chemruby 0.9.3
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- data/README +120 -0
- data/Rakefile +195 -0
- data/ext/extconf.rb +4 -0
- data/ext/subcomp.c +416 -0
- data/lib/chem.rb +130 -0
- data/lib/chem/appl.rb +1 -0
- data/lib/chem/appl/chem3dole.rb +36 -0
- data/lib/chem/appl/tinker/nucleic.rb +40 -0
- data/lib/chem/appl/tinker/tinker_reader.rb +43 -0
- data/lib/chem/data.rb +4 -0
- data/lib/chem/data/atomic_weight.rb +124 -0
- data/lib/chem/data/character.rb +2 -0
- data/lib/chem/data/electronegativity.rb +14 -0
- data/lib/chem/data/periodic_table.rb +6 -0
- data/lib/chem/data/prime_numbers.rb +1 -0
- data/lib/chem/data/vdw_radii.rb +1 -0
- data/lib/chem/db.rb +64 -0
- data/lib/chem/db/cansmi.rb +234 -0
- data/lib/chem/db/cdx.rb +1525 -0
- data/lib/chem/db/eps.rb +164 -0
- data/lib/chem/db/g98.rb +909 -0
- data/lib/chem/db/gspan.rb +130 -0
- data/lib/chem/db/iupac.rb +5 -0
- data/lib/chem/db/iupac/a_1.rb +46 -0
- data/lib/chem/db/iupac/iuparser.rb +226 -0
- data/lib/chem/db/iupac/iuparser.ry +97 -0
- data/lib/chem/db/iupac/postfix.rb +2 -0
- data/lib/chem/db/kcf.rb +390 -0
- data/lib/chem/db/kcf_glycan.rb +19 -0
- data/lib/chem/db/kegg.rb +516 -0
- data/lib/chem/db/linucs/linparser.rb +144 -0
- data/lib/chem/db/linucs/linucs.ry +53 -0
- data/lib/chem/db/mdl.rb +379 -0
- data/lib/chem/db/molconnz.rb +12 -0
- data/lib/chem/db/mopac.rb +88 -0
- data/lib/chem/db/msi.rb +107 -0
- data/lib/chem/db/pdb_dic.rb +115 -0
- data/lib/chem/db/pdf.rb +131 -0
- data/lib/chem/db/pubchem.rb +113 -0
- data/lib/chem/db/rmagick.rb +70 -0
- data/lib/chem/db/sdf.rb +37 -0
- data/lib/chem/db/smbl.rb +88 -0
- data/lib/chem/db/smiles.rb +2 -0
- data/lib/chem/db/smiles/smiles.ry +203 -0
- data/lib/chem/db/smiles/smiparser.rb +375 -0
- data/lib/chem/db/swf.rb +74 -0
- data/lib/chem/db/sybyl.rb +150 -0
- data/lib/chem/db/tinker.rb +77 -0
- data/lib/chem/db/types/type_cansmi.rb +9 -0
- data/lib/chem/db/types/type_cdx.rb +24 -0
- data/lib/chem/db/types/type_gspan.rb +31 -0
- data/lib/chem/db/types/type_kcf.rb +28 -0
- data/lib/chem/db/types/type_kcf_glycan.rb +26 -0
- data/lib/chem/db/types/type_kegg.rb +92 -0
- data/lib/chem/db/types/type_mdl.rb +31 -0
- data/lib/chem/db/types/type_pdf.rb +33 -0
- data/lib/chem/db/types/type_png.rb +31 -0
- data/lib/chem/db/types/type_rxn.rb +25 -0
- data/lib/chem/db/types/type_sdf.rb +25 -0
- data/lib/chem/db/types/type_sybyl.rb +30 -0
- data/lib/chem/db/types/type_xyz.rb +26 -0
- data/lib/chem/db/vector.rb +128 -0
- data/lib/chem/db/xyz.rb +39 -0
- data/lib/chem/model.rb +119 -0
- data/lib/chem/model/skeleton.rb +37 -0
- data/lib/chem/utils.rb +11 -0
- data/lib/chem/utils/geometry.rb +27 -0
- data/lib/chem/utils/graph_db.rb +146 -0
- data/lib/chem/utils/math.rb +17 -0
- data/lib/chem/utils/prop.rb +123 -0
- data/lib/chem/utils/sssr.rb +101 -0
- data/lib/chem/utils/sub.rb +78 -0
- data/lib/chem/utils/transform.rb +110 -0
- data/lib/chem/utils/traverse.rb +37 -0
- data/lib/chem/utils/ullmann.rb +134 -0
- data/lib/graph.rb +41 -0
- data/lib/graph/cluster.rb +20 -0
- data/lib/graph/morgan.rb +38 -0
- data/sample/frequent_subgraph.rb +46 -0
- data/sample/images/ex1.rb +11 -0
- data/sample/images/ex2.rb +4 -0
- data/sample/images/ex3.rb +5 -0
- data/sample/images/ex4.rb +17 -0
- data/sample/images/ex5.rb +10 -0
- data/sample/images/mol/adenine.mol +26 -0
- data/sample/images/mol/atp.mol +69 -0
- data/sample/images/temp/ex5.mol +344 -0
- data/sample/kegg_db.rb +116 -0
- data/setup.rb +1551 -0
- data/test/all.rb +6 -0
- data/test/coord_test.rb +17 -0
- data/test/ctab_test.rb +31 -0
- data/test/data/A_21.tar.gz +0 -0
- data/test/data/A_21/aceanthrylene.cdx +0 -0
- data/test/data/A_21/aceanthrylene.mol +40 -0
- data/test/data/A_21/acenaphthylene.cdx +0 -0
- data/test/data/A_21/acenaphthylene.mol +31 -0
- data/test/data/A_21/acephenanthrylene.cdx +0 -0
- data/test/data/A_21/acephenanthrylene.mol +40 -0
- data/test/data/A_21/anthracene.cdx +0 -0
- data/test/data/A_21/anthracene.mol +35 -0
- data/test/data/A_21/as-indacene.cdx +0 -0
- data/test/data/A_21/as-indacene.mol +31 -0
- data/test/data/A_21/azulene.cdx +0 -0
- data/test/data/A_21/azulene.mol +26 -0
- data/test/data/A_21/biphenylene.cdx +0 -0
- data/test/data/A_21/biphenylene.mol +31 -0
- data/test/data/A_21/chrysene.cdx +0 -0
- data/test/data/A_21/chrysene.mol +44 -0
- data/test/data/A_21/coronen.cdx +0 -0
- data/test/data/A_21/coronen.mol +59 -0
- data/test/data/A_21/fluoranthene.cdx +0 -0
- data/test/data/A_21/fluoranthene.mol +40 -0
- data/test/data/A_21/fluorene.cdx +0 -0
- data/test/data/A_21/fluorene.mol +33 -0
- data/test/data/A_21/heptacene.cdx +0 -0
- data/test/data/A_21/heptacene.mol +71 -0
- data/test/data/A_21/heptalene.cdx +0 -0
- data/test/data/A_21/heptalene.mol +30 -0
- data/test/data/A_21/heptaphene.cdx +0 -0
- data/test/data/A_21/heptaphene.mol +71 -0
- data/test/data/A_21/hexacene.cdx +0 -0
- data/test/data/A_21/hexacene.mol +62 -0
- data/test/data/A_21/hexaphene.cdx +0 -0
- data/test/data/A_21/hexaphene.mol +62 -0
- data/test/data/A_21/indene.cdx +0 -0
- data/test/data/A_21/indene.mol +24 -0
- data/test/data/A_21/iupac.txt +41 -0
- data/test/data/A_21/naphthacene.cdx +0 -0
- data/test/data/A_21/naphthacene.mol +44 -0
- data/test/data/A_21/naphthalene.cdx +0 -0
- data/test/data/A_21/naphthalene.mol +26 -0
- data/test/data/A_21/ovalene.cdx +0 -0
- data/test/data/A_21/ovalene.mol +78 -0
- data/test/data/A_21/pentacene.cdx +0 -0
- data/test/data/A_21/pentacene.mol +53 -0
- data/test/data/A_21/pentalene.cdx +0 -0
- data/test/data/A_21/pentalene.mol +22 -0
- data/test/data/A_21/pentaphene.cdx +0 -0
- data/test/data/A_21/pentaphene.mol +53 -0
- data/test/data/A_21/perylene.cdx +0 -0
- data/test/data/A_21/perylene.mol +49 -0
- data/test/data/A_21/phenalene.cdx +0 -0
- data/test/data/A_21/phenalene.mol +33 -0
- data/test/data/A_21/phenanthrene.cdx +0 -0
- data/test/data/A_21/phenanthrene.mol +35 -0
- data/test/data/A_21/picene.cdx +0 -0
- data/test/data/A_21/picene.mol +53 -0
- data/test/data/A_21/pleiadene.cdx +0 -0
- data/test/data/A_21/pleiadene.mol +44 -0
- data/test/data/A_21/pyranthrene.cdx +0 -0
- data/test/data/A_21/pyranthrene.mol +72 -0
- data/test/data/A_21/pyrene.cdx +0 -0
- data/test/data/A_21/pyrene.mol +40 -0
- data/test/data/A_21/rubicene.cdx +0 -0
- data/test/data/A_21/rubicene.mol +63 -0
- data/test/data/A_21/s-indacene.cdx +0 -0
- data/test/data/A_21/s-indacene.mol +31 -0
- data/test/data/A_21/tetraphenylene.cdx +0 -0
- data/test/data/A_21/tetraphenylene.mol +57 -0
- data/test/data/A_21/trinaphthylene.cdx +0 -0
- data/test/data/A_21/trinaphthylene.mol +71 -0
- data/test/data/A_21/triphenylene.cdx +0 -0
- data/test/data/A_21/triphenylene.mol +44 -0
- data/test/data/C00147.kcf +25 -0
- data/test/data/G00147.kcf +13 -0
- data/test/data/atp.mol +69 -0
- data/test/data/cyclohexane.mol +17 -0
- data/test/data/cyclohexane.ps +485 -0
- data/test/data/fullerene.mol +155 -0
- data/test/data/glycan +33 -0
- data/test/data/hypericin.cdx +0 -0
- data/test/data/hypericin.cdxml +596 -0
- data/test/data/hypericin.chm +0 -0
- data/test/data/hypericin.ct +85 -0
- data/test/data/hypericin.f1d +0 -0
- data/test/data/hypericin.f1q +0 -0
- data/test/data/hypericin.gif +0 -0
- data/test/data/hypericin.mol +88 -0
- data/test/data/hypericin.mol2 +159 -0
- data/test/data/hypericin.msm +123 -0
- data/test/data/hypericin.pdf +359 -0
- data/test/data/hypericin.png +0 -0
- data/test/data/hypericin.ps +0 -0
- data/test/data/hypericin.skc +0 -0
- data/test/data/hypericin2.gif +0 -0
- data/test/data/hypericin2.ps +0 -0
- data/test/data/kegg/genomes/hsa/hsa_enzyme.list +4 -0
- data/test/data/kegg/genomes/hsa/hsa_pfam.list +4 -0
- data/test/data/kegg/ligand/mol/C00147.mol +26 -0
- data/test/data/kegg/ligand/reaction +14 -0
- data/test/data/kegg/ligand/reaction.lst +1 -0
- data/test/data/kegg/ligand/reaction_mapformula.lst +3 -0
- data/test/data/reaction +14 -0
- data/test/data/reaction.lst +1 -0
- data/test/data/reaction_mapformula.lst +3 -0
- data/test/data/rxn/C00001.mol +6 -0
- data/test/data/rxn/C00011.mol +10 -0
- data/test/data/rxn/C00014.mol +6 -0
- data/test/data/rxn/C01010.mol +18 -0
- data/test/data/rxn/sample.rxn +50 -0
- data/test/data/rxn/substitution.rxn +45 -0
- data/test/data/test.eps +0 -0
- data/test/data/test.mol +28 -0
- data/test/data/test.sdf +143 -0
- data/test/data/test.skc +0 -0
- data/test/data/test.xyz +4 -0
- data/test/data/test_lf.sdf +143 -0
- data/test/heavy_test_pubchem.rb +16 -0
- data/test/multiple_test.rb +22 -0
- data/test/test_adj.rb +54 -0
- data/test/test_canonical_smiles.rb +46 -0
- data/test/test_cdx.rb +32 -0
- data/test/test_chem.rb +18 -0
- data/test/test_cluster.rb +19 -0
- data/test/test_db.rb +11 -0
- data/test/test_eps.rb +24 -0
- data/test/test_geometry.rb +11 -0
- data/test/test_gspan.rb +28 -0
- data/test/test_iupac.rb +36 -0
- data/test/test_kcf.rb +24 -0
- data/test/test_kcf_glycan.rb +10 -0
- data/test/test_kegg.rb +118 -0
- data/test/test_linucs.rb +21 -0
- data/test/test_mdl.rb +45 -0
- data/test/test_mol2.rb +62 -0
- data/test/test_morgan.rb +21 -0
- data/test/test_pdf.rb +12 -0
- data/test/test_prop.rb +86 -0
- data/test/test_rmagick.rb +15 -0
- data/test/test_sbdb.rb +23 -0
- data/test/test_sdf.rb +30 -0
- data/test/test_smiles.rb +84 -0
- data/test/test_sssr.rb +18 -0
- data/test/test_sub.rb +47 -0
- data/test/test_subcomp.rb +37 -0
- data/test/test_traverse.rb +29 -0
- data/test/test_writer.rb +13 -0
- data/test/test_xyz.rb +15 -0
- data/test/type_test.rb +25 -0
- metadata +290 -0
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1.4289 -2.0625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
31
|
+
2.1434 -1.6500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
32
|
+
2.1434 -0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
33
|
+
-1.4289 2.8875 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
34
|
+
-2.8579 0.4125 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
35
|
+
0.0000 2.8875 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
36
|
+
1.4289 2.8875 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
37
|
+
2.8579 0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
38
|
+
2.8579 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
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39
|
+
1.4289 -2.8875 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
40
|
+
0.0000 -2.8875 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
41
|
+
-1.4289 -2.8875 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
42
|
+
-2.8579 -0.4125 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
43
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+
1 2 1 0
|
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44
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+
2 3 2 0
|
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45
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+
3 4 1 0
|
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46
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+
4 5 2 0
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47
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+
5 6 1 0
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48
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+
6 1 2 0
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49
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+
4 7 1 0
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50
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+
7 8 1 0
|
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51
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+
8 9 2 0
|
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52
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+
9 10 1 0
|
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53
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+
10 5 1 0
|
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54
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+
8 11 1 0
|
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55
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+
11 12 2 0
|
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56
|
+
12 13 1 0
|
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57
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+
13 14 2 0
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58
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+
14 9 1 0
|
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59
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+
3 15 1 0
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60
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+
15 16 1 0
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61
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+
16 17 1 0
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62
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+
17 7 2 0
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63
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+
17 18 1 0
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64
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+
18 19 1 0
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65
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+
19 11 1 0
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66
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+
15 20 2 0
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67
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+
20 21 1 0
|
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68
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+
21 22 2 0
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69
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+
22 23 1 0
|
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70
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+
23 16 2 0
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71
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+
23 24 1 0
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72
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+
24 25 1 0
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73
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+
25 18 2 0
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74
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+
25 26 1 0
|
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75
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+
26 27 2 0
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76
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+
27 28 1 0
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77
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+
28 19 2 0
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78
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+
6 29 1 0
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79
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+
2 30 1 0
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80
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+
10 31 2 0
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81
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+
14 32 1 0
|
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82
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+
12 33 1 0
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83
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+
28 34 1 0
|
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84
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+
26 35 1 0
|
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85
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+
24 36 2 0
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86
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+
22 37 1 0
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87
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+
20 38 1 0
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88
|
+
M END
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|
@@ -0,0 +1,159 @@
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1
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+
# Name: Unnamed
|
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2
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+
# Creating user name: miki
|
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3
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+
# Creation time: Wed Sep 21 16:19:09 2005
|
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4
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+
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5
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+
# Modifying user name: miki
|
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6
|
+
# Modification time: Wed Sep 21 16:19:09 2005
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7
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+
|
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8
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+
@<TRIPOS>MOLECULE
|
|
9
|
+
Unnamed
|
|
10
|
+
67 70 1 1 0
|
|
11
|
+
SMALL
|
|
12
|
+
GAST_HUCK
|
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13
|
+
|
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14
|
+
|
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15
|
+
@<TRIPOS>ATOM
|
|
16
|
+
1 C1 -3.262565 -0.588014 -0.082185 C.3 1 <1> -0.020001
|
|
17
|
+
2 H2 -3.038988 -0.127168 -1.060674 H 1 <1> 0.032112
|
|
18
|
+
3 C3 -0.966863 -1.811332 -0.527477 C.3 1 <1> -0.046782
|
|
19
|
+
4 C4 0.184996 0.210827 1.395415 C.3 1 <1> -0.034356
|
|
20
|
+
5 C5 0.490033 -1.945216 0.011113 C.3 1 <1> -0.048934
|
|
21
|
+
6 C6 1.124074 -0.573792 0.416800 C.3 1 <1> -0.032177
|
|
22
|
+
7 C7 0.746489 1.629048 1.684431 C.3 1 <1> -0.049323
|
|
23
|
+
8 C8 2.616386 -0.651238 0.927178 C.3 1 <1> -0.023644
|
|
24
|
+
9 C9 2.204639 1.558281 2.204247 C.3 1 <1> -0.047008
|
|
25
|
+
10 C10 3.102285 0.820604 1.172452 C.3 1 <1> -0.006875
|
|
26
|
+
11 C11 3.544175 -1.250316 -0.182078 C.3 1 <1> -0.044608
|
|
27
|
+
12 C12 2.728260 -1.552265 2.205062 C.3 1 <1> -0.058963
|
|
28
|
+
13 C13 4.612647 0.955179 1.530799 C.3 1 <1> 0.084351
|
|
29
|
+
14 C14 5.056505 -1.153871 0.156867 C.3 1 <1> -0.023904
|
|
30
|
+
15 C15 5.491312 0.307192 0.421583 C.3 1 <1> 0.081351
|
|
31
|
+
16 O16 6.885968 0.255313 0.781139 O.3 1 <1> -0.389230
|
|
32
|
+
17 H17 -1.098539 0.845003 -0.192888 H 1 <1> 0.030888
|
|
33
|
+
18 H18 0.090437 -0.293389 2.363899 H 1 <1> 0.030645
|
|
34
|
+
19 C19 -2.110736 -1.950848 1.764990 C.3 1 <1> -0.058997
|
|
35
|
+
20 H20 1.142774 0.012528 -0.517506 H 1 <1> 0.030888
|
|
36
|
+
21 O21 4.902194 2.364882 1.635208 O.3 1 <1> -0.388947
|
|
37
|
+
22 H22 2.997980 1.377034 0.225106 H 1 <1> 0.033184
|
|
38
|
+
23 C23 -1.888378 -1.072789 0.488143 C.3 1 <1> -0.024730
|
|
39
|
+
24 C24 -1.232058 0.307738 0.763647 C.3 1 <1> -0.032219
|
|
40
|
+
25 C25 -2.328936 1.084926 1.526876 C.3 1 <1> -0.049129
|
|
41
|
+
26 C26 -3.656951 0.578264 0.881800 C.3 1 <1> -0.048017
|
|
42
|
+
27 C27 -4.339789 -1.674951 -0.425210 C.3 1 <1> 0.010335
|
|
43
|
+
28 C28 -5.391758 -1.995289 0.675492 C.3 1 <1> -0.049224
|
|
44
|
+
29 N29 -5.002461 -1.358241 -1.723284 N.3 1 <1> -0.305393
|
|
45
|
+
30 C30 -6.089178 -0.350414 -1.717836 C.3 1 <1> -0.012771
|
|
46
|
+
31 C31 -5.263363 -2.503048 -2.631898 C.3 1 <1> -0.012771
|
|
47
|
+
32 H32 -0.933714 -1.254217 -1.478210 H 1 <1> 0.027078
|
|
48
|
+
33 H33 -1.366647 -2.813320 -0.750106 H 1 <1> 0.027078
|
|
49
|
+
34 H34 0.501273 -2.643396 0.856954 H 1 <1> 0.026837
|
|
50
|
+
35 H35 1.072060 -2.411489 -0.798693 H 1 <1> 0.026837
|
|
51
|
+
36 H36 0.720507 2.234580 0.763436 H 1 <1> 0.026821
|
|
52
|
+
37 H37 0.124848 2.138262 2.439498 H 1 <1> 0.026821
|
|
53
|
+
38 H38 2.246632 1.059648 3.183891 H 1 <1> 0.026901
|
|
54
|
+
39 H39 2.556935 2.593046 2.349477 H 1 <1> 0.026901
|
|
55
|
+
40 H40 3.376532 -0.722093 -1.135023 H 1 <1> 0.027150
|
|
56
|
+
41 H41 3.326862 -2.316418 -0.349507 H 1 <1> 0.027150
|
|
57
|
+
42 H42 2.556110 -2.607570 1.951676 H 1 <1> 0.023525
|
|
58
|
+
43 H43 2.010909 -1.288627 2.989363 H 1 <1> 0.023525
|
|
59
|
+
44 H44 3.716726 -1.509320 2.674372 H 1 <1> 0.023525
|
|
60
|
+
45 H45 4.821488 0.481922 2.502898 H 1 <1> 0.062185
|
|
61
|
+
46 H46 5.312110 -1.774341 1.028334 H 1 <1> 0.029104
|
|
62
|
+
47 H47 5.644179 -1.541371 -0.692904 H 1 <1> 0.029104
|
|
63
|
+
48 H48 5.366211 0.884348 -0.512252 H 1 <1> 0.061898
|
|
64
|
+
49 H49 7.294090 1.109580 0.867943 H 1 <1> 0.209888
|
|
65
|
+
50 H50 -2.538045 -2.921914 1.478269 H 1 <1> 0.023525
|
|
66
|
+
51 H51 -2.796768 -1.483320 2.482272 H 1 <1> 0.023525
|
|
67
|
+
52 H52 -1.190680 -2.172274 2.316468 H 1 <1> 0.023525
|
|
68
|
+
53 H53 5.780854 2.561980 1.940968 H 1 <1> 0.209900
|
|
69
|
+
54 H54 -2.275228 0.838583 2.599702 H 1 <1> 0.026829
|
|
70
|
+
55 H55 -2.208542 2.176779 1.426007 H 1 <1> 0.026829
|
|
71
|
+
56 H56 -4.331612 0.256402 1.687925 H 1 <1> 0.026868
|
|
72
|
+
57 H57 -4.153440 1.396018 0.335064 H 1 <1> 0.026868
|
|
73
|
+
58 H58 -3.772505 -2.605476 -0.580480 H 1 <1> 0.046242
|
|
74
|
+
59 H59 -6.031491 -2.824454 0.337371 H 1 <1> 0.024481
|
|
75
|
+
60 H60 -4.920329 -2.301872 1.618476 H 1 <1> 0.024481
|
|
76
|
+
61 H61 -6.045071 -1.136394 0.881491 H 1 <1> 0.024481
|
|
77
|
+
62 H62 -6.206665 0.073542 -2.726510 H 1 <1> 0.039061
|
|
78
|
+
63 H63 -5.868660 0.480866 -1.036373 H 1 <1> 0.039061
|
|
79
|
+
64 H64 -7.043130 -0.810931 -1.418049 H 1 <1> 0.039061
|
|
80
|
+
65 H65 -5.672092 -2.159679 -3.594598 H 1 <1> 0.039061
|
|
81
|
+
66 H66 -4.328846 -3.043118 -2.847841 H 1 <1> 0.039061
|
|
82
|
+
67 H67 -5.981755 -3.200901 -2.176024 H 1 <1> 0.039061
|
|
83
|
+
@<TRIPOS>BOND
|
|
84
|
+
1 10 13 1
|
|
85
|
+
2 14 11 1
|
|
86
|
+
3 13 15 1
|
|
87
|
+
4 15 16 1
|
|
88
|
+
5 6 5 1
|
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89
|
+
6 9 10 1
|
|
90
|
+
7 15 14 1
|
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91
|
+
8 24 17 1
|
|
92
|
+
9 4 18 1
|
|
93
|
+
10 23 19 1
|
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94
|
+
11 23 3 1
|
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95
|
+
12 4 24 1
|
|
96
|
+
13 6 20 1
|
|
97
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+
14 13 21 1
|
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98
|
+
15 5 3 1
|
|
99
|
+
16 10 22 1
|
|
100
|
+
17 1 2 1
|
|
101
|
+
18 4 6 1
|
|
102
|
+
19 7 4 1
|
|
103
|
+
20 24 23 1
|
|
104
|
+
21 25 26 1
|
|
105
|
+
22 26 1 1
|
|
106
|
+
23 23 1 1
|
|
107
|
+
24 24 25 1
|
|
108
|
+
25 6 8 1
|
|
109
|
+
26 1 27 1
|
|
110
|
+
27 7 9 1
|
|
111
|
+
28 27 28 1
|
|
112
|
+
29 8 10 1
|
|
113
|
+
30 27 29 1
|
|
114
|
+
31 8 11 1
|
|
115
|
+
32 29 30 1
|
|
116
|
+
33 8 12 1
|
|
117
|
+
34 29 31 1
|
|
118
|
+
35 3 32 1
|
|
119
|
+
36 3 33 1
|
|
120
|
+
37 5 34 1
|
|
121
|
+
38 5 35 1
|
|
122
|
+
39 7 36 1
|
|
123
|
+
40 7 37 1
|
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124
|
+
41 9 38 1
|
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125
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+
42 9 39 1
|
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126
|
+
43 11 40 1
|
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127
|
+
44 11 41 1
|
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128
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+
45 12 42 1
|
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129
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+
46 12 43 1
|
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130
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+
47 12 44 1
|
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131
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+
48 13 45 1
|
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132
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+
49 14 46 1
|
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133
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+
50 14 47 1
|
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134
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+
51 15 48 1
|
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135
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+
52 16 49 1
|
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136
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+
53 19 50 1
|
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137
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+
54 19 51 1
|
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138
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+
55 19 52 1
|
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139
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+
56 21 53 1
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140
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+
57 25 54 1
|
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141
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+
58 25 55 1
|
|
142
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+
59 26 56 1
|
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143
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+
60 26 57 1
|
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144
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+
61 27 58 1
|
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145
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+
62 28 59 1
|
|
146
|
+
63 28 60 1
|
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147
|
+
64 28 61 1
|
|
148
|
+
65 30 62 1
|
|
149
|
+
66 30 63 1
|
|
150
|
+
67 30 64 1
|
|
151
|
+
68 31 65 1
|
|
152
|
+
69 31 66 1
|
|
153
|
+
70 31 67 1
|
|
154
|
+
@<TRIPOS>SUBSTRUCTURE
|
|
155
|
+
1 **** 1 TEMP 0 **** **** 0 ROOT
|
|
156
|
+
@<TRIPOS>NORMAL
|
|
157
|
+
@<TRIPOS>FF_PBC
|
|
158
|
+
FORCE_FIELD_SETUP_FEATURE Force Field Setup information
|
|
159
|
+
v1.0 0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 NONE 0 0 0 0 1 0 0 0 0 0 0 0 0
|
|
@@ -0,0 +1,123 @@
|
|
|
1
|
+
! Polygen 133
|
|
2
|
+
ChemNote molecule file created by CS ChemDraw�
|
|
3
|
+
* File format version number
|
|
4
|
+
90.0928
|
|
5
|
+
* File update version number
|
|
6
|
+
92.0319
|
|
7
|
+
*
|
|
8
|
+
* molecule name
|
|
9
|
+
Undefined Name
|
|
10
|
+
* empirical formula
|
|
11
|
+
Undefined Empirical Formula
|
|
12
|
+
* need 3D conversion?
|
|
13
|
+
1
|
|
14
|
+
* 3D displacement vector
|
|
15
|
+
0.000 0.000 0.000
|
|
16
|
+
* 3D rotation matrix
|
|
17
|
+
1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000
|
|
18
|
+
* 3D scale factor
|
|
19
|
+
0.000000
|
|
20
|
+
* 2D scale factor
|
|
21
|
+
1.000000
|
|
22
|
+
* 2D attributes
|
|
23
|
+
1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
|
|
24
|
+
* 3D attributes
|
|
25
|
+
0 0 0 0 0 0 0 0 0 0 0
|
|
26
|
+
* Global display attributes
|
|
27
|
+
1 0 1 12 256
|
|
28
|
+
* Atom List
|
|
29
|
+
* Atom# Lbl Type x y x y z bits chrg ichrg frag istp lp chrl ring frad name seg grp FLAGS sat dfoxid useroxid Sh_type Sh_nr Qstring
|
|
30
|
+
1 C 255 -389 -299 0 0 0 1 0.0 0 00
|
|
31
|
+
2 C 255 -389 -149 0 0 0 1 0.0 0 00
|
|
32
|
+
3 C 255 -259 -74 0 0 0 1 0.0 0 00
|
|
33
|
+
4 C 255 -129 -149 0 0 0 1 0.0 0 00
|
|
34
|
+
5 C 255 -129 -299 0 0 0 1 0.0 0 00
|
|
35
|
+
6 C 255 -259 -374 0 0 0 1 0.0 0 00
|
|
36
|
+
7 C 255 0 -74 0 0 0 1 0.0 0 00
|
|
37
|
+
8 C 255 130 -149 0 0 0 1 0.0 0 00
|
|
38
|
+
9 C 255 130 -299 0 0 0 1 0.0 0 00
|
|
39
|
+
10 C 255 0 -374 0 0 0 1 0.0 0 00
|
|
40
|
+
11 C 255 260 -74 0 0 0 1 0.0 0 00
|
|
41
|
+
12 C 255 390 -149 0 0 0 1 0.0 0 00
|
|
42
|
+
13 C 255 390 -299 0 0 0 1 0.0 0 00
|
|
43
|
+
14 C 255 260 -374 0 0 0 1 0.0 0 00
|
|
44
|
+
15 C 255 -259 75 0 0 0 1 0.0 0 00
|
|
45
|
+
16 C 255 -129 150 0 0 0 1 0.0 0 00
|
|
46
|
+
17 C 255 0 75 0 0 0 1 0.0 0 00
|
|
47
|
+
18 C 255 130 150 0 0 0 1 0.0 0 00
|
|
48
|
+
19 C 255 260 75 0 0 0 1 0.0 0 00
|
|
49
|
+
20 C 255 -389 150 0 0 0 1 0.0 0 00
|
|
50
|
+
21 C 255 -389 300 0 0 0 1 0.0 0 00
|
|
51
|
+
22 C 255 -259 375 0 0 0 1 0.0 0 00
|
|
52
|
+
23 C 255 -129 300 0 0 0 1 0.0 0 00
|
|
53
|
+
24 C 255 0 375 0 0 0 1 0.0 0 00
|
|
54
|
+
25 C 255 130 300 0 0 0 1 0.0 0 00
|
|
55
|
+
26 C 255 260 375 0 0 0 1 0.0 0 00
|
|
56
|
+
27 C 255 390 300 0 0 0 1 0.0 0 00
|
|
57
|
+
28 C 255 390 150 0 0 0 1 0.0 0 00
|
|
58
|
+
29 O 255 -259 -524 0 0 0 1 0.0 0 00
|
|
59
|
+
30 O 255 -519 -74 0 0 0 1 0.0 0 00
|
|
60
|
+
31 O 255 0 -524 0 0 0 1 0.0 0 00
|
|
61
|
+
32 O 255 260 -524 0 0 0 1 0.0 0 00
|
|
62
|
+
33 C 255 520 -74 0 0 0 1 0.0 0 00
|
|
63
|
+
34 C 255 520 75 0 0 0 1 0.0 0 00
|
|
64
|
+
35 O 255 260 525 0 0 0 1 0.0 0 00
|
|
65
|
+
36 O 255 0 525 0 0 0 1 0.0 0 00
|
|
66
|
+
37 O 255 -259 525 0 0 0 1 0.0 0 00
|
|
67
|
+
38 O 255 -519 75 0 0 0 1 0.0 0 00
|
|
68
|
+
* Bond List
|
|
69
|
+
* Bond# bond_type atom1 atom2 cis/trans length locked ring Sh_type Sh_nr Qorder Qtopol Qstereo
|
|
70
|
+
1 1 1 2
|
|
71
|
+
2 2 2 3
|
|
72
|
+
3 1 3 4
|
|
73
|
+
4 2 4 5
|
|
74
|
+
5 1 5 6
|
|
75
|
+
6 2 6 1
|
|
76
|
+
7 1 4 7
|
|
77
|
+
8 1 7 8
|
|
78
|
+
9 2 8 9
|
|
79
|
+
10 1 9 10
|
|
80
|
+
11 1 10 5
|
|
81
|
+
12 1 8 11
|
|
82
|
+
13 2 11 12
|
|
83
|
+
14 1 12 13
|
|
84
|
+
15 2 13 14
|
|
85
|
+
16 1 14 9
|
|
86
|
+
17 1 3 15
|
|
87
|
+
18 1 15 16
|
|
88
|
+
19 1 16 17
|
|
89
|
+
20 2 17 7
|
|
90
|
+
21 1 17 18
|
|
91
|
+
22 1 18 19
|
|
92
|
+
23 1 19 11
|
|
93
|
+
24 2 15 20
|
|
94
|
+
25 1 20 21
|
|
95
|
+
26 2 21 22
|
|
96
|
+
27 1 22 23
|
|
97
|
+
28 2 23 16
|
|
98
|
+
29 1 23 24
|
|
99
|
+
30 1 24 25
|
|
100
|
+
31 2 25 18
|
|
101
|
+
32 1 25 26
|
|
102
|
+
33 2 26 27
|
|
103
|
+
34 1 27 28
|
|
104
|
+
35 2 28 19
|
|
105
|
+
36 1 6 29
|
|
106
|
+
37 1 2 30
|
|
107
|
+
38 2 10 31
|
|
108
|
+
39 1 14 32
|
|
109
|
+
40 1 12 33
|
|
110
|
+
41 1 28 34
|
|
111
|
+
42 1 26 35
|
|
112
|
+
43 2 24 36
|
|
113
|
+
44 1 22 37
|
|
114
|
+
45 1 20 38
|
|
115
|
+
* Fragment List
|
|
116
|
+
* Fgmt# Label Atoms
|
|
117
|
+
* Bond Angles
|
|
118
|
+
* bond1 bond2 angle locked
|
|
119
|
+
* Dihedral Angles
|
|
120
|
+
* at1-cons at1 at2 at2-cons angle locked
|
|
121
|
+
* Planarity data
|
|
122
|
+
* User data area
|
|
123
|
+
* End of File
|