Author: bugman
Date: Wed Feb 20 12:13:00 2013
New Revision: 18523
URL: http://svn.gna.org/viewcvs/relax?rev=18523&view=rev
Log:
Merged revisions 18519-18522 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r18519 | bugman | 2013-02-20 11:44:33 +0100 (Wed, 20 Feb 2013) | 3 lines
Expanded the unit test of the generic_fns.structure.pdb_read.sheet()
function.
........
r18520 | bugman | 2013-02-20 11:45:21 +0100 (Wed, 20 Feb 2013) | 3 lines
Implemented the PDB SHEET record parsing function
generic_fns.structure.pdb_read.sheet().
........
r18521 | bugman | 2013-02-20 12:06:56 +0100 (Wed, 20 Feb 2013) | 3 lines
Extended the PDB ATOM record reading unit test to be of 80 characters in
length, as per the PDB definition.
........
r18522 | bugman | 2013-02-20 12:11:58 +0100 (Wed, 20 Feb 2013) | 6 lines
Created unit tests for the generic_fns.structure.pdb_write module.
This currently covers the atom(), helix() and sheet() functions (the last 2
are not yet
implemented).
........
Added:
branches/frame_order_testing/test_suite/unit_tests/_generic_fns/_structure/test_pdb_write.py
- copied unchanged from r18522,
trunk/test_suite/unit_tests/_generic_fns/_structure/test_pdb_write.py
Modified:
branches/frame_order_testing/ (props changed)
branches/frame_order_testing/generic_fns/structure/pdb_read.py
branches/frame_order_testing/test_suite/unit_tests/_generic_fns/_structure/__init__.py
branches/frame_order_testing/test_suite/unit_tests/_generic_fns/_structure/test_pdb_read.py
Propchange: branches/frame_order_testing/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Wed Feb 20 12:13:00 2013
@@ -1,1 +1,1 @@
-/trunk:1-18517
+/trunk:1-18522
Modified: branches/frame_order_testing/generic_fns/structure/pdb_read.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/generic_fns/structure/pdb_read.py?rev=18523&r1=18522&r2=18523&view=diff
==============================================================================
--- branches/frame_order_testing/generic_fns/structure/pdb_read.py (original)
+++ branches/frame_order_testing/generic_fns/structure/pdb_read.py Wed Feb 20
12:13:00 2013
@@ -1012,6 +1012,172 @@
raise RelaxImplementError('record')
+def sheet(record):
+ """Parse the SHEET record.
+
+ The following is the PDB v3.3 documentation
U{http://www.wwpdb.org/documentation/format33/sect5.html#SHEET}.
+
+ Overview
+ ========
+
+ SHEET records are used to identify the position of sheets in the
molecule. Sheets are both named and numbered. The residues where the sheet
begins and ends are noted.
+
+
+ Record Format
+ =============
+
+
______________________________________________________________________________________________
+ | | | |
|
+ | Columns | Data type | Field | Definition
|
+
|_________|______________|______________|____________________________________________________|
+ | | | |
|
+ | 1 - 6 | Record name | "SHEET " |
|
+ | 8 - 10 | Integer | strand | Strand number which starts at
1 for each strand |
+ | | | | within a sheet and increases
by one. |
+ | 12 - 14 | LString(3) | sheetID | Sheet identifier.
|
+ | 15 - 16 | Integer | numStrands | Number of strands in sheet.
|
+ | 18 - 20 | Residue name | initResName | Residue name of initial
residue. |
+ | 22 | Character | initChainID | Chain identifier of initial
residue in strand. |
+ | 23 - 26 | Integer | initSeqNum | Sequence number of initial
residue in strand. |
+ | 27 | AChar | initICode | Insertion code of initial
residue in strand. |
+ | 29 - 31 | Residue name | endResName | Residue name of terminal
residue. |
+ | 33 | Character | endChainID | Chain identifier of terminal
residue. |
+ | 34 - 37 | Integer | endSeqNum | Sequence number of terminal
residue. |
+ | 38 | AChar | endICode | Insertion code of terminal
residue. |
+ | 39 - 40 | Integer | sense | Sense of strand with respect
to previous strand in |
+ | | | | the sheet. 0 if first strand,
1 if parallel, and |
+ | | | | -1 if anti-parallel.
|
+ | 42 - 45 | Atom | curAtom | Registration. Atom name in
current strand. |
+ | 46 - 48 | Residue name | curResName | Registration. Residue name in
current strand. |
+ | 50 | Character | curChainId | Registration. Chain
identifier in current strand. |
+ | 51 - 54 | Integer | curResSeq | Registration. Residue
sequence number in current |
+ | | | | strand.
|
+ | 55 | AChar | curICode | Registration. Insertion code
in current strand. |
+ | 57 - 60 | Atom | prevAtom | Registration. Atom name in
previous strand. |
+ | 61 - 63 | Residue name | prevResName | Registration. Residue name in
previous strand. |
+ | 65 | Character | prevChainId | Registration. Chain
identifier in previous strand. |
+ | 66 - 69 | Integer | prevResSeq | Registration. Residue
sequence number in previous |
+ | | | | strand.
|
+ | 70 | AChar | prevICode | Registration. Insertion code
in previous strand. |
+
|_________|______________|______________|____________________________________________________|
+
+
+ Details
+ =======
+
+ - The initial residue for a strand is its N-terminus. Strand
registration information is provided in columns 39 - 70. Strands are listed
starting with one edge of the sheet and continuing to the spatially adjacent
strand.
+ - The sense in columns 39 - 40 indicates whether strand n is parallel
(sense = 1) or anti-parallel (sense = -1) to strand n-1. Sense is equal to
zero (0) for the first strand of a sheet.
+ - The registration (columns 42 - 70) of strand n to strand n-1 may be
specified by one hydrogen bond between each such pair of strands. This is
done by providing the hydrogen bonding between the current and previous
strands. No register information should be provided for the first strand.
+ - Split strands, or strands with two or more runs of residues from
discontinuous parts of the amino acid sequence, are explicitly listed. Detail
description can be included in the REMARK 700 .
+
+
+ Relationships to Other Record Types
+ ===================================
+
+ If the entry contains bifurcated sheets or beta-barrels, the relevant
REMARK 700 records must be provided. See the REMARK section for details.
+
+
+ Examples
+ ========
+
+ 1 2 3 4 5 6 7
8
+
12345678901234567890123456789012345678901234567890123456789012345678901234567890
+ SHEET 1 A 5 THR A 107 ARG A 110 0
+ SHEET 2 A 5 ILE A 96 THR A 99 -1 N LYS A 98 O THR A 107
+ SHEET 3 A 5 ARG A 87 SER A 91 -1 N LEU A 89 O TYR A 97
+ SHEET 4 A 5 TRP A 71 ASP A 75 -1 N ALA A 74 O ILE A 88
+ SHEET 5 A 5 GLY A 52 PHE A 56 -1 N PHE A 56 O TRP A 71
+ SHEET 1 B 5 THR B 107 ARG B 110 0
+ SHEET 2 B 5 ILE B 96 THR B 99 -1 N LYS B 98 O THR B 107
+ SHEET 3 B 5 ARG B 87 SER B 91 -1 N LEU B 89 O TYR B 97
+ SHEET 4 B 5 TRP B 71 ASP B 75 -1 N ALA B 74 O ILE B 88
+ SHEET 5 B 5 GLY B 52 ILE B 55 -1 N ASP B 54 O GLU B 73
+
+ The sheet presented as BS1 below is an eight-stranded beta-barrel. This
is represented by a nine-stranded sheet in which the first and last strands
are identical.
+
+ SHEET 1 BS1 9 VAL 13 ILE 17 0
+ SHEET 2 BS1 9 ALA 70 ILE 73 1 O TRP 72 N ILE 17
+ SHEET 3 BS1 9 LYS 127 PHE 132 1 O ILE 129 N ILE 73
+ SHEET 4 BS1 9 GLY 221 ASP 225 1 O GLY 221 N ILE 130
+ SHEET 5 BS1 9 VAL 248 GLU 253 1 O PHE 249 N ILE 222
+ SHEET 6 BS1 9 LEU 276 ASP 278 1 N LEU 277 O GLY 252
+ SHEET 7 BS1 9 TYR 310 THR 318 1 O VAL 317 N ASP 278
+ SHEET 8 BS1 9 VAL 351 TYR 356 1 O VAL 351 N THR 318
+ SHEET 9 BS1 9 VAL 13 ILE 17 1 N VAL 14 O PRO 352
+
+ The sheet structure of this example is bifurcated. In order to represent
this feature, two sheets are defined. Strands 2 and 3 of BS7 and BS8 are
identical.
+
+ SHEET 1 BS7 3 HIS 662 THR 665 0
+ SHEET 2 BS7 3 LYS 639 LYS 648 -1 N PHE 643 O HIS 662
+ SHEET 3 BS7 3 ASN 596 VAL 600 -1 N TYR 598 O ILE 646
+ SHEET 1 BS8 3 ASN 653 TRP 656 0
+ SHEET 2 BS8 3 LYS 639 LYS 648 -1 N LYS 647 O THR 655
+ SHEET 3 BS8 3 ASN 596 VAL 600 -1 N TYR 598 O ILE 646
+
+
+ @param record: The PDB SHEET record.
+ @type record: str
+ @return: The record name, strand number, sheet
identifier, number of strands in sheet, residue name of initial residue,
chain identifier of initial residue in strand, sequence number of initial
residue in strand, insertion code of initial residue in strand, residue name
of terminal residue, chain identifier of terminal residue, sequence number of
terminal residue, insertion code of terminal residue, sense of strand with
respect to previous strand, atom name in current strand, residue name in
current strand, chain identifier in current strand, residue sequence number
in current strand, insertion code in current strand, atom name in previous
strand, residue name in previous strand, chain identifier in previous strand,
residue sequence number in previous strand, insertion code in previous strand.
+ @rtype: tuple of str, int, str, int, str, str, int, str,
str, str, int, str, int, str, str, str, int, str, str, str, str, int, str
+ """
+
+ # Initialise.
+ fields = []
+
+ # Split up the record.
+ fields.append(record[0:6])
+ fields.append(record[7:10])
+ fields.append(record[11:14])
+ fields.append(record[14:16])
+ fields.append(record[17:20])
+ fields.append(record[21])
+ fields.append(record[22:26])
+ fields.append(record[26])
+ fields.append(record[28:31])
+ fields.append(record[32])
+ fields.append(record[33:37])
+ fields.append(record[37])
+ fields.append(record[38:40])
+ fields.append(record[41:45])
+ fields.append(record[45:48])
+ fields.append(record[49])
+ fields.append(record[50:54])
+ fields.append(record[54])
+ fields.append(record[56:60])
+ fields.append(record[60:63])
+ fields.append(record[64])
+ fields.append(record[65:69])
+ fields.append(record[69])
+
+ # Loop over the fields.
+ for i in range(len(fields)):
+ # Strip all whitespace.
+ fields[i] = fields[i].strip()
+
+ # Replace nothingness with None.
+ if fields[i] == '':
+ fields[i] = None
+
+ # Convert strings to numbers.
+ if fields[1]:
+ fields[1] = int(fields[1])
+ if fields[3]:
+ fields[3] = int(fields[3])
+ if fields[6]:
+ fields[6] = int(fields[6])
+ if fields[10]:
+ fields[10] = int(fields[10])
+ if fields[12]:
+ fields[12] = int(fields[12])
+ if fields[16]:
+ fields[16] = int(fields[16])
+ if fields[21]:
+ fields[21] = int(fields[21])
+
+ # Return the data.
+ return tuple(fields)
+
+
def ter(record):
"""Parse the TER record.
Modified:
branches/frame_order_testing/test_suite/unit_tests/_generic_fns/_structure/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/unit_tests/_generic_fns/_structure/__init__.py?rev=18523&r1=18522&r2=18523&view=diff
==============================================================================
---
branches/frame_order_testing/test_suite/unit_tests/_generic_fns/_structure/__init__.py
(original)
+++
branches/frame_order_testing/test_suite/unit_tests/_generic_fns/_structure/__init__.py
Wed Feb 20 12:13:00 2013
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2008 Edward d'Auvergne
#
+# Copyright (C) 2008-2013 Edward d'Auvergne
#
#
#
# This file is part of the program relax (http://www.nmr-relax.com).
#
#
#
@@ -20,7 +20,11 @@
###############################################################################
-__all__ = ['test_api_base',
- 'test__init__',
- 'test_internal',
- 'test_scientific']
+__all__ = [
+ 'test_api_base',
+ 'test__init__',
+ 'test_internal',
+ 'test_pdb_read',
+ 'test_pdb_write',
+ 'test_scientific'
+]
Modified:
branches/frame_order_testing/test_suite/unit_tests/_generic_fns/_structure/test_pdb_read.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/unit_tests/_generic_fns/_structure/test_pdb_read.py?rev=18523&r1=18522&r2=18523&view=diff
==============================================================================
---
branches/frame_order_testing/test_suite/unit_tests/_generic_fns/_structure/test_pdb_read.py
(original)
+++
branches/frame_order_testing/test_suite/unit_tests/_generic_fns/_structure/test_pdb_read.py
Wed Feb 20 12:13:00 2013
@@ -31,7 +31,7 @@
"""Test the pdb_read.atom() function."""
# Parse a PDB record.
- record = pdb_read.atom('ATOM 158 CG GLU 11 9.590
-1.041 -11.596 1.00 0.00 C')
+ record = pdb_read.atom('ATOM 158 CG GLU 11 9.590
-1.041 -11.596 1.00 0.00 C ')
# Test the elements.
self.assertEqual(record[0], 'ATOM')
@@ -82,3 +82,25 @@
# Test the elements.
self.assertEqual(record[0], 'SHEET')
+ self.assertEqual(record[1], 1)
+ self.assertEqual(record[2], 'BET')
+ self.assertEqual(record[3], 5)
+ self.assertEqual(record[4], 'GLY')
+ self.assertEqual(record[5], 'A')
+ self.assertEqual(record[6], 10)
+ self.assertEqual(record[7], None)
+ self.assertEqual(record[8], 'VAL')
+ self.assertEqual(record[9], 'A')
+ self.assertEqual(record[10], 17)
+ self.assertEqual(record[11], None)
+ self.assertEqual(record[12], 0)
+ self.assertEqual(record[13], None)
+ self.assertEqual(record[14], None)
+ self.assertEqual(record[15], None)
+ self.assertEqual(record[16], None)
+ self.assertEqual(record[17], None)
+ self.assertEqual(record[18], None)
+ self.assertEqual(record[19], None)
+ self.assertEqual(record[20], None)
+ self.assertEqual(record[21], None)
+ self.assertEqual(record[22], None)
r18523 - in /branches/frame_order_testing: ./ generic_fns/structure/ test_suite/unit_tests/_generic_fns/_structure/