Merge branch 'add_SCNet_icon' into 'master'

add SCNet and icon

See merge request !1

scripts/download_alphafold_params.sh

@@ -31,7 +31,8 @@ fi
 
 DOWNLOAD_DIR="$1"
 ROOT_DIR="${DOWNLOAD_DIR}/params"
-SOURCE_URL="https://storage.googleapis.com/alphafold/alphafold_params_2022-03-02.tar"
+# SOURCE_URL="https://storage.googleapis.com/alphafold/alphafold_params_2022-03-02.tar"
+SOURCE_URL="http://113.200.138.88:18080/aidatasets/project-dependency/alphafold/-/raw/master/pdb_mmcif_2023_09_13.tar.gz?ref_type=heads&inline=false"
 BASENAME=$(basename "${SOURCE_URL}")
 
 mkdir --parents "${ROOT_DIR}"

scripts/download_bfd.sh

@@ -33,7 +33,8 @@ DOWNLOAD_DIR="$1"
 ROOT_DIR="${DOWNLOAD_DIR}/bfd"
 # Mirror of:
 # https://bfd.mmseqs.com/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt.tar.gz.
-SOURCE_URL="https://storage.googleapis.com/alphafold-databases/casp14_versions/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt.tar.gz"
+# SOURCE_URL="https://storage.googleapis.com/alphafold-databases/casp14_versions/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt.tar.gz"
+SOURCE_URL="http://113.200.138.88:18080/aidatasets/project-dependency/alphafold/-/raw/master/bfd.tar.gz?inline=false"
 BASENAME=$(basename "${SOURCE_URL}")
 
 mkdir --parents "${ROOT_DIR}"

scripts/download_mgnify.sh

@@ -33,7 +33,8 @@ DOWNLOAD_DIR="$1"
 ROOT_DIR="${DOWNLOAD_DIR}/mgnify"
 # Mirror of:
 # ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/peptide_database/2018_12/mgy_clusters.fa.gz
-SOURCE_URL="https://storage.googleapis.com/alphafold-databases/casp14_versions/mgy_clusters_2018_12.fa.gz"
+# SOURCE_URL="https://storage.googleapis.com/alphafold-databases/casp14_versions/mgy_clusters_2018_12.fa.gz"
+SOURCE_URL="http://113.200.138.88:18080/aidatasets/project-dependency/alphafold/-/raw/master/mgnify.tar.gz?ref_type=heads&inline=false"
 BASENAME=$(basename "${SOURCE_URL}")
 
 mkdir --parents "${ROOT_DIR}"

scripts/download_pdb70.sh

@@ -31,7 +31,8 @@ fi
 
 DOWNLOAD_DIR="$1"
 ROOT_DIR="${DOWNLOAD_DIR}/pdb70"
-SOURCE_URL="http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/old-releases/pdb70_from_mmcif_200401.tar.gz"
+# SOURCE_URL="http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/old-releases/pdb70_from_mmcif_200401.tar.gz"
+SOURCE_URL="http://113.200.138.88:18080/aidatasets/project-dependency/alphafold/-/raw/master/pdb70.tar.gz?ref_type=heads&inline=false"
 BASENAME=$(basename "${SOURCE_URL}")
 
 mkdir --parents "${ROOT_DIR}"

scripts/download_pdb_mmcif.sh

@@ -62,4 +62,5 @@ done
 # Delete empty download directory structure.
 find "${RAW_DIR}" -type d -empty -delete
 
-aria2c "ftp://ftp.wwpdb.org/pub/pdb/data/status/obsolete.dat" --dir="${ROOT_DIR}"
+# aria2c "ftp://ftp.wwpdb.org/pub/pdb/data/status/obsolete.dat" --dir="${ROOT_DIR}"
+aria2c "http://113.200.138.88:18080/aidatasets/project-dependency/alphafold/-/raw/master/pdb_mmcif.tar.gz?ref_type=heads&inline=false" --dir="${ROOT_DIR}"

scripts/download_pdb_seqres.sh

@@ -31,7 +31,8 @@ fi
 
 DOWNLOAD_DIR="$1"
 ROOT_DIR="${DOWNLOAD_DIR}/pdb_seqres"
-SOURCE_URL="ftp://ftp.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt"
+# SOURCE_URL="ftp://ftp.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt"
+SOURCE_URL="http://113.200.138.88:18080/aidatasets/project-dependency/alphafold/-/raw/master/pdb_seqres.tar.gz?ref_type=heads&inline=false"
 BASENAME=$(basename "${SOURCE_URL}")
 
 mkdir --parents "${ROOT_DIR}"

scripts/download_small_bfd.sh

@@ -31,7 +31,8 @@ fi
 
 DOWNLOAD_DIR="$1"
 ROOT_DIR="${DOWNLOAD_DIR}/small_bfd"
-SOURCE_URL="https://storage.googleapis.com/alphafold-databases/reduced_dbs/bfd-first_non_consensus_sequences.fasta.gz"
+# SOURCE_URL="https://storage.googleapis.com/alphafold-databases/reduced_dbs/bfd-first_non_consensus_sequences.fasta.gz"
+SOURCE_URL="http://113.200.138.88:18080/aidatasets/project-dependency/alphafold/-/raw/master/small_bfd.tar.gz?ref_type=heads&inline=false"
 BASENAME=$(basename "${SOURCE_URL}")
 
 mkdir --parents "${ROOT_DIR}"

scripts/download_uniclust30.sh

@@ -33,7 +33,8 @@ DOWNLOAD_DIR="$1"
 ROOT_DIR="${DOWNLOAD_DIR}/uniclust30"
 # Mirror of:
 # http://wwwuser.gwdg.de/~compbiol/uniclust/2018_08/uniclust30_2018_08_hhsuite.tar.gz
-SOURCE_URL="https://storage.googleapis.com/alphafold-databases/casp14_versions/uniclust30_2018_08_hhsuite.tar.gz"
+# SOURCE_URL="https://storage.googleapis.com/alphafold-databases/casp14_versions/uniclust30_2018_08_hhsuite.tar.gz"
+SOURCE_URL="http://113.200.138.88:18080/aidatasets/project-dependency/alphafold/-/raw/master/uniclust30.tar.gz?ref_type=heads&inline=false"
 BASENAME=$(basename "${SOURCE_URL}")
 
 mkdir --parents "${ROOT_DIR}"

scripts/download_uniprot.sh

@@ -33,23 +33,24 @@ fi
 DOWNLOAD_DIR="$1"
 ROOT_DIR="${DOWNLOAD_DIR}/uniprot"
 
-TREMBL_SOURCE_URL="ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.fasta.gz"
+# TREMBL_SOURCE_URL="ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.fasta.gz"
+TREMBL_SOURCE_URL="http://113.200.138.88:18080/aidatasets/project-dependency/alphafold/-/raw/master/uniprot.tar.gz?ref_type=heads&inline=false"
 TREMBL_BASENAME=$(basename "${TREMBL_SOURCE_URL}")
-TREMBL_UNZIPPED_BASENAME="${TREMBL_BASENAME%.gz}"
+# TREMBL_UNZIPPED_BASENAME="${TREMBL_BASENAME%.gz}"
 
-SPROT_SOURCE_URL="ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz"
-SPROT_BASENAME=$(basename "${SPROT_SOURCE_URL}")
-SPROT_UNZIPPED_BASENAME="${SPROT_BASENAME%.gz}"
+# SPROT_SOURCE_URL="ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz"
+# SPROT_BASENAME=$(basename "${SPROT_SOURCE_URL}")
+# SPROT_UNZIPPED_BASENAME="${SPROT_BASENAME%.gz}"
 
 mkdir --parents "${ROOT_DIR}"
 aria2c "${TREMBL_SOURCE_URL}" --dir="${ROOT_DIR}"
-aria2c "${SPROT_SOURCE_URL}" --dir="${ROOT_DIR}"
+# aria2c "${SPROT_SOURCE_URL}" --dir="${ROOT_DIR}"
 pushd "${ROOT_DIR}"
 gunzip "${ROOT_DIR}/${TREMBL_BASENAME}"
-gunzip "${ROOT_DIR}/${SPROT_BASENAME}"
+# gunzip "${ROOT_DIR}/${SPROT_BASENAME}"
 
 # Concatenate TrEMBL and SwissProt, rename to uniprot and clean up.
-cat "${ROOT_DIR}/${SPROT_UNZIPPED_BASENAME}" >> "${ROOT_DIR}/${TREMBL_UNZIPPED_BASENAME}"
-mv "${ROOT_DIR}/${TREMBL_UNZIPPED_BASENAME}" "${ROOT_DIR}/uniprot.fasta"
-rm "${ROOT_DIR}/${SPROT_UNZIPPED_BASENAME}"
+# cat "${ROOT_DIR}/${SPROT_UNZIPPED_BASENAME}" >> "${ROOT_DIR}/${TREMBL_UNZIPPED_BASENAME}"
+# mv "${ROOT_DIR}/${TREMBL_UNZIPPED_BASENAME}" "${ROOT_DIR}/uniprot.fasta"
+# rm "${ROOT_DIR}/${SPROT_UNZIPPED_BASENAME}"
 popd

scripts/download_uniref90.sh

@@ -31,7 +31,8 @@ fi
 
 DOWNLOAD_DIR="$1"
 ROOT_DIR="${DOWNLOAD_DIR}/uniref90"
-SOURCE_URL="ftp://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref90/uniref90.fasta.gz"
+# SOURCE_URL="ftp://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref90/uniref90.fasta.gz"
+SOURCE_URL="http://113.200.138.88:18080/aidatasets/project-dependency/alphafold/-/raw/master/uniref90.tar.gz?ref_type=heads&inline=false"
 BASENAME=$(basename "${SOURCE_URL}")
 
 mkdir --parents "${ROOT_DIR}"