User 9d8db04821
16-10-2008 13:54:34
Hi,
I am currently using CheAxon's library for (very) basic handling of structures and reactions, i.e., reading form file and comparing, modifying, etc. exisitng structures or creating new structures from scratch. Nothing as fancy as databases, Markush queries, etc.
It seems like only the API is available as documentation for the fundamental chemaxon.struc package. While I am generally able to find my way through the framework in a lot of instances the API alone is not enough and I have to use "trial and error" - trying a method to see what it does.
As a practical example I would like to merge a number of fragments into one multi-fragment molecule. From the API I have found
but the description of these methods is hardly enough to really understand what they do. Also I was not able to find any method which gives the valency of an atom - I mean the number used internally to add implicit hydrogens and to do valence checks, etc. Or how the internals operate - it is mentioned that an instance of MolAtom can represent more than one atom, but I was not able to find how this works and what implications it does or does not have. The list is quite long, these just a few examples from the top of my head.
The rather long introduction above leads (finally :) to my question. Isn't there a kind of developers guide covering things as basic as creating molecules in memory, merging two molecules together, working with atoms, bonds, selections, and, in general, covering the chemaxon.struc package?
Thank you in advance,
Dim
I am currently using CheAxon's library for (very) basic handling of structures and reactions, i.e., reading form file and comparing, modifying, etc. exisitng structures or creating new structures from scratch. Nothing as fancy as databases, Markush queries, etc.
It seems like only the API is available as documentation for the fundamental chemaxon.struc package. While I am generally able to find my way through the framework in a lot of instances the API alone is not enough and I have to use "trial and error" - trying a method to see what it does.
As a practical example I would like to merge a number of fragments into one multi-fragment molecule. From the API I have found
| Code: |
void clonecopy(CGraph g) Makes another molecule identical to this one. void clonecopy(int[] iatoms, MoleculeGraph g) Copies the specified atoms and bonds of this graph to another one. void clonelesscopy(CGraph g) Copies to selection. |
but the description of these methods is hardly enough to really understand what they do. Also I was not able to find any method which gives the valency of an atom - I mean the number used internally to add implicit hydrogens and to do valence checks, etc. Or how the internals operate - it is mentioned that an instance of MolAtom can represent more than one atom, but I was not able to find how this works and what implications it does or does not have. The list is quite long, these just a few examples from the top of my head.
The rather long introduction above leads (finally :) to my question. Isn't there a kind of developers guide covering things as basic as creating molecules in memory, merging two molecules together, working with atoms, bonds, selections, and, in general, covering the chemaxon.struc package?
Thank you in advance,
Dim