[pull] master from nglviewer:master #76
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Only BufferGeometry is supported. Every BufferGeometry helper (e.g. BoxBufferGeometry) has been renamed to shorter name (e.g. BoxGeometry)
As it leverages many deprecated methods
replace with copy() + invert()
critical and high vulnerabilities were caused by dependencies related with Jest
Previous code was setting `_position` to an empty array. This was causing some bugs where the _position array was not filled with the proper values and remained empty.
`ALPHATEST` was previously used as a flag and a value in three.js `alphatest_fragment` chunk. It was superseded by the `USE_ALPHATEST` flag and the `alphaTest` value passed as a uniform. The declaration of the `alphaTest` uniform is made in the `alphatest_pars_fragment` chunk.
A SpotLight must have its distance set in real world coordinates. This was resulting in very dark scenes, where the position of the light or its intensity must take into account the bounding box. Directional Lights do not require this settings. They light the scene in a uniform manner from afar.
Changes in Three.js regarding light computation even with the `renderer.useLegacyLights` parameter enabled.
A banding effect was due to a loss of precision when copying the texture between render targets.
standard is a linter for js files. Note that it does not work on ts file, which makes the `npm run lint` command inneffective, except for the example files. With the upgrade, standard breaks when it can't find any files, and it reports many warnings for the example files (stylistic warnings). So it is also disabled for now.
…ghts #865 upgrade three js legacy lights
CIF reader from Mol* is wrapped in async calls which require to make the _parse function async in the binary cif parser.
mmCif files use the struct_conf table to define the alpha helices whereas the sheets are defined in the struct_sheet_range table. Alphafold modelCif files contain every DSSP assignation in the struct_conf table using DSSP mmcif codes (such as `TURN_TY1_P1`)
This table is available in "Updated mmcif files" distributed by PDBe. In this commit, the list of bonds defined for each residue is stored in a new dictionary in a ChemCompMap object. Bonds in the mmcif file are defined using atom names (e.g. CA), which need to be converted in indices in the atomList from a given residue type. The atomList contain list of indices of AtomTypes from the structure AtomMap. Given an atom index from the atomAlist, the AtomMap.get(idx) method returns an AtomType object that contains the atomname property.
Previously, the default was to use mmtf format server by RCSB. This format was containing the full connectivity, which is currently missing from bcif files distributed by RCSB. PDBe distributes "Updated" mmcif files, containing this data. The same content is available in their bcif files.
Jest cannot import code from ES modules which is the case of the modules from MolStar (not bundled). Jest code fails with some indications about tweaking jest config using the transformIgnorePattern property. After much trials and research I was not able to make it work and decided to switch the test runner to vitest, which solved the issue.
valueKind has 3 values: 0 if present, 1 if not present ('.' in Cif), 2 if unknown ('?' in Cif)
When splitting `(1,2,6,10,23,24)` against `(`, the first item is an empty string. The fix consists in filtering-out falsy values from the split array.
The CIF library returns `0` when a string column is converted to an int array. The fix here is to map the string array from the column using the String.charCodeAt() function.
In that case the `chainIndexDict` does not have the corresponding key. This fix still creates the corresponding `Entity` but with an empty chain list.
1015 binary cif support
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