install.py

import re
from defs import CRAWLTYPE_LINE as LINE, CRAWLTYPE_FILE as FILE


def _create_databank(name, reference, filelink, regex, crawltype,
                   parent_name=None):
    """
    Create a databank entry
    - a name
    - a crawltype, either LINE to obtain entries from lines in a single file,
      (like PDBFINDER) or FILE to presume that entries are files within a
      directory (like PDB)
    - a filelink, a macro for generating a link to a file, given it's pdbid,
      part simply means: the 2nd and 3rd character of the pdbid
    - a reference: link to a web page that explains the databank
    - a regex: a pattern that filenames/lines should match to be included as an
      entry.
    - a parent name: name of an other databank that it depends on. This field
      is not set for the root databank. Entries are considered missing if their
      parent has a certain pdbid entry, but the child has not. Obsolete is the
      opposite of missing.
    """
    doc = {
        'name': name,
        'crawltype': crawltype,
        'filelink': filelink,
        'reference': reference,
        'regex': regex
    }

    if parent_name:
        doc['parent_name'] = parent_name

    return doc

def create_databanks():
    docs = []
    docs.append(_create_databank('MMCIF','http://www.wwpdb.org/',
        'ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/mmCIF/${PART}/${PDBID}.cif.gz',
        re.compile(r'.*/([\w]{4})\.cif(\.gz)?'),FILE))
    docs.append(_create_databank('PDB','http://www.wwpdb.org/',
        'ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/pdb/${PART}/pdb${PDBID}.ent.gz',
        re.compile(r'.*/pdb([\w]{4})\.ent(\.gz)?'),FILE,'MMCIF'))
    docs.append(_create_databank('BDB','http://www.cmbi.umcn.nl/bdb/',
        'ftp://ftp.cmbi.umcn.nl/pub/molbio/data/bdb/${PART}/${PDBID}/${PDBID}.bdb',
        re.compile(r'.*/([\w]{4})\.bdb'),FILE,'PDB'))
    docs.append(_create_databank('DSSP','http://swift.cmbi.umcn.nl/gv/dssp/',
        'ftp://ftp.cmbi.umcn.nl/pub/molbio/data/dssp/${PDBID}.dssp',
        re.compile(r'.*/([\w]{4})\.dssp'),FILE,'MMCIF'))
    docs.append(_create_databank('HSSP','http://swift.cmbi.umcn.nl/gv/hssp/',
        'ftp://ftp.cmbi.umcn.nl/pub/molbio/data/hssp/${PDBID}.hssp.bz2',
        re.compile(r'.*/([\w]{4})\.hssp.bz2'),FILE,'DSSP'))
    docs.append(_create_databank('PDBFINDER','http://swift.cmbi.umcn.nl/gv/pdbfinder/',
        'ftp://ftp.cmbi.umcn.nl/pub/molbio/data/pdbfinder/PDBFIND.TXT.gz',
        re.compile(r'ID           : ([\w]{4})'),LINE,'PDB'))
    docs.append(_create_databank('PDBFINDER2','http://swift.cmbi.umcn.nl/gv/pdbfinder/',
        'ftp://ftp.cmbi.umcn.nl/pub/molbio/data/pdbfinder2/PDBFIND2.TXT.gz',
        re.compile(r'ID           : ([\w]{4})'),LINE,'PDBFINDER'))
    docs.append(_create_databank('NMR','http://www.bmrb.wisc.edu/',
        'ftp://ftp.wwpdb.org/pub/pdb/data/structures/all/nmr_restraints/${PDBID}.mr.gz',
        re.compile(r'.*/([\w]{4}).mr.gz'),FILE,'PDB'))
    docs.append(_create_databank('STRUCTUREFACTORS','http://www.pdb.org/',
        'ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/structure_factors/${PART}/r${PDBID}sf.ent.gz',
        re.compile(r'.*/r([\w]{4})sf\.ent\.gz'),FILE,'MMCIF'))
    docs.append(_create_databank('PDBREPORT','http://swift.cmbi.umcn.nl/gv/pdbreport/',
        'http://www.cmbi.umcn.nl/pdbreport/cgi-bin/nonotes?PDBID=${PDBID}',
        re.compile(r'pdbreport\/\w{2}\/(\w{4})\/pdbout\.txt'),FILE,'PDB'))
    docs.append(_create_databank('PDB_REDO','https://pdb-redo.eu/',
        "https://pdb-redo.eu/db/${PDBID}/${PDBID}_final.pdb",
        re.compile(r'\/\w{2}\/\w{4}\/(\w{4})_final\.pdb'),FILE,'STRUCTUREFACTORS'))
    docs.append(_create_databank('DSSP_REDO','http://swift.cmbi.umcn.nl/gv/dssp/',
        'ftp://ftp.cmbi.umcn.nl/pub/molbio/data/dssp_redo/${PDBID}.dssp',
        re.compile(r'.*/([\w]{4})\.dssp'),FILE,'PDB_REDO'))

    for lis in ['dsp','iod','sbh','sbr','ss1','ss2','tau','acc','cal','wat',
                'cc1','cc2','cc3','chi']:
        docs.append(_create_databank('WHATIF_PDB_%s' % lis, 'http://swift.cmbi.umcn.nl/whatif/',
            'ftp://ftp.cmbi.umcn.nl/pub/molbio/data/wi-lists/pdb/%s/${PDBID}/${PDBID}.%s.bz2' % (lis, lis),
            re.compile(r'.*/([\w]{4})\.' + lis + r'(\.bz2)?$'),FILE,'PDB'))
        docs.append(_create_databank('WHATIF_REDO_%s' % lis, 'http://swift.cmbi.umcn.nl/whatif/',
            'ftp://ftp.cmbi.umcn.nl/pub/molbio/data/wi-lists/redo/%s/${PDBID}/${PDBID}.%s.bz2' % (lis, lis),
            re.compile(r'.*/([\w]{4})\.' + lis + r'(\.bz2)?$'),FILE,'PDB_REDO'))

    scenames = { 'ss2': 'sym-contacts', 'iod': 'ion-sites'}
    for lis in scenames:
        docs.append(_create_databank('PDB_SCENES_%s' % lis, 'http://www.cmbi.umcn.nl/pdb-vis/',
            'ftp://ftp.cmbi.umcn.nl/pub/molbio/data/wi-lists/pdb/scenes/%s/${PDBID}/${PDBID}_%s.sce' % (lis, scenames[lis]),
            re.compile(r'.*/([\w]{4})_' + scenames[lis] + r'\.sce'),FILE,'WHATIF_PDB_%s' % lis))
        docs.append(_create_databank('REDO_SCENES_%s' % lis, 'http://www.cmbi.umcn.nl/pdb-vis/',
            'ftp://ftp.cmbi.umcn.nl/pub/molbio/data/wi-lists/redo/scenes/%s/${PDBID}/${PDBID}_%s.sce' % (lis, scenames[lis]),
            re.compile(r'.*/([\w]{4})_' + scenames[lis] + r'\.sce'),FILE,'WHATIF_REDO_%s' % lis))

    return docs