-chain, all atoms in the side chain are removed from the structure. If a violation is detected in the backbone, all atoms in the residue are removed. This behavior is changed by the always_remove_bb flag: when the flag is set to true all atoms in the residue are removed even if a violation is just detected in the side-chain

std::pair<EntityView,StereoChemistryInfo> DLLEXPORT_OST_MOL_ALG ost::mol::alg::CheckStereoChemistry ( const EntityView &  ent,
const StereoChemicalParams &  bond_table,
const StereoChemicalParams &  angle_table,
Real  bond_tolerance,
Real  angle_tolerance,
bool  always_remove_bb = false 
)

Filters a structure based on detected stereo-chemical violations. Entity version.

If a stereo-chemical violation (i.e., a bond or an angle with a value outside the range defined by the mean value, the standard deviation and the tolerance parameter) is detected in a residue's side-chain, all atoms in the side chain are removed from the structure. If a violation is detected in the backbone, all atoms in the residue are removed. This behavior is changed by the always_remove_bb flag: when the flag is set to true all atoms in the residue are removed even if a violation is just detected in the side-chain

void DLLEXPORT_OST_MOL_ALG ost::mol::alg::ConstructCBetas ( EntityHandle &  entity_handle,
bool  include_gly = false 
)
Real DLLEXPORT_OST_MOL_ALG ost::mol::alg::ContactOverlap ( const DistanceMatrixPtr &  lhs,
const DistanceMatrixPtr &  rhs,
Real  tolerance,
OverlapMode  mode = OM_RELATIVE,
Real  dist_limit = 1e6 
)
SimilarityMatrix DLLEXPORT_OST_MOL_ALG ost::mol::alg::ContactOverlapMap ( const DistanceMatrix &  dmat1,
const DistanceMatrix &  dmat2,
Real  tolerance,
OverlapMode  mode = OM_RELATIVE,
Real  max_dist = 1e6 
)
SimilarityMatrix DLLEXPORT_OST_MOL_ALG ost::mol::alg::ContactOverlapMap ( const ost::seq::AlignmentHandle target_tpl_aln,
Real  tolerance,
OverlapMode  mode = OM_RELATIVE,
Real  max_dist = 1e6 
)
SimilarityMatrix DLLEXPORT_OST_MOL_ALG ost::mol::alg::ContactOverlapMap ( const ost::seq::AlignmentHandle target_tpl_aln,
Real  tolerance,
int  idx_a,
int  idx_b 
)
ContactList DLLEXPORT_OST_MOL_ALG ost::mol::alg::Contacts ( const ost::mol::EntityView ent,
Real  min_dist,
Real  max_dist 
)

returns a a list of contacts between C-alpha atoms

GlobalRDMap DLLEXPORT_OST_MOL_ALG ost::mol::alg::CreateDistanceList ( const EntityView &  ref,
Real  max_dist 
)

Creates a list of distances to check during a Local Difference Distance Test.

Requires a reference structure and an inclusion radius (max_dist)

GlobalRDMap DLLEXPORT_OST_MOL_ALG ost::mol::alg::CreateDistanceListFromMultipleReferences ( const std::vector< EntityView > &  ref_list,
std::vector< Real > &  cutoff_list,
int  sequence_separation,
Real  max_dist 
)

Creates a list of distances to check during a Local Difference Distance Test starting from multiple reference structures.

Requires a list of reference structure and an inclusion radius (max_dist).

The structures in the list have to be properly prepared before being passed to the function. Corresponding residues in the structures must have the same residue number, the same chain name, etc. Gaps are allowed and automatically dealt with: if information about a distance is present in at least one of the structures, it will be considered.

If a distance between two atoms is shorter than the inclusion radius in all structures in which the two atoms are present, it is included in the list. However, if the distance is longer than the inclusion radius in at least one of the structures, it is not be considered a local interaction and is exluded from the list

The function takes care of residues with ambigous symmetric sidechains. To decide which naming convention to use, the functions computes a local distance score of each reference structure with the first reference structure in the list, using only non ambigously-named atoms. It picks then the naming convention that gives the highest score, guaranteeing that all references are processed with the correct atom names.

The cutoff list that will later be used to compute the Local Distance Difference Test score and the sequence separation parameter must be passed to the function. These parameters do not influence the output distance list, which always includes all distances within the provided max_dist (to make it consistent with the single-reference corresponding function). However, the parameters are used when dealing with the naming convention of residues with ambiguous nomenclature.

EntityHandle DLLIMPORT ost::mol::alg::CreateMeanStructure ( const CoordGroupHandle &  traj,
const EntityView &  selection,
int  from = 0,
int  to = -1,
unsigned int  stride = 1 
)
def ost::mol::alg::DefaultAngleStereoChemicalParams (  ) 

Definition at line 49 of file __init__.py.

def ost::mol::alg::DefaultBondStereoChemicalParams (  ) 

Definition at line 40 of file __init__.py.

def ost::mol::alg::DefaultClashingDistances (  ) 

Definition at line 31 of file __init__.py.

std::pair<Real,long int> DLLEXPORT_OST_MOL_ALG ost::mol::alg::DistanceRMSDTest ( const EntityView &  mdl,
const GlobalRDMap &  glob_dist_list,
Real  cap_distance,
int  sequence_separation = 0,
const String local_drmsdt_property_string = "" 
)

Calculates the Distance RMSD in a model, given a list of distances with their refence length.

Calculates the two values needed to determine the Distance RMSD Test score for a given model, i.e. the sum of the squared distance deviations and the total number of distances on which the sum was calculated. The function requires a list of distances for which the distance deviation has to be computed, together with a reference length for each of them. The function also requires a model on which the returned values are computed. Furthermore, the function requires a default deviation value to be used in the calculations when a distance is not present in the model.

The distance information needs to be stored in ian instance of the GlobalRDMap object. This object stores two distance lengths for each distance. This function uses the first of them as reference length and ignores the second.

The function only processes standard residues in the first chains of the model and of the reference For residues with symmetric sidechains (GLU, ASP, ARG, VAL, PHE, TYR), the naming of the atoms is ambigous. For these residues, the function computes the Distance RMSD score that each naming convention would generate when considering all non-ambigous surrounding atoms. The solution that gives lower score is then picked to compute the final Distance RMSD score for the whole model.

A sequence separation parameter can be passed to the function. If this happens, only distances between residues whose separation is higher than the provided parameter are considered when computing the score.

If a string is provided as an argument to the function, residue-per-residue statistics are stored as residue properties. Specifically, the local residue-based Distance RMSD score is stored in a float property as the provided string, while the residue-based sum of squared distances and the number of distances checked are saved in two properties named [string]_sum (a float property) and [string]_count (an int property).

void DLLEXPORT_OST_MOL_ALG ost::mol::alg::DomainsFromCOM ( const SimilarityMatrix &  sim,
ost::seq::AlignmentHandle  aln,
Real  tolerance,
int  idx_a = -1,
int  idx_b = -1 
)
Real DLLEXPORT_OST_MOL_ALG ost::mol::alg::DRMSD ( const EntityView &  v,
const GlobalRDMap &  global_dist_list,
Real  cap_distance,
int  sequence_separation = 0 
)

Computes the Distance RMSD Test given a list of distances to check and a model.

Computes the Local Distance RMSD Test on the provided model. Requires a list of distances to check and a model for which the score is computed, plus a default deviation value to be used when a distance is not present in the model.

A sequence separation parameter can be passed to the function. If this happens, only distances between residues whose separation is higher than the provided parameter are considered when computing the score.

Real ost::mol::alg::DSSPHBondEnergy ( const geom::Vec3 h_pos,
const geom::Vec3 n_pos,
const geom::Vec3 c_pos,
const geom::Vec3 o_pos 
) [inline]

Definition at line 31 of file sec_struct.hh.

void DLLEXPORT_OST_MOL_ALG ost::mol::alg::EntityToDensityRosetta ( const mol::EntityView &  entity_view,
img::MapHandle &  map,
const DensityType &  density_type,
Real  resolution,
bool  clear_map_flag = false,
Real  source_wavelength = 1.5418 
)

create a density representation of an entity in a density map

This function creates a density representation of the entity provided by the user in a density map, also provided by the user. The user can choose the type of density of the output map:

ROSETTA_HIGH_RESOLUTION gaussian spheres in real space to represent density, one per atom, see Dimaio et al., Refinement of Protein Structures into Low-Resolution Density Maps Using Rosetta. Journal of Molecular Biology (2009) pp. 1-10 ROSETTA_LOW_RESOLUTION guassian spheres in real space to represent density, one per residue. See reference above. Only useful at low resolution

The user can also choose if the density map should be cleared of its previous content before creating the density representation.

The user must also provide a resolution parameter.

This function will only create a density represenation of the entities (or portion of entities ) that fall within the borders of the map. The user must take care that this condition is verified for all entities for which he wants a representation.

void DLLEXPORT_OST_MOL_ALG ost::mol::alg::EntityToDensityScattering ( const mol::EntityView &  entity_view,
img::MapHandle &  map,
Real  falloff_start,
Real  falloff_end,
bool  clear_map_flag = false,
Real  source_wavelength = 1.5418 
)

create a density representation of an entity in a density map (using electron scattering factors)

This functions creates a density representation of the entity provided by the user in a density map, in Fourier space using the correct scattering factors for the elements involved.

The user can also choose if the density map should be cleared of its previous content before creating the density representation.

The density is generated in Fourier space. In order to avoid artifacts in the final density representation, the function avoids sharp frequency cutoffs by applying a Gaussian falloff. The user must provide the resolutions at which the cutoff should begin and end, as opposed to a single resolution cutoff value.

This function will only create a density represenation of the entities (or portion of entities ) that fall within the borders of the map. The user must take care that this condition is verified for all entities for which he wants a representation.

def ost::mol::alg::FillAngleStereoChemicalParamsFromFile (   filename  ) 

Definition at line 24 of file __init__.py.

def ost::mol::alg::FillBondStereoChemicalParamsFromFile (   filename  ) 

Definition at line 17 of file __init__.py.

ClashingDistances DLLEXPORT_OST_MOL_ALG ost::mol::alg::FillClashingDistances ( std::vector< String > &  stereo_chemical_props_file  ) 

Fills a list of reference clashing distances from the content of a parameter file.

Requires a list of strings holding the contents of a parameter file, one line per string

def ost::mol::alg::FillClashingDistancesFromFile (   filename  ) 

Definition at line 10 of file __init__.py.

StereoChemicalParams DLLEXPORT_OST_MOL_ALG ost::mol::alg::FillStereoChemicalParams ( const String header,
std::vector< String > &  stereo_chemical_props_file 
)

Fills a list of stereo-chemical statistics from the content of a parameter file.

Requires a list of strings holding the contents of a parameter file, one line per string The header can be 'Bonds' to read bond statistics or 'Angles' to read angle statistics

std::pair<EntityView,ClashingInfo> DLLEXPORT_OST_MOL_ALG ost::mol::alg::FilterClashes ( const EntityHandle &  ent,
const ClashingDistances &  min_distances,
bool  always_remove_bb = false 
)

Filters a structure based on detected clashes between non bonded atoms. Handle version.

If a clash between two atoms (distance shorter than reference clashing distance - tolerance threshold) is detected in a residue's side-chain, all atoms in the side chain are removed from the structure If a clash is detected in the backbone, all atoms in the residue are removed. This behavior is changed by the always_remove_bb flag: when the flag is set to true all atoms in the residue are removed even if a clash is just detected in the side-chain

std::pair<EntityView,ClashingInfo> DLLEXPORT_OST_MOL_ALG ost::mol::alg::FilterClashes ( const EntityView &  ent,
const ClashingDistances &  min_distances,
bool  always_remove_bb = false 
)

Filters a structure based on detected clashes between non bonded atoms. Entity version.

If a clash between two atoms (distance shorter than reference clashing distance - tolerance threshold) is detected in a residue's side-chain, all atoms in the side chain are removed from the structure If a clash is detected in the backbone, all atoms in the residue are removed. This behavior is changed by the always_remove_bb flag: when the flag is set to true all atoms in the residue are removed even if a clash is just detected in the side-chain

geom::Vec3List DLLIMPORT ost::mol::alg::GetPosListFromView ( const EntityView &  view  ) 
bool DLLEXPORT_OST_MOL_ALG ost::mol::alg::IsStandardResidue ( String  rn  ) 
SuperpositionResult DLLIMPORT ost::mol::alg::IterativeSuperposeSVD ( const geom::Vec3List pl1,
const geom::Vec3List pl2,
int  max_cycles,
Real  distance_threshold 
)

iterative superposition of two point lists

SuperpositionResult DLLIMPORT ost::mol::alg::IterativeSuperposeSVD ( const mol::EntityView &  ev1,
const mol::EntityView &  ev2,
int  max_cycles,
Real  distance_threshold,
bool  apply_transform 
)

iterative superposition

Real DLLEXPORT_OST_MOL_ALG ost::mol::alg::LDDTHA ( EntityView &  v,
const GlobalRDMap &  global_dist_list,
int  sequence_separation = 0 
)

Computes the Local Distance Difference High-Accuracy Test given a list of distances to check.

Computes the Local Distance Difference High-Accuracy Test (with threshold 0.5,1,2 and 4 Angstrom) Requires a list of distances to check and a model for which the score is computed

A sequence separation parameter can be passed to the function. If this happens, only distances between residues whose separation is higher than the provided parameter are considered when computing the score.

Real DLLEXPORT_OST_MOL_ALG ost::mol::alg::LocalDistanceTest ( const ost::mol::EntityView mdl,
const ost::mol::EntityView ref,
Real  max_dist,
Real  tolerance = 0.02,
bool  only_complete = false 
)
Real DLLEXPORT_OST_MOL_ALG ost::mol::alg::LocalDistDiffTest ( const ost::seq::AlignmentHandle aln,
Real  cutoff,
Real  max_dist,
int  ref_index = 0,
int  mdl_index = 1 
)

Calculates the Local Distance Difference Test score for a given model starting from an alignment between a reference structure and the model.

Calculates the Local Distance Difference Test score given an alignment between a model and a taget structure. Requires a threshold on which to calculate the score and an inclusion radius to determine the interatiomic distances to check. Obviously, the strucvtures of the model and the reference must be attached to the alignment. By default the first structure in the alignment is considered the reference and the second is considered the model, but this can be changed by passing to the function the indexes of the two structures in the ref_index and mdl_index parameters. BEWARE: This algorithm uses the old version of the Local Distance Difference Test (multiple cycles, single threshold, etc. ) and will give a slightly different result than the other functions

Real DLLEXPORT_OST_MOL_ALG ost::mol::alg::LocalDistDiffTest ( const EntityView &  mdl,
const EntityView &  target,
Real  cutoff,
Real  max_dist,
const String local_ldt_property_string = "" 
)

Calculates the Local Distance Difference Score for a given model with respect to a given target.

Calculates the Local Distance Difference Test score for a given model with respect to a given reference structure. Requires a model, a reference structure, a list of thresholds that are used to determine if distances are conserved, and an inclusion radius value used to determine which distances are checked.

The function only processes standard residues in the first chains of the model and of the reference For residues with symmetric sidechains (GLU, ASP, ARG, VAL, PHE, TYR), the naming of the atoms is ambigous. For these residues, the function computes the Local Distance Difference Test score that each naming convention would generate when considering all non-ambigous surrounding atoms. The solution that gives higher score is then picked to compute the final Local Difference Distance Score for the whole model.

If a string is provided as an argument to the function, residue-per-residue statistics are stored as residue properties. Specifically, the local residue-based lddt score is stored in a float property named as the provided string, while the residue-based number of conserved and total distances are saved in two int properties named [string]_conserved and [string]_total.

std::pair<long int,long int> DLLEXPORT_OST_MOL_ALG ost::mol::alg::LocalDistDiffTest ( const EntityView &  mdl,
const GlobalRDMap &  dist_list,
std::vector< Real cutoff_list,
int  sequence_separation = 0,
const String local_ldt_property_string = "" 
)

Calculates number of distances conserved in a model, given a list of distances to check and a model.

Calculates the two values needed to determine the Local Distance Difference Test for a given model, i.e. the number of conserved distances in the model and the number of total distances in the reference structure. The function requires a list of distances to check, a model on which the distances are checked, and a list of tolerance thresholds that are used to determine if the distances are conserved.

The function only processes standard residues in the first chains of the model and of the reference For residues with symmetric sidechains (GLU, ASP, ARG, VAL, PHE, TYR), the naming of the atoms is ambigous. For these residues, the function computes the Local Distance Difference Test score that each naming convention would generate when considering all non-ambigous surrounding atoms. The solution that gives higher score is then picked to compute the final Local Difference Distance Score for the whole model.

A sequence separation parameter can be passed to the function. If this happens, only distances between residues whose separation is higher than the provided parameter are considered when computing the score.

If a string is provided as an argument to the function, residue-per-residue statistics are stored as residue properties. Specifically, the local residue-based lddt score is stored in a float property named as the provided string, while the residue-based number of conserved and total distances are saved in two int properties named [string]_conserved and [string]_total.

std::vector< std::vector<Real> > DLLIMPORT ost::mol::alg::PariwiseDistanceMatrix ( const EntityView &  view  ) 
std::vector< std::vector<Real> > DLLIMPORT ost::mol::alg::PariwiseDistanceMatrix ( const EntityView &  view1,
const EntityView &  view2 
)
void ost::mol::alg::PrepareSSData ( const ost::mol::ResidueViewList res_list,
std::vector< int > &  res_indices,
std::vector< geom::Vec3 > &  ca_positions,
std::vector< int > &  donor_for_one,
std::vector< int > &  donor_for_two,
std::vector< int > &  connected_to_next 
)
void DLLEXPORT_OST_MOL_ALG ost::mol::alg::PrintGlobalRDMap ( const GlobalRDMap &  glob_dist_list  ) 

Prints all distances in a global distance list to standard output.

void DLLEXPORT_OST_MOL_ALG ost::mol::alg::PrintResidueRDMap ( const ResidueRDMap &  res_dist_list  ) 

Prints all distances in a residue distance list to standard output.

String ost::mol::alg::RawEstimateSS ( const std::vector< geom::Vec3 > &  ca_positions,
int  start_idx,
int  size,
const std::vector< int > &  donor_for_one,
const std::vector< int > &  donor_for_two,
const std::vector< int > &  connected_to_next 
)
bool DLLEXPORT_OST_MOL_ALG ost::mol::alg::ResidueNamesMatch ( const EntityView &  probe,
const EntityView &  reference,
bool  log_as_error = false 
)

Checks that residue types with the same ResNum in the two structures match.

Requires a reference structure and a probe structure. The function checks that all the residues in the reference structure that appear in the probe structure (i.e., that have the same ResNum) are of the same residue type. Chains are comapred by order, not by chain name (i.e.: the first chain of the reference will be compared with the first chain of the probe structure, etc.)

SuperpositionResult DLLIMPORT ost::mol::alg::SuperposeAtoms ( const mol::AtomViewList &  atoms1,
const mol::AtomViewList &  atoms2,
bool  apply_transform 
)

takes the corresponding atoms and superposes them

CoordGroupHandle DLLIMPORT ost::mol::alg::SuperposeFrames ( CoordGroupHandle &  cg,
EntityView &  sel,
EntityView &  ref_view,
int  begin = 0,
int  end = -1 
)

returns a superposed version of coord group, superposed on a reference view

CoordGroupHandle DLLIMPORT ost::mol::alg::SuperposeFrames ( CoordGroupHandle &  cg,
EntityView &  sel,
int  begin = 0,
int  end = -1,
int  ref = -1 
)

returns a superposed version of coord group, superposed on a reference frame

SuperpositionResult DLLIMPORT ost::mol::alg::SuperposeSVD ( const geom::Vec3List pl1,
const geom::Vec3List pl2 
)

superposes two pointlists

SuperpositionResult DLLIMPORT ost::mol::alg::SuperposeSVD ( const mol::EntityView &  ev1,
const mol::EntityView &  ev2,
bool  apply_transform 
)

superposes two entity views

bool DLLEXPORT_OST_MOL_ALG ost::mol::alg::Swappable ( const String rname,
const String aname 
)

Checks if an atom in a residue has a symmetry equivalent.

Returns true if the atom belongs to a residue with a symmetric side-chain and a symmetry equivalent atom exists. Returns false otherwise

String DLLEXPORT_OST_MOL_ALG ost::mol::alg::SwappedName ( const String name  ) 

Returns the name of the symmetry equivalent atom in residues with symmetric side-chains.

If the atom does belongs to a residue with a symmetric side-chain and if the atom has a symmetry equivalent, the function returns the name of the symmetry equivalent atom, otherwise it returns the name of the original atom

void DLLIMPORT ost::mol::alg::WrapEntityInPeriodicCell ( EntityHandle  eh,
const geom::Vec3  cell_center,
const geom::Vec3  ucell_size,
const geom::Vec3  ucell_angles = geom::Vec3(),
bool  group_res = true,
bool  follow_bond = true 
)

Variable Documentation

const char* LIGAND_CHAIN_NAME
const char* WATER_CHAIN_NAME
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