mol2 format, mol2--sybyl mol2 format,这怎么区别呢？ ml2是2D，mol2是3D？谢谢！
通过Open Babel,我们可以将这个坐标文件导出为一个smi文件,也就是SMILES表达式: dechin@ubuntu2004:~/projects/gitlab/dechin/src/vmd$ obabel -ixyz file.xyz -osmi -O file.smi 1 molecule converted (py37) dechin@ubuntu2004:~/projects/gitlab/dechin/src/vmd$cat file.smi C(CC)CCCC(=O)N mol ...
Open Babel is a chemical toolbox designed to speak the many languages of chemical data. - openbabel/NEWS at master · rwest/openbabel
Fix a typo to '-DHAVE_RAPIDJSON' lemniscati committed Oct 25, 2020 f9724a8 Commits on Oct 18, 2020 Merge pull request #2285 from dspoel/fix-obthermo … ghutchis committed Oct 18, 2020 Verified 43fffbd Merge pull request #2287 from baoilleach/smilesorder … ghutchis committed ...
我想用化合物的SMILES号转成MOL格式文件，但是用Open Babel 2.2.1似乎有点问题。带苯环的转换出来的...
3. Keep "smi -- SMILES format" as the INPUT FORMAT. 4. Check to select the "Input below (ignore input file)" checkbox. And enter the following SMILES string: F[C@@](Cl)(Br)I 5. Change the OUTPUT FORMAT to "sdf -- MDL MOL format" on the right side. ...
>obabel -ismi input.smi -O output.mol -gen3d (-f 6) And here are the first 10 molecules in SMILES notation: FCCCCCn1cc(c2c1ccnc2)C(=O)Nc1cccc2c1cccc2 O=C(c1nn(c2c1cccc2)CCN1CCCCC1)NC(c1ccccc1)(C)C FCCCCCn1cc(c2c1cccc2)C(=O)N[C@H](C(=O)N)C(C)C ...
2019/10/31 [Open Babel] How to draw structure from SMILES? Peng Yu 2019/10/30 Re: [Open Babel] Getting 3d coordinates from mol object Geoffrey Hutchison 2019/10/28 [Open Babel] issues reading recent gamess output for charge Bennion, Brian via OpenBabel-discuss 2019/10/28 Re: [Ope...
"babel -i fs ... -s SMILES" - Substructure Search with Index "babel -i fs ... -s query_file" - Substructure Search "babel -i fs ... -s query_file" - Exact Match Search Stereochemistry with Open Babel What Is Stereochemistry ...
0D stereoinformation in SMILES can be specified with [C@...] expressions. 0D Stereoinformation in SDF/MOL can be specified as atom parity codes. 2D Stereoinformation in SDF/MOL can be specified as bond stereo codes. 3D Stereoinformation in SDF/MOL can be specified as atom z-axis co...