Available for the Intel/Linux platform.
To download the software, the file files.tar.gz suffices.
The files structin_elements.dat and cvtstr_pref.dat should reside in the directory from where cvtstr.exe is called, otherwise environment variables STRUCTIN_ELEMENTS and/of CVTSTR_PREF should be set prior to calling cvtstr.exe. structin_elements.dat contains element and isotope data from the periodic table and cvtstr_pref.dat contains the preferences.
The executable cvtstr.exe can perform three tasks: file conversion, structure analysis, and plotting (Postscript file generation). For structure validation, the analysis mode should be used. The program has a simple command-line interface.
Two sample input files (sample.sdf and tartrates.sdf) are provided, illustrating some of the complaints the validation program can produce. Just call cvtstr.exe and reply with "A" (to request an analysis), "SFDILE" (to indicate an SD file), and "sample" or "tartrates".
The program produces two output files: for sample.sdf, these are sample_ana.sdf and sample_ana.txt. The sdfile contains canonicalized and standardized structural representations of the input molecules, except for those which had errors that prevented further analysis (e.g., too many atoms/bonds, valence violations). The text file contains the analysis results. For each input molecule a number of fields are calculated, e.g., for the fifth entry in sample.sdf (note that it is the fourth entry in the output!):
## 4 Chiral Absolute 1 1 0 0 354B626A IK C03066 NM 3-Hydroxy-L-glutamate TY 1 ST a SD 1 SU 1 BD 0 BU 0 RC 0 US a,C\,C|,C,N,C,O,O,O,C,O,O,1-2,1-3,1-4,2-5,2-6,3=7,3-8,5-9,9=10,9-11 UC n,C,C,C,N,C,O,O,O,C,O,O,1-2,1-3,1-4,2-5,2-6,3=7,3-8,5-9,9=10,9-11 MF C5H9NO5 MW 163.129 EM 163.0481 MZ 100% 163.0481
|ID||BioMeta Compound ID|
|IK||KEGG Compound ID|
|TY||structure type (3 = polymeric, 2 = generic, 1 = normal)|
|ST||stereochemistry (a= absolute, m = meso, r = relative, x = racemic, n = none)|
|SD||number of defined sp3 stereocenters|
|SU||number of undefined sp3 stereocenters|
|BD||number of defined stereo double bonds|
|BU||number of undefined stereo double bonds|
|RC||number of rings|
|US||unique (canonical) string including stereochemistry|
|UC||unique (canonical) string excluding stereochemistry|
|MZ||M/Z peak with abundance (currently only 100% and exact mass)|