Author: bugman
Date: Fri Jun 17 12:05:06 2011
New Revision: 13091
URL: http://svn.gna.org/viewcvs/relax?rev=13091&view=rev
Log:
Generating new user functions load_xyz() and __parse_models_xyz().
This is Han's patch https://gna.org/task/download.php?file_id=13247 attached
to the task
http://gna.org/task/?7404.
New user functions load_xyz() and __parse_models_xyz() were generated in
generic_fns/structures/internal.py based on the functions load_pdb() and
__parse_models().
Modified:
branches/xyz/generic_fns/structure/internal.py
Modified: branches/xyz/generic_fns/structure/internal.py
URL:
http://svn.gna.org/viewcvs/relax/branches/xyz/generic_fns/structure/internal.py?rev=13091&r1=13090&r2=13091&view=diff
==============================================================================
--- branches/xyz/generic_fns/structure/internal.py (original)
+++ branches/xyz/generic_fns/structure/internal.py Fri Jun 17 12:05:06 2011
@@ -280,6 +280,66 @@
records = []
# Skip the rest of this loop.
+ continue
+
+ # Append the line as a record of the model.
+ records.append(lines[i])
+
+ # If records is not empty then there are no models, so yield the lot.
+ if len(records):
+ yield model, records
+
+
+ def __parse_models_xyz(self, file_path):
+ """Generator function for looping over the models in the XYZ file.
+
+ @param file_path: The full path of the XYZ file.
+ @type file_path: str
+ @return: The model number and all the records for that
model.
+ @rtype: tuple of int and array of str
+ """
+
+ # Open the file.
+ file = open_read_file(file_path)
+ lines = file.readlines()
+ file.close()
+
+ # Check for empty files.
+ if lines == []:
+ raise RelaxError("The XYZ file is empty.")
+
+ # Init.
+ total_atom = 0
+ model = 0
+ records = []
+
+ # Loop over the data.
+ for i in xrange(len(lines)):
+ num=0
+ word=split(lines[i])
+ # Find the total atom number and the first model.
+ if (i==0) and (len(word)==1):
+ try:
+ total_atom = int(word[0])
+ num = 1
+ except:
+ raise RelaxError("The MODEL record " + repr(lines[i]) +
" is corrupt, cannot read the XYZ file.")
+
+ # End of the model.
+ if (len(records) == total_atom):
+ # Get the model number
+ model = num
+ print "model", model
+ num = num + 1
+
+ # Yield the info
+ yield model, records
+
+ # Reset the records.
+ records = []
+
+ # Skip all records prior to atom coordinates record.
+ if (len(word) != 4):
continue
# Append the line as a record of the model.
@@ -727,6 +787,108 @@
return True
+ def load_xyz(self, file_path, read_mol=None, set_mol_name=None,
read_model=None, set_model_num=None, verbosity=False):
+ """Method for loading structures from a XYZ file.
+
+ @param file_path: The full path of the XYZ file.
+ @type file_path: str
+ @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 XYZ 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 XYZ model numbers will be preserved, if
they exist.
+ @type set_model_num: None, int, or list of int
+ @keyword verbosity: A flag which if True will cause messages to
be printed.
+ @type verbosity: bool
+ @return: The status of the loading of the XYZ file.
+ @rtype: bool
+ """
+
+ # Initial print out.
+ if verbosity:
+ print("\nInternal relax XYZ parser.")
+
+ # Test if the file exists.
+ if not access(file_path, F_OK):
+ # Exit indicating failure.
+ return False
+
+ # Separate the file name and path.
+ path, file = os.path.split(file_path)
+
+ # Convert the structure reading args into lists.
+ if read_mol and not isinstance(read_mol, list):
+ read_mol = [read_mol]
+ if set_mol_name and not isinstance(set_mol_name, list):
+ set_mol_name = [set_mol_name]
+ if read_model and not isinstance(read_model, list):
+ read_model = [read_model]
+ if set_model_num and not isinstance(set_model_num, list):
+ set_model_num = [set_model_num]
+
+ # Loop over all models in the XYZ file.
+ mol_index=0
+ model_index = 0
+ orig_model_num = []
+ mol_conts = []
+ orig_mol_num = []
+ new_mol_name = []
+ for model_num, model_records in self.__parse_models_xyz(file_path):
+ # Only load the desired model.
+ if read_model and model_num not in read_model:
+ continue
+
+ # Store the original model number.
+ orig_model_num.append(model_index)
+
+ # Loop over the molecules of the model.
+ if read_mol and mol_index not in read_mol:
+ print "continue"
+ continue
+
+ # Set the target molecule name.
+ if set_mol_name:
+ new_mol_name.append(set_mol_name[mol_index])
+ else:
+ # Set the name to the file name plus the structure number.
+ new_mol_name.append(file_root(file) + '_mol' +
repr(mol_index))
+
+ # Store the original mol number.
+ orig_mol_num.append(mol_index)
+
+ # Generate the molecule container.
+ mol = MolContainer_xyz()
+
+ # Fill the molecular data object.
+ mol.fill_object_from_xyz(model_records)
+
+ # Store the molecule container.
+ mol_conts.append([])
+ mol_conts[model_index].append(mol)
+
+ # Increment the molecule index.
+ mol_index = mol_index + 1
+ print "mol_index_try", mol_index
+
+ # Increment the model index.
+ model_index = model_index + 1
+
+ # Create the structural data data structures.
+ self.pack_structs(mol_conts, orig_model_num=orig_model_num,
set_model_num=set_model_num, orig_mol_num=orig_mol_num,
set_mol_name=new_mol_name, file_name=file, file_path=path)
+
+ # Loading worked.
+ return True
+
+
def write_pdb(self, file, model_num=None):
"""Method for the creation of a PDB file from the structural data.
r13091 - /branches/xyz/generic_fns/structure/internal.py