Module sequence
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Module for handling the molecule, residue, and spin sequence.
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attach_protons()
Attach a single proton to all heteronuclei. |
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copy(pipe_from=None,
pipe_to=None,
preserve_select=False,
empty=True,
verbose=True)
Copy the molecule, residue, and spin sequence data from one data pipe
to another. |
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int
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display(sep=None,
mol_name_flag=False,
res_num_flag=False,
res_name_flag=False,
spin_num_flag=False,
spin_name_flag=False)
Display the molecule, residue, and/or spin sequence data. |
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generate(mol_name=None,
res_num=None,
res_name=None,
spin_num=None,
spin_name=None,
pipe=None,
select=True,
verbose=True)
Generate the sequence item-by-item by adding a single
molecule/residue/spin container as necessary. |
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read(file=None,
dir=None,
file_data=None,
spin_id_col=None,
mol_name_col=None,
res_num_col=None,
res_name_col=None,
spin_num_col=None,
spin_name_col=None,
sep=None,
spin_id=None)
Read the molecule, residue, and/or spin sequence data from file. |
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list of SpinContainer instances
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write(file,
dir=None,
sep=None,
mol_name_flag=True,
res_num_flag=True,
res_name_flag=True,
spin_num_flag=True,
spin_name_flag=True,
force=False)
Write the molecule, residue, and/or sequence data. |
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__package__ = ' pipe_control '
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Imports:
deepcopy,
search,
sys,
RelaxError,
RelaxDiffMolNumError,
RelaxDiffResNumError,
RelaxDiffSeqError,
RelaxDiffSpinNumError,
RelaxNoSequenceError,
RelaxSequenceError,
read_spin_data,
write_spin_data,
pipes,
return_interatom_list,
count_molecules,
count_residues,
count_spins,
create_molecule,
create_residue,
create_spin,
exists_mol_res_spin_data,
generate_spin_id,
return_molecule,
return_residue,
return_spin,
set_spin_element,
set_spin_isotope,
spin_loop,
check_pipe
copy(pipe_from=None,
pipe_to=None,
preserve_select=False,
empty=True,
verbose=True)
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Copy the molecule, residue, and spin sequence data from one data pipe
to another.
- Parameters:
pipe_from (str) - The data pipe to copy the sequence data from. This defaults to
the current data pipe.
pipe_to (str) - The data pipe to copy the sequence data to. This defaults to the
current data pipe.
preserve_select (bool) - A flag which if True will cause spin selections to be preserved.
empty - A flag which if True will create a molecule, residue, and spin
sequence in the target pipe lacking all of the spin data of the
source pipe. If False, then the spin data will also be copied.
verbose (bool) - A flag which if True will cause info about each spin to be
printed out as the sequence is generated.
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compare_sequence(pipe1=None,
pipe2=None,
fail=True)
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Compare the sequence in two data pipes.
- Parameters:
pipe1 (str) - The name of the first data pipe.
pipe2 (str) - The name of the second data pipe.
fail (bool) - A flag which if True causes a RelaxError to be raised.
- Returns: int
- 1 if the sequence is the same, 0 if different.
- Raises:
RelaxError - If the sequence is different and the fail flag is True.
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display(sep=None,
mol_name_flag=False,
res_num_flag=False,
res_name_flag=False,
spin_num_flag=False,
spin_name_flag=False)
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Display the molecule, residue, and/or spin sequence data.
This calls the write() function to do most of the work.
- Parameters:
sep (str or None) - The column seperator which, if None, defaults to whitespace.
mol_name_flag (bool) - A flag which if True will cause the molecule name column to be
written.
res_num_flag (bool) - A flag which if True will cause the residue number column to be
written.
res_name_flag (bool) - A flag which if True will cause the residue name column to be
written.
spin_name_flag (bool) - A flag which if True will cause the spin name column to be
written.
spin_num_flag (bool) - A flag which if True will cause the spin number column to be
written.
mol_name_flag (bool) - The column to contain the molecule name information.
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generate(mol_name=None,
res_num=None,
res_name=None,
spin_num=None,
spin_name=None,
pipe=None,
select=True,
verbose=True)
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Generate the sequence item-by-item by adding a single
molecule/residue/spin container as necessary.
- Parameters:
mol_name (str or None) - The molecule name.
res_num (int or None) - The residue number.
res_name (str or None) - The residue name.
spin_num (int or None) - The spin number.
spin_name (str or None) - The spin name.
pipe (str) - The data pipe in which to generate the sequence. This defaults
to the current data pipe.
select (bool) - The spin selection flag.
verbose (bool) - A flag which if True will cause info about each spin to be
printed out as the sequence is generated.
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read(file=None,
dir=None,
file_data=None,
spin_id_col=None,
mol_name_col=None,
res_num_col=None,
res_name_col=None,
spin_num_col=None,
spin_name_col=None,
sep=None,
spin_id=None)
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Read the molecule, residue, and/or spin sequence data from file.
- Parameters:
file (str) - The name of the file to open.
dir (str or None) - The directory containing the file (defaults to the current
directory if None).
file_data (list of lists) - An alternative to opening a file, if the data already exists in
the correct format. The format is a list of lists where the
first index corresponds to the row and the second the column.
spin_id_col (int or None) - The column containing the spin ID strings. If supplied, the
mol_name_col, res_name_col, res_num_col, spin_name_col, and
spin_num_col arguments must be none.
mol_name_col (int or None) - The column containing the molecule name information. If
supplied, spin_id_col must be None.
res_name_col (int or None) - The column containing the residue name information. If supplied,
spin_id_col must be None.
res_num_col (int or None) - The column containing the residue number information. If
supplied, spin_id_col must be None.
spin_name_col (int or None) - The column containing the spin name information. If supplied,
spin_id_col must be None.
spin_num_col (int or None) - The column containing the spin number information. If supplied,
spin_id_col must be None.
sep (str or None) - The column separator which, if None, defaults to whitespace.
spin_id (None or str) - The spin ID string used to restrict data loading to a subset of
all spins.
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Return a list of all proton spin containers attached to the given
spin.
- Parameters:
spin_hash (str) - The unique spin hash.
- Returns: list of SpinContainer instances
- The list of proton spin containers attached to the given spin.
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write(file,
dir=None,
sep=None,
mol_name_flag=True,
res_num_flag=True,
res_name_flag=True,
spin_num_flag=True,
spin_name_flag=True,
force=False)
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Write the molecule, residue, and/or sequence data.
This calls the lib.io.write_spin_data() function to do most of the
work.
- Parameters:
file (str) - The name of the file to write the data to.
dir (str or None) - The directory to contain the file (defaults to the current
directory if None).
sep (str or None) - The column seperator which, if None, defaults to whitespace.
mol_name_flag (bool) - A flag which if True will cause the molecule name column to be
written.
res_num_flag (bool) - A flag which if True will cause the residue number column to be
written.
res_name_flag (bool) - A flag which if True will cause the residue name column to be
written.
spin_name_flag (bool) - A flag which if True will cause the spin name column to be
written.
spin_num_flag - A flag which if True will cause the spin number column to be
written.
force (bin) - A flag which if True will cause an existing file to be
overwritten.
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