Author: bugman
Date: Wed Feb 27 19:40:48 2013
New Revision: 18573
URL: http://svn.gna.org/viewcvs/relax?rev=18573&view=rev
Log:
Created the structure.web_of_motion user function.
This is used to create a special PDB file which represents the atomic motions
between different
structural models. Identical atoms of the selected models are concatenated
into one model, within
a temporary internal structural object, and linked together using PDB CONECT
records.
Modified:
trunk/generic_fns/structure/main.py
trunk/user_functions/structure.py
Modified: trunk/generic_fns/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/structure/main.py?rev=18573&r1=18572&r2=18573&view=diff
==============================================================================
--- trunk/generic_fns/structure/main.py (original)
+++ trunk/generic_fns/structure/main.py Wed Feb 27 19:40:48 2013
@@ -916,6 +916,81 @@
raise RelaxError("No vectors could be extracted.")
+def web_of_motion(file=None, dir=None, models=None, force=False):
+ """Create a PDB representation of the motion between a set of models.
+
+ This will create a PDB file containing the atoms of all models, with
identical atoms links using CONECT records. This function only supports the
internal structural object.
+
+ @keyword file: The name of the PDB file to write.
+ @type file: str
+ @keyword dir: The directory where the PDB file will be placed.
If set to None, then the file will be placed in the current directory.
+ @type dir: str or None
+ @keyword models: The optional list of models to restrict this to.
+ @type models: list of int or None
+ @keyword force: The force flag which if True will cause the file
to be overwritten.
+ @type force: bool
+ """
+
+ # Test if the current data pipe exists.
+ pipes.test()
+
+ # Test if the structure exists.
+ if not hasattr(cdp, 'structure') or not cdp.structure.num_models() or
not cdp.structure.num_molecules():
+ raise RelaxNoPdbError
+
+ # Validate the models.
+ cdp.structure.validate_models()
+
+ # Check the structural object type.
+ if cdp.structure.id != 'internal':
+ raise RelaxError("The %s structure type is not supported." %
cdp.structure.id)
+
+ # Initialise the structural object.
+ web = Internal()
+
+ # Loop over the molecules.
+ for i in range(len(cdp.structure.structural_data[0].mol)):
+ # Alias the molecule of the first model.
+ mol1 = cdp.structure.structural_data[0].mol[i]
+
+ # Loop over the atoms.
+ for j in range(len(mol1.atom_name)):
+ # Loop over the models.
+ for k in range(len(cdp.structure.structural_data)):
+ # Alias.
+ mol = cdp.structure.structural_data[k].mol[i]
+
+ # Add the atom.
+ web.add_atom(mol_name=mol1.mol_name,
atom_name=mol.atom_name[j], res_name=mol.res_name[j], res_num=mol.res_num[j],
pos=[mol.x[j], mol.y[j], mol.z[j]], element=mol.element[j],
chain_id=mol.chain_id[j], segment_id=mol.seg_id[j],
pdb_record=mol.pdb_record[j])
+
+ # Loop over the models again, this time twice.
+ for k in range(len(cdp.structure.structural_data)):
+ for l in range(len(cdp.structure.structural_data)):
+ # Skip identical atoms.
+ if k == l:
+ continue
+
+ # The atom index.
+ index1 = j*len(cdp.structure.structural_data) + l
+ index2 = j*len(cdp.structure.structural_data) + k
+
+ # Connect to the previous atoms.
+ web.connect_atom(mol_name=mol1.mol_name, index1=index1,
index2=index2)
+
+ # The file path.
+ file_path = get_file_path(file, dir)
+
+ # Add '.pdb' to the end of the file path if it isn't there yet.
+ if not search(".pdb$", file_path):
+ file_path = file_path + '.pdb'
+
+ # Open the file for writing.
+ file = open_write_file(file_path, force=force)
+
+ # Write the structure.
+ web.write_pdb(file)
+
+
def write_pdb(file=None, dir=None, model_num=None, compress_type=0,
force=False):
"""The PDB writing function.
Modified: trunk/user_functions/structure.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/user_functions/structure.py?rev=18573&r1=18572&r2=18573&view=diff
==============================================================================
--- trunk/user_functions/structure.py (original)
+++ trunk/user_functions/structure.py Wed Feb 27 19:40:48 2013
@@ -838,6 +838,57 @@
uf.wizard_image = WIZARD_IMAGE_PATH + 'structure' + sep + '2JK4.png'
+# The structure.web_of_motion user function.
+uf = uf_info.add_uf('structure.web_of_motion')
+uf.title = "Create a PDB representation of motion between models using a web
of interconnecting lines."
+uf.title_short = "Web of motion between models."
+uf.add_keyarg(
+ name = "file",
+ py_type = "str",
+ arg_type = "file sel",
+ desc_short = "file name",
+ desc = "The name of the PDB file.",
+ wiz_filesel_wildcard = "PDB files (*.pdb)|*.pdb;*.PDB",
+ wiz_filesel_style = FD_SAVE
+)
+uf.add_keyarg(
+ name = "dir",
+ py_type = "str",
+ arg_type = "dir",
+ desc_short = "directory name",
+ desc = "The directory to save the file to.",
+ can_be_none = True
+)
+uf.add_keyarg(
+ name = "models",
+ py_type = "int_list",
+ desc_short = "model numbers",
+ desc = "Restrict the web to a subset of models.",
+ can_be_none = True
+)
+uf.add_keyarg(
+ name = "force",
+ default = False,
+ py_type = "bool",
+ desc_short = "force flag",
+ desc = "A flag which if set to True will cause any pre-existing files to
be overwritten."
+)
+# Description.
+uf.desc.append(Desc_container())
+uf.desc[-1].add_paragraph("This will create a PDB representation of the
motion between the atoms of a given set of structural models. Identical
atoms of the selected models are concatenated into one model, within a
temporary internal structural object, and linked together using PDB CONECT
records.")
+# Prompt examples.
+uf.desc.append(Desc_container("Prompt examples"))
+uf.desc[-1].add_paragraph("To create a web of motion for the models 1, 3,
and 5, type one of:")
+uf.desc[-1].add_prompt("relax> structure.web_of_motion('web.pdb', '.', [1,
3, 5])")
+uf.desc[-1].add_prompt("relax> structure.web_of_motion(file='web.pdb',
models=[1, 3, 5])")
+uf.desc[-1].add_prompt("relax> structure.web_of_motion(file='web.pdb',
dir='.', models=[1, 3, 5])")
+uf.backend = generic_fns.structure.main.web_of_motion
+uf.menu_text = "&web_of_motion"
+uf.wizard_size = (900, 600)
+uf.wizard_apply_button = False
+uf.wizard_image = WIZARD_IMAGE_PATH + 'structure' + sep + '2JK4.png'
+
+
# The structure.write_pdb user function.
uf = uf_info.add_uf('structure.write_pdb')
uf.title = "Writing structures to a PDB file."
r18573 - in /trunk: generic_fns/structure/main.py user_functions/structure.py