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ost::mol::alg Namespace Reference

Namespaces

 bb_lddt
 
 chain_mapping
 
 contact_score
 
 dockq
 
 hbond
 
 helix_kinks
 
 lddt
 
 ligand_scoring
 
 ligand_scoring_base
 
 ligand_scoring_lddtpli
 
 ligand_scoring_scrmsd
 
 qsscore
 
 qsscoring
 
 scoring
 
 stereochemistry
 
 structure_analysis
 
 superpose
 
 trajectory_analysis
 
 views
 

Data Structures

class  NACCESSAccessibilityParam
 
class  DSSPAccessibilityParam
 
struct  OverlapResult
 
class  AdjacencyBitmap
 
struct  BUInfo
 
struct  Contact
 
struct  LDT
 
class  DistanceMatrix
 
class  UniqueAtomIdentifier
 
struct  Domain
 
class  Domains
 
class  BondLengthInfo
 
class  ClashEvent
 
class  ClashingInfo
 
class  StereoChemicalBondViolation
 
class  StereoChemicalAngleViolation
 
class  StereoChemistryInfo
 
class  ClashingDistances
 
class  StereoChemicalParams
 
struct  FindMemParam
 
struct  StereoChemicalProps
 
struct  lDDTSettings
 
struct  lDDTLocalScore
 
class  lDDTScorer
 
struct  MolckSettings
 
class  PDBize
 
struct  SecStructureSegment
 
class  SimilarityMatrix
 
struct  SuperpositionResult
 
class  MeanSquareMinimizer
 

Typedefs

typedef std::vector< ContactContactList
 
typedef boost::shared_ptr< DistanceMatrixDistanceMatrixPtr
 
typedef std::pair< UniqueAtomIdentifier, UniqueAtomIdentifierUAtomIdentifiers
 
typedef std::map< std::pair< UniqueAtomIdentifier, UniqueAtomIdentifier >, std::pair< Real, Real > > ResidueRDMap
 
typedef std::map< ost::mol::ResNum, ResidueRDMapGlobalRDMap
 
typedef std::map< UniqueAtomIdentifier, int > ExistenceMap
 
typedef boost::shared_ptr< DomainsDomainsPtr
 
typedef std::map< int, DomainDomainsMap
 
typedef std::vector< SecStructureSegmentSecStructureSegments
 

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)
 
ost::mol::EntityHandle CreateBU (const ost::mol::EntityHandle &asu, const ost::io::MMCifInfoBioUnit &bu)
 
ost::mol::EntityHandle CreateBU (const ost::mol::EntityHandle &asu, const BUInfo &bu_info)
 
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 DLLIMPORT Contacts (const ost::mol::EntityView &ent, Real min_dist, Real max_dist)
 
void DLLIMPORT CalcContactNodeDegree (const ContactList &contacts)
 
Real DLLIMPORT ContactOverlap (const DistanceMatrixPtr &lhs, const DistanceMatrixPtr &rhs, Real tolerance, OverlapMode mode=OM_RELATIVE, Real dist_limit=1e6)
 
Real DLLIMPORT LocalDistanceTest (const ost::mol::EntityView &mdl, const ost::mol::EntityView &ref, Real max_dist, Real tolerance=0.02, bool only_complete=false)
 
SimilarityMatrix DLLIMPORT ContactOverlapMap (const ost::seq::AlignmentHandle &target_tpl_aln, Real tolerance, int idx_a, int idx_b)
 
SimilarityMatrix DLLIMPORT ContactOverlapMap (const ost::seq::AlignmentHandle &target_tpl_aln, Real tolerance, OverlapMode mode=OM_RELATIVE, Real max_dist=1e6)
 
SimilarityMatrix DLLIMPORT ContactOverlapMap (const DistanceMatrix &dmat1, const DistanceMatrix &dmat2, Real tolerance, OverlapMode mode=OM_RELATIVE, Real max_dist=1e6)
 
void DLLIMPORT 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, bool check=false)
 
StereoChemicalParams DLLEXPORT_OST_MOL_ALG FillStereoChemicalParams (const String &header, std::vector< String > &stereo_chemical_props_file, bool check=false)
 
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)
 
FindMemParam FindMembrane (ost::mol::EntityHandle &ent, bool assign_membrane_representation, bool fast)
 
FindMemParam FindMembrane (ost::mol::EntityView &ent, bool assign_membrane_representation, bool fast)
 
void GDT (const geom::Vec3List &mdl_pos, const geom::Vec3List &ref_pos, int window_size, int max_windows, Real distance_thresh, int &n_superposed, geom::Mat4 &transform)
 
std::pair< int, int > DLLEXPORT_OST_MOL_ALG ComputeCoverage (const EntityView &v, const GlobalRDMap &glob_dist_list)
 
bool DLLEXPORT_OST_MOL_ALG IsResnumInGlobalRDMap (const ResNum &resnum, const GlobalRDMap &glob_dist_list)
 
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 EntityView &v, std::vector< EntityView > &ref_list, const GlobalRDMap &glob_dist_list, lDDTSettings &settings)
 
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)
 
void DLLEXPORT_OST_MOL_ALG CleanlDDTReferences (std::vector< EntityView > &ref_list)
 
GlobalRDMap DLLEXPORT_OST_MOL_ALG PreparelDDTGlobalRDMap (const std::vector< EntityView > &ref_list, std::vector< Real > &cutoff_list, int sequence_separation, Real max_dist)
 
void DLLEXPORT_OST_MOL_ALG CheckStructure (EntityView &ent, StereoChemicalParams &bond_table, StereoChemicalParams &angle_table, ClashingDistances &nonbonded_table, Real bond_tolerance, Real angle_tolerance)
 
std::vector< lDDTLocalScore > DLLEXPORT_OST_MOL_ALG GetlDDTPerResidueStats (EntityView &model, GlobalRDMap &glob_dist_list, bool structural_checks, String label)
 
void DLLEXPORT_OST_MOL_ALG PrintlDDTPerResidueStats (std::vector< lDDTLocalScore > &scores, bool structural_checks, int cutoffs_length)
 
void MapNonStandardResidues (ost::mol::EntityHandle &ent, ost::conop::CompoundLibPtr lib, bool reprocess=true)
 
void RemoveAtoms (ost::mol::EntityHandle &ent, ost::conop::CompoundLibPtr lib, bool rm_unk_atoms, bool rm_non_std, bool rm_hyd_atoms, bool rm_oxt_atoms, bool rm_zero_occ_atoms, bool colored=true, bool reprocess=true)
 
void CleanUpElementColumn (ost::mol::EntityHandle &ent, ost::conop::CompoundLibPtr lib)
 
void Molck (ost::mol::EntityHandle &ent, ost::conop::CompoundLibPtr lib, const MolckSettings &settings, bool prune=true)
 
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, ost::conop::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, ost::conop::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, ost::conop::CompoundLibPtr lib)
 
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 DLLEXPORT_OST_MOL_ALG GetPosListFromView (const EntityView &view)
 
std::vector< Real > DLLEXPORT_OST_MOL_ALG CalculateAgreementWithDensityMap (const geom::Vec3List &vl, img::MapHandle &density_map)
 
Real DLLEXPORT_OST_MOL_ALG CalculateAverageAgreementWithDensityMap (const geom::Vec3List &vl, img::MapHandle &density_map)
 
void DLLEXPORT_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)
 
std::vector< std::vector< Real > > DLLEXPORT_OST_MOL_ALG PariwiseDistanceMatrix (const EntityView &view1, const EntityView &view2)
 
std::vector< std::vector< Real > > DLLEXPORT_OST_MOL_ALG PariwiseDistanceMatrix (const EntityView &view)
 
CoordGroupHandle DLLEXPORT_OST_MOL_ALG SuperposeFrames (CoordGroupHandle &cg, EntityView &sel, int begin=0, int end=-1, int ref=-1)
 
CoordGroupHandle DLLEXPORT_OST_MOL_ALG SuperposeFrames (CoordGroupHandle &cg, EntityView &sel, EntityView &ref_view, int begin=0, int end=-1)
 
SuperpositionResult DLLEXPORT_OST_MOL_ALG SuperposeAtoms (const mol::AtomViewList &atoms1, const mol::AtomViewList &atoms2, bool apply_transform)
 
SuperpositionResult DLLEXPORT_OST_MOL_ALG SuperposeSVD (const mol::EntityView &ev1, const mol::EntityView &ev2, bool apply_transform)
 
SuperpositionResult DLLEXPORT_OST_MOL_ALG SuperposeSVD (const geom::Vec3List &pl1, const geom::Vec3List &pl2)
 
SuperpositionResult DLLEXPORT_OST_MOL_ALG IterativeSuperposeSVD (const mol::EntityView &ev1, const mol::EntityView &ev2, int max_cycles, Real distance_threshold, bool apply_transform)
 
SuperpositionResult DLLEXPORT_OST_MOL_ALG IterativeSuperposeSVD (const geom::Vec3List &pl1, const geom::Vec3List &pl2, int max_cycles, Real distance_threshold)
 
Real DLLEXPORT_OST_MOL_ALG CalculateRMSD (const mol::EntityView &ev1, const mol::EntityView &ev2, const geom::Mat4 &transformation)
 
geom::Vec3List DLLEXPORT_OST_MOL_ALG AnalyzeAtomPos (const CoordGroupHandle &traj, const AtomHandle &a1, unsigned int stride=1)
 
geom::Vec3List DLLEXPORT_OST_MOL_ALG AnalyzeCenterOfMassPos (const CoordGroupHandle &traj, const EntityView &sele, unsigned int stride=1)
 
std::vector< Real > DLLEXPORT_OST_MOL_ALG AnalyzeDistanceBetwAtoms (const CoordGroupHandle &traj, const AtomHandle &a1, const AtomHandle &a2, unsigned int stride=1)
 
std::vector< Real > DLLEXPORT_OST_MOL_ALG AnalyzeAngle (const CoordGroupHandle &traj, const AtomHandle &a1, const AtomHandle &a2, const AtomHandle &a3, unsigned int stride=1)
 
std::vector< Real > DLLEXPORT_OST_MOL_ALG AnalyzeDistanceBetwCenterOfMass (const CoordGroupHandle &traj, const EntityView &sele1, const EntityView &sele2, unsigned int stride=1)
 
std::vector< Real > DLLEXPORT_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 > DLLEXPORT_OST_MOL_ALG AnalyzeRMSD (const CoordGroupHandle &traj, const EntityView &reference_view, const EntityView &sele, unsigned int stride=1)
 
Real DLLEXPORT_OST_MOL_ALG AnalyzeRMSF (const CoordGroupHandle &traj, const EntityView &selection, int from=0, int to=-1, unsigned int stride=1)
 
std::vector< Real > DLLEXPORT_OST_MOL_ALG AnalyzeMinDistance (const CoordGroupHandle &traj, const EntityView &view1, const EntityView &view2, unsigned int stride=1)
 
std::vector< Real > DLLEXPORT_OST_MOL_ALG AnalyzeMinDistanceBetwCenterOfMassAndView (const CoordGroupHandle &traj, const EntityView &view_cm, const EntityView &view_atoms, unsigned int stride=1)
 
std::vector< Real > DLLEXPORT_OST_MOL_ALG AnalyzeAromaticRingInteraction (const CoordGroupHandle &traj, const EntityView &view_ring1, const EntityView &view_ring2, unsigned int stride=1)
 
void DLLEXPORT_OST_MOL_ALG AnalyzeAlphaHelixAxis (const CoordGroupHandle &traj, const EntityView &prot_seg, geom::Vec3List &directions, geom::Vec3List &centers, unsigned int stride=1)
 
void DLLEXPORT_OST_MOL_ALG AnalyzeBestFitLine (const CoordGroupHandle &traj, const EntityView &prot_seg, geom::Vec3List &directions, geom::Vec3List &centers, unsigned int stride=1)
 
void DLLEXPORT_OST_MOL_ALG AnalyzeBestFitPlane (const CoordGroupHandle &traj, const EntityView &prot_seg, geom::Vec3List &normals, geom::Vec3List &origins, unsigned int stride=1)
 
EntityHandle DLLEXPORT_OST_MOL_ALG CreateMeanStructure (const CoordGroupHandle &traj, const EntityView &selection, int from=0, int to=-1, unsigned int stride=1)
 
std::vector< Real > DLLEXPORT_OST_MOL_ALG AnalyzeHelicity (const CoordGroupHandle &traj, const EntityView &prot_seg, unsigned int stride=1)
 
def FillClashingDistancesFromFile (filename)
 
def FillBondStereoChemicalParamsFromFile (filename)
 
def FillAngleStereoChemicalParamsFromFile (filename)
 
def DefaultClashingDistances ()
 
def DefaultBondStereoChemicalParams ()
 
def DefaultAngleStereoChemicalParams ()
 

Variables

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

Typedef Documentation

◆ ContactList

typedef std::vector<Contact> ContactList

Definition at line 35 of file contact_overlap.hh.

◆ DistanceMatrixPtr

typedef boost::shared_ptr<DistanceMatrix> DistanceMatrixPtr

Definition at line 58 of file contact_overlap.hh.

◆ DomainsMap

typedef std::map<int, Domain> DomainsMap

Definition at line 77 of file domain_find.hh.

◆ DomainsPtr

typedef boost::shared_ptr<Domains> DomainsPtr

Definition at line 32 of file domain_find.hh.

◆ ExistenceMap

typedef std::map<UniqueAtomIdentifier,int> ExistenceMap

Definition at line 98 of file distance_test_common.hh.

◆ GlobalRDMap

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.

◆ ResidueRDMap

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.

◆ SecStructureSegments

Definition at line 55 of file sec_structure_segments.hh.

◆ UAtomIdentifiers

Definition at line 83 of file distance_test_common.hh.

Enumeration Type Documentation

◆ AccessibilityAlgorithm

Enumerator
NACCESS 
DSSP 

Definition at line 28 of file accessibility.hh.

◆ DensityType

type of density being created by the EntityToDensity function

Enumerator
HIGH_RESOLUTION 
LOW_RESOLUTION 

Definition at line 13 of file entity_to_density.hh.

◆ OverlapMode

Enumerator
OM_RELATIVE 
OM_ABSOLUTE 

Definition at line 42 of file contact_overlap.hh.

Function Documentation

◆ Accessibility() [1/2]

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 
)

◆ Accessibility() [2/2]

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 
)

◆ AnalyzeAlphaHelixAxis()

void DLLEXPORT_OST_MOL_ALG ost::mol::alg::AnalyzeAlphaHelixAxis ( const CoordGroupHandle traj,
const EntityView prot_seg,
geom::Vec3List directions,
geom::Vec3List centers,
unsigned int  stride = 1 
)

◆ AnalyzeAngle()

std::vector<Real> DLLEXPORT_OST_MOL_ALG ost::mol::alg::AnalyzeAngle ( const CoordGroupHandle traj,
const AtomHandle a1,
const AtomHandle a2,
const AtomHandle a3,
unsigned int  stride = 1 
)

◆ AnalyzeAromaticRingInteraction()

std::vector<Real> DLLEXPORT_OST_MOL_ALG ost::mol::alg::AnalyzeAromaticRingInteraction ( const CoordGroupHandle traj,
const EntityView view_ring1,
const EntityView view_ring2,
unsigned int  stride = 1 
)

◆ AnalyzeAtomPos()

geom::Vec3List DLLEXPORT_OST_MOL_ALG ost::mol::alg::AnalyzeAtomPos ( const CoordGroupHandle traj,
const AtomHandle a1,
unsigned int  stride = 1 
)

◆ AnalyzeBestFitLine()

void DLLEXPORT_OST_MOL_ALG ost::mol::alg::AnalyzeBestFitLine ( const CoordGroupHandle traj,
const EntityView prot_seg,
geom::Vec3List directions,
geom::Vec3List centers,
unsigned int  stride = 1 
)

◆ AnalyzeBestFitPlane()

void DLLEXPORT_OST_MOL_ALG ost::mol::alg::AnalyzeBestFitPlane ( const CoordGroupHandle traj,
const EntityView prot_seg,
geom::Vec3List normals,
geom::Vec3List origins,
unsigned int  stride = 1 
)

◆ AnalyzeCenterOfMassPos()

geom::Vec3List DLLEXPORT_OST_MOL_ALG ost::mol::alg::AnalyzeCenterOfMassPos ( const CoordGroupHandle traj,
const EntityView sele,
unsigned int  stride = 1 
)

◆ AnalyzeDihedralAngle()

std::vector<Real> DLLEXPORT_OST_MOL_ALG ost::mol::alg::AnalyzeDihedralAngle ( const CoordGroupHandle traj,
const AtomHandle a1,
const AtomHandle a2,
const AtomHandle a3,
const AtomHandle a4,
unsigned int  stride = 1 
)

◆ AnalyzeDistanceBetwAtoms()

std::vector<Real> DLLEXPORT_OST_MOL_ALG ost::mol::alg::AnalyzeDistanceBetwAtoms ( const CoordGroupHandle traj,
const AtomHandle a1,
const AtomHandle a2,
unsigned int  stride = 1 
)

◆ AnalyzeDistanceBetwCenterOfMass()

std::vector<Real> DLLEXPORT_OST_MOL_ALG ost::mol::alg::AnalyzeDistanceBetwCenterOfMass ( const CoordGroupHandle traj,
const EntityView sele1,
const EntityView sele2,
unsigned int  stride = 1 
)

◆ AnalyzeHelicity()

std::vector<Real> DLLEXPORT_OST_MOL_ALG ost::mol::alg::AnalyzeHelicity ( const CoordGroupHandle traj,
const EntityView prot_seg,
unsigned int  stride = 1 
)

◆ AnalyzeMinDistance()

std::vector<Real> DLLEXPORT_OST_MOL_ALG ost::mol::alg::AnalyzeMinDistance ( const CoordGroupHandle traj,
const EntityView view1,
const EntityView view2,
unsigned int  stride = 1 
)

◆ AnalyzeMinDistanceBetwCenterOfMassAndView()

std::vector<Real> DLLEXPORT_OST_MOL_ALG ost::mol::alg::AnalyzeMinDistanceBetwCenterOfMassAndView ( const CoordGroupHandle traj,
const EntityView view_cm,
const EntityView view_atoms,
unsigned int  stride = 1 
)

◆ AnalyzeRMSD()

std::vector<Real> DLLEXPORT_OST_MOL_ALG ost::mol::alg::AnalyzeRMSD ( const CoordGroupHandle traj,
const EntityView reference_view,
const EntityView sele,
unsigned int  stride = 1 
)

◆ AnalyzeRMSF()

Real DLLEXPORT_OST_MOL_ALG ost::mol::alg::AnalyzeRMSF ( const CoordGroupHandle traj,
const EntityView selection,
int  from = 0,
int  to = -1,
unsigned int  stride = 1 
)

◆ AssignSecStruct() [1/2]

void ost::mol::alg::AssignSecStruct ( ost::mol::EntityHandle ent)

◆ AssignSecStruct() [2/2]

void ost::mol::alg::AssignSecStruct ( ost::mol::EntityView ent)

◆ CalcContactNodeDegree()

void DLLIMPORT ost::mol::alg::CalcContactNodeDegree ( const ContactList contacts)

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

◆ CalculateAgreementWithDensityMap()

std::vector<Real> DLLEXPORT_OST_MOL_ALG ost::mol::alg::CalculateAgreementWithDensityMap ( const geom::Vec3List vl,
img::MapHandle density_map 
)

◆ CalculateAverageAgreementWithDensityMap()

Real DLLEXPORT_OST_MOL_ALG ost::mol::alg::CalculateAverageAgreementWithDensityMap ( const geom::Vec3List vl,
img::MapHandle density_map 
)

◆ CalculateRMSD()

Real DLLEXPORT_OST_MOL_ALG ost::mol::alg::CalculateRMSD ( const mol::EntityView ev1,
const mol::EntityView ev2,
const geom::Mat4 transformation 
)

calculates RMSD for two entity view

◆ CBetaPosition() [1/2]

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 
)

◆ CBetaPosition() [2/2]

geom::Vec3 DLLEXPORT_OST_MOL_ALG ost::mol::alg::CBetaPosition ( const ResidueHandle residue,
Real  bond_length = 1.5 
)

◆ CheckStereoChemistry() [1/2]

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

◆ CheckStereoChemistry() [2/2]

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

◆ CheckStructure()

void DLLEXPORT_OST_MOL_ALG ost::mol::alg::CheckStructure ( EntityView ent,
StereoChemicalParams bond_table,
StereoChemicalParams angle_table,
ClashingDistances nonbonded_table,
Real  bond_tolerance,
Real  angle_tolerance 
)

◆ ClashScore() [1/3]

Real DLLEXPORT_OST_MOL_ALG ost::mol::alg::ClashScore ( const mol::AtomHandle atom,
const mol::EntityView ent_b 
)

calculate clash score of one single atom

Returns
floating point between 0 and 10
See also
The Hammer Example

◆ ClashScore() [2/3]

Real DLLEXPORT_OST_MOL_ALG ost::mol::alg::ClashScore ( const mol::EntityHandle ent_a,
const mol::EntityView ent_b 
)

calculate clash score between full entity and view

◆ ClashScore() [3/3]

Real DLLEXPORT_OST_MOL_ALG ost::mol::alg::ClashScore ( const mol::EntityView ent_a,
const mol::EntityView ent_b 
)

calculate clash score between two entity views

For each atom of ent_a the interaction with atoms of ent_b calculated.

Returns
0.0 if there are no clashes and a positive clash score otherwise.
See also
The Hammer Example

◆ CleanlDDTReferences()

void DLLEXPORT_OST_MOL_ALG ost::mol::alg::CleanlDDTReferences ( std::vector< EntityView > &  ref_list)

◆ CleanUpElementColumn()

void ost::mol::alg::CleanUpElementColumn ( ost::mol::EntityHandle ent,
ost::conop::CompoundLibPtr  lib 
)

◆ ComputeCoverage()

std::pair<int,int> DLLEXPORT_OST_MOL_ALG ost::mol::alg::ComputeCoverage ( const EntityView v,
const GlobalRDMap glob_dist_list 
)

◆ ConstructCBetas()

void DLLEXPORT_OST_MOL_ALG ost::mol::alg::ConstructCBetas ( EntityHandle entity_handle,
bool  include_gly = false 
)

◆ ContactOverlap()

Real DLLIMPORT ost::mol::alg::ContactOverlap ( const DistanceMatrixPtr lhs,
const DistanceMatrixPtr rhs,
Real  tolerance,
OverlapMode  mode = OM_RELATIVE,
Real  dist_limit = 1e6 
)

◆ ContactOverlapMap() [1/3]

SimilarityMatrix DLLIMPORT ost::mol::alg::ContactOverlapMap ( const DistanceMatrix dmat1,
const DistanceMatrix dmat2,
Real  tolerance,
OverlapMode  mode = OM_RELATIVE,
Real  max_dist = 1e6 
)

◆ ContactOverlapMap() [2/3]

SimilarityMatrix DLLIMPORT ost::mol::alg::ContactOverlapMap ( const ost::seq::AlignmentHandle target_tpl_aln,
Real  tolerance,
int  idx_a,
int  idx_b 
)

◆ ContactOverlapMap() [3/3]

SimilarityMatrix DLLIMPORT ost::mol::alg::ContactOverlapMap ( const ost::seq::AlignmentHandle target_tpl_aln,
Real  tolerance,
OverlapMode  mode = OM_RELATIVE,
Real  max_dist = 1e6 
)

◆ Contacts()

ContactList DLLIMPORT 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

◆ CopyConserved() [1/2]

bool DLLIMPORT ost::mol::alg::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

◆ CopyConserved() [2/2]

bool DLLIMPORT ost::mol::alg::CopyConserved ( ost::mol::ResidueHandle  src_res,
ost::mol::ResidueHandle  dst_res,
ost::mol::XCSEditor edi,
bool &  has_cbeta,
ost::conop::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

◆ CopyIdentical()

bool DLLIMPORT ost::mol::alg::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
src_res
dst_res
edi
has_cbetawill be set to true if the src_res has a cbeta and the dst_residue is not a glycine

◆ CopyModified()

bool DLLIMPORT ost::mol::alg::CopyModified ( ost::mol::ResidueHandle  src_res,
ost::mol::ResidueHandle  dst_res,
ost::mol::XCSEditor edi,
bool &  has_cbeta,
ost::conop::CompoundLibPtr  lib 
)

construct a dst_res with only atoms matching the standard aminoacid from src_res when src_res is an is modified

◆ CopyMSE()

bool DLLIMPORT ost::mol::alg::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

◆ CopyNonConserved()

bool DLLIMPORT ost::mol::alg::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.

◆ CopyResidue() [1/2]

bool DLLIMPORT ost::mol::alg::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

◆ CopyResidue() [2/2]

bool DLLIMPORT ost::mol::alg::CopyResidue ( ost::mol::ResidueHandle  src_res,
ost::mol::ResidueHandle  dst_res,
ost::mol::XCSEditor edi,
ost::conop::CompoundLibPtr  lib 
)

copies all atom of src_res to dst_res, requires a compound lib

◆ CreateBU() [1/2]

ost::mol::EntityHandle ost::mol::alg::CreateBU ( const ost::mol::EntityHandle asu,
const BUInfo bu_info 
)

◆ CreateBU() [2/2]

ost::mol::EntityHandle ost::mol::alg::CreateBU ( const ost::mol::EntityHandle asu,
const ost::io::MMCifInfoBioUnit bu 
)

◆ CreateDistanceList()

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)

◆ CreateDistanceListFromMultipleReferences()

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 excluded 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.

◆ CreateMeanStructure()

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

◆ DefaultAngleStereoChemicalParams()

def ost.mol.alg.DefaultAngleStereoChemicalParams ( )

Definition at line 49 of file __init__.py.

◆ DefaultBondStereoChemicalParams()

def ost.mol.alg.DefaultBondStereoChemicalParams ( )

Definition at line 40 of file __init__.py.

◆ DefaultClashingDistances()

def ost.mol.alg.DefaultClashingDistances ( )

Definition at line 31 of file __init__.py.

◆ DistanceRMSDTest()

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).

◆ DomainsFromCOM()

void DLLIMPORT ost::mol::alg::DomainsFromCOM ( const SimilarityMatrix sim,
ost::seq::AlignmentHandle  aln,
Real  tolerance,
int  idx_a = -1,
int  idx_b = -1 
)

◆ DRMSD()

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.

◆ DSSPHBondEnergy()

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.

◆ EntityToDensityRosetta()

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.

◆ EntityToDensityScattering()

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.

◆ FillAngleStereoChemicalParamsFromFile()

def ost.mol.alg.FillAngleStereoChemicalParamsFromFile (   filename)

Definition at line 24 of file __init__.py.

◆ FillBondStereoChemicalParamsFromFile()

def ost.mol.alg.FillBondStereoChemicalParamsFromFile (   filename)

Definition at line 17 of file __init__.py.

◆ FillClashingDistances()

ClashingDistances DLLEXPORT_OST_MOL_ALG ost::mol::alg::FillClashingDistances ( std::vector< String > &  stereo_chemical_props_file,
bool  check = false 
)

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

◆ FillClashingDistancesFromFile()

def ost.mol.alg.FillClashingDistancesFromFile (   filename)

Definition at line 10 of file __init__.py.

◆ FillStereoChemicalParams()

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

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

◆ FilterClashes() [1/2]

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

◆ FilterClashes() [2/2]

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

◆ FindMembrane() [1/2]

FindMemParam ost::mol::alg::FindMembrane ( ost::mol::EntityHandle ent,
bool  assign_membrane_representation,
bool  fast 
)

◆ FindMembrane() [2/2]

FindMemParam ost::mol::alg::FindMembrane ( ost::mol::EntityView ent,
bool  assign_membrane_representation,
bool  fast 
)

◆ GDT()

void ost::mol::alg::GDT ( const geom::Vec3List mdl_pos,
const geom::Vec3List ref_pos,
int  window_size,
int  max_windows,
Real  distance_thresh,
int &  n_superposed,
geom::Mat4 transform 
)

◆ GetlDDTPerResidueStats()

std::vector<lDDTLocalScore> DLLEXPORT_OST_MOL_ALG ost::mol::alg::GetlDDTPerResidueStats ( EntityView model,
GlobalRDMap glob_dist_list,
bool  structural_checks,
String  label 
)

◆ GetPosListFromView()

geom::Vec3List DLLEXPORT_OST_MOL_ALG ost::mol::alg::GetPosListFromView ( const EntityView view)

◆ IsResnumInGlobalRDMap()

bool DLLEXPORT_OST_MOL_ALG ost::mol::alg::IsResnumInGlobalRDMap ( const ResNum resnum,
const GlobalRDMap glob_dist_list 
)

◆ IsStandardResidue()

bool DLLEXPORT_OST_MOL_ALG ost::mol::alg::IsStandardResidue ( String  rn)

◆ IterativeSuperposeSVD() [1/2]

SuperpositionResult DLLEXPORT_OST_MOL_ALG ost::mol::alg::IterativeSuperposeSVD ( const geom::Vec3List pl1,
const geom::Vec3List pl2,
int  max_cycles,
Real  distance_threshold 
)

iterative superposition of two point lists

◆ IterativeSuperposeSVD() [2/2]

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

iterative superposition

◆ LDDTHA()

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.

◆ LocalDistanceTest()

Real DLLIMPORT 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 
)

◆ LocalDistDiffTest() [1/4]

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.

◆ LocalDistDiffTest() [2/4]

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.

◆ LocalDistDiffTest() [3/4]

Real DLLEXPORT_OST_MOL_ALG ost::mol::alg::LocalDistDiffTest ( const EntityView v,
std::vector< EntityView > &  ref_list,
const GlobalRDMap glob_dist_list,
lDDTSettings settings 
)

Wrapper around LocalDistDiffTest.

◆ LocalDistDiffTest() [4/4]

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

◆ MapNonStandardResidues()

void ost::mol::alg::MapNonStandardResidues ( ost::mol::EntityHandle ent,
ost::conop::CompoundLibPtr  lib,
bool  reprocess = true 
)

◆ Molck()

void ost::mol::alg::Molck ( ost::mol::EntityHandle ent,
ost::conop::CompoundLibPtr  lib,
const MolckSettings settings,
bool  prune = true 
)

◆ PariwiseDistanceMatrix() [1/2]

std::vector< std::vector<Real> > DLLEXPORT_OST_MOL_ALG ost::mol::alg::PariwiseDistanceMatrix ( const EntityView view)

◆ PariwiseDistanceMatrix() [2/2]

std::vector< std::vector<Real> > DLLEXPORT_OST_MOL_ALG ost::mol::alg::PariwiseDistanceMatrix ( const EntityView view1,
const EntityView view2 
)

◆ PreparelDDTGlobalRDMap()

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

◆ PrepareSSData()

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 
)

◆ PrintGlobalRDMap()

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.

◆ PrintlDDTPerResidueStats()

void DLLEXPORT_OST_MOL_ALG ost::mol::alg::PrintlDDTPerResidueStats ( std::vector< lDDTLocalScore > &  scores,
bool  structural_checks,
int  cutoffs_length 
)

◆ PrintResidueRDMap()

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.

◆ RawEstimateSS()

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 
)

◆ RemoveAtoms()

void ost::mol::alg::RemoveAtoms ( ost::mol::EntityHandle ent,
ost::conop::CompoundLibPtr  lib,
bool  rm_unk_atoms,
bool  rm_non_std,
bool  rm_hyd_atoms,
bool  rm_oxt_atoms,
bool  rm_zero_occ_atoms,
bool  colored = true,
bool  reprocess = true 
)

◆ ResidueNamesMatch()

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.)

◆ StericEnergy()

Real DLLEXPORT_OST_MOL_ALG ost::mol::alg::StericEnergy ( const geom::Vec3 pos1,
Real  r1,
const geom::Vec3 pos2,
Real  r2 
)

calculate steric energy of two atoms

◆ SuperposeAtoms()

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

takes the corresponding atoms and superposes them

◆ SuperposeFrames() [1/2]

CoordGroupHandle DLLEXPORT_OST_MOL_ALG 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

◆ SuperposeFrames() [2/2]

CoordGroupHandle DLLEXPORT_OST_MOL_ALG 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

◆ SuperposeSVD() [1/2]

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

superposes two pointlists

◆ SuperposeSVD() [2/2]

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

superposes two entity views

◆ Swappable()

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

◆ SwappedName()

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

◆ WrapEntityInPeriodicCell()

void DLLEXPORT_OST_MOL_ALG 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

◆ LIGAND_CHAIN_NAME

const char* LIGAND_CHAIN_NAME
extern

◆ POLYPEPTIDE_CHAIN_NAMES

const char* POLYPEPTIDE_CHAIN_NAMES
extern

◆ WATER_CHAIN_NAME

const char* WATER_CHAIN_NAME
extern