Scoring based on chemical shift ranges.
bioppmscore add
bioppmscore clear
bioppmscore fragscore
bioppmscore get
bioppmscore score
bioppmscore add resName atomName shiftAvg shiftSDev
Add an atom type to the internal library specifying the average shift and standard deviation range for the chemical shift of that type of atom. This command is normally used when NMRViewJ starts up to input values from a database of shifts from the BMRB.
bioppmscore clear
Clear the internal database of atom type shifts.
bioppmscore fragscore scoreLimit dataList residueList
This command works the same as the "bioppmscore score" command, but takes a list of data values and residues and returns a list of scores for each residue in the list. If a given residue score is below the scoreLimit a "-" character will be present at that position in the score list.
bioppmscore get ?resName atomName ??
Without any arguments this returns a list of the residue names that are currently in the shift database.
bioppmscore score scoreLimit atomName atomPPM ?atomName2 atomPPM2 ...?
Returns a list of residue names and scores based on the specified list of atom names and chemical shifts. The score is calculated based on the average value and standard deviation of the chemical shifts for each residue and atom in the internal database. The score value is a Chi Square based probability value that ranges from 0.0 to 1.0 with higher values indicating a higher probability of the residue type being consistent with the specified chemical shifts.
Multidimensional clustering of a list of data values.
Clusters the specified values. The result consists of two lists. The second list is a list of the positions of the "prototypes" (the center position of each cluster). The first list consists of a pair of values for each input value. The first member of the pair is the cluster (index of the prototypes 0, 1 ...) to which the pair belongs. The second member of the pair is the index of the original value as input to the command.
export ?-mode modeType ?-fileName fileName?? windowName
Export a graphical representation of the specified window into a file. If no optional arguments are specified then a dialog will appear in which the file format can be selected and a file name entered. If a mode is specified without the fileName the file will be named export.mode (i.e. export.png or export.ps). Currently supported vector modes are ps, pdf, svg and emf. Bitmap modes are gif, jpg, png, and bmp.
Read MMCIF files.
mmcif close
mmcif comp_atoms
mmcif comp_bonds
mmcif mmcifxyz
mmcif next
mmcif open
mmcif put
mmcif close
Not yet documented
mmcif comp_atoms
Not yet documented
mmcif comp_bonds
Not yet documented
mmcif mmcifxyz
Not yet documented
mmcif next
Not yet documented
mmcif open
Not yet documented
mmcif put
Not yet documented
Interact with molecular structures.
mol add
mol atoms
mol calcbonds
mol calcRMSD
mol canonname
mol center
mol color
mol colortype
mol coordsets
mol displaytype
mol distance
mol draw
mol entities
mol equiv
mol gencoord
mol getcenter
mol labeltype
mol lines
mol list
mol listatoms
mol listbonds
mol listresidues
mol molname
mol negshapetype
mol new
mol nstructures
mol points
mol posshapetype
mol radius
mol remove
mol selcyclecount
mol select
mol serial
mol setatomprop
mol setbondprop
mol setbonds
mol site
mol smiles
mol structures
mol tablemodel
mol tree
mol unselect
mol add molName compound | water | polymer | name
Adds a new entity of the specified type and with the specified name to the specified molecule.
mol atoms molName
Return a list of all atoms in the specified molecule.
mol calcbonds molName
This command adds bonds between any pairs of atoms that are currently selected and whose inter-atom distance is less than 1.8 Angstroms.
mol calcRMSD molName
Calculates the rms position across multiple structure models for each atom in the specified molecule. The calculated rms is stored in the "bFactor" field for each atom (and can be queried with the "nv_atom elem bfactor atomSpecifier" command).
mol canonname molName
Rename the atoms in a molecule so that they canonical names. That is, names that will be the same no matter what order the atoms or their bonds were input in. The algorithm used does not conform to any standard.
mol center molName ?structureNum?
Centers the coordinates of the molecule so that the average x, y and z positions are 0.0. If the optional structureNum argument is included then only the coordinates for the specified structure (model) will be centered.
mol color atoms | bonds | red green blue
Set the display color for selected atoms or bonds to the specified values. The red, green and blue values are to be specified as floating point numbers between 0.0 and 1.0.
mol colortype
Not yet documented
mol coordsets molName
Return a list of the names of all the coordinate sets in the specified molecule. In the terminology of NMRViewJ, a coordset is essentially the equivalent of an "assymetric unit" in crystallographic terminology.
mol displaytype
Sets the type of display to be used when displaying molecules. With no arguments the command returns a list of acceptable types. Currently the list is: "none wire hwire bwire ball pball cpk"
mol distance molFilter1 molFilter2
Returns the distance between the atom(s) selected with molFilter1 and the atom(s) selected with molFilter2. If the filters match more than one atom then the distance between the average position of each set of atoms is used.
mol draw
unused
mol entities molName
Return a list of the names of all entities (polymers, ligands etc.) in the specified molecule.
mol equiv atomSpecifier
Return a list describing atoms that are chemically? equivalent to this one.
mol gencoord molName
Generate 3D coordinates from internal coordinates (bond lengths, bond angles and dihedral angles).
mol getcenter molName ?structureNum?
Returns, as a three element list, the coordinates of the average position of all atoms in the specified molecule. If the optional structureNum parameter is included then only the coordinates of that structure (model) are used.
mol labeltype ?molName type?
Sets the type of label to be used when displaying molecules. With no arguments the command returns a list of acceptable types. Currently the list is: "none label fc symbol number both ffc ss residue charge value title mname string bond custom name ppm"
mol lines molName
Returns a list of coordinates representing 3D lines between all bonds with the DISPLAY property set.
mol list
Return a list of all molecules currently in memory.
mol listatoms ?molName display?
Returns a list of all currently selected atoms. With the optional arguments returns a list of all atoms in the specified molecule that have their DISPLAY property set.
mol listbonds molName
Returns a list of all currently selected bonds in the specified molecule.
mol listresidues molName entity
Return a list of residues in the indicated entity of the indicated molecule. The list consists of alternating residue numbers and residue names: "1 GLY 2 ARG 3 TYR ..."
mol molname molName?
Returns the name of the currently active molecule. If the optional argument is included sets the currently active molecule to the one named.
mol negshapetype molName type?
The molecular display of atoms can be done with a shape based on the state of some molecular property. This command gets, or sets, the type of shape to be used when the property is positive. Current shape types are a circle, square or triangle.
mol new molName
Create a new molecule with the specified name. If a molecule with this name already exists an error will be thrown.
mol nstructures molName
Each molecule can multiple structure sets (models) associated with it. This command returns the number of structures.
mol points
Not yet documented
mol posshapetype molName type?
The molecular display of atoms can be done with a shape based on the state of some molecular property. This command gets, or sets, the type of shape to be used when the property is positive. Current shape types are a circle, square or triangle.
mol radius atoms | bonds | radius
Set the display radius for selected atoms or bonds to the specified value.
mol remove all | molName1 | molName2...
Remove the specified molecules. If the literal word "all" is used then all molecules are removed.
mol selcyclecount
Not yet documented
mol select atoms ?-inverse ?-append? molFilter bonds mode residues mode
Mark atoms, bonds or residues in the current molecule as selected. Selected items will be used in subsequent operations such as setting colors and other properties or listing selected items.
Selecting residues, at present, requires first selecting atoms. Then the "mol select residues atom" command will select all atoms in any residues that currently have selected atoms. The mode argument is currently required, but the actual value is ignored.
mol serial molName fileName
Serialize the Java object representing the molecule and write to the specified file. Expert use only.
mol setatomprop molName propertyNum 0 | 1 |
Each atom can have a set of boolean properties associated with it. This command sets the state of the property (at present specified with an integer value, 0, 1...,15) for any selected atoms.
mol setbondprop molName propertyNum 0 | 1 |
Each bond can have a set of boolean properties associated with it. This command sets the state of the property (at present specified with an integer value, 0, 1...) for any selected bonds. In the current implementation the only property available is the DISPLAY property and the propertyNum value is ignored.
mol setbonds
unused
mol site set siteName | get | siteName | within | siteName tolerance
Sets of atoms can be grouped as sites within the molecule. With the "set" option all currently selected atoms are stored in a site list with the specified name. The get option selects all atoms within the named site and returns the number of selected atoms. The within option sets the selected atoms to be all atoms that are both currently selected and within tolerance distance of any atom in the named site.
mol smiles newMolName smilesString
Generates a molecule from the specified SMILES string. Only available in dataChord (not NMRViewJ).
mol structures molName ?active | | select args?
Each molecule can multiple structure sets (models) associated with it. This command allows the user to select particular sets to be used for actions such as superimposing the structures. If the optional argument active or select are not used this command returns a list of the integer numbers corresponding to each structure set in the molecule. With the "active" argument the command returns a list of currently selected structures. The "select" argument can be used with a list of selections to select or deselect specific structures. The args are a series of structure numbers or the wildcard character "*" interspersed with optional "+" or "-" characters. Any structure numbers occuring after a "+" character will be selected. Any structure numbers occuring after a "-" character will be deseelcted. For example, *mol select molName select + - **3 would select all structures but structure 3.
mol tablemodel
The list of atoms can be displayed in a Swank table. This updates any tables to use the currently active model in their display.
mol tree atomName t | p | a |
Operations on molecule as a "tree" structure. Only available in dataChord.
mol unselect ?last? | | all
With no parameters or the literal word "last", the last atom that was selected is unselected. With the literal word "all" then all atoms are unselected.
Query and set atom-based values for current molecule.
nv_atom add
nv_atom coords
nv_atom elem
nv_atom num
nv_atom remove
nv_atom add atomSpecifier newName newElement bondOrder
Add an atom to the molecule bonded to the specified atom. Doesn't currently set up proper parent/child relationships.
nv_atom coords
Returns a list of coordinate values for the atom in the following format:
If more than one structure (model) is available for the model the "structureNum x y z" values will be repeated for each structure.
nv_atom elem elemName atomNum [value]
Returns the value of 'elemName' for 'atomNum'. If the optional argument is included the command sets the element to the value specified. The valid values for 'elemName' are:
Chemical Shift Ambiguity Index Value Definitions
| Index Value | Definition |
|---|---|
| 1 | Unique (geminal atoms and geminal methyl groups with identical chemical shifts are assumed to be assigned to stereospecific atoms) |
| 2 | Ambiguity of geminal atoms or geminal methyl proton groups |
| 3 | Aromatic atoms on opposite sides of symmetrical rings (e.g. Tyr HE1 and HE2 protons |
| 4 | Intraresidue ambiguities (e.g. Lys HG and HD protons or Trp HZ2 and HZ3 protons) |
| 5 | Interresidue ambiguities (Lys 12 vs. Lys 27) |
| 9 | Ambiguous, specific ambiguity not defined |
nv_atom num atomSpecifier
Returns 1 or -1 depending on whether the specified exists (1) or doesn't exist (-1).
nv_atom remove atomSpecifier
Remove the specified atom.
Analyze NMR datasets
nv_dataset analyze
nv_dataset blkheadersize
nv_dataset blksize
nv_dataset close
nv_dataset complex
nv_dataset compress
nv_dataset create
nv_dataset datatype
nv_dataset dims
nv_dataset fileheadersize
nv_dataset flush
nv_dataset freqdomain
nv_dataset get
nv_dataset hpick
nv_dataset label
nv_dataset littleendian
nv_dataset lvl
nv_dataset name
nv_dataset ndim
nv_dataset negcolor
nv_dataset nucleus
nv_dataset open
nv_dataset parsync
nv_dataset path
nv_dataset peakpick
nv_dataset poscolor
nv_dataset posneg
nv_dataset ppm2pt
nv_dataset property
nv_dataset pt2ppm
nv_dataset put
nv_dataset rdims
nv_dataset readpoint
nv_dataset ref
nv_dataset refpt
nv_dataset refunits
nv_dataset rename
nv_dataset rename
nv_dataset scale
nv_dataset scanget
nv_dataset scanput
nv_dataset scanstart
nv_dataset sf
nv_dataset size
nv_dataset solvent
nv_dataset sw
nv_dataset title
nv_dataset vector
nv_dataset wrhead
nv_dataset writable
nv_dataset analyze datasetName [-d1 dimRange] [-d2 dimRange] ...
Analyzes the data in the specified region of the spectrum 'spectrumName'.
The elements of the list or Tcl variable are described below:
| Element | Description |
|---|---|
| volume | the sum of the points in the region. |
| evolume | the sum of the points in an elliptical region around the center of the peak. The width of each axis of the ellipse is determined as a ratio of the linewidth that should theoretically give an optimal signal to noise ratio of the volume estimate. |
| max | the maximum value from the region. |
| min | the minimum value from the region. |
| extreme | the most extreme (maximum or minimum) value from the region. |
| center | the value at the center of the region. |
| jitter | the largest value (of the same sign as center point) within a certain tolerance (+/- 25% of the region width) of the center of the cursor region. |
| n | The number of datapoints in the region. |
| mean | the mean of the values in the region. |
| sdev | the standard deviation of the values in the region. |
| scale | The current scale value for the dataset (same as retrieved with "nv_dataset scale") |
| p1b | The first (beginning) data point along dimension 1 of the region. Similar values are present for any other dimensions. |
| p1e | The last (ending) data point along dimension 1 of the region. Similar values are present for any other dimensions. |
| max1 | The position of the maximum along dimension 1 of the region. Similar values are present for any other dimensions. |
A convenient way to put the list of values into a Tcl array variable (other than the default Nv_Value variable) is the following: array set dataValues [nv_dataset analyze hsqc.nv -d1 8 9 -d2 110 117] You could print out these values like this:
parray dataValues
dataValues(center) = 0.982547
dataValues(evolume) = 478.424618923
dataValues(extreme) = 4.420222
dataValues(jitter) = 3.618867
dataValues(max) = 4.420222
dataValues(max0) = 8.48848862769
dataValues(max1) = 111.181070777
dataValues(mean) = 0.0203823353443
dataValues(min) = -0.70917875
dataValues(n) = 23387
dataValues(p0b) = 642
dataValues(p0e) = 898
dataValues(p1b) = 242
dataValues(p1e) = 332
dataValues(scale) = 1000000.0
dataValues(sdev) = 0.292174502012
dataValues(volume) = 476.681676697</literallayout>nv_dataset blkheadersize dataset [newValue]
Some datasets, like NMRViewJ's own, are divided into a series of blocks. Each block may have a header of information and this command will return the size of the block header in bytes. Of the dataset types commonly used by NMRViewJ, only VNMR files typically have non-zero blockheader size. If 'newValue' is given the block header size will be changed to that value. 'newValue' must be a integer. Only change this if you really know what you are doing.
nv_dataset blksize datasetName iDim [newValue]
Returns the number of bytes per block in 'datasetName' for the dimension 'iDim'. If 'newValue' is given the block size will be changed to that value. 'newValue' must be a integer. Only change this if you really know what you are doing.
nv_dataset close datasetName [datasetName2] ...
Closes all datasets listed in the argument.
nv_dataset complex dataset iDim [newValue]
Returns the complex flag of the dimension specified. If 'newValue' is given, it sets the flag to that value. Valid values are 0 (real data) and 1 (complex data).
nv_dataset compress
Experimental
nv_dataset create fileName dim1Size dim2Size ...
Create a dataset named 'fileName'. The number of dimensions is determined by the number of 'dim?Size' arguments. The size of each dimension should be specified with the dimSize parameters.
nv_dataset datatype dataset [newValue]
Returns the type of numbers used to represent data values. 0: four byte floating point, 1: four byte integers. If 'newValue' is given the data type will be changed to that value.
nv_dataset dims datasetName nDims dim1Size dim1BlockSize ...
Sets the number of dataset dimensions and their sizes in one command. For example nv_dataset hsqc.nv 2 1024 64 512 65 would set the dataset to have two dimensions, the first one having 1024 data points, divided into blocks of 64 datapoints, and the second one having 512 data points, also divided into blocks of 64 datapoints.
nv_dataset fileheadersize dataset [newValue]
Some datasets, like NMRViewJ's own, have a header. This is an area that precedes that actual data, and may contain reference information or information about the layout of the actual data. This command will return the size of the file header in bytes. If 'newValue' is given the file header size will be changed to that value. 'newValue' must be a integer. Only change this if you really know what you are doing.
nv_dataset flush datasetName
Flush the memory buffers for the dataset to disk. This is only relevant for datasets that have been opened with write access.
nv_dataset freqdomain datasetName dim [isFreqDomain]
This command returns whether or not the dataset values are in the time (0) or frequency (1) domain along the specified dimension. This is used when vectors are read from the dataset. Some operations on the vectors will, for example, properly adjust referencing based on whether the vector is in the time or frequencey domain.
nv_dataset get datasetName [-d1 dimRange] [-d2 dimRange] ... -obj vecName
Extracts the datapoints from the specified region of the spectrum. The data is read into the vector 'vecName'. The limits of each dimension are specified by 'dimRange'. If no range is given for a dimension the range of all points in that dimensioln are extracted. The default unit for 'dimRange' is ppm but appending "p" to the end of a number changes it to data points (for example "-d1 1p 113p" would extract all points between data points 1 and 113). For brevity, the second number of a range may be excluded if the span of the range is 0 (for example "-d1 1.2" is equivalent to "-d1 1.2 1.2").
nv_dataset hpick
Unsupported experimental tool for picking peaks based on an HSVD analysis
nv_dataset label datasetName dim [arg]
Returns the label name for the dimension 'dim' of dataset 'datasetName'. If the optional argument is specified, the label is changed to 'arg'.
nv_dataset littleendian dataset [newValue]
Returns whether the dataset uses little endian byte order. If 'newValue' is given the dataset parameter specifiying the byte order will be changed to that value.
nv_dataset lvl datasetName [newLvl]
Returns the level the dataset will be drawn at in spectral windows. This value is used when a dataset is initial assigned to a window. Changing the contour level with "nv_win lvl" will override this value. If the 'newLvl' argument is given, the level will be set to it.
nv_dataset name
Returns the full file name (including the directory path) of the dataset.
nv_dataset ndim datasetName [dims]
Returns the number of dimensions of the dataset 'datasetName'. If the 'dims' argument is given the dataset's number of dimensions is set to it. Changing this value should only be done if you know what you are doing.
nv_dataset negcolor datasetName [newValue]
Returns the color used for negative contours when the dataset is drawn in a spectral windows. This value is used when a dataset is initially assigned to a window. Changing the color with "nv_win negcolor" command will override this value. If the 'newLvl' argument is given, the negative color will be set to it.
nv_dataset nucleus datasetName iDim [newValue]
Returns the nucleus name assoiciated with the dimension iDim. If 'newValue' is given, the nucleus name is set the that value.
nv_dataset open [[-wr | | -r] [-name newName] fileName]
Opens a compatible dataset named fileName. The complete path to the file is required for 'fileName'. However, further references to the file within NMRView use only the name of the file, or by 'newName' if the -name option is set. The -wr and -r options set the write access of the file. If -wr is set the file is opened with read/write access, if -r is set the file is opened read-only. The default option is read-only if no option is given. If no options are specified the command returns a list of the currently open files.
nv_dataset parsync datasetName dimNum
NMRViewJ can maintain two copies of the reference units, reference value, reference point, and sw for each dataset dimension. One value (the write value) is updated when a vector is written to the dataset (with the value present in that vector). The second value (the read value) is returned when a vector is read from the dataset. After processing a dataset this command can be used to set all the read values to the write values for the specified dimension.
nv_dataset path datasetName
Returns the full file name (including the directory path) of the dataset. (Same as the nv_dataset name command).
nv_dataset peakpick datasetName
Picks peaks for 'datasetName' and places them in a new list named 'datasetName'.
nv_dataset poscolor
Returns the color used for positive contours when the dataset is drawn in a spectral windows. This value is used when a dataset is initially assigned to a window. Changing the color with "nv_win poscolor" command will override this value. If the 'newLvl' argument is given, the negative color will be set to it.
nv_dataset posneg dataset [newValue]
Returns whether the dataset should show positive, negative or both frequencies when the dataset is examined. Values of 1 and 2 coorespond to positive and negative frequencies only, respectively. A value of 3 corresponds to both frequencies. If the 'newValue' argument is given posneg is set to that value.
nv_dataset ppm2pt datasetName iDim ppmVal
Returns the closest point to 'ppmVal' on the demension 'iDim' of the dataset 'datasetName'.
nv_dataset property datasetName propertyName [newValue]
Datasets can have a series of properties associated with them. These are specified as name values. Returns the value of a property with the specified propertyName. If newValue is specified the property will be set to that value. If the property doesn't exist it will be created.
nv_dataset pt2ppm datasetName iDim point
Returns the ppm value that cooresponds with 'point' on the dimension 'iDim' of the dataset 'datasetName'.
nv_dataset put datasetName [-d1 dimRange] [-d2 dimRange] ... -obj vecName
Writes the datapoints from a vector specified by 'vecName' to the specified region of the spectrum. Only datapoints withing the range given for each dimention are written. The limits of each dimension are specified by 'dimRange'. If no range is given for a dimension the range of all points in that dimensioln are written. The default unit for 'dimRange' is ppm but appending "p" to the end of a number changes it to data points (for example "-d1 1p 113p" would write all points between data points 1 and 113). For brevity, the second number of a range may be excluded if the span of the range is 0 (for example "-d1 1.2" is equivalent to "-d1 1.2 1.2"). The data is extracted from the dataset specified by 'datasetName'.
nv_dataset rdims dataset [newValue]
Returns the number of real dimensions of the dataset. If the 'newValue' argument is given, the number of real dimensions will be set to it.
nv_dataset readpoint
Not yet documented
nv_dataset ref nv_datasetName dim [arg]
Returns the chemical shift at the reference point for dimension 'dim' of dataset 'nv_datasetName'. If the optional argument is specified, the chemical shift is changed to the new value. For example,
nv_dataset refpt nv_datasetName dim [arg]
Returns the datapoint at which the reference chemical shift is specified for dimension 'dim' of dataset 'nv_datasetName'. If the optional argument is specified, the data point used for reference is changed to 'arg'. For example,
nv_dataset refunits dataset dim [arg]
Returns the reference units for the dimension given. If the optional argument is given then the reference units are set to that value.
nv_dataset rename dataset newName
Changes the name of 'dataset' to 'newName', all further references to the dataset should be 'newName'.
nv_dataset rename dataset newName
Changes the name of 'dataset' to 'newName', all further references to the dataset should be 'newName'.
nv_dataset scale dataset [newScale]
All datasets in NMRView have a scale parameter. This is used to put the numbers used for contouring or peak intensities or volumes in a more user friendly range. The scale is typically set to 1.0e6. This command returns the scale of the dataset. If the 'newScale' argument is given, the scale will be set to it.
nv_dataset scanget datasetName
Each time this command is called a vector will be read from 'datasetName' and stored into a vector. The dataset dimension and vector name must first be setup with the "nv_dataset scanstart" command. The vectors are not necessarily read in sequential order from the matrix. Instead, they are read in an optimal order as defined by the dataset layout. If data is succesfully read, the command will return "1", if the end of the matrix is reached the command will return "0". Thus the command
nv_dataset scanput datasetName
This command is analogous to the "nv_dataset scanget" command, but writes data from a vector to the matrix, rather than reading it.
nv_dataset scanstart datasetName dimNumber vectorName
Sets up various internal parameters for an optimized scan through the dataset using the "nv_dataset scanget" and "nv_dataset scanput" commands. The 'datasetName' parameter refers to the dataset that will be scanned. The axis that the data will be read from or written to is specified by 'dimNumber'. The 'vectorName' argument specifies the name of the vector in to which data will be read by the "nv_dataset scanget" command, or written to with the "nv_dataset scanput" command.
nv_dataset sf nv_datasetName dim [arg]
Returns the spectrometer frequency for dimension 'dim' of dataset 'nv_datasetName'. If the optional argument is specified, the spectrometer frequency is changed to the new value. For example,
nv_dataset size datasetName dimNum
Returns the number of points in 'datasetName' along the dimension 'dimNum'.
nv_dataset solvent datasetName [newValue]
Returns the solvent used in the experiement, for reference. The value must first be set by including the 'newValue' argument.
nv_dataset sw nv_datasetName dim [arg]
Returns the sweepwidth set for dimension 'dim' of dataset 'nv_datasetName'. If the optional argument is specified, the sweepwidth is changed to the new value. For example,
nv_dataset title datasetName [newValue]
Returns the title set for the dataset. This will initially be blank but can be set by including the 'newValue' argument. To create a title longer than one word place them in quotes.
nv_dataset vector vectorName
Creates a new dataset from the vector 'vectorName'. The name of the dataset created will be the same as the vector given.
nv_dataset wrhead datasetName
Writes the dataset header to disk. Do this after changing reference information. This is only operable for datasets that have been opened with write access.
nv_dataset writable datasetName writable
Datasets are generally opened as read-only files. If you want to change values in the file, either information in the file header, or actual data values, you need to have the file open in a writable mode. This can be done either when opening the file, or after it is opened using this command. Changing the writable status of an already opened file will acually, at a low level, close the file and reopen it with the specified mode.
Identify atoms consistent with chemical shift values.
Search for assignments consistent with a set of patterns that specify chemical shifts, atom types, and tolerances. Normally used to suggest assignments for a peak, but because the search parameters are explicitly specified values (rather than a specific peak) it can be used in more general searches.
Atom patterns are of the format residue.atom where residue is specified as the letter "i" or "j" and atom specifies an atom pattern, possibly using a wildcard character "" to match multiple characters. For example, "i.hn", "i.ca", or "j.c". In any given assignment, the patterns with the same residue character (i or j) must match the same residue. That is, if the patterns are "i.hn" and "i.ha" a possible assignment could be 35.hn and 35.ha, but not 35.hn and 36.ha. The relation parameter specifies that the assignment atom for one pattern is bonded to the assignment pattern for another atom. Thus, with patterns "i.h(D2)" and "i.n" a possible match could be 35.hn and 35.n since the 35.hn is the descendent (chemically bonded to) the atom matched for dimension 2 (this is represented by D2 on dimension 1). Atoms 35.ha and 35.n would not match this pattern. They have the same residue, but atom 35.ha is not directly bonded to 35.n. For an atom to match its chemical shift must be within the specified tolerance of the ppm in the pattern. A full pattern would look like: i.h(D2)@7.3~0.2.
Interact with lists of NOEs.
nv_noe add
nv_noe check
nv_noe clear
nv_noe elem
nv_noe extract
nv_noe n
nv_noe off
nv_noe on
nv_noe uniq
nv_noe write
nv_noe add atomSpecifier1 atomSpecifier2 lower upper
Add an NOE type constraint to the list. Constraint will be between the atoms that match atomSpecifier1 and atomSpecifier2 and will have the specified lower and upper constraint distances.
nv_noe check
Not present in NMRViewJ
nv_noe clear
Clear the noe list.
nv_noe elem elemSpecifier iNoe [value]
Returns the value of the the element specified with the
'elemSpecifier' for the NOE specified with the
vol The peak volume of the peak this noe came from.
nv_noe extract peakList ?-all?
Search the specified 'peakList' for entries that have two named protons. For each such peak enter an noe into the noe list. If the optional argument '-all' is specified, extract NOEs for peaks that have multiplet (ambiguous) assignments. Otherwise, only extract unambiguous peaks.
nv_noe n
Returns the number of noes in the noe list.
nv_noe off noeSpecifier
Inactivate constraint so it won't be used when exporting constraint lists.
nv_noe on noeSpecifier
Activate constraint so it willbe used when exporting constraint lists.
nv_noe uniq
Not present in NMRViewJ
nv_noe write
Unused
Analyze and manipulate spectral peak lists.
nv_peak add
nv_peak addlist
nv_peak analyze
nv_peak changelistener
nv_peak closest
nv_peak cluster
nv_peak compare
nv_peak compress
nv_peak couple
nv_peak dataset
nv_peak delete
nv_peak delregion
nv_peak dim
nv_peak display
nv_peak dmatch
nv_peak elem
nv_peak find
nv_peak fit
nv_peak fold
nv_peak getpeak
nv_peak idlast
nv_peak idnum
nv_peak idtol
nv_peak inbox
nv_peak inregion
nv_peak jfit
nv_peak labels
nv_peak lfit
nv_peak link
nv_peak lists
nv_peak maplink
nv_peak match
nv_peak mknoelist
nv_peak n
nv_peak name
nv_peak nearest
nv_peak panel
nv_peak pattern
nv_peak precision
nv_peak ref
nv_peak relation
nv_peak remove
nv_peak renumber
nv_peak scale
nv_peak score
nv_peak sf
nv_peak show
nv_peak sort
nv_peak status
nv_peak sw
nv_peak swap
nv_peak template
nv_peak undelete
nv_peak undelregion
nv_peak unlink
nv_peak updatecouplings
nv_peak write
nv_peak writexml
nv_peak zlink
nv_peak add peakList ?numPeaks?
Appends a peak to the end of the peak list 'peakList' and returns the new peak's number. The peak position, width and other attributes are set to zero. If the optional argument numPeaks is specified then that number of peaks will be added to the list. The peak number of the last peak added will be returned.
nv_peak addlist listName label1 [label2] [label3] ...
Creates a new list with the name 'listName'. The number of dimensions is determined by the number of 'label' arguments, and each of these arguments specifies the name of a dimension. For example,
nv_peak analyze datasetName -p1 plane -p2 plane peakSpecifiers ...
Analyze the region of 'datasetName' contained within the bounds of the all peaks given as 'peakSpecifiers'. One or more peaks may be specified. If more than one peak is specified, then the region is the smallest region that can encompass all the specified peak bounds. If the number of dimensions of the peak is less than the number of dimensions of the spectrum, then the additional plane specifiers are necessary. For example, to evaluate the region of a 2D peak in a 3D spectrum, where each plane is a different relaxation time.
See the documentation for the "nv_dataset analyze" command for information on the data returned by the command.
nv_peak changelistener register | unregister | listName procedure
Whenever a change is made to a peak or peak list a Tcl procedure can be called. This command is used to register or unregister a particular procedure for a given peak list. If changes are made in rapid succession to a peak list then the multiple events will be collapsed into a single event, otherwise the large number of calls to the event procedure could take too long to process.
nv_peak closest peakList ?xppm1 xppm2 yppm1 yppm2 ...?
Returns the number of the peak closest to the center of the specified region. If the peakList argument is not specified, the peaklist used is the first peak list assigned to the currently active window. If the position arguments are not specified, they are taken from the position of the crosshair cursors in the active window. If positions are specified as arguments, the peakList to be used must also be specified. .
nv_peak cluster peakList1 peakList2 ...
This command clusters together the peaks in one or more peak lists. Lists can be clustered based on the chemical shifts in one or more dimensions. The dimensions and tolerances used are specified with the peak template command. All peaks that fall within the same cluster are linked together.
nv_peak compare
Not implemented
nv_peak compress peakList
Compresses 'peakList' by permanently removing peaks that have been marked for deletion. Use care with this command, after compression deleted peaks cannot be restored!
nv_peak couple [-ignore | -inphase | -anti] | -wDim min max ... peakList
Couples together peaks that are within the specified tolerances. For example,
would couple together any peaks whose centers were between 0 and 3 Hz apart in the first dimension, and between 0 and 20 Hz apart in the second dimension, and whose intensities had the same sign.
nv_peak dataset peakList ?dataset?
Returns the dataset associated with 'peakList'. If the 'dataset' argument is present, 'dataset' is set to be associated with 'peakList'.
nv_peak delete peakSpecifier
Deletes one peak or an entire peak list. If the peakSpecifier does not have any "." characters, that is it describes only a list not a specific peak, then the entire list will be removed. Deleting an entire peak list cannot be undone. Otherwise, it marks the peak described with 'peakSpecifier' for deletion. The peak can be restored with the "nv_peak undel" command, or from the peak analysis window. The peak is permanently lost if the peak list is compressed with the "nv_peak compress" command. Peaks marked for deletion are not saved in the database when the database is written.
nv_peak delregion peakList ?xppm1 xppm2 yppm1 yppm2 ...?
Marks for deletion the peaks in the peak list whose centers are in the active box. If the peakList argument is not specified, the peaklist used is the first peak list assigned to the currently active window. If the position arguments are not specified, they are taken from the position of the crosshair cursors in the active window. If positions are specified as arguments, the peakList to be used must also be specified. .
nv_peak dim
Not yet documented
nv_peak display [peakList]
Draw boxs and labels at the position of all the peaks in the peak list. The peak list displayed is the active list if "LIST" argument is not specified, otherwise the specified list is displayed. For example, "peak display noesy", would display all the peaks in the peak list named "noesy". Display occurs in the active window. The peak-display list can also be set in the PEAK_ATTRIBUTES_PANEL.
nv_peak dmatch [listA listB]
Not implemented
nv_peak elem
Returns the value of the element specified by 'elemSpecifier' for the peak 'peakSpecifier'. If the optional argument is included the command sets the element to the value specified. The valid elements are:
| Element | Description |
|---|---|
| Labe l | The chemical shift of along the specified dimension. |
| Label.P | The chemical shift of along the specified dimension. |
| Label.W | The peak width for the specified dimension. |
| Label.L | The atom label for the specified dimension. |
| Label.E | The peak error message for the specified dimension. |
| Label.B | The bounds for the specified dimension. |
| Label.J | The J-coupling for the specified dimension. |
| Label.U | The user-comment for the specified dimension. |
| int | The peak intensity. |
| vol | The peak volume. |
| status | The peak status (deleted or not) |
| flag0 | The peak lock status (locked or not) |
| comment | The peak comment |
For example,
nv_peak elem 15N.W hnco.45
would return the peak width for the 15N dimension of peak 45 of the list hnco.
nv_peak find peakList ppm1 ppm2 ...
Returns a list of the numbers of the peaks in the specified peak list that are within a specified tolerance of the specified chemical shifts (ppm1, ppm2 ...). The tolerance and peak dimensions to test are specified with the "nv_peak template" command, see below.
nv_peak fit dataset -range r1 r2? peak1 ?peak2 peak3 ...?
Does a lineshape fit to the specified peaks. Currently only works for 1D peaks.
nv_peak fold peakSpecifier up | down |
Increments or decrements the chemical shift of the specified peak by an amount corresponding to one "sweep width". The peakSpecifier must include a dimension field. For example, "hnco.32.0". The sweep width value is taken from that associated with the peak's list, and may be set with the "nv_peak sw" command. By default it is the value in the dataset from which the peaks are derived.
nv_peak getpeak peakSpecifier
Returns a list of parameters describing the peak.
nv_peak idlast peakList
Returns the identifier number of the last peak in the specified peakList
nv_peak idnum peakSpecifier
Returns the peakID corresponding to the ordinal of 'peakSpecifier'. For example, with a list that has peaks 0, 2, 3...,
nv_peak idtol listName [idTol1] [idTol2] ...
Returns or sets the tolerance used by the idpeak command for 'listName'. A value must be specified for each dimension of the list. For example,
nv_peak inbox peakList ?xppm1 xppm2 yppm1 yppm2 ...?
Returns a list of peaks in the specified region. If the peakList argument is not specified, the peaklist used is the first peak list assigned to the currently active window. If the position arguments are not specified, they are taken from a region between the crosshair cursors in the active window. If positions are specified as arguments, the peakList to be used must also be specified. The peaks in the list are sorted according to their distance from the center of the box. For example, "peak inbox hmqc" would find the peaks in the peak list named "hmqc" that are within the cursor box in the active window.
nv_peak inregion listName ppm1_1 ppm1_2 ?ppm2_1 ppm2_2?
Returns a list of peaks in the specified region. There must be a pair of ppm limit values for each dimension of the peak list.
nv_peak jfit dataset -range r1 r2 -amp -lwamp -rms -maxdev? peak1 ?peak2 peak3 ...?
Does a lineshape fit to the specified peaks. Currently only works for 1D peaks.
nv_peak labels peakList ?label1 label2 ...?
Returns the labels for the various dimensions of 'peakList'. If the labels parameters are included then set the dimension labels for the peak list. There must be one label argument for each dimension of the list.
nv_peak lfit
Not yet documented
nv_peak link peakSpecifier1 ?peakSpecifier2 ...?
Creates a link between the first peak listed and any additional peaks listed. If only one peak is given a list of peaks linked that peak is returned. The format of the peakSpecifier must include the link dimension as well as the list name/number and peak number. For example, noesy.35.1 specifies dimension 1 of peak 35 of list noesy and noesy.40.N specifies the dimension labeled "N" of peak 40 of list noesy.
nv_peak lists
Returns the names of all peak lists currently loaded.
nv_peak maplink
Experimental. Not yet documented
nv_peak match peakList arg ...
Returns a list of peaks for which any of the peak labels match the argument(s). For example, "nv_peak match noesy 14.hn" returns the peak specifiers for any peaks in the list "noesy" that had a label of "14.hn" in any dimension. Wild cards are accepted. For example, "nv_peak match 33.c" returns the peak specifiers for peaks in any of the lists that had a carbon of residue 33 as the peak label. It is also possible to use multiple arguments. For example, "nv_peak -match noesy 14.ha 15.hn" returns peaks of the list "noesy" that had labels of 14.ha and 15.hn.
nv_peak mknoelist peakList nDim lab1 lab2 .. labnDim maxDis i0
Not implemented.
nv_peak n peakList
Returns the number of peaks in 'peakList'.
nv_peak name peakList newName
Changes the name of 'peakList' to 'newName'.
nv_peak nearest peakList ?xppm1 xppm2 yppm1 yppm2 ...?
Returns a list of peaks close to the center of the specified region. If the peakList argument is not specified, the peaklist used is the first peak list assigned to the currently active window. If the position arguments are not specified, they are taken from a region around the positon of the first crosshair cursor in the active window. If positions are specified as arguments, the peakList to be used must also be specified.
nv_peak panel ?peakSpecifier?
If the peakSpecifier argument is provided this command will changes the peak analysis window to display information about the specified peak. The command also returns as its result the nv_peakSpecifier for the peak active in the peak analysis window. Implemented using the Tcl scripts NvPeakSetPeak and NvPeakGetPeak
nv_peak pattern listName [pattern1] [pattern2] ...
Returns or sets the pattern used by the idpeak command (and potentially other commands as well). The pattern is in the form of an atomSpecifier, typically with the letters "i" or "j" replacing the residue field. For example:
This command needs to be extended to allow more complicated expressions.
nv_peak precision peakList ?precision1 precision2 ...?
Return, or sets, the precision used in returning chemical shift data for the peak list. One value is returned for each of the list's dimensions. If one value is included as an argument for each peak dimension then the precision parameter for the peak list will be set to the specified values.
nv_peak ref peakList ref1 ref2 ...?
Get or set reference values for each dimension of the peak list. These values are not presently used for anything???
nv_peak relation peakList ?relation?
Returns the relation fields that specify the "familial" relation between peak dimensions of 'peakList'. If the 'relation' argument is given, the relation is set to that for 'peakList'. Dimensions that are the parent of other dimensions would be specified as P(1). Where the "1" is an integer that specifys the dimension that the specified field is the parent of. For example, a 1H, 15N sqc experiment might have the relation: "" P(1), indicating that the atom of the second dimension (the nitrogen) is the parent of the atom of the first dimension (the proton).
nv_peak remove peakList
Removes the specified peak list. Deprecated. Use "nv_peak delete peakList" instead.
nv_peak renumber
Renumbers the list so that there are no gaps in the id numbers for the peaks.
nv_peak scale peakList ?scaleVale?
Gets or sets a scale value for the peak list. The scale value is used in the peak table when calculating the normalized atom number (N). The calculated value is the peak volume divided by the scale value.
nv_peak score
Calculate a score of the fit of a peak with dataset values. Only works with 1D data at present.
nv_peak sf peakList [sf1] [sf2] ...
Returns the spectrometer frequency for each dimension of the peak list. The spectrometer frequencies for a peak list are set to those of the spectrum it was picked from. If the sf1, sf2 ... arguments are included the spectrometer frequencies are changed to the specified values.
nv_peak show [peakSpecifier]
Unused. The functionality of this command from NMRViewC is now entirely implemented with Tcl scripts.
nv_peak sort listName ?iDim ascending?
Sorts the peaks in the specified list. With no optional arguments the peaks are sorted based on the peak position in the first dimension and in ascending order. The peak dimension can be specified with the iDim parameter (0, 1, .. Warning: we may change the numbering from 1,2 ... in the future). If the ascending option is specified as "0", the peaks will be sorted in descending order.
nv_peak status peakSpecifier [peakStatus]
Returns the status flag for the peak specified with the peakSpecifier argument. If the optional peakStatus argument is included the status flag of the specified peak is set to the specified value. Peaks with negative status values are marked for deletion. They do not appear when the list is displayed on a spectra and will be permanently removed when the list is compressed.
nv_peak sw peakList [sw1] [sw2] ...
Returns the sweepwidth for each dimension of 'peakList'. The sweepwidths for a peak list are initially set to those of the spectrum that it was picked from. If the optional sw1, sw2 ... arguments are included the sweepwidths are changed to the specified values.
nv_peak swap peakList label1 label2
Not yet implemented in NvJ.
nv_peak template peakList [name] [ppm] ...
Specifies a template to be used by the nv_peak find and peak dmatch commands, and returns the current template. For example, if the template is specificied as,
nv_peak undelete peakSpecifier
Unmarks 'peakSpecifier' for deletion. A peak is permanently lost if it is marked for deletion when the peak list is compressed.
nv_peak undelregion peakList ?xppm1 xppm2 yppm1 yppm2 ...?
Undeletes the peaks in the peak list whose centers are in the active box. If the peakList argument is not specified, the peaklist used is the first peak list assigned to the currently active window. If the position arguments are not specified, they are taken from the position of the crosshair cursors in the active window. If positions are specified as arguments, the peakList to be used must also be specified. .
nv_peak unlink peakSpecifier
Removes any links between 'peakSpecifier' and all peaks currently linked to it. If the peakSpecifier includes the dimension then only that dimension will be unlinked, otherwise all dimensions of the peak will be unlinked.
nv_peak updatecouplings
Not yet documented.
nv_peak write -xml | | -star listName channelName
Write peaks in XML (non standardized version, subject to change) or STAR Version 2 formats.
nv_peak writexml
Write peaks in XML (non standardized version, subject to change) format.
nv_peak zlink peakList
All links of peaks from 'peakList' are zeroed.
Worth with clusters of peaks.
nv_pkcluster fragment
nv_pkcluster fragshifts
nv_pkcluster get
nv_pkcluster last
nv_pkcluster link
nv_pkcluster new
nv_pkcluster overlap
nv_pkcluster ppm
nv_pkcluster prune
nv_pkcluster scoreres
nv_pkcluster scoreseq
nv_pkcluster unlink
nv_pkcluster fragment clusterAnalyzerName iClust
Return the fragment (a series of clusters) that contains contains the specified cluster.
nv_pkcluster fragshifts clusterAnalyzerName fragment
Returns a list of chemical shifts and matching peaks for the clusters in the fragment.
nv_pkcluster get clusterAnalyzerName clusterIndex
Return a list of all peaks in the specified cluster.
nv_pkcluster last clusterAnalyzerName
Return the peak identifier for the last peak in the reference list. This should be the last possible cluster identififer.
nv_pkcluster link clusterAnalyzerName iClust ?jClust?
If jClust is not specified, then return the clusters that are linked to iClust. If it is specified then link the two clusters together.
nv_pkcluster new clusterAnalyzerName refList list1 linkDim1 list2 linkDim2 ...
Creates a new cluster analyzer tool. Multiple cluster analyzers can be present so each one needs a name (clusterAnalyzerName). In RunAbout each cluster must contain one peak from a reference list. The reference list is specified with the refList argument. The remaining arguments come in pairs, a peak list to be included in the cluster analysis, and a dimension name for the list to be used when linking through the carbons. The list used for a reference list can also be listed as a linking list.
nv_pkcluster overlap clusterAnalyzerName iClust jClust
Return the scores and overlapping peaks between the two specified clusters. If either cluster index is set to -1, then all clusters are compared to the other cluster.
nv_pkcluster ppm clusterAnalyzerName iClust peakDimName
Return the average chemical shift of the specified peak dimension (either the proton or nitrogen) in the iClust cluster.
nv_pkcluster prune
Not yet documented.
nv_pkcluster scoreres clusterAnalyzerName iClust jClust
Return a series of scores indicating how well this pair of clusters could match different residue types.
nv_pkcluster scoreseq clusterAnalyzerName molName entityName fragmentList
Return a list of scores and possible matchings of the fragment (a sequence of clusters) against the specified molecular entity. Each possible matching is a list consisting of the starting residue, the score (a Bayesian probability), and the chemical shift and peak matches for each cluster in the fragment.
nv_pkcluster unlink clusterAnalyzerName clusterIndex1 clusterIndex2
Remove the link between the specified clusters.
Deprecated
nv_residue resNum [varName]
Deprecated
Query and assign resonances.
nv_resonance assign
nv_resonance clear
nv_resonance label
nv_resonance n
nv_resonance peakdims
nv_resonance assign resonanceID ?atomSpecifier?
Return, or set, the atom assigned to the specified resonance. The atomSpecifier must correspond to an existing atom.
nv_resonance clear
Clear the list of all resonances. Use with caution.
nv_resonance label resonanceID ?label?
Return, or set, the label assigned to the specified resonance. The label can be any arbitrary text, and doesn't need to correspond to an existing atom.
nv_resonance n
Return the number of resonances.
nv_resonance peakdims resonanceID
Return a list of all peak dimensions linked to the specific resonance.
Read molecular structures.
nv_sread pdb
nv_sread pdbx
nv_sread ressd
nv_sread sd
nv_sread seq
nv_sread xpsf
nv_sread xyz
nv_sread pdb fileName
Read Protein Data Bank format files. This is the standard way to read in pdb files. NMRView first reads the pdb file to determine the amino acid sequence. Next, it reads the corresponding residues from the PEGASUS residue library. Finally, it reads coordinates from the pdb file for those atoms that have names matching the names in the residue library. Atoms, that do not have a match in the residue library will not be entered into the PEGASUS structure list. Atoms that are in the residue library but not in pdb file, will be included in structure list but will not be displayed. The file will be read from directory $SDIR where SDIR is a TCL variable. SDIR can be set in the preference panel or on the command line. The default value for SDIR is ".".
nv_sread pdbx
Not yet documented
nv_sread ressd fileName ?fileContent? molName
Reads sdfile (also mol) files from specified fileName. The molecule data read from the file (or fileContent string) is used to create a new compound within the specified molecule, rather than creating a new molecule. If fileContent is specified then the the molecular structure is read directly from the provided string.
nv_sread sd fileName ?fileContent?
Reads sdfile (also mol) files from specified fileName. If fileContent is specified then the the molecular structure is read directly from the provided string.
nv_sread seq seqName
Read in residues from residue library based on sequence in file filename.
nv_sread xpsf fileName
Not yet implemented. Reads a file in the format produced by XPLOR. This is a alternative method to the "nv_sread seq" command to obtain atom, residue and connectivity information. Coordinates must be read in with the "nv_sread xyz" or "nv_sread grp" commands. The directory used is the same as that used with "sread -pdb" command.
nv_sread xyz fileName strct
Reads the PDB file filename and attempts to match the atoms to atoms in the structure in memory. If atoms match by residue name, atom name, sequence number, chain id, and alternate identifier then the coordinates corresponding to each atom matched are assigned the value of the coordinates of that atom in file. The coordinates are read into the structure specified by the "strct" parameter. The directory used is the same as that used with "sread -pdb" command.
Write molecular structures.
nv_swrite ppm
nv_swrite sxyz
nv_swrite ppm
Not yet documented
nv_swrite sxyz
Not yet documented
Control spectral windows.
nv_win aclear
nv_win active
nv_win addtag
nv_win adim
nv_win attributes
nv_win axis
nv_win axisline
nv_win bbox
nv_win bgcolor
nv_win bind
nv_win border
nv_win box
nv_win busy
nv_win caldelta
nv_win canvasx
nv_win canvasy
nv_win center
nv_win cget
nv_win clear
nv_win clm
nv_win closest
nv_win configure
nv_win coords
nv_win copy
nv_win copyimage
nv_win create
nv_win cross1
nv_win cross1x
nv_win cross1y
nv_win cross2
nv_win cross2x
nv_win cross2y
nv_win crosscolor
nv_win crosshair
nv_win crossmode
nv_win crossstate
nv_win cursor
nv_win czoom
nv_win dataset
nv_win datatitles
nv_win dcoffset
nv_win defer
nv_win delete
nv_win delregion
nv_win deltaoffset
nv_win dim
nv_win dispeaks
nv_win display
nv_win draw
nv_win drawlist
nv_win drawpeak
nv_win dtag
nv_win edit
nv_win erasepeak
nv_win expand
nv_win export
nv_win find
nv_win full
nv_win gettags
nv_win grid
nv_win hit
nv_win inbox
nv_win index
nv_win integrals
nv_win interp
nv_win itemcget
nv_win itemconfigure
nv_win jadd
nv_win jmode
nv_win label
nv_win links
nv_win lower
nv_win lvl
nv_win masked
nv_win maxveclen
nv_win mode
nv_win move
nv_win name
nv_win ndim
nv_win nearest
nv_win neg
nv_win negcolor
nv_win negwidth
nv_win new
nv_win newtype
nv_win nlvls
nv_win object
nv_win open
nv_win paste
nv_win peak_col_off
nv_win peak_col_on
nv_win peak_col_type
nv_win peak_dis_type
nv_win peak_lab_type
nv_win peak_off
nv_win peak_types
nv_win peakattributes
nv_win peaklist
nv_win pick
nv_win pix2ppm
nv_win plot
nv_win pos
nv_win poscolor
nv_win poswidth
nv_win ppm
nv_win ppmmax
nv_win previous
nv_win pt
nv_win raise
nv_win refreshcrosshairs
nv_win region
nv_win regioncolor
nv_win repfile
nv_win scale
nv_win scale1d
nv_win search
nv_win selectdataset
nv_win selectpeak
nv_win shift
nv_win show
nv_win showpeaks
nv_win slice
nv_win stop
nv_win svg
nv_win thread
nv_win transformer
nv_win type
nv_win wait
nv_win winpeak
nv_win xdim
nv_win xoffset
nv_win xshear
nv_win ydim
nv_win yoffset
nv_win z2dim
nv_win zdim
nv_win zoom
nv_win aclear clearMode?
Unused in NvJ
nv_win active windowName
Returns the pathName of the active window. If the optional argument is present then it sets the active window to the specified window.
nv_win addtag tagOrId ?tagOrId tagOrId ...?
Same as Tk canvas "addtag" subcommand
nv_win adim dimNum
Sets the z2 (or a) display dimension of the active window to dimNum.
nv_win attributes
Display the Spectrum Attributes window. Does this by calling the Tcl proc "spectrum::showAttrPanel"
nv_win axis axis axis1 axis2
Returns a 0 or 1 specifying whether or not the bottom and top axis (and left and right) labels and tick marks should be drawn. If the axis1 and axis2 arguments are specified the respective axes are turned on or off as specified. The values are specified as boolean values (0/1, yes/no, on/off or true/false). For example, to turn the labels and tic marks for both the bottom and top axis off
nv_win axisline axis axis1 axis2
Returns a 0 or 1 specifying whether or not the bottom and top axis (and left and right) line should be drawn. If the axis1 and axis2 arguments are specified the respective axis lines are turned on or off as specified. The values are specified as boolean values (0/1, yes/no, on/off or true/false). For example, to turn the axis lines for both the bottom and top axis off
nv_win bbox
Same as Tk canvas "bbox" subcommand
nv_win bgcolor newColor
Returns the current color used for the background of the active spectrum window. If the optional parameter, newColor, is specified, then the background is set to that value. This command is redundant to "nv_win configure -bg".
nv_win bind bind tagOrId ?sequence? ?command?
Same as Tk canvas "bind" subcommand
nv_win border axis border1 border2
Returns the borders for the left and right sides, or top and bottom, of the plot region in the active window. If the border1 and border2 arguments are specified the appropriate borders are set to the specified values. The values are specified in units of pixels.
nv_win box xVal yVal 0 | 1 |
Use this command to draw a temporary box on the spectrum. Generally this would be used from a mouse binding to draw a resizable box. With a mode value 0f "0", the xVal and yVal arguments set the position (in pixels) of the starting corner of the box. With a mode value of "1", the xVal and yVal arguments set the ending corner of the box and redraws the box.
nv_win busy
Returns the value "1" if the spectrum is actively being drawn and "0" if the spectrum drawing is idle.
nv_win caldelta mode
This determines how the ofsets between 1D vectors are calculated when more than one spectrum (or row) is drawn in a single window.
nv_win canvasx
Not yet documented
nv_win canvasy
Not yet documented
nv_win center ?xPos yPos?
Shift view displayed in spectrum window to center on the specified xPos and yPos positions (in ppm) If these arguments are not included the x and y position is taken from the current position of the first crosshair (usually black). The width and hieght of the displayed region is unchanged by this command.
nv_win cget
Not yet documented
nv_win clear
Has no observable effect in NMRViewJ
nv_win clm ?-dataset datasetName? contourLevelMultiplier?
Returns the contour level multiplier used in the active window. If the optional argument is specified the contour level multiplier in the active window is set to contourLevelMultiplier. For example, "nv_win clm 1.5", sets the contour level multiplier in active window to 1.5.
nv_win closest
Unused, use corresponding "nv_peak" command.
nv_win configure
Not yet documented
nv_win coords
Same as Tk canvas "coords" subcommand
nv_win copy
Copy data about active window into a buffer.
nv_win copyimage
Puts graphic representation of spectrum on to the system clipboard where it can be pasted into other applications.
nv_win create
Same as Tk canvas "create" subcommand
nv_win cross1 x y?
Returns the coordinates (in ppm) of CrossHair_1 in the active window. If the optional arguments are specified the position of CrossHair_1 is set to x, y. For example, "nv_win cross1 3.2 4.3", sets CrossHair_1 in the active window to (3.2,4.3) in ppms.
nv_win cross1x x?
Returns the x coordinate (in ppm) of CrossHair_1 in the active window. If the optional argument are specified the x value of CrossHair_1 is set to x. For example, "nv_win cross1x 3.2", sets x value of CrossHair_1 in the active window to 3.2 in ppms. The y value is unchanged.
nv_win cross1y y?
Returns the y coordinate (in ppm) of CrossHair_1 in the active window. If the optional argument are specified the y value of CrossHair_1 is set to y. For example, "nv_win cross1x 3.2", sets y value of CrossHair_1 in the active window to 3.2 in ppms. The x value is unchanged.
nv_win cross2 x y?
Returns the coordinates (in ppm) of CrossHair_2 in the active window. If the optional arguments are specified the position of CrossHair_1 is set to x, y. For example, "nv_win cross2 3.2 4.3", sets CrossHair_2 in the active window to (3.2,4.3) in ppms.
nv_win cross2x x?
Returns the x coordinate (in ppm) of CrossHair_2 in the active window. If the optional argument are specified the x value of CrossHair_2 is set to x. For example, "nv_win cross2x 3.2", sets x value of CrossHair_2 in the active window to 3.2 in ppms. The y value is unchanged.
nv_win cross2y y?
Returns the y coordinate (in ppm) of CrossHair_2 in the active window. If the optional argument are specified the y value of CrossHair_2 is set to y. For example, "nv_win cross2x 3.2", sets y value of CrossHair_2 in the active window to 3.2 in ppms. The x value is unchanged.
nv_win crosscolor 1 | 2 | color
Returns the color used for drawing the first or second crosshair. If the optional color argument is used the specified crosshair is set to that color.
nv_win crosshair crossHair xVal yVal mode mouseType
Provides low level control of the crosshairs (as compared to the cross1, cross2 etc. commands). The crossHair parameter should be 1 or 2, to specify the first or second crosshairs. The "xVal" and "yVal" parameters set the crosshair positon (in pixels). The mode parameter specifies the action that should happen when the command is executed. The mouseType specifies whether the crosshair behaviour should be appropriate for a one (1) button or three (3) button mouse. It defaults to "1" if not specified.
nv_win crossmode 1 | 2 | x | y | xyMode
Returns the current mode for the specified crosshair line. For example, nv_win crossmode 1 x would return the mode for the vertical (x) line of the first crosshaird. The returned value is either 0 or 1, with 0 indicating that the crosshair line is inactive and will not appear on the dspectrum, and 1 indicating that the crosshair line is active and will appear on the spectrum. The optional xyMode value can be specified to set the cross mode to inactive (0) or active (1).
nv_win crossstate 1 | 2 | x | y |
Returns the current state for the specified crosshair line. For example, nv_win crossmode 1 x would return the state for the vertical (x) line of the first crosshair. The returned value is either 0 or 1, with 0 indicating that the crosshair line is not currently displayed, and 1 indicating that the crosshair line is currently visible on the spectrum. Note that if a crosshair is visible, then the mode is set to 0, it will still return a state value of 1, even though setting the mode to 0 will have made the crosshair disappear.
nv_win cursor cursorType?
Returns, and optionally sets, the current cursor type for the window. This command is redundant with the "nv_win configure -crosshair" command. Note that changing the cursor will change the actions that happen when the mouse is clicked or dragged in the window. For example, setting the cursorType to "crosshair" will cause crosshairs to be drawn when the mouse is clicked or dragged.
nv_win czoom
Not yet implemented
nv_win dataset datasetName1 datasetName2 ...?
Returns the name(s) of the dataset(s) used in the active window. If the optional argument is specified the datasets for the active window are set to the specified value(s). For example, "nv_win dataset noesy.mat", sets the dataset for the active window to "noesy.mat". The specified dataset must have been opened previously. An unlimited number of datasets may be assigned to the window.
nv_win datatitles drawTitles
Returns 0 or 1 to indicate whether or not the title of the dataset should be drawn in the spectrum window. If the optional boolean value is included then the the state of title drawing will be changed to the specified value. The title is normally drawn in the lower left corner of the spectrum. By default, the title value for a dataset is set to the name of the dataset, but it can be changed with the "nv_dataset title" command.
nv_win dcoffset ?0 | 1? |
Returns, or sets if the optional argument is included, the state of automatic dcoffset mode. This mode only effects the display of vectors (either true 1D spectra, or slices of higher dimensional spectra). If selected then the spectrum will be offset so that the edges of the spectrum will be displayed at zero. This is accomplished by subtracting a straight line calculated between the left and right edges. The offset is dynamically calculated as the spectrum plot limits are changed. The effect is only really appropriate when the spectrum is positioned so that the left and right eddges are "baseline" regions.
nv_win defer on off?
If set to "On" then don't defer drawing the spectrum until set to "Off"
nv_win delete tagOrId tagOrID ...?
Delete eah of the spectrum canvas items given by each tagOrID, and return an empty string.
nv_win delregion
Unused, use corresponding "nv_peak" command.
nv_win deltaoffset ?offsetValue?
Returns, or sets if the offsetValue argument is included, the offset between 1D spectra when multiple spectra are displayed in one window. Whether or not this value is used depends on the state of the parameter set with the "nv_win caldelta" command.
nv_win dim displayDimType?
Returns the display type as 0 (1Dx), 1 (1Dy) or 2 (2D). If the optional displayDimType argument the display type is set as specified.
nv_win dispeaks peakListName1 peakListName2 ...?
Returns the name of the peak lists to be displayed in the active window. If the optional argument is specified the display peak list for the active window is set to the specified values. For example, "nv_win dispeaks list1", sets the peak list for the active window to "list1". Whenever this window is redrawn the peaks from the specified lists will be displayed. A practically unlimited number of peak lists may be specified. To cancel peak display for the window use the "nv_peak dispeaks {}". See also the PEAK ATTRIBUTES PANEL.
nv_win display
Not used
nv_win draw ?peaks?
Draws the current window. If the optional "peaks" argument (literally the word "peaks") is added then only refresh the display of peaks and shapes in the spectrum.
nv_win drawlist ?-dataset datasetName? ?"row1 row2 ..."?
Returns or specifies a list of rows of a dataset that should be drawn. This is only appropriate for arrayed one dimensional spectra or two dimensional spectra when they are drawn as a series of 1D vectors.
nv_win drawlist "1 5 30"
would draw the first, fifth, and thirtieth, row of the spectrum. Specifying an empty list nv_win drawlist "" will restore the drawing of all rows.
nv_win drawpeak
Not yet documented
nv_win dtag
Same as Tk canvas "dtag" subcommand
nv_win edit
Same as "nv_win copy". Deprecated.
nv_win erasepeak
Unused
nv_win expand
Draws expansion (area in cursor box) of active window.
nv_win export
Export a graphical representation of the active window to a file. The command first displays a dialog box from which the user can choose one of a variety of export formats including vector formats such as PDF, SVG EMF,and PostScript, and bitmap formats such as GIF, PNG, and JPEG.
nv_win find searchCommand ?arg arg ...?
Same as Tk canvas find command.
nv_win full
Draws full expansion of active window.
nv_win gettags
Same as Tk canvas "gettags" subcommand
nv_win grid
Not implemented in NMRViewJ. The grid command is a toggle command. If grids are off in the active window it causes a grid of points to be drawn in the active spectral window. The grid of points will be removed when the window is redrawn. If grids are currently on in the active window the grid command removes the grid. Each point in the grid is located at the position of a point in the file.
nv_win hit tagOrID x y
Returns a parameter indicating the point on a displayed shape that is closest to the x and y values. Only some shape types, for example molecules, support this feature.
nv_win inbox
Unused, use corresponding "nv_peak" command.
nv_win index
Same as Tk canvas "index" subcommand
nv_win integrals state | scale | offset | ?value?
New experimental code for displaying 1D integrals
nv_win interp
Not yet documented
nv_win itemcget
Same as Tk canvas "itemcget" subcommand
nv_win itemconfigure
Same as Tk canvas "itemconfigure" subcommand
nv_win jadd
For adding popup menus to spectrum. Do not use.
nv_win jmode jmodType?
Returns the method for displaying peaks that have J-values (coupling constants) greater than 0.0. With jmodType 0, a single peak is displayed with the J-value added to the peak width. With jmodType 1, two peaks are displayed with their centers shifted by the J-value.
nv_win label axisName axisLabel
Returns the label for the specified axis of the spectrum. If the optional argument 'axisLabel' is specified then set the label to the specified value.
nv_win links ?0 | 1? |
Returns, or sets if the optional argument is included, the whether lines sould be drawn between linked peaks. This feature is experimental.
nv_win lower
Same as Tk canvas "lower" subcommand
nv_win lvl ?-dataset datasetName? Level?
Returns the contour level of the active window. If the optional argument is specified the contour level of the active window is set to Level. For example, "nv_win lvl 0.2" sets the contour level in active window to 0.2.
nv_win masked
Do not use
nv_win maxveclen ?value?
Drawing of 1D vectors can be sped up by not drawing all data points. The parameter returned or set by this command indicates the maximum number of points to be used in drawing a vector. Defaults to 2048. If set to 0, all points are drawn.
nv_win mode live record play
Returns the drawing mode. Not currently supported
nv_win move
Same as Tk canvas "move" subcommand
nv_win name
Returns name of current window.
nv_win ndim ?-dataset datasetName?
Return the number of dimensions of the matrix currently displayed in the window. If more than one dataset is displayed in the window, the number of dimensions of the first dataset will be returned.
nv_win nearest
Unused, use corresponding "nv_peak" command.
nv_win neg ?-dataset datasetName? ?0 | 1? |
Return, or set if optional argument is included, whether or not negative contour levels should be drawn.
nv_win negcolor ?-dataset datasetName? colorName?
Returns the color corresponding to the color used for negative contours in the active window. If the optional argument is specified the color for negative contours in the active window is set to colorName. For example, "nv_win negcolor red" sets the color for negative contours in the active window to red.
nv_win negwidth ?-dataset datasetName? ?width?
Returns the width of lines used for drawing negative contours in the active window. If the optional argument is specified the width for negative contours in the active window is set to width. For example, "nv_win negwidth 2" sets the width for negative contours in the active window to 2.
nv_win new
Unused
nv_win newtype
Allows adding a new type of canvas shape to the spectrum. To do this custom Java code must be written to implement the new type.
nv_win nlvls ?-dataset datasetName? nLevels
Returns the number of contour levels used in the active window. If the optional argument is specified the number of contour levels in the active window is set to nLevels. For example, "nv_win nlvl 5", sets the number of contour levels in active window to 5.
nv_win object
Do not use
nv_win open
Return a list of currently open spectrum windows.
nv_win paste
Paste data from the copy buffer into active window and draw contour plot.
nv_win peak_col_off colorName
Returns the name of the color used to draw peak boxes that are not on (or between, if a range of planes is used) the displayed plane. If the optional argument is specified the color is set to that value in the active window.
nv_win peak_col_on colorName
Returns the name of the color used to draw peak boxes that are on (or between, if a range of planes is used) the displayed plane. If the optional argument is specified the value is set in the active window.
nv_win peak_col_type arg
plane, assigned, error, status
If set to the value "plane", peak boxes are colored according to their closeness to the display plane, as determined by the peak_off, peak_col_off, and peak_col_on parameters. If set to the value "assigned", peak boxes are colored according to the peak labels. If any peak dimension has a "?", in the label field the peak boxes is colored as specified by the peak_col_off argument, otherwise it is colored as specified with the peak_col_on.
nv_win peak_dis_type arg
"peak", "simulated","label", "none"
Returns a number (0-3) corresponding to the manner in which peaks from the peak list are displayed in the spectral window. If set to 0, peaks are drawn as boxes with widths corresponding to the peak width. If the value is 1, peaks are drawn as simulated contours. If the value is 2, only the peak label is draw. If the value is 3, the peak is drawn as a single ellipse. The peak width parameter is then assumed to be the line width. The number of contours and their levels are determined by the "nv_win nlvl", "nv_win lvl", and "nv_win clm" commands. If the optional argument is specified the value is set in the active window. See also the PEAK ATTRIBUTES PANEL.
nv_win peak_lab_type labType
number label residue atom cluster user comment summary
This parameter determines what type of label is drawn next to each peak box. The choices are as follows:
nv_win peak_off nPlanes
This parameter determines which peaks are displayed on 3 or 4 dimensional spectra. If the plane of a peak is closest to the display plane, it is displayed with the color specified by the peak_col_on parameter. If it is not on the display plane, but is within nPlanes of the display plane it is displayed with the color specified by the peak_col_off paramter. Otherwise it is not displayed. See also the PEAK ATTRIBUTES PANEL.
nv_win peak_types ?type1 type2 ...?
compound minor solvent contaminant impurity chemshiftref quantityref comboref water artifact
nv_win peakattributes
Not used in NMRViewJ
nv_win peaklist
Not used in NMRViewJ
nv_win pick xVal yVal jiggle"
Find peak or dataset in window at within jiggle range of position specified with the xVal and yVal. First, displayed peaks are scanned to find one overlapping the specified position. If one or more are found the return value is "peak PeakSpecifier" where "peak" is the literal word peak, and peakSpecifier is a value specifiying the closest peak to the position. If no peaks are found within the jiggle range, the window is searched for a 1D spectra that is within range. If one is found the return value is "dataset datasetName" where "dataset" is the literal word dataset, and datasetName is the name of the dataset closest to to the specified position.
nv_win pix2ppm xVal yVal
Returns, as a Tcl list, the x and y chemical shifts that correspond to the specified pixel positions. This is useful for converting positions returned from mouse or key bindings to a chemical shift position in the spectrum.
nv_win plot all?
Unused in NMRViewJ. Use the print command instead.
nv_win pos ?-dataset datasetName? ?0 | 1? |
Return, or set if optional argument is included, whether or not positive contour levels should be drawn.
nv_win poscolor ?-dataset datasetName? colorName?
Returns the color corresponding to the color used for positive contours in the active window. If the optional argument is specified the color for positive contours in the active window is set to colorName. For example, "nv_win poscolor black" sets the color for positive contours in the active window to black.
nv_win poswidth ?-dataset datasetName? ?width?
Returns the width of lines used for drawing negative contours in the active window. If the optional argument is specified the width for negative contours in the active window is set to width. For example, "nv_win negwidth 2" sets the width for negative contours in the active window to 2.
nv_win ppm axis ?value1 value2?
Returns the plot limits, in units of ppm, for the specified axis. If the optional value1 and value2 arguments are included, then set the plot limits to those specified. For example
nv_win ppmmax axis
Returns the minimum and maximum plot limits, in units of ppm, for the specified dimension.
nv_win previous
Draw previous expansion (up to 8 previous expansions are stored.)
nv_win pt axis ?value1 value2
Returns the plot limits, in units of points, for the specified axis. If the optional minValue and maxValue arguments are included, then set the plot limits to those specified. For example
nv_win raise
Same as Tk canvas "raise" subcommand
nv_win refreshcrosshairs
Unused
nv_win region clear | | get | | add x1 x2 | | adjust x1 x2 | set | x1 x2 | | display 0/1
Spectra can have colored regions displayed on them. At present this is only useful for 1D spectra. This subcommand allows the user to specify the regions to be displayed.
nv_win regioncolor ?regionColor?
Return, or set, the color to be used when drawing regions on the spectrum. Use the "nv_win region" command to set the regions to be displayed.
nv_win repfile datasetName repFileName
This command can be used to assign a copy of a dataset to the window. The datasetName specifies the dataset to be copied, and repFileName specifies the new name to be used when adjusting parameters for the new copy within the window. An actual copy of the data is not made, the original dataset is the source of all data used for display. But, the parameters such as contour levels and contour colors can be controlled independently for the original and "replica" dataset. This command was originaly developed so sets of 1D vectors from a pseudo-2D file could be independently controlled. Rows in each dataset (or replica) are selected for display with the "nv_win drawlist" command. A given dataset can be replicated an unlimited number of times within the same spectrum window.
nv_win scale
Same as Tk canvas "scale" subcommand
nv_win scale1d scaleValue
Returns the scale value used for drawing 1D spectra (including slices). If the optional argument, scaleValue, is included the command sets the scale value to that specified.
nv_win search
Unused
nv_win selectdataset ?-append? ?datasetName
One dimensional datasets can be displayed in a highlighted mode if they are selected. With no arguments, this command return a list of currently selected datasets. If datasetName is specified then set that dataset to be selected. If the "-append" flag is included then any previously selected datasets are left selected, otherwise only the specified dataset will be selected after completion of the command.
nv_win selectpeak ?-append? ?peakSpecifier?
Peaks can be displayed in a highlighted mode if they are selected. With no arguments, this command return a list of currently selected peaks. If peakSpecifier is included then set that peak to be selected. If the "-append" flag is included then any previously selected peaks are left selected, otherwise only the specified peak will be selected after completion of the command.
nv_win shift xShiftPPM yShiftPPM
Shift the displayed region of the spectrum by the specified amounts.
nv_win show
Not used
nv_win showpeaks
Unused
nv_win slice state | position | offset | draw | dimName ?slice?
Returns the boolean state of the cursor slices. If a slice is turned on then a realtime vector slice is drawn across the spectra in a direction specified by the axis. If the option on|off value is specified then set the state to the value specified. For example, to draw slices parallel to the x axis when the cursor is moved
nv_win stop
Stop drawing the current spectrum. Useful if it is taking a long time to draw the spectrum and you want to intterupt the drawing process, perhaps so you adjust parameters.
nv_win svg
Unused. Use "nv_win export" instead.
nv_win thread 0 | 1 |
Report or set whether the spectrum should be drawn in its own thread of execution. Expert use only.
nv_win transformer transformerName m0 m10 m01 m11 m02 m12
Sets the elements of the specified affine transform used in drawing shapes on the spectrum. Expert use only.
nv_win type tagOrID
Return the type of the item given by tagOrId, such as rectangle or text.
nv_win wait
This command will not return until drawing in the active window is completed. Useful in scripts to ensure that drawing is done before some parameter is changed and the spectrum drawn again.
nv_win winpeak ?off | expand | expandfix | plane? |
Returns or sets a flag to be used by scripts that can update the spectrum region to display the region surrounding a specified peak. This command only sets or returns the flag, any useful activity is done via scripts that scan the list of spectrum windows for ones that have the paramter set to something other than "off".
nv_win xdim dimNum
Sets the x display dimension of the active window to dimNum.
nv_win xoffset offsetValue
Returns the offset value used for drawing 1D spectra parallel to the x axis (including slices). The value can range from 0 to 1 and specifies the position of the zero value for the spectra. If the optional argument, offsetValue, is included the command sets the offset value to that specified.
nv_win xshear ?shearValue?
Returns or sets a shearValue to be used when drawing 2D datasets. Typically this is used in a stack plot mode so that subsequent rows of the spectra are drawn above and offset to the right relative to the previous row.
nv_win ydim dimNum
Sets the y display dimension of the active window to dimNum.
nv_win yoffset offsetValue
Returns the offset value used for drawing 1D spectra parallel to the y axis (including slices). The value can range from 0 to 1 and specifies the position of the zero value for the spectra. If the optional argument, offsetValue, is included the command sets the offset value to that specified.
nv_win z2dim dimNum
Sets the z2 display dimension of the active window to dimNum.
nv_win zdim dimNum
Sets the z display dimension of the active window to dimNum.
nv_win zoom in | | out | | f1 f2 f3 f4
Zooms spectra region in or out. If the argument is "in" the window is zoomed in to show a smaller region of the spectrum. The four directions (two each for x and y axes) are adjusted by 0.25 times the existing spectral width. If the argument is "out" then the window is zoomed out to show a larger region of the spectrum. If four numbers are specified then the zooming is done by the factors specified, with negative values zooming in and positive values zooming out.
Non-linear regression fitting of XY data.
nv_xy auxnames
nv_xy equations
nv_xy fit
nv_xy gen
nv_xy npar
nv_xy auxnames equationNum
Return a list of the names of any auxiliary parameters.
nv_xy equations
Return a list of the equations available for fitting.
nv_xy fit -xvec xvec -yvec yvec -xlist xlist -ylist ylist -clvl clvl -nsim nsim -equation equationNum -sdev calc | input | set | sdev -guesses guessList -aux auxList
Fit the xy data to the specified equation. Data for the fit can either come from vecmat objects, using the -xvec and -yvec arguments, or from Tcl lists, using the -xlist and -ylist arguments.
nv_xy gen [param1] [param2] ...
Generate simulated data using the parameters specified with 'param1' 'param2' ... The simulated data will be returned in the vector specified by the 'yObject' parameter of the "nv_xy objects" method. By default this is the vector fit_y.
nv_xy npar equationNum
Return the number of parameters for the specified equation.
Print windows.
Prints the specified window. Page orientation can be set with the -landscape or -portrait flags. If -autoselect is used then if the window is wider than it is high then landscape mode will be used, otherwise portrait will be used. If -silent is specified then no print dialog will be displayed and the file will be printed to the default printer. If -sizetofit is specified the page size will be based on the dimensions of the printed window. The margin around the printed area can be set with the marginValue.
Read NMR-STAR (version 2) files.
star close
star discon
star mmcifxyz
star next
star open
star peak
star ppm
star put
star xyz
star close
Not yet documented
star discon
Not yet documented
star mmcifxyz
Not yet documented
star next
Not yet documented
star open
Not yet documented
star peak
Not yet documented
star ppm
Not yet documented
star put
Not yet documented
star xyz
Not yet documented
Read and write NMR-STAR (Version 3) files.
star3 clear
star3 close
star3 get
star3 loop
star3 open
star3 process
star3 saveframe
star3 scan
star3 write
star3 clear
Discard current STAR file. This doesn't delete any molecules, peak lists or other data structures.
star3 close
Close the datafile that the STAR file was read from.
star3 get starSpecifier
Get the value corresponding to the specified tag.
star3 loop count starSelector | | tags starSelector | | values starSelector | | row starSelector
count starName.saveframe.category: Return the number of rows in the loop.
star3 open fileName
Opens the specified NMR-STAR 3 file. This only opens the actual file, but doesn't read (see "star3 scan") or process (see "star3 process") the data.
star3 process
Processes the imported STAR 3 file by looking for specific save frames that NMRViewJ handles (at present these are the ones for datasets, molecules, peak lists, resonance, chemical shifts, and RunAbout parameters).
star3 saveframe list | | categories starSelector | | tags starSelector
Retreive information about the save frames in the loaded STAR file.
list: Return a list of saveframes in the file.
star3 scan
Reads the previously opened file into memory.
star3 write fileChannel
Writes the current STAR file data to the specified file channel. The file channel must have been opened with Tcl commands.
set f1 [open test.str w] star3 write $f1 close $f1
Math and statistics with vectors and matrices.
vecmat add
vecmat addmul
vecmat apsl
vecmat autophase
vecmat axscale
vecmat base64todouble
vecmat base64tofloat
vecmat bcmed
vecmat bcpoly
vecmat bcsmooth
vecmat bcwhit
vecmat bucket
vecmat bytes
vecmat cnew
vecmat comb
vecmat complex
vecmat compress
vecmat convert
vecmat copy
vecmat copyrange
vecmat cow
vecmat cshift
vecmat cwtd
vecmat cwtidbaseline
vecmat dalist
vecmat dc
vecmat dcfid
vecmat decompress
vecmat deconv
vecmat delete
vecmat dm1d
vecmat dwell
vecmat esmooth
vecmat exchange
vecmat expd
vecmat extend
vecmat fconvert
vecmat fdss
vecmat fp
vecmat freqdomain
vecmat fromasdf
vecmat ft
vecmat genbase
vecmat gensignal
vecmat genspec
vecmat get
vecmat getbytes
vecmat gf
vecmat gm
vecmat gmb
vecmat hft
vecmat hsvd
vecmat idbase
vecmat idintegrals
vecmat ift
vecmat imag
vecmat input
vecmat integrate
vecmat list
vecmat list2vec
vecmat mag
vecmat max
vecmat min
vecmat negatepairs
vecmat new
vecmat object
vecmat ones
vecmat output
vecmat phase
vecmat poly
vecmat power
vecmat psmooth
vecmat random
vecmat range
vecmat real
vecmat ref
vecmat resize
vecmat reverse
vecmat rft
vecmat sb
vecmat scale
vecmat sdev
vecmat set
vecmat setcolumn
vecmat setrow
vecmat shift
vecmat size
vecmat sort
vecmat split
vecmat status
vecmat svd
vecmat sw
vecmat swap
vecmat tdpoly
vecmat trap
vecmat tri
vecmat trim
vecmat zero
vecmat zf
vecmat zv_mlt
vecmat add vecName value
Add the specified value to each element of the specified vector. If the vector is complex the value is added only to the real part of each element.
vecmat addmul vecName1 vecName2 ?scale?
Add the two vectors element by element and store the result in vector vecName1. If the scale parameter is present each element of vector vecName2 is multiplied by the scale value before being added to the corresponding element of vector vecName1. The vectors must be of the same length and same type (real or complex). The command returns vecName1 as a result.
vecmat apsl center start width asym
Calculate a zero order phase value that will optimize the symmetry of a spectral peak. The center of the peak is specified by the center argument, the first data points to compare the symmetry of are the points at center-start and center+start. The last points to be compared are at center-start-width and center+start+width. The asym value should normally be set to 0.
vecmat autophase vecName ?-mode flat | max? | ?-first firstPoint? ?-last lastPoint? ?-winsize winSize?
Calculate a zero order phase parameter. If mode is "flat" (the default), then a systematic search is done for a phase parameter that maximizes the flatness of the spectral baseline. The winsize parameter (default = 60) is used in identifying baseline regions and is only used in "flat" mode. If mode is "max", a search is done to maximize the integral of the spectrum. This method is only appropriate for spectra that do not have significant negative components in the well phased spectrum. The first and last parameter values are used only in the "max" mode and are used to specify the region over which the integral is calculated. If they are not specified the entire spectrum is used.
vecmat axscale vecName ?value?
Used as a generic equivalent of the spectrum frequency. Used when calculating referencing and adjusting referencing during some vector manipulations. When a vector is loaded from an NMR dataset this value is set to the spectometer frequency for the dimension that the vector is parallel to.
vecmat base64todouble vecName values
Convert a string of base 64 encoded data points that represent double precision floating point values into values in the vector. The vector will be resized to exactly accomadate the number of values in the string.
vecmat base64tofloat vecName values
Convert a string of base 64 encoded data points that represent double precision floating point values into values in the vector. The vector will be resized to exactly accomadate the number of values in the string.
vecmat bcmed vecName frac
Correct the baseline of the specified vector using the median method. The window size used in the analysis is set by multiplying the frac parameter times the number of extrema in the vector.
vecmat bcpoly vecName ?-winsize winSize? ?-ratio ratioValue? ?-order orderValue?
Correct the baseline of the specified vector using a polynomial fit to the values of the baseline data points of the vector. The fitted polynomial is then subtacted from the original vector to produce the corrected vector. Baseline regions are identified as regions with signals that exceed the standard deviation of the noise of the vector by more than a ratio of ratioValue (default = 10.0). The standard deviation of the spectrum is estimated by dividing the vector into regions of size winSize, calculating the standard deviation in each range, and then estimating the overall noise standard deviation from a sorted list of the standard deviations of each region.
vecmat bcsmooth vecName smoothSize winSize ratio
Correct the baseline of the specified vector by calculating a smoothed baseline. The smoothed baseline is then subtacted from the original vector to produce the corrected vector. Baseline regions are identified as regions with signals that exceed the standard deviation of the noise of the vector by more than a ratio of ratioValue (default = 10.0). The standard deviation of the spectrum is estimated by dividing the vector into regions of size winSize, calculating the standard deviation in each range, and then estimating the overall noise standard deviation from a sorted list of the standard deviations of each region. The smoothed baseline is calculated within each baseline region by averaging adjacent datapoints over a region of size smoothSize. Smoothed baseline points in non-baseline regions are calculated by linear interpolation between the adjacent smoothed baseline points.
vecmat bcwhit vecName ?-winsize winSize? ?-lamda lambda? ?-order order? ?-minsize minSize? ?-baseline 0 | 1? |
Correct the baseline of the specified vector using a calculating a smoothed baseline using the Whitaker "perfect smoothing" algorithm. The smoothed baseline is then subtacted from the original vector to produce the corrected vector. Baseline regions are first identified as regions of low intensity after calculating the derivative of the spectrum using a continuous wavelet transform.
vecmat bucket vectorName nBuckets
The vector is bucketed by adding adjacent data points. The vector size after this operation will be equal to the specified number of buckets. Thre original vector size must be a multiple of the number of buckets. Each resulting data point will represent the sum of winSize data points where winSize is equal to size/nBuckets.
vecmat bytes byteValues
Returns a handle to a Java object corresponding to an array of bytes (byte[]) containing the values in the supplied argument.
vecmat cnew length vecName
Creates a complex vector with the name 'vecName' and the size 'length'. The vector will be initialized with all real and imaginary components set to zero.
vecmat comb
Not yet documented
vecmat complex vecName
Converts a real vector into a complex vector of the same number of components. The real part of each value is set to the corresponding value in the original vector. The imaginary part of each value is set to zero. If the original vector is already complex no action is taken and no errors are reported.
vecmat compress vecName
Experimental vector compression. Not yet documented
vecmat convert ?-swap | -noswap? | ?-float | -int? | vecName data
Imports a byte array stored in data into the specified vector. If -swap is specified the byte order of the data will be reversed as it is imported. If -float is specified the data bytes are converted as if they represent 4 byte floating point numbers, otherwise they are converted as 4 byte integers. Note: the actual data stored in vectors is always 8 byte double precision floating point. The type of the vector refered to by vecName determines whether the data is converted as real or complex values. The vector will be resized to exactly accomadate the number of data values in data.
vecmat copy vecName1 vecName2
Copy vector vecName1 into vector vecName2. If the destination vector doesn't exist it will be created. It's type (real/complex) and size will be adjusted if necessary to conform to that of the source vector.
vecmat copyrange vecName1 vecName2 srcPos destPos length
Copy the specified range of values of vector vecName1 into vector vecName2. If the destination vector doesn't exist it will be created. It's type (real/complex) and size will be adjusted if necessary to conform to that of the source vector.
vecmat cow
Not yet implemented.
vecmat cshift vecName shiftAmount
Circular shift of the data points in the specified vector by the specified amount.
vecmat cwtd vecName winSize
Calculate the first derivative of the vector using a continuous wavelet transform.
vecmat cwtidbaseline vecName ?-winsize winsize? ?-minsize minSize?
Indentify baseline regions by using a continous wavelet transform calculation of the first derivative of the vector. After the derivative is calculated the data values are replaced by their power (rr+ii). An estimate of the noise level of the vector is then calculated. Baseline regions are set as areas where intensities are never higher than a certain multiple of the noise level. The result is a list of points demarcating the start and end of baseline regions.
vecmat dalist vecName
Many mathematical and statistical calculations can be done using access to the built Colt library. Some of these calculations require the data in the format of a Java object of the DoubleArrayList class. This command will return a double array list containing the data values in the vector. If the vector is complex an ObjectArrayList is returned containing complex value objects.
vecmat dc vecMat ?-fraction fraction?
Subtracts from each data point the average value of two regions, one at the begining and one at the end of the vector. The optional fraction argument (default = 0.05) specifies the fractional size of the vector used for each of the two regions. The vector must be real (not complex).
vecmat dcfid vecMat fraction fraction
Subtracts from each data point the average value of the set of data points at the end of the vector. The fraction argument specifies the fractional size of the vector used for the region. The vector must be complex (not real).
vecmat decompress vecName
Experimental vector decompression. Not yet documented
vecmat deconv
Not yet documented
vecmat delete vecName1 vecName2 ...
Delete the specified vectors.
vecmat dm1d vecName dm1D
Many mathematical and statistical calculations can be done using access to the built Colt library. Some of these calculations require the data in the format of a Java object of the DoubleMatrix1D class. This command will such an object containing the data values in the vector. This only works for vectors of type real. If the optional dm1D object is provided data in the provided object will be put into the vector. The vector will be resized to conform to the size of the DoubleMatrix1D object.
vecmat dwell vecName ?dwell?
Vectors have a dwell time associated with them. This corresponds to the time between data points in time domain mode, and 1/sweepwidth in frequency domain mode. The dwell time is updated when vectors are read from datasets, and is used for adjusting the referencing of the data and calculating time-dependent apodization functions.
vecmat esmooth
Not yet documented
vecmat exchange vecName
Interchange the real and imaginary components of each data point of a complex valued vector. Throws an error if the dataset is not complex.
vecmat expd vecName ?-lb lb? ?-firstpoint firstPoint?
Multiply vector by an exponentially decaying apodization function. The decay rate is specified as a "line-broadening" parameter in Hz.
vecmat extend vecMat ?-fitstart fitStart? ?-fitend fitEnd? ?-ncoef nCoef? ?-predictstart predictStart? ?-predictend predictEnd? ?-threshold threshold? ?-mode mode?
Performs linear prediction to extend the data at either the beginning or end of the original data. Linear prediction is performed by using the SVD (Singluar Value Decomposition) algorithm.
vecmat fconvert vecName data
Equivalent to "vecmat convert -noswap -float vecName data"
vecmat fdss vecMat -center center -start start -end end
Perform a frequency domain solvent suppression on the specified vector. This is done phasing the spectrum to optimally symmetrize the baseline around the solvent peak, converting the data from complex to real, zeroing the solvent region, converting the data back to complex with a hilbert transform, and then restoring the original phase. The parameters used are the same as described in the "vecmat apsl" command.
vecmat fp vecName ?-fp fpValue?
Multiply the first piont of the vector by the specified fpValue (default = 0.5).
vecmat freqdomain vecMat 0 1?
Return, or set if the optional argument is included, the state of the frequency domain flag. A value of 0 indicates the data is in the "time domain" and a value of 1 indicates that the data is in the "frequency domain". Changing this value does not modify the data in any way, but will effect automated adjustment of the referencing that may happen after other data manipulations.
vecmat fromasdf vecName data
Import data stored in the data argument into the specified vector. The data must be values in the ASDF format.
vecmat ft vecName
Execute a Fast Fourier Transform on the data. An error will be thrown if the data is not complex. If the data size is not equal to a power of 2 it will be resized to the next higher size that is a power of 2.
vecmat genbase vecName order winSize bcVec
Perform the same operation as that done by "vecmat bcpoly", but do not modify the input vector. Instead the calculated baseline is stored in the vector named with the bcVec argument. The bcVec vector must already exist.
vecmat gensignal vecName ?-f freq? ?-d decay? ?-p phase? ?-a amplitude?
Add a sinusoidal signal with the specified parameters to the vector. The vector must exist and be complex. The new signal is added to any data values already present.
vecmat genspec vecName parameterVec
Add Lorentzian signals to the vector. The vector must exist and be real. Parameters for the signal are stored in the vector parameterVec in the order amplitude, phase, frequency, decay rate.
vecmat get vecMat index
Returns the data value stored at position index (counts from 0). If the vector is complex the real and imaginary values will be returned as a list of two values.
vecmat getbytes vecName
Return a handle to an object containing an array of bytes corresponding to the data in the vector.
vecmat gf vecName -gf gf -gfs gfs -firstpoint firstPoint
Apply a gaussian apodization. Vector must have an appropriate dwell time set.
vecmat gm -g1 g1 -g2 g2 -g3 g3 -firstpoint firstPoint
Apply a gaussian multiplication to vector.
double e = Math.PI g1 dwellTime; double ga = 0.6 Math.PI g2 dwellTime; double gb = ga g3 * (size - 1);
for (int i = 0; i < size; i++) { double g = gb - (ga i); apodVec[i] = Math.exp((e i) - (g * g)); }
vecmat gmb vecName ?-gb gb? ?-lb lb? ?-firstpoint firstPoint?
Gaussian multiplication
double e = Math.PI g1 dwellTime; double ga = 0.6 Math.PI g2 dwellTime; double gb = ga g3 * (size - 1);
for (int i = 0; i < size; i++) { double g = gb - (ga i); apodVec[i] = Math.exp((e i) - (g * g)); }
vecmat hft vecName
Hilbert transform of the specified vector. Vector must be real or an error will be thrown.
vecmat hsvd
Not yet documented
vecmat idbase vecName winSize ?ratio?
Returns a list of data point positions that mark the beginning and end of baseline regions.
vecmat idintegrals vecName winSize ?ratio regionWidth joinWidth extendSize minThreshold?
Returns a list of data point positions that mark the beginning and end of integral regions.
vecmat ift vecName
Inverse Fourier Transform
vecmat imag vecName
Converts a complex vector to a real vector with values that correspond to the imaginary components of the original vector. If the vector is already real it is unchanged and no error is thrown. Returns the name of the input vector.
vecmat input vecName fileName ?columnNum?
Reads values from a text file of numbers. If columnNum is specified and the data is arranged as columns values will be taken from the specified column (counting from 0). Columns are formed by splitting each row on any white space (space or tab characters). If the specified vector is complex then each row must have at least two columns and the real value will be taken from the first (or columnNum) column and the imaginary from the next value on the row.
vecmat integrate vecName ?firstIndex lastIndex?
Replace the data points in the vector with the cumulative sum of data points over the specified range. If the optional parameters are not included the entire vector is integrated.
vecmat list
Return a list of existing vector names.
vecmat list2vec vecName list
The specified vector is resized to the length of the specified Tcl list and then the values in the list are stored in order into the vector. Values in the list must be parsable as floating point numbers or an error will be thrown. If the vector is complex then real and imaginary values will be taken from alternate values in the list.
vecmat mag vecName
If the specified vector is complex then replace each value with the magnitude "sqrt(rr+ii)" of each existing complex value. The resultant vector will be real. If the specified vector is already real no action will be taken and no error will be thrown.
vecmat max vecName ?firstPoint lastPoint?
Locate the maximum value in the vector. Return, as the result, a two element list where the first value is the maximum value and the second value is the index at which it occurred. If the vector is complex the maximum located is the value with largest magnitude. If the optional arguments are included then the search for a maximum is done only in the specified range.
vecmat min vecName ?firstPoint lastPoint?
Locate the minimum value in the vector. Return, as the result, a two element list where the first value is the minimum value and the second value is the index at which it occurred. If the vector is complex the minimum located is the value with smallest magnitude. If the optional arguments are included then the search for a minimum is done only in the specified range.
vecmat negatepairs vecName
Set every other pair of data values to the negative of the current value.
vecmat new size vecName
Create a new vector with name vecName and the specified size.
vecmat object vecName
Returns a handle to the underlying vector object.
vecmat ones vecName
Sets all values in the vector to 1.0 if the vector is real, and 1.0+i0.0 if the vector is complex.
vecmat output vecName fileName?
Output the vector values to either standard output (if there is no fileName argument) or to the named file.
vecmat phase vecName p0 p1
Phase correct the vector using the provided zero order (p0) and first order (p1) phase values.
vecmat poly xVector yVector order coefVector
Fit a polynomial equation of the specified order to the x and y values taken from xVector and yVector. The polynomial coefficients are stored in the coefVector. The command returns as a result the rms deviation between the fitted polynomial and the original data.
vecmat power vecName
If the specified vector is complex then replace each value with the power "(rr+ii)" of each existing complex value. The resultant vector will be real. If the specified vector is already real no action will be taken and no error will be thrown.
vecmat psmooth vecName ?-lambda lambda?
Smooth the values in the vector using the Whitaker perfect smoother algorithm.
vecmat random vecName
Set values to the random numbers generated with the Java Math.random() method.
vecmat range vecName first last value
Sets data points in the range of the specified vector starting at point first to point last to value.
vecmat real vecName
Converts a complex vector to a real vector with values that correspond to the real components of the original vector. If the vector is already real it is unchanged and no error is thrown. Returns the name of the input vector.
vecmat ref
Not yet documented
vecmat resize vecmat newSize
Resize the vector to the specified size (which can be either larger or smaller than existing size). If the vector doesn't already exist it will be created.
vecmat reverse vecName
Reverse the vector.
vecmat rft vecName
Apply a Fast Fourier Transform optimized for real data.
vecmat sb vecName ?-offset offset? ?-end end? ?-power power? ?-size size? ?-c firstPoint?
Multiply the specified vector by a "sine bell" apodization window with the specified parameters.
vecmat scale vecMat scaleValue
Multiply each element of the vector by the specified scaleValue.
vecmat sdev vecName winSize ?nWindows?
Estimates the standard deviation of values in noise regions of the spectrum. This is done by first dividing the vector into regions of size winSize. Then the standard deviation of each region is calculated. The region standard deviations are sorted and the average of the standard deviation is taken over the nWindows regions with smallest standard deviations.
vecmat set vecName index realValue ?imagValue?
Sets the value at position index in the specified vector. If the vector is of type real then only one value (realValue) should be provided. If the vector is of type complex then both a real and imaginary value can be provided. If the imaginary value is not provided it is set to 0.0.
vecmat setcolumn
Not yet documented
vecmat setrow
Not yet documented
vecmat shift vecName shiftAmount
Shift each data point right or left by the specified number of data points. Positive shiftAmounts shift points to the right and negative to the left.
vecmat size vectorName
Returns the size of the specified vector.
vecmat sort
Not yet documented (does not sort the vector).
vecmat split vecName realVecName imagVecName
Puts the real values of complex array vecName into the real vector realVecName and the imaginar values of vecName into imagVecName. If realVecName or imagVecName don't exist they will be created.
vecmat status vecName
Return status information about the vector. Three values are returned: r/c indicating real/complex, the size of the vector, and the capacity of the vector. The capacity is the size the vector can grow to without allocating additional memory.
vecmat svd
Not yet documented
vecmat sw vecName sw
Vectors have a dwell time associated with them. This corresponds to the time between data points in time domain mode, and 1/sweepwidth in frequency domain mode. The dwell time is updated when vectors are read from datasets, and is used for adjusting the referencing of the data and calculating time-dependent apodization functions. This parameter allows setting or getting the dwell via its inverse, the sweep width.
vecmat swap vecName
Swaps the byte order in vector. Doesn't just change a flag, but actually reverses the order of bytes in each data value.
vecmat tdpoly vecName ?-order order? ?-start start? ?-winsize winsize?
Fits a polynomial equation to the vector and then subtracts the calculated polynomial from the original data. Useful for solvent suppression.
vecmat trap vecMat ?-pt1 pt1? ?-pt2 pt2?
Multiply the vector by a trapazoidally shaped apodization function.
vecmat tri vecMat ?-pt1 pt1? ?-lheight lHeight2? ?-rheight rHeight?
Multiply the vector by a triangularly shaped apodization function.
vecmat trim vecMat ?-left | -middle | -right? | ?-pt1 pt1? ?-newsize newSize?
Trim the vector to a new size. If the -left, -middle, or -right arguments are specified the new vector size will be half the original size and the vector will contain the data points from the indicated region. If the -pt1 and -newsize arguments are used, the vector will be of newSize size and contain the original points starting at pt1.
vecmat zero vecName
Sets all values in the vector to 0.0 if the vector is real, and 0.0+i0.0 if the vector is complex.
vecmat zf vecMat -factor factor
Extend the vector with zeros up to a size that is a power of 2. With a factor of 0 the vector is extended to the first size that is a power of 2. With each additional increment of factor the final size is twice that with the previous factor.
vecmat zv_mlt
Not yet documented
Load and VNMR parameter files.
vnmr exists
vnmr get
vnmr load
vnmr remove
vnmr exists handleName parameterName
Returns 0 or 1 indicating whetherspecified parameter exists in the parameter set specified with handleName.
1
vnmr get handleName parameterName
Get the value of the specified parameter from the parameter set specified with handleName.
7509.62
vnmr load procParFileData
Reads in the specified VNMR procpar file data. Returns a handle that can be used to refer to these parameters. The data must have been previously read and stored in to a Tcl variable. For exampe:
set f1 [open /Users/brucejohnson/data/proton.fid/procpar] set d [read $f1] close $f1 vnmr load $d
By working this way data can be loaded not only from normal files, but other sources such as network sockets.
vnmr remove handleName
Remove the specified parameter set from memory.