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This document describes the Python api to VIDA. VIDA uses the Python programming language to internally script user actions. Most users actions have a corresponding Python function that is called to perform the action and save it in the journal file.
This document does not describe how to program in Python or any of the built-in features already accessible through the Python scripting interface. You can find out more information about Python at the Python website, http://python.org/.
Every Python function called by VIDA automatically blocks user interaction from the GUI and restores it when the function is completed. (The one exception is the stop sign by the progress bar which can always be used to halt Python scripts and functions)
Advanced users can look at the Blocking functions which control this behavior. These functions should be used with caution as they can have strange artifacts during some function calls.
If you are importing a Python function from a library or a user supplied function, you may wish to use vfapp.scriptDoWork() and vfapp.scriptStopWork(). These functions force VIDA to look for GUI events after every Python function call. Standard usage is:
def myFunction():
vfapp.scriptDoWork()
try:
... perform Python functions here
finally:
vfapp.scriptStopWork()
Placing the functions in a try...finally block ensure that the GUI blocking is appropriately turned off when the function ends or an exception is caught.
(OEKey key, string str, string data)Add a piece of data to the object specified by key. This piece of data will also appear in the spreadsheet ( a new column will be created if the column doesn't already exist. )
This is an easy way to annotate molecules or atoms for instance.
() -> VFDataBase *Return the VFDataTable Object for datatable name.
(string name, bool throwError) -> VFDataTable *Return the list of all internal datatables.
(string datatable, string columnName, bool genericData)Add a column to datatable datatable with the name columnName. If columnName already exists in the datatable, it will be ignored.
(string datatable)Commit any outstanding changes to the internal database.
() -> stringReturns the name of the current datatable. e.g. 'Molecules'. This function is deprecated and the DatatableCurrentGet function should be used instead.
() -> stringReturns the name of the current datatable. e.g. 'Molecules'.
(string datatable) -> boolSets the current datatable.
(string datatable, integer row, string header) -> stringReturn the string representation of the data in the datatable named datatable for the row row and the column named header.
(string datatable, string name)Delete the column named column. Note that this delets column from all datatables.
(string ss) -> boolReturns True if datatable is editable.
(string ss, bool val)Sets datatable to be editable if val is True, otherwise sets datatable to be read-only.
(string datatable, OEDataFilter filter, string name, bool staticView, bool permaFilter)
(string datatable, string filter, string name, bool staticView, bool permaFilter)
Create a new datatable view from the datatable named datatable using the filter defined in filter. The new view is named name. filter is an arbitrary python expression that is applied to every row in the datatable.
This expression may assume that a local variable ROW is assigned to the row currently being evaluated. e.g.
DatatableData(DatatableCurrent(), ROW, foo)returns the string representation of the data in column foo for the current datatable. Note: the current datatable may not be datatable.
(integer listid, string name)Generate a filtered datatable with name name from the list listid.
If name is already in the datatable, it will be renamed name1, name2 and so on.
(string datatable, string name) -> [string, ...]
(string datatable, integer index) -> [string, ...]
Returns string representations of the entire column for the datatable named datatable for column name or, alternatively, for column index by index.
(string datatable) -> intReturns the row index for the first active or selected row for the datatable named datatable.
() -> [string, ...]
(string datatable, string filename, int row, int width, int height) -> boolWrite an image file to the file specified by filename for the datatable named datatable at the row specified by row. The size of the image is specified by width and height.
(string datatable) -> intReturn the number of rows for the datatable named datatable.
(string datatable) -> [string, ...]Return a list of all the names of all the headers for the datatable named datatable.
(string spreadsheet, integer row) -> bool
(string datatable, int row, string func) -> doubleDatatableMolNumberFunctions calculate molecular data that returns a numeric value.
datatable identifies the datatable containing the molecule and row is the datatable row with the molecule.
The function func to compute is one of:
"mw" Molecular weight.
"Num Atoms" Number of atoms in the molecule.
"Num Bonds" number of bonds in the molecule.
- "Carbon-Hetero ratio" the ratio of carbons to hetero atoms in the molecule.
Returns -1 if there are no carbons.
"Energy" The molecular energy of the molecule as specified in the input file.
"Actual Charge" The sum of the partial charges on all atoms as specified in the input file.
"Formal Charge" The sum of the formal charges on all atoms.
"Halide Count" The number of halogen atoms in the molecule.
"Num Carbons" The number of carbon atoms in the molecule.
"Num Formal Charges" The number of more atoms with a specified formal charge.
"Num Heavy Atoms" The number of heavy atoms (non hydrogen) in the molecule.
"Num Hetero Atoms" The number of hetero atoms in the molecule.
"Num Hydrogens" The number of hydrogen atoms in the molecule.
"Num Rigid Bonds" The number of rigid bonds in the molecule.
"Nom Rotatable Bonds" The number of rotatable bonds in the molecule.
"Num Chiral Atoms" returns the number of chiral atoms in the molecule.
"Num Chiral Bonds" returns the number of chiral bonds in the molecule.
(string datatable, int row, string func) -> stringDatatableMolNumberFunctions calculate molecular data that returns a string value.
datatable identifies the datatable containing the molecule and row is the datatable row with the molecule.
The function func to compute is one of:
o 'molformula' the molecular formula for the molecule.
(string datatable) -> intReturn the number of rows for the datatable named datatable.
(string filename) -> bool
(string datatable, integer row, string header, string value, bool update)Set the cell data for the datatable named datatable at row for the column named header to the string value value.
If update is true, immediately update the datatable. Set this to false if you are updating a bunch of data and then call DatatableUpdateContents(ss).
(string datatable, string col, string expr)A datatable expression defines an arbitrary piece of python code to call that generates data to be displayed in the datatable.
DatatableSetExpression creates a new column named col for the datatable named datatable using the function defined by expr.
This expression may assume that a local variable ROW is assigned to the row currently being evaluated. e.g.
DatatableData(DatatableCurrent(), ROW, foo)returns the string representation of the data in column foo for the current datatable which, for this function, is always datatable.
(string datatable, integer row, [string, ...] headers, [string, ...] rows, bool update)Set data in the datatable named datatable. row is the row index to set. headers defines the names of the columns to set and rows is the string representation of the data.
Note: headers[i] should be the name of the column for row[i].
The update parameter is no longer used and is kept for backwards compatabillity.
(string filename) -> bool
(integer scope)This function restores the default atom coloring to those atoms within the specified scope.
()This function updates the default atom coloring palette based on whether or not the application is using a dark or light colored background scheme. This function is called internally and should not by called by the user.
(integer scope)This function provides a quick way to mark a molecule (or set of atoms) as a reference structure. The coloring function that is applied colors all carbon atoms the current application 'reference' color (default is green). The 'reference' color can be changed in the preferences.
(integer scope)This function provides a quick way to color a molecule (or set of atoms) based on associated residue information. The default coloring that is applied uses the 'Shapely' color scheme for coloring residues. The residue colors can be changed in the preferences:
* ALA Medium Green [140,255,140] * GLY White [255,255,255] * LEU Olive Green [ 69, 94, 69] * SER Medium Orange [255,112, 66] * VAL Light Purple [255,140,255] * THR Dark Orange [184, 76, 0] * LYS Royal Blue [ 71, 71,184] * ASP Dark Rose [160, 0, 66] * ILE Dark Green [ 0, 76, 0] * ASN Light Salmon [255,124,112] * GLU Dark Brown [102, 0, 0] * PRO Dark Grey [ 82, 82, 82] * ARG Dark Blue [ 0, 0,124] * PHE Olive Grey [ 83, 76, 66] * GLN Dark Salmon [255, 76, 76] * TYR Medium Brown [140,112, 76] * HIS Medium Blue [112,112,255] * CYS Medium Yellow [255,255,112] * MET Light Brown [184,160, 66] * TRP Olive Brown [ 79, 70, 0] * ASX Medium Purple [255, 0,255] * GLX Medium Purple [255, 0,255] * PCA Medium Purple [255, 0,255] * HYP Medium Purple [255, 0,255] * A Light Blue [160,160,255] * C Light Orange [255,140, 75] * G Medium Salmon [255,112,112] * T Light Green [160,255,160] * Default Medium Purple [255, 0,255]
(OESystem::OEColor color, integer scope)
(integer element, OESystem::OEColor color, integer scope)
This function sets the color of the atoms in the specified scope to be the specified color c.
() -> boolReturns whether or not the application is using the atom color palette designed for dark colored backgrounds. Otherwise, the application is using the atom color palette designed for light colored backgrounds. Both of these palettes can be edited in the preferences.
(bool dark)Sets whether or not the application is using the atom color palette designed for dark colored backgrounds. Otherwise, the application is using the atom color palette designed for light colored backgrounds. Both of these palettes can be edited in the preferences.
() -> OESystem::OEColor
(integer elem) -> OESystem::OEColor
Returns the current default atom color. The default atom color is applied to every atom that does not have its own specific default color assigned. Calling this function with the elem parameter returns the specific default color associated with the passed element number (e.g. carbon = 6).
(OESystem::OEColor color)
(integer elem, OESystem::OEColor color)
Sets the current default atom color. The default atom color is applied to every atom that does not have its own specific default color assigned. Calling this function with the elem parameter sets the specific default color associated with the passed element number (e.g. carbon = 6).
() -> floatReturns the current radius of atom selection halo. The atom selection halo is a transparent white surface with the specified radius drawn around the current selected set of atoms. If the DistanceControlsVisibility property is set (see DistanceControlsVisibilitySet/Get functions), only atoms falling within this radius will be displayed.
(float radius, bool notify) -> floatSets the current radius of atom selection halo. The atom selection halo is a transparent white surface with the specified radius drawn around the current selected set of atoms. If the DistanceControlsVisibility property is set (see DistanceControlsVisibilitySet/Get functions), only atoms falling within this radius will be displayed.
() -> integer
(OEKey key) -> integer
Returns the current default hydrogen display style - 0 for no hydrogens, 1 for polar hydrogens only, and 2 for all hydrogens.
(integer style)Sets the current default hydrogen display style. Valid style parameter values are 0 for no hydrogens, 1 for polar hydrogens only, and 2 for all hydrogens.
(integer style, integer scope)Sets the hydrogen display style for all the molecules in the specified scope. Valid style parameter values are 0 for no hydrogens, 1 for polar hydrogens only, and 2 for all hydrogens.
() -> stringReturns the default label displayed on atoms. The default is "None". See the AtomLabelSetScoped function for more information about label types.
(string label)Sets the default label displayed on atoms. The default is "None". See the AtomLabelSetScoped function for more information about label types.
(OEKey k, string label) -> boolSets the label on the specified atom. The parameter label contains the text of the label and the parameter key specifies which atom this label should apply to. See the AtomLabelSetScoped function for more information about label types.
(string label, integer scope) -> boolSets the current label displayed on the atoms in the specified scope. Label types include:
* "none" or "" * "index" or "%i" * "element" or "%e" * "name" or "%n" * "type" or "%t" * "inttype" or "%it" * "implicit hcount" or "%h" * "formal charge" or "%f" * "partial charge" or "%p" * "residue info" or "%r" * "degree" or "%d" * "ischiral" or "%c" * "chirality" or "%chi" * "hasstereospecified" or "%sts" * "symmetry class" or "%sy" * "isinring" or "%rng" * "oechem idx" or "%oei" * "map index" or "%m" * "read order" or "%ro" * "isotope" or "%iso" * "hcount" or "%h" * "residue info (ca)" or "%car" * "bfactor" or "%cab" * "degree" or "%d" * "hybrid" or "%hyb" * "comment" or "%cm" * "%gd(x)" - where x specifies the desired piece of generic data to use as the label
() -> stringReturns the default atom style. The default is "small". See the AtomStyleSetScoped function for more information about atom styles.
(integer scope) -> integerReturns the style of the atoms in the specified scope. If there are multiple styles present, the return type is "mixed". See the AtomStyleSetScoped function for more information about atom styles.
() -> stringReturns the default atom style for large molecules, where large is determined by whether or not the number of atoms in the molecule exceeds the specified cutoff. For more information on this cutoff, see the MoleculeSizeCutoff function. The default is "none". See the AtomStyleSetScoped function for more information about atom styles.
(string atomStyle)
(integer style)
Sets the default atom style for large molecules, where large is determined by whether or not the number of atoms in the molecule exceeds the specified cutoff. This function accepts either a string or an enumerated representation as its parameter. The default is "none". For more information on this large molecule atom cutoff, see the MoleculeSizeCutoff function. See the AtomStyleSetScoped function for more information about atom styles.
() -> stringReturns the default atom style for nucleic acids. The default is to mirror the large molecule atom style. See the AtomStyleLargeSet function for more information about large molecules and see the AtomStyleSetScoped function for more information about atom styles.
Note: this function is a placeholder for a future implementation and therefore does not currently have any effect.
(string atomStyle)
(integer style)
Sets the default atom style for nucleic acids. This function accepts either a string or an enumerated representation as its parameter. The default is to mirror the large molecule atom style. See the AtomStyleLargeSet function for more information about large molecules and see the AtomStyleSetScoped function for more information about atom styles.
Note: this function is a placeholder for a future implementation and therefore does not currently have any effect.
(string atomStyle)
(integer style)
Sets the default atom style. This function accepts either a string or an enumerated representation as its parameter. The default is "small". See the AtomStyleSetScoped function for more information about atom styles.
(string atomStyle, integer scope)
(integer style, integer scope)
Sets the display style for the specified atoms. This function accepts either a string or an enumerated representation as its parameter. Available atom styles include:
* "small" atoms are drawn as small sized spheres * "medium" atoms are drawn as medium sized spheres * "large" atoms are drawn as large sized spheres * "stars" atoms are drawn as stars * "radii" atoms are drawn as spheres with radii equivalent to their VDW radii * "none" atoms are not drawn, but are still considered visible and thus selectable * "hidden" atoms are not drawn and are not considered visible and thus are not selectable
(string style) -> integerThis function returns the enumerated type associated the specified string atoms style representation. See the AtomStyleSetScoped function for more information about atom styles.
(integer style) -> stringThis function returns the text string associated with the specified enumerated atom style representation. See the AtomStyleSetScoped function for more information about atom styles.
() -> floatThis function is currently a placeholder for future functionality.
(float ballStickRatio) -> floatThis function is currently a placeholder for future functionality.
(integer scope)This function restores the default bond coloring to those bonds within the specified scope.
(OESystem::OEColor color, integer scope)This function sets the color of the bonds in the specified scope to be the specified color c.
(integer id) -> boolReturns whether or not aromatic bonds should be drawn as aromatic or instead in kekule format for the molecule with the specified id.
(integer id, bool aromatic) -> boolSets whether or not aromatic bonds should be drawn as aromatic or instead in kekule format for the molecule with the specified id.
() -> boolReturns the global property which specifies whether or not explicit hydrogens should be displayed.
(bool hide) -> boolSets the global property which specifies whether or not explicit hydrogens should be displayed.
() -> boolReturns the global property which specifies whether or not explicit non-bonded atoms should be displayed.
(bool hide) -> boolSets the global property which specifies whether or not explicit non-bonded atoms should be displayed.
() -> stringReturns the default label displayed on bonds. The default is "None". See the BondLabelSetScoped function for more information about label types.
(string label)Sets the default label displayed on bonds. The default is "None". See the BondLabelSetScoped function for more information about label types.
(OEKey k, string label) -> boolSets the label on the specified bond. The parameter label contains the text of the label and the parameter key specifies which bond this label should apply to. See the BondLabelSetScoped function for more information about label types.
(string label, integer scope) -> boolSets the current label displayed on the bonds in the specified scope. Label types include:
* "none" or "" * "index" or "%i" * "order" or "%o" * "length" or "%l" * "type" or "%t" * "inttype" or "%it" * "ischiral" or "%c" * "chirality" or "%chi" * "hasstereospecified" or "%sts" * "oechem idx" or "%oei" * "%gd(x)" - where x specifies the desired piece of generic data to use as the label
() -> floatReturns the line width (in pixels) to be used when drawing bonds in "line" or "wireframe" styles.
(float width) -> floatSets the line width (in pixels) to be used when drawing bonds in "line" or "wireframe" styles.
() -> floatReturns the radius of the cylinders to be used when drawing bonds in "cylinder" style.
(float radius) -> floatSets the radius of the cylinders to be used when drawing bonds in "cylinder" style.
() -> boolReturns the global property which specifies whether or not aromatic bonds should be drawn as aromatic or instead in kekule format.
(bool show) -> boolSets the global property which specifies whether or not aromatic bonds should be drawn as aromatic or instead in kekule format.
() -> boolReturns the global property which specifies whether or not dipolar bonds should be drawn as directed bonds.
(bool show) -> boolSets the global property which specifies whether or not dipolar bonds should be drawn as directed bonds.
() -> boolReturns the global property which specifies whether or not bond orders should be displayed.
(bool show) -> boolSets the global property which specifies whether or not bond orders should be displayed.
() -> stringReturns the default bond style. The default is "cylinders". See the BondStyleSetScoped function for more information about bond styles.
(integer scope) -> integerReturns the style of the bonds in the specified scope. If there are multiple styles present, the return type is "mixed". See the BondStyleSetScoped function for more information about bond styles.
() -> stringReturns the default bond style for large molecules, where large is determined by whether or not the number of atoms in the molecule exceeds the specified cutoff. For more information on this cutoff, see the MoleculeSizeCutoff function. The default is "lines". See the BondStyleSetScoped function for more information about bond styles.
(string bondstyle)
(integer style)
Sets the default bond style for large molecules, where large is determined by whether or not the number of atoms in the molecule exceeds the specified cutoff. This function accepts either a string or an enumerated representation as its parameter. The default is "lines". For more information on this large molecule atom cutoff, see the MoleculeSizeCutoff function. See the BondStyleSetScoped function for more information about bond styles.
() -> stringReturns the default bond style for nucleic acids. The default is to mirror the large molecule bond style. See the BondStyleLargeSet function for more information about large molecules and see the BondStyleSetScoped function for more information about bond styles.
Note: this function is a placeholder for a future implementation and therefore does not currently have any effect.
(string bondstyle)
(integer style)
Sets the default bond style for nucleic acids. This function accepts either a string or an enumerated representation as its parameter. The default is to mirror the large molecule atom style. See the AtomStyleLargeSet function for more information about large molecules and see the AtomStyleSetScoped function for more information about atom styles.
Note: this function is a placeholder for a future implementation and therefore does not currently have any effect.
(string bondstyle)
(integer style)
Sets the default bond style. This function accepts either a string or an enumerated representation as its parameter. The default is "cylinders". See the BondStyleSetScoped function for more information about bond styles.
(string bondstyle, integer scope)
(integer style, integer scope)
Sets the display style for the specified bonds. This function accepts either a string or an enumerated representation as its parameter. Available bonds styles include:
* "lines" bonds are drawn as lines * "cylinders" bonds are drawn as cylinders * "none" bonds are not drawn, but are still considered visible and thus selectable * "hidden" bonds are not drawn and are not considered visible and thus are not selectable
(string style) -> integerThis function returns the enumerated type associated the specified string bond style representation. See the BondStyleSetScoped function for more information about bond styles.
(integer style) -> stringThis function returns the text string associated with the specified enumerated bond style representation. See the BondStyleSetScoped function for more information about bond styles.
(OEKey ) -> OESystem::OEColorReturns the color of the object specified by the OEKey parameter key.
(OEKey , OESystem::OEColor var2)Sets the color of the object specified by the OEKey parameter key to be the specified color.
(OESystem::OEColor , integer scope)Sets the color for all of the objects in the specified scope to be the specified color.
(integer scope)Assigns a "unique" color to each individual object found in the specified scope. For large numbers of objects in the scope, the colors used may eventually repeat.
() -> boolReturns whether or not an atom's or bond's distance from the selected set will affect its visibility. The distance cutoff is specified by the AtomHaloSet function.
(bool state)Sets whether or not an atom's or bond's distance from the selected set will affect its visibility. The distance cutoff is specified by the AtomHaloSet function.
() -> boolReturns whether or not the application has drawing of atoms and bonds enabled. Ordinarily, this function should not need to be called by the user.
(bool draw) -> boolSets whether or not the application has drawing of atoms and bonds enabled. Ordinarily, this function should not need to be called by the user.
() -> boolReturns whether or not axes should be drawn in the application's 3D display.
(bool draw) -> boolSets whether or not axes should be drawn in the application's 3D display.
() -> boolReturns whether or not the application has drawing of labels enabled.
(bool draw) -> boolSets whether or not the application has drawing of labels enabled.
() -> boolReturns whether or not the application has matrix (or tiled) displays enabled.
(bool draw) -> boolSets whether or not the application has matrix (or tiled) displays enabled.
() -> boolReturns whether or not the application has drawing of symmetry enabled.
(bool draw) -> boolSets whether or not the application has drawing of symmetry enabled.
() -> boolReturns whether or not the application has drawing of titles enabled.
(bool draw) -> boolSets whether or not the application has drawing of symmetry enabled.
() -> boolReturns whether or not the application has drawing of unit cells enabled.
(bool draw) -> boolSets whether or not the application has drawing of symmetry enabled.
() -> [integer, ...]Returns of a list of IDs corresponding to all the visible objects.
(OEKey key)This function adds the molecule corresponding to the specified key to the list of targets to be considered when displaying hydrogen bonds. Calling this function on a molecule will cause hydrogens to be added to that molecule if they are not already present.
(integer scope)This function adds of the molecules in the specified scope to the list of targets to be considered when displaying hydrogen bonds. Calling this function on a molecule will cause hydrogens to be added to that molecule if they are not already present.
()This function clears the list of molecule targets to be consdered when displaying hydrogen bonds.
() -> OESystem::OEColorReturns the current color being used when drawing hydrogen bonds.
(OESystem::OEColor )Sets the color to be used when drawing hydrogen bonds.
(OEKey key)This function removes the molecule corresponding to the specified key from the list of molecule targets to be consdered when displaying hydrogen bonds.
(integer scope)This function removes all of the molecules in the specified scope from the list of molecule targets to be consdered when displaying hydrogen bonds.
() -> boolReturns whether or not external hydrogen bonds (those between two separate molecules) should be displayed if present.
(bool show)Sets whether or not external hydrogen bonds (those between two separate molecules) should be displayed if present.
() -> boolReturns whether or not internal hydrogen bonds should be displayed if present.
(bool show)Sets whether or not internal hydrogen bonds should be displayed if present.
() -> OESystem::OEColorReturns the default color to be used when displaying halos.
(OESystem::OEColor c)Sets the default color to be used when displaying halos.
(OEKey ) -> OESystem::OEColorReturns the color of the halo associated with the specified atom key.
(OEKey k, OESystem::OEColor c)
(OEKey k, string var2)
Sets the color of the halo associated with the specified atom key.
(OESystem::OEColor , integer scope)
(string , integer scope)
Sets the color of the halos associated with the atoms in the specified scope.
(OEKey ) -> floatReturns the radius of the halo associated with the specified atom key.
(OEKey , string var2)
(OEKey , float var2)
Sets the radius of the halo associated with the specified atom key.
(string , integer scope)
(float , integer scope)
Sets the radius of the halos associated with the atoms in the specified scope.
(OEKey ) -> floatReturns the scaling factor for the size of the halo associated with the specified atom key.
(OEKey , string var2)
(OEKey , float var2)
Sets the scaling factor for the size of the halo associated with the specified atom key.
(string , integer scope)
(float , integer scope)
Sets the scaling factor for the size of the halo associated with the atoms in the specified scope.
(integer scope) -> intReturns 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.
(string type, integer scope) -> intReturns 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.
(integer scope)This function restores the default label coloring to those labels within the specified scope.
(integer scope)Clears the labels on all the atoms and bonds in the specified scope.
(OESystem::OEColor c, integer scope)This function sets the color of the labels in the specified scope to be the specified color c.
() -> OESystem::OEColorThis function returns the default color for labels.
(OESystem::OEColor c)This function sets the default color for labels.
() -> boolReturns whether or not labels are drawn using a fixed size on the screen or whether they scale with zooming of the scene.
(bool fixed)Sets whether or not labels are drawn using a fixed size on the screen or whether they scale with zooming of the scene.
(OEKey k, bool polarOnly)This function adds hydrogens to the molecule associated with the specified key. If the polarOnly parameter is set, only polar hydrogens will be added.
(bool polarOnly, integer scope)This function adds hydrogens to the molecules int the specified scope. If the polarOnly parameter is set, only polar hydrogens will be added.
(string atomStyle, string bondStyle, integer scope)Set the combined style for atoms and bonds.
o atomStyle is the style to set the atom , see AtomStyleSetScoped. o bondStyle is the style to set the bond, see BondStyleSetScoped. o scope is the default scope to use.
(string property, string params, integer scope)This color colors all the molecules in the specified scope according to the scheme specified by the property parameter. Valid properties include:
* "amino" * "bfactor" * "chain" * "charge" * "cpk" * "cpknew" * "formal charge" * "group" * "hbond" * "hydrophobicity" * "partial charge" * "shapely"If the specified property is hydrophobicity, the specific scale to be used can be specified in the params parameter. Valid scale options include:
* "charifson" * "eisenberg" * "kytedolittle" * "whiteoctanol"For more details on the specifics of these coloring scheme, please see the user manual.
(integer scope)This function restores the default atom and bond coloring to those atoms and bonds in the specified scope. It is essentially equivalent to calling AtomClearColorScoped followed by BondClearColorScoped.
() -> boolReturns whether or not the application is using either the atom or residue color palette designed for dark colored backgrounds. Otherwise, the application is using the atom color palettes designed for light colored backgrounds. All of these palettes can be edited in the preferences. For more information, see the functions AtomDarkColorsGet and ResidueDarkColorsGet.
(bool dark)Sets whether or not the application is using the atom and residue color palettes designed for dark colored backgrounds. Otherwise, the application is using the atom color palettes designed for light colored backgrounds. All of these palettes can be edited in the preferences. For more information, see the functions AtomDarkColorsSet and ResidueDarkColorsSet.
() -> boolReturns whether or not the application is using the high quality molecule representations as opposed to standard models.
(bool show) -> boolSets whether or not the application is using the high quality molecule representations as opposed to standard models.
() -> integerReturns the atom number cutoff at which point a molecule is considered to be a "large" molecule. The default is 255.
(integer size)Sets the atom number cutoff at which point a molecule is considered to be a "large" molecule. The default is 255.
() -> stringReturns the default molecule style. The default is "stick". See the MoleculeStyleSetScoped function for more information about molecule styles.
(integer scope) -> integerReturns the style of the molecules in the specified scope. If there are multiple styles present, the return type is "mixed". See the MoleculeStyleSetScoped function for more information about molecule styles.
() -> stringReturns the default molecule style for large molecules, where large is determined by whether or not the number of atoms in the molecule exceeds the specified cutoff. For more information on this cutoff, see the MoleculeSizeCutoff function. The default is "wireframe". See the MoleculeStyleSetScoped function for more information about moleceule styles.
(string style)
(integer style)
Sets the default molecule style for large molecules, where large is determined by whether or not the number of atoms in the molecule exceeds the specified cutoff. For more information on this cutoff, see the MoleculeSizeCutoff function. The default is "wireframe". See the MoleculeStyleSetScoped function for more information about moleceule styles.
() -> stringReturns the default molecule style for nucleic acids. The default is to mirror the large molecule style. See the MoleculeStyleLargeSet function for more information about large molecules and see the MoleculeStyleSetScoped function for more information about molecule styles.
Note: this function is a placeholder for a future implementation and therefore does not currently have any effect.
(string style)
(integer style)
Sets the default molecule style for nucleic acids. The default is to mirror the large molecule style. See the MoleculeStyleLargeSet function for more information about large molecules and see the MoleculeStyleSetScoped function for more information about molecule styles.
Note: this function is a placeholder for a future implementation and therefore does not currently have any effect.
(string atomStyle)
(integer style)
Sets the default molecule style. This function accepts either a string or an enumerated representation as its parameter. The default is "stick". See the MoleculeStyleSetScoped function for more information about molecule styles.
(string atomStyle, integer scope)
(integer style, integer scope)
Sets the display style for the specified molecules. This function accepts either a string or an enumerated representation as its parameter. Available molecule styles include:
* "ball and stick" molecules are drawn in ball and stick mode * "cpk" molecules are drawn in CPK mode * "stars" molecules are drawn in star mode * "stick" molecules are drawn in stick mode * "wireframe" molecules are drawn in wireframe mode * "none" molecules are not drawn, but are still considered visible and thus selectable * "hidden" molecules are not drawn and are not considered visible and thus are not selectable
(string style) -> integerThis function returns the enumerated type associated the specified string molecule style representation. See the MoleculeStyleSetScoped function for more information about molecule styles.
(integer style) -> stringThis function returns the text string associated with the specified enumerated molecule style representation. See the MolStyleSetScoped function for more information about molecule styles.
(integer pane)In matrix (tiled) mode, sets the specified pane to be the active pane in the display. Ordinarily, this function should not need to be called by the user.
()This function updates the default residue coloring palette based on whether or not the application is using a dark or light colored background scheme. This function is called internally and should not by called by the user.
() -> boolReturns whether or not the application is using the residue color palette designed for dark colored backgrounds. Otherwise, the application is using the residue color palette designed for light colored backgrounds. Both of these palettes can be edited in the preferences.
(bool dark)Sets whether or not the application is using the residue color palette designed for dark colored backgrounds. Otherwise, the application is using the residue color palette designed for light colored backgrounds. Both of these palettes can be edited in the preferences.
() -> OESystem::OEColor
(integer res) -> OESystem::OEColor
Returns the current default residue color. The default residue color is applied to every residue that does not have its own specific default color assigned. Calling this function with the res parameter returns the specific default color associated with the passed residue index.
(OESystem::OEColor c)
(integer res, OESystem::OEColor c)
Sets the current default residue color. The default residue color is applied to every residue that does not have its own specific default color assigned. Calling this function with the res parameter sets the specific default color associated with the passed residue index.
() -> boolReturns whether or not a border is drawn (in matrix mode) around the cell containing the focused object.
(bool draw)Sets whether or not a border is drawn (in matrix mode) around the cell containing the focused object.
() -> stringReturns the display style for the individual cells when the application is in matrix mode. Available styles are: "OnePerView", "LockedOnAll", and "LockedPerView".
(string mode) -> stringSets the display style for the individual cells when the application is in matrix mode. Available styles are: "OnePerView", "LockedOnAll", and "LockedPerView".
()This function selects every molecule that is currently visible.
(string query, bool mark, integer scope)This function selects every molecule in the specified scope based on whether or not it matches the specified substructure query. Valid query inputs include SMILES, SMARTS, and IUPAC as well as common names. The IUPAC and common name to structure conversion is performed by the Ogham toolkit.
([OEKey, ...] atomsKeys)This function selects the objects corresponding to each of the keys specified in the parameter list keys.
(integer id, bool selected)This function sets the selected property on the object corresponding to the specified id. The selected parameter specifies whether or not the object should either be selected or unselected.
() -> floatReturns the alpha buffer coloring blending factor for selection colors. The default value is 1.0 which corresponds to zero blending with the selection color being the one displayed. A value of 0.0 also corresponds to zero blending but with the underlying color being the one displayed. A value of 0.5 corresponds to even blending of the underlying color and the selected color.
(float alpha) -> floatSets the alpha buffer coloring blending factor for selection colors. The default value is 1.0 which corresponds to zero blending with the selection color being the one displayed. A value of 0.0 also corresponds to zero blending but with the underlying color being the one displayed. A value of 0.5 corresponds to even blending of the underlying color and the selected color.
() -> OESystem::OEColorThis function returns the default color for titles.
(OESystem::OEColor c)This function returns the default color for titles.
() -> boolReturns whether or not titles are drawn at the top of the scene or the bottom of the scene.
(bool top)Sets whether or not titles are drawn at the top of the scene or the bottom of the scene.
(OEKey , integer alpha)This function sets the transparency of the object associated with the specified key. The transparency is determined by the specified parameter alpha which corresponds to the desired alpha value of the object's color. Alpha can range from 0 (completely transparent) to 255 (completely opaque).
(integer alpha, integer scope)This function sets the transparency of all the objects in the specified scope. The transparency is determined by the specified parameter alpha which corresponds to the desired alpha value of the object's color. Alpha can range from 0 (completely transparent) to 255 (completely opaque).
()This function notifies the style widget that it should update itself due to changes that might affect its display.
(integer id) -> boolReturns whether or not reentrant grids are automatically contoured at the center of the scene.
(integer id, bool center) -> boolSets whether or not reentrant grids are automatically contoured at the center of the scene. If this is set to true, translating the center of the scene will cause the grids to be recontoured as the scene moves.
() -> boolReturns whether or not reentrant grids are automatically recontoured when the center of the scene is changed.
(float radius, float scale) -> boolSets the radius and scale parameters used in determining how to contour a reentrant grid around the center of the scene.
(bool autocontour)Sets whether or not reentrant grids are automatically recontoured when the center of the scene is changed.
(integer id) -> [float, ...]
(integer id, [float, ...] var2) -> [float, ...]
Returns the scene center position associated with the specified contour.
(integer id, integer index) -> OESystem::OEColorReturn the color of the grid contour specified by the grid id and contour index.
(integer index, integer scope) -> OESystem::OEColorReturns the color of the grid contours in the specified scope at contour index index. This color is determined by looking at the first contour found in the specified scope.
(integer id, integer index, OESystem::OEColor color) -> OESystem::OEColorFor grid id in scope set the color of contour index to color.
(integer index, OESystem::OEColor color, integer scope) -> OESystem::OEColorFor all grids in scope set the color of contour index to color.
(OEKey , OESystem::OEColor var2)This function sets the color of the contour associated with the specified key.
(OESystem::OEColor , integer scope)This function sets the color of the contours in the specified scope.
(integer id) -> integerReturns the number of contours for grid id.
(integer scope) -> intReturns 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.
(integer id)
(integer id, float threshold)
(integer id, float threshold, OESystem::OEColor color)
Create a new contour for grid id.
() -> integerThis function is obsolete and has been deprecated.
(integer id) -> integerThis function is obsolete and has been deprecated.
(integer id)Delete all contours for grid id.
(integer id, integer index)Delete contour index for grid id. All contours with indices greater than index will now be at their current index - 1.
(integer id, float threshold)Delete all contours abouve threshold for grid id.
Contour indices will be reassigned.
(integer id) -> boolReturns whether or not the contour should be drawn as a solid surface or as a mesh.
(integer id, bool draw) -> boolSets whether or not the contour should be drawn as a solid surface or as a mesh.
(bool draw, integer scope)Returns the style of contour drawing for the surfaces in scope.
See ContourDrawAsSurfaceGet.
Essentially returns the state of the first grid found in scope.
(integer id) -> stringIf "surface" the contours are drawn as a surface, otherwise the contour is drawn as a mesh.
(integer id, string var2)If set to "surface" the contours are drawn as a surface, otherwise the contour is drawn as a mesh.
(string , integer scope)Set the drawstyle to all contours in scope.
(integer id) -> boolReturns true if grid id is contoured over the whole grid.
Returns false if only the portion near the center of the scene is contoured.
(integer id, bool entire) -> boolIf true contour the entire extent of grid id, otherwise only contour the portion near the center of the drawing scene.
(integer id, integer vertex, bool maskVis) -> integerReserved for internal use.
(integer scope) -> [integer, ...]
(integer id) -> [float, ...]Get all contour levels from each contour drawn for grid id.
(integer index, bool hide)
(integer id, integer index, bool hide)
This function controls the visibility of the contour specified by the grid id and contour index. If the hide parameter is set to true, the contour is hidden, otherwise the contour is shown.
(integer id, integer index) -> boolThis function returns whether or not the contour specified by the grid id and contour index is hidden or not.
(integer index, bool hide)
(integer id, integer index, bool hide)
This function controls the visibility of the contour specified by the grid id and contour index. If the hide parameter is set to true, the contour is hidden, otherwise the contour is shown.
(integer id, integer index) -> floatReturns the contour level for grid id at index id.
(int index, integer scope) -> floatReturns the contour level for index id for the first grid in scope.
(integer id, integer index, float thresh) -> floatSet the level for the contour at index index to thresh for grid id.
(integer index, float thresh, integer gridType, integer scope)Set the level for the contour at index index to thresh for all grids in scope.
(bool increase, integer scope)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.
(float level, integer scope)This function sets the contour level of all the contours in the specified scope to the value specified by the parameter level.
(integer id) -> floatReturns the line width for drawing mesh contours.
(integer id, float rad) -> floatSet the line width to width for drawing mesh contours.
(integer oerid) -> floatReturns the maximum allowable contour threshold for grid id.
(integer scope) -> floatReturns the maximum allowable contour threshod for the first grid found in scope.
(integer oerid) -> floatReturns the minimum allowable contour threshold for grid id.
(integer scope) -> floatReturns the minimum allowable contour threshod for the first grid found in scope.
() -> boolReturns whether or not contours are selectable by picking.
(bool pickable)Sets whether or not contours are selectable by picking.
(integer id) -> floatReturns the radius used when generating contours for crystallographic grids.
(integer id, float rad) -> floatSets the radius used when generating contours for crystallographic grids.
(integer id) -> floatReturn the contouring resolution for drawing the contours in angstroms. A lower resolution samples more grid points, but requires more memory.
(integer id, float rad) -> floatSet the contouring resolution in angstroms. Lower values sample more grid points and generate finer visualizations but require more memory.
(OEKey , integer var2)Sets the transparency of the contour associated with the specified key. The transparency is determined by the alpha parameter which corresponds to the color alpha value which can range from 0 (completely transparent) to 255 (completely opaque).
(integer scope)Add a single contour to all grids of type type in scope.
(integer scope) -> intReturn the number of contours of all grids of type type in scope. This essentially returns the number of contours of the first grid found.
(integer scope) -> floatReturns the maximum allowable threshold for the first grid found of type type in scope.
(integer scope) -> floatReturns the minimum allowable threshold for the first grid found of type type in scope.
(integer scope)Remove the last contour from all grids of type type in scope.
(integer index, float thresh, integer scope)Set the contour level for the contour at index for all grids of type type in scope.
() -> boolReturns true if the contours are being drawn. Returns false if no contours are being drawn.
(bool draw) -> boolIf draw is true, then draw all contours for each visible grid. Otherwise no contours are drawn.
(OEKey k, bool property) -> integerCreate an electrostatis 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 seperate entity from id.
(OEKey k, float res) -> integerCreates a gaussian grid representation for the molecule associated with the specified key at the specified resolution.
(OEKey k, float res) -> integerCreates a gaussian product grid representation for the molecule associated with the specified key at the specified resolution.
(integer gridType, integer index) -> OESystem::OEColorReturns the default contour color for contour index for grids of type gridType.
(integer gridType, integer index, OESystem::OEColor color)Set the default contour color for contour index for grids of type gridType.
(integer gridType, integer index) -> floatReturns the default contour level for contour index for grids of type gridType.
(integer gridType, integer index, float thresh)Set the default contour level thresh for contour index for grids of type gridType.
(integer gridType) -> boolReturns the default drawing style for contours of grid with type gridType.
If true, then the surface is drawn as a solid surface, otherwise the surface is drawn as a mesh.
(integer gridType, bool asSurf)Set the default drawing style asSurf for contours of grid with type gridType.
If asSurf is true, then the surface is drawn as a solid surface, otherwise the surface is drawn as a mesh.
(integer gridType) -> integerReturns the default number of contours for grids of type gridType.
(integer gridType, integer count)Set the default number of contours for grids of type gridType to count.
(integer id, bool update)Initialize a grid to it's default contours, colors and levels.
(integer id) -> boolNormalizes a grid. This finds the sigma for the grid and divides all grid points by that value.
() -> boolReturns true if grid corners are being shown false if not.
Grid corners are indicators of the extent of visible grids. They are useful for displaying uncontoured grids and showing whether grid space and molecules intersect.
(bool show)Set show to true to show grid corners, false if not.
Grid corners are indicators of the extent of visible grids. They are useful for displaying uncontoured grids and showing whether grid space and molecules intersect.
(bool show) -> integerReserved for internal use.
(integer id) -> integerCreates a gaussian grid representation for the specified grid.
(integer oerid) -> integerReturns the type of grid for grid id.
(integer scope) -> integerReturns the type of grid for the first grid found in scope.
(integer id, integer gridType)Set the grid type of grid id to gridType.
(integer gridType, integer scope)Scoped version of GridTypeSet.
(integer scope) -> integerReturns 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.
(bool show, integer scope)If show is true, attach and show electrostatic grids to all molecules in scope.
If show if false, hide all attached electrostatic grids to molecules in scope.
() -> OESystem::OEColor
(OESystem::OEColor c)
() -> OESystem::OEColor
(OESystem::OEColor c)
() -> bool
(bool interactive)
() -> OESystem::OEColor
(OESystem::OEColor c)
() -> bool
(bool show)
(bool expand) -> string
(bool expand) -> string
()
()
()
()
(integer id)
(integer id)
() -> [integer, ...]
() -> [integer, ...]
(integer column)
(integer column)
()
()
()
()
() -> bool
() -> bool
() -> bool
() -> bool
() -> bool
() -> bool
() -> bool
() -> bool
(string fname) -> integer
(string fname) -> integer
() -> bool
(bool on)
([integer, ...] pos)
([integer, ...] pos)
(integer column)
(integer column)
() -> bool
() -> bool