docs of isolated topics

Author: sbittrich

.gitignore

@@ -1 +1,2 @@
-site/
+site/
+.idea

docs/data-access-tools/convert-to-bcif.md

@@ -0,0 +1,37 @@
+# Convert CIF to BinaryCIF
+BinaryCIF is an efficient, binary flavor of the CIF format.
+
+This script reads data in CIF format and converts it lossless to a BinaryCIF file that can be read by Mol* or other 
+applications.
+
+## Example
+    node lib/commonjs/cli/cif2bcif/index.js file.cif file.bcif
+
+## Usage
+| Argument | Description |
+| --- | --- |
+| `src` | Source CIF to convert (can be gzipped) |
+| `out` | Generated BinaryCIF output path |
+| `-c` | Path to optional config file |
+| `-f` | Path to optional filter file |
+
+    index.js [-h] [-c CONFIG] [-f FILTER] src out
+
+### Config file
+Controls how certain columns will be encoded. This is a JSON array of instructions:
+```ts
+interface EncodingStrategyHint {
+    categoryName: string,
+    columnName: string,
+    encoding: 'pack' | 'rle' | 'delta' | 'delta-rle',
+    precision?: number
+}
+```
+Identify a particular CIF columns by its name and override the encoding by Integer Packing, Run-Length Encoding, Delta 
+Encoding, or Delta & Run-Length Encoding. You can optionally control the precision if dealing with float values.
+
+### Filter file
+Specifies which categories and columns will be written. This is a plain text file, each line represents one entry. 
+You can specify explicitly which categories or columns to include by adding `category_name` or 
+`category_name.field_name`. You can also choose to ignore some categories or columns by adding `!category_name` or 
+`!category_name.field_name`.

docs/data-access-tools/create-ccd-table.md

@@ -0,0 +1,20 @@
+# Create table from CCD
+The [Chemical Component Dictionary (CCD)](https://www.wwpdb.org/data/ccd) is as an external reference file describing all residue and small molecule 
+components found in PDB entries. The Protonation Variants Companion Dictionary (PVCD) enumerates protonation variants of
+canonical amino acids.
+
+This script bundles all `chem_comp_bond` information from the CCD and the PVCD into a single file for later use.
+Optionally, it can also generate a second output file that contains all `chem_comp_atom` information.
+
+## Example
+    node --max-old-space-size=4096 lib/commonjs/cli/chem-comp-dict/create-table.js build/data/ccb.bcif -b
+
+## Usage
+| Argument | Description |
+| --- | --- |
+| `out` | Generated file output path |
+| `--forceDownload`, `-f` | Force download of CCD and PVCD |
+| `--binary`, `-b` | Output as BinaryCIF |
+| `--ccaOut`, `-a` | File output path of optionally generated chem_comp_atom |
+
+    create-table.js [-h] [--forceDownload] [--binary] [--ccaOut CCAOUT] out

docs/data-access-tools/extract-ccd-ions.md

@@ -0,0 +1,16 @@
+# Extract ions from CCD
+The [Chemical Component Dictionary (CCD)](https://www.wwpdb.org/data/ccd) is as an external reference file describing all residue and small molecule 
+components found in PDB entries.
+
+This script extracts all ions from the CCD and provides their names as TypeScript set.
+
+## Example
+    node --max-old-space-size=4096 lib/commonjs/cli/chem-comp-dict/create-ions.js src/mol-model/structure/model/types/ions.ts
+
+## Usage
+| Argument | Description |
+| --- | --- |
+| `out` | Generated file output path |
+| `--forceDownload`, `-f` | Force download of CCD |
+
+    create-ions.js [-h] [--forceDownload] out