Merge branch 'docs' into setup-improvements

examples/monomer/fasta_dir/6kwc.fasta

+>6KWC_1
+GSTIQPGTGYNNGYFYSYWNDGHGGVTYTNGPGGQFSVNWSNSGEFVGGKGWQPGTKNKVINFSGSYNPNGNSYLSVYGWSRNPLIEYYIVENFGTYNPSTGATKLGEVTSDGSVYDIYRTQRVNQPSIIGTATFYQYWSVRRNHRSSGSVNTANHFNAWAQQGLTLGTMDYQIVAVQGYFSSGSASITVS

examples/monomer/inference.sh

+#!/bin/bash
+export LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$LD_LIBRARY_PATH
+export LIBRARY_PATH=$CONDA_PREFIX/lib:$LIBRARY_PATH
+
+export FASTA_DIR=./fasta_dir
+export OUTPUT_DIR=./
+export PRECOMPUTED_ALIGNMENT_DIR=./alignments
+export MMCIF_DIR=/mmcifs    # UPDATE with path to your mmcifs directory 
+
+python3 run_pretrained_openfold.py $FASTA_DIR \
+  $MMCIF_DIR \
+  --output_dir $OUTPUT_DIR \
+  --config_preset model_1_ptm \
+  --model_device "cuda:0" \
+  --data_random_seed 42 \
+  --use_precomputed_alignments $PRECOMPUTED_ALIGNMENT_DIR