Author: bugman
Date: Thu Jul 7 11:06:32 2011
New Revision: 13476
URL: http://svn.gna.org/viewcvs/relax?rev=13476&view=rev
Log:
Updated all of the molecule user function docstrings.
Modified:
branches/gui_testing/prompt/molecule.py
Modified: branches/gui_testing/prompt/molecule.py
URL:
http://svn.gna.org/viewcvs/relax/branches/gui_testing/prompt/molecule.py?rev=13476&r1=13475&r2=13476&view=diff
==============================================================================
--- branches/gui_testing/prompt/molecule.py (original)
+++ branches/gui_testing/prompt/molecule.py Thu Jul 7 11:06:32 2011
@@ -27,7 +27,7 @@
# relax module imports.
from base_class import User_fn_class, _build_doc
import arg_check
-from generic_fns.mol_res_spin import copy_molecule, create_molecule,
delete_molecule, display_molecule, id_string_doc, name_molecule, type_molecule
+from generic_fns.mol_res_spin import ALLOWED_MOL_TYPES, copy_molecule,
create_molecule, delete_molecule, display_molecule, id_string_doc,
name_molecule, type_molecule
class Molecule(User_fn_class):
@@ -54,13 +54,14 @@
# The function doc info.
copy._doc_title = "Copy all data associated with a molecule."
+ copy._doc_title_short = "Copy a molecule."
copy._doc_args = [
["pipe_from", "The data pipe containing the molecule from which the
data will be copied. This defaults to the current data pipe."],
- ["mol_from", "The molecule identifier string of the molecule to copy
the data from."],
+ ["mol_from", "The molecule ID string of the molecule to copy the
data from."],
["pipe_to", "The data pipe to copy the data to. This defaults to
the current data pipe."],
- ["mol_to", "The molecule identifier string of the molecule to copy
the data to."]]
+ ["mol_to", "The molecule ID string of the molecule to copy the data
to."]]
copy._doc_desc = """
- This function will copy all the data associated with a molecule to a
second molecule. This includes residue and spin system information. The new
molecule must not yet exist.
+ This will copy all the data associated with a molecule to a second
molecule. This includes residue and spin system information. The new
molecule name must be unique.
"""
copy._doc_examples = """
To copy the molecule data from the molecule 'GST' to the new
molecule 'wt-GST', type:
@@ -95,11 +96,12 @@
# The function doc info.
create._doc_title = "Create a new molecule."
+ create._doc_title_new = "New molecule."
create._doc_args = [
["mol_name", "The name of the molecule."],
["type", "The type of molecule."]]
create._doc_desc = """
- This function will add a new molecule data container to the relax
data storage object. The same molecule name cannot be used more than once.
The molecule type need not be specified. However if it given, it should be
one of 'protein', 'RNA', 'DNA', 'organic molecule', 'inorganic molecule',
'other'.
+ This adds a new molecule data container to the relax data storage
object. The same molecule name cannot be used more than once. The molecule
type need not be specified. However if it given, it should be one of
'protein', 'RNA', 'DNA', 'organic molecule', 'inorganic molecule', 'other'.
"""
create._doc_examples = """
To create the molecules 'Ap4Aase', 'ATP', and 'MgF4', type:
@@ -119,7 +121,7 @@
print(text)
# The argument checks.
- arg_check.is_str(mol_id, 'molecule identification string')
+ arg_check.is_str(mol_id, 'molecule ID string')
# Execute the functional code.
delete_molecule(mol_id=mol_id)
@@ -127,9 +129,9 @@
# The function doc info.
delete._doc_title = "Delete molecules."
delete._doc_args = [
- ["mol_id", "The molecule identifier string."]]
+ ["mol_id", "The molecule ID string."]]
delete._doc_desc = """
- This function can be used to delete a single or sets of molecules.
+ This can be used to delete a single or sets of molecules.
"""
delete._doc_additional = [id_string_doc]
_build_doc(delete)
@@ -143,15 +145,16 @@
print(text)
# The argument checks.
- arg_check.is_str(mol_id, 'molecule identification string',
can_be_none=True)
+ arg_check.is_str(mol_id, 'molecule ID string', can_be_none=True)
# Execute the functional code.
display_molecule(mol_id=mol_id)
# The function doc info.
display._doc_title = "Display the molecule information."
+ display._doc_title_short = "Molecule information."
display._doc_args = [
- ["mol_id", "The molecule identifier string."]]
+ ["mol_id", "The molecule ID string."]]
display._doc_additional = [id_string_doc]
_build_doc(display)
@@ -166,7 +169,7 @@
print(text)
# The argument checks.
- arg_check.is_str(mol_id, 'molecule identification string',
can_be_none=True)
+ arg_check.is_str(mol_id, 'molecule ID string', can_be_none=True)
arg_check.is_str(name, 'new molecule name')
arg_check.is_bool(force, 'force flag')
@@ -176,11 +179,11 @@
# The function doc info.
name._doc_title = "Name a molecule."
name._doc_args = [
- ["mol_id", "The molecule identification string corresponding to one
or more molecules."],
+ ["mol_id", "The molecule ID string corresponding to one or more
molecules."],
["name", "The new molecule name."],
["force", "A flag which if True will cause the molecule to be
renamed."]]
name._doc_desc = """
- This function simply allows molecules to be named (or renamed).
+ This simply allows molecules to be named (or renamed).
"""
name._doc_examples = """
To rename the molecule 'Ap4Aase' to 'Inhib Ap4Aase', type one of:
@@ -204,7 +207,7 @@
print(text)
# The argument checks.
- arg_check.is_str(mol_id, 'molecule identification string',
can_be_none=True)
+ arg_check.is_str(mol_id, 'molecule ID string', can_be_none=True)
arg_check.is_str(type, 'molecule type')
arg_check.is_bool(force, 'force flag')
@@ -213,29 +216,22 @@
# The function doc info.
type._doc_title = "Set the molecule type."
+ type._doc_title_short = "Set molecule type."
type._doc_args = [
- ["mol_id", "The molecule identification string corresponding to one
or more molecules."],
+ ["mol_id", "The molecule ID string corresponding to one or more
molecules."],
["type", "The molecule type."],
["force", "A flag which if True will cause the molecule to type to
be overwritten."]]
type._doc_desc = """
- This function allows the type of the molecule to be specified. It
can be one of:
-
- 'protein'
- 'organic molecule',
- 'DNA/RNA hybrid',
- 'polydeoxyribonucleotide',
- 'polypeptide(D)',
- 'polypeptide(L)',
- 'polyribonucleotide',
- 'polysaccharide(D)',
- 'polysaccharide(L)',
- 'other'.
- """
+ This allows the type of the molecule to be specified. It can be one
of:
+
+ """
+ for name in ALLOWED_MOL_TYPES:
+ type._doc_desc = "%s '%s'\n" % (type._doc_desc, name)
type._doc_examples = """
- To set the molecule 'Ap4Aase' to the 'polypeptide(L)' type, type one
of:
-
- relax> molecule.type('#Ap4Aase', 'polypeptide(L)', True)
- relax> molecule.type(mol_id='#Ap4Aase', type='polypeptide(L)',
force=True)
+ To set the molecule 'Ap4Aase' to the 'protein' type, type one of:
+
+ relax> molecule.type('#Ap4Aase', 'protein', True)
+ relax> molecule.type(mol_id='#Ap4Aase', type='protein', force=True)
"""
type._doc_additional = [id_string_doc]
_build_doc(type)
r13476 - /branches/gui_testing/prompt/molecule.py