In [1]:

    

from __future__ import print_function

from Bio import PDB


    

In [2]:

    

repository = PDB.PDBList()
repository.retrieve_pdb_file('1TUP', pdir='.')


    

    




Structure exists: './pdb1tup.ent' 






    
Out[2]:





'./pdb1tup.ent'

In [3]:

    

rec_types = {
    #single line
    'HEADER': [(str, 11, 49), (str, 50, 58), (str, 62, 65)],
    #multi_line
    'SOURCE': [(int, 7, 9), (str, 10, 78)],
    #multi_rec
    'LINK' : [(str, 12, 15), (str, 16, 16), (str, 17, 19), (str, 21, 21), (int, 22, 25),
              (str, 26, 26), (str, 42, 45), (str, 46, 46), (str, 47, 49), (str, 51, 51),
              (int, 52, 55), (str, 56, 56), (str, 59, 64), (str, 66, 71), (float, 73, 77)],
    'HELIX': [(int, 7, 9), (str, 11, 13), (str, 15, 17), (str, 19, 19), (int, 21, 24),
              (str, 25, 25), (str, 27, 29), (str, 31, 31),
              (int, 33, 36), (str, 37 ,37), (int, 38, 39), (str, 40, 69), (int, 71, 75)],
    'SHEET': [(int, 7, 9), (str, 11, 13), (int, 14, 15), (str, 17, 19), (str, 21, 21),
              (int, 22, 24), (str, 26, 26), (str, 28, 30),
              (str, 32, 32), (int, 33, 36), (str, 37, 37), (int, 38, 39), (str, 41, 44),
              (str, 45, 47), (str, 49, 49), (int, 50, 53), (str, 54, 54), (str, 56, 59),
              (str, 60, 62), (str, 64, 64), (int, 65, 68), (str, 69, 69)],
}

def parse_pdb(hdl):
    for line in hdl:
        line = line[:-1]  # remove \n but not other whitespace
        toks = []
        for section, elements in rec_types.items():
            if line.startswith(section):
                for fun, start, end in elements:
                    try:
                        toks.append(fun(line[start: end + 1]))
                    except ValueError:
                        toks.append(None)  # eg continuation
                yield (section, toks)
        if len(toks) == 0:
            yield ('UNKNOWN', line)


    

In [4]:

    

hdl = open('pdb1tup.ent')
done_rec = set()
for rec in parse_pdb(hdl):
    if rec[0] == 'UNKNOWN' or rec[0] in done_rec:
        continue
    print(rec)
    done_rec.add(rec[0])


    

    




('HEADER', ['NTITUMOR PROTEIN/DNA                   ', '11-JUL-95', '1TUP'])
('SOURCE', [None, 'MOL_ID: 1;                                                           '])
('HELIX', [1, '  1', 'SER', 'A', 166, ' ', 'HIS', 'A', 168, ' ', 5, '                              ', 3])
('SHEET', [1, '  A', 4, 'ARG', 'A', 11, ' ', 'GLY', 'A', 112, ' ', 0, '    ', '   ', ' ', None, ' ', '    ', '   ', ' ', None, ' '])
('LINK', ['ZN  ', ' ', ' ZN', 'A', 951, ' ', ' SG ', ' ', 'CYS', 'A', 176, ' ', '  1555', '  1555', 2.33])

In [5]:

    

multi_lines = ['SOURCE']

#assume multi is just a string
def process_multi_lines(hdl):
    current_multi = ''
    current_multi_name = None
    for rec_type, toks in parse_pdb(hdl):
        if current_multi_name is not None and current_multi_name != rec_type:
            yield current_multi_name, [current_multi]
            current_multi = ''
            current_multi_name = None
        if rec_type in multi_lines:
            current_multi += toks[1].strip().rstrip() + ' '
            current_multi_name = rec_type
        else:
            if len(current_multi) != 0:
                yield current_multi_name, [current_multi]
                current_multi = ''
                current_multi_name = None                
            yield rec_type, toks
    if len(current_multi) != 0:
        yield current_multi_name, [current_multi]


    

In [6]:

    

hdl = open('pdb1tup.ent')
done_rec = set()
for rec in process_multi_lines(hdl):
    if rec[0] == 'UNKNOWN' or rec[0] in done_rec:
        continue
    print(rec)
    done_rec.add(rec[0])


    

    




('HEADER', ['NTITUMOR PROTEIN/DNA                   ', '11-JUL-95', '1TUP'])
('SOURCE', ['MOL_ID: 1; SYNTHETIC: YES; MOL_ID: 2; SYNTHETIC: YES; MOL_ID: 3; ORGANISM_SCIENTIFIC: HOMO SAPIENS; ORGANISM_COMMON: HUMAN; ORGANISM_TAXID: 9606; CELL_LINE: A431; CELL: HUMAN VULVA CARCINOMA; EXPRESSION_SYSTEM: ESCHERICHIA COLI; EXPRESSION_SYSTEM_TAXID: 562; EXPRESSION_SYSTEM_PLASMID: PET3D '])
('HELIX', [1, '  1', 'SER', 'A', 166, ' ', 'HIS', 'A', 168, ' ', 5, '                              ', 3])
('SHEET', [1, '  A', 4, 'ARG', 'A', 11, ' ', 'GLY', 'A', 112, ' ', 0, '    ', '   ', ' ', None, ' ', '    ', '   ', ' ', None, ' '])
('LINK', ['ZN  ', ' ', ' ZN', 'A', 951, ' ', ' SG ', ' ', 'CYS', 'A', 176, ' ', '  1555', '  1555', 2.33])

In [7]:

    

def get_spec_list(my_str):
    #ignoring escape characters
    spec_list = {}
    elems = my_str.strip().strip().split(';')
    for elem in elems:
        toks = elem.split(':')
        spec_list[toks[0].strip()] = toks[1].strip()
    return spec_list

struct_types = {
    'SOURCE': [get_spec_list] 
}

def process_struct_types(hdl):
    for rec_type, toks in process_multi_lines(hdl):
        if rec_type in struct_types.keys():
            funs = struct_types[rec_type]
            struct_toks = []
            for tok, fun in zip(toks, funs):
                struct_toks.append(fun(tok))
            yield rec_type, struct_toks
        else:
            yield rec_type, toks


    

In [8]:

    

hdl = open('pdb1tup.ent')
for rec in process_struct_types(hdl):
    if rec[0] != 'SOURCE':
        continue
    print(rec)


    

    




('SOURCE', [{'SYNTHETIC': 'YES', 'MOL_ID': '3', 'EXPRESSION_SYSTEM': 'ESCHERICHIA COLI', 'EXPRESSION_SYSTEM_TAXID': '562', 'ORGANISM_SCIENTIFIC': 'HOMO SAPIENS', 'CELL': 'HUMAN VULVA CARCINOMA', 'EXPRESSION_SYSTEM_PLASMID': 'PET3D', 'CELL_LINE': 'A431', 'ORGANISM_TAXID': '9606', 'ORGANISM_COMMON': 'HUMAN'}])

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