Author: bugman
Date: Mon Dec 2 10:47:35 2013
New Revision: 21733
URL: http://svn.gna.org/viewcvs/relax?rev=21733&view=rev
Log:
Implemented the structure.read_gaussian user function.
This will read the final structural data out of a Gaussian log file.
Modified:
trunk/lib/structure/internal/molecules.py
trunk/lib/structure/internal/object.py
trunk/pipe_control/structure/main.py
trunk/user_functions/structure.py
Modified: trunk/lib/structure/internal/molecules.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/structure/internal/molecules.py?rev=21733&r1=21732&r2=21733&view=diff
==============================================================================
--- trunk/lib/structure/internal/molecules.py (original)
+++ trunk/lib/structure/internal/molecules.py Mon Dec 2 10:47:35 2013
@@ -23,12 +23,14 @@
"""The objects representing molecules in the internal structural object."""
# Python module imports.
+from re import search
from string import digits
from warnings import warn
# relax module import.
from data_store.relax_xml import fill_object_contents, xml_to_object
from lib.errors import RelaxError, RelaxFromXMLNotEmptyError
+from lib.periodic_table import periodic_table
from lib.structure import pdb_read
from lib.warnings import RelaxWarning
@@ -154,6 +156,54 @@
# Else, throw a warning.
warn(RelaxWarning("Cannot determine the element associated with atom
'%s'." % atom_name))
+
+
+ def _parse_gaussian_record(self, record):
+ """Parse the Gaussian log record string and return an array of the
corresponding atomic information.
+
+ The format of the Gaussian log records is::
+
__________________________________________________________________________________________
+ | | |
|
+ | Columns | Data type | Description
|
+
|_________|______________|_______________________________________________________________|
+ | | |
|
+ | 1 | int | "Center Number" - the sequential atom
number. |
+ | 2 | int | "Atomic Number" - the atomic number.
|
+ | 3 | int | "Atomic Type" - the atomic type?
|
+ | 4 | float | X coordinate in Angstrom
|
+ | 5 | float | Y coordinate in Angstrom
|
+ | 6 | float | Z coordinate in Angstrom
|
+
|_________|______________|_______________________________________________________________|
+
+
+ @param record: The single line Gaussian record.
+ @type record: str
+ @return: The list of atomic information
+ @rtype: list of str
+ """
+
+ # Skip the header.
+ if search("---------", record):
+ return None
+ if search("Center", record):
+ return None
+ if search("Number", record):
+ return None
+
+ # Initialise.
+ word = record.split()
+
+ # Proper records.
+ if len(word) == 6:
+ # Convert strings to numbers.
+ atom_number = int(word[0])
+ atomic_num = int(word[1])
+ x = float(word[3])
+ y = float(word[4])
+ z = float(word[5])
+
+ # Return the atomic info.
+ return atom_number, atomic_num, x, y, z
def _parse_xyz_record(self, record):
@@ -276,6 +326,32 @@
self.bonded[index2].append(index1)
+ def fill_object_from_gaussian(self, records):
+ """Method for generating a complete Structure_container object from
the given Gaussian log records.
+
+ @param records: A list of structural Gaussian log records.
+ @type records: list of str
+ """
+
+ # Loop over the records.
+ for record in records:
+ # Parse the record.
+ data = self._parse_gaussian_record(record)
+
+ # Nothing to do.
+ if data == None:
+ continue
+
+ # Unpack.
+ atom_number, atomic_num, x, y, z = data
+
+ # Translate the atomic number to the atom name.
+ atom_name = periodic_table.lookup_z_to_symbol(atomic_num)
+
+ # Add.
+ self.atom_add(atom_name=atom_name, atom_num=atom_number, pos=[x,
y, z], element=atom_name)
+
+
def fill_object_from_pdb(self, records, alt_loc_select=None):
"""Method for generating a complete Structure_container object from
the given PDB records.
Modified: trunk/lib/structure/internal/object.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/structure/internal/object.py?rev=21733&r1=21732&r2=21733&view=diff
==============================================================================
--- trunk/lib/structure/internal/object.py (original)
+++ trunk/lib/structure/internal/object.py Mon Dec 2 10:47:35 2013
@@ -28,6 +28,7 @@
import os
from os import F_OK, access, curdir, sep
from os.path import abspath
+from re import search
from string import ascii_uppercase
from warnings import warn
@@ -235,6 +236,59 @@
# Average vector.
if hetID == 'AVE':
return 'Average vector'
+
+
+ def _parse_models_gaussian(self, file_path):
+ """Generator function for looping over the models in the Gaussian
log file.
+
+ @param file_path: The full path of the Gaussian log 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 Gaussian log file is empty.")
+
+ # Init.
+ found = False
+ str_index = 0
+ total_atom = 0
+ model = 0
+ records = []
+
+ # Loop over the data.
+ for i in range(len(lines)):
+ # Found a structure.
+ if search("Standard orientation", lines[i]):
+ found = True
+ str_index = 0
+ continue
+
+ # End of the model.
+ if found and str_index > 4 and search("---------", lines[i]):
+ # Yield the info
+ yield records
+
+ # Reset.
+ records = []
+ found = False
+
+ # Not a structure line.
+ if not found:
+ continue
+
+ # Append the line as a record of the model.
+ records.append(lines[i])
+
+ # Increment the structure line index.
+ str_index += 1
def _parse_pdb_connectivity_annotation(self, lines):
@@ -1622,6 +1676,67 @@
return mol
+ def load_gaussian(self, file_path, set_mol_name=None,
set_model_num=None, verbosity=False):
+ """Method for loading structures from a Gaussian log file.
+
+ @param file_path: The full path of the Gaussian log file.
+ @type file_path: str
+ @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 set_model_num: Set the model number of the loaded molecule.
If set to None, then the Gaussian log 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 Gaussian
log file.
+ @rtype: bool
+ """
+
+ # Initial printout.
+ if verbosity:
+ print("\nInternal relax Gaussian log 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_name = os.path.split(file_path)
+
+ # The absolute path.
+ path_abs = abspath(curdir) + sep + path
+
+ # Set up the molecule name data structure.
+ if set_mol_name:
+ if not isinstance(set_mol_name, list):
+ set_mol_name = [set_mol_name]
+ else:
+ set_mol_name = [file_root(file_name) + '_mol1']
+
+ # Set up the model number data structure.
+ if set_model_num:
+ if not isinstance(set_model_num, list):
+ set_model_num = [set_model_num]
+ else:
+ set_model_num = [1]
+
+ # Loop over all models in the Gaussian log file, doing nothing so
the last model records are stored.
+ for model_records in self._parse_models_gaussian(file_path):
+ pass
+
+ # Generate the molecule container.
+ mol = MolContainer()
+
+ # Fill the molecular data object.
+ mol.fill_object_from_gaussian(model_records)
+
+ # Create the structural data data structures.
+ self.pack_structs([[mol]], orig_model_num=[1],
set_model_num=set_model_num, orig_mol_num=[0], set_mol_name=set_mol_name,
file_name=file_name, file_path=path, file_path_abs=path_abs)
+
+ # Loading worked.
+ return True
+
+
def load_pdb(self, file_path, read_mol=None, set_mol_name=None,
read_model=None, set_model_num=None, alt_loc=None, verbosity=False,
merge=False):
"""Method for loading structures from a PDB file.
Modified: trunk/pipe_control/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/structure/main.py?rev=21733&r1=21732&r2=21733&view=diff
==============================================================================
--- trunk/pipe_control/structure/main.py (original)
+++ trunk/pipe_control/structure/main.py Mon Dec 2 10:47:35 2013
@@ -617,6 +617,52 @@
# Print out.
write_spin_data(file=sys.stdout, mol_names=mol_names, res_nums=res_nums,
res_names=res_names, spin_nums=spin_nums, spin_names=spin_names)
+
+
+def read_gaussian(file=None, dir=None, set_mol_name=None,
set_model_num=None, verbosity=1, fail=True):
+ """Read structures from a Gaussian log file.
+
+
+ @keyword file: The name of the Gaussian log file to read.
+ @type file: str
+ @keyword dir: The directory where the Gaussian log file is
located. If set to None, then the file will be searched for in the current
directory.
+ @type dir: str or None
+ @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 set_model_num: Set the model number of the loaded molecule.
+ @type set_model_num: None, int, or list of int
+ @keyword fail: A flag which, if True, will cause a RelaxError
to be raised if the Gaussian log file does not exist. If False, then a
RelaxWarning will be trown instead.
+ @type fail: bool
+ @keyword verbosity: The amount of information to print to screen.
Zero corresponds to minimal output while higher values increase the amount of
output. The default value is 1.
+ @type verbosity: int
+ @raise RelaxFileError: If the fail flag is set, then a RelaxError is
raised if the Gaussian log file does not exist.
+ """
+
+ # Test if the current data pipe exists.
+ pipes.test()
+
+ # The file path.
+ file_path = get_file_path(file, dir)
+
+ # Try adding '.log' to the end of the file path, if the file can't be
found.
+ if not access(file_path, F_OK):
+ file_path_orig = file_path
+ file_path = file_path + '.log'
+
+ # Test if the file exists.
+ if not access(file_path, F_OK):
+ if fail:
+ raise RelaxFileError('Gaussian log', file_path_orig)
+ else:
+ warn(RelaxNoPDBFileWarning(file_path))
+ return
+
+ # Place the structural object into the relax data store.
+ if not hasattr(cdp, 'structure'):
+ cdp.structure = Internal()
+
+ # Load the structures.
+ cdp.structure.load_gaussian(file_path, set_mol_name=set_mol_name,
set_model_num=set_model_num, verbosity=verbosity)
def read_pdb(file=None, dir=None, read_mol=None, set_mol_name=None,
read_model=None, set_model_num=None, alt_loc=None, verbosity=1, merge=False,
fail=True):
Modified: trunk/user_functions/structure.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/user_functions/structure.py?rev=21733&r1=21732&r2=21733&view=diff
==============================================================================
--- trunk/user_functions/structure.py (original)
+++ trunk/user_functions/structure.py Mon Dec 2 10:47:35 2013
@@ -607,6 +607,58 @@
uf.wizard_height_desc = 300
uf.wizard_size = (800, 600)
uf.wizard_image = WIZARD_IMAGE_PATH + 'structure' + sep + 'load_spins.png'
+
+
+# The structure.read_gaussian user function.
+uf = uf_info.add_uf('structure.read_gaussian')
+uf.title = "Reading structures from Gaussian log files."
+uf.title_short = "Gaussian log structure reading."
+uf.add_keyarg(
+ name = "file",
+ py_type = "str",
+ arg_type = "file sel",
+ desc_short = "file name",
+ desc = "The name of the Gaussian log file.",
+ wiz_filesel_wildcard = "Gaussian log files
(*.log)|*.log;*.log.gz;*.log.bz2",
+ wiz_filesel_style = FD_OPEN
+)
+uf.add_keyarg(
+ name = "dir",
+ py_type = "str",
+ arg_type = "dir",
+ desc_short = "directory name",
+ desc = "The directory where the file is located.",
+ can_be_none = True
+)
+uf.add_keyarg(
+ name = "set_mol_name",
+ py_type = "str_or_str_list",
+ desc_short = "setting of molecule names",
+ desc = "Set the names of the read molecules. If unset, then the
molecules will be automatically labelled based on the file name or other
information. This can either be a single name or a list of names.",
+ can_be_none = True
+)
+uf.add_keyarg(
+ name = "set_model_num",
+ py_type = "int_or_int_list",
+ desc_short = "setting of model numbers",
+ desc = "Set the model numbers of the loaded molecules. This can be a
single number or list of numbers.",
+ can_be_none = True
+)
+# Description.
+uf.desc.append(Desc_container())
+uf.desc[-1].add_paragraph("The atomic positions from a Gaussian log file can
be read into relax. If optimisation has been preformed, the last set of
atomic coordinates from the log will be read to obtain the final structure.
The log file can be Gzip or Bzip2 compressed.")
+uf.desc[-1].add_paragraph("The setting of molecule names is used to name the
molecules within the Gaussian file. If not set, then the molecules will be
named after the file name, with the molecule number appended if more than one
exists. By setting the molecule name or setting the model number, the loaded
structure can be stored as a specific model or as a different molecule.")
+# Prompt examples.
+uf.desc.append(Desc_container("Prompt examples"))
+uf.desc[-1].add_paragraph("To load all structures from the Gaussian file
'taxol.log' in the directory '~/logs', including all models and all
molecules, type one of:")
+uf.desc[-1].add_prompt("relax> structure.read_gaussian('taxol.log',
'~/logs')")
+uf.desc[-1].add_prompt("relax> structure.read_gaussian(file='taxol.log',
dir=logs')")
+uf.backend = pipe_control.structure.main.read_gaussian
+uf.menu_text = "read_&gaussian"
+uf.gui_icon = "oxygen.actions.document-open"
+uf.wizard_height_desc = 400
+uf.wizard_size = (900, 600)
+uf.wizard_image = WIZARD_IMAGE_PATH + 'structure' + sep + 'read_xyz.png'
# The structure.read_pdb user function.
r21733 - in /trunk: lib/structure/internal/ pipe_control/structure/ user_functions/