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categories: Engineering,June,2009,EisaA

Awk for Chemical Engineers

A style seen in many Awk libraries is lots of small scripts, each handling a very specific task.

A good example of this style is Eiso Ab's library of scripts for chemical engineering. Shown below are dozens of his scripts. His library is an interesting example of real-world Awk programming.

You can download a tgz of all awk and other scripts from http://www.nmr.chem.uu.nl/~eiso/scripts.tgz. Please direct all bugs and , questions to eiso@nmr.chem.uu.nl

help ass2shift.awk (Jan-23-2008) purpose: read in anything with assignments or chemical shifts check consistency and write a shift list
help ppm2prot.awk (Jun-12-12:15) generate an xeasy .prot file from another shift.list or ppm.out file
help xpk2peaks.awk (Sep-20-2007)
help pdb2iupac.awk (Feb-11-2005)
help pdb2pdb.awk (Jun-12-12:17) purpose: - reformat ATOM records for various conventions - set B-factors for residues and/or atoms
help seq2shift.awk (Nov-21-2007) fill shift list with chemical shift statistics from a database , currently the cyana lib file.
help predict.awk (Jun-12-12:16) purpose : make list of predicted peaks from shift-lists
help addass.awk (Feb-11-2005)
help reref.awk (Jun-12-12:18) compare referencing for one or two peaklists in a 2D-histogram see also plotpeaks.awk
help plotpeaks.awk (Jun-12-12:15) plot peaks in a 2D graph useful for comparing referencing between peak files or within domains of one peakfile, see also reref.awk
help calib.awk (Jul-13-2005) determining calibration parameters from bruker acqu file use: calib.awk temp=298 acqu [1] Wishart, D.S; Sykes, B.D. (1995) J. Biomol. NMR., 6, 135-140 1H, 13C and 15N chemical shift referencing in biomolecular NMR
help mergeshift.awk (Jun-12-12:12)
help gmx2nmr.awk (Jun-12-12:10) opposite of nmr2gmx.awk convert gmx topology distance and orientation restraints
help nmr2gmx.awk (Jun-16-13:55) make gromacs topology files for distance restraints and dipolar coupling data
help diffshift.awk (Apr-23-10:33) compare shift lists e.g. diffshift.awk [ options ] shiftlist1 shiftlist2
help complete_assignments.awk (Sep-20-2007) adds assignments in xeasy peaklist where one atom of a proton-heteroatom couple is assigned and the remaining assignment is clear.
help peaks-project.awk (Jun-12-12:13) make lower dimension projections from xeasy peak files
help peaks-unfold.awk (Jun-12-12:14) unfolds peaks in xeasy peaks files
help unwatergate.awk (Feb-14-2005) undo the effect of watergate water suppression on peak intensities in nmrview xpk files
help colorchain2mac.awk (Feb-15-2005) make molmol macro for rainbow-colored spline
help seq2seq.awk (Sep-20-2007) convert protein aminoacid sequence files from oneletter to threeletter format and vice versa.
help seq2shift.awk (Nov-21-2007) fill shift list with chemical shift statistics from a database , currently the cyana lib file.
help makehbonds.awk (Feb-11-2005)
help sparkysave2peaks.awk (Sep-21-2006) convert sparky save files to xeasy peakslist
help peaks2sparky.awk (Jun-12-12:14) create sparky readable peaklists (.list) example: peaks2sparky.awk protein.seq protein.prot c13-cycle7.peaks
help addass2sparkysave.awk (Feb-11-2005)
help shifts2sparky-rl.awk (Sep-20-2007)
help check_hetero_atom.awk (May-15-2007)
help splitass.awk (Feb-11-2005)
help splitnoa.awk (Feb-11-2005)
help pdb2ariapdb.awk (Feb-11-2005)
help tblcount.awk (Aug-15-2005) make a table with numbers of ambiguous and unambiguous intra/seq/medium/long/inter-dom restraints it needs a2ps to format the output.
help upl2tbl.awk (Jun-12-12:20) very simple converter for xeasy .upl files to xplor/cns .tbl files
help tbl2upl.awk (Apr-22-2005) convert (ambiguous) distance restraints in xplor *.tbl file to xeasy/cyana .upl/lol file Use: tbl2upl.awk name.(seq|pdb) unambig.tbl > out.upl
help filterpeaks.awk (May-26-2005) filter peaklist for diagonal,water,lowest/highest intensities
help tabstat.awk (Jun-12-12:21) get stats on values in columns of tables
help linestat.awk (Jun-12-12:10) perform statistic on a certain number of columns of each line
help qual-col.awk (Jun-12-12:17) purpose: color residues according to whatcheck bad/poor scores. creates molmol macros
help make_IDR.awk (Jun-12-12:11) purpose: create restraints for working with proxy residues
help add-linkers.awk (Sep-20-2007)
help cyana-renum-lib.awk (Sep-20-2007) renumber the atoms a cyana residue library entry
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