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Taking link templates outside and use them as parameter for greater f…
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…lexibility
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@olegsobolev
olegsobolev committed Nov 1, 2024
1 parent c65483b commit b2a2b58
Showing 1 changed file with 45 additions and 46 deletions.
91 changes: 45 additions & 46 deletions iotbx/pdb/fetch.py
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Original file line number Diff line number Diff line change
Expand Up @@ -33,60 +33,59 @@
import os


def get_link(mirror, entity, pdb_id=None, emdb_number=None):
all_links_dict = {
'rcsb': {
'model_pdb': 'https://files.rcsb.org/pub/pdb/data/structures/divided/pdb/{mid_id}/pdb{pdb_id}.ent.gz',
'model_cif': 'https://files.rcsb.org/pub/pdb/data/structures/divided/mmCIF/{mid_id}/{pdb_id}.cif.gz',
'sequence': 'https://www.rcsb.org/fasta/entry/{pdb_id}',
'sf': 'https://files.rcsb.org/download/{pdb_id}-sf.cif.gz',
'em_map': 'https://files.rcsb.org/pub/emdb/structures/EMD-{emdb_number}/map/emd_{emdb_number}.map.gz',
'em_half_map_1': 'https://files.rcsb.org/pub/emdb/structures/EMD-{emdb_number}/other/emd_{emdb_number}_half_map_1.map.gz',
'em_half_map_2': 'https://files.rcsb.org/pub/emdb/structures/EMD-{emdb_number}/other/emd_{emdb_number}_half_map_2.map.gz',
},
'pdbe': {
'model_pdb': 'https://ftp.ebi.ac.uk/pub/databases/pdb/data/structures/divided/pdb/{mid_id}/pdb{pdb_id}.ent.gz',
'model_cif': 'https://ftp.ebi.ac.uk/pub/databases/pdb/data/structures/divided/mmCIF/{mid_id}/{pdb_id}.cif.gz',
'sequence': 'https://www.ebi.ac.uk/pdbe/entry/pdb/{pdb_id}/fasta',
'sf': 'https://www.ebi.ac.uk/pdbe/entry-files/download/r{pdb_id}sf.ent',
'em_map': 'https://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-{emdb_number}/map/emd_{emdb_number}.map.gz',
'em_half_map_1': 'https://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-{emdb_number}/other/emd_{emdb_number}_half_map_1.map.gz',
'em_half_map_2': 'https://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-{emdb_number}/other/emd_{emdb_number}_half_map_2.map.gz',
},
'pdbj': {
'model_pdb': 'https://ftp.pdbj.org/pub/pdb/data/structures/divided/pdb/{mid_id}/pdb{pdb_id}.ent.gz',
'model_cif': 'https://ftp.pdbj.org/pub/pdb/data/structures/divided/mmCIF/{mid_id}/{pdb_id}.cif.gz',
'sequence': 'https://pdbj.org/rest/newweb/fetch/file?cat=pdb&type=fasta&id={pdb_id}',
'sf': 'https://data.pdbjpw1.pdbj.org/pub/pdb/data/structures/divided/structure_factors/{mid_id}/r{pdb_id}sf.ent.gz',
'em_map': 'https://ftp.pdbj.org/pub/emdb/structures/EMD-{emdb_number}/map/emd_{emdb_number}.map.gz',
'em_half_map_1': 'https://ftp.pdbj.org/pub/databases/emdb/structures/EMD-{emdb_number}/other/emd_{emdb_number}_half_map_1.map.gz',
'em_half_map_2': 'https://ftp.pdbj.org/pub/databases/emdb/structures/EMD-{emdb_number}/other/emd_{emdb_number}_half_map_2.map.gz',
},
# 'pdb-redo': {
# 'model_pdb': 'https://pdb-redo.eu/db/{pdb_id}/{pdb_id}_final.pdb',
# 'model_cif': 'https://pdb-redo.eu/db/{pdb_id}/{pdb_id}_final.cif',
# # these are from RCSB because PDB-redo does not have them
# 'sequence': 'https://www.rcsb.org/fasta/entry/{pdb_id}',
# 'sf': 'https://files.rcsb.org/download/{pdb_id}-sf.cif',
# 'map': 'https://files.rcsb.org/pub/emdb/structures/EMD-{emdb_number}/map/emd_{emdb_number}.map.gz',
# },
}

all_links_dict = {
'rcsb': {
'model_pdb': 'https://files.rcsb.org/pub/pdb/data/structures/divided/pdb/{mid_id}/pdb{pdb_id}.ent.gz',
'model_cif': 'https://files.rcsb.org/pub/pdb/data/structures/divided/mmCIF/{mid_id}/{pdb_id}.cif.gz',
'sequence': 'https://www.rcsb.org/fasta/entry/{pdb_id}',
'sf': 'https://files.rcsb.org/download/{pdb_id}-sf.cif.gz',
'em_map': 'https://files.rcsb.org/pub/emdb/structures/EMD-{emdb_number}/map/emd_{emdb_number}.map.gz',
'em_half_map_1': 'https://files.rcsb.org/pub/emdb/structures/EMD-{emdb_number}/other/emd_{emdb_number}_half_map_1.map.gz',
'em_half_map_2': 'https://files.rcsb.org/pub/emdb/structures/EMD-{emdb_number}/other/emd_{emdb_number}_half_map_2.map.gz',
},
'pdbe': {
'model_pdb': 'https://ftp.ebi.ac.uk/pub/databases/pdb/data/structures/divided/pdb/{mid_id}/pdb{pdb_id}.ent.gz',
'model_cif': 'https://ftp.ebi.ac.uk/pub/databases/pdb/data/structures/divided/mmCIF/{mid_id}/{pdb_id}.cif.gz',
'sequence': 'https://www.ebi.ac.uk/pdbe/entry/pdb/{pdb_id}/fasta',
'sf': 'https://www.ebi.ac.uk/pdbe/entry-files/download/r{pdb_id}sf.ent',
'em_map': 'https://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-{emdb_number}/map/emd_{emdb_number}.map.gz',
'em_half_map_1': 'https://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-{emdb_number}/other/emd_{emdb_number}_half_map_1.map.gz',
'em_half_map_2': 'https://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-{emdb_number}/other/emd_{emdb_number}_half_map_2.map.gz',
},
'pdbj': {
'model_pdb': 'https://ftp.pdbj.org/pub/pdb/data/structures/divided/pdb/{mid_id}/pdb{pdb_id}.ent.gz',
'model_cif': 'https://ftp.pdbj.org/pub/pdb/data/structures/divided/mmCIF/{mid_id}/{pdb_id}.cif.gz',
'sequence': 'https://pdbj.org/rest/newweb/fetch/file?cat=pdb&type=fasta&id={pdb_id}',
'sf': 'https://data.pdbjpw1.pdbj.org/pub/pdb/data/structures/divided/structure_factors/{mid_id}/r{pdb_id}sf.ent.gz',
'em_map': 'https://ftp.pdbj.org/pub/emdb/structures/EMD-{emdb_number}/map/emd_{emdb_number}.map.gz',
'em_half_map_1': 'https://ftp.pdbj.org/pub/databases/emdb/structures/EMD-{emdb_number}/other/emd_{emdb_number}_half_map_1.map.gz',
'em_half_map_2': 'https://ftp.pdbj.org/pub/databases/emdb/structures/EMD-{emdb_number}/other/emd_{emdb_number}_half_map_2.map.gz',
},
# 'pdb-redo': {
# 'model_pdb': 'https://pdb-redo.eu/db/{pdb_id}/{pdb_id}_final.pdb',
# 'model_cif': 'https://pdb-redo.eu/db/{pdb_id}/{pdb_id}_final.cif',
# # these are from RCSB because PDB-redo does not have them
# 'sequence': 'https://www.rcsb.org/fasta/entry/{pdb_id}',
# 'sf': 'https://files.rcsb.org/download/{pdb_id}-sf.cif',
# 'map': 'https://files.rcsb.org/pub/emdb/structures/EMD-{emdb_number}/map/emd_{emdb_number}.map.gz',
# },
}

assert mirror in ['rcsb', 'pdbe', 'pdbj']
if entity not in all_links_dict[mirror].keys():
def get_link(mirror, entity, pdb_id=None, emdb_number=None, link_templates=all_links_dict):
assert mirror in link_templates.keys()
if entity not in link_templates[mirror].keys():
return None
if entity == 'map':
assert emdb_number
else:
assert pdb_id
mid_pdb_id = pdb_id[1:3]
return all_links_dict[mirror][entity].format(mid_id=mid_pdb_id, pdb_id=pdb_id, emdb_number=emdb_number)
return link_templates[mirror][entity].format(mid_id=mid_pdb_id, pdb_id=pdb_id, emdb_number=emdb_number)

def valid_pdb_id(id):
return len(id) == 4 and re.match("[1-9]{1}[a-zA-Z0-9]{3}", id)

def fetch(id, entity='model_pdb', mirror="rcsb", emdb_number=None):
def fetch(id, entity='model_pdb', mirror="rcsb", emdb_number=None, link_templates=all_links_dict):
"""
Locate and open a data file for the specified PDB ID and format, either in a
local mirror or online.
Expand All @@ -103,7 +102,7 @@ def fetch(id, entity='model_pdb', mirror="rcsb", emdb_number=None):
if not valid_pdb_id(id):
raise Sorry("Invalid pdb id %s. Must be 4 characters, 1st is a number 1-9." % id)

url = get_link(mirror, entity, pdb_id=id, emdb_number=emdb_number)
url = get_link(mirror, entity, pdb_id=id, emdb_number=emdb_number, link_templates=link_templates)
need_to_decompress = url.split('.')[-1] == 'gz' and entity.find('map') < 0

try :
Expand All @@ -121,12 +120,12 @@ def write_data_to_disc(fname, data):
with open(fname, "wb") as f:
f.write(data.read())

def fetch_and_write(id, entity='model_pdb', mirror='rcsb', emdb_number=None, log=None):
def fetch_and_write(id, entity='model_pdb', mirror='rcsb', emdb_number=None, link_templates=all_links_dict, log=None):
"""
Frontend for fetch(...), writes resulting data to disk.
"""
try :
data = fetch(id, entity, mirror=mirror, emdb_number=emdb_number)
data = fetch(id, entity, mirror=mirror, emdb_number=emdb_number, link_templates=link_templates)
except RuntimeError as e :
print(str(e),file=log)
return None
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