charge for more than one fragment

If more than one fragment in input file. The charges of all the atoms can be calculated by visual interface,but not all can be calculated by command line.





Such as mol file as followed.


129927-33-9


three fragments





68 67 1 V2000


-1.8184 2.4716 -0.5785 C 0 0 0


-3.0870 3.0980 -0.0595 C 0 0 0


-0.8826 2.1688 0.5935 C 0 0 0


-2.1495 1.1910 -1.3007 C 0 0 0


-1.1755 3.3746 -1.4803 O 0 0 0


-3.3865 4.4111 -0.3700 C 0 0 0


-3.9539 2.3575 0.7225 C 0 0 0


0.3740 1.4671 0.0746 C 0 0 0


-0.4886 3.4768 1.2826 C 0 0 0


-2.7613 0.1908 -0.6473 O 0 0 0


-1.8642 1.0647 -2.4680 O 0 0 0


-4.5503 4.9859 0.1062 C 0 0 0


-5.1174 2.9321 1.1985 C 0 0 0


1.3098 1.1643 1.2465 C 0 0 0


0.4472 3.1740 2.4546 C 0 0 0


-2.9660 -1.0877 -1.3045 C 0 0 0


-5.4142 4.2474 0.8926 C 0 0 0


1.7038 2.4723 1.9356 C 0 0 0


-3.6050 -2.0249 -0.3663 C 0 0 0


-3.8671 -0.8948 -2.5258 C 0 0 0


-1.6163 -1.6535 -1.7507 C 0 0 0


-4.1146 -2.7724 0.3819 C 0 0 0


-4.7536 -3.7096 1.3200 C 0 0 0


-4.9606 -5.0030 0.6551 N 0 0 0


-5.5979 -5.8869 1.6403 C 0 0 0


-5.9471 -4.7772 -0.4098 C 0 0 0


-4.6930 -7.0920 1.9048 C 0 0 0


-5.4513 -5.4168 -1.7082 C 0 0 0


13.4682 -0.8541 0.5232 O 0 0 0


22.0882 -1.1846 -0.2435 Cl 0 0 0


-1.2340 1.3627 0.0000 H 0 0 0


-0.6655 4.0909 0.0000 H 0 0 0


-2.6962 4.9559 0.0000 H 0 0 0


-3.8451 1.4849 0.0000 H 0 0 0


-0.3501 0.9681 0.0000 H 0 0 0


0.5012 0.5970 0.0000 H 0 0 0


-0.2236 4.3153 0.0000 H 0 0 0


-1.3288 3.7361 0.0000 H 0 0 0


-4.6593 5.8585 0.0000 H 0 0 0


-5.8083 2.3881 0.0000 H 0 0 0


1.0448 0.3258 0.0000 H 0 0 0


2.1500 0.9050 0.0000 H 0 0 0


1.1713 3.6730 0.0000 H 0 0 0


0.3200 4.0441 0.0000 H 0 0 0


-6.2487 4.5247 0.0000 H 0 0 0


2.5253 2.1586 0.0000 H 0 0 0


2.0760 3.2690 0.0000 H 0 0 0


-3.6830 -0.0349 0.0000 H 0 0 0


-4.7270 -0.7107 0.0000 H 0 0 0


-4.0512 -1.7547 0.0000 H 0 0 0


-1.9563 -2.4645 0.0000 H 0 0 0


-0.8053 -1.9935 0.0000 H 0 0 0


-1.2763 -0.8425 0.0000 H 0 0 0


-5.2467 -2.9815 0.0000 H 0 0 0


-5.6121 -3.9001 0.0000 H 0 0 0


-6.2559 -5.3035 0.0000 H 0 0 0


-6.2445 -6.4829 0.0000 H 0 0 0


-6.0084 -3.9000 0.0000 H 0 0 0


-6.7687 -5.0908 0.0000 H 0 0 0


-5.3962 -7.6200 0.0000 H 0 0 0


-4.1650 -7.7952 0.0000 H 0 0 0


-3.9898 -6.5640 0.0000 H 0 0 0


-6.1463 -5.9555 0.0000 H 0 0 0


-4.9126 -6.1118 0.0000 H 0 0 0


-4.7563 -4.8781 0.0000 H 0 0 0


12.5888 -0.8541 0.0000 H 0 0 0


14.3476 -0.8541 0.0000 H 0 0 0


22.9676 -1.1846 0.0000 H 0 0 0


1 2 1 0


1 3 1 0


1 4 1 0


1 5 1 0


2 6 2 0


2 7 1 0


3 8 1 0


3 9 1 0


4 10 1 0


4 11 2 0


6 12 1 0


7 13 2 0


8 14 1 0


9 15 1 0


10 16 1 0


12 17 2 0


14 18 1 0


16 19 1 0


16 20 1 0


16 21 1 0


19 22 3 0


22 23 1 0


23 24 1 0


24 25 1 0


24 26 1 0


25 27 1 0


26 28 1 0


13 17 1 0


15 18 1 0


3 31 1 0


5 32 1 0


6 33 1 0


7 34 1 0


8 35 1 0


8 36 1 0


9 37 1 0


9 38 1 0


12 39 1 0


13 40 1 0


14 41 1 0


14 42 1 0


15 43 1 0


15 44 1 0


17 45 1 0


18 46 1 0


18 47 1 0


20 48 1 0


20 49 1 0


20 50 1 0


21 51 1 0


21 52 1 0


21 53 1 0


23 54 1 0


23 55 1 0


25 56 1 0


25 57 1 0


26 58 1 0


26 59 1 0


27 60 1 0


27 61 1 0


27 62 1 0


28 63 1 0


28 64 1 0


28 65 1 0


29 66 1 0


29 67 1 0


30 68 1 0


M END


$$$$








command : cxcalc inputfile charge


The charges of two small fragments can't be calculated.





Thanks!

Hi,





This is the normal behaviour of the charge calculation in cxcalc. cxcalc tool performs the calculation on the largest fragment of the input molecule.





cxcalc is a batch processing tool, it is mainly used for calculating results on a number of molecules stored in an SDfile. If there are (for example) 1000 molecules in the SDfile on which we run the calculation, then we expect to get 1000 results, even if there are molecules with more than one fragment in that file. That's why we have to return one result/molecule.





Best regards,


Zsolt