Author: bugman
Date: Thu Dec 18 17:16:03 2008
New Revision: 8223
URL: http://svn.gna.org/viewcvs/relax?rev=8223&view=rev
Log:
Add structural object load_pdb() methods now take the read_mol, set_mol_name,
read_model, set_model_num args.
Modified:
branches/multi_structure/generic_fns/structure/api_base.py
branches/multi_structure/generic_fns/structure/internal.py
branches/multi_structure/generic_fns/structure/main.py
branches/multi_structure/generic_fns/structure/scientific.py
Modified: branches/multi_structure/generic_fns/structure/api_base.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_structure/generic_fns/structure/api_base.py?rev=8223&r1=8222&r2=8223&view=diff
==============================================================================
--- branches/multi_structure/generic_fns/structure/api_base.py (original)
+++ branches/multi_structure/generic_fns/structure/api_base.py Thu Dec 18
17:16:03 2008
@@ -285,7 +285,7 @@
warn(RelaxWarning("The structure file " + `self.file[i]`
+ " cannot be found in the current directory or the directory of the results
file."))
- def load_pdb(self, file_path, model=None, struct_index=None,
verbosity=False):
+ def load_pdb(self, file_path, read_mol=None, set_mol_name=None,
read_model=None, set_model_num=None, struct_index=None, verbosity=False):
"""Prototype method stub for loading structures from a PDB file.
This inherited prototype method is a stub which, if the
functionality is desired, should be
@@ -294,8 +294,21 @@
@param file_path: The full path of the PDB file.
@type file_path: str
- @param model: The structural model to use.
- @type model: int
+ @keyword read_mol: The molecule(s) to read from the file,
independent of model. The
+ molecules are determined differently by the
different parsers, but
+ are numbered consecutively from 1. If set
to None, then all
+ molecules will be loaded.
+ @type read_mol: None, int, or list of int
+ @keyword set_mol_name: Set the names of the molecules which are
loaded. If set to None,
+ then the molecules will be automatically
labelled based on the file
+ name or other information.
+ @type set_mol_name: None, str, or list of str
+ @keyword read_model: The PDB model to extract from the file. If
set to None, then all
+ models will be loaded.
+ @type read_model: None, int, or list of int
+ @keyword set_model_num: Set the model number of the loaded molecule.
If set to None, then
+ the PDB model numbers will be preserved, if
they exist.
+ @type set_model_num: None, int, or list of int
@param struct_index: The index of the structure. This optional
argument can be useful
for reloading a structure.
@type struct_index: int
Modified: branches/multi_structure/generic_fns/structure/internal.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_structure/generic_fns/structure/internal.py?rev=8223&r1=8222&r2=8223&view=diff
==============================================================================
--- branches/multi_structure/generic_fns/structure/internal.py (original)
+++ branches/multi_structure/generic_fns/structure/internal.py Thu Dec 18
17:16:03 2008
@@ -841,13 +841,26 @@
return data
- def load_pdb(self, file_path, model=None, struct_index=None,
verbosity=False):
+ def load_pdb(self, file_path, read_mol=None, set_mol_name=None,
read_model=None, set_model_num=None, struct_index=None, verbosity=False):
"""Method for loading structures from a PDB file.
@param file_path: The full path of the PDB file.
@type file_path: str
- @param model: The PDB model to use. If None, all models
will be loaded.
- @type model: int or None
+ @keyword read_mol: The molecule(s) to read from the file,
independent of model. The
+ molecules are determined differently by the
different parsers, but
+ are numbered consecutively from 1. If set
to None, then all
+ molecules will be loaded.
+ @type read_mol: None, int, or list of int
+ @keyword set_mol_name: Set the names of the molecules which are
loaded. If set to None,
+ then the molecules will be automatically
labelled based on the file
+ name or other information.
+ @type set_mol_name: None, str, or list of str
+ @keyword read_model: The PDB model to extract from the file. If
set to None, then all
+ models will be loaded.
+ @type read_model: None, int, or list of int
+ @keyword set_model_num: Set the model number of the loaded molecule.
If set to None, then
+ the PDB model numbers will be preserved, if
they exist.
+ @type set_model_num: None, int, or list of int
@param struct_index: The index of the structure. This optional
argument can be useful
for reloading a structure.
@type struct_index: int
Modified: branches/multi_structure/generic_fns/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_structure/generic_fns/structure/main.py?rev=8223&r1=8222&r2=8223&view=diff
==============================================================================
--- branches/multi_structure/generic_fns/structure/main.py (original)
+++ branches/multi_structure/generic_fns/structure/main.py Thu Dec 18
17:16:03 2008
@@ -236,7 +236,7 @@
cdp.structure = Internal()
# Load the structures.
- cdp.structure.load_pdb(file_path, model, verbosity=verbosity)
+ cdp.structure.load_pdb(file_path, read_mol=read_mol,
set_mol_name=set_mol_name, read_model=read_model,
set_model_num=set_model_num, verbosity=verbosity)
# Load into Molmol (if running).
molmol.open_pdb()
Modified: branches/multi_structure/generic_fns/structure/scientific.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_structure/generic_fns/structure/scientific.py?rev=8223&r1=8222&r2=8223&view=diff
==============================================================================
--- branches/multi_structure/generic_fns/structure/scientific.py (original)
+++ branches/multi_structure/generic_fns/structure/scientific.py Thu Dec 18
17:16:03 2008
@@ -520,13 +520,26 @@
return data
- def load_pdb(self, file_path, model=None, struct_index=None,
verbosity=False):
+ def load_pdb(self, file_path, read_mol=None, set_mol_name=None,
read_model=None, set_model_num=None, struct_index=None, verbosity=False):
"""Function for loading the structures from the PDB file.
@param file_path: The full path of the file.
@type file_path: str
- @param model: The PDB model to use. If None, all models
will be loaded.
- @type model: int or None
+ @keyword read_mol: The molecule(s) to read from the file,
independent of model. The
+ molecules are determined differently by the
different parsers, but
+ are numbered consecutively from 1. If set
to None, then all
+ molecules will be loaded.
+ @type read_mol: None, int, or list of int
+ @keyword set_mol_name: Set the names of the molecules which are
loaded. If set to None,
+ then the molecules will be automatically
labelled based on the file
+ name or other information.
+ @type set_mol_name: None, str, or list of str
+ @keyword read_model: The PDB model to extract from the file. If
set to None, then all
+ models will be loaded.
+ @type read_model: None, int, or list of int
+ @keyword set_model_num: Set the model number of the loaded molecule.
If set to None, then
+ the PDB model numbers will be preserved, if
they exist.
+ @type set_model_num: None, int, or list of int
@param struct_index: The index of the structure. This optional
argument can be useful
for reloading a structure.
@type struct_index: int
r8223 - in /branches/multi_structure/generic_fns/structure: api_base.py internal.py main.py scientific.py