|
FELIX Version 2004 for IRIX & Linux Command Reference Guide |
Who should use this guide
What FCL does
Things to be familiar with
Workstation requirements
Related books
Typographical conventions
1. Introduction
What is FCL?
Using this guide
FCL command line
Symbols and expressions
Macros
Menus
The database
Operating system access
2. FCL basics
The FCL prompt
Commands and command arguments
Case sensitivity
Errors in FCL commands
Display and context effects
Line continuation
File prefixes and suffixes
Macro file formats
Comment symbols
Tabs and spacing
3. Symbols and expressions
Reserved symbols
User-defined symbols
Symbol substitution
Local symbols
Global symbols
Arithmetic expressions
Integer vs. real expressions
Complex mathematical functions
Database functions
4. Macros
Macro directories
Writing macros
Executing macros
Passing arguments to macros
Loops
Text scrolling
Interrupting a macro
oop application: Reversing a matrix
Loop application: Accessing the database
Branching statements
go statements
gto statements
gif statements
if statements
if/then/else statements
ifx statements
exr statements
Macro-specific commands
com statements
err statements
ty and tym statements
Using FELIX to build macros
Some simple macro applications
Reading files
Plotting multiple files
5. Menus and control panels
The menu commands
Changing the menubar interface
Control panels
Output commands
Input commands
Control-panel dependencies and special behaviors
Finding your way through the menu interface
6. Real-time displays
Graphical interface tools
Buttons
Sliders
Option menus
Text entry boxes
Writing real-time display menus and macros
A very simple example
7. The database
Structure of the database
The database schema
Creating database information
Database command structure
Database files
Database entities
Database items and elements
Database item lists
dba list subcommands
Creating lists of information
Spreadsheet interface
A. Command reference
abl -- Automatic baseline flattening
abp -- Automatic baseline point selection using FLATT algorithm
abq -- Automatic selection of baseline points
abs -- Absolute value replacement of work
adb -- Add work to buffer
add -- Add number to work
aln -- Antilogarithm (exponential) of work
alt -- Alternating real/imaginary
ann -- Annotate plot
aph -- Autophase spectrum
arr -- Arrow annotation
bas -- Baseline points manipulation
bc -- Baseline correct
bft -- Bruker-Fourier transform
bir -- Read database from Insight II
bit -- Bit manipulation operators
biw -- Write database to Insight II
bld -- Build a matrix file
bml -- Get molecule name
bun -- Set bundle mode
by, bye -- Exit FELIX
cal -- Macro call
cdf -- Conditional define
cfg -- Configure memory
cgd -- Change values in the control panel
chi -- Calculate minimum chi-square value
cl -- Close a data file
clr -- Clear frame
cls -- Close output file
cmb -- Change symbol on the user interface
cmd -- List commands
cmx -- Close matrix file(s)
cnj -- Complex conjugate
cnv -- Time-domain convolution
com -- Execute FELIX commands in macros
cp -- Contour plot
cpl -- Real to complex
csh -- Circular signed shift
csl -- Circular shift left
csp -- Cubic spline baseline correction
csr -- Circular shift right
cur -- Cursor control
dba -- Database facility
dbc -- Oversampled baseline correction
dbl -- Double data size
def -- Define a symbol
der -- Derivative
dft -- Fast Fourier transform of digitally oversampled data
dr -- Draw work space and stack
drb -- Display brother cross peaks
drx -- Display cross peaks
dst, exd, don, dof -- Distributed processing commands
eif -- Macro end of block if
els -- Macro else block
em -- Exponential multiply
ena -- Enable multiple cursors
end -- Macro end statement
env -- Get a UNIX environment variable
err -- Macro branch on error condition
esc -- Test for escape key event
eva -- Evaluate expression and assign to symbol
ex -- Execute a macro
exc -- Exchange real and imaginary
exm -- Execute Multiple Macros
exp -- Expanded display
exr -- Execute a macro and return
fit -- Fit 1D peaks
flf -- FaceLift baseline correction
fli -- Frequency list manipulation
flp -- Low-point fold of work space
flt -- FLATT baseline flattening
fol -- Fold work space in half
for -- Loop for macros
fpo -- Pop FELIX window
fpu -- Push FELIX window
fra -- Manipulate graphics frames
ft -- Fast Fourier transform
ful -- Full display
fxp -- Filter cross peaks
get -- Get a symbol value
gf -- Generate FID
gif -- Macro arithmetic goto
gm -- Gaussian/Lorentzian window
gmh -- Gaussian multiply in Hz
go -- Macro unconditional branch
gre -- Greek text annotation
gto -- Macro case goto
gsp -- Generate spectrum
gv -- Get value
hav -- Halve data size
hcp -- Hard copy plot
hft -- Hilbert transform
idf -- Is defined
if -- Macro if conditional branch
Advanced if conditionals
Macro if conditional block execution
ift -- Inverse Fourier transform
inq -- Inquire If file exists
ins -- Insight II-FELIX inter-process communication
int -- Integral
inv -- Inverse of workspace
ip -- Intensity plot
jcp -- Calculate J-coupling constant
kw -- Kaiser window
ld -- List data
ldb -- Load buffer into work space
lim -- Matrix limits
lin -- Line annotation
lis -- List symbol table
lm -- List macro
loa -- Load vector from matrix
log -- Natural logarithm of work space
lmd -- Load theoretical vector
lpf -- Linear predict first points
lpl -- Linear predict last points
lps -- Solvent suppression using linear prediction
lpx -- General linear prediction
lrl -- Find local extremum
lvo -- Load volume time course
lwb -- Load work space from bundle
mat -- Open matrix
md -- Model data
mf -- Matched filter
mgv -- Matrix get data value
mpv-Matrix put data value
mmp -- Display memory map
mnu -- Menu manager
ms -- Magnitude spectrum
mul -- Multiply the work space by a number
mwb -- Multiply work by buffer
nd2 -- Neighbor detection in 2D NOESY spectrum
nd3 -- Neighbor detection in 3D NOESY spectrum
nex -- Next
no -- Generate random noise
nop -- No operation
nor -- Normalize data
np -- Null plot
old -- Recall old limits
opn -- Open output file
opt -- Felix option license inquiry or license checkin and checkout
ord -- Matrix dimension order
ovc -- Overlay contour plot
pd2 -- Prototype pattern detection in 2D
pd3 -- Prototype pattern detection in 3D
pen -- Define a new colored pen
ph -- Phase correction
pic -- Peak pick and label
For ND Spectra:
pla -- Redisplay 3D object
pol -- Polynomial baseline correction
pop -- Pop the display stack
ppm -- Convert Between points and PPM
prb -- Residue type probability scoring
prf -- Formatted print
ps -- Power spectrum
psa -- Suggest assignment for a set of patterns
psh -- Push the work space onto the buffer stack
pso -- Polynomial-based solvent suppression
puf -- Formatted put
pur -- Purge symbol table
put -- Put record
pv -- Put value
pxp -- Automated peak assignment
qsb -- Skewed sinebell window
qss -- Skewed sinebell squared window
ra -- Read ASCII data
rb -- Read Bruker file
re -- Read a file (old format)
rea -- Read record from ASCII file
rec -- Rectangle annotation
red -- Reduce complex to real
ref -- Set shift reference
ret -- Macro subroutine return
rev -- Reverse
rf -- Read Felix for Windows file
rft -- Real Fourier transform
rj -- Read JEOL file
rm -- Read macro
rmx -- Reference matrix
rn -- Read file (new format)
rph -- Real-time phase
rpl -- Real-time polynomial baseline correction
rv -- Read Varian file
sar -- Autoscreen command
sb -- Sinebell window
sca -- Scale factor for dimension
seg -- Integral segments
sep -- Separate real and imaginary
set -- Set work space to a value
shl -- Shift left
shr -- Shift right
smo -- Binomial smooth
sp -- Stack plot
sqz -- Squeeze a matrix
srv -- Set range to value
ss -- Sinebell squared window
ssh -- Signed shift
ssp -- Synthesize spectrum from peak list
ste -- Stella peak picker
stb -- Store work space to buffer
sto -- Store vector to matrix
str -- String manipulation operators
sub -- Sub-string extraction
swb -- Store work space to bundle
sys -- Execute system commands
tex -- Text annotation
til -- Tile plot
tim -- A basic clock and chronograph
tm -- Trapezoidal multiplication
ty -- Type text
tyf -- Type a file of text to the user
tym -- Type text to motif
unf -- Unfold work
ver -- FELIX version number and release date
vol -- Integrate cross peak volumes
wa -- Write an ASCII data file
wai -- Wait a while
wm -- Write macro
wn -- Write a file (new format)
wr -- Write a file (old format)
xpa -- Cross-peak assignments from shifts and spins
xpk -- Cross-peak operations
xpl -- Make a list of peaks
xps -- Generate spins and shifts from cross peaks
xsh -- Exchange stack head with work space
xss -- Simulated annealing assignment functions
xyl -- Atom list manipulation
xyp -- X,Y data pair manipulation
xyz -- Atom manipulation
ze -- Zero workspace
zf -- Zero fill
zgt -- Zero greater than
zi -- Zero imaginary
zlt -- Zero less than
zr -- Zero real
zp -- Null plot
B. Symbol reference
absint -- Absolute intensity
absmg1, absmg2, absmg3, absmg4 -- Absolute magnitude peak search window size
animat -- Animation switch
annang -- Annotation angle
annasz -- Annotation arrow size
anncol -- Annotation color
annfil -- Annotation file
annlst -- Annotation line style
annpfx -- Annotation prefix
annsiz -- Annotation text size
annunt -- Annotation units
autox, autoy, autoz -- Autorotation X-, Y-, and Z-angle increments
autpse -- Autorotation pause
autrot -- Autorotation switch
cntrot -- Autorotation count
axsobj -- Axis object switch
axtype -- 1D Axis type
b1size, b2size, b3size, b4size -- Matrix brick size
basent -- Baseline points entity
bcfrac -- Baseline correct fraction
bckrad -- Back-calculation cutoff radius
bigpt -- Big point in workspace
blkwht -- Black/White reverse switch
button -- Button status
celpxx -- Cell X pixels
celpxy -- Cell Y pixels
center -- Center plot switch
chi -- Minimum chi-square value
clmode -- Contour level mode
cntrot -- Autorotation count
colcur -- Color of cursor
conmod -- Contour spacing modifier
contyp -- Contour interpolation type
cutoff -- Cutoff for stack plot
cycle -- Color cycle length
d1size, d2size, d3size, d4size -- Matrix size
d1vect, d2vect, d3vect, d4vect -- Current vector
datfil -- 1D Data file
datpfx -- 1D Data file prefix
datsiz -- Data size
datype -- Data type
dbafil -- Database file
dbapfx -- Database file prefix
deltax, deltay -- Delta x and y for stack plot
dimen -- Number of Matrix Dimensions
dimplt -- Number of plot dimensions
disply -- Current display type
draw3d -- 3D capability switch
drwbox -- Draw box switch
drwclv -- Draw contour levels switch
drwpks -- Draw peaks switch
drwxpk -- Draw cross peaks switch
dspmod -- Display mode
erase -- Erase display switch
etcpfx -- Runtime files prefix
first -- First point
flxver -- FELIX version number
fontsw -- Font switch
fontsz -- Font size
frsize -- Frame size
gbroad -- Gaussian coefficient
gibbs -- Gibbs filter switch
graysc -- Gray scale switch
grid -- Grid switch
gridco -- Grid color
gridst -- Grid style
hafwid -- Halfwidth factor
harddv -- Hardcopy destination
hardmo -- Hardcopy mode
hardx0, hardy0, hardxs, hardys -- Hardcopy origin and size
hfwid1, hfwid2, hfwid3, hfwid4 -- Minimum peak half width
hilim -- Current plot region high limits
hndshk -- HPGL plotter handshake
inbias, inslop -- Integral bias and slope corrections
intolp -- Integral overlap
item -- Menu item
iwidth -- Interval width for baseline correction
keyhit -- Keyboard character struck
last -- Last point
lbroad -- Line broadening
level -- Contour level
linpts -- Lines/Points for draw command
loc3x0, loc3x1, loc3y0,loc3y1, loc3z0, loc3z1 -- 3D Locator endpoint coordinates
lolim1, hilim1, lolim2, hilim2, lolim3, hilim3, lolim4,hilim4 -- Current plot region low and high limits
macfil -- Macro file
macpfx -- Macro file prefix
matfil -- Matrix file
matpfx -- Matrix file prefix
maxvol -- Maximum volume slots in entity
mdlcf1, mdlcf2 -- Model data coefficients 1 and 2 (matrix factor)
mdlpke -- Model data peak entity ID
mdlvle -- Model data volume entity ID
mdlvsl -- Model data volume slot number
menu -- Menu name selected
mframe -- Matrix framesize
minzee -- Cutoff Z-magnetization for back-calculation
mnufil -- Menu file
mnumod -- Default frame position
mnupfx -- Menu file prefix
mscale -- Matrix scale factor
msgfil -- Message file
msgpfx -- Message file prefix
msgc1, msgc2, msgi1, msgi2, msgr1, msgr2 -- Character, integer, and real message parameters
ndctyp -- Normalized device coordinate type
newhpglc -- control contouring in HPGL plots
newpostc -- control contouring in PostScript plots
nframe -- Number of stack frames
nlevel -- Number of contour levels
norval -- Normalization value
objmem -- Object memory size limit
order1, order2, order3, order4 -- Matrix dimension order
orient -- Postscript orientation
ovrlap -- Stack overlap
paphgt -- Paper height
papwid -- Paper width
pennum -- Starting color
phase0 -- Zero-order phase
phase1 -- First-order phase
picent -- 1D peaks entity
pivot -- phase correction pivot
pksent -- Cross peak entity
pksobj -- Peaks object switch
pkstyl -- 1D peak display style
pkunit -- Units for picking peaks
plotd1, plotd2, plotd3, plotd4 -- Plot dimension
pltann -- Annotation switch
pltmod -- Plot mode
pltobj -- Plot object switch
pltusr -- Position plot manually switch
posneg -- Negative level switch
ppmmod -- PPM mode switch
proj1 -- Type of 1D projection onto x axis
proj2 -- Type of 1D projection onto y axis
projct -- Graphics projection type
projsz -- Size of 1D projections
pwidth -- Pen width
redraw -- Automatic backing store of plots
refpt -- Reference point
refsh -- Reference shift
rowinc -- Row increment
scale -- Plot scale factor
schfil -- Schema file
schpfx -- Schema file prefix
segent -- Integral segments entity
segint -- Segmented integral switch
sfreq -- Spectrometer frequency
slant -- Character slant angle
smalpt -- Small point in workspace
stack -- Stack depth
status -- Command status
steang -- Stereo angle
stereo -- Stereo switch
stesep -- Stereo separation
stkord -- 1D Stack display order
swidth -- Spectral width
taucee -- Correlation time
thick -- Character thickness
thresh -- Threshold for 1D peakpick
title -- Spectrum title
tphas0, tphas1 -- Total zero and first-order phase
value -- Data value
vector -- Vectors in bundle
verify -- Macro verification mode
volent -- Volume entity name
volobj -- Volume object switch
wshift -- Sinebell shift
wskew -- Sinebell skew
x0pnt, y0pnt, x1pnt, y1pnt -- Cursor position
xangle, yangle, zangle -- Euler angles
xcells, ycells -- Number of character cells
xpixel, ypixel -- Number of pixels
xpklbl -- Cross peak label switch
xsize, ysize -- Plot size
xwalk, ywalk -- Walking menu position
xyzent -- Coordinate entity
xzero, yzero -- Plot origin
y0pnt
y1pnt
yangle
ycells
ypixel
ysize
ywalk
yzero
zangle
C. Macro examples
4dv.mac
diag.mac
dss.mac
eval_point.mac
lpf_d2.mac
madd.mac
msub.mac
mult.mac
old2new.mac
psi.mac
psr.mac
rev_bundle.mac
zap.mac