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OpenStructure
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OpenStructure
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Namespaces | |
| namespace | helix_kinks |
| namespace | structure_analysis |
| namespace | superpose |
| namespace | trajectory_analysis |
| namespace | views |
Data Structures | |
| 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 | UniqueAtomIdentifier |
| Contains the infomation needed to uniquely identify an atom in a structure. More... | |
| struct | SecStructureSegment |
| a consecutive secondary structure element More... | |
| 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 | SuperposerSVD |
| efficiently superpose a bunch of models with the same number of atoms Choose either two EntityViews or two AtomViewLists. More... | |
Typedefs | |
| 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 std::vector < SecStructureSegment > | SecStructureSegments |
Enumerations | |
| enum | DensityType { HIGH_RESOLUTION, LOW_RESOLUTION } |
| typedef std::map<UniqueAtomIdentifier,int> ExistenceMap |
Definition at line 95 of file local_dist_diff_test.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 92 of file local_dist_diff_test.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 86 of file local_dist_diff_test.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 80 of file local_dist_diff_test.hh.
| enum DensityType |
type of density being created by the EntityToDensity function
Definition at line 13 of file entity_to_density.hh.
| 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 |
||
| ) |
| 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 |
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| ) |
| 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 |
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| ) |
| geom::Vec3List DLLEXPORT_OST_MOL_ALG ost::mol::alg::AnalyzeAtomPos | ( | const CoordGroupHandle & | traj, |
| const AtomHandle & | a1, | ||
| unsigned int | stride = 1 |
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| ) |
| 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 |
||
| ) |
| 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 |
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| ) |
| geom::Vec3List DLLEXPORT_OST_MOL_ALG ost::mol::alg::AnalyzeCenterOfMassPos | ( | const CoordGroupHandle & | traj, |
| const EntityView & | sele, | ||
| unsigned int | stride = 1 |
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| ) |
| 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 |
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| ) |
| std::vector<Real> DLLEXPORT_OST_MOL_ALG ost::mol::alg::AnalyzeDistanceBetwAtoms | ( | const CoordGroupHandle & | traj, |
| const AtomHandle & | a1, | ||
| const AtomHandle & | a2, | ||
| unsigned int | stride = 1 |
||
| ) |
| std::vector<Real> DLLEXPORT_OST_MOL_ALG ost::mol::alg::AnalyzeDistanceBetwCenterOfMass | ( | const CoordGroupHandle & | traj, |
| const EntityView & | sele1, | ||
| const EntityView & | sele2, | ||
| unsigned int | stride = 1 |
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| ) |
| std::vector<Real> DLLEXPORT_OST_MOL_ALG ost::mol::alg::AnalyzeHelicity | ( | const CoordGroupHandle & | traj, |
| const EntityView & | prot_seg, | ||
| unsigned int | stride = 1 |
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| ) |
| std::vector<Real> DLLEXPORT_OST_MOL_ALG ost::mol::alg::AnalyzeMinDistance | ( | const CoordGroupHandle & | traj, |
| const EntityView & | view1, | ||
| const EntityView & | view2, | ||
| unsigned int | stride = 1 |
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| ) |
| 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 |
||
| ) |
| 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 |
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| ) |
| Real DLLEXPORT_OST_MOL_ALG ost::mol::alg::AnalyzeRMSF | ( | const CoordGroupHandle & | traj, |
| const EntityView & | selection, | ||
| int | from = 0, |
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| int | to = -1, |
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| unsigned int | stride = 1 |
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| ) |
| 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
| geom::Vec3 DLLEXPORT_OST_MOL_ALG ost::mol::alg::CBetaPosition | ( | const ResidueHandle & | residue, |
| Real | bond_length = 1.5 |
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| ) |
| 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 |
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| ) |
| EntityView 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 |
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| ) |
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
| EntityView 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 |
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| ) |
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
| void DLLEXPORT_OST_MOL_ALG ost::mol::alg::ConstructCBetas | ( | EntityHandle & | entity_handle, |
| bool | include_gly = false |
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| ) |
| GlobalRDMap 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 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 DLLEXPORT_OST_MOL_ALG 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 48 of file __init__.py.
| def ost.mol.alg.DefaultBondStereoChemicalParams | ( | ) |
Definition at line 39 of file __init__.py.
| def ost.mol.alg.DefaultClashingDistances | ( | ) |
Definition at line 30 of file __init__.py.
| 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 23 of file __init__.py.
| def ost.mol.alg.FillBondStereoChemicalParamsFromFile | ( | filename | ) |
Definition at line 16 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, | |
| default_clashing_distance, | |||
| default_tolerance | |||
| ) |
Definition at line 9 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
| EntityView 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
| EntityView 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
| geom::Vec3List DLLEXPORT_OST_MOL_ALG ost::mol::alg::GetPosListFromView | ( | const EntityView & | view | ) |
| bool ost::mol::alg::IsStandardResidue | ( | String | rn | ) |
| SuperpositionResult DLLEXPORT_OST_MOL_ALG ost::mol::alg::IterativeSuperposition | ( | mol::EntityView & | ev1, |
| mol::EntityView & | ev2, | ||
| int | ncycles, | ||
| 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.
| 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, |
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| const String & | local_ldt_property_string = "" |
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| ) |
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.
| 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.
| 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
| void ost::mol::alg::PrintGlobalRDMap | ( | const GlobalRDMap & | glob_dist_list | ) |
Prints all distances in a global distance list to standard output.
| void ost::mol::alg::PrintResidueRDMap | ( | const ResidueRDMap & | res_dist_list | ) |
Prints all distances in a residue distance list to standard output.
| 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
| 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
| 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
| SuperpositionResult DLLEXPORT_OST_MOL_ALG ost::mol::alg::SuperposeSVD | ( | const mol::EntityView & | ev1, |
| const mol::EntityView & | ev2, | ||
| bool | apply_transform | ||
| ) |
superposes two entity views
| SuperpositionResult DLLEXPORT_OST_MOL_ALG ost::mol::alg::SuperposeSVD | ( | const std::vector< geom::Vec3 > & | pl1, |
| const std::vector< geom::Vec3 > & | pl2 | ||
| ) |
superposes two pointlists
| void DLLEXPORT_OST_MOL_ALG ost::mol::alg::WrapEntityInPeriodicCell | ( | EntityHandle | eh, |
| const geom::Vec3 | cell_center, | ||
| const geom::Vec3 | basis_vec | ||
| ) |
1.8.1.1