LACS

Liya Wang's (wangli@cshl.edu) code from 2012-11-30 with a few bits of python added.

PubMed ID: 19436955

doi: 10.1007/s10858-009-9324-0

Tested on matlab 2011b linux x86_64 (centos 5).

Initial version: run in matlab:

>> LACS( 'test_in.txt', 'test_out.txt' );

generates test_out.txt and offset_test_out.txt.

To build a "standalone" exe at NMRFAM:

/opt/MATLAB/R2011b/bin/mcc -m -W main -R '-nojvm,-nodisplay' -I /root/lacs_test/ -d /root/lacs_test/bin/ LACS 

• 2m07_1_A.lacs_in - input test data.
• 2m07_1_A.lacs_out - corresp. output plot

See scripts in the python subdirectory for examples of dealing with LACS input and output files.

Input matrix

%4.0f      %3.0f      %7.2f      %7.2f      %7.2f      %7.2f     %7.2f     %7.2f  %7.2f
seq_No      resid      CA         CB         HA         C         H         N      pH

CA..N are CS values for corresp. atoms except for GLY "HA" is (HA2 + HA3)/2. Use -100.0 for missing values.

resid is from the lookup table:

{ "ALA" : 1, "CYS" : 2, "ASP" : 3, "GLU" : 4,
"PHE" : 5, "GLY" : 6, "HIS" : 7, "ILE" : 8,
"LYS" : 9, "LEU" : 10, "MET" : 11, "ASN" : 12,
"PRO" : 13, "GLN" : 14, "ARG" : 15, "SER" : 16,
"THR" : 17, "VAL" : 18, "TRP" : 19, "TYR" : 20,
"X" : 21 }

Output

% lacs codes: 0: outlier, 1: normal, 2: endpoints for line 1, 3: endpoints for line 2
% seq label x_name y_name x_val y_val lacs_code
...
% offsets:
OFFATOMS:     CA    CB    HA     C     H     N
OFFVALUES:  0.25  0.25 -----  0.95 -0.06 -0.62

See example.svg: rows with lacs codes 2 and 3 are used to draw the cyan "midlines", rows with code 1: to draw the "normal" values in blue, and code 0: the outlier in red.

Sample drawing code is in python/lacs2svg_pychart.py