Frank Delaglio, Ph.D.

19804 Maycrest Way
Germantown MD 20876 USA

301 806-0867
delaglio@nmrscience.com


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 Some procedures, however, may rarely be used, were added only for development purposes, or may be superseded by more recent additions to the software.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.