Create MolecularSystem class

[khs26]

I am planning to create a MolecularSystem class inheriting from BaseSystem. Its purpose will be to:

• Act as a superclass for AMBERSystem and any future CHARMM, GROMOS etc. style systems;
• Identify topological features of molecular symmetry;
• Allow for interconversion between AMBER, CHARMM and other potentials;
• Implement easy I/O and visual representations.

The two important classes for this will be MolecularSystem and Atom, which are outlined below:

class MolecularSystem(BaseSystem)
    atoms
    bonds
    angles
    torsions
    topology_search()
    import_pdb()
    import_xyz()

class Atom()
    mass
    element
    charge
    lj_terms[]
    bonded_atoms[]

[ruehle]

Hey,

I think that should go into a separate Topology class - as it is done for the rigid bodies already. The rigid body topology needs massive cleanup, but i think keeping the topology separate is the better idea.

Then the system class is responsible for the algorithms and the Topology for the data structures. I also have a topology for crystal systems.

[js850]

victor, can you be more specific? your non-existent documentation makes
it hard to use what you've done as an example.

On 19/03/13 17:00, Kyle Sutherland-Cash wrote:

I am planning to create a MolecularSystem class inheriting from
BaseSystem. Its purpose will be to:

• Act as a superclass for AMBERSystem and any future CHARMM, GROMOS
  etc. style systems;
• Identify topological features of molecular symmetry;
• Allow for interconversion between AMBER, CHARMM and other potentials;
• Implement easy I/O and visual representations.

The two important classes for this will be MolecularSystem and Atom,
which are outlined below:

|class MolecularSystem(BaseSystem)
atoms
bonds
angles
torsions
topology_search()
import_pdb()
import_xyz()

class Atom()
mass
element
charge
lj_terms[]
bonded_atoms[]
|

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[ruehle]

I on purpose wasn't more specific regarding my example. I think the current aatopology is not very well structured. What I wanted to say is that I think we should do more or less exactly what Kyle suggested, but in a separate topology class rather than the system class. Then we have the data structures (Molecules, Atoms, Bonds, ...) separated from the choice of algorithms (system class). I also prefer the idea to have it separated into smaller sub components.

We should sit have a chat on which parts might be similar in molecular systems, angle axis systems and crystal systems to design a more uniform interface - but by no means keep the existing one. One thing which also should go into the topology is a reference to the current boundary conditions used, e.g. cubic pbc, open system, triclinic, ...