Python select_pdb_fragment Examples

Example #1

File: rna_get_distances.py Project: mmagnus/rna-pdb-tools

def get_residues(pdb_fn, restraints, verbose):
    residues = set()
    for h in restraints:
        a = h[0]
        b = h[1]
        a = a[0] + ':' + a[1:]
        residues.add(a)  # A19
        b = b[0] + ':' + b[1:]
        residues.add(b)
    # set(['A:41', 'A:9', 'A:10', 'A:16'])

    selection = ','.join(residues)
    selection_parsed = select_pdb_fragment(selection, separator=",", splitting="[,:;]")

    residues = parse_pdb(pdb_fn, selection_parsed)

    # get mb
    for r in residues:
        if 'N9' in residues[r]:  # A,G
            residues[r]['mb'] = residues[r]['N9'] - ((residues[r]['N9'] - residues[r]['C6']) / 2)
        else:  # A,G
            residues[r]['mb'] = residues[r]['N1'] - ((residues[r]['N1'] - residues[r]['C4']) / 2)
    for r in residues:
        if verbose:
            logger.info(' '.join(['mb for ', str(r), str(residues[r]['mb'])]))
    return residues

Example #2

def get_residues(pdb_fn, restraints, verbose):
    residues = set()
    for h in restraints:
        a = h[0]
        b = h[1]
        a = a[0] + ':' + a[1:]
        residues.add(a)  # A19
        b = b[0] + ':' + b[1:]
        residues.add(b)
    # set(['A:41', 'A:9', 'A:10', 'A:16'])

    selection = ','.join(residues)
    selection_parsed = select_pdb_fragment(selection,
                                           separator=",",
                                           splitting="[,:;]")

    residues = parse_pdb(pdb_fn, selection_parsed)

    # get mb
    for r in residues:
        if 'N9' in residues[r]:  # A,G
            residues[r]['mb'] = residues[r]['N9'] - (
                (residues[r]['N9'] - residues[r]['C6']) / 2)
        else:  # A,G
            residues[r]['mb'] = residues[r]['N1'] - (
                (residues[r]['N1'] - residues[r]['C4']) / 2)
    for r in residues:
        if verbose:
            logger.info(' '.join(['mb for ', str(r), str(residues[r]['mb'])]))
    return residues

Example #3

File: rna_calc_rmsd.py Project: MingleiYang/rna-tools

    return parser


# main
if __name__ == '__main__':
    parser = get_parser()
    args = parser.parse_args()

    input_files = args.files  # opts.input_dir
    rmsds_fn = args.rmsds_fn
    target_fn = args.target_fn
    method = args.method

    print('method:', method)

    target_selection = select_pdb_fragment(args.target_selection)
    model_selection = select_pdb_fragment(args.model_selection)

    if target_selection:
        if args.verbose:
            print('  target_selection: #', args.target_selection,
                  target_selection)
            ts = target_selection
            print(ts)
            resides_in_total = 0
            for i in target_selection:
                print((i, len(ts[i])))  # chain string, a list of residues
                resides_in_total += len(ts[i])
            print('in total:', resides_in_total)

    if model_selection:

Example #4

File: rna_calc_rmsd.py Project: mmagnus/rna-pdb-tools

                        help="verbose")

    parser.add_argument('files', help='files', nargs='+')

    return parser
# main
if __name__ == '__main__':
    parser = get_parser()
    args = parser.parse_args()

    input_files = args.files  # opts.input_dir
    rmsds_fn = args.rmsds_fn
    target_fn = args.target_fn
    method = args.method
    print('method:', method)
    target_selection = select_pdb_fragment(args.target_selection)
    model_selection = select_pdb_fragment(args.model_selection)
    if target_selection:
        if args.verbose:
            print('  target_selection: #', args.target_selection, target_selection)
            ts = target_selection
            print(ts)
            resides_in_total = 0
            for i in target_selection:
                print((i, len(ts[i]))) # chain string, a list of residues
                resides_in_total += len(ts[i])
            print('in total:', resides_in_total)
    if model_selection:
        if args.verbose:
            print('  model_selection:  ', len(model_selection), args.model_selection, model_selection)
            resides_in_total = 0