Index of Rbq - Lua Interface Functions
207 total function(s)
last updated Tue Dec 14 16:06:01 2004
Function Categories
descrip
Adds a new atom type to the list of atom types used in the forcefield.
params
number iElement = element
number fVdwRadius = van der waals radius
number fCharge = electrical charge on atom
string sName = name of the new atom type
returns
number iNewAtomType = number of new atom type
or
nil if error
notes
Use rbq_SetForceObjProperty() to set the atom type of an atom to the newly-defined type.
seealso
rbq_SetForceObjProperty()
descrip
Adds a force object to a force group.
params
number iForceGroup = index of force group in custom force container
number iPdb = index of pdb in document
number iDynSeg = index of dynamic segment in pdb
number iRes = index of force object in dyn seg
returns
number bRet = 1
or
nil if error
notes
seealso
rbq_CreateForceGroup(), rbq_EnableCustomForceContainer()
descrip
Adds a menu item to the main window menu. Typically used in building submenus and commands in the Script menu.
params
QPopupMenu *pMenu ptr to the menu which will add the param item
string sMenuItemName name of item, as shown in menu
string sDescrip description of item, as shown in tooltip
string sCmd command to be executed when item is clicked
returns
number bRet = 1 or nil
notes
seealso
rbq_GetTopMenu(), rbq_AddSubmenu(), rbq_ClearScriptMenu()
descrip
Applies param force to param node of param force object at param position.
params
number iPdb = index of pdb in document
number iDynSeg = index of dynamic segment in pdb
number iRes = index of force object in dyn seg
number iNode = index of node in force object
numbers x, y, z = position of force application
nubers fx, fy, fz = components of force
returns
1 if success, else nil if error
notes
This function is used by scripts that apply 'driving forces' to influence a simulation. The script object should call this function from within the 'fiTick.lua' event script, so that the force will be properly applied during the forcefield timestep. If the position of application of force on the node is displaced from the node center-of-mass, the applied force will also produce a torque on the node.
seealso
rbq_AddNodeTorque()
descrip
Applies param toraue to param node of param force object at param position.
params
number iPdb = index of pdb in document
number iDynSeg = index of dynamic segment in pdb
number iRes = index of force object in dyn seg
number iNode = index of node in force object
nubers tx, ty, tz = components of torque
returns
1 if success, else nil if error
notes
This function is used by scripts that apply 'driving forces' to influence a simulation. The script object should call this function from within the 'fiTick.lua' event script, so that the torque will be properly applied during the forcefield timestep.
seealso
rbq_AddNodeForce()
descrip
Adds an inter-residue bond between a static residue and previous residue in chain.
params
number iPdb = index of pdb in document
number iChain = index of chain in pdb
number iRes = index of residue in chain
number iAtom = index of atom in residue
number jAtom = index of atom in previous residue
returns
number bRet = 1 if success, else nil if error
notes
The current implementation only creates inter-residue betweens between residues that are in a standard sequence direction. For nucleic acids, this means that the PDB sequence of residues corresponds to a 5' to 3' sequence. For proteins, this means the PDB sequence corresponds to an amino to carboxyl sequence of residues. This function can be used to create bonds between residues which are in a reversed sequence.
seealso
descrip
Adds a variable to the context of an executing script. The variable is persistent between intervals of execution of script code, such as the tick() function, which is called every idle cycle. The variable is accessed within script code through the lua functions setglobal() and getglobal().
params
string sScriptObjectName name of script object
string sVarName name of variable to be added
string sVal initial value of variable
returns
number bRet = 1 or nil
notes
If the script object is in a fail state, the variable will not be added and nil will always be returned. Currently, the name and value parameters must be non-zero in length.
seealso
rbq_CreateScriptObject(), rbq_SetScriptObjectVar(), rbq_GetScriptObjectVar(), rbq_IsScriptObjectFailStateSet(), lua functions setglobal(), getglobal()
descrip
Adds a line separator to a menu. This is used to separate groups of menu items.
params
QPopupMenu *pMenu
returns
number bRet = 1 or nil
notes
seealso
rbq_AddMenuItem(), rbq_AddSubmenu(), rbq_GetTopMenu(), rbq_ClearScriptMenu()
descrip
Creates a submenu in the param parent menu.
params
QPopupMenu *pParentMenu ptr to menu which adds the submenu
const char *szSubmenuName name of submenu, as shown in the parent menu
returns
userdata QPopupMenu *pSubmenu
notes
seealso
rbq_GetTopMenu()
descrip
Appends a PDB ATOM record to param file with param atom data.
params
string sFilename
number bHetAtom
number iAtomSerial
string sAtomName
string sResidueName
string sChainId
number iResidueSequenceNum
numbers x, y, z = atom position coordinates
returns
number bRet = 1
or
nil if error
notes
seealso
rbq_IsHetAtom(), rbq_GetAtomSerial(), rbq_GetAtomPdbName(), rbq_GetResidueName(), rbq_GetAtomPos()
descrip
Calculates the RMS difference between the backbone atoms of 2 pdb chains.
params
string sPdbChainI
string sPdbChainJ
returns
number fRet = RMS value
string sStatus
or
number fRet = -1
string sStatus if error
notes
The chains must belong to currently-loaded PDB models. The calculation can only be done if there is a sequence map file for the two chains, where the sequence file is located in the 'seq' subdirectory and named '<sPdbChainI>-<sPdbChainJ>.smap'.
The RMS difference is calculated as sqrt( sum( i = 1, i = N, (dist_iA_iB)^2 ) / N ) where N is the number of common backbone atoms in chains A and B and dist_ia_ib is the distance between the backbone atom i in chain A and backbone atom i in chain B.
seealso
descrip
Resets cumulative interaction counts in forcefield.
params
returns
notes
seealso
rbq_GetFfCumInteractionCount()
descrip
Deletes all dynamic menu items which have been added to the top-level script menu. This method is typically called prior to recreating the script submenu structure
params
returns
notes
seealso
CreateScriptMenu.lua
descrip
Closes a stream for detailed reporting of forcefield interactions.
params
returns
number bRet = 1 or 0
notes
seealso
rbq_OpenFfReportStream(), rbq_SetFfReportCondition()
descrip
Disables reporting of status by the command processor after execution of commands. The previous enable state is pushed onto a stack, allowing for nested calls of rbq_CmdStatusOff() and rbq_CmdStatusRestore().
params
returns
notes
If an error occurs at some point in script processing, command status is automatically reenabled.
seealso
rbq_CmdStatusRestore(), rbq_EnableCommandStatus(), rbq_IsCmdStatusEnabled()
descrip
Restores previous enable state of command status reporting by the command processor.
params
returns
notes
seealso
rbq_CmdStatusOff(), rbq_IsCmdStatusEnabled()
descrip
Adds a new force group to a custom force container.
params
number bMoveGroup = enables movement of the objects as a group
number bIntraGroupForceCalc = enables force calculations between objects in group
returns
number iForceGroup = index of created force group
or
nil if error
notes
The created group is empty. To add force objects to the group, call rbq_AddForceObjectToGroup(). If bIntraGroupForceCalc is true, then individual movement of the objects in the group will also be enabled.
seealso
rbq_AddForceObjectToGroup(), rbq_EnableCustomForceContainer()
descrip
Creates a persistent object which can execute user-defined code. The object is created and stored in a list of objects referred to as annotations. The object can execute drawing, idle processing and keyboard handling code as defined in lua script files located in a subdirectory associated with the object.
params
string sObjectName
number bTimeUser
[number bKeyboardUser]
returns
number bCreated = 1 or nil
notes
seealso
rbq_GetFreeGraphicObjectName(), rbq_AddScriptObjectVar(), CRbqScriptObject.
descrip
Returns number of seconds since the Epoch (1/1/1970).
params
returns
number iTimeInSeconds
notes
seealso
descrip
Deletes the named pdb object.
params
string sPdbName
returns
number bRet = 1 if success, else nil if error
string sStatus
notes
seealso
rbq_InsPdbFile()
descrip
Sets draw state of the backbone segments between residues for the current selection.
params
number iShow = 1 or 0
[number iEchoCmd = 1 or 0]
returns
number bRet = 1 or nil
notes
Probably should be renamed to 'rbq_SetDrawBackbone()' to avoid confusion with rbq_DrawXXX() functions.
seealso
rbq_DrawCovalent(), rbq_DrawSpacefill()
descrip
Draws param text as a bitmap at param position and color.
params
string sText
numbers x, y, z = starting position of text
numbers r, g, b = (red, green, blue) color vector (scalar range: [0 - 1])
returns
number bRet = 1
or
nil if error
notes
The text is drawn in a predefined font style and size. The font is mono-spaced. The text is drawn at a fixed orientation at the param location in 3D space, and its visibility is affected by the location of the current viewpoint. For the proper persistent display of the text, this function should be called from the draw event script of a script object.
seealso
rbq_DrawOrthoText()
descrip
Draws a block arrow.
params
numbers x0, y0, z0 = start point
numbers x1, y1, z1 = end point
numbers r, g, b = color
number t = thickness (-1 for auto-calc)
returns
number bRet = 1 or nil
notes
seealso
descrip
Draws a box with param size.
params
numbers w, h, d = size of box
returns
number bRet = 1 or nil
notes
The location used to draw the box must be previously defined using the functions rbq_SetDrawMatrix() or rbq_TranslateDrawMatrix(). The color to draw the box must be previously defined with rbq_SetDrawColor().
seealso
rbq_DrawBoxLc(), rbq_DrawCylinder(), rbq_DrawSphere(), rbq_DrawLine(), rbq_SetDrawMatrix(), rbq_SetDrawColor(), rbq_PushDrawMatrix(), rbq_PopDrawMatrix(), rbq_TranslateDrawMatrix(), rbq_RotateDrawMatrix()
descrip
Draws a box with param location, size and color.
params
numbers m00, ..., m015 = transform matrix of box location
numbers w, h, d = size of box
numbers r, g, b = color of box
returns
number bRet = 1 or nil
notes
seealso
rbq_DrawBox()
descrip
Sets draw state of the covalent bonds between atoms for the current selection.
params
int iShow = 1 or 0,
[int iEchoCmd = 1 or 0]
returns
number bRet = 1 or nil
notes
Probably should be renamed to 'rbq_SetDrawCovalent()' to avoid confusion with rbq_DrawXXX() functions.
seealso
rbq_DrawSpacefill(), rbq_DrawBackbone()
descrip
Draws the appearance of a covalent bond.
params
numbers xi, yi, zi = position of atom i
number iEl = element of atom i
numbers xj, yj, zj = position of atom j
number jEl = element of atom j
number fSize = radius of covalent bond
[numbers r, g, b = color of bond]
returns
number bRet = 1 or nil
notes
This function is typically used in annotations and schematic simulations that represent the making or breaking of covalent bonds. If the color parameters are not given, the bond halves will be drawn using the CPK of the atoms.
seealso
descrip
Draws a cylinder with param size.
params
number radius = radius
number height = height
returns
number bRet = 1 or nil
notes
The location and color used to draw the cylinder must be previously defined using the functions rbq_SetDrawMatrix() and rbq_SetDrawColor().
seealso
rbq_DrawCylinderLc(), rbq_DrawBox(), rbq_DrawSphere(), rbq_DrawLine(), rbq_SetDrawMatrix(), rbq_SetDrawColor(), rbq_PushDrawMatrix(), rbq_PopDrawMatrix(), rbq_TranslateDrawMatrix(), rbq_RotateDrawMatrix(),
descrip
Draws a cylinder with param location, size and color.
params
numbers m00, ..., m015 = transform matrix defining location
number radius = radius
number height = height
numbers r, g, b = color
returns
number bRet = 1 or nil
notes
The orientation of the cylinder when the transform is the identity matrix is with the base at the origin and the apex pointing down the +z axis.
seealso
descrip
Draws a line with param endpoints and color.
params
numbers x0, y0, z0 = starting point of line
numbers x1, y1, z1 = ending point of line
numbers r, g, b = color of line
returns
notes
seealso
rbq_DrawBoxLc(), rbq_DrawCylinderLc(), rbq_DrawSphereLc()
descrip
Draws a quadrilateral polygon in orthographic projection.
params
numbers v0x, v0y, v0z = upper-left corner
numbers v1x, v1y, v1z = lower-left corner
numbers v2x, v2y, v2z = lower-right corner
numbers v3x, v3y, v3z = upper-right corner
numbers r, g, b = color
number fTrans = transparency
returns
number bRet = 1 or nil
notes
This function can be used to draw a semi-transparent background that can serve as a 'billboard' for orthographic text. The coordinates { x, y, z } that define the boundaries of the quadrilateral are window pixel coordinates, where the upper-left corner begins at (0, 0). The positive x and y directions increase to the right and down. The z coordinate must be in the range (-2, -1].
If fTrans = 0, the quad is completely opaque. If fTrans = 1, the quad is completely transparent.
seealso
rbq_DrawOrthoText()
descrip
Draws param text as a bitmap text at param screen position and color.
params
string sText
numbers col, row = starting position of text
numbers r, g, b = (red, green, blue) color vector (scalar range: [0 - 1])
returns
number bRet = 1
or
nil if error
notes
Orthographic text is overlaid on the graphics window independently from the current view location and orientation. Col 0, Row 0 start in the upper-left corner of the screen. For the proper persistent display of the text, this function should be called from the draw event script of a script object.
seealso
rbq_DrawBitmapText(), rbq_DrawOrthoQuad()
descrip
Draws a quad polygon with param vertices.
params
numbers x, y, z = pt0
numbers x, y, z = pt1
numbers x, y, z = pt2
numbers x, y, z = pt3
returns
number bRet = 1 or nil
notes
The normal of the polygon should have been set with a prior call to rbq_SetGlNormal(). The vertices should have a positive winding order. The color of the polygon is determined by the most recent 'rbq_SetDrawColor()' call.
seealso
rbq_SetDrawColor(), rbq_SetGlNormal()
descrip
Sets draw state of the vdw boundary spheres for atoms for the current selection.
params
int iShow = 1 or 0
[int iEchoCmd = 1 or 0]
returns
number bRet = 1 or nil
notes
Probably should be renamed to 'rbq_SetDrawSpacefill()' to avoid confusion with rbq_DrawXXX() functions.
seealso
rbq_DrawCovalent(), rbq_DrawBackbone()
descrip
Draws a sphere at param position with param radius and param color.
params
number radius = radius
returns
number bRet = 1 or nil
notes
seealso
rbq_DrawSphereLc(), rbq_DrawCylinder(), rbq_DrawBox(), rbq_DrawLine(), rbq_SetDrawMatrix(), rbq_SetDrawColor(), rbq_PushDrawMatrix(), rbq_PopDrawMatrix(), rbq_TranslateDrawMatrix(), rbq_RotateDrawMatrix()
descrip
Draws a sphere at param position with param radius and param color.
params
numbers x, y, z = origin
number radius = radius
numbers r, g, b = color
returns
number bRet = 1 or nil
notes
seealso
rbq_DrawSphere(), rbq_DrawCylinder(), rbq_DrawBox(), rbq_DrawLine(), rbq_SetDrawMatrix(), rbq_SetDrawColor(), rbq_PushDrawMatrix(), rbq_PopDrawMatrix(), rbq_TranslateDrawMatrix(), rbq_RotateDrawMatrix()
descrip
Draws a wireframe arc with param endpoints and radius.
params
number fBegAngle = beginning angle of arc, in degrees
number fEndAngle = beginning angle of arc, in degrees
number fRadius = radius of arc
numbers xC, yC, zC = center point of arc
numbers vXx, vXy, vXz = +x axis in plane of arc
numbers vYx, vYy, vYz = +y axis in plane of arc
returns
number bRet = 1 or nil
notes
By default, the arc is drawn with normal pointing down the +z axis, located at the origin. fBegAngle should be positive and less than fEndAngle. To draw an arc in the opposite direction, reverse the look direction vector.
seealso
rbq_DrawCylinderLc(), rbq_DrawBox(), rbq_DrawSphere(), rbq_DrawLine(), rbq_SetDrawMatrix(), rbq_SetDrawColor(), rbq_PushDrawMatrix(), rbq_PopDrawMatrix(), rbq_TranslateDrawMatrix(), rbq_RotateDrawMatrix(),
descrip
Enables reporting of status by the command processor after execution of commands. This does not affect the stack of saved states used by rbq_CmdStatusOff() and rbq_CmdStatusRestore()
params
number iEnable
returns
notes
seealso
rbq_EnableCommandEcho()
descrip
Enables interactions of force objects in a custom force container.
params
number iEnable = 1 or 0
returns
notes
seealso
rbq_AddForceObjectToGroup(), rbq_CreateForceGroup()
descrip
Flag used to enable/disable drawing in the graphics window.
params
number iEnable = 1 or 0
returns
notes
seealso
descrip
Enables call of lua_error() on error in rbq lua api functions, terminating subsequent execution of lua code.
params
number iEnable = 1 or 0
returns
notes
seealso
rbq_IsLuaErrorEnabled()
descrip
Enables display of 'save current document' dialog on document closing. This flag is typically used in script automation to bypass the display of this dialog.
params
number iEnable = 1 or 0
returns
notes
seealso
rbq_IsSaveDocQueryEnabled()
descrip
Outputs the param text message to the application stderr (typically, a text widget).
params
string sMsg
returns
notes
seealso
rbq_StdOut()
descrip
Returns true if an annotation with the param name exists.
params
string sAnnName
returns
number iRet = 1 or nil
notes
seealso
descrip
Returns the full path to the base directory of the rbq application.
params
returns
string sDir
notes
The path uses unix separators ('/') and does not have a terminating separator.
seealso
descrip
Returns the element number for the param static atom, as specified by the param indices.
params
number iPdb
number iChain
number iRes
number iAtom
returns
number iEl
or
nil
notes
The return value is the atomic number of the element (H = 1, He = 2, etc.). If the element type for the atom is invalid, the value 0 (zero) will be returned. For dynamic atoms, use rbq_GetForceObjProperty().
seealso
rbq_GetAtomPos(), rbq_GetElementColor(), rbq_GetElementVdwRadius(), rbq_GetForceObjProperty()
descrip
Returns the full index from the param full atom name.
params
string sName = 'pdbName.chainId.resName.atomName'
returns
number iPdb
number iChain
number iRes
number iAtom
or
nil
notes
Dynamic atoms are also supported by this function.
seealso
rbq_GetAtomName(), rbq_GetPdbIndexFromName(), rbq_GetChainIndex(), rbq_GetResidueIndex(), rbq_GetObjectIndexFromName()
descrip
Returns the full dotted name of the static atom specified by the param indices.
params
number iPdb
number iChain
number iRes
number iAtom
returns
string sName
or
nil
notes
Example: if 1tra pdb is the first loaded static model then rbq_GetAtomName( 0, 0, 0, 0 ) should return '1tra.a.G1.OXT'. For dynamic atoms, use rbq_GetForceObjProperty().
seealso
rbq_GetAtomPdbName(), rbq_GetAtomIndex(), rbq_GetForceObjProperty()
descrip
Returns the string from the atom name field of the PDB ATOM record of the static atom specified by the param indices.
params
number iPdb
number iChain
number iRes
number iAtom
returns
string sName
or
nil
notes
This will be the full string from the PDB atom name field, including any spaces. Example: if 1tra pdb is the first loaded static model then rbq_GetAtomPdbName( 0, 0, 0, 0 ) should return ' OXT'.
seealso
rbq_GetAtomName(), rbq_GetAtomSerial()
descrip
Returns the position for the param static atom, as specified by the param indices.
params
number iPdb
number iChain
number iRes
number iAtom
returns
numbers x, y, z
or
nil
notes
For dynamic atoms, use rbq_GetForceObjProperty().
seealso
rbq_GetBackboneAtomPos(), rbq_GetAtomElement(), rbq_GetForceObjProperty()
descrip
Returns the PDB atom serial number for the param static atom, as specified by the param indices.
params
number iPdb
number iChain
number iRes
number iAtom
returns
number iAtomSerial
or
nil if invalid index
notes
The serial number is for an atom as originally read from an ATOM or HETATOM record in a PDB file.
seealso
rbq_GetAtomPdbName()
descrip
Returns a number that identifies the 'AtomType' of the static atom with param indices. This 'AtomType' value is used as a handle to associate certain chemical and forcefield properties with the atom. If an extended atom type has not been associated with this atom, its atom type number will be the same as its element atomic number.
params
number iPdb
number iChain
number iRes
number iAtom
returns
number iAtomType
or
nil if invalid index
notes
By default, the initial atom type of an atom is the atomic number of its element. Subsequently, the atom may be set to a more specific type of atom by assigning an atom type number to it. The atom type numbers begin after the atomic number of the final element that is defined in the program. For dynamic atoms, the atom type can be obtained with rbq_GetForceObjProperty().
seealso
rbq_SetAtomType(), rbq_GetAtomElement(), rbq_GetFirstAtomTypeId(), rbq_GetTotalAtomTypes(), rbq_GetAtomTypeVdwRadius(), rbq_GetForceObjProperty()
descrip
Returns the id of the atom type that is identified by the param name.
params
string sAtomTypeName
returns
int iAtomType = numerical id of atom type (first atom type id + ordinal position of atom type)
or
nil if error
notes
Atom types are used to define chemical properties of particular types of atoms. These are types that are more specific than just the element of the atom. For example, an atom type can refer to the valence-bond structure of an atom, such as 'Carbon_Sp3'.
Or, the atom type may be even more specific and refer to the properties of a particular atom within a particular biomolecular residue, such as 'Nitrogen_Arg_NH1'.
This function does not return the atom type id of an actual atom. Use rbq_GetAtomType() for that.
seealso
rbq_GetAtomTypeName(), rbq_GetFirstAtomTypeId(), rbq_GetTotalAtomTypes(), rbq_GetAtomType()
descrip
Returns the name for the param atom type.
params
int iAtomType = numerical id of atom type (first atom type id + ordinal position of atom type)
returns
string sName
or
nil if error (atom type value is not valid).
notes
The atom type names can be retrieved by calling rbq_GetAtomTypeName(). If the param type number is a numeric value corresponding to an element, nil will be returned.
seealso
rbq_SetAtomTypeVdwRadius(), rbq_GetElementVdwRadius(), rbq_GetAtomTypeName(), rbq_GetFirstAtomTypeId(), rbq_GetTotalAtomTypes()
descrip
Returns vdw radius for param atom type.
params
string sAtomTypeName
returns
number fRadius
or
nil if error
notes
The atom type names can be retrieved by calling rbq_GetAtomTypeName().
seealso
rbq_GetAtomTypeName(), rbq_SetAtomTypeVdwRadius(), rbq_GetElementVdwRadius(), rbq_GetTotalAtomTypes(), rbq_GetFirstAtomTypeId()
descrip
Returns the coordinate of the backbone atom of a residue. For an amino acid residue, this is the alpha-carbon atom. For a nucleic acid residue, it is the phosphate atom.
params
number iPdb
number iChain
nubmer iRes
returns
numbers x, y, z
or
nil if invalid param index
notes
seealso
rbq_GetAtomPos()
descrip
Returns the width and height, in pixels, of characters in the fixed-font bitmap text.
params
returns
number iWidth
number iHeight
notes
The height value includes the pixels for the full line-height of the row of characters.
seealso
rbq_DrawBitmapText(), rbq_DrawOrthoText()
descrip
Returns the 3D coordinates which represent the geometrical center of the param chain object. This is the center of the axial-aligned bounding box around the vdw radii of all the atoms in the pdb object.
params
number iPdb
number iChain
returns
numbers x, y, z
or
nil if invalid index
notes
seealso
rbq_GetPdbBoxCenter(), rbq_GetResidueBoxCenter(), rbq_GetObjectBoxCenter(), rbq_GetSelectionCenter()
descrip
Returns the PDB file COMPOUND description for the param chain.
params
number iPdb
number iChain
returns
string sChainDescrip
or
nil if error or not found
notes
seealso
rbq_GetChainName()
descrip
Returns the pdb and chain index of the named chain.
params
string sChainName (format: 'PdbName.ChainId')
returns
number iPdb
number iChain
or
nil if invalid name
notes
seealso
rbq_GetChainName(), rbq_GetPdbIndexFromName(), rbq_GetResidueIndex(), rbq_GetAtomIndex(), rbq_GetObjectIndexFromName()
descrip
Returns the 3D coordinates which represent the mass center of the param chain object. This is calculated from all the atoms in the chain.
params
number iPdb
number iChain
returns
numbers x, y, z
or
nil if invalid index.
notes
seealso
rbq_GetChainBoxCenter(), rbq_GetPdbMassCenter(), rbq_GetResidueMassCenter()
descrip
Returns the dotted name (PdbName.ChainId) for the chain specified by the param index.
params
number iPdb
number iChain
returns
string sName
or
nil if invalid index
notes
The param indices are 0-based.
seealso
rbq_GetChainIndexFromName(), rbq_GetChainDescrip(), rbq_GetPdbName(), rbq_GetResidueName()
descrip
Returns the cpk color for the param element.
params
number iElement
returns
numbers r, g, b
or
nil if invalid element
notes
seealso
rbq_GetAtomElement(), rbq_GetElementVdwRadius()
descrip
Returns the number of an element from param full element name.
params
string sName
returns
number iElement
notes
If a valid name is not specified, the number 0 is returned (invalid element). Example: when called with the name 'Hydrogen', the value '1' would be returned.
seealso
descrip
Returns the cpk color for the param element.
params
number iElement
returns
numbers fMass
or
nil if invalid element
notes
seealso
rbq_GetAtomElement(), rbq_GetElementVdwRadius()
descrip
Returns the vanderwaals radius for the param element.
params
number iElement
returns
numbers r, g, b
or
nil if invalid element
notes
seealso
rbq_GetAtomTypeVdwRadius(), rbq_GetAtomElement(), rbq_GetElementMass()
descrip
Returns name of param energy type, as used in reporting of energy totals.
params
number iType = { 0, ..., (iTotalTypes - 1) }
returns
string sType = { "steric", "torsion", "covalent", "electro", "hbond", "ringStack" }
or
number bRet = nil if invalid iType
notes
seealso
rbq_GetTotalEnergy(), rbq_GetTotalEnergyTypes()
descrip
Returns total number of interactions of param energy type that occurred since the cumulative counts were reset.
params
int iType = { 0, ..., iTotalEnergyTypes - 1 }
returns
number fCount
or
nil if error
notes
seealso
rbq_GetTotalEnergyTypes(), rbq_GetEnergyName(), rbq_GetTimestepInteractionCount(), rbq_ClearFfCumInteractionCounts()
descrip
Returns true if forcefield run state is enabled.
params
returns
number bRet = 1 or nil
notes
rbq_IsForcefieldRunning() is a duplicate of this function.
seealso
rbq_IsForcefieldRunning()
descrip
Returns a text string which describes the names and values of all forcefield parameters. Format is: ' \n' ...
params
returns
string sRet = concatenated lines of forcefield param name and value.
notes
Some forcefield context variables associated with statistical recording are not included.
seealso
descrip
Returns ith filename specified by a filespec.
params
string sFileSpec
number iFile
[number bExcludeDirs = 1]
returns
string sFileName
or
nil
notes
iFile index is 0-based. If bExcludeDirs is set, files that are directories will not be returned.
seealso
rbq_GetTotalFiles()
descrip
Returns the numerical id of the first atom type.
params
returns
number iFirstAtomType
notes
This can be used to enumerate the atom type names. The value of the first atom type is 1 greater than the atomic number of the final defined element.
seealso
rbq_GetTotalAtomTypes(), rbq_GetAtomTypeName(), rbq_GetTotalElements()
descrip
Returns the most recent rotation of param node of param force object.
params
number iPdb Index of pdb in document
number iDynSeg Index of dynamic segment in pdb
number iRes Index of force object in dyn seg
number iNode Index of node in force object
returns
numbers hmf[0] ... hmf[15]
or
number bRet = nil if error
notes
Recording of the node rotation must first be enabled by a call to rbq_SetForceObjProperty( "enableRecordNodeMove" ). If no rotation of the node has been recorded, the identity matrix is returned.
seealso
rbq_SetForceObjProperty(), rbq_GetForceObjectRecordedNodeTranslation()
descrip
Returns the most recent translation of param node of param force object.
params
number iPdb Index of pdb in document
number iDynSeg Index of dynamic segment in pdb
number iRes Index of force object in dyn seg
number iNode Index of node in force object
returns
numbers hmf[0] ... hmf[15]
or
number bRet = nil if error
notes
Recording of the node translation must first be enabled by a call to rbq_SetForceObjProperty( "enableRecordNodeMove" ). If no translation of the node has been recorded, the identity matrix is returned.
seealso
rbq_GetForceObjectRecordedNodeRotation(), rbq_SetForceObjProperty()
descrip
Returns the value of the param property of the param force object.
params
number iPdb = index of pdb in document
number iDynSeg = index of dynamic segment in pdb
number iRes = index of force object in dyn seg
string sProperty = property name and additional args if any
returns
string sPropertyValue
or
nil if error
notes
Currently, the large number of distinct properties of force objects are all accessed through a single pair of rbq-lua interface functions. To retrieve a particular property value, the following property names and arguments are used.
| Property name and arguments | Format of returned string | Description of returned property value |
|---|
| 'atomElement <iAtomInRes>' | iEl | element of atom |
| 'atomName <iAtomInRes>' | sAtomName | name of atom |
| 'atomPos <iAtomInRes>' | x y z | position of atom |
| 'atomOwnerNode <iAtomInRes>' | iNode | index of owner node of atom |
| 'atomType <iAtomInRes>' | iType | 'atom type' of atom |
| 'boxCenter' | x y z | box center of force object |
| 'hbAcceptAtomName <iAccept>' | sHbaAtomName | name of atom in hydrogen bond acceptor <iAccept> |
| 'hbAcceptAtomPos <iAccept>' | x y z | position of atom in hydrogen bond acceptor <iAccept> |
| 'hbAcceptElectronPos <iAccept>' | x y z | position of electron in hydrogen bond acceptor <iAccept> |
| 'hbAcceptMaxDonorPtr <iAccept>' | iPtr | memory ptr address of a hydrogen bond donor that most strongly interacts with hydrogen bond acceptor <iAccept> |
| 'hbAcceptMaxPotential <iAccept>' | fPot | potential energy of interaction wth hydrogen bond donor that most strongly interacts with hydrogen bond acceptor <iAccept> |
| 'hbAcceptPtr <iAccept>' | iPtr | memory ptr address of hydrogen bond acceptor <iAccept> |
| 'hbDonorAtomName <iDonor>' | sHbdAtomName | name of atom in hydrogen bond donor <iDonor> |
| 'hbDonorAtomPos <iDonor>' | x y z | position of atom in hydrogen bond donor <iDonor> |
| 'hbDonorHydroPos <iDonor>' | x y z | position of hydrogen in hydrogen bond donor <iDonor> |
| 'hbDonorPtr <iDonor>' | iPtr | memory ptr address of hydrogen bond donor <iDonor> |
| 'intraResBonds' | sAtomIdxs | pairs of atom indices for all intra-residue bonds within the force object |
| 'name' | sName | name of force object |
| 'nodeAngVelocity <iNode>' | x y z | angular velocity of node <iNode> |
| 'nodeChildren <iNode>' | sChildNodeIdxs | space-delimited string of indices of nodes that are direct children of node <iNode> |
| 'nodeCom <iNode>' | x y z | center of mass of node <iNode> |
| 'nodeForce <iNode>' | x y z | total force on node <iNode> |
| 'nodeFrame <iNode>' | hm00 ... hm15 | homogeneous transform matrix for node <iNode> |
| 'nodeParent <iNode>' | sParentNodeIdx | index of parent of node <iNode> if any, else -1 |
| 'nodeTorque <iNode>' | x y z | total torque of node <iNode> |
| 'nodeVelocity <iNode>' | x y z | velocity of node <iNode> |
| 'prevResBond' | sAtomIdxs | space-delimited string of indices of atom in this force object bonded to atom in previous force object, if any |
| 'selectedState' | bSel | selected state of force object (1 or 0) |
| 'nodeSelectedState <iNode>' | bNodeSel | selected state of node <iNode> (1 or 0) |
| 'totalAtoms' | iTotalAtoms | total atoms in force object |
| 'totalAtomsInNode <iNode>' | iTotalAtoms | total atoms in node <iNode> |
| 'totalHbAccepts' | iTotalAccepts | total hydrogen bond acceptors in force object |
| 'totalHbDonors' | iTotalDonors | total hydrogen bond donors in force object |
| 'totalNodes' | iTotalDonors | total nodes in force object |
seealso
rbq_SetForceObjProperty()
descrip
Returns a name which is not currently being used by any other graphic object. Typically, this is used for creating new script objects, which use a unique name as a handle for various operations.
params
[string sHint]
returns
string sName
notes
If a starting name is given as a hint, numerical prefixes are added to the starting name until a unused name is specified.
seealso
rbq_CreateScriptObject()
descrip
Returns a homogeneous transform matrix with a rotation created by the CGrTransformMatrix class.
params
number fDeg
numbers vx, vy, vz
numbers cx, cy, cz
returns
numbers hm00 ... hm15
notes
seealso
descrip
Returns width and height of graphics win, in pixels.
params
returns
number fWidth
number fHeight
notes
seealso
rbq_GetMainWinSize()
descrip
Creates a dialog box to receive a text string entered by the user.
params
string sPrompt = text in dialog window describing what input is desired
string sCaption = caption of dialog window
[string sDefaultInput = default value to appear in text box of dialog]
returns
string sRet
or
nil if user cancelled
notes
seealso
descrip
Creates a dialog box to receive a text string entered by the user, which specifies a 3 coordinate vector.
params
[string sPrompt]
returns
numbers x, y, z
or
nil if user cancelled or an error in conversion occurred.
notes
If conversion failed, an error message is output to app stderr.
seealso
descrip
Returns the ith inter-residue bond for the param residues.
params
number iPdb
number iChain
number iRes = index of a residue in iChain
number jRes = index of an adjacent residue in iChain
number iBond
returns
number iAtom = index of atom in iRes
number jAtom = index of atom in jRes
or
nil if invalid index or if iRes and jRes are not adjacent residues
notes
The bond is specified as a pair of indices to the atoms within the residues.
seealso
rbq_GetTotalInterResidueBonds(), rbq_GetIntraResidueBond()
descrip
Returns the ith intra-residue bond for the param residue.
params
number iPdb
number iChain
number iRes
number iBond = ith bond in iRes
returns
number iAtom = index of first atom in iBond
number jAtom = index of second atom in iBond
or
nil if invalid index
notes
The bond is specified as a pair of indices to the atoms within the residue.
seealso
rbq_GetTotalIntraResidueBonds(), rbq_GetInterResidueBond()
descrip
Returns the amount of free stack space in the lua scripting context.
params
returns
number iStackSpace
notes
A function call with an excessive number of parameters can cause the Lua stack to overflow.
seealso
descrip
Returns width and height of main window, in pixels.
params
returns
number iWidth
number iHeight
notes
This is the size of the entire window including the frame (non-client area). The actual enclosed client area will be a smaller size.
seealso
rbq_GetGraphicsWinSize()
descrip
Returns the current frame number of the movie.
params
returns
number iFrame
notes
seealso
descrip
Returns the current playback direction of the movie.
params
returns
number iPlaybackDir = 1 or -1
notes
seealso
descrip
Returns the bounding box center of the param object.
params
string sObjName
returns
numbers x, y, z
or
nil if invalid name
notes
Force objects not currently supported by this method, use rbq_GetForceObjProperty() instead.
seealso
rbq_GetObjectMassCenter(), rbq_GetObjectExtent()
descrip
Returns the index of the static or dynamic object from the param name.
params
string sObjName
returns
number bDynObj = 1 or 0
number iPdb
[number iChain or (iTotalStaticChains + iSeg)]
[number iRes or iDynRes]
[number iAtom or iDynAtom]
or
nil if object not found from name
notes
The number of arguments returned depends upon the type of object specified by the param name. Currently, the corollary of this function, to get the object name from index, is not defined. One of the more explict functions listed in the seealso section below must be used instead.
seealso
rbq_GetPdbIndex(), rbq_GetChainIndex(), rbq_GetResidueIndex(), rbq_GetAtomIndex() rbq_GetPdbName(), rbq_GetChainName(), rbq_GetResidueName(), rbq_GetForceObjProperty()
descrip
Returns the mass center of the param object.
params
string sObjName
returns
numbers x, y, z
or
nil if invalid name
notes
This function supports both static and dynamic objects.
seealso
rbq_GetObjectBoxCenter(), rbq_GetObjectExtent()
descrip
Returns the geometrical boundaries of the param object. These are the bounds of the axial-aligned bounding box around the vdw radii of all atoms in the object.
params
string sObjName
returns
numbers xMin, yMin, zMin, xMax, yMax, zMax
or
nil if invalid name
notes
seealso
rbq_GetObjectBoxCenter(), rbq_GetObjectMassCenter()
descrip
Returns the 3D coordinates which represent the geometrical center of the param pdb object. This is the center of the axial-aligned bounding box around the vdw radii of all the atoms in the pdb object.
params
number iPdb
returns
numbers x, y, z
or
nil if invalid index
notes
seealso
rbq_GetChainBoxCenter(), rbq_GetResidueBoxCenter(), rbq_GetSelectionCenter()
descrip
Returns the name of the file used to load the pdb object with the param index. The index refers to the position of the pdb object in the list of pdb objects loaded into the current document (0-based index).
params
number iPdb
returns
string sFileName
or
nil if invalid index.
notes
seealso
rbq_GetPdbName()
descrip
Returns the 3D coordinates which represent the center of mass of the param pdb object. This is calculated from all the atoms in the pdb object.
params
number iPdb
returns
numbers x, y, z
or
nil if invalid index
notes
seealso
rbq_GetPdbBoxCenter(), rbq_GetChainMassCenter(), rbq_GetResidueMassCenter(), rbq_GetSelectionMassCenter()
descrip
Returns the name of the pdb object with the param index. The index refers to the position of the pdb object in the list of pdb objects loaded into the current document (0-based index).
params
number iPdb
returns
string sName
or
nil if invalid index.
notes
seealso
rbq_SetPdbName(), rbq_GetPdbIndexFromName(), rbq_GetChainName(), rbq_GetResidueName(), rbq_GetPdbFileName()
descrip
Returns the 0-based index of the pdb object with the param name. The index refers to the position of the pdb object in the list of pdb objects loaded into the current document (0-based index).
params
string sName
returns
number iPdb or nil
notes
seealso
rbq_GetPdbName(), rbq_GetChainIndex(), rbq_GetResidueIndex(), rbq_GetAtomIndex(), rbq_GetObjectIndexFromName()
descrip
Returns the homogeneous transform matrix which represents the position of the param pdb object. The transform represents all accumulated translations and rotations which have been applied to the pdb object from its initial state as loaded from a PDB file.
params
number iPdb 0-based index of pdb object loaded into the current document
returns
number m0, m1, ... , m15
or
nil if invalid pdb index
notes
seealso
rbq_SetPdbTransformMatrix()
descrip
Returns the geometrical center of the residue specified by the param indices. The geometrical center is the center of the axial-aligned bounding box which contains vdw bounds of the residue atoms.
params
numbers iPdb, iChain, iRes
returns
numbers x, y, z
or
nil if invalid index
notes
seealso
rbq_GetResidueMassCenter()
descrip
Returns the center of mass of the residue specified by the param indices.
params
numbers iPdb, iChain, iRes
returns
numbers x, y, z
or
nil if invalid index.
notes
seealso
rbq_GetResidueBoxCenter(), rbq_GetPdbMassCenter(), rbq_GetChainMassCenter()
descrip
returns the color of the param residue.
params
number iPdb
number iChain
number iRes
returns
number r
number g
number b
notes
seealso
descrip
Returns the 0-based index of the residue with the param name.
params
string sFullResName (Pdb.Chain.Res)
returns
numbers iPdb, iChain, iRes
or
nil if invalid index.
notes
seealso
rbq_GetResidueName(), rbq_GetPdbIndexFromName(), rbq_GetChainIndex(), rbq_GetAtomIndex(), rbq_GetObjectIndexFromName()
descrip
Returns a list of residue names belonging to the param chain J which intersect the param residue I. The intersection is between the axial-aligned bounding boxes of the residues.
params
string sPdbChainResI : name of source pdb and chain (ex: '1ffk.0.A2602')
string sPdbChainJ : name of target pdb and chain (ex: '1tra.a')
number fResExtBound : distance beyond residue bounding boxes to check for intersection
returns
number bRet : 1 on success, else 0
string sResJList : " ..." (ex: "C69 G71 C72 C73 G74" )
string sStatus : error message on fail
notes
seealso
descrip
Returns the full name of the residue with the param index. The returned name consists of 3 components: the pdb object name, chain id and residue sequence name, separated by '.'. Example: (0, 0, 0) will return '1tra.a.G1' for 1tra.pdb loaded as the first pdb object in the document.
params
numbers iPdb, iChain, iRes
returns
string sName
or
nil if invalid index
notes
seealso
rbq_GetResidueIndex(), rbq_GetPdbName(), rbq_GetChainName(), rbq_GetAtomName()
descrip
Returns name of param script object.
params
number iScriptObject index of script object in document
returns
string sSoName name of script object
notes
seealso
rbq_GetTotalScriptObjects()
descrip
Returns the value of the param var of the param script object.
params
string sScriptObjName
string sVarName
returns
string sVal
or
number nil if invalid var name
notes
If the script object is in a fail state, nil will always be returned.
seealso
rbq_CreateScriptObject(), rbq_AddScriptObjectVar(), rbq_SetScriptObjectVar(), rbq_IsScriptObjectFailStateSet()
descrip
Returns the name of the script object var with param index.
params
string sScriptObjName
int iVarIndex
returns
string sName
or
number nil if invalid var index or script object name
notes
seealso
rbq_GetTotalScriptObjectVars()
descrip
Returns the 0-based indices of all fully selected pdb objects. The definition of a fully selected pdb is one that has all static chains selected, with all residues in each chain selected.
params
returns
[number iPdb0 [, iPdb1...]]
or
nil if no pdbs are selected
notes
seealso
rbq_GetSelectedChainIndex(), rbq_GetSelectedResidueIndex()
descrip
Returns the (iPdb, iChain) index of the ith selected chain. The ith selected chain is determined by iterating all selected static chains in all pdb objects.
params
number iSelChain
returns
number iPdb, iChain
or
nil if iSelChain not found
notes
A chain is considered selected only if all residues in the chain are fully-selected. Param and return indices are 0-based.
seealso
rbq_GetTotalSelectedChains(), rbq_GetSelectedPdbs(), rbq_GetSelectedResidueIndex()
descrip
Returns the (iPdb, iChain, iRes) index of the ith selected static residue. The ith selected residue is determined by iterating all selected residues in all pdb objects.
params
number iSelRes (0-based)
returns
numbers iPdb, iChain, iRes
or
number nil if iSelRes not found
notes
For dynamic residues, use rbq_GetForceObjProperty().
seealso
rbq_GetTotalSelectedResidues(), rbq_GetSelectedPdbs(), rbq_GetSelectedChainIndex(), rbq_GetSelectedResidueIndexes(),
descrip
Returns a set of residue indices for all selected static residues, up to the param total.
params
number iMaxResToReturn
returns
[number iPdb0, iChain0, iRes0 [, iPdb1, iChain1, iRes1, ...]]
notes
Because the lua stack is limited in size, returning indicies for a large selection could easily blow it out.
seealso
rbq_GetSelectedPdbs(), rbq_GetSelectedChainIndex(), rbq_GetSelectedResidueIndex()
descrip
Returns the geometrical center of the current selection. This is the center of the bounding box around the union of all selected objects.
params
returns
numbers x, y, z
notes
If there is no current selection, the origin point should be returned. The center of selection is the center-of-mass of all selected objects.
seealso
rbq_GetSelectionExtent(), rbq_GetObjectMassCenter()
descrip
Returns the color used for selected objects, if selection coloring is enabled.
params
returns
numbers r, g, b
notes
seealso
descrip
Returns the geometrical extent of the current selection. This is the extent of the bounding box around the union of all selected objects.
params
returns
numbers xMin, yMin, zMin, xMax, yMax, zMax
notes
If there is no current selection, a zero-extent will be returned.
seealso
rbq_GetSelectionCenter(), rbq_GetObjectExtent()
descrip
Returns value of current forcefield timestep
params
returns
number iCurTimestep
notes
This count is incremented each time a forcefield timestep is done. It is reset to 0 when a new document is opened.
seealso
descrip
Returns total number of interactions of param energy type that occurred in most recent timestep.
params
int iType = { 0, ..., iTotalEnergyTypes - 1 }
returns
number iCount
or
nil if error
notes
seealso
rbq_GetTotalEnergyTypes(), rbq_GetEnergyName(), rbq_GetFfCumInteractionCount()
descrip
Returns a ptr to the top-level menu in the application main window.
params
string sMenuName
returns
userdata QPopupMenu*
notes
seealso
rbq_AddSubmenu(), rbq_AddMenuItem()
descrip
Returns the total number of atoms in the param residue.
params
number iPdb
number iChain
number iRes
returns
number iTotalAtomsInResidue
or
nil if invalid param
notes
seealso
rbq_GetTotalResiduesInChain()
descrip
Returns the total number of atom types.
params
returns
number iTotalAtomTypes
notes
Atom types are used to extend the default properties of atoms as defined by their element type. If a PDB atom is present in a list of nucleic, metal or amino-acid atom types, it will be assigned user-customizable chemical parameters such as vdw radius and charge.
seealso
rbq_GetFirstAtomTypeId(), rbq_GetAtomTypeName(), rbq_GetTotalElements()
descrip
Returns total number of chains in param pdb object.
params
number iPdb
returns
number iTotalChains
or
nil if invalid param
notes
Param index is 0-based.
seealso
rbq_GetTotalPdbs(), rbq_GetTotalResiduesInChain()
descrip
Returns total number of dynamic segments in param pdb object.
params
number iPdb
returns
number iTotalDynamicSegments
or
nil if invalid param
notes
seealso
rbq_GetTotalForceObjectsInDynamicSegment()
descrip
Returns total number of defined elements.
params
returns
number iTotalElements
notes
This function is typically used for iterating elements in element property functions. The value of the first valid element is 1 (Hydrogen). Because the value 0 is reserved as representing an invalid element, the total number of elements is defined as 1 greater than the value of the final element. Therefore, the total number of elements can be thought of as the total number of actual defined element, plus 1, where the 'extra' element is the invalid element at the beginning of the enumeration. The enumeration of atom types begins after the value of the final element, so the value of the first atom type is also equal to the total number of defined elements.
seealso
rbq_GetElementMass(), rbq_GetElementVdwRadius(), rbq_GetFirstAtomTypeId(), rbq_GetTotalAtomTypes()
descrip
Returns total energy [of param type] from most recent timestep.
params
[string sType = { "steric", "torsion", "covalent", "electro", "hbond", "ringStack" }]
returns
number fTotal
or
nil
notes
If no type is specified, the total of all types is returned.
seealso
rbq_GetEnergyName()
descrip
Returns total number of energy types, as used in energy reporting.
params
returns
number iTotalTypes
notes
seealso
rbq_GetEnergyName(), rbq_GetTotalEnergy()
descrip
Returns total filenames specified by a filespec.
params
string sFileSpec
[number bExcludeDirs = 1]
returns
number iTotal
notes
If bExcludeDirs is set, files that are directories will not be counted.
seealso
rbq_GetFile()
descrip
Returns total number of force objects in param dynamic segment.
params
number iPdb
number iDynSeg
returns
number iTotalForceObjects
or
nil if invalid param
notes
seealso
rbq_GetTotalDynamicSegmentsInPdb()
descrip
Returns the total number of inter-residue bonds between the param residues. These are the covalent bonds between the atoms that link the adjacent residues.
params
number iPdb
number iChain
number iRes = index of a residue in iChain
number jRes = index of an adjacent residue in iChain
returns
number iTotalInterResBonds
or
nil if invalid index or if residues are not adjacent
notes
Indices are 0-based. Either the previous or the next residue index may be given first in the param list, the order does not matter.
seealso
rbq_GetTotalIntraResidueBonds(), rbq_GetInterResidueBond()
descrip
Returns the total number of intra-residue bonds within the param residue. These are the covalent bonds between the atoms within a single residue.
params
number iPdb
number iChain
number iRes
returns
number iTotalIntraResBonds
or
nil if invalid index
notes
The indices are 0-based.
seealso
rbq_GetTotalInterResidueBonds(), rbq_GetIntraResidueBond()
descrip
Returns total number of frames in the currently loaded movie.
params
returns
number iTotalFrames
notes
seealso
descrip
Returns total number of pdb objects loaded in current document.
params
returns
number iTotalPdbsInDocument
notes
seealso
rbq_GetTotalChainsInPdb(), rbq_GetTotalResiduesInChain()
descrip
Returns total number of residues in param chain of param pdb object.
params
numbers iPdb, iChain
returns
number iTotalResidues
or
nil if invalid param index
notes
Param indices are 0-based.
seealso
rbq_GetTotalPdbs(), rbq_GetTotalChainsInPdb(), rbq_GetTotalAtomsInResidue()
descrip
Returns the total number of script objects that currently exist.
params
returns
number iTotal
notes
seealso
rbq_GetScriptObjectName()
descrip
Returns the total number of variables for the script object with param name.
params
string sSoName = name of script object
returns
number iTotalVars
or
nil if script object not found
notes
This function can be used for iterating script object variables.
seealso
rbq_GetScriptObjectVarName()
descrip
Returns the total number of selected chains in the current document.
params
returns
number iTotalSelChains
notes
seealso
rbq_GetSelectedChainIndex(), rbq_GetTotalSelectedResidues()
descrip
Returns the total number of selected residue in the current document.
params
returns
number iTotalSelRes
notes
seealso
rbq_GetSelectedResidueIndex(), rbq_GetTotalSelectedChains()
descrip
Returns the coordinates of the center point of the current view, in world frame coordinates.
params
returns
numbers x, y, z
notes
seealso
rbq_GetViewUpDir(), rbq_GetViewLookDir(), rbq_GetViewRotCenter(), rbq_GetViewMatrix()
descrip
Returns the vector of the current view look direction, in world frame coordinates.
params
returns
numbers x, y, z
notes
seealso
rbq_GetViewUpDir(), rbq_GetViewCenter(), rbq_GetViewMatrix(), rbq_GetViewRotCenter()
descrip
Returns the homogeneous matrix of the current view.
params
returns
numbers m00, ..., m15
notes
seealso
rbq_GetViewCenter(), rbq_GetViewLookDir(), rbq_GetViewRotCenter(), rbq_GetViewUpDir()
descrip
Returns the coordinates of the current view rotation center, in world frame coordinates.
params
returns
numbers x, y, z
notes
This is the center point around which the view rotates.
seealso
rbq_GetViewCenter(), rbq_GetViewLookDir(), rbq_GetViewUpDir(), rbq_GetViewMatrix()
descrip
Returns the vector of the current view up direction, in world frame coordinates.
params
returns
numbers x, y, z
notes
seealso
rbq_GetViewLookDir(), rbq_GetViewCenter(), rbq_GetViewMatrix(), rbq_GetViewRotCenter()
descrip
Returns true if there is at least one currently selected object.
params
returns
number bHaveSel = 1 if selected
or
nil if no seleciton
notes
seealso
descrip
Submits the param command to the application command processor.
params
string sCommand
returns
number bProcessedOk: true or nil
notes
This is the script input equivalent to command input done by the user interactively through the command input dialog box. This function allows scripts to input all defined internal commands. The status after processing the command is output to the status window, unless it has been disabled by rbq_CmdStatusOff().
seealso
rbq_EnableCommandStatus(), rbq_EnableCommandEcho(), rbq_CmdStatusOff(), rbq_CmdStatusRestore(),
descrip
Inserts the param pdb file into the current document.
params
string sFile
[number iEchoCmd = 1]
returns
number bLoaded: true or nil
notes
seealso
rbq_OpenPdbFile(), rbq_DeletePdbObject()
descrip
Returns true if 'add-to-selection' mode is on. When this is on, the current selection is maintained as subsequent selection commands cause objects to be added to or removed from the current selection. When this mode is off, the current selection is cleared just prior to the execution of a new selection command.
params
returns
number bRet = 1 or nil
notes
seealso
descrip
Returns true if option to center view on newly-inserted object is set.
params
returns
number bRet = 1 or nil
notes
seealso
descrip
Returns true if the param chain has at least one element being drawn.
params
number iPdb, iChain
returns
number bVisible: true or nil
notes
seealso
descrip
Returns true if command processing status is being output to the status window.
params
returns
number bEnabled: 1 or nil
notes
seealso
descrip
Returns true if 'ff fo creatSingleAtomNodes' option is on.
params
returns
number bSet: 1 or nil
notes
seealso
descrip
Returns true if param file exists.
params
string sPath
returns
number bExists: true or nil
notes
File is considered to exist if file information for the param name was obtained in a call to the C runtime function _stat().
seealso
descrip
Returns true if log scaling of force display arrows is set.
params
returns
number bSet = 1 or nil
notes
seealso
descrip
Returns true if timestep movement in the forcefield is enabled.
params
returns
number bEnabled = 1 or nil
notes
seealso
descrip
Returns true if the forcefield is running.
params
returns
number bRunning = 1 or nil
notes
rbq_GetFfRunState() is a duplicate of this function.
seealso
rbq_GetFfRunState()
descrip
Returns true if the param force object has covalent bonds being drawn.
params
numbers iPdb, iSeg, iRes
returns
number bVisible: 1 or nil
notes
seealso
descrip
Returns true if param static PDB atom is from a HETATM record.
params
numbers iPdb, iChain, iRes, iAtom
returns
number 1 if het atom, else 0
or
nil if invalid index
notes
seealso
descrip
Returns true if call of lua_error() on error in rbq lua api functions is enabled.
params
returns
number bRet = 1 or nil
notes
seealso
rbq_EnableLuaError()
descrip
Returns true if movie is paused.
params
returns
number 1 or nil
notes
seealso
rbq_PauseMovie()
descrip
Returns true if movie is stopped.
params
returns
number 1 or nil
notes
seealso
descrip
Returns true if param residue is a nucleic acid residue.
params
numbers iPdb, iChain, iRes
returns
number 1 if nucleic, else 0
or
nil if invalid index
notes
Currently, only static model residues are supported. Currently, the criterion for being a nucleic residue is the existence of an atom in the residue with PDB name ' P ' or containing a '*' character in the name.
seealso
descrip
Returns true if param static residue is selected.
params
numbers iPdb, iChain, iRes
returns
number bRet = 1
or
number bRet = nil if error
notes
This function applies to static residues only. For dynamic residues, use rbq_GetForceObjProperty().
seealso
descrip
Returns true if display of 'save current document' dialog on document closing is enabled.
params
returns
number bRet = 1 or nil
notes
seealso
rbq_EnableSaveDocQuery()
descrip
Returns true if the fail state of the param script object is set.
params
string sScriptObjectName
returns
number bFail = 1
or
nil if fail state is not set or the script object is not found from param name.
notes
The fail state is set for a script object if an error occurs while running one of its event scripts, or if an error occurred in setting or getting its global variables. An error in running an event script is defined by a non-zero return value from the lua_dofile() function. See the Lua reference manual, section 5.8 for details. The user can also force such a non-zero return result by doing an explict call to error() in the script code.
seealso
descrip
Returns true if script object tick events are enabled.
params
returns
number bEnabled = 1 if enabled, else nil
notes
seealso
descrip
Display a message box dialog to the user.
params
string sMsg
string sCaption = "Message"
number iShowCancel
returns
number bRet = 1 if user hit Ok, else 0
notes
seealso
descrip
Opens a stream for detailed reporting of forcefield interactions.
params
returns
number bRet = 1 or 0
notes
seealso
rbq_SetFfReportCondition(), rbq_CloseFfReportStream()
descrip
Creates a new document and new pdb object from the param file.
params
string sFile
returns
number bLoaded: true or nil
notes
The current document will be closed prior to creating the new document. If changes have been made in the current document, a save dialog will appear prompting for user input.
seealso
rbq_InsPdbFile()
descrip
Sets pause state of movie.
params
number iPause = 1 or 0
returns
number bRet = 1 or nil
notes
seealso
rbq_IsMoviePaused()
descrip
Restores current model matrix from stack.
params
returns
notes
Used to restore the graphics state saved by an earlier call to rbq_PushDrawMatrix(). This function is typically called after various drawing functions such as rbq_TranslateDrawMatrix() have changed the graphics state. This function is just a wrapper for the OpenGL function glPopMatrix().
seealso
rbq_PushDrawMatrix(), rbq_TranslateDrawMatrix(), rbq_RotateDrawMatrix(), rbq_DrawBox(), rbq_DrawCylinder(), rbq_DrawSphere(), rbq_DrawLine()
descrip
Saves current model matrix on stack.
params
returns
notes
Used to save state for various drawing functions such as rbq_DrawBox(). This function is just a wrapper for the OpenGL function glPushMatrix().
seealso
rbq_PopDrawMatrix(), rbq_TranslateDrawMatrix(), rbq_RotateDrawMatrix(), rbq_DrawBox(), rbq_DrawCylinder(), rbq_DrawSphere(), rbq_DrawLine()
descrip
Increments the progress of a progress dialog by param percent.
params
number iInc
returns
notes
seealso
rbq_ProgressBar_Init(), rbq_ProgressBar_SetDone(), rbq_ProgressBar_WasCancelled()
descrip
Displays a progress dialog with param description. The initial progress is set to zero.
params
string sProgressDescrip
returns
notes
seealso
rbq_ProgressBar_IncPercentDone(), rbq_ProgressBar_SetDone(), rbq_ProgressBar_WasCancelled()
descrip
Completes and closes the currently displayed progress dialog.
params
returns
notes
seealso
rbq_ProgressBar_Init(), rbq_ProgressBar_IncPercentDone(), rbq_ProgressBar_WasCancelled()
descrip
Returns true if the user pressed the cancel button during display of the progress dialog.
params
returns
number 1 or nil
notes
seealso
rbq_ProgressBar_Init(), rbq_ProgressBar_IncPercentDone(), rbq_ProgressBar_SetDone()
descrip
Calls the tick event for the forcefield movie recorder.
params
returns
number bRet = 1 if a frame was recorded, else nil
notes
This is a way for recording movies independently of the forcefield timestep. The movie must currently be in the recording state for this function to have an effect. The condition that determines whether a frame will be played back as a result of this call depends on the current movie playback rate.
seealso
rbq_TickPlaybackMovie()
descrip
Sets redraw flag, indicating that redrawing in the graphics window is needed.
params
returns
notes
The redraw flag is checked every idle tick.
seealso
descrip
Rotates current drawing model matrix by param degrees about param vector.
params
number fDeg
numbers x, y, z
returns
number bRet = 1 or nil
notes
Used to set state for various drawing functions such as rbq_DrawBox(). This function is just a wrapper for the OpenGL function glRotatef().
seealso
rbq_TranslateDrawMatrix(), rbq_PushDrawMatrix(), rbq_PopDrawMatrix()
descrip
Rotates param force object about param vector around param point by param degrees.
params
numbers iPdb, iSeg, iRes = index of force object
number deg = degrees to rotate
numbers rx, ry, rz = vector about which rotation will be done (world frame).
numbers cx, cy, cz = center point around which rotation will be done (world frame).
returns
number bRet = 1 or nil if error
notes
seealso
rbq_TranslateForceObject(), rbq_RotateForceObjectNode(), rbq_TransformForceObject(), rbq_TransformForceObjectNode(), rbq_RotatePdb()
descrip
Rotates atoms of param force object around bond of param node by param degrees.
params
number iPdb = index of pdb in document
number iDynSeg = index of dynamic segment in pdb
number iRes = index of force object in dyn seg
number iNode = index of node in force object
number fDeg = degrees to rotate
number bFwdNodes = flag to indicate which side of node to rotate.
returns
number bRet = 1 or nil
notes
The direction flag determines whether upstream or downstream nodes are rotated in conjunction with the param node. The nodes of a force object are organized in a tree where each node may have a parent node and one or more child nodes. Upstream refers to ancestor nodes, downstream refers to descendant nodes. If the node is the very first node in the segment, then there is no parent node and no defined axis of rotation, therefore no rotation will be done for this root node.
The axis of rotation is the vector defined from the center-of-mass point of the param node to the center-of-mass point of the parent node. The center point of rotation is around the node center-of-mass point.
seealso
rbq_RotateForceObject(), rbq_TranslateForceObject(), rbq_TransformForceObject(), rbq_TransformForceObjectNode()
descrip
Rotates the param pdb by param degrees about the param vector around the param point.
params
number iPdb = index of pdb to rotate
number fDeg = degrees to rotate
numbers vx, vy, vz = vector about which rotation will be done (world frame).
numbers cx, cy, cz = center point around which rotation will be done (world frame).
returns
number bRet = 1
or
nil if invalid index
notes
seealso
rbq_TranslatePdb(), rbq_SetPdbTransformMatrix(), rbq_RotateForceObject()
descrip
params
number deg = degrees to rotate selection
numbers x, y, z = vector about which to rotate (world frame)
returns
number bRet = 1
or
number bRet = nil
string sStatus if error
notes
The center point of the rotation will be the center of the current selection. If there is a dynamic segment selection, it will be rotated. Else, the pdb model selection will be rotated, if fully selected. If there is no current selection, or only a partial static selection, no rotation will be done and nil will be returned.
seealso
rbq_RotateSelectionCen(), rbq_TranslateSelection()
descrip
params
number deg = degrees to rotate selection
numbers x, y, z = vector about which to rotate (world frame)
numbers xc, yc, zc = point around which to rotate (world frame)
returns
number bRet = 1
or
number bRet = nil
string sStatus if error
notes
If there is a dynamic segment selection, it will be rotated. Else, the pdb model selection will be rotated, if fully selected. If there is no current selection, or only a partial static selection, no rotation will be done and nil will be returned.
seealso
rbq_RotateSelection(), rbq_TranslateSelection()
descrip
Selects the param pdb object.
params
int iPdb
returns
number bSelected: true or nil
notes
seealso
descrip
Sets a vdw radius for param atom type.
params
string sAtomTypeName
number fRadius
returns
number bSet = 1
or
nil if error
notes
The atom type names can be retrieved by calling rbq_GetAtomTypeName().
seealso
rbq_GetAtomTypeVdwRadius(), rbq_GetElementVdwRadius(), rbq_GetAtomTypeName(), rbq_GetTotalAtomTypes()
descrip
Enables echoing of input command string to status window.
params
number iEnable = iEchoLevel = { 0 = none, 1 = console, 2 = menu, 3 = script, 4 = mouse, 5 = all }
returns
number bRet 1 or nil
notes
seealso
rbq_EnableCommandStatus()
descrip
Sets the value of the param var of the currently-executing script object, if any.
params
string sVarName
string sVarValue
returns
number bRet = 1 or nil
notes
This function provides support in script object event scripts to address the changed design of script object data access. This change involved the removal of 'implicit' saving of global data in the script object environment. This function makes it easier to explicitly save script object data, without needing to know the name of the currently-executing script object. If no current script object event script is running, nil will be returned. If the param var does not exist for the current script object, nil will be returned. If the script object is in a fail state, no value will be set and nil will always be returned. Currently, the name and value parameters must be non-zero in length.
seealso
rbq_SetScriptObjectVar(),
descrip
Sets param color as current drawing color.
params
numbers r, g, b
returns
number bRet = 1
or
nil if invalid param count
notes
Used to set graphics state for various drawing functions such as rbq_DrawBox(). This function is just a wrapper for the OpenGL function glColor3fv().
seealso
rbq_DrawBox(), rbq_DrawCylinder(), rbq_DrawSphere(), rbq_SetDrawMatrix()
descrip
Sets param matrix as current drawing model matrix.
params
numbers m00, ..., m15 = coordinates of homogeneous model matrix
returns
number bRet = 1 or nil if invalid param count
notes
Used to set state for various drawing functions such as rbq_DrawBox(). This function is just a wrapper for the OpenGL function glMultMatrixf().
seealso
rbq_SetDrawColor(), rbq_PushDrawMatrix(), rbq_PopDrawMatrix(), rbq_TranslateDrawMatrix(), rbq_RotateDrawMatrix()
descrip
Sets the current normal direction used for drawing polygons.
params
numbers x, y, z
returns
number bRet = 1 or nil if invalid param count
notes
Used to set graphics state for various drawing functions such as rbq_DrawQuad(). This function is just a wrapper for the OpenGL function glNormal3fv().
seealso
rbq_DrawQuad(), rbq_SetDrawColor()
descrip
Sets the param frame number as the current frame of the currently loaded movie.
params
number iFrame
returns
number bRet = 1 or nil
notes
seealso
rbq_GetMovieFrame()
descrip
Closes a stream for detailed reporting of forcefield interactions.
params
string sForceType = { "steric" }
numbers iPdb, iSeg, iRes index of 1st force object
numbers jPdb, jSeg, jRes index of 2nd force object
returns
number bRet = 1
or
nil if error
notes
seealso
rbq_OpenFfReportStream(), rbq_CloseFfReportStream()
descrip
Sets the value of the param property of the param force object.
params
number iPdb = index of pdb in document
number iDynSeg = index of dynamic segment in pdb
number iRes = index of force object in dyn seg
string sPropertyAndVal = property name and additional args if any
returns
number bRet = 1 or nil if error
notes
Currently, the large number of distinct properties of force objects are all accessed through a single pair of rbq-lua interface functions. To set a particular property value, the following property names and arguments are used.
| Property name and arguments | Description of set property value |
|---|
| 'enableExternalForceCalc <iEnable>' | enables interaction with other force objects |
| 'enableInternalForceCalc <iEnable>' | enables internal force interactions betwen atoms of this force object |
| 'enableNodeMove <iNode> <iEnable>' | enables timestep movement of node <iNode> |
| 'enableRecordNodeMove <iNode> <iEnable>' | enables recording of movement of <iNode> |
| 'setAtomType <iAtom> <iAtomType>' | sets the atom type number of <iAtom> |
| 'setNodeVelocity <iNode> <vx vy vz>' | sets velocity of <iNode> |
| 'setNodeAngVelocity <iNode> <vx vy vz>' | sets angular velocity of <iNode> |
seealso
rbq_GetForceObjProperty()
descrip
params
number iDir = 1 or -1
returns
nubmer bRet = 1 or nil
notes
seealso
rbq_GetMoviePlaybackDir()
descrip
Sets the name of the pdb object with the param index. The index refers to the position of the pdb object in the list of pdb objects loaded into the current document (0-based index).
params
number iPdb
string sName
returns
number bRet = 1
or
nil if error
notes
The name cannot contain the characters {' ', '.', '-' }
seealso
rbq_GetPdbName()
descrip
Sets the 4x4 homogeneous transform matrix of the param pdb object. This is used to adjust the position and orientation of a pdb object relative to its initial one as loaded from the PDB file.
params
number iPdb
numbers m0, ... , m15
returns
nubmer bRet = 1 or nil
notes
seealso
rbq_GetPdbTransformMatrix(), rbq_RotatePdb(), rbq_TranslatePdb()
descrip
Sets the color of the param residue.
params
numbers iPdb, iChain, iRes
numbers fRed, fGreen, fBlue
returns
number bRet = 1 or nil
notes
seealso
descrip
Sets the value of the param var of the param script object.
params
string sScriptObjName
string sVarName
string sVarValue
returns
number bRet = 1 or nil
notes
If the script object is in a fail state, no value will be set and nil will always be returned. Currently, the name and value parameters must be non-zero in length.
seealso
rbq_CreateScriptObject(), rbq_AddScriptObjectVar(), rbq_GetScriptObjectVar(), rbq_IsScriptObjectFailStateSet()
descrip
Sets the draw state of the annotation with the param name.
params
string sAnnotationName
number iShow (0 = hide, 1 = show, 2 = toggle)
returns
number bRet = 1 on success
or
number nil
string sStatus
notes
seealso
descrip
Sets the cursor to a wait indicator (hourglass) or a normal indicator.
params
number iShow (0 = show normal, 1 = show wait)
returns
notes
seealso
descrip
Spawns an external process as specified by a cmd line string.
params
string sCmdLine (args separated by whitespace)
string sWorkingDir
number bWait = 1 or 0
returns
number iRet = exit status (if wait ) or process handle (if no wait)
or
number nil, string sStatus if error
notes
spawnvp() is used, so the PATH environmental variable will be used to search for the command to execute.
seealso
rbq_TerminateProcess()
descrip
Outputs param string to the application status window.
params
string sMsg
returns
notes
seealso
rbq_ErrOut()
descrip
Does immediate timestep of the forcefield (independently of the event-driven stepping).
params
returns
number bRet = 1
or
number bRet = nil if an error occurred during the forcefield timestep.
notes
seealso
descrip
Terminates the param process
params
number iProcessHandle
returns
number bRet = 1
or
number nil
notes
seealso
rbq_SpawnProcess()
descrip
Pre-multiplies the param homogeneous transform matrix to the param force object.
params
numbers iPdb, iSeg, iRes = index of force object
numbers hmf00, ..., hmf15 = homogeneous transform matrix.
returns
number bRet = 1 or nil if error
notes
The positions of the atoms in the force object are automatically updated in this function after the param transform is applied. This function is equivalent to calling rbq_TransformForceObjectNode() for all nodes and then calling rbq_UpdateAtomPositions().
seealso
rbq_TransformForceObjectNode(), rbq_RotateForceObject(), rbq_TranslateForceObject(), rbq_RotateForceObjectNode()
descrip
Pre-multiplies the param homogeneous transform matrix to the param node of the param force object.
params
numbers iPdb, iSeg, iRes, iNode = index of force object node
numbers hmf00, ..., hmf15 = homogeneous transform matrix.
returns
number bRet = 1 or nil
notes
The caller must subsequently call rbq_UpdateForceObjectAtomPositions() to update the node atoms with the new transform.
seealso
rbq_UpdateForceObjectAtomPositions(), rbq_RotateForceObjectNode(), rbq_TransformForceObject(), rbq_RotateForceObject(), rbq_TranslateForceObject()
descrip
Translates current drawing model matrix by param vector.
params
numbers x, y, z
returns
number bRet = 1 or nil
notes
Used to set state for various drawing functions such as rbq_DrawBox(). This function is just a wrapper for the OpenGL function glTranslatef().
seealso
rbq_RotateDrawMatrix(), rbq_PushDrawMatrix(), rbq_PopDrawMatrix()
descrip
Translates param force object by param vector.
params
numbers iPdb, iSeg, iRes = index of force object
numbers tx, ty, tz = vector by which force object is translated (world frame).
returns
number bRet = 1 or nil if error
notes
seealso
rbq_RotateForceObject(), rbq_TransformForceObject(), rbq_TranslatePdb()
descrip
Translates the param pdb by the param vector.
params
number iPdb
numbers x, y, z
returns
number bRet = 1
or
nil if invalid index
notes
seealso
rbq_RotatePdb(), rbq_SetPdbTransformMatrix(), rbq_TranslateForceObject()
descrip
Translates the current selection by the param vector.
params
numbers x, y, z
returns
number bRet = 1 on success
or
number nil
string sStatus if error
notes
If there is a dynamic segment selection, it will be translated. Else, the pdb model selection will be translated, if fully selected. If there is no current selection, or only a partial static selection, no rotation will be done and nil will be returned.
seealso
rbq_RotateSelection(), rbq_RotateSelectionCen()
descrip
Updates all atoms in param force object with positions defined by the force object node frames.
params
numbers iPdb, iSeg, iRes = index of force object
returns
number bRet = 1
or
nil if invalid index
notes
After calling rbq_TransformForceObjectNode(), the caller must subsequently call rbq_UpdateForceObjectAtomPositions() to update the positions of the node atoms with the new transform.
seealso
rbq_TransformForceObjectNode()
descrip
Spawns a MS Windows process as specified by cmd line and show state.
params
string sCmdLine (args separated by whitespace)
number iShow (0 = minimized, 1 = normal, 2 = maximized)
returns
number bRet = 1 on success
or
nil
notes
Hack for demo! (couldn't set show state with rbq_SpawnProcess).
seealso