xyza2pipe

The xyza2pipe provides a cross conversion environment of higher dimensional NMR spectra (2D/3D/4D) between the following systems: NMRPipe, UCSF/Sparky, NMRView, XEASY (16bit)/CARA and Azara/ANSIG. It is possible to read VNMR (Agilent, formerly Varian) or XWinNMR (Bruker) binary spectra. This is open-source version branched from Olivia project.

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)	Projection	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` or `pipe2proj --out proj.ft;`	`pipe2ucsf --out proj.ucsf` `pipe2nv --out proj.nv` `pipe2xeasy --out proj.16` `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](http://en.wikipedia.org/wiki/Endianness 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

Acknowledgments

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.
Nicholas Fitzkee, Mississippi State University, for reporting invalid Sparky spectra issue.
Maxim Mayzel, Swedish NMR Centrum, for reporting invalid block size when data size is odd.
Ekaterina Burakova, Ludwig-Maximilians-Universität München, for reporting issue in reading UCSF 4D spectra header.
Douglas J. Kojetin, Scripps Research, for reporting issue of inconsistency between data point and block size in NMRView/NMRFx format.
Henry Wetton, ETH Zurich, for reporting inconsistency of XEASY parameter filename.

Release notes

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.
Feb 07, 2017: Released v1.0.0 @ GitHub, Inc. under Apache License V2.
Jun 30, 2017: Released v1.0.1, Fixed invalid header of UCSF spectra file.
Jun 30, 2017: Released v1.0.2, Set big endian as default for UCSF spectra.
Oct 12, 2017: Released v1.0.3, Fixed problem with block size when data size is odd.
Feb 28, 2019: Released v1.0.4, Fixed problem in reading UCSF 4D spectra header.
Feb 24, 2021: Released v1.0.5, Resolved inconsistency between data point and block size [Issue #3]. v1.0.3 and v1.0.4 users should update to v1.0.5 or later.
Feb 20, 2024: Released v1.0.6, Fixed inconsistency of XEASY parameter filename [Issue #4].

Executable files

add2pipe: 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
  --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: 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
  --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: 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
  --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: 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
  --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: 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
  --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: 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
  --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: 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
  --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: 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]

defl2pipe: 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: 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

pipe2azara: 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: 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: 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: stdin stream → UCSF spectra

 pipe2ucsf -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]

pipe2xeasy: 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: 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]

ucsf2pipe: 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

vnmr2pipe: 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: 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]

xwnmr2pipe: 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: 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]

Name		Name	Last commit message	Last commit date
Latest commit History 61 Commits
LICENSE		LICENSE
Makefile		Makefile
NOTICE		NOTICE
README.md		README.md
add2pipe.c		add2pipe.c
addazara2pipe.c		addazara2pipe.c
addnv2pipe.c		addnv2pipe.c
adducsf2pipe.c		adducsf2pipe.c
addvnmr2pipe.c		addvnmr2pipe.c
addxeasy2pipe.c		addxeasy2pipe.c
addxwnmr2pipe.c		addxwnmr2pipe.c
azara2pipe.c		azara2pipe.c
checkazara.c		checkazara.c
checkdefl.c		checkdefl.c
checklabel.c		checklabel.c
checknv.c		checknv.c
checkpipe.c		checkpipe.c
checkucsf.c		checkucsf.c
checkvnmr.c		checkvnmr.c
checkxeasy.c		checkxeasy.c
checkxwnmr.c		checkxwnmr.c
checkxyza.c		checkxyza.c
cnvhdr.c		cnvhdr.c
defl2pipe.c		defl2pipe.c
initpars.c		initpars.c
libMath.c		libMath.c
libMath.h		libMath.h
libMatrix.c		libMatrix.c
libMatrix.h		libMatrix.h
libString.c		libString.c
libString.h		libString.h
nv2pipe.c		nv2pipe.c
openazara.c		openazara.c
opennv.c		opennv.c
openpipe.c		openpipe.c
openucsf.c		openucsf.c
openvnmr.c		openvnmr.c
openxeasy.c		openxeasy.c
openxwnmr.c		openxwnmr.c
openxyza.c		openxyza.c
pipe2azara.c		pipe2azara.c
pipe2nv.c		pipe2nv.c
pipe2proj.c		pipe2proj.c
pipe2ucsf.c		pipe2ucsf.c
pipe2xeasy.c		pipe2xeasy.c
pipe2xyza.c		pipe2xyza.c
pullazara.c		pullazara.c
pullnv.c		pullnv.c
pullproj.c		pullproj.c
pullucsf.c		pullucsf.c
pullxeasy.c		pullxeasy.c
pullxyza.c		pullxyza.c
pushadd.c		pushadd.c
pushaddazara.c		pushaddazara.c
pushaddnv.c		pushaddnv.c
pushadducsf.c		pushadducsf.c
pushaddvnmr.c		pushaddvnmr.c
pushaddxeasy.c		pushaddxeasy.c
pushaddxwnmr.c		pushaddxwnmr.c
pushazara.c		pushazara.c
pushnv.c		pushnv.c
pushucsf.c		pushucsf.c
pushvnmr.c		pushvnmr.c
pushxeasy.c		pushxeasy.c
pushxwnmr.c		pushxwnmr.c
pushxyza.c		pushxyza.c
ucsf2pipe.c		ucsf2pipe.c
vendorpar.c		vendorpar.c
vendorpar.h		vendorpar.h
vnmr2pipe.c		vnmr2pipe.c
xeasy2float.c		xeasy2float.c
xeasy2pipe.c		xeasy2pipe.c
xwnmr2pipe.c		xwnmr2pipe.c
xyza2pipe.c		xyza2pipe.c
xyza2pipe.h		xyza2pipe.h

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xyza2pipe

Conversion, Transposing, Combination and 2D Projection

Special notes

Resolving endianness

Acknowledgments

Release notes

Executable files

add2pipe: Two NMRPipe spectra → Combination → stdout stream

addazara2pipe: Two Azara spectra → Combination → stdout stream

addnv2pipe: Two NMRView spectra → Combination → stdout stream

adducsf2pipe: Two UCSF spectra → Combination → stdout stream

adducsf2pipe: Two VNMR spectra → Combination → stdout stream

addxeasy2pipe: Two XEASY spectra → Combination → stdout stream

addxwnmr2pipe: Two XWinNMR spectra → Combination → stdout stream

azara2pipe: Azara spectra → stdout stream

defl2pipe: Deflates dimensionarity into 2D spectra → stdout stream

nv2pipe: NMRView spectra → stdout stream

pipe2azara: stdin stream → Azara spectra

pipe2nv: stdin stream → NMRView spectra

pipe2proj: stdin stream → Integration → NMRPipe spectra (with --out option) or stdout stream (without --out option)

pipe2ucsf: stdin stream → UCSF spectra

pipe2xeasy: stdin stream → XEASY spectra

pipe2xyza: stdin stream → NMRPipe spectra (with --out option) or stdout stream (without --out option)

ucsf2pipe: UCSF spectra → stdout stream

vnmr2pipe: VNMR (Agilent, formerly Varian) binary spectra → stdout stream

xeasy2pipe: XEASY spectra → stdout stream

xwnmr2pipe: XWinNMR (Bruker) binary spectra → stdout stream

xyza2pipe: NMRPipe spectra → stdout stream

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yokochi47/xyza2pipe

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Repository files navigation

xyza2pipe

Conversion, Transposing, Combination and 2D Projection

Special notes

Resolving endianness

Acknowledgments

Release notes

Executable files

add2pipe: Two NMRPipe spectra → Combination → stdout stream

addazara2pipe: Two Azara spectra → Combination → stdout stream

addnv2pipe: Two NMRView spectra → Combination → stdout stream

adducsf2pipe: Two UCSF spectra → Combination → stdout stream

adducsf2pipe: Two VNMR spectra → Combination → stdout stream

addxeasy2pipe: Two XEASY spectra → Combination → stdout stream

addxwnmr2pipe: Two XWinNMR spectra → Combination → stdout stream

azara2pipe: Azara spectra → stdout stream

defl2pipe: Deflates dimensionarity into 2D spectra → stdout stream

nv2pipe: NMRView spectra → stdout stream

pipe2azara: stdin stream → Azara spectra

pipe2nv: stdin stream → NMRView spectra

pipe2proj: stdin stream → Integration → NMRPipe spectra (with --out option) or stdout stream (without --out option)

pipe2ucsf: stdin stream → UCSF spectra

pipe2xeasy: stdin stream → XEASY spectra

pipe2xyza: stdin stream → NMRPipe spectra (with --out option) or stdout stream (without --out option)

ucsf2pipe: UCSF spectra → stdout stream

vnmr2pipe: VNMR (Agilent, formerly Varian) binary spectra → stdout stream

xeasy2pipe: XEASY spectra → stdout stream

xwnmr2pipe: XWinNMR (Bruker) binary spectra → stdout stream

xyza2pipe: NMRPipe spectra → stdout stream

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