md-highlighter README

md-highlighter is a simple extension to highlight files about molecular modeling and molecular dynamics simulation. Specially, it supports NAMD/CHARMM and some of Amber file formats.

Features

Supported format:

• NAMD: rtf, pdb, prm, psf, str, inp
• Amber: in, prmtop, inpcrd, prepin, frcmod
• Gromacs: gro, atp, rtp, mtp (pmx), ...
• small molecule: sdf, mol2 (modified from gromacs helper), ...
• PLUMED: .plumed.dat
• upcoming: (AmberTools leap), lib,...

For gromacs-related files, please install gromacs-helper. For VMD, install TCL. For Gaussian, install Gaussian Input File (gjf). But maybe I'll make my own syntaxes.

Tested in theme "Atom One Light".

This extension is created with the help of ChatGPT and New Bing.

Gallery

Install to explore more file types!

Conventions

• variable.other.residue-number (except psf,gro)
• entity.name.type.residue-name
• constant.numeric.atom-number (except gro,lib)
• entity.name.tag.atom-name
• support.type.atom-type
• constant.numeric.mass
• constant.numeric.coordinate
• string.quoted.charge (rtf,psf,mol2,prepi, except rtf)
• string.quoted.element-symbol
• string.quoted.bond-number
• string.quoted.velocity
• support.type.segment-name (except psf)
• entity.name.function: a different kind of blue

But different file types might rendered with different colors...

Known Issues

• Are the files too colorful?
• PDB: CONNECT and TER highlight later terms
• RTF: the structure depiction after ! is italic...
• atom names
  • with ', +, - in them are matched by \\S+ but not [A-Z+-']
  • not always start with numbers (-?\\+?[A-Z]+[0-9]*[A-Z0-9_]*)
  • MTP: the last word in rotations
• Amber .in files include various types; so do Gromacs .itp file
• PRMTOP: E-01, normal constant?
• FRCMOD: I know atomtypes can only be 1/2 characters long. Matching with this may solve the mismatching problem
• LIB: later section not read and implemented
• MTP/RTP: cannot match the last atom name?
• not fully tested files for OPLS series and more force field, where naming conventions might be different

TODO:

• add self-defined colors for aminoacids types (polar, nonpolar, etc.)
• add self-defined colors like pink, etc.
• sdf file?

Release Notes

see CHANGELOG

For more information

Welcome to contact me for any problems: gxf1212@zju.edu.cn

Enjoy!