Xyza2pipe src

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various conversion programs.

Contents

Features

Cross conversion environment of NMR spectra

Cross conversion environment

This software package provides cross conversion environment for NMR 2D/3D/4D spectra among the following systems: NMRPipe, UCSF/Sparky, NMRView, XEASY (16bit)/CARA and Azara/ANSIG. And one-way conversion from VNMR (Agilent, formerly Varian) binary spectra and XWinNMR (Bruker) binary spectra.

Conversion, Transposing, Combination and 2D Projection

  • It supports transposing like NMRPipe does.
  • Usage and parameter arguments are equivalent to NMRPipe.
  • How to use:
Make a pipeline between importer and exporter of any combinations below.
  • Conversion and transposing:
Importer: File (reading) → Stream (stdout) Exporter: Stream (stdin) → File (writing)
xyza2pipe --in filename.ft (2D)
xyza2pipe --in filename%03d.ft (3D)
xyza2pipe --in filename%02d%03d.ft (4D)
ucsf2pipe --in filename.ucsf
nv2pipe --in filename.nv
xeasy2pipe --in filename.16
azara2pipe --in filename.spc
vnmr2pipe --in filename (2D)
vnmr2pipe --in filename%d or filename (3D/4D)
xwnmr2pipe --in 2rr/3rrr/4rrrr
pipe2xyza --out filename.ft (2D)
pipe2xyza --out filename%03d.ft (3D)
pipe2xyza --out filename%02d%03d.ft (4D)
pipe2ucsf --out filename.ucsf
pipe2nv --out filename.nv
pipe2xeasy --out filename.16
pipe2azara --out filename.spc
  • Combination:
Importer: File (reading) → Stream (stdout) Exporter: Stream (stdin) → File (writing)
add2pipe --in1 file1.ft --in2 file2.ft
adducsf2pipe --in1 file1.ucsf --in2 file2.ucsf
addnv2pipe --in1 file1.nv --in2 file2.nv
addxeasy2pipe --in1 file1.16 --in2 file2.16
addazara2pipe --in1 file1.spc --in2 file2.spc
addvnmr2pipe --in1 file1 --in2 file2
addxwnmr2pipe --in1 file1 --in2 file2
pipe2xyza --out filename.ft (2D)
pipe2xyza --out filename%03d.ft (3D)
pipe2xyza --out filename%02d%03d.ft (4D)
pipe2ucsf --out filename.ucsf
pipe2nv --out filename.nv
pipe2xeasy --out filename.16
pipe2azara --out filename.spc
  • 2D Projection:
Importer: File (reading) → Stream (stdout) Exporter: Stream (stdin) → File (writing)
xyza2pipe --in filename%03d.ft (3D)
xyza2pipe --in filename%02d%03d.ft (4D)
ucsf2pipe --in filename.ucsf
nv2pipe --in filename.nv
xeasy2pipe --in filename.16
azara2pipe --in filename.spc
vnmr2pipe --in filename%d or filename (3D/4D)
xwnmr2pipe --in 3rrr/4rrrr
pipe2proj --out proj.ft
pipe2proj | pipe2ucsf --out proj.ucsf
pipe2proj | pipe2nv --out proj.nv
pipe2proj | pipe2xeasy --out proj.16
pipe2proj | pipe2azara --out proj.spc


  • Effective pipeline combinations (conversion and transposing):
    • To transpose NMRPipe formatted spectra, Type xyza2pipe | pipe2xyza.
    • To convert (UCSF→NMRPipe) and transpose, Type ucsf2pipe | pipe2xyza.
    • To convert (NMRView→NMRPipe) and transpose, Type nv2pipe | pipe2xyza.
    • To convert (XEASY→NMRPipe) and transpose, Type xeasy2pipe | pipe2xyza.
    • To convert (Azara→NMRPipe) and transpose, Type azara2pipe | pipe2xyza.

    • To transpose UCSF formatted spectra, Type ucsf2pipe | pipe2ucsf.
    • To convert (NMRView→UCSF) and transpose, Type nv2pipe | pipe2ucsf.
    • To convert (XEASY→UCSF) and transpose, Type xeasy2pipe | pipe2ucsf.
    • To convert (Azara→UCSF) and transpose, Type azara2pipe | pipe2ucsf.
    • To convert (NMRPipe→UCSF) and transpose, Type xyza2pipe | pipe2ucsf.

    • To transpose NMRView formatted spectra, Type nv2pipe | pipe2nv.
    • To convert (XEASY→NMRView) and transpose, Type xeasy2pipe | pipe2nv.
    • To convert (Azara→NMRView) and transpose, Type azara2pipe | pipe2nv.
    • To convert (NMRPipe→NMRView) and transpose, Type xyza2pipe | pipe2nv.
    • To convert (UCSF→NMRView) and transpose, Type ucsf2pipe | pipe2nv.

    • To transpose XEASY formatted spectra, Type xeasy2pipe | pipe2xeasy.
    • To convert (Azara→XEASY) and transpose, Type azara2pipe | pipe2xeasy.
    • To convert (NMRPipe→XEASY) and transpose, Type xyza2pipe | pipe2xeasy.
    • To convert (UCSF→XEASY) and transpose, Type ucsf2pipe | pipe2xeasy.
    • To convert (NMRView→XEASY) and transpose, Type nv2pipe | pipe2xeasy.

    • To transpose Azara formatted spectra, Type azara2pipe | pipe2azara.
    • To convert (NMRPipe→Azara) and transpose, Type xyza2pipe | pipe2azara.
    • To convert (UCSF→Azara) and transpose, Type ucsf2pipe | pipe2azara.
    • To convert (NMRView→Azara) and transpose, Type nv2pipe | pipe2azara.
    • To convert (XEASY→Azara) and transpose, Type xeasy2pipe | pipe2azara.

    • To convert (VNMR→NMRPipe) and transpose, Type vnmr2pipe | pipe2xyza.
    • To convert (VNMR→UCSF) and transpose, Type vnmr2pipe | pipe2ucsf.
    • To convert (VNMR→NMRView) and transpose, Type vnmr2pipe | pipe2nv.
    • To convert (VNMR→XEASY) and transpose, Type vnmr2pipe | pipe2xeasy.
    • To convert (VNMR→Azara) and transpose, Type vnmr2pipe | pipe2azara.

    • To convert (XWinNMR→NMRPipe) and transpose, Type xwnmr2pipe | pipe2xyza.
    • To convert (XWinNMR→UCSF) and transpose, Type xwnmr2pipe | pipe2ucsf.
    • To convert (XWinNMR→NMRView) and transpose, Type xwnmr2pipe | pipe2nv.
    • To convert (XWinNMR→XEASY) and transpose, Type xwnmr2pipe | pipe2xeasy.
    • To convert (XWinNMR→Azara) and transpose, Type xwnmr2pipe | pipe2azara.


  • Example:
ucsf2pipe --in ./hnco.ucsf | pipe2xyza --out ./data/hnco%03d.ft
nv2pipe   --in ./hnca.nv   | pipe2xyza --out ./data/hnca%03d.ft

Special notes

Monolithic NMRPipe format is compatible with this program. See examples below.

  • Example (how to handle monolithic NMRPipe format):
 xyza2pipe --in  data%03d.ft > data.ft [NMRPipe(regular)    → NMRPipe(monolithic)]
 pipe2xyza --out data%03d.ft < data.ft [NMRPipe(monolithic) → NMRPipe(regular)]
 pipe2ucsf --out data.ucsf   < data.ft [NMRPipe(monolithic) → UCSF]
 pipe2nv   --out data.nv     < data.ft [NMRPipe(monolithic) → NMRView]

Several format conversions, such as NMRView→NMRPipe, UCSF→NMRPipe, VNMR→NMRPipe and XEASY→NMRPipe, cause to lose apodization information. This may affect result of NOESY back calculation in the Olivia system. For that cases, the conversion program assumes square of sine bell window function for direct observation axis (NMRPipe -fn SP -off 0.5 -end 0.98 -pow 2.0) and sine bell window function for the other axes (NMRPipe -fn SP -off 0.5 -end 0.98 -pow 1.0). If you want to retrieve correct apodization conditions, You should apply Fourier Transform again using either NMRPipe or Azara. On the other hand, Azara→NMRPipe conversion succeeds all apodization information and phase settings. While NMRPipe→Azara conversion doesn't.

xeasy2pipe requires a parameter file. The parameter file name should be *.param (parameter) for *.16 (XEASY spectra) where the asterisk (*) indicates common name.
azara2pipe also requires a parameter file, which was implicitly generated by Azara at the execution time. The parameter file name should be *.spc.par and the asterisk (*) indicates common name of the Azara spectra *.spc.
vnmr2pipe always requires a path to a directory that includes either procpar or procpar3d file.
xwnmr2pipe requires properly situated parameter files, known as acqu*s and proc*s.

pipe2proj is used to make NMRPipe formatted 2D projection of spectra.

  • Example:
xyza2pipe --in ./data/hnco%03d.ft | pipe2proj --out hnco_proj.ft

add2pipe is used to combine two NMRPipe formatted spectra like addNMR command.

  • Example:
add2pipe --in1 hsqc1.ft --in2 hsqc2.ft --add | pipe2xyza --out add_hsqc.ft
add2pipe --in1 hsqc1.ft --in2 hsqc2.ft --sub | pipe2xyza --out diff_hsqc.ft

defl2pipe is used to deflate dimensionarity of pseudo arrayed NMRPipe 3D/4D spectra into regular 2D spectra.

Resolving endianness

In relation to the endianness issue, program will try to detect proper endianess of file for CPU you used currently. However azara format is definitely endian dependent. If you fail in spectra conversion using pipe2azara, pipe2nv, pipe2ucsf, pipe2xeasy or pipe2xyza, Try to use '--swap' option which reverses byte order of data region.

NOTE: Improper endianness leads to crash viewer applications, to generate unrecognized file format or to generate radial spectra.

  • Example (how to settle the endianness issue in the case of conversion from Azara to NMRPipe):
If the following pipeline command leads to generate radial spectra in some configuration. 
azara2pipe --in ./hsqc.spc | pipe2xyza --out ./hsqc.ft

In our experience, '--swap' option is helpful, where the option changes the byte order of data region of the NMRPipe file.
azara2pipe --in ./hsqc.spc | pipe2xyza --swap --out ./hsqc.ft
                                         ^^^^

Download

This cross conversion environment is a part of the Olivia system:

http://fermi.pharm.hokudai.ac.jp/olivia/preview/

Meanwhile, a stand-alone version that you can use freely is also available (Last update: Nov/26/2015):

http://fermi.pharm.hokudai.ac.jp/olivia/documents/xyza2pipe.tgz

Acknowledgments

Thanks to:

  • Bruce D. Ray, NMR Center IUPUI, for general suggestions.
  • Miklos Guttman, University of California, San Diego, for contribution to support UCSF format.
  • Alexander Eletsky, University at Buffalo, for contribution to support XEASY format with code supply.
  • Tomohide Saio, Rutgers University, for contribution to develop auto-repair mechanism against partially broken file.
  • Pascal Mercier, University of Alberta, for alternative spectral regulation method relying on the origin frequency.
  • Naohiro Kobayashi, Osaka University, for reporting NMRView spectra conversion issue.

Release note

  • Oct/31/2011 ucsf2pipe and nv2pipe commands detect incorrect header information and fix them automatically.
  • Feb/14/2012 Fixed vnmr2pipe problems (distorted 2D spectra and shifted 3D spectra) and added support for varian 3D/4D complex spectra.
  • Feb/22/2012 Fixed Makefile.
  • Mar/16/2012 Added alternative spectral regulation method relying on the origin frequency. (--orig option)
  • Oct/01/2012 Fixed auto repairing routine to support pseudo-zerofill of ucsf and nv file.
  • Jan/30/2014 Added defl2pipe command to enforce dimensionarity to 2D spectra.
  • Jun/26/2015 Fixed invalid header of NMRView and UCSF spectra file.
  • Nov/16/2015 pipe2xyza allows inline transposing if filename is not specified.

Want peak list conversion?

Peak list conversion

The Olivia system provides peak list conversion among the following systems: Olivia's index format, NMRWish's tab format, Sparky's list format, NMRView's xpk format and XEASY's peaks format.

Source files

add2pipe.c

[Program] Two NMRPipe spectra → Combination → stdout stream.
add2pipe -i/--in1 inTemplate1(2D/3D/4D) -j/--in2 inTemplate2(2D/3D/4D)
 -a/--add inTemplate1 + inTemplate2 (default)
 -s/--sub inTemplate1 - inTemplate2
 -m/--mul inTemplate1 * inTemplate2
 -d/--div inTemplate1 / inTemplate2
 --c1   Scale factor for inTemplate1 (default=1.0)
 --c2   Scale factor for inTemplate2 (default=1.0)
 --xLAB X-Axis Label
 --yLAB Y-Axis Label
 --zLAB Z-Axis Label
 --aLAB A-Axis Label
 --xCAR X-Axis Center [ppm]
 --yCAR Y-Axis Center [ppm]
 --zCAR Z-Axis Center [ppm]
 --aCAR A-Axis Center [ppm]

addazara2pipe.c

[Program] Two Azara spectra → Combination → stdout stream.
addazara2pipe -i/--in1 inTemplate1(2D/3D/4D) -j/--in2 inTemplate2(2D/3D/4D)
 -a/--add inTemplate1 + inTemplate2 (default)
 -s/--sub inTemplate1 - inTemplate2
 -m/--mul inTemplate1 * inTemplate2
 -d/--div inTemplate1 / inTemplate2
 --c1   Scale factor for inTemplate1 (default=1.0)
 --c2   Scale factor for inTemplate2 (default=1.0)
 --xLAB X-Axis Label
 --yLAB Y-Axis Label
 --zLAB Z-Axis Label
 --aLAB A-Axis Label
 --xCAR X-Axis Center [ppm]
 --yCAR Y-Axis Center [ppm]
 --zCAR Z-Axis Center [ppm]
 --aCAR A-Axis Center [ppm]

addnv2pipe.c

[Program] Two NMRView spectra → Combination → stdout stream.
addnv2pipe -i/--in1 inTemplate1(2D/3D/4D) -j/--in2 inTemplate2(2D/3D/4D)
 -a/--add inTemplate1 + inTemplate2 (default)
 -s/--sub inTemplate1 - inTemplate2
 -m/--mul inTemplate1 * inTemplate2
 -d/--div inTemplate1 / inTemplate2
 --c1   Scale factor for inTemplate1 (default=1.0)
 --c2   Scale factor for inTemplate2 (default=1.0)
 --xLAB X-Axis Label
 --yLAB Y-Axis Label
 --zLAB Z-Axis Label
 --aLAB A-Axis Label
 --xCAR X-Axis Center [ppm]
 --yCAR Y-Axis Center [ppm]
 --zCAR Z-Axis Center [ppm]
 --aCAR A-Axis Center [ppm]

adducsf2pipe.c

[Program] Two UCSF spectra → Combination → stdout stream.
adducsf2pipe -i/--in1 inTemplate1(2D/3D/4D) -j/--in2 inTemplate2(2D/3D/4D)
 -a/--add inTemplate1 + inTemplate2 (default)
 -s/--sub inTemplate1 - inTemplate2
 -m/--mul inTemplate1 * inTemplate2
 -d/--div inTemplate1 / inTemplate2
 --c1   Scale factor for inTemplate1 (default=1.0)
 --c2   Scale factor for inTemplate2 (default=1.0)
 --xLAB X-Axis Label
 --yLAB Y-Axis Label
 --zLAB Z-Axis Label
 --aLAB A-Axis Label
 --xCAR X-Axis Center [ppm]
 --yCAR Y-Axis Center [ppm]
 --zCAR Z-Axis Center [ppm]
 --aCAR A-Axis Center [ppm]

adducsf2pipe.c

[Program] Two VNMR spectra → Combination → stdout stream.
addvnmr2pipe -i/--in1 inTemplate1(2D/3D/4D) -j/--in2 inTemplate2(2D/3D/4D)
 -p/--pdir1   A directory that includes VNMR procpar file1. (default=".")
 -q/--pdir2   A directory that includes VNMR procpar file2. (default=".")
 -a/--add inTemplate1 + inTemplate2 (default)
 -s/--sub inTemplate1 - inTemplate2
 -m/--mul inTemplate1 * inTemplate2
 -d/--div inTemplate1 / inTemplate2
 --c1   Scale factor for inTemplate1 (default=1.0)
 --c2   Scale factor for inTemplate2 (default=1.0)
 --xLAB X-Axis Label
 --yLAB Y-Axis Label
 --zLAB Z-Axis Label
 --aLAB A-Axis Label
 --xCAR X-Axis Center [ppm]
 --yCAR Y-Axis Center [ppm]
 --zCAR Z-Axis Center [ppm]
 --aCAR A-Axis Center [ppm]

addxeasy2pipe.c

[Program] Two XEASY spectra → Combination → stdout stream.
addxeasy2pipe -i/--in1 inTemplate1(2D/3D/4D) -j/--in2 inTemplate2(2D/3D/4D)
 -a/--add inTemplate1 + inTemplate2 (default)
 -s/--sub inTemplate1 - inTemplate2
 -m/--mul inTemplate1 * inTemplate2
 -d/--div inTemplate1 / inTemplate2
 --c1   Scale factor for inTemplate1 (default=1.0)
 --c2   Scale factor for inTemplate2 (default=1.0)
 --xLAB X-Axis Label
 --yLAB Y-Axis Label
 --zLAB Z-Axis Label
 --aLAB A-Axis Label
 --xCAR X-Axis Center [ppm]
 --yCAR Y-Axis Center [ppm]
 --zCAR Z-Axis Center [ppm]
 --aCAR A-Axis Center [ppm]

addxwnmr2pipe.c

[Program] Two XWinNMR spectra → Combination → stdout stream.
addxwnmr2pipe -i/--in1 inTemplate1(2D/3D/4D) -j/--in2 inTemplate2(2D/3D/4D)
 -a/--add inTemplate1 + inTemplate2 (default)
 -s/--sub inTemplate1 - inTemplate2
 -m/--mul inTemplate1 * inTemplate2
 -d/--div inTemplate1 / inTemplate2
 --c1   Scale factor for inTemplate1 (default=1.0)
 --c2   Scale factor for inTemplate2 (default=1.0)
 --xLAB X-Axis Label
 --yLAB Y-Axis Label
 --zLAB Z-Axis Label
 --aLAB A-Axis Label
 --xCAR X-Axis Center [ppm]
 --yCAR Y-Axis Center [ppm]
 --zCAR Z-Axis Center [ppm]
 --aCAR A-Axis Center [ppm]

azara2pipe.c

[Program] Azara spectra → stdout stream.
azara2pipe -i/--in inTemplate(2D/3D/4D)
 -x  Output X-Vector first
 -y  Output Y-Vector first
 -z  Output Z-Vector first
 -a  Output A-Vector first
 --xLAB  X-Axis Label
 --yLAB  Y-Axis Label
 --zLAB  Z-Axis Label
 --aLAB  A-Axis Label
 --xCAR  X-Axis Center [ppm]
 --yCAR  Y-Axis Center [ppm]
 --zCAR  Z-Axis Center [ppm]
 --aCAR  A-Axis Center [ppm]

checkazara.c

File check for Azara spectra.

checklabel.c

Checks axis label and convert proper name if it's required.

checknv.c

File check for NMRView spectra.

checkpipe.c

(stdin) streaming header (NMRPipe formatted) check.

checkucsf.c

File check for UCSF spectra.

checkvnmr.c

File check for VNMR spectra.

checkxeasy.c

File check for XEASY spectra.
Originally written by Masashi Yokcohi.
Modified by Alexander Eletsky - Special patches to handle submatrix tiling, permutation properly.

checkxwnmr.c

File check for XWinNMR spectra.

checkxyza.c

File check for NMRPipe spectra.

cnvhdr.c

Converts header structure.

defl2pipe.c

[Program] Deflates dimensionarity into 2D spectra → stdout stream.
defl2pipe -i/--in inTemplate(2D/3D/4D)
 -x  Output X-Vector first
 -y  Output Y-Vector first
 -z  Output Z-Vector first
 -a  Output A-Vector first
 --xLAB  X-Axis Label
 --yLAB  Y-Axis Label
 --zLAB  Z-Axis Label
 --aLAB  A-Axis Label
 --xCAR  X-Axis Center [ppm]
 --yCAR  Y-Axis Center [ppm]
 --zCAR  Z-Axis Center [ppm]
 --aCAR  A-Axis Center [ppm]

nv2pipe.c

[Program] NMRView spectra → stdout stream.
nv2pipe -i/--in inTemplate(2D/3D/4D)
 -x  Output X-Vector first
 -y  Output Y-Vector first
 -z  Output Z-Vector first
 -a  Output A-Vector first
 --xLAB  X-Axis Label
 --yLAB  Y-Axis Label
 --zLAB  Z-Axis Label
 --aLAB  A-Axis Label
 --xCAR  X-Axis Center [ppm]
 --yCAR  Y-Axis Center [ppm]
 --zCAR  Z-Axis Center [ppm]
 --aCAR  A-Axis Center [ppm]
 --ndim  dimCount

openazara.c

Opens Azara spectra.

opennv.c

Opens NMRView spectra.

openpipe.c

Opens streaming (NMRPipe formatted) spectra.

openucsf.c

Opens UCSF spectra.

openvnmr.c

Opens VNMR spectra.

openxeasy.c

Opens XEASY spectra.
Originally written by Masashi Yokcohi.
Modified by Alexander Eletsky - Special patches to handle submatrix tiling, permutation properly.
Modified by Masashi Yokcohi - Simplified implementation.

openxwnmr.c

Opens XWinNMR spectra.

openxyza.c

Opens NMRPipe spectra.

pipe2azara.c

[Program] (stdin) stream → Azara spectra.
pipe2azara -o/--out outTemplate(2D/3D/4D)
 -s/--swap  Byteswap data
 -l/--left  Left shift observable carrier frequency by sw/2
 -g/--orig  Rely on the origin frequency for spectral regulation
 --xLAB  X-Axis Label
 --yLAB  Y-Axis Label
 --zLAB  Z-Axis Label
 --aLAB  A-Axis Label
 --xCAR  X-Axis Center [ppm]
 --yCAR  Y-Axis Center [ppm]
 --zCAR  Z-Axis Center [ppm]
 --aCAR  A-Axis Center [ppm]

pipe2nv.c

[Program] (stdin) stream → NMRView spectra.
pipe2nv -o/--out outTemplate(2D/3D/4D)
 -s/--swap  Byteswap data
 -p/--pswap Byteswap parameter
 -l/--left  Left shift observable carrier frequency by sw/2
 -g/--orig  Rely on the origin frequency for spectral regulation
 --xLAB  X-Axis Label
 --yLAB  Y-Axis Label
 --zLAB  Z-Axis Label
 --aLAB  A-Axis Label
 --xCAR  X-Axis Center [ppm]
 --yCAR  Y-Axis Center [ppm]
 --zCAR  Z-Axis Center [ppm]
 --aCAR  A-Axis Center [ppm]

pipe2proj.c

[Program] (stdin) stream → Integration → NMRPipe spectra (with --out option), or stdout stream (without --out option).
pipe2proj -o/--out outTemplate
 -s/--swap  Byteswap data
 -r/--right Right shift observable carrier frequency by sw/2
 -a/--abs   Absolute mode
 --xLAB X-Axis Label
 --yLAB Y-Axis Label
 --zLAB Z-Axis Label
 --aLAB A-Axis Label
 --xCAR X-Axis Center [ppm]
 --yCAR Y-Axis Center [ppm]
 --zCAR Z-Axis Center [ppm]
 --aCAR A-Axis Center [ppm]

pipe2ucsf.c

[Program] (stdin) stream → UCSF spectra.
pipe2ucsf -o/--out outTemplate(2D/3D/4D)
 -s/--swap  Byteswap data
 -p/--pswap Byteswap parameter
 -l/--left  Left shift observable carrier frequency by sw/2
 -g/--orig  Rely on the origin frequency for spectral regulation
 --xLAB  X-Axis Label
 --yLAB  Y-Axis Label
 --zLAB  Z-Axis Label
 --aLAB  A-Axis Label
 --xCAR  X-Axis Center [ppm]
 --yCAR  Y-Axis Center [ppm]
 --zCAR  Z-Axis Center [ppm]
 --aCAR  A-Axis Center [ppm]

pipe2xeasy.c

[Program] (stdin) stream → XEASY spectra.
pipe2xeasy -o/--out outTemplate(2D/3D/4D)
 -s/--swap  Byteswap data
 -l/--left  Left shift observable carrier frequency by sw/2
 -g/--orig  Rely on the origin frequency for spectral regulation
 --xLAB  X-Axis Label
 --yLAB  Y-Axis Label
 --zLAB  Z-Axis Label
 --aLAB  A-Axis Label
 --xCAR  X-Axis Center [ppm]
 --yCAR  Y-Axis Center [ppm]
 --zCAR  Z-Axis Center [ppm]
 --aCAR  A-Axis Center [ppm]

pipe2xyza.c

[Program] (stdin) stream → NMRPipe spectra (with --out option), or stdout stream (without --out option).
pipe2xyza -o/--out outTemplate(2D/3D/4D)
 -x  Output X-Vector first
 -y  Output Y-Vector first
 -z  Output Z-Vector first
 -a  Output A-Vector first
 -s/--swap  Byteswap data
 -r/--right Right shift observable carrier frequency by sw/2
 --xLAB  X-Axis Label
 --yLAB  Y-Axis Label
 --zLAB  Z-Axis Label
 --aLAB  A-Axis Label
 --xCAR  X-Axis Center [ppm]
 --yCAR  Y-Axis Center [ppm]
 --zCAR  Z-Axis Center [ppm]
 --aCAR  A-Axis Center [ppm]

pullazara.c

Receives stream and writes Azara spectra.

pullnv.c

Receives stream and writes NMRView spectra.

pullproj.c

Receives steam and writes NMRPipe spectra (Projection).

pullucsf.c

Receives stream and writes UCSF spectra.

pullxeasy.c

Receives stream and writes XEASY spectra.

pullxyza.c

Receives stream and writes NMRPipe spectra.

pushadd.c

Streaming function for combined NMRPipe spectra.

pushaddazara.c

Streaming function for combined Azara spectra.

pushaddnv.c

Streaming function for combined NMRView spectra.

pushadducsf.c

Streaming function for combined UCSF spectra.

pushaddxeasy.c

Streaming function for combined XEASY spectra.

pushazara.c

Streaming function for Azara spectra.

pushnv.c

Streaming function for NMRView spectra.

pushucsf.c

Streaming function for UCSF spectra.

pushvnmr.c

Streaming function for VNMR spectra.

pushxeasy.c

Streaming function for XEASY spectra.

pushxwnmr.c

Streaming function for XWinNMR spectra.

pushxyza.c

Streaming function for NMRPipe spectra.

ucsf2pipe.c

[Program] UCSF spectra → stdout stream.
ucsf2pipe -i/--in inTemplate(2D/3D/4D)
 -x  Output X-Vector first
 -y  Output Y-Vector first
 -z  Output Z-Vector first
 -a  Output A-Vector first
 --xLAB  X-Axis Label
 --yLAB  Y-Axis Label
 --zLAB  Z-Axis Label
 --aLAB  A-Axis Label
 --xCAR  X-Axis Center [ppm]
 --yCAR  Y-Axis Center [ppm]
 --zCAR  Z-Axis Center [ppm]
 --aCAR  A-Axis Center [ppm]
 --ndim  dimCount

vendorpar.c

Parameter reader library for both VNMR (Agilent, formerly Varian) and XWinNMR (Bruker).

vnmr2pipe.c

[Program] VNMR (Agilent, formerly Varian) binary spectra → stdout stream.
vnmr2pipe -i/--in inTemplate(2D/3D/4D)
 -p/--pdir    A directory that includes VNMR procpar file. (default=".")
 -e/--extLeft Extract left hand of X-Axis.
 -c/--adjCAR  Adjust indirect carrier frequencies according to 1H calibration.
 -h/--adjH2O  Adjust all carrier frequencies assuming transmitter is set to H2O solvent.
 -x  Output X-Vector first
 -y  Output Y-Vector first
 -z  Output Z-Vector first
 --xLAB  X-Axis Label
 --yLAB  Y-Axis Label
 --zLAB  Z-Axis Label
 --aLAB  A-Axis Label
 --xCAR  X-Axis Center [ppm]
 --yCAR  Y-Axis Center [ppm]
 --zCAR  Z-Axis Center [ppm]
 --aCAR  A-Axis Center [ppm]
 --ndim  dimCount
 NOTE: User's phase correction is effective only in hyper-complex 2D spectra.
 --rp  0th Order X-Phase [deg]
 --lp  1st Order X-Phase [deg]
 --rp1 0th Order Y-Phase [deg]
 --lp1 1st Order Y-Phase [deg]

xeasy2pipe.c

[Program] XEASY spectra → stdout stream.
xeasy2pipe -i/--in inTemplate(2D/3D/4D)
 -x  Output X-Vector first
 -y  Output Y-Vector first
 -z  Output Z-Vector first
 -a  Output A-Vector first
 --xLAB  X-Axis Label
 --yLAB  Y-Axis Label
 --zLAB  Z-Axis Label
 --aLAB  A-Axis Label
 --xCAR  X-Axis Center [ppm]
 --yCAR  Y-Axis Center [ppm]
 --zCAR  Z-Axis Center [ppm]
 --aCAR  A-Axis Center [ppm]

xeasy2float.c

Converts scale from float (32bit) to XEASY (16bit): xeasy2float(unsigned char *x16).
Converts scale from XEASY (16bit) to float (32bit): float2xeasy(float x, unsigned char *lo16).
Originally written by Ralf W. Glaser - Native pipe2xeasy converter (some_spscan_methods.cc).
Modified by Masashi Yokochi - Translation from C++ to C language.

xwnmr2pipe.c

[Program] XWinNMR (Bruker) binary spectra → stdout stream.
xwnmr2pipe -i/--in inTemplate(2D/3D/4D)
 -e/--extLeft Extract left hand of X-Axis.
 -x  Output X-Vector first
 -y  Output Y-Vector first
 -z  Output Z-Vector first
 -a  Output A-Vector first
 --xLAB  X-Axis Label
 --yLAB  Y-Axis Label
 --zLAB  Z-Axis Label
 --aLAB  A-Axis Label
 --xCAR  X-Axis Center [ppm]
 --yCAR  Y-Axis Center [ppm]
 --zCAR  Z-Axis Center [ppm]
 --aCAR  A-Axis Center [ppm]
 --ndim  dimCount

xyza2pipe.c

[Program] NMRPipe spectra → stdout stream.
xyza2pipe -i/--in inTemplate(2D/3D/4D)
 -x  Output X-Vector first
 -y  Output Y-Vector first
 -z  Output Z-Vector first
 -a  Output A-Vector first
 --xLAB  X-Axis Label
 --yLAB  Y-Axis Label
 --zLAB  Z-Axis Label
 --aLAB  A-Axis Label
 --xCAR  X-Axis Center [ppm]
 --yCAR  Y-Axis Center [ppm]
 --zCAR  Z-Axis Center [ppm]
 --aCAR  A-Axis Center [ppm]

Other source files

Other source files in the directory without credit title were all written by Masashi Yokochi.



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