Namespaces | |
namespace | alg |
namespace | impl |
namespace | mm |
Data Structures | |
class | AtomBase |
base class for AtomHandle and AtomView More... | |
class | AtomHandle |
Handle to atom datatype. More... | |
class | AtomView |
definition of AtomView More... | |
class | BondHandle |
chemical bond More... | |
struct | BondTableEntry |
struct | BondTable |
class | Builder |
class | ChainBase |
base class for ChainHandle and ChainView More... | |
class | ChainHandle |
linear chain of residues More... | |
class | ChainView |
definition of ChainView More... | |
struct | ChemClass |
struct | ChemType |
class | CoordFrame |
class | CoordGroupHandle |
coordinate group, for trajectories and such More... | |
class | CoordSource |
coordinate source More... | |
class | EditorBase |
base class for entity editors More... | |
class | EntityBase |
definition of EntityBase More... | |
class | EntityHandle |
Protein or molecule. More... | |
class | EntityObserver |
class | EntityPropertyMapper |
class | EntityView |
definition of EntityView More... | |
class | EntityVisitor |
EntityVisitor interface. More... | |
class | EntityViewVisitor |
EntityViewVisitor interface. More... | |
class | ICSEditor |
editor for internal molecule coordinates More... | |
class | InMemCoordSource |
in-memory coordinate source More... | |
class | NotConnectedError |
Error to indicate that two atoms that are supposed to be connected are not. More... | |
struct | Prop |
struct | PropertyError |
struct | QueryFlag |
query flags More... | |
class | Query |
Selection Query. More... | |
struct | QueryErrorDesc |
class | QueryError |
class | QueryState |
Holds state used during query evaluation. More... | |
class | QueryViewWrapper |
class | ResidueBase |
base class for ResidueHandle and ResidueView More... | |
class | ResidueHandle |
Residue handle. More... | |
class | ResNum |
class | ResidueView |
residue view More... | |
struct | SecStructure |
Secondary structure types as defined by DSSP. For convenience, the enum values match the characters used in the DSP file format. More... | |
class | SpatialOrganizer |
spatial organizer More... | |
class | SurfaceHandle |
struct | SurfaceVertex |
struct | SurfaceTri |
class | TorsionHandle |
Named torsion (dihedral) angle. More... | |
struct | ViewAddFlag |
Flags to control the behaviour when adding handles to views. More... | |
class | XCSEditor |
external coordinate system editor More... | |
Typedefs | |
typedef std::vector< BondHandle > | BondHandeList |
typedef boost::shared_ptr < CoordFrame > | CoordFramePtr |
typedef std::vector < CoordFramePtr > | CoordFrameList |
typedef boost::shared_ptr < CoordSource > | CoordSourcePtr |
typedef boost::shared_ptr < EntityObserver > | EntityObserverPtr |
typedef std::pair< EntityView, EntityView > | EntityViewPair |
typedef std::vector< ChainHandle > | ChainHandleList |
typedef std::vector < ResidueHandle > | ResidueHandleList |
typedef std::vector< AtomHandle > | AtomHandleList |
typedef std::vector < TorsionHandle > | TorsionHandleList |
typedef std::vector< BondHandle > | BondHandleList |
typedef std::vector< EntityHandle > | EntityHandleList |
typedef boost::shared_ptr < InMemCoordSource > | InMemCoordSourcePtr |
typedef uint | QueryFlags |
typedef String | ResidueKey |
typedef std::vector< ResNum > | ResNumList |
typedef std::vector< SurfaceTriID > | SurfaceTriIDList |
typedef std::vector < SurfaceVertexID > | SurfaceVertexIDList |
typedef std::vector < SurfaceHandle > | SurfaceHandleList |
typedef unsigned int | SurfaceVertexID |
typedef unsigned int | SurfaceTriID |
typedef std::vector < SurfaceVertex > | SurfaceVertexList |
typedef geom::Transform | Transform |
typedef boost::shared_ptr < AtomViewData > | AtomViewDataPtr |
typedef boost::weak_ptr < AtomViewData > | AtomViewDataWeakPtr |
typedef std::vector< AtomView > | AtomViewList |
typedef boost::shared_ptr < ResidueViewData > | ResidueViewDataPtr |
typedef boost::weak_ptr < ResidueViewData > | ResidueViewDataWeakPtr |
typedef std::vector< ResidueView > | ResidueViewList |
typedef boost::shared_ptr < ChainViewData > | ChainViewDataPtr |
typedef boost::weak_ptr < ChainViewData > | ChainViewDataWeakPtr |
typedef std::vector< ChainView > | ChainViewList |
typedef boost::shared_ptr < EntityViewData > | EntityViewDataPtr |
typedef boost::weak_ptr < EntityViewData > | EntityViewDataWeakPtr |
typedef std::vector< EntityView > | EntityViewList |
typedef std::vector < QueryViewWrapper > | QueryViewWrapperList |
typedef int | ViewAddFlags |
Enumerations | |
enum | ChainType { CHAINTYPE_POLY, CHAINTYPE_NON_POLY, CHAINTYPE_WATER, CHAINTYPE_POLY_PEPTIDE_D, CHAINTYPE_POLY_PEPTIDE_L, CHAINTYPE_POLY_DN, CHAINTYPE_POLY_RN, CHAINTYPE_POLY_SAC_D, CHAINTYPE_POLY_SAC_L, CHAINTYPE_POLY_DN_RN, CHAINTYPE_UNKNOWN, CHAINTYPE_MACROLIDE, CHAINTYPE_CYCLIC_PSEUDO_PEPTIDE, CHAINTYPE_POLY_PEPTIDE_DN_RN, CHAINTYPE_N_CHAINTYPES } |
enum | EditMode { BUFFERED_EDIT, UNBUFFERED_EDIT } |
Functions | |
DLLEXPORT_OST_MOL std::ostream & | operator<< (std::ostream &os, const AtomBase &atom) |
DLLEXPORT_OST_MOL std::ostream & | operator<< (std::ostream &os, const BondHandle &bond) |
DLLEXPORT_OST_MOL std::ostream & | operator<< (std::ostream &os, const ChainBase &chain) |
ChainType DLLEXPORT_OST_MOL | ChainTypeFromString (const StringRef identifier) |
ChainType DLLEXPORT_OST_MOL | ChainTypeFromString (const String &identifier) |
String DLLEXPORT_OST_MOL | StringFromChainType (ChainType type) |
DLLEXPORT_OST_MOL CoordFrame | CreateCoordFrame (const geom::Vec3List &atom_pos, const geom::Vec3 &cell_size=geom::Vec3(), const geom::Vec3 &cell_angles=geom::Vec3()) |
DLLEXPORT_OST_MOL void | GetIndices (const EntityView &sele, std::vector< unsigned long > &indices) |
DLLEXPORT_OST_MOL void | GetMasses (const EntityView &sele, std::vector< Real > &masses) |
DLLEXPORT_OST_MOL void | GetIndicesAndMasses (const EntityView &sele, std::vector< unsigned long > &indices, std::vector< Real > &masses) |
DLLEXPORT_OST_MOL void | GetPositions (const EntityView &sele, std::vector< geom::Vec3 > &ref_pos) |
DLLEXPORT_OST_MOL void | GetCaIndices (const EntityView &segment, std::vector< unsigned long > &indices_ca) |
DLLEXPORT_OST_MOL void | GetCaCONIndices (const EntityView &segment, std::vector< unsigned long > &indices_ca, std::vector< unsigned long > &indices_c, std::vector< unsigned long > &indices_o, std::vector< unsigned long > &indices_n) |
DLLEXPORT_OST_MOL CoordGroupHandle | CreateCoordGroup (const AtomHandleList &atoms) |
DLLEXPORT_OST_MOL std::ostream & | operator<< (std::ostream &os, const EntityBase &ent) |
Prop::ID DLLIMPORT | PropertyIDFromString (const String &prop) |
Prop DLLIMPORT | PropertyFromString (const String &prop) |
DLLIMPORT std::ostream & | operator<< (std::ostream &os, const ResidueBase &residue) |
bool DLLIMPORT | InSequence (const ResidueHandle &residue_one, const ResidueHandle &residue_two) |
std::ostream & | operator<< (std::ostream &os, const ResNum &n) |
DLLIMPORT SurfaceHandle | BuildSurface (const EntityView &ev, Real probe_radius, Real patch_size) |
DLLIMPORT SurfaceHandle | CreateSurface () |
DLLIMPORT std::ostream & | operator<< (std::ostream &os, const SurfaceHandle &surf) |
Real DLLIMPORT | DihedralAngle (const AtomHandle &a1, const AtomHandle &a2, const AtomHandle &a3, const AtomHandle &a4) |
DLLIMPORT std::ostream & | operator<< (std::ostream &os, const TorsionHandle &torsion) |
void DLLIMPORT | TransferConnectivity (EntityHandle dest, const std::map< ResidueHandle, ResidueHandle > &to_from) |
bool | operator< (const ResidueHandle &lhs, const ResidueHandle &rhs) |
std::pair< EntityView, EntityView > DLLIMPORT | CompareViews (const EntityView &view1, const EntityView &view2) |
EntityHandle DLLIMPORT | CreateEntityFromView (const EntityView &view, bool include_exlusive_atoms, EntityHandle handle=EntityHandle()) |
def | Transform |
def | MergeCoordGroups |
create bounding box from entity | |
geom::Cuboid DLLEXPORT_OST_MOL | BoundingBoxFromEntity (const EntityHandle &ent) |
geom::Cuboid DLLEXPORT_OST_MOL | BoundingBoxFromEntity (const EntityView &ent) |
geom::Cuboid DLLEXPORT_OST_MOL | BoundingBoxFromAtoms (const AtomHandleList &atoms) |
typedef std::vector<AtomHandle> AtomHandleList |
Definition at line 30 of file handle_type_fw.hh.
typedef boost::shared_ptr<AtomViewData> AtomViewDataPtr |
Definition at line 28 of file view_type_fw.hh.
typedef boost::weak_ptr<AtomViewData> AtomViewDataWeakPtr |
Definition at line 30 of file view_type_fw.hh.
typedef std::vector<AtomView> AtomViewList |
Definition at line 31 of file view_type_fw.hh.
typedef std::vector<BondHandle> BondHandeList |
Definition at line 135 of file bond_handle.hh.
typedef std::vector<BondHandle> BondHandleList |
Definition at line 37 of file handle_type_fw.hh.
typedef std::vector<ChainHandle> ChainHandleList |
Definition at line 26 of file handle_type_fw.hh.
typedef boost::shared_ptr<ChainViewData> ChainViewDataPtr |
Definition at line 40 of file view_type_fw.hh.
typedef boost::weak_ptr<ChainViewData> ChainViewDataWeakPtr |
Definition at line 42 of file view_type_fw.hh.
typedef std::vector<ChainView> ChainViewList |
Definition at line 43 of file view_type_fw.hh.
typedef std::vector<CoordFramePtr> CoordFrameList |
Definition at line 207 of file coord_frame.hh.
typedef boost::shared_ptr<CoordFrame> CoordFramePtr |
Definition at line 206 of file coord_frame.hh.
typedef boost::shared_ptr<CoordSource> CoordSourcePtr |
Definition at line 37 of file coord_source.hh.
typedef std::vector<EntityHandle> EntityHandleList |
Definition at line 40 of file handle_type_fw.hh.
typedef boost::shared_ptr<EntityObserver> EntityObserverPtr |
Definition at line 26 of file entity_observer_fw.hh.
typedef boost::shared_ptr<EntityViewData> EntityViewDataPtr |
Definition at line 46 of file view_type_fw.hh.
typedef boost::weak_ptr<EntityViewData> EntityViewDataWeakPtr |
Definition at line 48 of file view_type_fw.hh.
typedef std::vector<EntityView> EntityViewList |
Definition at line 49 of file view_type_fw.hh.
typedef std::pair<EntityView, EntityView> EntityViewPair |
Definition at line 349 of file entity_view.hh.
typedef boost::shared_ptr<InMemCoordSource> InMemCoordSourcePtr |
Definition at line 32 of file in_mem_coord_source.hh.
typedef uint QueryFlags |
typedef std::vector<QueryViewWrapper> QueryViewWrapperList |
Definition at line 51 of file view_type_fw.hh.
typedef std::vector<ResidueHandle> ResidueHandleList |
Definition at line 28 of file handle_type_fw.hh.
typedef String ResidueKey |
Definition at line 125 of file residue_prop.hh.
typedef boost::shared_ptr<ResidueViewData> ResidueViewDataPtr |
Definition at line 34 of file view_type_fw.hh.
typedef boost::weak_ptr<ResidueViewData> ResidueViewDataWeakPtr |
Definition at line 36 of file view_type_fw.hh.
typedef std::vector<ResidueView> ResidueViewList |
Definition at line 37 of file view_type_fw.hh.
typedef std::vector<ResNum> ResNumList |
Definition at line 126 of file residue_prop.hh.
typedef std::vector<SurfaceHandle> SurfaceHandleList |
Definition at line 87 of file surface_handle.hh.
typedef unsigned int SurfaceTriID |
Definition at line 63 of file surface_prop.hh.
typedef std::vector<SurfaceTriID> SurfaceTriIDList |
Definition at line 35 of file surface_handle.hh.
typedef unsigned int SurfaceVertexID |
Definition at line 56 of file surface_prop.hh.
typedef std::vector<SurfaceVertexID> SurfaceVertexIDList |
Definition at line 36 of file surface_handle.hh.
typedef std::vector<SurfaceVertex> SurfaceVertexList |
Definition at line 65 of file surface_prop.hh.
typedef std::vector<TorsionHandle> TorsionHandleList |
Definition at line 34 of file handle_type_fw.hh.
typedef geom::Transform Transform |
Definition at line 5 of file transform.hh.
typedef int ViewAddFlags |
Definition at line 71 of file view_type_fw.hh.
enum ChainType |
CHAINTYPE_POLY |
polymer |
CHAINTYPE_NON_POLY |
non-polymer |
CHAINTYPE_WATER |
water |
CHAINTYPE_POLY_PEPTIDE_D |
(D) amino acid sequence |
CHAINTYPE_POLY_PEPTIDE_L |
(L) amino acid sequence |
CHAINTYPE_POLY_DN |
polydeoxyribonucleotide |
CHAINTYPE_POLY_RN |
polyribonucleotide |
CHAINTYPE_POLY_SAC_D |
polysaccharide(D) |
CHAINTYPE_POLY_SAC_L |
polysaccharide(L) |
CHAINTYPE_POLY_DN_RN |
polydeoxyribonucleotide/ -ribonucleotide hybrid |
CHAINTYPE_UNKNOWN |
guess what |
CHAINTYPE_MACROLIDE |
macrolide |
CHAINTYPE_CYCLIC_PSEUDO_PEPTIDE |
cyclic-pseudo-peptide |
CHAINTYPE_POLY_PEPTIDE_DN_RN |
peptide nucleic acid |
CHAINTYPE_N_CHAINTYPES |
no. of chain types |
Definition at line 31 of file chain_type.hh.
enum EditMode |
Definition at line 31 of file editor_type_fw.hh.
geom::Cuboid DLLEXPORT_OST_MOL ost::mol::BoundingBoxFromAtoms | ( | const AtomHandleList & | atoms | ) |
create bounding box from atom list
geom::Cuboid DLLEXPORT_OST_MOL ost::mol::BoundingBoxFromEntity | ( | const EntityView & | ent | ) |
create bounding box from entity view
geom::Cuboid DLLEXPORT_OST_MOL ost::mol::BoundingBoxFromEntity | ( | const EntityHandle & | ent | ) |
create bounding box from entity handle
DLLIMPORT SurfaceHandle ost::mol::BuildSurface | ( | const EntityView & | ev, | |
Real | probe_radius, | |||
Real | patch_size | |||
) |
Create a ChainType item for a given string.
identifier | String to be translated |
ChainType DLLEXPORT_OST_MOL ost::mol::ChainTypeFromString | ( | const StringRef | identifier | ) |
std::pair<EntityView, EntityView> DLLIMPORT ost::mol::CompareViews | ( | const EntityView & | view1, | |
const EntityView & | view2 | |||
) |
compare two entity views
IntegrityError | if trying to compare two views that do not point to the same entity. |
first
contains the elements that are in view1
, but not in view2
, second
contains the elements that are in view2
but not in view1
DLLEXPORT_OST_MOL CoordFrame ost::mol::CreateCoordFrame | ( | const geom::Vec3List & | atom_pos, | |
const geom::Vec3 & | cell_size = geom::Vec3() , |
|||
const geom::Vec3 & | cell_angles = geom::Vec3() | |||
) |
DLLEXPORT_OST_MOL CoordGroupHandle ost::mol::CreateCoordGroup | ( | const AtomHandleList & | atoms | ) |
EntityHandle DLLIMPORT ost::mol::CreateEntityFromView | ( | const EntityView & | view, | |
bool | include_exlusive_atoms, | |||
EntityHandle | handle = EntityHandle() | |||
) |
create new entity handle from entity view
This function behaves exactly like EntityHandle::Copy(), except that only atoms, residues, chains and bonds that are present in the view will be copied.
view | is the view to be converted to a handle | |
include_exlusive_atoms | if true, atoms that are part of an exclusive bond (only one bond partner is included in the view) will also be included in the new entity handle. | |
handle | If invalid a new entity will be created. If valid, the atoms, residues, chains, bonds and torsions will be added to handle. This is useful to combine several entities into one. |
DLLIMPORT SurfaceHandle ost::mol::CreateSurface | ( | ) |
Real DLLIMPORT ost::mol::DihedralAngle | ( | const AtomHandle & | a1, | |
const AtomHandle & | a2, | |||
const AtomHandle & | a3, | |||
const AtomHandle & | a4 | |||
) |
DLLEXPORT_OST_MOL void ost::mol::GetCaCONIndices | ( | const EntityView & | segment, | |
std::vector< unsigned long > & | indices_ca, | |||
std::vector< unsigned long > & | indices_c, | |||
std::vector< unsigned long > & | indices_o, | |||
std::vector< unsigned long > & | indices_n | |||
) |
Writes the backbone indices of all residues in the EntityView into the provided list.
DLLEXPORT_OST_MOL void ost::mol::GetCaIndices | ( | const EntityView & | segment, | |
std::vector< unsigned long > & | indices_ca | |||
) |
Writes the indices of all atoms in the EntityView into the provided list.
DLLEXPORT_OST_MOL void ost::mol::GetIndices | ( | const EntityView & | sele, | |
std::vector< unsigned long > & | indices | |||
) |
This function returns a vector containing the atom indices of the atoms in an EntityView; it is used to accelerate the extraction of information from a trajectory
DLLEXPORT_OST_MOL void ost::mol::GetIndicesAndMasses | ( | const EntityView & | sele, | |
std::vector< unsigned long > & | indices, | |||
std::vector< Real > & | masses | |||
) |
conveniece for GetIndices and GetMasses in one call
DLLEXPORT_OST_MOL void ost::mol::GetMasses | ( | const EntityView & | sele, | |
std::vector< Real > & | masses | |||
) |
This function returns a vector containing the atom masses of the atoms in an EntityView; it is used together with GetIndices to accelerate the extraction of RMSD from a trajectory
DLLEXPORT_OST_MOL void ost::mol::GetPositions | ( | const EntityView & | sele, | |
std::vector< geom::Vec3 > & | ref_pos | |||
) |
Writes the positions of all atoms in the EntityView into the provided vec3 list.
bool DLLIMPORT ost::mol::InSequence | ( | const ResidueHandle & | residue_one, | |
const ResidueHandle & | residue_two | |||
) |
Test if two residues are in next in sequence.
Tests whether two residues are next in sequence and if they are connected by a bond. At the moment, this is only implemented for peptides
def ost::mol::MergeCoordGroups | ( | coord_groups | ) |
Merge several separate coord groups into one. The coord groups must have the same number of atoms. In case no coord group is supplied, None will be returned.
Definition at line 35 of file __init__.py.
bool ost::mol::operator< | ( | const ResidueHandle & | lhs, | |
const ResidueHandle & | rhs | |||
) |
Definition at line 33 of file transfer_connectivity.hh.
DLLIMPORT std::ostream& ost::mol::operator<< | ( | std::ostream & | os, | |
const TorsionHandle & | torsion | |||
) |
DLLIMPORT std::ostream& ost::mol::operator<< | ( | std::ostream & | os, | |
const SurfaceHandle & | surf | |||
) |
std::ostream& ost::mol::operator<< | ( | std::ostream & | os, | |
const ResNum & | n | |||
) | [inline] |
Definition at line 128 of file residue_prop.hh.
DLLIMPORT std::ostream& ost::mol::operator<< | ( | std::ostream & | os, | |
const ResidueBase & | residue | |||
) |
DLLEXPORT_OST_MOL std::ostream& ost::mol::operator<< | ( | std::ostream & | os, | |
const EntityBase & | ent | |||
) |
DLLEXPORT_OST_MOL std::ostream& ost::mol::operator<< | ( | std::ostream & | os, | |
const ChainBase & | chain | |||
) |
DLLEXPORT_OST_MOL std::ostream& ost::mol::operator<< | ( | std::ostream & | os, | |
const BondHandle & | bond | |||
) |
DLLEXPORT_OST_MOL std::ostream& ost::mol::operator<< | ( | std::ostream & | os, | |
const AtomBase & | atom | |||
) |
String DLLEXPORT_OST_MOL ost::mol::StringFromChainType | ( | ChainType | type | ) |
Return the String identifier for a given type.
type | ChainType to be translated |
void DLLIMPORT ost::mol::TransferConnectivity | ( | EntityHandle | dest, | |
const std::map< ResidueHandle, ResidueHandle > & | to_from | |||
) |
def ost::mol::Transform | ( | tf = None |
) |
Definition at line 24 of file __init__.py.