Author: bugman
Date: Tue May 20 18:41:57 2008
New Revision: 6167
URL: http://svn.gna.org/viewcvs/relax?rev=6167&view=rev
Log:
Wrote the load_pdb() structural API method for the internal relax object.
This involved the addition of the following private methods:
__generate_object_from_pdb
__parse_models
__parse_pdb_record
Modified:
1.3/generic_fns/structure/internal.py
Modified: 1.3/generic_fns/structure/internal.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/internal.py?rev=6167&r1=6166&r2=6167&view=diff
==============================================================================
--- 1.3/generic_fns/structure/internal.py (original)
+++ 1.3/generic_fns/structure/internal.py Tue May 20 18:41:57 2008
@@ -23,10 +23,15 @@
# Module docstring.
"""Module containing the internal relax structural object."""
+# Python module imports.
+from re import search
+from string import split, strip
# relax module imports.
from api_base import Base_struct_API
+from data import Data as relax_data_store
from relax_errors import RelaxError
+from relax_io import open_read_file
@@ -42,11 +47,29 @@
id = 'internal'
- def __init__(self):
- """Initialise the structural object."""
-
- # Reinitialise the data object to an empty structure container.
- self.structural_data = Structure_container()
+ def __generate_object_from_pdb(self, records):
+ """Method for generating a complete Structure_container object from
the given PDB records.
+
+ @param records: A list of structural PDB records.
+ @type records: list of str
+ @return: The structural object containing all the atomic
information in the PDB
+ records.
+ @rtype: Structure_container instance
+ """
+
+ # Initialise the structural object.
+ str_obj = Structure_container()
+
+ # Loop over the records.
+ for record in records:
+ # Parse the record.
+ record = self.__parse_pdb_record(record)
+
+ # Add the atom.
+ self.atom_add(pdb_record=record[0], atom_name=record[2],
res_name=record[4], chain_id=record[5], res_num=record[6], pos=[record[8],
record[9], record[10]], segment_id=record[13], element=record[14])
+
+ # Return the structural object.
+ return str_obj
def __get_chemical_name(self, hetID):
@@ -104,6 +127,154 @@
# Unknown hetID.
raise RelaxError, "The residue ID (hetID) " + `hetID` + " is not
recognised."
+
+
+ def __parse_models(self, file_path):
+ """Generator function for looping over the models in the PDB file.
+
+ @param file_path: The full path of the PDB 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()
+
+ # Init.
+ model = None
+ records = []
+
+ # Loop over the data.
+ for i in xrange(len(lines)):
+ # A new model record.
+ if search('^MODEL', lines[i]):
+ model = int(split(lines[i])[1])
+
+ # Skip all records prior to the first ATOM record.
+ if not search('^ATOM', lines[i]) and not len(records):
+ continue
+
+ # End of the model.
+ if search('^ENDMDL', lines[i]):
+ # Yield the info.
+ yield model, records
+
+ # Reset the records.
+ 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_pdb_record(self, record):
+ """Parse the PDB record string and return an array of the
corresponding atomic information.
+
+ The format of the ATOM and HETATM records is::
+
__________________________________________________________________________________________
+ | | | |
|
+ | Columns | Data type | Field | Definition
|
+
|_________|______________|______________|________________________________________________|
+ | | | |
|
+ | 1 - 6 | Record name | "ATOM" |
|
+ | 7 - 11 | Integer | serial | Atom serial number.
|
+ | 13 - 16 | Atom | name | Atom name.
|
+ | 17 | Character | altLoc | Alternate location
indicator. |
+ | 18 - 20 | Residue name | resName | Residue name.
|
+ | 22 | Character | chainID | Chain identifier.
|
+ | 23 - 26 | Integer | resSeq | Residue sequence number.
|
+ | 27 | AChar | iCode | Code for insertion of
residues. |
+ | 31 - 38 | Real(8.3) | x | Orthogonal coordinates
for X in Angstroms. |
+ | 39 - 46 | Real(8.3) | y | Orthogonal coordinates
for Y in Angstroms. |
+ | 47 - 54 | Real(8.3) | z | Orthogonal coordinates
for Z in Angstroms. |
+ | 55 - 60 | Real(6.2) | occupancy | Occupancy.
|
+ | 61 - 66 | Real(6.2) | tempFactor | Temperature factor.
|
+ | 73 - 76 | LString(4) | segID | Segment identifier,
left-justified. |
+ | 77 - 78 | LString(2) | element | Element symbol,
right-justified. |
+ | 79 - 80 | LString(2) | charge | Charge on the atom.
|
+
|_________|______________|______________|________________________________________________|
+
+
+ The format of the TER record is::
+
__________________________________________________________________________________________
+ | | | |
|
+ | Columns | Data type | Field | Definition
|
+
|_________|______________|______________|________________________________________________|
+ | | | |
|
+ | 1 - 6 | Record name | "TER " |
|
+ | 7 - 11 | Integer | serial | Serial number.
|
+ | 18 - 20 | Residue name | resName | Residue name.
|
+ | 22 | Character | chainID | Chain identifier.
|
+ | 23 - 26 | Integer | resSeq | Residue sequence number.
|
+ | 27 | AChar | iCode | Insertion code.
|
+
|_________|______________|______________|________________________________________________|
+
+
+ @param record: The single line PDB record.
+ @type record: str
+ @return: The list of atomic information, each element
corresponding to the PDB fields
+ as defined in "Protein Data Bank Contents Guide:
Atomic Coordinate Entry
+ Format Description" version 2.1 (draft), October 25,
1996.
+ @rtype: list of str
+ """
+
+ # Initialise.
+ fields = []
+
+ # Split up the record.
+ fields.append(record[0:6])
+ fields.append(record[6:11])
+ fields.append(record[12:16])
+ fields.append(record[16])
+ fields.append(record[17:20])
+ fields.append(record[21])
+ fields.append(record[22:26])
+ fields.append(record[26])
+ fields.append(record[30:38])
+ fields.append(record[38:46])
+ fields.append(record[46:54])
+ fields.append(record[54:60])
+ fields.append(record[60:66])
+ fields.append(record[72:76])
+ fields.append(record[76:78])
+ fields.append(record[78:80])
+
+ # Loop over the fields.
+ for i in xrange(len(fields)):
+ # Strip all whitespace.
+ fields[i] = strip(fields[i])
+
+ # Replace nothingness with None.
+ if fields[i] == '':
+ fields[i] = None
+
+ # Convert strings to numbers.
+ if fields[1]:
+ fields[1] = int(fields[1])
+ if fields[6]:
+ fields[6] = int(fields[6])
+ if fields[8]:
+ fields[8] = float(fields[8])
+ if fields[9]:
+ fields[9] = float(fields[9])
+ if fields[10]:
+ fields[10] = float(fields[10])
+ if fields[11]:
+ fields[11] = float(fields[11])
+ if fields[12]:
+ fields[12] = float(fields[12])
+
+ # Return the atomic info.
+ return fields
def __validate_data_arrays(self):
@@ -170,6 +341,62 @@
# Update the bonded array structure.
self.structural_data.bonded[index1].append(index2)
self.structural_data.bonded[index2].append(index1)
+
+
+ def load_pdb(self, file_path, model=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 structural model to use.
+ @type model: int
+ @keyword verbosity: A flag which if True will cause messages to be
printed.
+ @type verbosity: bool
+ """
+
+ # Initial print out.
+ if verbosity:
+ print "Internal relax PDB parser.\n"
+
+ # Store the file name (with full path).
+ self.file_name = file_path
+
+ # Store the model number.
+ self.model = model
+
+ # Use pointers (references) if the PDB data exists in another run.
+ for data_pipe in relax_data_store:
+ if hasattr(data_pipe, 'structure') and
data_pipe.structure.file_name == file_path and data_pipe.structure.model ==
model and data_pipe.structure.id == 'internal':
+ # Make a pointer to the data.
+ self.structural_data = data_pipe.structure.structural_data
+
+ # Print out.
+ if verbosity:
+ print "Using the structures from the data pipe " +
`data_pipe.pipe_name` + "."
+ for i in xrange(len(self.structural_data)):
+ print self.structural_data[i]
+
+ # Exit this function.
+ return
+
+ # Print out.
+ if verbosity:
+ if type(model) == int:
+ print "Loading structure " + `model` + " from the PDB file."
+ else:
+ print "Loading all structures from the PDB file."
+
+ # Loop over all models in the PDB file.
+ for model_num, records in self.__parse_models(file_path):
+ # Only load the desired model.
+ if model != None and model != model_num:
+ continue
+
+ # Generate the structural data object.
+ str_obj = self.__generate_object_from_pdb(records)
+
+ # Place the structure in 'self.structural_data'.
+ self.structural_data.append(str_obj)
def terminate(self):
r6167 - /1.3/generic_fns/structure/internal.py