Re: [Rdkit-discuss] mass of proton

2013-06-22 Thread Yingfeng Wang
Greg,

I totally got two cases. The inchi formats of them are InChI=1S/p+1
and InChI=1S/H2/h1H. The former has been reported. The mass of later is
1.007825032. So I think it could also be a bug.

Yingfeng


On Sat, Jun 22, 2013 at 5:26 AM, Greg Landrum greg.land...@gmail.comwrote:

 Hi Yingfeng,

 On Fri, Jun 21, 2013 at 4:40 PM, Yingfeng Wang ywang...@gmail.com wrote:

 With the following code,

  from rdkit import Chem
  from rdkit.Chem import Descriptors
  from rdkit.Chem import AllChem
  a = Chem.MolFromSmiles([H+])
  Descriptors.ExactMolWt(a)
 0.0


 snip


 Is it normal?


 Nope. It's a bug. Thanks for reporting it!

 -greg



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Re: [Rdkit-discuss] mass of proton

2013-06-22 Thread Yingfeng Wang
Greg,

I also got some 'bad' inchi data, which are given in the end of this mail.

Yingfeng

These data crashed my script.

InChI=1S/ClHO2/c2-1-3/h(H,2,3)/p-1
InChI=1S/H2O3Te/c1-4(2)3/h(H2,1,2,3)/p-2
InChI=1S/C5H13NO4S/c1-6(2,3)4-5-10-11(7,8)9/h4-5H2,1-3H3
InChI=1S/CH6O3Te/c1-5(2,3)4/h5H,1H3,(H2,2,3,4)/p-2
InChI=1S/ClHO3/c2-1(3)4/h(H,2,3,4)
InChI=1S/CCl2/c2-1-3
InChI=1S/C26H44N7O17P3S/c1-4-5-6-17(35)54-10-9-28-16(34)7-8-29-24(38)21(37)26(2,3)12-47-53(44,45)50-52(42,43)46-11-15-20(49-51(39,40)41)19(36)25(48-15)33-14-32-18-22(27)30-13-31-23(18)33/h11,13-15,19-21,25,36-37,44,51H,4-10,12H2,1-3H3,(H,28,34)(H,29,38)(H,42,43)(H2,27,30,31)(H2,39,40,41)/q-4/t15-,19-,20-,21+,25-/m1/s1
InChI=1S/C12H22O14P/c13-1-4-6(15)8(17)9(18)11(24-4)26-12(3-14)10(19)7(16)5(25-12)2-23-27(20,21)22/h4-11,13-19H,1-3H2,(H,20,21,22)/t4-,5-,6-,7-,8+,9+,10+,11-,12-/m1/s1

And I got warning messages of the following data.
InChI=1S/C9H8N5O5/c1-2(15)5(16)3-8(18)14(19)6-4(11-3)7(17)13-9(10)12-6/h8,18-19H,1H3,(H2,10,13,17)/q-1
[15:29:14] WARNING:  Problems/mismatches: Mobile-H( Hydrogens: Number;
Mobile-H groups: Attachment points, Number; Charge(s): Do not match)
InChI=1S/C3H3N2O/c6-3-1-4-2-5-3/h1-2H,(H,5,6)
[15:29:15] WARNING:  Problems/mismatches: Mobile-H( Mobile-H groups:
Attachment points, Number)
InChI=1S/C55H69N4O6.Mg/c1-13-39-34(7)41-29-46-48(38(11)60)36(9)43(57-46)27-42-35(8)40(52(58-42)50-51(55(63)64-12)54(62)49-37(10)44(59-53(49)50)28-45(39)56-41)23-24-47(61)65-26-25-33(6)22-16-21-32(5)20-15-19-31(4)18-14-17-30(2)3;/h17,19,21,25,27-29,34-35,39-40,51H,13-16,18,20,22-24,26H2,1-12H3,(H-,56,57,58,59,60,62);/q-1;+2/p-1/b31-19+,32-21+,33-25+;/t34-,35+,39-,40+,51-;/m1./s1
[15:29:16] WARNING:  Problems/mismatches: Mobile-H( Hydrogens: Number;
Mobile-H groups: Number; Charge(s): Do not match)
InChI=1S/C9H14N5O8/c10-8-11-5-3(6(18)12-8)14(22)9(20,7(19)13(5)21)4(17)2(16)1-15/h2,4,7,15-17,19-22H,1H2,(H2,10,12,18)/q-1
[15:29:22] WARNING:  Problems/mismatches: Mobile-H( Mobile-H groups:
Attachment points, Number)
InChI=1S/C14H19N7O9S/c15-5(1-7(22)23)13(26)20-31(27,28)29-2-6-9(24)10(25)14(30-6)21-4-19-8-11(16)17-3-18-12(8)21/h3-6,9-10,14,24-25H,1-2,15H2,(H4,16,17,18,20,22,23,26)/p-2/t5-,6+,9+,10+,14+/m0/s1
[15:29:22] WARNING:  Problems/mismatches: Mobile-H( Proton balance: Does
not match)
InChI=1S/C9H14N5O6/c10-9-12-6-4(7(18)13-9)11-3(8(19)14(6)20)5(17)2(16)1-15/h2-3,5,8,11,15-17,19-20H,1H2,(H2,10,13,18)/q-1
[15:29:23] WARNING:  Problems/mismatches: Mobile-H( Mobile-H groups:
Attachment points, Number)
InChI=1S/C30H32O20/c31-7-17-22(39)24(41)26(43)29(49-17)47-15-2-9(1-13(34)21(15)38)28-16(5-11-12(33)3-10(32)4-14(11)46-28)48-30-27(44)25(42)23(40)18(50-30)8-45-20(37)6-19(35)36/h1-5,17-18,22-27,29-31,39-44H,6-8H2,(H4-,32,33,34,35,38)/q-1/t17-,18-,22?,23-,24+,25+,26?,27-,29-,30?/m1/s1
[15:29:23] WARNING:  Problems/mismatches: Mobile-H( Hydrogens: Locations or
number, Number; Mobile-H groups: Attachment points, Number; Charge(s): Do
not match)
InChI=1S/HO3P/c1-4(2)3/h(H-,1,2,3)/q-2
[15:29:24] WARNING:  Problems/mismatches: Mobile-H( Charge(s): Do not match)
InChI=1S/C10H7NO3/c12-9-5-8(10(13)14)11-7-4-2-1-3-6(7)9/h1-5H,(H,11,12)(H,13,14)/p-2
[15:29:24] WARNING:  Problems/mismatches: Mobile-H( Proton balance: Does
not match)
InChI=1S/C16H24IN6O10PS/c1-3-7(2)9(17)15(26)22-35(29,30)33-34(27,28)31-4-8-11(24)12(25)16(32-8)23-6-21-10-13(18)19-5-20-14(10)23/h5-9,11-12,16,24-25H,3-4H2,1-2H3,(H4,18,19,20,22,26,27,28)/p-2/t7-,8+,9?,11+,12+,16+/m0/s1
[15:29:24] WARNING:  Problems/mismatches: Mobile-H( Proton balance: Does
not match)
InChI=1S/C8H8NOS/c10-9-8(11)6-7-4-2-1-3-5-7/h1-5H,6H2,(H-,9,10,11)/q-1
[15:29:27] WARNING:  Problems/mismatches: Mobile-H( Hydrogens: Locations or
number, Number; Mobile-H groups: Attachment points, Number; Charge(s): Do
not match)
InChI=1S/C18H18N4O6S4/c1-3-21-13-7-5-11(31(23,24)25)9-15(13)29-17(21)19-20-18-22(4-2)14-8-6-12(32(26,27)28)10-16(14)30-18/h5-10H,3-4H2,1-2H3,(H,23,24,25)(H,26,27,28)/q+1/p-2
[15:29:27] WARNING:  Problems/mismatches: Mobile-H( Proton balance: Does
not match)
InChI=1S/C27H33N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H5,28,29,30,34,42,43,44,45,46,47)/p-3/t14-,15+,16+,19-,20+,21+,26+/m0/s1
[15:29:27] WARNING:  Problems/mismatches: Mobile-H( Proton balance: Does
not match)
InChI=1S/C17H21N4O9P/c1-7-3-9-10(4-8(7)2)21(15-13(18-9)16(25)20-17(26)19-15)5-11(22)14(24)12(23)6-30-31(27,28)29/h3-4,11-12,14,22-24H,5-6H2,1-2H3,(H3,20,25,26,27,28,29)/p-3/t11-,12+,14-/m0/s1
[15:29:27] WARNING:  Problems/mismatches: Mobile-H( Proton balance: Does
not match)
InChI=1S/C13H20O3/c1-9(14)5-6-11-12(2,3)7-10(15)8-13(11,4)16/h5,10,15-16H,7-8H2,1-4H3/t6-,10-,13+/m0/s1
[15:29:28] Allene-style stereochemistry is not supported yet and will be
ignored.