Structure Exercise: MolSystem, Coord

(1) Load project (which has Molecule with name 'CcpnMol' in it).

Create Molecule with name 'CcpnMol' and sequence 'WHATSTHISCCPNAPILIKE'.
Use Molecule Exercise code to do this.

(2) Create a MolSystem.
  mandatory arguments: code

Create two MolSystem.Chains.
  mandatory arguments: code=['A', 'B'], molecule

Note: this creates MolSystem.Residues, ChainFragments and Atoms automatically.

Print out empirical formula, formal charge and molecular mass of either chain.
Print out molecular mass of molSystem.
Print out sequence (ccpCodes) of residues in either chain.

(3) Create StructureEnsemble.
  mandatory arguments: ensembleId, molSystem

Create Model.
  mandatory arguments: None

Create two MolStructure.Chains.
  mandatory arguments: code (same as MolSystem.Chain.code).

Note: this does not create MolStructure.Residues and Atoms automatically

Create MolStructure.Residues for residues in chain with seqId between 3 and 6 (inclusive).
  mandatory arguments: seqId, seqCode (seqId same as MolSystem.Residue.seqId).

Create MolStructure.Atoms for non-H atoms.
  mandatory arguments: name (same as MolSystem.Atom.name)

Create MolStructure.Coord for each atom.
  mandatory arguments: model
  other interesting arguments: x, y, z

(4) Save project.

(5) Use FormatConverter readCoordinates() to read PDB files.
Need and a list of PDB files.
Can optionally specify a MolecularSystem and/or a StructureEnsemble.
Can optionally specify a NamingSystem.

Use ccpnmr.format.converters.PdbFormat.
Or try ccpnmr.format.converter.PseudoPdbFormat.

Two steps:

  Constructor for PdbFormat and PseudoPdbFormat:
    mandatory arguments: project
    optional arguments: verbose=1

  Function pdbFormatObject.readCoordinates():
    mandatory arguments: fileNames
    optional arguments: minimalPrompts=1, linkAtoms=0
    optional argument for PseudoPdbFormat: forceNamingSystemName='PDB_REMED'

Print out number of chains, residues, atoms for created MolSystem.
Print out number of models for created StructureEnsemble.
