NMRWish TCL Library Procedures

This particular reference page lists the NMRWish TCL Library Procedures. These are TCL scripts which perform generally useful functions, intended for use by other TCL application scripts. For example, the TCL library procedure getArgD is used by other scripts to extract argument values from the command-line.

Like getArgD, many of these TCL procedures are used frequently in the various application scripts which are part of the NMRPipe system. Some procedures, however, may rarely be used, were added only for development purposes, or may be superseded by more recent additions to the software. In an attempt to indicate which procedures are used most frequently, the reference list includes an instance count. In the current version of this Reference List, the instance count tallies how often NMRPipe's developer Frank Delaglio has used a procedure or option in a script during both routine use and research and development of the software.

NMRWish TCL Library Procedures

Name	Instances	Description	Common Arguments (Instances)
arg2array	0	Store a list of arguments on the command line in a TCL array.
dynEvalTensor	0	Compute Dipolar Coupling or Pseudo-Contact Shift tensor parameters for a timestep in a DYNAMO molecular structure calculation.
dynExit	36	Exit from a DYNAMO molecular structure calculation.
dynGetPDBDisuList	2	Identify atom pairs likely to be involved in S-S bonds from a PDB file read as a DYNAMO object.
dynGetPDBSeqStr	7	Create DATA SEQUENCE lines from the residue sequence in a PDB file read as a DYNAMO object.
dynNAAngles	0	Extract angles associated with Nucleic Acid PDB file read as a DYNAMO object.
dynReadGMC	61	Read a DYNAMO molecular structure calculation GMC environment (GMC, Generic Molecular Coordinates).	`-gmc (61)` `-pdb (61)` `-r1 (28)` `-rN (28)` `-torsion (27)` `-ac (9)` `-uangle (1)` `-noe (1)`
dynSimulateAnnealing	60	Perform a DYNAMO Simulated Annealing Calculation with Initialization, High-Temperature, and Cooling Stages.	`-graph (59)` `-print (59)` `-sa (59)` `-fc (56)` `-rasmol (47)` `-nocenter (19)` `-notensorProc (16)` `-tensorProc (12)` `-norasmol (8)`
estSpecNoise	12	Estimate the standard deviation of the baseline noise in the named NMRPipe-format data.
expand	0	Expand a string into a list of its individual characters.
extractArray	0	Extract all index/value pairs from an array.
extractSaupe	8	Dipolar Coupling Analysis Utility
findClusters	5	Cluster Analysis on Objects in a List
flagLoc	1298	Find the location of a flag in the command line.
get15NDim	11	Return the axis name of the 15N dimension in an NMRPipe-format header.
get15NTabVar	21	Get the name of the variable (column) in an NMRPipe-format peak table associated with amide-nitrogen (15N) chemical shift in PPM.
getAbsMax	6	Return the value with the greatest absolute value in a list.
getAbsMin	0	Return the value with the smallest absolute value in a list.
getArgD	2525	Extract the named argument's value from the command line if it can be found.
getArgDN	32	Set a TCL array variables from an argument's value in the command line if it can be found.
getArrayList	2	Extract array contents as a list.
getAtomEntry	4	Find an atom's entry (row number) in a PDB file.
getAvg	72	Return the average of values in a list.
getAvgAngle	31	Returns the average of a list of angles in degrees.
getChi2	0	Computes the chi-square statistic on the difference between two lists, given the corresponding uncertainties.
getChiAngle	2	Extract chi sidechain angles for a given residue in a PDB file.
getDefinedAngles	3	Returns a list of angles in degrees with "undefined" values (> 999) removed.
getDim	0	Return the dimension location (1, 2, etc) associated with the axis name in an NMRPipe-format header.
getDimKeyword	18	Return the keyword (CUR_XDIM, CUR_YDIM, etc) associated with the axis name in an NMRPipe-format header.
getDirectDim	11	Return the axis name of the directly-acquired dimension in an NMRPipe-format header.
getEListAvg	13	Get the average of values for a GDB database table variable (column) from a list of entries (rows).
getEListMax	0	Get the maximum value of a GDB database table variable (column) from a list of entries (rows).
getEListMin	0	Get the minimum value of a GDB database table variable (column) from a list of entries (rows).
getEListStat	11	Apply a given TCL function to compute a statistic using a list of entries (rows) from a GDB database table.
getEListStdDev	0	Get the standard deviation for a GDB database table variable (column) from a list of entries (rows).
getEListSum	0	Get the sum of values for a GDB database table variable (column) from a list of entries (rows).
getEListVals	0	Extract all values associated with a GDB database table variable (column) from a list of entries (rows).
getFileBytes	6	Returns the size of a file in bytes, with options for compressed data.	`-estimate (3)` `-exact (1)`
getFirstLevel	6	Calculate a contour height from a range.
getFormat	0	Reformat values in list, for example to give a uniform number of decimal places.
getHNTabVar	21	Get the name of the variable (column) in an NMRPipe-format peak table associated with amide-proton (HN) chemical shift in PPM.
getHist	4	Build histogram values for lists of X/Y pairs.
getIndirectDim	8	Return the "third dimension" axis name in an NMRPipe-format header for amide-detected 3D data.
getIndirectTabVar	14	Get the name of the variable (column) in an NMRPipe-format peak table associated with the "third" dimension chemical shift of an amide-detected 3D data.
getIota	0	Return a numeric list with equal spacing between values.
getKeyData	26	Get the DATA information associated with a given keyword.
getListArgD	307	Extract the named argument's list of values from the command line if it can be found.
getMax	97	Return the maximum value in a list.
getMaxRes	15	Extract the largest residue number from a PDB file read as a GDB database table.
getMedian	27	Return the median of values in a list, return value is an average of two values for lists with even numbers of points.
getMin	79	Return the minimum value in a list.
getMinRes	14	Extract the smallest residue number from a PDB file read as a GDB database table.
getNAAngles	2	Extract angles associated with Nucleic Acid PDB file read as a GDB database table.
getNAResName3	0	Return the 3-character residue name associated with the given nucleaic residue name.
getNthResName	29	Get the name of the given residue in a PDB file.
getNthTensor	79	Extract tensor parameters from a Dipolar Coupling result.
getOmegaAngle	9	Extract omega backbone angles for a given residue in a PDB file.
getPChi	2	Return the Chi-square probability given a list of residuals, their associated uncertainties, and the number of degrees of freedom.
getPDBDisuList	2	Identify atom pairs likely to be involved in S-S bonds from a PDB file read as a GDB database table.
getPDBSeqList	3	Extract sequence information from a PDB file read as a GDB database table.
getPDBSeqStr	0	Create DATA SEQUENCE lines from the residue sequence in a PDB file read as a GDB database table.
getPDF	5	Create a 1D probability density distribution from lists of X/Y pairs.
getPDFCoords	4	Get coordinates for the X-axis of a 1D probability density function.
getParmI	93	Extract an integer parameter from an NNRPipe-format header.
getPearsonR	12	Return the Pearson's R correlation coefficient.
getPhiPsiAngles	18	Extract phi/psi backbone angles for a given residue in a PDB file.
getQuadSize	4	Return 1 if the given dimension is real-only, 2 if complex.
getRMS	48	Return the RMS (Root Mean Square) of values in a list.
getROIStat	14	Perform a computation on intensities from a given spectral region-of-interest (ROI.
getRange	0	Return the range (maximum - minimum) of values in a list.
getRepeat	0	Create a list by repeating a value.
getResName1	36	Return the 1-character residue name associated with the given amino acid residue name.
getResName3	19	Return the 3-character residue name associated with the given amino acid residue name.
getReverse	2	Returns a list with the order of its items reversed.
getSaupeAngle	17	Compute the angle between two Dipolar Coupling alignment tensors.
getScale	0	Return the value that minimizes the residual between values in two lists.
getSeqList	62	Extract residue sequence information from DATA statements in a table into a TCL array.
getSeqListSeqStr	2	Create DATA SEQUENCE lines from the residue sequence list.
getSequence	0	Extract the protein residue sequence from a PDB file read as a GDB database table.
getSimpleMedian	0	Return the median of values in a list; return value is always an element from the list.
getSpecRange	0	Find the ranges of intensities in an NMRPipe-format data file.
getStdDev	56	Return the standard deviation of values in a list.
getStdDevAngle	36	Returns the standard deviation of a list of angles in degrees.
getSum	18	Return the sum of values in a list.
getSumSq	8	Return the sum of squares of values in a list.
getTabAvg	3	Get the average of values of a variable (row) in a GDB database table.
getTabKeyItem	0	Get the value associated with a given DATA keyword in a table.
getTabKeyLength	3	Get a number of items associated with a DATA keyword in a table.
getTabKeyList	0	Get a list of DATA keywords in a table.
getTabMax	32	Get the maximum value of a variable (row) in a GDB database table.
getTabMin	26	Get the minimum value of a variable (row) in a GDB database table.
getTabStat	0	Apply a given TCL function to compute a statistic using all values extracted from a GDB database table variable (column).
getTabStatU	2	Apply a given TCL function to compute a statistic using all values extracted from a GDB database table variable (column), with undefined values skipped.
getTabStdDev	0	Get the standard deviation of values of a variable (row) in a GDB database table.
getTabSum	0	Get the sum of values of a variable (row) in a GDB database table.
getTabTextCount	0	Get the number of text items in a table.
getTabTextInfo	0	Extract table text items into a TCL array.
getTabVals	7	Extract all values associated with a GDB database table variable (column).
getTau	2	Extract the Tau value from the given NMRPipe-format data file.
getVsStat	12	Computes a statistic on the difference of two numerical lists of the same length.
getWAvg	24	Return the weighted average of values in a list.
getWRMS	6	Return the weighted RMS (Root Mean Square) of values in a list.
initMiniPlot	11	Initialize settings for multiple "postage stamp" PostScript plots.	`-landscape (1)` `-pxn (1)` `-bwx (1)` `-bwy (1)` `-bdx (1)` `-bdy (1)` `-bg (1)`
initResNames	48	Initialize the list of canonical residue names for common amino acids.
isAscending	0	Return 1 if the given numerical list is ascending.
isDescending	0	Return 1 if the given numerical list is descending.
isFlag	5	Return 1 if argument is a valid flag.
isInt	4	Test if argument contains only one or more digits 0-9.
isMonotonic	0	Return 1 if the given numerical list is monotonic.
linterp	0	Interpolate XY pairs in numerical lists.
listDisjoint	4	Returns the unique elements in one list but not in the other.
listIntersect	6	Returns the unique elements common to two lists.
listUnion	6	Returns the unique elements in the combined contents of two lists.
listUniq	6	Returns the unique members in a list.
loadArray	3	Read the contents of a TCL array from a file.
loadArrayDB	0	Read the contents of one or more TCL arrays from files in a directory.
lselect	22	Select items in one list according to 1 and 0 values in a corresponding list.
metro	0	Combinatorial optimization by metropolis method.
name2fmt	0	Convert a file name to an NMRPipe format template (i.e. test001.dat to test%03d.dat).
nextFlag	9	Find the location of the next flag in the command line.
nextMiniPlot	11	Prepare to draw the next "postage stamp" plot.
nextPower2	3	Return the smallest power of two equal to or greater than the given argument.
okExit	8	Display a Dialog Box asking permission to exit an application.
okWrite	7	Display a Dialog Box asking permission to overwrite a file.
pdbNAAngles	0	Extract angles associated with Nucleic Acid structures.
permList	8	Form all permutations of the elements in the given list taken N at a time.
polySolve	0	Return the solution coefficients to a polynomial least squares problem.
probePDBSrc	0	Identify PDB file contents as protein or nucleic acid.
rClip	17	Clip a variable's value.
rOrder	3	Numerical Utility
rSwap	0	Swap the contents of two TCL variables.
rdFDATA	65	Read the NMRPipe-format header from the named file.
rdFDATAU	6	Read the NMRPipe-format header from a data file opened for reading.
removeElement	0	Remove an element from a list by its location.
removeNullElements	2	Remove null items from a list.
sameList	2	Test whether two lists have the same unique members.
setArgD	30	Change the value of an argument in the command line if it can be found.	`-xLAB (6)` `-yT (6)` `-yMODE (6)` `-yLAB (6)` `-aq2D (6)`
setColors	3	Set some typical colors used for graphical interface items such as buttons. OBSOLETE.
setFlag	0	Change a flag in the command line.
setFlagD	0	Change a flag in the command line if it can be found.
setFonts	41	Set some typical font names for use in an NMRWish graphical application.
setListArgD	6	Change an argument's list of values in the command line if it can be found.	`-comment (6)`
setOSType	38	Set some operating-system dependent variables. OBSOLETE.
showError	79	Display a Dialog Box indicating an error.
simplePermutation	4	Form all permutations of the elements in the given list.
simplePermutationN	0	Form all permutations of the elements in the given list taken N at a time.
storeArray	4	Save the contents of a TCL array as a file.
storeArrayDB	0	Save the contents of one or more TCL arrays as files in a directory.
wrFDATA	3	Write the NMRPipe-format header to the named file.

Frank Delaglio, Ph.D.