Build combined topology files

[tomnewport]

A topology file defines a number of molecules:

[ molecules ]
Protein 1
POPG 229
POPC 117
W 7601
NA+ 440
CL- 213

These are usually included in .itp files. Grompp can produce a preprocessed output using the -pp flag. I would like to propose the following steps:

1. Collect: input.mdp, input.top, input.gro, moltype_name
2. Grompp inputs to produce a combined.top for the topology
3. Create a blank combined.itp file with a moltype specification for moltype_name
4. For each moltype in the molecules section of combined.top:
   1. Find the moltype definition in combined.top
   2. Renumber all atoms in all tables
   3. Add all tables to tables in combined.itp
5. Add combined.itp as an #include in combined.top

   Tables

.itp files can contain a number of tables. The following are the only ones which will be considered:

Thanks to GromacsWrapper.

[ moleculetype ]

This creates a new subsection within the file and defines a new moltype. Fields are:

• name - name of the molecule
• nrexcl - bond-based exclusions

  [ atoms ]

This defines atoms. Fields are:

• id - atom id within the moltype
• type - atom type (from atomtypes table)
• resnr - residue number
• residu - residue name
• atom - atom name
• cgnr - charge group number
• charge - coulomb charge on atom

  [ bonds ]

• ai - from atom id
• aj - to atom id
• funct - bond function
• c0 - bond length
• c1 - force constant

  [ angles ]

ai aj ak funct c0 c1

[ dihedrals ]

ai aj ak al funct c0 c1 c2

[ pairs ]

ai aj funct c0 c1

Adding to a single moleculegroup

1. Fetch uncommented parts of lines
   1. if ; is in the line:
      1. Take the bit of the line before the ;
   2. strip whitespace
   3. If line != "":
      1. split line on whitespace
      2. if that produces the expected number of parts
      3. resolve any atom references (a[ijkl])
   4. add greatest existing atom_id to all the atom ids
   5. add greatest existing cgnr to all the atom cgnrs

It would also be nice to be able to do a pass over the table to check the .gro and .itp match up.