PerlMol - Features
What follows is a list of the main features currently implemented in the
PerlMol toolkit, along with their status, according to this code:
| Basic functionality only (very incomplete) | 1
|
| Partially implemented | 2
|
| Mostly implemented (missing minor features or optimizations) | 3
|
| Fully implemented | 4
|
Note that even level 1 features work, it's just that they don't do
everything yet. For details about missing features and possible problems, see
the appropriate manpage.
Basic functions
| Clone molecules | 3
|
| Delete atoms and bonds | 3
|
| Combine/separate molecules (connected graphs) | 3
|
Geometric functions
| Calculate distances, angles, and dihedrals from cartesian coordinates | 4
|
| Find shortest distance between two molecules | 3
|
| Cartesian coordinates from internal coordinates | 4
|
| Z-matrix builder: create an internal coordinate
representation of a molecule from scratch using the Cartesian coordinates
| 3
|
| 3D molecule structure builder: generate atomic coordinates from a connection table
| 1
|
| Calculate the centroid and best-fit plane of a ring | 4
|
Topological functions
| Create bonds from cartesian coordinates | 3
|
| Automatically assign formal bond orders | 3
|
| Ring perception (including SSSR) | 3
|
| Detect aromaticity | 2
|
| Substructure matching | 3
|
| Formula matching | 4
|
| Canonicalization / topological symmetry perception | 4
|
| Z-matrix builder: create an internal coordinate
representation of a molecule from scratch using the Cartesian coordinates
| 3
|
Input/output and file formats
| MDL Molfile parser/writer | 2
|
| MDL SDF file parser/writer | 2
|
| PDB file parser/writer | 2
|
| SMILES parser/writer | 3
|
| Unique SMILES generator | 3
|
| SMARTS parser | 3
|
| Sybyl Line Notation (SLN) parser/writer | 2
|
| Midas/Chimera atom specification language parser | 2
|
| Formula parser/formatter | 4
|
| Formula pattern parser | 4
|
| Mopac input file parser/writer | 3
|
| XYZ format file parser/writer | 4
|
| VRML format file writer | 3
|
| Perl Data::Dumper file format | 4
|
| A "printf" for molecules and atoms | 3
|
Data
| Relative atomic masses | 4
|
| Exact isotope masses | 4
|
Mini-language
| Mok - "an AWK for molecules" | 3
|
Frequently Asked Question: When will feature X be implemented?
Answer: I usually add features when I need them. Some features I
will never need, so they are not likely to be implemented by me. However, if
you implement the feature you need and want to donate it so that
I can add it to the PerlMol distribution, I'll be happy to do so. Any feedback
is welcome, however, even if I can't implement the feature myself.
