hi, using OB I've encountered some rather unexpected behavior whentrying to use the --canonical flag: If I apply the babel (or obabel) command with the --canonical flag repeatedly to the same structure I get different results
e.g., if i start with a molecule can-gefitinib.xyz a small molecule drug with a fairly normal geometry(included below) and say: prompt> /usr/local/babel3/bin/obabel -ixyz can-gefitinib.xyz -oxyz -O b3-1-can-gefitinib.xyz --canonical prompt> /usr/local/babel3/bin/obabel -ixyz b3-1-can-gefitinib.xyz -oxyz -O b3-2-can-gefitinib.xyz --canonical prompt> /usr/local/babel3/bin/obabel -ixyz b3-2-can-gefitinib.xyz -oxyz -O b3-3-can-gefitinib.xyz --canonical prompt> /usr/local/babel3/bin/obabel -ixyz b3-3-can-gefitinib.xyz -oxyz -O b3-4-can-gefitinib.xyz --canonical prompt> /usr/local/babel3/bin/obabel -ixyz b3-4-can-gefitinib.xyz -oxyz -O b3-5-can-gefitinib.xyz --canonical I find that the order of atoms in b3-1-can-gefitinib.xyz is different from that in b3-2-can-gefitinib.xyzwhile b3-1-can-gefitinib.xyz has the same order as b3-3-can-gefitinib.xyz, etc ...happens, both with version 2.4 and 3. I tried this with mdl mol files and here the result is as expected (all files identical),so this might occur with xyz files only, but since no warning is issued when combiningxyz files and the --canonical flag this is rather dangerous.. mic 55 gefitinib H -0.10480 -5.19460 -0.98040 C 0.24530 -4.21620 -0.67490 N -0.68720 -3.35590 -0.23500 N 1.57150 -3.99530 -0.77970 C -0.21040 -2.15190 0.13380 C 2.01390 -2.78280 -0.40280 N -1.15770 -1.20930 0.60570 C 1.13450 -1.79750 0.07530 C 3.36800 -2.46510 -0.47600 C -2.51530 -1.00340 0.31370 H -0.85170 -0.72990 1.44800 C 1.60850 -0.53300 0.46630 H 4.07220 -3.20990 -0.84400 C 3.84720 -1.21000 -0.08900 C -3.01950 -1.32450 -0.95030 C -3.37250 -0.47610 1.28410 H 0.94090 0.23920 0.83590 C 2.96360 -0.25130 0.38000 O 5.18110 -0.94720 -0.17950 H -2.37500 -1.72260 -1.72960 C -4.36850 -1.12040 -1.24080 H -2.98380 -0.22450 2.26900 C -4.72140 -0.27150 0.99350 O 3.41870 0.98410 0.76170 C 5.98010 -1.25020 0.96230 H -4.75600 -1.36800 -2.22460 C -5.21950 -0.59370 -0.26910 Cl -5.76680 0.37870 2.19690 C 3.46790 1.98780 -0.24290 H 7.01550 -0.98040 0.73710 H 5.93780 -2.32070 1.18670 H 5.64820 -0.67070 1.82950 F -6.51340 -0.40260 -0.56390 C 3.23370 3.34540 0.40570 H 2.74780 1.79530 -1.04760 H 4.46890 1.97030 -0.68910 C 1.86870 3.41410 1.08300 H 3.39940 4.15530 -0.31050 H 3.98880 3.48680 1.19060 N 0.80650 3.17060 0.10930 H 1.75190 4.39540 1.56120 H 1.82130 2.66710 1.88490 C -0.50760 3.14330 0.76650 C 0.82080 4.19400 -0.94540 H -0.54390 2.34230 1.51380 H -0.69680 4.09550 1.27870 C -1.60000 2.89960 -0.27080 H 0.69400 5.19410 -0.51090 H 1.74840 4.18480 -1.52360 C -0.30350 3.92660 -1.94200 H -1.49620 1.91520 -0.74280 H -2.58400 2.93570 0.20740 O -1.56660 3.91380 -1.27560 H -0.33310 4.72180 -2.69390 H -0.15890 2.97600 -2.47000
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