Ejemplo n.º 1
0
 c_help = 'Atom ids to use for alignment (default = all heavy atoms)'
 parser = argparse.ArgumentParser(description=description,
                              formatter_class=argparse.RawDescriptionHelpFormatter)
 parser.add_argument('-i', '--allow_inversion', help=i_help, action='store_true')
 parser.add_argument('-f', '--output_format', help=f_help, default='cml')
 parser.add_argument('-c', '--center_id', help=c_help, action='append', type=int)
 parser.add_argument('ref_file', help='cml file containing the reference conformer that all others will be aligned to')
 parser.add_argument('input_files', help='cml files containing the other conformers to be algigned',
                 nargs='+')
 args = parser.parse_args()
 input_names = args.input_files
 if len(input_names) == 1 and '*' in input_names[0]:
     # If the shell is dumb (powershell/cmd.exe), glob input files ourselves
     from glob import glob
     input_names = glob(input_names[0])
 mols = [molecule.from_cml(i) for i in input_names]
 ref_mol = molecule.from_cml(args.ref_file)
 ref_num_atoms = len(ref_mol.atoms)
 if args.center_id:
     center_ids = [i - 1 for i in args.center_id]
 else:
     center_ids = [i.get_id() for i in ref_mol.atoms if i.num > 1]
 for each_id in center_ids:
     if not (0 <= each_id < ref_num_atoms):
         raise ValueError, 'The atom id to align molecules at must be a valid atom id for the molecule, i.e. an integer between between 1 and %d inclusive.' %ref_num_atoms
 for each_mol in mols:
     if len(each_mol.atoms) != ref_num_atoms:
         raise ValueError, 'Not all molecules to be aligned have the same number of atoms. Please retry with conformers of only one molecule'
 ref_center = numpy.array([i.coords for i in ref_mol.atoms if i.get_id() in center_ids])
 ref_mol.translate(-1*ref_center.mean(axis=0))
 input_names = [path.split(i) for i in input_names]
Ejemplo n.º 2
0
                                  formatter_class=argparse.RawDescriptionHelpFormatter)
 parser.add_argument('-s', '--scaling', help=scaling_help, type=float,
                     default=None)
 parser.add_argument('-d', '--delta', help=delta_help, type=int, default=30)
 parser.add_argument('-i', '--allow_inversion', help=i_help, action='store_true')
 parser.add_argument('-o', '--output_name', help=o_help)
 parser.add_argument('-f', '--output_format', help=f_help, default='cml')
 parser.add_argument('-r', '--ring_generation', help=r_help, default=-1, type=int)
 parser.add_argument('-a', '--avoid_division', help=a_help, action='store_true')
 parser.add_argument('-b', '--break_at', help=b_help, action='append', type=int, nargs=2)
 parser.add_argument('file_name', help='cml file containing the molecule')
 args = parser.parse_args()
 vary_rings = args.ring_generation
 fix_or_split = []
 try:
     mol = molecule.from_cml(args.file_name)
 except:
     msg = 'Reading molecule failed. Please check that the file a) exists and b) is a .cml molecule file'
     raise RuntimeError(msg)
 if args.output_name is None:
     in_name = os.path.normpath(args.file_name)
     in_path_name, in_file_name = os.path.split(in_name)
     base_file_name = os.path.join(in_path_name, 'Conformer_{0}_' + in_file_name)
     # Make sure that the file extension is appropriate to the contents of the file
     if args.output_format == 'xyz':
         base_file_name = os.path.splitext(base_file_name)[0] + '.xyz'
     elif args.output_format == 'gauss':
         base_file_name = os.path.splitext(base_file_name)[0] + '.gjf'
     elif args.output_format != 'cml':
         base_file_name = os.path.splitext(base_file_name)[0] + '.inp'
 else:
Ejemplo n.º 3
0
 parser = argparse.ArgumentParser(description=description,
                                  formatter_class=argparse.RawDescriptionHelpFormatter)
 parser.add_argument('-i', '--allow_inversion', help=i_help, action='store_true')
 parser.add_argument('-f', '--output_format', help=f_help, default='cml')
 parser.add_argument('-c', '--center_id', help=c_help, action='append', type=int)
 parser.add_argument('ref_file', help='cml file containing the reference ' +
                     'conformer that all others will be aligned to')
 parser.add_argument('input_files', help='cml files containing the other ' +
                     'conformers to be algigned', nargs='+')
 args = parser.parse_args()
 input_names = args.input_files
 if len(input_names) == 1 and '*' in input_names[0]:
     # If the shell is dumb (powershell/cmd.exe), glob input files ourselves
     from glob import glob
     input_names = glob(input_names[0])
 mols = [molecule.from_cml(i) for i in input_names]
 ref_mol = molecule.from_cml(args.ref_file)
 ref_num_atoms = len(ref_mol.atoms)
 if args.center_id:
     center_ids = [i - 1 for i in args.center_id]
 else:
     center_ids = [i.get_id() for i in ref_mol.atoms if i.num > 1]
 for each_id in center_ids:
     if not (0 <= each_id < ref_num_atoms):
         raise ValueError('The atom id to align molecules at must be a valid ' +
                          'atom id for the molecule, i.e. an integer between ' +
                          'between 1 and %d inclusive.' % ref_num_atoms)
 for each_mol in mols:
     if len(each_mol.atoms) != ref_num_atoms:
         raise ValueError('Not all molecules to be aligned have the same ' +
                          'number of atoms. Please retry with conformers ' +
Ejemplo n.º 4
0
    parser.add_argument('-n', '--no_rmsd', help=n_help, action='store_true')
    parser.add_argument('-a', '--automatic', help=a_help, action='store_true')
    parser.add_argument('-i', '--allow_inversion', help=i_help, action='store_true')
    parser.add_argument('-u', '--uniqueness_cutoff', type=float, help=u_help, default=1.0)
    parser.add_argument('-H', '--use_hierachical_clustering', help=c_help, action='store_true')
    parser.add_argument('input_files', help='cml files containing the conformers to be analysed',
                        nargs='+')
    # Prepare input
    args = parser.parse_args()
    input_names = args.input_files
    for idx, i in enumerate(input_names):
        if '*' in i:
         # If the shell is dumb (powershell/cmd.exe), glob input files ourselves

            input_names[idx:idx + 1] = glob(i)
    mols = [molecule.from_cml(i) for i in input_names]
    for i in mols:
        canonicalise(i)
    # Clean up the molecule names for pretty-printing
    mol_names = [path.splitext(path.split(i)[1])[0] for i in input_names]

    writer = csv.writer(args.output_name)
    if args.use_hierachical_clustering:
        cluster = cluster_hierarchy
    else:
        cluster = cluster_kmeans
    # Validate input
    if len(set([len(i.atoms) for i in mols])) != 1:
        raise ValueError, 'Not all molecules to be analysed have the same number of atoms. Please retry with conformers of only one molecule'
    if args.rmsd_arrange not in ['t', 'b', 'i']:
        raise ValueError, 'RMSD arrangement must be by [t]orsion clustering, [b]ounding box clustering, or conformer [i]d'
Ejemplo n.º 5
0
                         formatter_class=argparse.RawDescriptionHelpFormatter)
 parser.add_argument('-s', '--scaling', help=scaling_help, type=float,
                     default=None)
 parser.add_argument('-d', '--delta', help=delta_help, type=int, default=30)
 parser.add_argument('-i', '--allow_inversion', help=i_help, action='store_true')
 parser.add_argument('-o', '--output_name', help=o_help)
 parser.add_argument('-f', '--output_format', help=f_help, default='cml')
 parser.add_argument('-r', '--ring_generation', help=r_help, default=-1, type=int)
 parser.add_argument('-a', '--avoid_division', help=a_help, action='store_true')
 parser.add_argument('-b', '--break_at', help=b_help, action='append', type=int, nargs=2)
 parser.add_argument('file_name', help='cml file containing the molecule')
 args = parser.parse_args()
 vary_rings = args.ring_generation
 fix_or_split = []
 try:
     mol = molecule.from_cml(args.file_name)
 except:
     msg = 'Reading molecule failed. Please check that the file a) exists and b) is a .cml molecule file'
     raise RuntimeError(msg)
 if args.output_name is None:
     in_name = os.path.normpath(args.file_name)
     in_path_name, in_file_name = os.path.split(in_name)
     base_file_name = os.path.join(in_path_name, 'Conformer_{0}_' + in_file_name)
     # Make sure that the file extension is appropriate to the contents of the file
     if args.output_format == 'xyz':
         base_file_name = os.path.splitext(base_file_name)[0] + '.xyz'
     elif args.output_format == 'gauss':
         base_file_name = os.path.splitext(base_file_name)[0] + '.gjf'
     elif args.output_format != 'cml':
         base_file_name= os.path.splitext(base_file_name)[0] + '.inp'
 else:
Ejemplo n.º 6
0
    parser.add_argument('-H',
                        '--use_hierachical_clustering',
                        help=c_help,
                        action='store_true')
    parser.add_argument('input_files',
                        help='cml files containing the conformers' +
                        ' to be analysed',
                        nargs='+')
    # Prepare input
    args = parser.parse_args()
    input_names = args.input_files
    for idx, i in enumerate(input_names):
        if '*' in i:
            # If the shell is dumb (powershell/cmd.exe), glob input files ourselves
            input_names[idx:idx + 1] = glob(i)
    mols = [molecule.from_cml(i) for i in input_names]
    for i in mols:
        canonicalise(i)
    # Clean up the molecule names for pretty-printing
    mol_names = [path.splitext(path.split(i)[1])[0] for i in input_names]

    writer = csv.writer(args.output_name)
    if args.use_hierachical_clustering:
        cluster = cluster_hierarchy
    else:
        cluster = cluster_kmeans
    # Validate input
    if len(set([len(i.atoms) for i in mols])) != 1:
        raise ValueError(
            'Not all molecules to be analysed have the same number ' +
            'of atoms. Please retry with conformers of only one molecule')