Re: [Open Babel] Problem with --gen3D Open Babel 2.3.1
The problem is solved in the 2.3.2 release! Thank you very much. > I'm on trunk version and conversion is successful. > > [maciek@fokus ~]$ obabel > -:"OP(=O)(O)OC[C@H]1O[C@H]([C@@H]([C@@H]1O)OCC(=O)c1c2cc3c3cc2ccc1)n1cnc2c(=O)[nH]c(N)nc12" > -ismi -omol2 --gen3d > @MOLECULE > * > 65 70 0 0 0 > SMALL > GASTEIGER > > @ATOM > 1 O 2.4378 -1.0815 -1.3719 O.3 1 LIG1 > -0.3026 > 2 P 3.0749 -0.3174 -2.6155 P.3 1 LIG1 > 0.4724 > 3 O 2.7869 -0.9641 -3.9250 O.2 1 LIG1 > -0.2275 > 4 O 2.39471.1237 -2.5121 O.3 1 LIG1 > -0.3026 > 5 O 4.6155 -0.0562 -2.2781 O.3 1 LIG1 > -0.2841 > 6 C 4.92810.6358 -1.0775 C.3 1 LIG1 > 0.0878 > 7 C 6.44000.7658 -0.9139 C.3 1 LIG1 > 0.1134 > 8 H 6.63371.27870.0371 H 1 LIG1 > 0.0647 > 9 O 7.0680 -0.5260 -0.8323 O.3 1 LIG1 > -0.3456 > 10 C 8.4243 -0.3312 -1.2825 C.3 1 LIG1 > 0.1669 > 11 H 9.01260.0714 -0.4460 H 1 LIG1 > 0.0866 > 12 C 8.32860.6891 -2.4259 C.3 1 LIG1 > 0.1325 > 13 H 8.09330.1773 -3.3661 H 1 LIG1 > 0.0668 > 14 C 7.10531.5310 -2.0602 C.3 1 LIG1 > 0.1138 > 15 H 6.45641.6286 -2.9389 H 1 LIG1 > 0.0647 > 16 O 7.44322.8443 -1.6133 O.3 1 LIG1 > -0.3864 > 17 O 9.53861.4395 -2.5310 O.3 1 LIG1 > -0.3616 > 18 C 9.67442.1744 -3.7350 C.3 1 LIG1 > 0.1110 > 19 C 11.00512.9408 -3.8305 C.2 1 LIG1 > 0.1891 > 20 O 11.06663.9722 -4.5000 O.2 1 LIG1 > -0.2896 > 21 C 12.22722.3768 -3.1511 C.ar1 LIG1 > 0.0274 > 22 C 13.28463.1806 -2.6386 C.ar1 LIG1 > -0.0067 > 23 C 13.38434.5856 -2.7792 C.ar1 LIG1 > -0.0456 > 24 C 14.49745.3100 -2.3189 C.ar1 LIG1 > -0.0173 > 25 C 14.60696.6928 -2.5271 C.ar1 LIG1 > -0.0540 > 26 C 15.73127.3914 -2.0859 C.ar1 LIG1 > -0.0612 > 27 C 16.75626.7180 -1.4275 C.ar1 LIG1 > -0.0612 > 28 C 16.65885.3451 -1.2088 C.ar1 LIG1 > -0.0540 > 29 C 15.53584.6327 -1.6521 C.ar1 LIG1 > -0.0173 > 30 C 15.43453.2538 -1.4549 C.ar1 LIG1 > -0.0463 > 31 C 14.34162.5283 -1.9439 C.ar1 LIG1 > -0.0166 > 32 C 14.32391.1430 -1.7498 C.ar1 LIG1 > -0.0540 > 33 C 13.32020.3686 -2.3061 C.ar1 LIG1 > -0.0605 > 34 C 12.31320.9818 -3.0393 C.ar1 LIG1 > -0.0506 > 35 N 9.0010 -1.6299 -1.5935 N.ar1 LIG1 > -0.2854 > 36 C 9.1117 -2.6662 -0.6901 C.ar1 LIG1 > 0.1005 > 37 N 9.7437 -3.7105 -1.1934 N.ar1 LIG1 > -0.2286 > 38 C 10.0575 -3.3272 -2.4693 C.ar1 LIG1 > 0.1721 > 39 C 10.8003 -4.0264 -3.5002 C.ar1 LIG1 > 0.2803 > 40 O 11.3004 -5.1305 -3.4030 O.2 1 LIG1 > -0.2654 > 41 N 10.9390 -3.2641 -4.6565 N.ar1 LIG1 > -0.2934 > 42 H 11.5202 -3.6693 -5.3707 H 1 LIG1 > 0.1716 > 43 C 10.5123 -1.9716 -4.7838 C.ar1 LIG1 > 0.1950 > 44 N 10.8575 -1.3503 -5.9379 N.pl3 1 LIG1 > -0.3289 > 45 N 9.8361 -1.3330 -3.8695 N.ar1 LIG1 > -0.1963 > 46 C 9.6292 -2.0498 -2.7375 C.ar1 LIG1 > 0.1712 > 47 H 1.5706 -1.4615 -1.6035 H 1 LIG1 > 0.2220 > 48 H 2.25031.4923 -3.4028 H 1 LIG1 > 0.2220 > 49 H 4.50590.0926 -0.2269 H 1 LIG1 > 0.0592 > 50 H 4.48231.6356 -1.1203 H 1 LIG1 > 0.0592 > 51 H 6.98833.4857 -2.1865 H 1 LIG1 > 0.2100 > 52 H 8.87002.9152 -3.7947 H 1 LIG1 > 0.0643 > 53 H 9.59961.5131 -4.6068 H 1 LIG1 > 0.0643 > 54 H 12.60145.1378 -3.2940 H 1 LIG1 > 0.0630 > 55 H 13.81827.2328 -3.0467 H 1 LIG1 > 0.0624 > 56 H 15.80628.4609 -2.2602 H 1 LIG1 > 0.0618 > 57 H 17.63367.2590 -1.0851 H 1 LIG1 > 0.0618 > 58 H 17.46964.8314 -0.6973 H 1 LIG1 > 0.0624 > 59 H 16.23872.7318 -0.9381 H 1 LIG1 > 0.0630 > 60 H 15.11470.6480 -1.1888 H 1 LIG1 > 0.0624 > 61 H 13.3210 -0.7101 -2.1754 H 1 LIG1 > 0.0618 > 62 H 11.58160.3470 -3.5196 H 1 LIG1 > 0.0625 > 63 H 8.7236 -2.60070.3194
Re: [Open Babel] Problem with --gen3D Open Babel 2.3.1
I'm on trunk version and conversion is successful. [maciek@fokus ~]$ obabel -:"OP(=O)(O)OC[C@H]1O[C@H]([C@@H]([C@@H]1O)OCC(=O)c1c2cc3c3cc2ccc1)n1cnc2c(=O)[nH]c(N)nc12" -ismi -omol2 --gen3d @MOLECULE * 65 70 0 0 0 SMALL GASTEIGER @ATOM 1 O 2.4378 -1.0815 -1.3719 O.3 1 LIG1 -0.3026 2 P 3.0749 -0.3174 -2.6155 P.3 1 LIG10.4724 3 O 2.7869 -0.9641 -3.9250 O.2 1 LIG1 -0.2275 4 O 2.39471.1237 -2.5121 O.3 1 LIG1 -0.3026 5 O 4.6155 -0.0562 -2.2781 O.3 1 LIG1 -0.2841 6 C 4.92810.6358 -1.0775 C.3 1 LIG10.0878 7 C 6.44000.7658 -0.9139 C.3 1 LIG10.1134 8 H 6.63371.27870.0371 H 1 LIG10.0647 9 O 7.0680 -0.5260 -0.8323 O.3 1 LIG1 -0.3456 10 C 8.4243 -0.3312 -1.2825 C.3 1 LIG10.1669 11 H 9.01260.0714 -0.4460 H 1 LIG10.0866 12 C 8.32860.6891 -2.4259 C.3 1 LIG10.1325 13 H 8.09330.1773 -3.3661 H 1 LIG10.0668 14 C 7.10531.5310 -2.0602 C.3 1 LIG10.1138 15 H 6.45641.6286 -2.9389 H 1 LIG10.0647 16 O 7.44322.8443 -1.6133 O.3 1 LIG1 -0.3864 17 O 9.53861.4395 -2.5310 O.3 1 LIG1 -0.3616 18 C 9.67442.1744 -3.7350 C.3 1 LIG10.1110 19 C 11.00512.9408 -3.8305 C.2 1 LIG10.1891 20 O 11.06663.9722 -4.5000 O.2 1 LIG1 -0.2896 21 C 12.22722.3768 -3.1511 C.ar1 LIG10.0274 22 C 13.28463.1806 -2.6386 C.ar1 LIG1 -0.0067 23 C 13.38434.5856 -2.7792 C.ar1 LIG1 -0.0456 24 C 14.49745.3100 -2.3189 C.ar1 LIG1 -0.0173 25 C 14.60696.6928 -2.5271 C.ar1 LIG1 -0.0540 26 C 15.73127.3914 -2.0859 C.ar1 LIG1 -0.0612 27 C 16.75626.7180 -1.4275 C.ar1 LIG1 -0.0612 28 C 16.65885.3451 -1.2088 C.ar1 LIG1 -0.0540 29 C 15.53584.6327 -1.6521 C.ar1 LIG1 -0.0173 30 C 15.43453.2538 -1.4549 C.ar1 LIG1 -0.0463 31 C 14.34162.5283 -1.9439 C.ar1 LIG1 -0.0166 32 C 14.32391.1430 -1.7498 C.ar1 LIG1 -0.0540 33 C 13.32020.3686 -2.3061 C.ar1 LIG1 -0.0605 34 C 12.31320.9818 -3.0393 C.ar1 LIG1 -0.0506 35 N 9.0010 -1.6299 -1.5935 N.ar1 LIG1 -0.2854 36 C 9.1117 -2.6662 -0.6901 C.ar1 LIG10.1005 37 N 9.7437 -3.7105 -1.1934 N.ar1 LIG1 -0.2286 38 C 10.0575 -3.3272 -2.4693 C.ar1 LIG10.1721 39 C 10.8003 -4.0264 -3.5002 C.ar1 LIG10.2803 40 O 11.3004 -5.1305 -3.4030 O.2 1 LIG1 -0.2654 41 N 10.9390 -3.2641 -4.6565 N.ar1 LIG1 -0.2934 42 H 11.5202 -3.6693 -5.3707 H 1 LIG10.1716 43 C 10.5123 -1.9716 -4.7838 C.ar1 LIG10.1950 44 N 10.8575 -1.3503 -5.9379 N.pl3 1 LIG1 -0.3289 45 N 9.8361 -1.3330 -3.8695 N.ar1 LIG1 -0.1963 46 C 9.6292 -2.0498 -2.7375 C.ar1 LIG10.1712 47 H 1.5706 -1.4615 -1.6035 H 1 LIG10.2220 48 H 2.25031.4923 -3.4028 H 1 LIG10.2220 49 H 4.50590.0926 -0.2269 H 1 LIG10.0592 50 H 4.48231.6356 -1.1203 H 1 LIG10.0592 51 H 6.98833.4857 -2.1865 H 1 LIG10.2100 52 H 8.87002.9152 -3.7947 H 1 LIG10.0643 53 H 9.59961.5131 -4.6068 H 1 LIG10.0643 54 H 12.60145.1378 -3.2940 H 1 LIG10.0630 55 H 13.81827.2328 -3.0467 H 1 LIG10.0624 56 H 15.80628.4609 -2.2602 H 1 LIG10.0618 57 H 17.63367.2590 -1.0851 H 1 LIG10.0618 58 H 17.46964.8314 -0.6973 H 1 LIG10.0624 59 H 16.23872.7318 -0.9381 H 1 LIG10.0630 60 H 15.11470.6480 -1.1888 H 1 LIG10.0624 61 H 13.3210 -0.7101 -2.1754 H 1 LIG10.0618 62 H 11.58160.3470 -3.5196 H
Re: [Open Babel] Problem with --gen3D Open Babel 2.3.1
Have you tried it with OB 2.3.2? Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2013/1/20 David García Aristegui > OK, is an open bug http://sourceforge.net/p/openbabel/bugs/833/ > > > Hello, i'm trying to assign 3D coordinates to this SMILES structure > > > > OP(=O)(O)OC[C@H]1O[C@H]([C@@H]([C@ > @H]1O)OCC(=O)c1c2cc3c3cc2ccc1)n1cnc2c(=O)[nH]c(N)nc12 > > > > obabel is unable to resolve the structure > > > > time obabel --gen3D -ismi 3.3_30.smi -omol2 -O 3.3_30.mol2 > > 1 molecule converted > > > > real 6m8.107s > > user 6m7.947s > > sys 0m0.020s > > > > But the mol2 files looks like... > > > > @MOLECULE > > * > > 65 70 0 0 0 > > SMALL > > GASTEIGER > > > > @ATOM > > 1 O -nan -nan -nan O.3 1 LIG1 > > -0.3026 > > 2 P -nan -nan -nan P.3 1 LIG1 > > 0.4724 > > 3 O -nan -nan -nan O.2 1 LIG1 > > -0.2275 > > (...) > > > > Any ideas, is this a known bug? > > Best > > > regards.-- > > Master HTML5, CSS3, ASP.NET, MVC, AJAX, Knockout.js, Web API and > > much more. Get web development skills now with LearnDevNow - > > 350+ hours of step-by-step video tutorials by Microsoft MVPs and experts. > > SALE $99.99 this month only -- learn more at: > > > http://p.sf.net/sfu/learnmore_122812___ > > OpenBabel-discuss mailing list > > OpenBabel-discuss@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > > > > > > -- > Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, > MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current > with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft > MVPs and experts. ON SALE this month only -- learn more at: > http://p.sf.net/sfu/learnmore_123012 > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnmore_123012___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Problem with --gen3D Open Babel 2.3.1
OK, in the News section of the Openbabel main page is announced "2011-10-17 Open Babel 2.3.1 Released only", i'm downloading the 2.3.2 release. I will try to do the conversion with the new release, but the bug is "Milestone: 2.3.x". By the way, would you be so kind to try to do the conversion, if you have a 2.3.2 version available? Best regards. > Have you tried it with OB 2.3.2? > > > Pozdrawiam, | Best regards, > Maciek Wójcikowski > mac...@wojcikowski.pl > > > 2013/1/20 David García Aristegui > >> OK, is an open bug http://sourceforge.net/p/openbabel/bugs/833/ >> >> > Hello, i'm trying to assign 3D coordinates to this SMILES structure >> > >> > OP(=O)(O)OC[C@H]1O[C@H]([C@@H]([C@ >> @H]1O)OCC(=O)c1c2cc3c3cc2ccc1)n1cnc2c(=O)[nH]c(N)nc12 >> > >> > obabel is unable to resolve the structure >> > >> > time obabel --gen3D -ismi 3.3_30.smi -omol2 -O 3.3_30.mol2 >> > 1 molecule converted >> > >> > real 6m8.107s >> > user 6m7.947s >> > sys 0m0.020s >> > >> > But the mol2 files looks like... >> > >> > @MOLECULE >> > * >> > 65 70 0 0 0 >> > SMALL >> > GASTEIGER >> > >> > @ATOM >> > 1 O -nan -nan -nan O.3 1 LIG1 >> > -0.3026 >> > 2 P -nan -nan -nan P.3 1 LIG1 >> > 0.4724 >> > 3 O -nan -nan -nan O.2 1 LIG1 >> > -0.2275 >> > (...) >> > >> > Any ideas, is this a known bug? >> > Best >> > >> regards.-- >> > Master HTML5, CSS3, ASP.NET, MVC, AJAX, Knockout.js, Web API and >> > much more. Get web development skills now with LearnDevNow - >> > 350+ hours of step-by-step video tutorials by Microsoft MVPs and >> experts. >> > SALE $99.99 this month only -- learn more at: >> > >> http://p.sf.net/sfu/learnmore_122812___ >> > OpenBabel-discuss mailing list >> > OpenBabel-discuss@lists.sourceforge.net >> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >> > >> >> >> >> >> -- >> Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, >> MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current >> with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft >> MVPs and experts. ON SALE this month only -- learn more at: >> http://p.sf.net/sfu/learnmore_123012 >> ___ >> OpenBabel-discuss mailing list >> OpenBabel-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >> > -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnmore_123012 ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Problem with --gen3D Open Babel 2.3.1
OK, is an open bug http://sourceforge.net/p/openbabel/bugs/833/ > Hello, i'm trying to assign 3D coordinates to this SMILES structure > > OP(=O)(O)OC[C@H]1O[C@H]([C@@H]([C@@H]1O)OCC(=O)c1c2cc3c3cc2ccc1)n1cnc2c(=O)[nH]c(N)nc12 > > obabel is unable to resolve the structure > > time obabel --gen3D -ismi 3.3_30.smi -omol2 -O 3.3_30.mol2 > 1 molecule converted > > real 6m8.107s > user 6m7.947s > sys 0m0.020s > > But the mol2 files looks like... > > @MOLECULE > * > 65 70 0 0 0 > SMALL > GASTEIGER > > @ATOM > 1 O -nan -nan -nan O.3 1 LIG1 > -0.3026 > 2 P -nan -nan -nan P.3 1 LIG1 > 0.4724 > 3 O -nan -nan -nan O.2 1 LIG1 > -0.2275 > (...) > > Any ideas, is this a known bug? > Best > regards.-- > Master HTML5, CSS3, ASP.NET, MVC, AJAX, Knockout.js, Web API and > much more. Get web development skills now with LearnDevNow - > 350+ hours of step-by-step video tutorials by Microsoft MVPs and experts. > SALE $99.99 this month only -- learn more at: > http://p.sf.net/sfu/learnmore_122812___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnmore_123012 ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
