Running cxcalc from a script.

Hi all. I'm running cxcalc to extract features for a compound from a CGI script. However, some features return with a blank value when I run cxcalc from my CGI script, and when I run the exact same command directly from the command line, it works fine. My CGI is written in python, but I dont think this has anything to do with the problem. I'm speculating that I need to have some sort of environment variable or permission set.





Anyways, here is the command I'm running:





$HOME/marvin/marvinbeans/bin/cxcalc $HOME/public_html/cgi-bin/tempFiles/tempfile3727340.sdf acceptorcount accsitecount aliphaticatomcount aliphaticbondcount aliphaticringcount aromaticatomcount aromaticbondcount aromaticringcount atomcount bondcount carboaromaticringcount carboringcount chainatomcount chainbondcount cyclomaticnumber donorcount donsitecount exactmass fusedaliphaticringcount fusedaromaticringcount fusedringcount heteroaromaticringcount heteroringcount largestringsize logp mass molpol pi plattindex psa randicindex refractivity resonantcount ringatomcount ringbondcount ringcount ringcountofatom rotatablebondcount smallestringsize szegedindex tautomercount





When this command is run from the command lilne, the result looks fine:





id acceptorcount accsitecount Aliphatic atom count Aliphatic bond count Aliphatic ring count Aromatic atom count Aromatic bond count Aromatic ring count Atom count Bond count Carboaromatic ring countCarbo ring count Chain atom count Chain bond count Cyclomatic number donorcount donsitecount Exact mass Fused aliphatic ring count Fused aromatic ring count Fused ring count Heteroaromatic ring count Hetero ring count Largest ring size logP Mass molecular pI Platt index PSA Randic index Refractivity count Ring atom count Ring bond count Ring count Ring count of atom Rotatable bond count Smallest ring size Szeged index count


1 5 7 9 10 0 12 12 2 30 31 2 2 9 10 2 2 2 310.032062 00 0 0 0 6 3.63 310.683 27.24 3.50 60 58.20 9.97 75.07 148 12 12 2 0 2 6 1414 5








However, when I run it from the CGI script, I get the following:





id acceptorcount accsitecount Aliphatic atom count Aliphatic bond count Aliphatic ring count Aromatic atom count Aromatic bond count Aromatic ring count Atom count Bond count Carboaromatic ring countCarbo ring count Chain atom count Chain bond count Cyclomatic number donorcount donsitecount Exact mass Fused aliphatic ring count Fused aromatic ring count Fused ring count Heteroaromatic ring count Hetero ring count Largest ring size logP Mass molecular pI Platt index PSA Randic index Refractivity count Ring atom count Ring bond count Ring count Ring count of atom Rotatable bond count Smallest ring size Szeged index count


1 5 9 10 0 12 12 2 30 31 2 2 9 10 2 310.032062 00 0 0 0 6 3.63 310.683 27.24 3.50 60 58.20 9.97 75.07 148 12 12 2 0 2 6 5








Note how some of the fields are blank. The blank fields are:





accsitecount, donorcount, donsitecount, szegedindex





Can anyone give me any ideas about why some of the plugins are working, but some are not?





Thanks,





-Roman








P.S. here are the contents of the SDF file:











AAA


Marvin 05310620013D





21 22 0 0 0 0 999 V2000


-1.5923 0.5738 -1.2720 C 0 0 0 0 0 0 0 0 0 0 0 0


-1.2370 -0.4277 -0.5396 N 0 0 0 0 0 0 0 0 0 0 0 0


-0.8068 1.7240 -1.2553 C 0 0 0 0 0 0 0 0 0 0 0 0


-1.7557 -1.5426 -0.1333 C 0 0 0 0 0 0 0 0 0 0 0 0


-1.0260 -2.3950 0.5215 N 0 0 0 0 0 0 0 0 0 0 0 0


-2.6216 0.5166 -1.9338 O 0 0 0 0 0 0 0 0 0 0 0 0


0.6284 1.6739 -1.2226 C 0 0 0 0 0 0 0 0 0 0 0 0


-1.4261 3.0168 -1.2357 C 0 0 0 0 0 0 0 0 0 0 0 0


-2.9169 -1.8514 -0.3529 O 0 0 0 0 0 0 0 0 0 0 0 0


0.1480 -2.3140 1.1452 C 0 0 0 0 0 0 0 0 0 0 0 0


2.6556 -2.3267 2.3032 C 0 0 0 0 0 0 0 0 0 0 0 0


-2.7189 3.2001 -1.2423 F 0 0 0 0 0 0 0 0 0 0 0 0


1.3208 0.5673 -1.2546 F 0 0 0 0 0 0 0 0 0 0 0 0


4.1988 -2.3083 2.9831 Cl 0 0 0 0 0 0 0 0 0 0 0 0


0.9015 -3.5301 1.1188 C 0 0 0 0 0 0 0 0 0 0 0 0


0.6230 -1.1111 1.7737 C 0 0 0 0 0 0 0 0 0 0 0 0


2.1970 -3.5424 1.7082 C 0 0 0 0 0 0 0 0 0 0 0 0


1.9122 -1.1107 2.3686 C 0 0 0 0 0 0 0 0 0 0 0 0


0.7632 4.1242 -1.1397 C 0 0 0 0 0 0 0 0 0 0 0 0


-0.6497 4.2023 -1.1769 C 0 0 0 0 0 0 0 0 0 0 0 0


1.4023 2.8612 -1.1635 C 0 0 0 0 0 0 0 0 0 0 0 0


2 1 1 0 0 0 0


3 1 1 0 0 0 0


4 2 1 0 0 0 0


5 4 1 0 0 0 0


6 1 2 0 0 0 0


7 3 1 0 0 0 0


8 3 2 0 0 0 0


9 4 2 0 0 0 0


10 5 1 0 0 0 0


11 18 1 0 0 0 0


12 8 1 0 0 0 0


13 7 1 0 0 0 0


14 11 1 0 0 0 0


15 10 2 0 0 0 0


16 10 1 0 0 0 0


17 15 1 0 0 0 0


18 16 2 0 0 0 0


19 20 2 0 0 0 0


20 8 1 0 0 0 0


21 7 2 0 0 0 0


19 21 1 0 0 0 0


11 17 2 0 0 0 0


M END


> <CAS>


035367-38-5





> <NAME>


DIFLUBENZURON





> <WS>


8.000000000000000e-002





> <WS Temperature>


25





> <WS Data Type>


EXP





> <WS Reference>


TOMLIN,C (1997); pH 7





> <Kow>


3.880000000000000e+000





> <Kow Data Type>


EXP





> <Kow Reference>


SOTOMATSU,T ET AL. (1987)





> <VP>


9.000000000000001e-010





> <VP Temperature>


25





> <VP Data Type>


EXP





> <VP Reference>


WAUCHOPE,RD ET AL. (1991A)





> <HL>


4.600000000000000e-009





> <HL Temperature>


25





> <HL Data Type>


EST





> <HL Reference>


VP/WSOL





> <OH>


1.400000000000000e-010





> <OH Temperature>


25





> <OH Data Type>


EST





> <OH Reference>


ATKINOSN,R (1988)





> <MP>


239





$$$$

Hi,





We are examining the problem.





May be it is related to license handling: without a license key only one run is allowed for each plugin. Most of our cxcalc calculations "share" one plugin (e.g.: acceptorcount, accsitecount, donorcount, donsitecount belong to HBDAPlugin).





Do you have license keys for our plugins? Are they set in both cases (command line and CGI)?





Our software tools are free for academic users and non-commercial web sites. Follow this link if you would like to subscribe for the free usage or need more details: http://www.chemaxon.com/licensing.html





See also: http://www.chemaxon.com/jchem/doc/user/Licenses.html





Please attach the SDF file as attachment, because in this format it is hardly usable.





Regards,


Zsolt

You were right, it was a license problem. I forgot that the CGI script runs under the user "apache" and so I had to have a copy of my licenses in the apache user's .chemaxon directory as well. Thank you for your help.