AMF DOCUMENTATION
ENG
This project introduces a new molecule-containing file format - called Absolute Molecule Format - which concurrently aims to make molecular modelling more accesible and comprehendable. Although various types of molecule files exist, this specific file format generically utilizes the improvisations on legibility of file format, and file size.
One of the most striking advantages of the "Absolute Molecule Format" is its unparalleled legibility. The structure of molecules, being complex and intricate, demands a representation that can be easily interpreted by both humans and computational algorithms. .amf format achieves this by employing a clear and intuitive syntax that captures the intricate details of chemical entities in a comprehensible manner. This feature makes this new molecule file format outstand from other formats.
Another remarkable feature of .amf format is its low memory consumption. The special format occupies much less memory than other molecule file formats. For example:
.amf format |
.xyz format |
.pdb format |
|---|---|---|
Glucose molecule file |
Glucose molecule file |
Glucose molecule file |
AMF file |
XYZ file |
PDB file |
866 bytes |
1,204 bytes (~1Kb) |
2,002 bytes (~2Kb) |
This page is a reference for *.amf format keywords.
| Keyword | Description | USAGE |
|---|
| ORI | Builds an origin which can be named and then summoned by that name. | ORI [ORIGIN_NAME] |
| STOP | This keyword should be put at the last line of an ORI block to seperate the blocks. | STOP |
| INS | Invokes an origin. The origin needs to be declared beforehand. | INS [ORIGIN_NAME] [X] [Y] [Z] |
| ATOM | Instructs to create an atom. Can be drawn 2D or 3D afterward. | ATOM [ID] [ATOM_NUMBER] [X] [Y] [Z] |
| BND | Similar to the ATOM keyword, creates a bond between atoms. | BND [ID] [BOND_TYPE] [ATOM_ID_1] [ATOM_ID_2] |
| EXP | For explanation; can be written anything. Must be declared at the start of the file. | EXP [EXPLANATION] |
| STT | Starts the building part. All invokes,bond and atom placements must be done here. | STT |
| STP | Finishes the building part. | STP |
| END | Indicates that the file has ended. It must be put at the end of the file. | END |
For any questions or unclear statements, contact me Through here
PyPi Link: PyPi
The python library can be installed to the machine via the following command:
pip install amfpy-python
Source Code on GitHub: GitHub Link