5.1.4.5.2. Gromacs TOP - BLOCKS boiler-plate code
5.1.4.5.2.1. Classes
- class gromacs.fileformats.blocks.System[source]
Top-level class containing molecule topology.
Contains all the parameter types (AtomTypes, BondTypes, … ) and molecules.
- class gromacs.fileformats.blocks.Molecule[source]
Class that represents a Molecule
Contains all the molecule attributes: atoms, bonds, angles dihedrals. Also contains settle, cmap and exclusion sections, if present.
- class gromacs.fileformats.blocks.Atom[source]
Class that represents an Atom
Contains only the simplest atom attributes, that are contained like in section example below.
Molecule
cantains anatoms
that’s a list-container forAtom
instances.
- class gromacs.fileformats.blocks.Param(format)[source]
Class that represents an abstract Parameter.
This class is the parent to AtomType, BondType and all the other parameter types.
The class understands a parameter line and that a
comment
that may follow. CMapType is an exception (it’s a multi-line parameter).convert()
provides a rudimentary support for parameter unit conversion between GROMACS and CHARMM notation: change kJ/mol into kcal/mol and nm into Angstrom.disabled
for supressing output when writing-out to a file.
5.1.4.5.2.2. History
Sources adapted from code by Reza Salari https://github.com/resal81/PyTopol