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define_locations.txt
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# Defined locations -----------------------------------------------------------
# WARNING: This is a system file. Do not edit or move
# PARSING: Fields are separated by " : ".
# Lines with one field determine the sector of the location dict.
# The sector FSYSPATH is defined just after the FSYS sector is parsed.
# Lines with two fields define a key-value pair.
# Initial tabs are part of the key, and they specify the dependence of
# the folder.
# Values can be composed by two subfields divided by ' + '. The first
# field is interpreted as a keyword of the FSYSPATH sector. The second
# is interpreted as plain text.
# -----------------------------------------------------------------------------
# File system for ensembles of structures =====================================
TREE
str : structures
seq : sequences
aln : alignments
seqaln : seq_alns
straln : str_alns
# Main file system ============================================================
# The tag <main> will be replaced with the address of the database
FSYSPATH
src : <src>
main : <main>
database : database
selection : selection
whole : whole_structs
chains : chains
old : .old
alns : alignments
stralns : stralns
strseqalns : str_seqalns
seqseqalns : seq_seqalns
ENCpdbs : EncoMPASS_structures
source : source_files
PDB : PDB
PDBpdbs : pdb
PDBmmcifs : mmcif
PDBobs : obsolete_pdb
PDBfastas : fasta
PDBxmls : xml
PDBjsons : json
PDBstats : statistics
PDBTM : PDBTM
PDBTMpdbs : pdb
PDBTMxmls : xml
OPM : OPM
OPMpdbs : pdb
OPMjsons : json
UniProt : UniProt
logs : logs
cache : cache
TMPcoords : tmp_coords
locusts_log : locusts
symmetry : symmetry
ananas_log : ananas
cesymm_log : cesymm
cesymm_from_symd_log : cesymm_from_symd
cesymm_low_thr_log : cesymm_low_thr
cesymm_minlen_log : cesymm_minlen
cesymm_order_log : cesymm_order
cesymm_quat_minlen_log : cesymm_quat_minlen
cesymm_rmsd_2_5_log : cesymm_rmsd_2_5
cesymm_rmsd_3_log : cesymm_rmsd_3
mssd_log : mssd
neighbors_log : neighbors
images_cesymm_symd_log : images_cesymm_symd
images_transfer_log : images_transfer
quatsymm_log : quatsymm
symd_log : symd
transfer_log : transfer
symmetries : symmetries
ananas : ananas
cesymm : cesymm
cesymm_from_symd : cesymm_from_symd
cesymm_low_thr : cesymm_low_thr
cesymm_minlen : cesymm_minlen
cesymm_order : cesymm_order
cesymm_quat_minlen : cesymm_quat_minlen
cesymm_rmsd_2_5 : cesymm_rmsd_2_5
cesymm_rmsd_3 : cesymm_rmsd_3
quatsymm : quatsymm
quatsymm_pngs : pngs
quatsymm_jsons : jsons
quatsymm_super : super
mssd : mssd
neighbors : neighbors
symd : symd
symmtemp : temp
transfer : transfer
webarchive : webarchive
3dmol_whole : whole_structs_json
3dmol_chains : chains_json
analysis_wholejsons : analysis_whole_structs_json
analysis_wholepngs : analysis_whole_structs_pngs
analysis_wholesuper : analysis_whole_structs_super
analysis_chainsjsons : analysis_chains_json
analysis_chainspngs : analysis_chains_pngs
analysis_chainssuper : analysis_chains_super
symm_wholejsons : symm_whole_structs_json
symm_wholepngs : symm_whole_structs_pngs
symm_chainsjsons : symm_chains_json
symm_chainspngs : symm_chains_pngs
transfer_chainsjsons : transfer_chains_json
transfer_chainspngs : transfer_chains_pngs
transfer_chainssuper : transfer_chains_super
analysis : analysis
stfig : static_figures
ancache : analysis_cache
analyses : analysis
images : images
images_figs : images_figs
images_figs_whole : whole_structs
images_figs_chain : chains
images_pml : images_pymolscripts
images_pml_whole : whole_structs
images_pml_chain : chains
estimators : estimators
nlists : neighbor_lists
seqneighs : seq_neighbors
strneighs : str_neighbors
totneighs : tot_neighbors
distributions : distributions
distributions_figs : distributions_figs
distributions_data : distributions_data
densityscatter : densityscatter
densityscatter_figs : densityscatter_figs
densityscatter_maps : densityscatter_maps
polar : polarplots
polar_figs : polarplots_figs
polar_data : polarplots_data
polar_maps : polarplots_maps
DSSP : DSSP
topologies : topologies
topologies_figs : topologies_figs
topologies_data : topologies_data
databasewide : databasewide_graphs
# System files ================================================================
SYSFILES
H_options : main + .options.dat
H_filters : main + .filters.dat
H_locations : main + .locations.dat
H_topologytype : database + .topology_classification.dat
H_instraln : database + .straln_instructions.dat
H_scheduledalns : database + .scheduled_alignments.dat
H_toporigapollo : main + .toporigapollo.txt
OPMlastddate : OPM + .lastdownload_date.txt
OPMarchive : OPM + OPM_archive.dat
excludedwhole : whole + exclusions.txt
excludedchains : chains + exclusions.txt
excludedstralnchains : chains + exclusions_from_instructions.txt
chaindata : chains + chain_database.txt
missingpdbfiles : PDBpdbs + missing_files.txt
missingfastafiles : PDBfastas + missing_files.txt
webwhole : webarchive + web_archive_whole.xml
webchain : webarchive + web_archive_chain.xml
runinppm : main + .run_in_ppm.pkl
OPMdata : main + .opm_archive.pkl
neighborstable : main + neighbors_table.txt
neighborstlist : main + neighbors_tot_list.txt
neighborsselist : main + neighbors_seq_list.txt
neighborsstlist : main + neighbors_str_list.txt
symmwebwhole : webarchive + symmetry_web_archive_whole.xml
symmwebchain : webarchive + symmetry_web_archive_chain.xml
ignoredpasscodes : src + ignored_passport_codes.txt
slurmtemplate : src + template_manager.txt
seqid_py : src + seqid.py
pdbquery : src + pdb_query.json
pdbdownload : src + batch_download.sh
pdbatomdict : src + pdb_atom_dictionary.txt
delcodes : src + deletion_codes.txt
delmsg : src + deletion_messages.txt
OPMreprchart : OPM + representatives.txt
summarytable : main + summary_table.txt
structurewise_table : main + structurewise_table.txt
uniprot_all : UniProt + all_entries.fasta
data_structure_template : cache + str_data_template.json
sifts_uniprot : UniProt + pdb_chain_uniprot.tsv
# pdb_tmchains : symmetry + .pdb_tmchains.dat
# opmfullstruct : opmrepofullstruct + opm_data.pkl
cesymm_completed : cesymm + cesymm_completed.list
symd_completed : symd + symd_completed.list
mssd_symmetries_whole : mssd + mssd_symmetries_whole
mssd_symmetries_chains : mssd + mssd_symmetries_chains
OPMsecondary : OPMjsons + secondary.json
background : databasewide + densitylines.png
squashin : src + squashfs_include_list.txt
# External addresses ==========================================================
# Other external addresses written in the instruction file and figuring under
# the sector PATHS of the "options" dict will be reported here as well
EXTERNAL
opmliburl : http://opm.phar.umich.edu/classes_dl.php?type=1
opmrefsemiurl : http://opm.phar.umich.edu/protein.php?pdbid=
opmrelsemiurl : http://opm.phar.umich.edu/protein.php?extrapdb=
opmpdbsemiurl : http://opm.phar.umich.edu/pdb/
pdbmainsemiurl_UPPER : http://www.rcsb.org/pdb/explore/explore.do?structureId=
pdbpagestaticurl : https://www.rcsb.org/structure/
pdbsemiurl_UPPERpdbgz : http://www.rcsb.org/pdb/files/
pdbobsurl_UPPER : http://www.rcsb.org/pdb/explore/obsolete.do?obsoleteId=
pdbfastasemiurl_UPPER : http://www.rcsb.org/pdb/download/downloadFastaFiles.do?structureIdList=
pdbfastasemiurl_ending : &compressionType=uncompressed