Object Functions¶
The functions detailed in this section provide a mechanism to add, delete, modify, and organize the many types of objects (e.g. molecules, grids, and surfaces) available in VIDA.
Add¶
unsigned int Add(OESystem::OEBase &, unsigned int listID = 0)
Adds the specified object to the application and returns a unique ID associated with that object. If the optional listID argument is provided, then the object is added to the specified list. Otherwise, a new list is created and the object is added to it.
AddCSVSmiles¶
unsigned int AddCSVSmiles( const std::string &smiles,
const std::vector<std::string> &headers,
const std::vector<std::string> &values,
const std::string &filename = "",
unsigned int listid = 0)
Adds a new molecule from SMILES with the optional associated data. smiles species the SMILES string to parse, headers is a list of column names corresponding to the data specified in values, filename is an optional filename to attribute this molecule to, and listid is the ID of the list to which this molecule will be added. If listid is zero, a new list will be created.
Returns the ID of the list to which the molecule was added.
AddURLMol¶
unsigned int AddURLMol( const std::string &url,
const std::string &urlFunc,
const std::vector<std::string> &headers,
const std::vector<std::string> &values,
const std::string &filename,
unsigned int listid)
Reserved for future implementation.
AtomDataGet¶
AtomData AtomDataGet(const OEPropDB::OEKey &key )
Returns an AtomData object populated with information about the atom specified by the parameter key.
CheckIn¶
bool CheckIn(OESystem::OEBase &)
Checks the specified Python accessible object back into the main VIDA application which will synchronize any changes made to the object in Python with the object in VIDA. The object in question must have been checked out of VIDA prior to being checked back in.
See GridCheckOut,
MoleculeCheckOut, and
SurfaceCheckOut.
ChildrenGet¶
std::vector<OEPropDB::OEKey> ChildrenGet(unsigned int id)
std::vector<OEPropDB::OEKey> ChildrenGet(const OEPropDB::OEKey &)
Returns a list of keys corresponding to any child objects associated with the specified object.
ContourCloudJitterDefaultGet¶
float ContourCloudJitterDefaultGet()
Returns the value (between 0.0 and 1.0) indicated by the Jitter slider on the Contours panel.
ContourCloudJitterGet¶
float ContourCloudJitterGet(unsigned int id)
Returns the jitter value assigned to grid id. The jitter value is used when the contour is displayed with the “cloud” style, and represents the degree to which the grid vertex positions are to be randomized. Jitter values range from 0.0 (no jitter) to 1.0 (jitter equal to the grid spacing).
ContourCloudJitterSet¶
float ContourCloudJitterSet(unsigned int id, float jitter)
Sets the jitter value to be used when grid id is displayed with the “cloud” style. Jitter values range from 0.0 (no jitter) to 1.0 (jitter equal to the grid spacing).
ContourCountScoped¶
int ContourCountScoped(unsigned int scope = BestScope)
Returns the number of contours for all grids in scope.
This returns the number of contours for the focused grid or the first grid found in the given scope.
ContourCreate¶
void ContourCreate(unsigned int id=0)
void ContourCreate(unsigned int id, float threshold)
void ContourCreate(unsigned int id, float threshold,
const OESystem::OEColor &color)
Create a new contour for grid id.
ContourCreateSurface¶
unsigned int ContourCreateSurface(unsigned int id, unsigned int contourIndex)
Create a contour surface for the surface defined by the repository id id for the contour referenced by contourIndex.
ContourDeleteByIndex¶
void ContourDeleteByIndex(unsigned int id, unsigned int index)
Delete contour index for grid id. All contours with indices greater than index will now be at their current index - 1.
ContourDeleteByThreshold¶
void ContourDeleteByThreshold(unsigned int id, float threshold)
Delete all contours above threshold for grid id. Contour indices will be reassigned.
ContourExtractIsoSurface¶
unsigned int ContourExtractIsoSurface(unsigned int id, unsigned int vertex,
bool maskVis=true)
Reserved for internal use.
ContourFixAsSurfaceScoped¶
std::vector<unsigned int>
ContourFixAsSurfaceScoped(unsigned int scope = BestScope)
Creates an actual surface object for each contour in the specified scope. Returns a list of IDs corresponding to the generated surfaces.
ContourGetAll¶
std::vector<float> ContourGetAll(unsigned int id=0)
Get all contour levels from each contour drawn for grid id.
ContourLevelForIndexGet¶
float ContourLevelForIndexGet(unsigned int id, unsigned int index)
Returns the contour level for grid id at index id.
ContourLevelForIndexGetScoped¶
float ContourLevelForIndexGetScoped(int index,
unsigned int scope = BestScope)
Returns the contour level for index id for the first grid in scope.
ContourLevelForIndexSet¶
float ContourLevelForIndexSet(unsigned int id, unsigned int index, float thresh)
Set the level for the contour at index index to thresh for grid id.
ContourLevelForIndexSetScoped¶
void ContourLevelForIndexSetScoped(unsigned int index, float thresh,
unsigned int gridType=UINT_MAX,
unsigned int scope = BestScope)
Set the level for the contour at index index to thresh for all grids in scope.
ContourLevelNudgeScoped¶
void ContourLevelNudgeScoped(bool increase,
unsigned int scope = BestScope)
This function increases or decreases the contour value for the contours in the specified scope by 0.1 depending on whether the increase parameter is set to true or false.
ContourLevelSetScoped¶
void ContourLevelSetScoped(float level,
unsigned int scope = BestScope)
This function sets the contour level of all the contours in the specified scope to the value specified by the parameter level.
ContourMax¶
float ContourMax(unsigned int oerid)
Returns the maximum allowable contour threshold for grid id.
ContourMaxScoped¶
float ContourMaxScoped(unsigned int scope = BestScope)
Returns the maximum allowable contour threshold for the first grid found in scope.
ContourMin¶
float ContourMin(unsigned int oerid)
Returns the minimum allowable contour threshold for grid id.
ContourMinScoped¶
float ContourMinScoped(unsigned int scope = BestScope)
Returns the minimum allowable contour threshold for the first grid found in scope.
ContourRadiusGet¶
float ContourRadiusGet(unsigned int id=0)
Returns the radius used when generating contours for crystallographic grids.
ContourRadiusSet¶
float ContourRadiusSet(unsigned int id, float rad)
Sets the radius used when generating contours for crystallographic grids.
ContourResolutionGet¶
float ContourResolutionGet(unsigned int id=0)
Return the contouring resolution for drawing the contours in Angstroms. A lower resolution samples more grid points, but requires more memory.
ContourResolutionSet¶
float ContourResolutionSet(unsigned int id, float rad)
Set the contouring resolution in Angstroms. Lower values sample more grid points and generate finer visualizations but require more memory.
ContourTypedAddScoped¶
void ContourTypedAddScoped(unsigned int scope = BestScope)
Add a single contour to all grids of type type in scope.
ContourTypedCountScoped¶
int ContourTypedCountScoped(unsigned int scope = BestScope)
Return the number of contours of all grids of type type in scope. This essentially returns the number of contours of the first grid found.
ContourTypedMaxScoped¶
float ContourTypedMaxScoped(unsigned int scope = BestScope)
Returns the maximum allowable threshold for the first grid found of type type in scope.
ContourTypedMinScoped¶
float ContourTypedMinScoped(unsigned int scope = BestScope)
Returns the minimum allowable threshold for the first grid found of type type in scope.
ContourTypedRemoveScoped¶
void ContourTypedRemoveScoped(unsigned int scope = BestScope)
Remove the last contour from all grids of type type in scope.
ContourTypedSetLevelForIndexScoped¶
void ContourTypedSetLevelForIndexScoped(unsigned int index, float thresh,
unsigned int scope = BestScope)
Set the contour level for the contour at index for all grids of type type in scope.
ContourVolume¶
float ContourVolume(unsigned int id, unsigned int contourIndex)
Return the enclosed volume of Grid id’s contour at index contourIndex.
Delete¶
void Delete(unsigned int id)
void Delete(const std::vector<unsigned int> &)
void Delete(const std::vector<OEPropDB::OEKey> &)
void Delete(const OEPropDB::OEKey &, bool all=false)
Deletes the specified object(s) from the current session. It is important to note that this does NOT delete the actual files (or entries within files) associated with the specified objects.
DeleteAll¶
void DeleteAll(bool force=false)
Clears the application back to a clean state with nothing loaded.
DeleteScoped¶
void DeleteScoped(unsigned int scope, bool inScope)
Scoped version of Delete but with the
additional option to specify whether to delete everything within the scope
or everything not within the scope using the inScope parameter.
FindByDataScoped¶
std::vector<OEPropDB::OEKey> FindByDataScoped(const std::string &query,
unsigned int scope = AllScope)
Reserved for future implementation.
FindByQueryScoped¶
std::vector<OEPropDB::OEKey> FindByQueryScoped(const OEPropDB::OEKey &query,
unsigned int scope = AllScope)
std::vector<OEPropDB::OEKey> FindByQueryScoped(const OEPropDB::OEKey &query,
unsigned int atoms,
unsigned int bonds,
unsigned int scope = AllScope)
Uses the specified molecule as a query to search the specified scope. Returns a list of keys corresponding to molecules that match the specified query.
FindBySMARTSScoped¶
std::vector<OEPropDB::OEKey> FindBySMARTSScoped(const std::string &smarts,
unsigned int scope = AllScope)
Uses the specified SMARTS pattern as a query to search the specified scope. Returns a list of keys corresponding to molecules that match the specified SMARTS pattern.
FindBySimilarityScoped¶
std::vector<OEPropDB::OEKey> FindBySimilarityScoped(const OEPropDB::OEKey &query,
float similarity,
unsigned int scope = AllScope)
Searches the specified scope for molecules with a Lingo similarity greater than the specified similarity cutoff with the specified molecule query.
FindByTitleScoped¶
std::vector<OEPropDB::OEKey> FindByTitleScoped(const std::string &expr,
unsigned int scope = AllScope)
Uses the specified title query as a regular expression to search the specified scope for molecules whose title match the expression.
FindInRepository¶
void FindInRepository()
This function prompts the user to specify a query to search the contents of the application repository. The user then has the option to select some, none, or all of the hits to be placed in a new list.
FindOnDisk¶
void FindOnDisk()
This function prompts the user to specify a query to search a specific region of the user’s hard drive for molecules matching the query. The user then has the option to load some, none, or all of the files containing the hits. This function will load the entire file where a hit was discovered as opposed to just the hits in that file.
GridAdd¶
unsigned int GridAdd(OESystem::OESkewGrid &grd, unsigned int listID = 0)
unsigned int GridAdd(OESystem::OEScalarGrid &grd, unsigned int listID = 0)
Adds the specified Python grid object to VIDA. If the optional listID argument is provided, then the grid is added to the specified list. Otherwise, a new list is created and the grid is added to it.
GridCheckIn¶
bool GridCheckIn(OESystem::OESkewGrid &grd,
unsigned int checkInType = OECheckInType_UnknownChange)
bool GridCheckIn(OESystem::OEScalarGrid &grd,
unsigned int checkInType = OECheckInType_UnknownChange)
Checks the specified Python accessible grid back into the main VIDA application which will synchronize any changes made to the grid in Python with the grid in VIDA. The grid in question must have been checked out of VIDA prior to being checked back in.
The checkInType parameter tells VIDA what type of changes were made to the grid in order to optimize the check in process. There are multiple allowable values for this parameter which can be OR’d together if necessary:
OECheckInType_ConformerChange
OECheckInType_CoordinateChange
OECheckInType_DataChange
OECheckInType_GraphChange
OECheckInType_NoChange
OECheckInType_RenderChange
OECheckInType_AnnotationChange
OECheckInType_UnknownChange
GridCheckOut¶
bool GridCheckOut(OESystem::OESkewGrid &grd, unsigned int id)
bool GridCheckOut(OESystem::OEScalarGrid &grd, unsigned int id)
Checks out a copy of the grid specified by id into the specified Python grid object (grd). Returns whether or not the check out process succeeded.
The checked out grid can be modified in Python, but those changes will not be
applied to the original grid in VIDA until the modified grid is
checked back in using the
GridCheckIn command.
GridCopy¶
unsigned int GridCopy(unsigned int id)
Creates a copy of the specified grid and returns the ID of the newly created copy.
GridCreateElectrostaticsGrid¶
unsigned int GridCreateElectrostaticsGrid(OEPropDB::OEKey k,
bool property=false)
Create an electrostatics grid for molecule id.
If property is true, then this grid is attached to id and does not show up in the list window. These grids cannot be saved to disk.
If property is false, then this grid is created as a separate entity from id.
GridCreateGaussian¶
unsigned int GridCreateGaussian(const OEPropDB::OEKey &k, float res)
Creates a gaussian grid representation for the molecule associated with the specified key at the specified resolution.
GridCreateGaussianProduct¶
unsigned int GridCreateGaussianProduct(const OEPropDB::OEKey &k, float res)
Creates a gaussian product grid representation for the molecule associated with the specified key at the specified resolution.
GridDefaultContourLevelByIndexGet¶
float GridDefaultContourLevelByIndexGet(unsigned int gridType,
unsigned int index)
Returns the default contour level for contour index for grids of type gridType.
GridDefaultContourLevelByIndexSet¶
void GridDefaultContourLevelByIndexSet(unsigned int gridType,
unsigned int index, float thresh)
Set the default contour level thresh for contour index for grids of type gridType.
GridDefaultNumContoursGet¶
unsigned int GridDefaultNumContoursGet(unsigned int gridType)
Returns the default number of contours for grids of type gridType.
GridDefaultNumContoursSet¶
void GridDefaultNumContoursSet(unsigned int gridType, unsigned int count)
Set the default number of contours for grids of type gridType to count.
GridInitializeContours¶
void GridInitializeContours(unsigned int id, bool update=true)
Initialize a grid to its default contours, colors and levels.
GridNormalize¶
bool GridNormalize(unsigned int id)
Normalizes a grid. This finds the sigma for the grid and divides all grid points by that value.
GridRegularize¶
unsigned int GridRegularize(unsigned int id)
Regularizes the specified skew grid. Returns the ID of the newly created regular scalar grid.
GridToGaussianGrid¶
unsigned int GridToGaussianGrid(unsigned int id)
Creates a gaussian grid representation for the specified grid.
GridTypeGetScoped¶
unsigned int GridTypeGetScoped(unsigned int scope = BestScope)
Returns the type of grid for the first grid found in scope.
GridTypeSet¶
void GridTypeSet(unsigned int id, unsigned int gridType)
Set the grid type of grid id to gridType.
GridTypeSetScoped¶
void GridTypeSetScoped(unsigned int gridType,
unsigned int scope = BestScope)
Scoped version of GridTypeSet.
GridWorkingGetScoped¶
unsigned int GridWorkingGetScoped(unsigned int scope = BestScope)
Returns the ID for the “working grid” which is determined in the following order: grid associated with selected contour, grid which is currently focused, grid which is a child object of the currently focused object, or lastly the first grid found in the current default scope.
HasGridChildrenScoped¶
int HasGridChildrenScoped(unsigned int scope = BestScope)
Returns whether or not any of the molecules in the specified scope have visible grids attached to them. Returns 0 for none of the molecules have visible grids, 1 for all molecules have visible grid, and 2 for at least one has a visible grid.
HasSurfaceChildrenScoped¶
int HasSurfaceChildrenScoped(const std::string &type,
unsigned int scope = BestScope)
Returns whether or not any of the molecules in the specified scope have visible surfaces attached to them. Returns 0 for none of the molecules have visible surfaces, 1 for all molecules have visible surface, and 2 for at least one has a visible surface.
Initialize¶
void Initialize(unsigned int id)
void Initialize(const OEPropDB::OEKey &)
Initializes the specified object for display. This function is automatically called on objects that are loaded into VIDA and ordinarily should not need to be called by the user.
IsAGrid¶
bool IsAGrid(unsigned int id)
bool IsAGrid(const OEPropDB::OEKey &k)
Returns whether or not the specified object is a grid.
IsAMolecule¶
bool IsAMolecule(unsigned int id)
bool IsAMolecule(const OEPropDB::OEKey &k)
Returns whether or not the specified object is a molecule.
IsAReflection¶
bool IsAReflection(unsigned int id)
bool IsAReflection(const OEPropDB::OEKey &k)
Returns whether or not the specified object is a reflection.
IsASmallMolecule¶
bool IsASmallMolecule(unsigned int id)
bool IsASmallMolecule(const OEPropDB::OEKey &k)
Returns whether or not the specified object is a small molecule.
IsASurface¶
bool IsASurface(unsigned int id)
bool IsASurface(const OEPropDB::OEKey &k)
Returns whether or not the specified object is a surface.
KeyGet¶
OEPropDB::OEKey KeyGet(const OESystem::OEBase &)
OEPropDB::OEKey KeyGet(const OESystem::OEBase &, const OEPropDB::OEKey &pkey)
Returns the key associated with the specified OEBase object. If the object’s parent key is known, that can be passed as a parameter as well to aid the key determination process.
KeyIDGet¶
unsigned int KeyIDGet(const OEPropDB::OEKey &)
Returns the ID associated with the specified key.
KeyParentIDGet¶
unsigned int KeyParentIDGet(const OEPropDB::OEKey &)
Returns the ID of the parent object associated with the specified key. This function should be used for child object types such as atoms, bonds, triangles, and vertices.
KeySourceIDGet¶
unsigned int KeySourceIDGet(const OEPropDB::OEKey &)
Returns the ID of the parent object associated with a specified key. This function should be used for top-level object types such as molecules, grids, and surfaces in situations where these objects have been added as children to another object.
KeyTypeGet¶
std::string KeyTypeGet(const OEPropDB::OEKey &)
Returns a string representation of the object type associated with the specified key. Return values include:
“Atom”
“Bond”
“Grid”
“Mol”
“Surface”
“Triangle”
“Vertex”
KeysGet¶
std::vector<OEPropDB::OEKey> KeysGet(unsigned int id)
Returns a list of all the keys for the specified ID. For most objects, the list returned will contain a single entry; however, for multi-conformer molecules, the list will include a key for each individual conformer.
ListAddObject¶
bool ListAddObject(unsigned int listid, unsigned int objectid)
Adds the object specified by objectid to the list specified by listid.
ListAddObjects¶
bool ListAddObjects(unsigned int listid,
const std::vector<unsigned int> &ids)
Adds the objects specified by the list of IDs (ids) to the list specified by listid.
ListGetNames¶
std::vector<std::string> ListGetNames()
Returns a list of the names of all the current lists.
ListGetObjectLists¶
std::vector<unsigned int> ListGetObjectLists(unsigned int objectid)
Returns a list of all the lists to which the object specified by objectid belongs.
ListGetObjects¶
std::vector<unsigned int> ListGetObjects(unsigned int listid)
Returns a list of IDs of all the objects contained within the list specified by listid.
ListMoveObject¶
bool ListMoveObject(unsigned int srclist, unsigned int dstlist,
unsigned int objectid)
Moves the object specified by objectid from the list specified by srclist to the list specified by dstlist.
ListMoveObjects¶
bool ListMoveObjects(unsigned int srclist, unsigned int dstlist,
const std::vector<unsigned int> &ids)
Moves the objects specified by list of IDs (ids) from the list specified by srclist to the list specified by dstlist.
ListNew¶
unsigned int ListNew(const std::string &name)
unsigned int ListNew(const std::string &name,
const std::vector<unsigned int> &ids)
unsigned int ListNew(const std::string &name,
const std::vector<OEPropDB::OEKey> &keys)
Creates a new list with the specified name. If a list of IDs or keys is specified with this call, all of the objects corresponding to those IDs or keys will be added to the list.
Returns the ID of the created list.
ListNewAnd¶
unsigned int ListNewAnd(const std::vector<unsigned int> &ids)
Creates a new list containing all of the objects that each appear in every list specified by the list of IDs (ids).
Returns the ID of the created list.
ListNewMarked¶
unsigned int ListNewMarked(const std::string &name="")
Creates a new list containing all the currently marked objects. Objects will not be removed from this list if they are subsequently unmarked.
Returns the ID of the created list.
ListNewOr¶
unsigned int ListNewOr(const std::vector<unsigned int> &ids)
Creates a new list containing all of the objects in all of the lists specified by the list of IDs (ids).
Returns the ID of the created list.
ListNewXor¶
unsigned int ListNewXor(const std::vector<unsigned int> &ids)
Creates a new list containing all of the objects that each appear only once among all the lists specified by the list of IDs (ids).
Returns the ID of the created list.
ListRemoveObject¶
bool ListRemoveObject(unsigned int listid, unsigned int objectid)
Removes the object specified by objectid from the list specified by listid.
ListRemoveObjects¶
bool ListRemoveObjects( unsigned int listid,
const std::vector<unsigned int> &ids )
Removes the object(s) specified by the list of IDs (ids) from the list specified by listid.
ListSubsetMarked¶
unsigned int ListSubsetMarked(unsigned int id, bool match)
Creates a new list containing a subset of the objects contained within the list specified by id. If the match parameter is True, the subset will contain all of the marked objects in the source list, if match is False, the subset will contain all of the non-marked objects in the source list.
Returns the ID of the created list.
ListSubsetQuery¶
unsigned int ListSubsetQuery(unsigned int id, const std::string &, bool match)
Creates a new list containing a subset of the objects contained within the list specified by id. If the match parameter is True, the subset will contain all of the objects that match the specified query in the source list, if match is Fale, the subset will contain all of the objects which fail to match the specified query in the source list. The query parameter can be specified as a SMARTS, a SMILES, or an IUPAC name.
Returns the ID of the created list.
MoleculeAdd¶
unsigned int MoleculeAdd(const std::string &, unsigned int listID = 0)
unsigned int MoleculeAdd(OEChem::OEMCMolBase &, unsigned int listID = 0)
Adds a new molecule to VIDA. There are two implementations of this function. The first implementation expects a hexadecimal encoded OEB string specifying a molecule. The second implementation expects a Python molecule object.
If the optional listID argument is provided, then the molecule is added to the specified list. Otherwise, a new list is created and the molecule is added to it.
Returns the ID assigned to the newly added molecule or zero if the add failed for any reason.
MoleculeCheckIn¶
bool MoleculeCheckIn(OEChem::OEMCMolBase &mol,
unsigned int checkInType = OECheckInType_UnknownChange )
Checks the specified Python accessible molecule back into the main VIDA application which will synchronize any changes made to the molecule in Python with the molecule in VIDA. The molecule in question must have been checked out of VIDA prior to being checked back in.
The checkInType parameter tells VIDA what type of changes were made to the molecule in order to optimize the check in process. There are multiple allowable values for this parameter which can be OR’d together if necessary:
OECheckInType_ConformerChange
OECheckInType_CoordinateChange
OECheckInType_DataChange
OECheckInType_GraphChange
OECheckInType_NoChange
OECheckInType_RenderChange
OECheckInType_AnnotationChange
OECheckInType_UnknownChange
MoleculeCheckOut¶
bool MoleculeCheckOut(OEChem::OEMCMolBase &mol, unsigned int id)
Checks out a copy of the molecule specified by id into the specified Python molecule object (mol). Returns whether or not the check out process succeeded.
The checked out molecule can be modified in Python, but those changes will not
be applied to the original molecule in VIDA until the modified molecule
is checked back in using the
MoleculeCheckIn command.
MoleculeComponentNamesGet¶
std::vector<std::string> MoleculeComponentNamesGet(unsigned int id)
Returns a list of names of the individual components of the molecule
specified by id based on PDB related subsets.
MoleculeExamine¶
bool MoleculeExamine(OEChem::OEMCMolBase &, unsigned int id)
bool MoleculeExamine(OEChem::OEMCMolBase &, const OEPropDB::OEKey &key)
Copies the molecule associated with the specified ID or key into the specified Python molecule object. Returns True if the copy happened successfully. In cases where a script needs read-only access to a molecule, MoleculeExamine provides a much faster way to retrieve molecules than MoleculeCheckOut or MoleculeGet. Molecules retrieved using MoleculeExamine cannot be checked back in using MoleculeCheckIn.
MoleculeGet¶
bool MoleculeGet(OEChem::OEMCMolBase &, unsigned int id)
bool MoleculeGet(OEChem::OEMCMolBase &, const OEPropDB::OEKey &key)
OEChem::OEMol MoleculeGet(unsigned int id)
OEChem::OEMol MoleculeGet(const OEPropDB::OEKey &key)
Copies the molecule associated with the specified ID or key into the specified Python molecule object. Returns whether or not the copy happened successfully.
MoleculeHasComponents¶
bool MoleculeHasComponents(unsigned int id)
Returns whether or not the molecule specified by id contains multiple
distinct components.
MoleculeMaxResidueGet¶
int MoleculeMaxResidueGet(unsigned int id)
Returns the largest residue index of all the residues contained within the specified molecule.
MoleculeMergeScoped¶
unsigned int MoleculeMergeScoped(unsigned int scope = BestScope,
const std::string &name="Merged",
unsigned int listid=0)
Merges all of the molecules in the specified scope into a single new molecule.
The name parameter specifies the new molecule’s name and the listid
parameter specifies in which list to place this new molecule. If listid
is 0, a new list will be created to contain the created molecule.
MoleculeNewSubset¶
std::vector<unsigned int> MoleculeNewSubset(unsigned int listid,
unsigned int id, bool pdb)
std::vector<unsigned int> MoleculeNewSubset(unsigned int listid,
unsigned int id, unsigned int scope,
bool unmatched)
std::vector<unsigned int> MoleculeNewSubset(unsigned int listid,
unsigned int id,
const std::vector<std::vector<unsigned int> > &parts)
This function creates a series of new molecules from the given molecule based on its internal components determined by OEChem using the OEDetermineComponents function.
MoleculeNewSubsetScoped¶
std::vector<unsigned int> MoleculeNewSubsetScoped(unsigned int listid,
unsigned int scope, bool pdb)
std::vector<unsigned int> MoleculeNewSubsetScoped(unsigned int listid,
unsigned int mscope,
unsigned int scope,
bool unmatched)
This function creates a series of new molecules from the given scope based on its internal components determined by OEChem using the OEDetermineComponents function.
MoleculeResidueNameSetScoped¶
void MoleculeResidueNameSetScoped(const std::string &name,
unsigned int scope = BestScope)
Renames all the residues in the specified scope.
MoleculeResidueSet¶
int MoleculeResidueSet(unsigned int id, int residueNum,
bool incrementPerRes=false)
Sets the residue number of every residue in the specified molecule to the specified value (residueNum). The incrementPerRes parameter is currently reserved for future expansion.
MoleculeSetProperty¶
void MoleculeSetProperty(const std::vector<OEPropDB::OEKey> &keys,
unsigned char action, std::string prop, bool state)
Reserved for internal use.
MoleculeSizeCutoffGet¶
unsigned int MoleculeSizeCutoffGet()
Returns the atom number cutoff at which point a molecule is considered to be a “large” molecule. The default is 255.
MoleculeSizeCutoffSet¶
void MoleculeSizeCutoffSet(unsigned int size)
Sets the atom number cutoff at which point a molecule is considered to be a “large” molecule. The default is 255.
MoleculeUpdate¶
bool MoleculeUpdate(OEChem::OEMCMolBase &)
Updates the original molecule stored in VIDA with any changes that may have been made to the specified Python molecule.
NameGet¶
std::string NameGet(unsigned int)
std::string NameGet(const OEPropDB::OEKey &)
Returns the name of the object specified by either its ID or key.
NameSet¶
void NameSet(unsigned int, const std::string &)
void NameSet(const OEPropDB::OEKey &, const std::string &)
Sets the name of the object specified by either its ID or key.
OEFuseKeyGroups¶
OEKeyGroup OEFuseKeyGroups(const std::vector<OEKeyGroup> &k1,
unsigned char type)
Fuses the specified keys groups into a single key group.
OEKeyIterToVector¶
std::vector<OEPropDB::OEKey>
OEKeyIterToVector(OESystem::OEIterBase<const OEPropDB::OEKey> *iterbase)
Converts a key iterator into a list of keys.
PropertyTypeGet¶
unsigned int PropertyTypeGet(const std::string &type)
Returns the integer property type for the string type. See
KeyTypeGet for a list of types.
SDDataGet¶
std::string SDDataGet(unsigned int id, const std::string &tag)
std::string SDDataGet(const OEPropDB::OEKey &key, const std::string &tag)
Returns the SD data associated with the specified tag on the specified object.
SDDataHas¶
bool SDDataHas(unsigned int id, const std::string &tag)
bool SDDataHas(const OEPropDB::OEKey &key, const std::string &tag)
Returns whether or not the specified object contains SD data with the specified tag.
SDDataSet¶
void SDDataSet(unsigned int id, const std::string &tag, const std::string &data)
void SDDataSet(const OEPropDB::OEKey &key, const std::string &tag,
const std::string &data)
Sets the value of the SD data associated with the specified tag on the specified object.
SurfaceAdd¶
unsigned int SurfaceAdd(OESpicoli::OESurface &surf, unsigned int listID = 0)
Adds a new Python surface object to VIDA. Returns the ID assigned to the newly added surface or zero if the add failed for any reason. If the optional listID argument is provided, then the surface is added to the specified list. Otherwise, a new list is created and the surface is added to it.
SurfaceBestFloodScoped¶
int SurfaceBestFloodScoped(unsigned int scope = BestScope)
Return the largest flood value for all surfaces in the given scope. A flood value defines the surface being scribed.
SurfaceCheckIn¶
bool SurfaceCheckIn(OESpicoli::OESurface &surf,
unsigned int checkInType = OECheckInType_UnknownChange)
Checks the specified Python accessible surface back into the main VIDA application which will synchronize any changes made to the surface in Python with the surface in VIDA. The surface in question must have been checked out of VIDA prior to being checked back in.
The checkInType parameter tells VIDA what type of changes were made to the surface in order to optimize the check in process. There are multiple allowable values for this parameter which can be OR’d together if necessary:
OECheckInType_ConformerChange
OECheckInType_CoordinateChange
OECheckInType_DataChange
OECheckInType_GraphChange
OECheckInType_NoChange
OECheckInType_RenderChange
OECheckInType_AnnotationChange
OECheckInType_UnknownChange
SurfaceCheckOut¶
bool SurfaceCheckOut(OESpicoli::OESurface &surf, unsigned int id)
Checks out a copy of the surface specified by id into the specified Python surface object (surf). Returns whether or not the check out process succeeded.
The checked out surface can be modified in Python, but those changes will not
be applied to the original surface in VIDA until the modified surface is
checked back in using the
SurfaceCheckIn command.
SurfaceCreate¶
unsigned int SurfaceCreate(const std::string &, const OEPropDB::OEKey &key,
bool property=false)
Create a surface of type type based on the molecule represented by key.
If property is true, then make the surface a property surface that is bound to the molecule.
SurfaceCreateScoped¶
bool SurfaceCreateScoped(const std::string &, bool single_surface=false,
unsigned int scope = BestScope)
Create a surface of type type for each molecule in scope.
If property is true, then make the surface a property surface that is bound to the molecule.
SurfaceCropDistance¶
void SurfaceCropDistance(unsigned int id, float distance)
Retains the section of the surface specified by oerid to a distance dist from the selected set of atoms.
SurfaceCropDistanceFrom¶
void SurfaceCropDistanceFrom(const OEPropDB::OEKey &s, const OEPropDB::OEKey &,
float distance)
Retains the section of the surface specified by s based on its distance to another object. The reference object can be a molecule or another surface. The distance cutoff is measured in Angstroms.
SurfaceCropScribedScoped¶
void SurfaceCropScribedScoped(unsigned int scope = BestScope)
Retains the section of all surfaces in scope to a distance dist from the selected set of atoms.
SurfaceCropUnscribedScoped¶
void SurfaceCropUnscribedScoped(unsigned int scope = BestScope)
Remove the scribed sections of all scribed surfaces in scope.
SurfaceGenerateBox¶
unsigned int SurfaceGenerateBox(float x, float y, float z, float width,
float height, float depth)
Creates and returns the id of a surface representing a box as determined by the parameters x, y, z, width, height, and depth.
SurfaceGenerateSphere¶
unsigned int SurfaceGenerateSphere(float x, float y, float z, float radius,
int level=10)
Creates and returns the id of a surface representing a sphere as determined by the parameters x, y, z, and radius. The level parameter specifies how many iterations should be used in determining the quality of the surface.
SurfaceGenerateSpline¶
unsigned int SurfaceGenerateSpline(const std::vector<float> &coords,
int splineResolution, int seq_res,
int cross_res, float width, float thick,
int splineType, int style)
Creates and returns the id of a surface representing a spline as determined by the parameters coords, splineResolution, seq_res, cross_res, width, thick, splineType, and style.
SurfacePickTriangle¶
void SurfacePickTriangle(unsigned int oerid, const OEPropDB::OEKey &trikey,
bool addtriangle=false)
Pick a surface triangle specified by trikey. Ordinarily, this function does not need to be called.
SurfaceProbeRadiusGet¶
float SurfaceProbeRadiusGet()
Get the probe radius used when creating surfaces.
SurfaceProbeRadiusSet¶
float SurfaceProbeRadiusSet(float radius)
Set the probe radius to radius that is used when creating surfaces.
SurfaceResolutionSet¶
float SurfaceResolutionSet(float res)
Set the resolution used when creating surfaces. The resolution is set to resolution.
SurfaceRestoreScoped¶
void SurfaceRestoreScoped(unsigned int scope = BestScope)
Restore all surfaces in scope to their original states.
SurfaceScribeScoped¶
void SurfaceScribeScoped(int flood,
unsigned int scope = BestScope)
Scribe all scribed surfaces in scope to include all portions of the surface that fall within flood. Ordinarily, this function does not need to be called.
SurfaceSetPotentialFromGrid¶
void SurfaceSetPotentialFromGrid(unsigned int id, unsigned int gridid)
Sets the surface potential for the specified surface using the values in the specified grid.
SurfaceSetPotentialFromGridScoped¶
void SurfaceSetPotentialFromGridScoped(unsigned int gridid,
unsigned int scope = BestScope)
Sets the surface potential for all the surfaces in the specified scope using the values in the specified grid.
SymmetryNumOperators¶
unsigned int SymmetryNumOperators(unsigned int id)
This function returns the number of symmetry operators for the specified id.
SymmetryOperatorEnabledGet¶
bool SymmetryOperatorEnabledGet(unsigned int id, unsigned int operatorNumber)
SymmetryOperatorEnabledSet¶
bool SymmetryOperatorEnabledSet(unsigned int id, unsigned int operatorNumber,
bool enable)
SymmetryRadiusGet¶
float SymmetryRadiusGet()
SymmetryRadiusSet¶
float SymmetryRadiusSet(float r)
SymmetryRealize¶
unsigned int SymmetryRealize(unsigned int id, bool make_new_mol,
std::vector<float> center=std::vector<float>(),
float radius=0.0f)
XRayAutoMapCalculationPrefsSet¶
void XRayAutoMapCalculationPrefsSet()
void XRayAutoMapCalculationPrefsSet(const std::string &map1,
const std::string &map2="")
Set the map types for maps which should be calculated automatically after reading a reflection file.
XRayCalculateMap¶
unsigned int XRayCalculateMap(unsigned int map_id,
unsigned int refln_id,
std::string map_type)
unsigned int XRayCalculateMap(unsigned int map_id,
unsigned int refln_id,
unsigned int map_type)
This set of overloaded functions calculates a map for the set of reflection data specified by ‘refln_id’. If ‘map_id’ is non-zero, then the map replaces the grid with that ID. Otherwise, an entirely new map is created. The string ‘map_type’ parameter may be one of: Fo, Fc, 2Fo-Fc, Fo-Fc, 3Fo-2Fc, 5Fo-3Fc, Fo*Fo, or Fo*FOM, while the integer version may be one of: 0 Fo, 1 Fc, 2 TwoFoFc, 3 FoFc, 4 ThreeFoTwoFc, 5 FiveFoThreeFc, 8 FoSquared, 9 FoFom.
XRayCalculatePhases¶
bool XRayCalculatePhases(unsigned int refln_id,
unsigned int model_id)
This is experimental, and should not be called by the user.
XRayGetCell¶
std::vector<float> XRayGetCell(unsigned int id)
Returns the cell constants for the given object in a list, in the order a, b, c, Alpha, Beta, Gamma.
XRayGetSpaceGroup¶
std::string XRayGetSpaceGroup(unsigned int id)
Returns the spacegroup name for the given object.
XRayMTZColumnNamesCurrentDefaultsGet¶
std::vector<std::string> XRayMTZColumnNamesCurrentDefaultsGet()
XRayMTZColumnNamesGet¶
std::vector<std::string> XRayMTZColumnNamesGet()
bool XRayMTZColumnNamesGet(std::vector<std::string> &names)
Fills up the input list/vector with the MTZ file column names as specified by XRayMTZColumnNamesSet. Unless XRayMTZColumnNamesSet was called with the permanent flag, this function will only work once per call to XRayMTZColumnNamesSet.
This function returns True if it successfully filled out the list/vector, or False otherwise.
XRayMTZColumnNamesSet¶
void XRayMTZColumnNamesSet(const std::vector<std::string> &names,
bool permanent=false)
Stores a list of column names for mtz files. The next time an MTZ file is read, instead of prompting the user, the column names are taken from the list/vector passed to this function. The column names are in the order Fo, Phi, Fc, PhiC, Sigma, FOM, RFree. If the permanent flag is set to True, then these values are used instead of prompting until the program exits. If permanent is false, then the values are only used once.
In a script, there’s no reason to call this command instead of pre-specifying the prompt results with PromptResponseVectMulti, as shows up in the journal file. However, if creating a function which will read an MTZ file directly then this command is needed since the PromptResponse commands don’t work in interactive commands.
XRayMTZColumnNamesStandardDefaultsGet¶
std::vector<std::string> XRayMTZColumnNamesStandardDefaultsGet()
XRaySetCrystalParams¶
bool XRaySetCrystalParams(unsigned int id,
unsigned int from_object_id)
bool XRaySetCrystalParams(unsigned int id,
std::vector<float> cell,
unsigned int sg)
bool XRaySetCrystalParams(unsigned int id,
std::vector<float> cell,
const std::string &sgname)
bool XRaySetCrystalParams(unsigned int id, float a, float b,
float c, float alpha, float beta,
float gamma, unsigned int sg)
bool XRaySetCrystalParams(unsigned int id, float a, float b,
float c, float alpha, float beta,
float gamma, const std::string &sgname)
Set the crystal parameters for the given reflection. The parameters may be specified in multiple ways, which are obvious from the names of the arguments.
XRayValidMaptypes¶
std::string XRayValidMaptypes(unsigned int refln_id)
Not all map types are available for every reflection data set, since not all files have all required data for every possible map calculation. For example, a reflection data set without Fc data will not be able to calculate any map types which require Fc. This function returns (as a string), the valid map types for the given reflection data set. The string is a concatenation of all available map types, with each type separated by the ‘|’ character.