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I have some questions regarding generation of mol files-

  1. For bond block the numbering can be done at random or it has to follow some order

  2. Also in the atom block the order in which atoms occur can it be random or again it has to follow any order

  3. Is order of numbering done in bond block and atom block related

  4. Is there any free software which converts mol files to structure

Here is a sample structure with mol file- enter image description here

  Sample

 22 23  0  0  0  0  0  0  0  0999 V2000
   -2.5962    2.2535    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5962    0.7512    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2958    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.7512    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.2535    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2958    3.0047    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6479    1.7042    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
    1.3005    3.0047    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2958    4.5070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2958   -1.5023    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3005    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3005   -1.5023    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6009   -2.2535    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8967   -1.5023    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8967    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6009    0.7512    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1972   -2.2535    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    2.6009   -3.7559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8967    3.0047    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1972    3.7559    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1455    4.3052    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
    3.9014   -4.5070    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  1  6  1  0  0  0  0
  1 19  1  0  0  0  0
  5  8  2  0  0  0  0
  6  9  1  0  0  0  0
  3 10  2  0  0  0  0
  4 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 15 16  1  0  0  0  0
 11 16  2  0  0  0  0
 14 17  1  0  0  0  0
 13 18  1  0  0  0  0
 19  7  1  0  0  0  0
 19 20  1  0  0  0  0
 19 21  1  0  0  0  0
 18 22  2  0  0  0  0
M  END
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    $\begingroup$ Can you explain, how the answer to your previous question does not cover your current question. For example, I read there, that the hydrogen atoms are stored implicitly. $\endgroup$ – Martin - マーチン Jul 5 '15 at 9:58
  • $\begingroup$ @Martin-マーチン Yeah sorry for that.i will edit and remove that part of my question..But still others questions were not covered in my last post $\endgroup$ – LifeIsGood Jul 5 '15 at 11:11
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For bond block the numbering can be done at random or it has to follow some order

Bonds don't need to be in any particular order, although usually bonds are created first for atom 1, then atom 2, etc. However, the first bond could be between atom 101 and atom 100 if you wish.

Also in the atom block the order in which atoms occur can it be random or again it has to follow any order

Atoms can be in any order. Some programs use "canonical ordering" so that the same molecule will always have the same atomic order, but this is rarely used because it can be time-consuming.

Is order of numbering done in bond block and atom block related

As indicated above, both the atom and bond blocks could be in random order. The relation, obviously, is that for a given molecular structure, there will be bonds between bonded atom pairs.

Is there any free software which converts mol files to structure

There are many, but you don't describe whether you want 3D (presumably) or 2D structures.

Personally, I suggest Avogadro which can create 3D coordinates for files.

If you're generating a large batch of 3D structures, you will likely want to use Open Babel or RDKit or something similar. Both are open source and free.

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  • $\begingroup$ Thanks a lot.I still have a question. In the mol file I have provided in that consider first six lines of bond block.1 is connected with 2,2with 3,3-4,4-5,1-6.So in this they have started from 1 and then continued and returned to 1 after 4-5.Can I just finish up 1 first then go to 2 and so on.I mean can I write this way- 1-2, 1-6, 1-19, 2-3. So,I finished up 1 and then started 2. Can I do this way? $\endgroup$ – LifeIsGood Jul 5 '15 at 18:02
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    $\begingroup$ You can enter the bonds in any order, since they will be read separately. Yes, you could write all the bonds of atom 1 and then 2, etc. or any way you see fit. $\endgroup$ – Geoff Hutchison Jul 5 '15 at 18:04
  • $\begingroup$ Sorry but I have another question.Can x,y,z coordinates in atom blocks be random if I have to write mol file by hand without any software?Because looking at the picture how is it possible to tell precise coordinates of the atoms? $\endgroup$ – LifeIsGood Jul 5 '15 at 18:09
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    $\begingroup$ No, they cannot be random. In this case, it's a 2D structure, so the Z coordinate should be uniformly 0.0, and the Mol file marked as such. The X and Y coordinates should be mapped out by the image, since 2D structures have meaningless bond lengths - they're for display purposes much like the image. But if you want image -> structure, I suggest OSRA which is open source and already does this. $\endgroup$ – Geoff Hutchison Jul 5 '15 at 18:12

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