Xavier Robin authored 1 year ago and Xavier Robin committed 1 year ago

An overflow would happen when the residue contains unknown atoms that
are not in the compound, and can prevent bonds from being properly
created in ConnectAtomsOfResidue.

This reverts commit 9153648f.

The intention of this commit was to fix potential issues when operating on a
dihedral connecting 4 atoms where at least 3 atoms are exactly on a line.
Dihedrals are ill defined in this case but "expected behaviour"
(whatever that means) is tested as a unit test.
A fail was observed in two cases. First case that triggered commit
9153648f, second case that showed that the
problem is not solved. Therefore reverting to original state in order to find
different solution.

There are two use cases for this parameter: 1) decide whether a chain
mapping problem is actually solvable by naive enumeration and crash out if not
2) As a decision whether one should use naive enumeration or a heuristic
approach for chain mapping.

For the latter, n_max_naive meant the number of chains in the underlying
structure. Now its number of possible mappings for both cases.

- Make original structures available as attribute in mol.alg.Scorer object.
  Thats the actual input structures without Molck etc.
- Ensure unique interface definitions by lexicographically sorting the respective
  chain name lists
- Optionally dump additional alignment information in the compare-structures action.
  Explicitely dump residue numbers etc. of the aligned residues.

requested by Andriy. Computes all IPS metrics on a per-interface basis

requested by Andriy. Computes all ICS metrics on a per-interface basis

Coordinates are delta encoded. That means the first element corresponds
to the first coordinate and all the following elements are the
respective diffs. The first element is potentially much larger than
the rest and can cause excessive integer packing due to overflows.
This change stores that first element separately.

Not sure why this doesn't cause an error here, but the code is invalid.

The chain naming strategy can be read in the documentation

- parameters for rotamers are derived from PDB structures by ourselves
- removed LOSSY and INFER_POSITIONS options. User can now just give a
  max error and OMF will figure out by itself the best strategy.
- Increased accuracy by storing angle differences in rotamer compression.
  That means: instead of blindly using the angles from the derived parameters,
  we sacrifice 4 bits to store differences to that optimal angle.
- CANNOT LOAD OMF FILES FROM PREVIOUS VERSIONS ANYMORE

SDF V2000 supports up to 999 atoms/bonds. For more we need to implement
the V3000 format. For now we throw an error.

The RCSB ModelServer SDF files contain counts line with only 33
characters. Although invalid, they can be read by RDKit (which only
requires 6 characters). This commit emmulates the behavior of RDKit.

- Required data is extracted from MMCifInfoBioUnit object and fed into a
  custom BUInfo object
- BUInfo object can be serialized into bytestring
- Chain names in biounit have following naming scheme:
  <idx>.<asu_chain_name>. idx -> n-th copy of ASU chain with n
  starting from 1.
- Properties are copied from whatever is stored in assymetric unit
- Chain properties copied: ChainType (CHAINTYPE_POLY etc.)
- Residue properties copied: OLC, sec struct, ChemClass (PEPTIDE_LINKING etc.),
  ChemType(AMINOACIDS etc.), IsProtein flag, IsLigand flag
- Atom properties copied: name, element, occupancy, bfactor, ishetatm