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< Contact >	ContactList
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, Domain >	DomainsMap
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.

typedef std::map<ost::mol::ResNum,ResidueRDMap> 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.

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.

typedef std::vector<SecStructureSegment> SecStructureSegments

Definition at line 46 of file sec_structure_segments.hh.

typedef std::pair<UniqueAtomIdentifier,UniqueAtomIdentifier> UAtomIdentifiers

Definition at line 83 of file distance_test_common.hh.

---

Enumeration Type Documentation

enum AccessibilityAlgorithm

Enumerator:

NACCESS
DSSP

Definition at line 28 of file accessibility.hh.

enum 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.

enum OverlapMode

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* POLYPEPTIDE_CHAIN_NAMES

const char* WATER_CHAIN_NAME