PDBE-6878: Sort nodes of graph based on residue id and chain (#25)
* Improving depiction diagrams for dative bonds to metal (like HEM) (#19)
* Dative bonds to metals that break valency that than
charge adjustment
* ZERO order bond to metals that break valency
rather than charge adjustment.
ZERO order results in dotted line in depictions.
* Alter DATIVE bonds to ZERO order for diagrams as
this results in dotted lines in depictions but
keeps good angles in CPT diagram
DATIVE bonds to metals that break valency
rather than charge adjustment.
* sort nodes before assigning id to boundmolecule
* test for boundmolecule equivalence
* bumped up version
* correct alignment of atom names in PDB files
* formatting the file
* updated to use custom PDB writing instead of RDKit MolToPDBBlock
* removed MAN as its mapping is for soe reason missing from unichem API
* change bond type from dative to single for inchi calculation
* use inchi_from_mol from mol_tools for inchi calcualtion
* removed altering of bond type while exproting svg, as mol2D is is generated using dative bond and it is only used for depiction
* store mol instead of smiles in SubstructureMapping
* updated doc to use refactored SubstructureMapping model
* strip new line only. RDKit checks for the 3D label in column 21-22
* removed formal charge from PDB files
* alters bondtype from dative to zero for depiction
* linting and formatting
* added changes
* updated rdkit version
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Co-authored-by: Oliver Smart <[email protected]>
Co-authored-by: roshan <“[email protected]”>
