date:20180924

Re: [Rdkit-discuss] [ext] online sdf to mol2 converter

2018-09-24 Thread John Mayfield

The joy of aromaticity models. Via Noel if you're running the (dev/master)
version of OpenBabel you can specify *-aa* to take the aromaticity from the
input. For example

>obabel -:o11 -omol2 -aa
> @MOLECULE
> *
>  5 5 0 0 0
> SMALL
> GASTEIGER
> @ATOM
>   1 O   0.0.0. O.2 1  UNL1 -0.4473
>   2 C   0.0.0. C.ar 1
> UNL10.1798
>   3 C   0.0.0. C.ar 1
> UNL10.0439
>   4 C   0.0.0. C.ar 1
> UNL10.0439
>   5 C   0.0.0. C.ar 1
> UNL10.1798
> @BOND
>  1 1 2   ar
>  2 2 3   ar
>  3 3 4   ar
>  4 4 5   ar
>  5 1 5   ar
> 1 molecule converted
> >obabel -:O1C=CC=C1 -omol2 -aa
> @MOLECULE
> *
>  5 5 0 0 0
> SMALL
> GASTEIGER
> @ATOM
>   1 O   0.0.0. O.2 1  UNL1 -0.4473
>   2 C   0.0.0. C.2 1 UNL10.1798
>   3 C   0.0.0. C.2 1 UNL10.0439
>   4 C   0.0.0. C.2 1 UNL10.0439
>   5 C   0.0.0. C.2 1 UNL10.1798
> @BOND
>  1 1 21
>  2 2 32
>  3 3 41
>  4 4 52
>  5 1 51
> 1 molecule converted


However Mol2 support is still not likely to be great.

On Mon, 24 Sep 2018 at 16:14, Volkamer, Andrea 
wrote:

> Maybe try NAOMI from Matthias Rarey's group (
> https://www.zbh.uni-hamburg.de/forschung/amd/software/naomi.html)
>
> Best, Andrea
>
> 
>
> Prof. Dr. Andrea Volkamer
>
> In-silico Toxicology Group
> ,
> Institute of Physiology, Charité Universitätsmedizin Berlin
>
> Campus Mitte: Virchowweg 6, 10117 Berlin
>
> Phone: +49 30 - 450 528 504
> E-Mail: andrea.volka...@charite.de
> --
> *Von:* Thomas Evangelidis [teva...@gmail.com]
> *Gesendet:* Montag, 24. September 2018 16:37
> *An:* RDKit Discuss
> *Betreff:* [ext] [Rdkit-discuss] online sdf to mol2 converter
>
> Greetings,
>
> Is anybody aware of a good sdf to mol2 file converter that is not based
> on OpenBabel? I want to avoid problems like the following, which I
> currently solve with Maestro. Basically, the problem is with O40 which
> -according to antechamber from AmberTools- should be sp3 within a
> non-aromatic pentameric ring, as opposed to OpenBabel which wants it to
> be sp2 within an aromatic pentameric ring.
>
> OpenBabel (AmberTools complain about the valence of O40):
>
> @MOLECULE
> BACE7
>  98 102 0 0 0
> SMALL
> GASTEIGER
>
> @ATOM
>   1 C   4.49061.0444  -22.8214 C.3 1  LIG1
>  -0.0624
>   2 C   4.89220.9339  -21.3406 C.3 1  LIG1
>  -0.0421
>   3 C   4.7328   -0.5268  -20.8573 C.3 1  LIG1
>  -0.0504
>   4 C   5.8712   -1.4883  -21.3104 C.3 1  LIG1
>  -0.0528
>   5 C   5.8678   -2.8681  -20.5852 C.3 1  LIG1
>  -0.0516
>   6 C   5.7796   -2.6627  -19.0768 C.3 1  LIG1
>  -0.0371
>   7 C   6.0082   -3.8328  -18.1147 C.3 1  LIG1
> 0.0156
>   8 N   5.0491   -3.7436  -16.9811 N.am1  LIG1
>  -0.2907
>   9 C   5.3910   -3.1904  -15.7259 C.2 1  LIG1
> 0.2471
>  10 O   4.9860   -3.7155  -14.6679 O.2 1  LIG1
>  -0.2700
>  11 C   6.1926   -1.9707  -15.7016 C.ar1  LIG1
> 0.0384
>  12 C   7.2723   -1.8151  -14.8219 C.ar1  LIG1
>  -0.0373
>  13 C   8.0748   -0.6639  -14.8950 C.ar1  LIG1
> 0.0383
>  14 C   7.75940.3295  -15.8386 C.ar1  LIG1
>  -0.0373
>  15 C   6.65290.1798  -16.6946 C.ar1  LIG1
> 0.0381
>  16 C   5.9088   -0.9874  -16.6449 C.ar1  LIG1
>  -0.0375
>  17 C   6.37581.1928  -17.7374 C.2 1  LIG1
> 0.2444
>  18 O   7.35751.7202  -18.3089 O.2 1  LIG1
>  -0.2702
>  19 N   5.05411.4981  -18.2116 N.am1  LIG1
>  -0.3060
>  20 C   4.83152.5154  -19.2554 C.3 1  LIG1
> 0.0508
>  21 C   4.04791.9160  -20.4590 C.3 1  LIG1
>  -0.0295
>  22 C   4.12783.7525  -18.6377 C.3 1  LIG1
> 0.0859
>  23 C   4.96604.3781  -17.5041 C.3 1  LIG1
> 0.0240
>  24 N   4.28425.5876  -17.0101 N.3 1  LIG1
>  -0.3095
>  25 C   5.17776.6776  -16.6101 C.3 1  LIG1
> 0.0213
>  26 C   6.01187.1928  -17.7645 C.ar1  LIG1
>  -0.0333
>  27 C   7.41347.0911  -17.6697 C.ar1  LIG1
>  -0.0573
>  28 C   8.23017.5127  -18.7170 C.ar1  LIG1
>  -0.0612
>  29 C   7.6590

Re: [Rdkit-discuss] [ext] online sdf to mol2 converter

2018-09-24 Thread Volkamer, Andrea

Maybe try NAOMI from Matthias Rarey's group 
(https://www.zbh.uni-hamburg.de/forschung/amd/software/naomi.html)

Best, Andrea



Prof. Dr. Andrea Volkamer

In-silico Toxicology 
Group,
 Institute of Physiology, Charité Universitätsmedizin Berlin

Campus Mitte: Virchowweg 6, 10117 Berlin
Phone: +49 30 - 450 528 504
E-Mail: andrea.volka...@charite.de

Von: Thomas Evangelidis [teva...@gmail.com]
Gesendet: Montag, 24. September 2018 16:37
An: RDKit Discuss
Betreff: [ext] [Rdkit-discuss] online sdf to mol2 converter

Greetings,

Is anybody aware of a good sdf to mol2 file converter that is not based on 
OpenBabel? I want to avoid problems like the following, which I currently solve 
with Maestro. Basically, the problem is with O40 which -according to 
antechamber from AmberTools- should be sp3 within a non-aromatic pentameric 
ring, as opposed to OpenBabel which wants it to be sp2 within an aromatic 
pentameric ring.

OpenBabel (AmberTools complain about the valence of O40):

@MOLECULE
BACE7
 98 102 0 0 0
SMALL
GASTEIGER

@ATOM
  1 C   4.49061.0444  -22.8214 C.3 1  LIG1   -0.0624
  2 C   4.89220.9339  -21.3406 C.3 1  LIG1   -0.0421
  3 C   4.7328   -0.5268  -20.8573 C.3 1  LIG1   -0.0504
  4 C   5.8712   -1.4883  -21.3104 C.3 1  LIG1   -0.0528
  5 C   5.8678   -2.8681  -20.5852 C.3 1  LIG1   -0.0516
  6 C   5.7796   -2.6627  -19.0768 C.3 1  LIG1   -0.0371
  7 C   6.0082   -3.8328  -18.1147 C.3 1  LIG10.0156
  8 N   5.0491   -3.7436  -16.9811 N.am1  LIG1   -0.2907
  9 C   5.3910   -3.1904  -15.7259 C.2 1  LIG10.2471
 10 O   4.9860   -3.7155  -14.6679 O.2 1  LIG1   -0.2700
 11 C   6.1926   -1.9707  -15.7016 C.ar1  LIG10.0384
 12 C   7.2723   -1.8151  -14.8219 C.ar1  LIG1   -0.0373
 13 C   8.0748   -0.6639  -14.8950 C.ar1  LIG10.0383
 14 C   7.75940.3295  -15.8386 C.ar1  LIG1   -0.0373
 15 C   6.65290.1798  -16.6946 C.ar1  LIG10.0381
 16 C   5.9088   -0.9874  -16.6449 C.ar1  LIG1   -0.0375
 17 C   6.37581.1928  -17.7374 C.2 1  LIG10.2444
 18 O   7.35751.7202  -18.3089 O.2 1  LIG1   -0.2702
 19 N   5.05411.4981  -18.2116 N.am1  LIG1   -0.3060
 20 C   4.83152.5154  -19.2554 C.3 1  LIG10.0508
 21 C   4.04791.9160  -20.4590 C.3 1  LIG1   -0.0295
 22 C   4.12783.7525  -18.6377 C.3 1  LIG10.0859
 23 C   4.96604.3781  -17.5041 C.3 1  LIG10.0240
 24 N   4.28425.5876  -17.0101 N.3 1  LIG1   -0.3095
 25 C   5.17776.6776  -16.6101 C.3 1  LIG10.0213
 26 C   6.01187.1928  -17.7645 C.ar1  LIG1   -0.0333
 27 C   7.41347.0911  -17.6697 C.ar1  LIG1   -0.0573
 28 C   8.23017.5127  -18.7170 C.ar1  LIG1   -0.0612
 29 C   7.65908.0307  -19.8750 C.ar1  LIG1   -0.0583
 30 C   6.26568.1500  -19.9835 C.ar1  LIG1   -0.0445
 31 C   5.44307.7541  -18.9156 C.ar1  LIG1   -0.0539
 32 C   5.66018.6452  -21.2852 C.3 1  LIG1   -0.0215
 33 C   4.75339.8610  -21.0668 C.3 1  LIG1   -0.0586
 34 C   4.90027.5146  -21.9875 C.3 1  LIG1   -0.0586
 35 O   3.94404.7344  -19.6282 O.3 1  LIG1   -0.3887
 36 C   9.2604   -0.5139  -14.0265 C.ar1  LIG10.2271
 37 N   9.6773   -1.4569  -13.1548 N.ar1  LIG1   -0.2175
 38 C  10.7852   -0.9156  -12.6169 C.ar1  LIG10.0663
 39 C  11.00060.3233  -13.1739 C.ar1  LIG10.1125
 40 O  10.04220.5438  -14.0357 O.2 1  LIG1   -0.4436
 41 C   3.7184   -4.3654  -17.1815 C.3 1  LIG10.0487
 42 C   3.6849   -5.7921  -16.6077 C.3 1  LIG1   -0.0422
 43 C   2.5948   -3.4594  -16.6885 C.ar1  LIG1   -0.0273
 44 C   2.1036   -2.4496  -17.5372 C.ar1  LIG1   -0.0568
 45 C   1.0992   -1.5797  -17.1055 C.ar1  LIG1   -0.0614
 46 C   0.5629   -1.7113  -15.8244 C.ar1  LIG1   -0.0617
 47 C   1.0304   -2.7139  -14.9731 C.ar1  LIG1   -0.0614
 48 C   2.0402   -3.5825  -15.3976 C.ar1  LIG1   -0.0568
 49 H   5.96441.2247  -21.2739 H   1  LIG10.0299
 50 H   5.7964

[Rdkit-discuss] online sdf to mol2 converter

2018-09-24 Thread Thomas Evangelidis

Greetings,

Is anybody aware of a good sdf to mol2 file converter that is not based on
OpenBabel? I want to avoid problems like the following, which I currently
solve with Maestro. Basically, the problem is with O40 which -according to
antechamber from AmberTools- should be sp3 within a non-aromatic pentameric
ring, as opposed to OpenBabel which wants it to be sp2 within an aromatic
pentameric ring.

OpenBabel (AmberTools complain about the valence of O40):

@MOLECULE
BACE7
 98 102 0 0 0
SMALL
GASTEIGER

@ATOM
  1 C   4.49061.0444  -22.8214 C.3 1  LIG1   -0.0624
  2 C   4.89220.9339  -21.3406 C.3 1  LIG1   -0.0421
  3 C   4.7328   -0.5268  -20.8573 C.3 1  LIG1   -0.0504
  4 C   5.8712   -1.4883  -21.3104 C.3 1  LIG1   -0.0528
  5 C   5.8678   -2.8681  -20.5852 C.3 1  LIG1   -0.0516
  6 C   5.7796   -2.6627  -19.0768 C.3 1  LIG1   -0.0371
  7 C   6.0082   -3.8328  -18.1147 C.3 1  LIG10.0156
  8 N   5.0491   -3.7436  -16.9811 N.am1  LIG1   -0.2907
  9 C   5.3910   -3.1904  -15.7259 C.2 1  LIG10.2471
 10 O   4.9860   -3.7155  -14.6679 O.2 1  LIG1   -0.2700
 11 C   6.1926   -1.9707  -15.7016 C.ar1  LIG10.0384
 12 C   7.2723   -1.8151  -14.8219 C.ar1  LIG1   -0.0373
 13 C   8.0748   -0.6639  -14.8950 C.ar1  LIG10.0383
 14 C   7.75940.3295  -15.8386 C.ar1  LIG1   -0.0373
 15 C   6.65290.1798  -16.6946 C.ar1  LIG10.0381
 16 C   5.9088   -0.9874  -16.6449 C.ar1  LIG1   -0.0375
 17 C   6.37581.1928  -17.7374 C.2 1  LIG10.2444
 18 O   7.35751.7202  -18.3089 O.2 1  LIG1   -0.2702
 19 N   5.05411.4981  -18.2116 N.am1  LIG1   -0.3060
 20 C   4.83152.5154  -19.2554 C.3 1  LIG10.0508
 21 C   4.04791.9160  -20.4590 C.3 1  LIG1   -0.0295
 22 C   4.12783.7525  -18.6377 C.3 1  LIG10.0859
 23 C   4.96604.3781  -17.5041 C.3 1  LIG10.0240
 24 N   4.28425.5876  -17.0101 N.3 1  LIG1   -0.3095
 25 C   5.17776.6776  -16.6101 C.3 1  LIG10.0213
 26 C   6.01187.1928  -17.7645 C.ar1  LIG1   -0.0333
 27 C   7.41347.0911  -17.6697 C.ar1  LIG1   -0.0573
 28 C   8.23017.5127  -18.7170 C.ar1  LIG1   -0.0612
 29 C   7.65908.0307  -19.8750 C.ar1  LIG1   -0.0583
 30 C   6.26568.1500  -19.9835 C.ar1  LIG1   -0.0445
 31 C   5.44307.7541  -18.9156 C.ar1  LIG1   -0.0539
 32 C   5.66018.6452  -21.2852 C.3 1  LIG1   -0.0215
 33 C   4.75339.8610  -21.0668 C.3 1  LIG1   -0.0586
 34 C   4.90027.5146  -21.9875 C.3 1  LIG1   -0.0586
 35 O   3.94404.7344  -19.6282 O.3 1  LIG1   -0.3887
 36 C   9.2604   -0.5139  -14.0265 C.ar1  LIG10.2271
 37 N   9.6773   -1.4569  -13.1548 N.ar1  LIG1   -0.2175
 38 C  10.7852   -0.9156  -12.6169 C.ar1  LIG10.0663
 39 C  11.00060.3233  -13.1739 C.ar1  LIG10.1125
 40 O  10.04220.5438  -14.0357 O.2 1  LIG1   -0.4436
 41 C   3.7184   -4.3654  -17.1815 C.3 1  LIG10.0487
 42 C   3.6849   -5.7921  -16.6077 C.3 1  LIG1   -0.0422
 43 C   2.5948   -3.4594  -16.6885 C.ar1  LIG1   -0.0273
 44 C   2.1036   -2.4496  -17.5372 C.ar1  LIG1   -0.0568
 45 C   1.0992   -1.5797  -17.1055 C.ar1  LIG1   -0.0614
 46 C   0.5629   -1.7113  -15.8244 C.ar1  LIG1   -0.0617
 47 C   1.0304   -2.7139  -14.9731 C.ar1  LIG1   -0.0614
 48 C   2.0402   -3.5825  -15.3976 C.ar1  LIG1   -0.0568
 49 H   5.96441.2247  -21.2739 H   1  LIG10.0299
 50 H   5.79642.8799  -19.6624 H   1  LIG10.0524
 51 H   3.14623.4322  -18.2096 H   1  LIG10.0624
 52 H   3.5467   -4.5027  -18.2736 H   1  LIG10.0548
 53 H   3.41500.7979  -22.9558 H   1  LIG10.0232
 54 H   5.10040.3599  -23.4465 H   1  LIG10.0232
 55 H   4.66522.0788  -23.1866 H   1  LIG10.0232
 56 H   4.7166   -0.4534  -19.7587 H   1  LIG10.0268
 57 H   3.7500   -0.9452  -21.1700 H   1  LIG10.0268
 58 H   5.7965   -1.6618  -22.4043 H   1  LIG10.0265
 59 H

Re: [Rdkit-discuss] [ext] online sdf to mol2 converter

Re: [Rdkit-discuss] [ext] online sdf to mol2 converter

[Rdkit-discuss] online sdf to mol2 converter

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