Author: bugman
Date: Tue May 20 11:02:11 2008
New Revision: 6142
URL: http://svn.gna.org/viewcvs/relax?rev=6142&view=rev
Log:
Module rename.
Added:
1.3/generic_fns/structure/internal.py
- copied unchanged from r6141, 1.3/generic_fns/structure/internal_pdb.py
Removed:
1.3/generic_fns/structure/internal_pdb.py
Removed: 1.3/generic_fns/structure/internal_pdb.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/internal_pdb.py?rev=6141&view=auto
==============================================================================
--- 1.3/generic_fns/structure/internal_pdb.py (original)
+++ 1.3/generic_fns/structure/internal_pdb.py (removed)
@@ -1,447 +1,0 @@
-###############################################################################
-#
#
-# Copyright (C) 2003-2008 Edward d'Auvergne
#
-#
#
-# This file is part of the program relax.
#
-#
#
-# relax is free software; you can redistribute it and/or modify
#
-# it under the terms of the GNU General Public License as published by
#
-# the Free Software Foundation; either version 2 of the License, or
#
-# (at your option) any later version.
#
-#
#
-# relax is distributed in the hope that it will be useful,
#
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
#
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#
-# GNU General Public License for more details.
#
-#
#
-# You should have received a copy of the GNU General Public License
#
-# along with relax; if not, write to the Free Software
#
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
-#
#
-###############################################################################
-
-# Module docstring.
-"""Module containing the internal relax structural object."""
-
-
-# relax module imports.
-from api_base import Base_struct_API
-from relax_errors import RelaxError
-
-
-
-class Internal(Base_struct_API):
- """The internal relax structural data object.
-
- The structural data object for this class is a dictionary of arrays.
The keys correspond to the
- 'atom_id' strings. The elements of the array are:
-
- 0. Atom number.
- 1. The record name (one of ATOM, HETATM, or TER).
- 2. Atom name.
- 3. Residue name.
- 4. Chain ID.
- 5. Residue number.
- 6. The x coordinate of the atom.
- 7. The y coordinate of the atom.
- 8. The z coordinate of the atom.
- 9. Segment ID.
- 10. Element symbol.
- 11. Bonded atom number 1. Element 11 onwards correspond to the
bonded atoms, this number
- being unlimited.
- """
-
- # Identification string.
- id = 'internal'
-
-
- def __init__(self):
- """Initialise the structural object."""
-
- # Reinitialise the data object to an empty dictionary.
- self.structural_data = {}
-
-
- def __get_chemical_name(self, hetID):
- """Method for returning the chemical name corresponding to the given
residue ID.
-
- The following names are currently returned::
- ________________________________________________
- | | |
- | hetID | Chemical name |
- |________|_____________________________________|
- | | |
- | TNS | Tensor |
- | COM | Centre of mass |
- | AXS | Tensor axes |
- | SIM | Monte Carlo simulation tensor axes |
- |________|_____________________________________|
-
-
- @param res: The residue ID.
- @type res: str
- @return: The chemical name.
- @rtype: str
- """
-
- # Tensor.
- if hetID == 'TNS':
- return 'Tensor'
-
- # Centre of mass.
- if hetID == 'COM':
- return 'Centre of mass'
-
- # Tensor axes.
- if hetID == 'AXS':
- return 'Tensor axes'
-
- # Monte Carlo simulation tensor axes.
- if hetID == 'SIM':
- return 'Monte Carlo simulation tensor axes'
-
- # Pivot point.
- if hetID == 'PIV':
- return 'Pivot point'
-
- # Cone object.
- if hetID == 'CON':
- return 'Cone'
-
- # Average vector.
- if hetID == 'AVE':
- return 'Average vector'
-
- # Unknown hetID.
- raise RelaxError, "The residue ID (hetID) " + `hetID` + " is not
recognised."
-
-
- def atom_add(self, atom_id=None, record_name='', atom_name='',
res_name='', chain_id='', res_num=None, pos=[None, None, None],
segment_id='', element=''):
- """Method for adding an atom to the structural data object.
-
- This method will create the key-value pair for the given atom.
-
-
- @param atom_id: The atom identifier. This is used as the key
within the dictionary.
- @type atom_id: str
- @param record_name: The record name, e.g. 'ATOM', 'HETATM', or 'TER'.
- @type record_name: str
- @param atom_name: The atom name, e.g. 'H1'.
- @type atom_name: str
- @param res_name: The residue name.
- @type res_name: str
- @param chain_id: The chain identifier.
- @type chain_id: str
- @param res_num: The residue number.
- @type res_num: int
- @param pos: The position vector of coordinates.
- @type pos: list (length = 3)
- @param segment_id: The segment identifier.
- @type segment_id: str
- @param element: The element symbol.
- @type element: str
- """
-
- # Initialise the key-value pair.
- self.structural_data[atom_id] = []
-
- # Fill the positions.
- self.structural_data[atom_id].append(len(self.structural_data))
- self.structural_data[atom_id].append(record_name)
- self.structural_data[atom_id].append(atom_name)
- self.structural_data[atom_id].append(res_name)
- self.structural_data[atom_id].append(chain_id)
- self.structural_data[atom_id].append(res_num)
- self.structural_data[atom_id].append(pos[0])
- self.structural_data[atom_id].append(pos[1])
- self.structural_data[atom_id].append(pos[2])
- self.structural_data[atom_id].append(segment_id)
- self.structural_data[atom_id].append(element)
-
-
- def atom_connect(self, atom_id=None, bonded_id=None):
- """Method for connecting two atoms within the data structure object.
-
- This method will find the atom number corresponding to both the
atom_id and bonded_id.
- The bonded_id atom number will then be appended to the atom_id
array. Because the
- connections work both ways, the atom_id atom number will be appended
to the bonded_id atom
- array as well.
-
-
- @param atom_id: The atom identifier. This is used as the key
within the dictionary.
- @type atom_id: str
- @param bonded_id: The second atom identifier. This is used as the
key within the
- dictionary.
- @type bonded_id: str
- """
-
- # Find the atom number corresponding to atom_id.
- if self.structural_data.has_key(atom_id):
- atom_num = self.structural_data[atom_id][0]
- else:
- raise RelaxError, "The atom corresponding to the atom_id " +
`atom_id` + " doesn't exist."
-
- # Find the atom number corresponding to bonded_id.
- if self.structural_data.has_key(bonded_id):
- bonded_num = self.structural_data[bonded_id][0]
- else:
- raise RelaxError, "The atom corresponding to the bonded_id " +
`bonded_id` + " doesn't exist."
-
- # Add the bonded_id to the atom_id array.
- self.structural_data[atom_id].append(bonded_num)
-
- # Add the atom_id to the bonded_id array.
- self.structural_data[bonded_id].append(atom_num)
-
-
- def terminate(self, atom_id_ext='', res_num=None):
- """Method for terminating the chain by adding a TER record to the
structral data object.
-
- @param atom_id_ext: The atom identifier extension.
- @type atom_id_ext: str
- @param res_num: The residue number.
- @type res_num: int
- """
-
- # The name of the last residue.
- atomic_arrays = self.structural_data.values()
- atomic_arrays.sort()
- last_res = atomic_arrays[-1][3]
-
- # Add the TER 'atom'.
- self.atom_add(atom_id='TER' + atom_id_ext, record_name='TER',
res_name=last_res, res_num=res_num)
-
-
- def write_pdb_file(self, file):
- """Method for the creation of a PDB file from the structural data.
-
- A number of PDB records including HET, HETNAM, FORMUL, HETATM, TER,
CONECT, MASTER, and END
- are created. To create the non-standard residue records HET,
HETNAM, and FORMUL, the data
- structure 'het_data' is created. It is an array of arrays where the
first dimension
- corresponds to a different residue and the second dimension has the
elements:
-
- 0. Residue number.
- 1. Residue name.
- 2. Chain ID.
- 3. Total number of atoms in the residue.
- 4. Number of H atoms in the residue.
- 5. Number of C atoms in the residue.
-
-
- @param file: The PDB file object. This object must be
writable.
- @type file: file object
- """
-
- # Sort the atoms.
- #################
-
- # Convert the self.structural_data structure from a dictionary of
arrays to an array of arrays and sort it by atom number.
- atomic_arrays = self.structural_data.values()
- atomic_arrays.sort()
-
-
- # Collect the non-standard residue info.
- ########################################
-
- # Initialise some data.
- H_count = 0
- C_count = 0
- het_data = []
-
- # Loop over the atomic data.
- for array in atomic_arrays:
- # Skip all ATOM and TER records.
- if array[1] != 'HETATM':
- continue
-
- # The residue number and element.
- res_num = array[5]
- element = array[10]
-
- # If the residue is not already stored initialise a new het_data
element.
- # (residue number, residue name, chain ID, number of atoms,
number of H, number of C, number of N).
- if not het_data or not res_num == het_data[-1][0]:
- het_data.append([array[5], array[3], array[4], 0, 0, 0, 0])
-
- # Total atom count.
- het_data[-1][3] = het_data[-1][3] + 1
-
- # Proton count.
- if element == 'H':
- het_data[-1][4] = het_data[-1][4] + 1
-
- # Carbon count.
- elif element == 'C':
- het_data[-1][5] = het_data[-1][5] + 1
-
- # Nitrogen count.
- elif element == 'N':
- het_data[-1][6] = het_data[-1][6] + 1
-
- # Unsupported element type.
- else:
- raise RelaxError, "The element " + `element` + " was
expected to be one of ['H', 'C', 'N']."
-
-
- # The HET records.
- ##################
-
- # Print out.
- print "Creating the HET records."
-
- # Write the HET records.
- for het in het_data:
- file.write("%-6s %3s %1s%4s%1s %5s %-40s\n" % ('HET',
het[2], het[1], het[0], '', het[3], ''))
-
-
- # The HETNAM records.
- #####################
-
- # Print out.
- print "Creating the HETNAM records."
-
- # Loop over the non-standard residues.
- residues = []
- for het in het_data:
- # Test if the residue HETNAM record as already been written
(otherwise store its name).
- if het[1] in residues:
- continue
- else:
- residues.append(het[1])
-
- # Get the chemical name.
- chemical_name = self.__get_chemical_name(het[1])
-
- # Write the HETNAM records.
- file.write("%-6s %2s %3s %-55s\n" % ('HETNAM', '', het[1],
chemical_name))
-
-
- # The FORMUL records.
- #####################
-
- # Print out.
- print "Creating the FORMUL records."
-
- # Loop over the non-standard residues and generate and write the
chemical formula.
- residues = []
- for het in het_data:
- # Test if the residue HETNAM record as already been written
(otherwise store its name).
- if het[1] in residues:
- continue
- else:
- residues.append(het[1])
-
- # Initialise the chemical formula.
- formula = ''
-
- # Protons.
- if het[4]:
- if formula:
- formula = formula + ' '
- formula = formula + 'H' + `het[4]`
-
- # Carbon.
- if het[5]:
- if formula:
- formula = formula + ' '
- formula = formula + 'C' + `het[5]`
-
- # Nitrogen
- if het[6]:
- if formula:
- formula = formula + ' '
- formula = formula + 'N' + `het[6]`
-
- # The FORMUL record (chemical formula).
- file.write("%-6s %2s %3s %2s%1s%-51s\n" % ('FORMUL', het[0],
het[1], '', '', formula))
-
-
- # Add the atomic coordinate records (ATOM, HETATM, and TER).
- ############################################################
-
- # Print out.
- print "Creating the atomic coordinate records (ATOM, HETATM, and
TER)."
-
- # Loop over the atomic data.
- for array in atomic_arrays:
- # Write the ATOM record.
- if array[1] == 'ATOM':
- file.write("%-6s%5s %4s%1s%3s %1s%4s%1s
%8.3f%8.3f%8.3f%6.2f%6.2f %4s%2s%2s\n" % ('ATOM', array[0], array[2],
'', array[3], array[4], array[5], '', array[6], array[7], array[8], 1.0, 0,
array[9], array[10], ''))
-
- # Write the HETATM record.
- if array[1] == 'HETATM':
- file.write("%-6s%5s %4s%1s%3s %1s%4s%1s
%8.3f%8.3f%8.3f%6.2f%6.2f %4s%2s%2s\n" % ('HETATM', array[0], array[2],
'', array[3], array[4], array[5], '', array[6], array[7], array[8], 1.0, 0,
array[9], array[10], ''))
-
- # Write the TER record.
- if array[1] == 'TER':
- file.write("%-6s%5s %3s %1s%4s%1s\n" % ('TER',
array[0], array[3], array[4], array[5], ''))
-
-
- # Create the CONECT records.
- ############################
-
- # Print out.
- print "Creating the CONECT records."
-
- connect_count = 0
- for array in atomic_arrays:
- # No bonded atoms, hence no CONECT record is required.
- if len(array) == 10:
- continue
-
- # The atom number.
- atom_num = array[0]
-
- # Initialise some data structures.
- flush = 0
- bonded_index = 0
- bonded = ['', '', '', '']
-
- # Loop over the bonded atoms.
- for i in xrange(len(array[11:])):
- # End of the array, hence create the CONECT record in this
iteration.
- if i == len(array[11:])-1:
- flush = 1
-
- # Only four covalently bonded atoms allowed in one CONECT
record.
- if bonded_index == 3:
- flush = 1
-
- # Get the bonded atom name.
- bonded[bonded_index] = array[i+11]
-
- # Increment the bonded_index value.
- bonded_index = bonded_index + 1
-
- # Generate the CONECT record and increment the counter.
- if flush:
- # Write the CONECT record.
- file.write("%-6s%5s%5s%5s%5s%5s%5s%5s%5s%5s%5s%5s\n" %
('CONECT', atom_num, bonded[0], bonded[1], bonded[2], bonded[3], '', '', '',
'', '', ''))
-
- # Increment the CONECT record count.
- connect_count = connect_count + 1
-
- # Reset the flush flag, the bonded atom count, and the
bonded atom names.
- flush = 0
- bonded_index = 0
- bonded = ['', '', '', '']
-
-
- # MASTER record.
- ################
-
- # Print out.
- print "Creating the MASTER record."
-
- # Write the MASTER record.
- file.write("%-6s %5s%5s%5s%5s%5s%5s%5s%5s%5s%5s%5s%5s\n" %
('MASTER', 0, 0, len(het_data), 0, 0, 0, 0, 0, len(self.structural_data), 1,
connect_count, 0))
-
-
- # END.
- ######
-
- # Print out.
- print "Creating the END record."
-
- # Write the END record.
- file.write("END\n")
r6142 - in /1.3/generic_fns/structure: internal.py internal_pdb.py