[pull] master from nglviewer:master #68
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The multiple TER records in this PDB each trigger the creation of a new chain in the chain store. As there is no chain name in the file, the calculateChainName function is called and recomputes new chains based on connectivity and chemical type.
In some cases the original number of chains could have been greater than the number of chains after the calculateChainnames execution. As the chainCount in the modelStore was not reset, it was possible to execute the model.eachChain() callback more times than the actual number of chain, over references that were non longer valid. A side effect of this was the creation of PDB files that contained duplicated sections. This fix ensures that the chainCount value in the modelStore is consistent with the execution of the `addChain` function.
Previously it was set from column 7 and left justified. This was breaking some tools such as the receptor preparation script from the AutoDock MGLTools which parses a number from the substring [10:14].
This was due to a double increment in the same loop.
To conform with PDB format v3.3
Fix pdbwriter model format
Fix calculate chain names
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