Create a independent PDB sanitize step before entering the haddock3 pipeline

[joaomcteixeira]

After the discussions in #140 and #142. PR #144 implements what is here discussed. The preprocessing steps happen before the haddock3 pipeline when the original input date is copied to the run_dir/data folder. The aim is also to have a CLI that the user can run and correct the PDBs (or dry-run) before submittting.

Done:

The list follows the execution order defined in the process_pdbs function, order matters:

• ANISOU records can be discarded (use pdb_keepcoord)
• REMARK lines are discarded (use pdb_keepcoord)
• Select altloc with the highest occupancy (waiting for Improved pdb_selaltloc pdb-tools#117 to be merged)
• sets all occupancy to 1.00 (uses pdb_occ)
• Rename the MSE residues (selenomethionine) to MET. Also if MSE are defined as HETATM, make them ATOM.
• Rename HSD, HSE, HIE, HID to HIS and convert them also to ATOM if needed.
• Corrects charge in ions
• Supports all residues defined in cns/toppar/*.top files. Automatically retrieves new residues from those files.
• Convert ATOM to HETATM for residues that are expected to be HETATM. If the user provides .top file also residues defined there get converted to HETATM if needed.
• Convert HETATM to ATOM for residues that should be ATOM and are defined as HETATM (these are natural and modified aminoacids)
• Remove unsupported HETATM. Accepts user .top file.
• Remove unsupported ATOM.
• Insertions (AARG, BARG) (uses pdb_fixinsert)
• Renumbers atoms (uses pdb_reatom starting at 1)
• Renumbers residues (uses pdb_reres starting at 1)
• pdb_tidy (waiting Correct MODEL, END and ENDMDL in pdb_tidy pdb-tools#119)
• address Weird behaviour when PDB input files have no chainID #138
• If input PDBs have the same chain ID (in different files) these are corrected such that all PDBs have different chains.

Todo

• Residues in the same chain cannot have repeated numbering
• If there is a gap in the sequence, the gap must be maintained (from the above list nothing corrects for this, so it should be as is, to be tested)
• All models in an ensemble (MODEL) should be equal, that is, same labels.
• Add flag to skip the preprocessing step

Probably good to check what our current 2.4 server machinery is doing in terms of input PDB validation

[rvhonorato]

I've added more points, the server also has checks specific to the moleculetypes

[joaomcteixeira]

When a PDB has multiple chains, what should be the behaviour? Keep only one chain or homogenize all chains to the same identifier?

[amjjbonvin]

Ideally we should offer different options to the user (I guess part of some config file): 1) Select a specific chain and sanitize 2) Keep all chains, shift the numbering to avoid overlap in residue numbering and assign a unique chainID

[joaomcteixeira]

Are ligands always given in independent PDBs, or can they be given in the same PDB together with the protein? And if the latter is the case, should HETATM be all at the end of the file, with TER, same chain?

[rvhonorato]

They can be either separated or together with any moleculetype actually, before or after the ATOM. Not sure about the effect of the TER record.

[joaomcteixeira]

pdb_tidy will add TER if there is an ATOM/HETATM break. If that can't be the case, I need to add something to tidy.

[rvhonorato]

Related? haddocking/pdb-tools#101

[amjjbonvin]

Sounds fine to me. And again, the ligand might be part of a PDB of a separate PDB on its own, depends on the docking scenario

…

pdb_tidy will add TER if there is an ATOM/HETATM break. If that can't be the case, I need to add something to tidy.