Preparing to open the repository to public

README.md

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 Folddisco is a bioinformatics tool for indexing and searching
 for discontinous motifs in protein structures.
 
+## Command
+### Installation
+```bash
+# Default
+cargo install --features foldcomp --path .
+```
+
+### Indexing
+```bash
+# default for small databases
+folddisco index -p <PDB_DIR|FOLDCOMP_DB> -i <INDEX_PATH> -t <THREADS> 
+# For large databases (number of structures > 65536). This will generate a 8GB fixed-size offset file
+folddisco index -p <PDB_DIR|FOLDCOMP_DB> -i <INDEX_PATH> -t <THREADS> -m big
+
+# Setting the number of bins and feature
+folddisco index -p <PDB_DIR|FOLDCOMP_DB> -i <INDEX_PATH> -t <THREADS> -d <DISTANCE_BINS> -a <ANGLE_BINS> -y <FEATURE_TYPE>
+```
+
+```bash
+# Example
+# Indexing human proteome with 12 threads
+folddisco index -p h_sapiens -i index/h_sapiens_folddisco -t 12
+```
+
+You can also download pre-built index files 
+- [Human proteome](https://foldcomp.steineggerlab.workers.dev/h_sapiens_folddisco.tar.gz)
+- [E. coli proteome](https://foldcomp.steineggerlab.workers.dev/e_coli_folddisco.tar.gz)
+
+### Querying
+```bash
+# default
+folddisco query -i <INDEX> -p <QUERY_PDB> -q <QUERY_RESIDUES> -r -t <THREADS>
+# -r flag is for residue matching & rmsd calculation
+# -v flag is for verbose output (measures step-by-step runtime)
+
+# Using the whole structure as a query
+folddisco query -i <INDEX> -p <QUERY_PDB> -r -t <THREADS>
+
+# Using query.txt file
+folddisco query -i <INDEX> -q <QUERY_FILE> -r -t <THREADS>
+
+# Using distance and angle threshold
+folddisco query -i <INDEX> -p <QUERY_PDB> -q <QUERY_RESIDUES> -d <DISTANCE_THRESHOLD> -a <ANGLE_THRESHOLD> -r -t <THREADS>
+```
+
+```bash
+# Example
+# Zinc finger query to human proteome
+folddisco query -i index/h_sapiens_folddisco -p query/1G2F.pdb -q F207,F212,F225,F229 -r -d 0.5 -a 5 -t 12
+folddisco query -i index/h_sapiens_folddisco -q query/zinc_finger.txt -r -d 0.5 -a 5 -t 12
+
+# Serine protease query to human proteome
+folddisco query -i index/h_sapiens_folddisco -p query/4CHA.pdb -q B57,B102,C195 -r -t 12
+folddisco query -i index/h_sapiens_folddisco -q query/serine_protease.txt -r -t 12
+```
+
+
+## Index list
+- `index/`
+  - `h_sapiens_folddisco`: Human proteome, 23K structures
+  - `e_coli_folddisco`: E. coli proteome, 4K structures
+
+## Example query list
+- `query/`
+  - `1G2F.pdb`: Zinc finger protein
+  - `4CHA.pdb`: Serine protease
+  - `1LAP.pdb`: Aminopeptidase
+  - `zinc_finger.txt`: 1G2F.pdb F207,F212,F225,F229
+  - `serine_protease.txt`: 4CHA.pdb B57,B102,C195
+  - `aminopeptidase.txt`: 1LAP.pdb 250,255,273,332,334
+  - `knottin.txt`: 2N6N.pdb 3,10,15,16,21,23,28,30
 
 
 ## Contributor

query/aminopeptidase.txt

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+query/1LAP.pdb	250,255,273,332,334	

query/knottin.txt

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+query/2N6N.pdb	3,10,15,16,21,23,28,30	

query/serine_peptidase.txt

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+query/4CHA.pdb	B57,B102,C195	

query/zinc_finger.txt

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+query/1G2F.pdb	F207,F212,F225,F229	

query/zinc_finger_with_output.txt

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+query/1G2F.pdb	F207,F212,F225,F229	./zinc_finger.folddisco.out.tsv