ChemAxon Forum Archive » Structure based predictions: Calculator Plugins & Chemical Terms

command CXCALC -S modify the CTAB block

User 247a2c5018

11-01-2006 16:31:07

I run :





cxcalc -S 2005-03-03_10.sdf logp > titi.sdf





In the new Sdfile titi.sdf, the CTAB block bas been modified.


Is it possible to store the same CTAB block than the original Sdfile (2005-03-03_10.sdf)?

ChemAxon 43e6884a7a

11-01-2006 16:41:32

Please send an example

User 247a2c5018

11-01-2006 22:23:34

input sdfile : titi.sdf


Code:



  -ISIS-  09140515022D





  0  0  0     0  0              0 V3000


M  V30 BEGIN CTAB


M  V30 COUNTS 18 19 0 0 0


M  V30 BEGIN ATOM


M  V30 1 I 6.61667 -0.4875 0 0 CHG=-1


M  V30 2 N 5.2824 -4.21672 0 0 CFG=3


M  V30 3 C 4.49756 -3.13999 0 0


M  V30 4 C 3.78613 -2.72754 0 0


M  V30 5 C 3.0718 -3.1422 0 0


M  V30 6 C 3.07307 -3.96514 0 0


M  V30 7 C 3.78867 -4.37343 0 0


M  V30 8 C 4.49884 -3.96294 0 0


M  V30 9 C 5.76176 -3.54962 0 0


M  V30 10 C 5.26896 -2.88056 0 0


M  V30 11 C 5.48353 -2.07182 0 0


M  V30 12 C 6.59794 -3.57965 0 0


M  V30 13 N 6.24539 -1.73376 0 0


M  V30 14 C 7.14174 -2.94443 0 0


M  V30 15 C 6.98203 -2.12403 0 0


M  V30 16 H 5.53977 -5.00056 0 0


M  V30 17 C 5.82917 -1.02083 0 0


M  V30 18 C 6.95 -1.31667 0 0


M  V30 END ATOM


M  V30 BEGIN BOND


M  V30 1 1 7 8


M  V30 2 2 9 10


M  V30 3 1 10 11


M  V30 4 1 2 9


M  V30 5 1 9 12


M  V30 6 1 10 3


M  V30 7 1 11 13


M  V30 8 1 8 2


M  V30 9 1 12 14


M  V30 10 2 3 8


M  V30 11 1 13 15


M  V30 12 1 14 15


M  V30 13 1 3 4


M  V30 14 1 2 16


M  V30 15 2 4 5


M  V30 16 1 13 17


M  V30 17 1 5 6


M  V30 18 1 13 18


M  V30 19 2 6 7


M  V30 END BOND


M  V30 BEGIN COLLECTION


M  V30 MDLV30/HILITE ATOMS=(18 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18) -


M  V30 BONDS=(19 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19)


M  V30 END COLLECTION


M  V30 END CTAB


M  END





$$$$












output after cxcalc -S titi.sdf > toto.sdf





Code:



  Marvin  01110623182D         





 18 19  0  0  0  0            999 V2000


    3.5446   -0.2612    0.0000 I   0  5  0  0  0  0  0  0  0  0  0  0


    2.8299   -2.2590    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0


    2.4094   -1.6821    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0


    2.0283   -1.4612    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0


    1.6456   -1.6833    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0


    1.6463   -2.1242    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0


    2.0296   -2.3429    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0


    2.4101   -2.1230    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0


    3.0867   -1.9016    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0


    2.8227   -1.5432    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0


    2.9376   -1.1099    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0


    3.5346   -1.9177    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0


    3.3457   -0.9288    0.0000 N   0  3  3  0  0  0  0  0  0  0  0  0


    3.8259   -1.5774    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0


    3.7404   -1.1379    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0


    2.9677   -2.6789    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0


    3.1228   -0.5469    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0


    3.7232   -0.7054    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0


  7  8  1  0  0  0  0


  9 10  2  0  0  0  0


 10 11  1  0  0  0  0


  2  9  1  0  0  0  0


  9 12  1  0  0  0  0


 10  3  1  0  0  0  0


 11 13  1  0  0  0  0


  8  2  1  0  0  0  0


 12 14  1  0  0  0  0


  3  8  2  0  0  0  0


 13 15  1  0  0  0  0


 14 15  1  0  0  0  0


  3  4  1  0  0  0  0


  2 16  1  0  0  0  0


  4  5  2  0  0  0  0


 13 17  1  0  0  0  0


  5  6  1  0  0  0  0


 13 18  1  0  0  0  0


  6  7  2  0  0  0  0


M  CHG  2   1  -1  13   1


M  END


>  <LOGP>


-2,54





$$$$






-------------------------





=> the CTAB block has been changed and a LOGP value is added at the end of the output sdfile


but I don't want that the CTAB block changed


is it possible?

User 247a2c5018

12-01-2006 08:57:10

the command is : output after cxcalc -S titi.sdf logp > toto.sdf

User 247a2c5018

12-01-2006 09:05:32

input :








-ISIS- 02100513522D





27 29 0 0 0 0 0 0 0 0999 V2000


-0.3806 0.4917 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


-0.3818 -0.3357 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


0.3331 -0.7485 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


1.0495 -0.3352 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


1.0466 0.4953 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


0.3313 0.9045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


1.7646 -0.7466 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


1.7659 -1.5716 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0


2.4784 -0.3329 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0


3.9074 -0.3307 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


4.6225 -0.7421 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0


3.9061 0.4943 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0


4.6238 -1.5671 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


5.3363 -0.3285 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


6.0486 -0.7400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


6.7619 -0.3271 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


6.7611 0.4988 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


6.0409 0.9100 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


5.3305 0.4947 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


3.1875 -0.7417 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0


3.1858 -1.5667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


2.6746 -2.1985 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


1.8738 -2.0697 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


1.3628 -2.7007 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


1.6543 -3.4603 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


2.4616 -3.5851 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


2.9691 -2.9529 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


11 13 1 0 0 0 0


1 2 2 0 0 0 0


11 14 1 0 0 0 0


4 7 1 0 0 0 0


14 15 2 0 0 0 0


3 4 2 0 0 0 0


15 16 1 0 0 0 0


7 8 2 0 0 0 0


16 17 2 0 0 0 0


17 18 1 0 0 0 0


7 9 1 0 0 0 0


18 19 2 0 0 0 0


19 14 1 0 0 0 0


9 20 1 0 0 0 0


4 5 1 0 0 0 0


20 21 1 4 0 0 0


20 10 1 0 0 0 0


21 22 1 0 0 0 0


2 3 1 0 0 0 0


22 23 2 0 0 0 0


10 11 1 0 0 0 0


23 24 1 0 0 0 0


5 6 2 0 0 0 0


24 25 2 0 0 0 0


10 12 2 0 0 0 0


25 26 1 0 0 0 0


6 1 1 0 0 0 0


26 27 2 0 0 0 0


27 22 1 0 0 0 0


M END


> <vrac> (3963)


50





$$$$











output :











Marvin 01120610032D





27 29 0 0 0 0 999 V2000


-0.3810 0.4923 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


-0.3822 -0.3361 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


0.3335 -0.7493 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


1.0507 -0.3356 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


1.0478 0.4959 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


0.3317 0.9055 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


1.7666 -0.7474 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


1.7679 -1.5734 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0


2.4812 -0.3333 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0


3.9118 -0.3311 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


4.6277 -0.7429 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0


3.9105 0.4949 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0


4.6290 -1.5689 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


5.3423 -0.3289 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


6.0554 -0.7408 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


6.7695 -0.3275 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


6.7687 0.4994 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


6.0477 0.9110 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


5.3365 0.4953 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


3.1911 -0.7425 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0


3.1894 -1.5685 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


2.6776 -2.2010 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


1.8759 -2.0720 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


1.3643 -2.7037 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


1.6562 -3.4642 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


2.4644 -3.5891 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


2.9724 -2.9562 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


11 13 1 0 0 0 0


1 2 2 0 0 0 0


11 14 1 0 0 0 0


4 7 1 0 0 0 0


14 15 2 0 0 0 0


3 4 2 0 0 0 0


15 16 1 0 0 0 0


7 8 2 0 0 0 0


16 17 2 0 0 0 0


17 18 1 0 0 0 0


7 9 1 0 0 0 0


18 19 2 0 0 0 0


19 14 1 0 0 0 0


9 20 1 0 0 0 0


4 5 1 0 0 0 0


20 21 1 4 0 0 0


20 10 1 0 0 0 0


21 22 1 0 0 0 0


2 3 1 0 0 0 0


22 23 2 0 0 0 0


10 11 1 0 0 0 0


23 24 1 0 0 0 0


5 6 2 0 0 0 0


24 25 2 0 0 0 0


10 12 2 0 0 0 0


25 26 1 0 0 0 0


6 1 1 0 0 0 0


26 27 2 0 0 0 0


27 22 1 0 0 0 0


M END


> <vrac>


50





> <LOGP>


4,02





$$$$

ChemAxon 43e6884a7a

12-01-2006 09:17:03

The input is V3000 type SDfile and the output is V2000 SDfile.


You can convert the output to V3000 type using


Code:
molconvert sdf:V3 toto.sdf >toto2.sdf



However the CTAB block will still not be the same. There is no way to keep the same CTAB block as CTAB is not a canonical format.


I am not sure if this is useful, but you can generate canonical strings using SMIILES:


Code:
 cxcalc -i smiles:a-H 1.sdf logp >toto2.sdf

User 247a2c5018

12-01-2006 09:29:17

for the second example , it is a V2000 format and yet the CTAB block has been changed after CXCALC -S





WHich option to avoid this change of CTAB block?

ChemAxon 43e6884a7a

12-01-2006 10:53:40

Please see may previous response: "However the CTAB block will still not be the same. There is no way to keep the same CTAB block as CTAB is not a canonical format."

User 247a2c5018

12-01-2006 11:21:35

Oh yes I understand your last post.


So is there any way to calculate LOGP by command line from a sdfile and at the output, just add the LOGP value for each structure in the input Sdfile without any change?

ChemAxon 43e6884a7a

12-01-2006 11:33:44

I don't think that we have any tool to support that, but we will discuss this. My colleague, Nora, who deals with these issues is off this week, so it might take some time to get back.

User 247a2c5018

13-01-2006 09:05:21

I run :





cxcalc logp titi.sdf > toto.txt








in toto.txt, I have





id logP


1 4,02








Is it possible to have only "4,02"?

ChemAxon fb166edcbd

14-01-2006 14:28:48

Yes, you should use the "-N hi" (no header and ID) cxcalc option:





Code:



cxcalc -N hi logp titi.sdf






About the CTAB differences: if the -S (SDF output) option is specified,


cxcalc outputs the input molecules with calculation results in SDF tags. In order to do this, an import/export operation is performed. If the CTAB changes during this process then the CTAB is changed. I think usually there are no changes, but some minor changes may occur mainly if you use a different software (e.g. ISIS) to draw the molecules and Marvin might change some flags (e.g. no-parity to either-parity in the atom block). What type of CTAB changes do you think of?