Author: bugman
Date: Tue Feb 19 22:41:03 2013
New Revision: 18509
URL: http://svn.gna.org/viewcvs/relax?rev=18509&view=rev
Log:
Implemented the generic_fns.structure.pdb_read.helix() function.
Modified:
trunk/generic_fns/structure/pdb_read.py
Modified: trunk/generic_fns/structure/pdb_read.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/structure/pdb_read.py?rev=18509&r1=18508&r2=18509&view=diff
==============================================================================
--- trunk/generic_fns/structure/pdb_read.py (original)
+++ trunk/generic_fns/structure/pdb_read.py Tue Feb 19 22:41:03 2013
@@ -417,6 +417,139 @@
# Not implemented yet.
raise RelaxImplementError('formul')
+
+
+def helix(record):
+ """Parse the HELIX record.
+
+ The following is the PDB v3.3 documentation
U{http://www.wwpdb.org/documentation/format33/sect5.html#HELIX}.
+
+ Overview
+ ========
+
+ HELIX records are used to identify the position of helices in the
molecule. Helices are named, numbered, and classified by type. The residues
where the helix begins and ends are noted, as well as the total length.
+
+
+ Record Format
+ =============
+
+
______________________________________________________________________________________________
+ | | | |
|
+ | Columns | Data type | Field | Definition
|
+
|_________|______________|______________|____________________________________________________|
+ | | | |
|
+ | 1 - 6 | Record name | "HELIX " |
|
+ | 8 - 10 | Integer | serNum | Serial number of the helix.
This starts at 1 and |
+ | | | | increases incrementally.
|
+ | 12 - 14 | LString(3) | helixID | Helix identifier. In addition
to a serial number, |
+ | | | | each helix is given an
alphanumeric character |
+ | | | | helix identifier.
|
+ | 16 - 18 | Residue name | initResName | Name of the initial residue.
|
+ | 20 | Character | initChainID | Chain identifier for the
chain containing this |
+ | | | | helix.
|
+ | 22 - 25 | Integer | initSeqNum | Sequence number of the
initial residue. |
+ | 26 | AChar | initICode | Insertion code of the initial
residue. |
+ | 28 - 30 | Residue name | endResName | Name of the terminal residue
of the helix. |
+ | 32 | Character | endChainID | Chain identifier for the
chain containing this |
+ | | | | helix.
|
+ | 34 - 37 | Integer | endSeqNum | Sequence number of the
terminal residue. |
+ | 38 | AChar | endICode | Insertion code of the
terminal residue. |
+ | 39 - 40 | Integer | helixClass | Helix class (see below).
|
+ | 41 - 70 | String | comment | Comment about this helix.
|
+ | 72 - 76 | Integer | length | Length of this helix.
|
+
|_________|______________|______________|____________________________________________________|
+
+ Details
+ =======
+
+ - Additional HELIX records with different serial numbers and identifiers
occur if more than one helix is present.
+ - The initial residue of the helix is the N-terminal residue.
+ - Helices are classified as follows:
+
+ _____________________________________________________
+ | | CLASS NUMBER |
+ | TYPE OF HELIX | (COLUMNS 39 - 40) |
+ |_______________________________|___________________|
+ | | |
+ | Right-handed alpha (default) | 1 |
+ | Right-handed omega | 2 |
+ | Right-handed pi | 3 |
+ | Right-handed gamma | 4 |
+ | Right-handed 3 - 10 | 5 |
+ | Left-handed alpha | 6 |
+ | Left-handed omega | 7 |
+ | Left-handed gamma | 8 |
+ | 2 - 7 ribbon/helix | 9 |
+ | Polyproline | 10 |
+ |_______________________________|___________________|
+
+
+ Relationships to Other Record Types
+ ===================================
+
+ There may be related information in the REMARKs.
+
+
+ Example
+ =======
+
+ 1 2 3 4 5 6 7
8
+
12345678901234567890123456789012345678901234567890123456789012345678901234567890
+ HELIX 1 HA GLY A 86 GLY A 94 1
9
+ HELIX 2 HB GLY B 86 GLY B 94 1
9
+
+ HELIX 21 21 PRO J 385 LEU J 388 5
4
+ HELIX 22 22 PHE J 397 PHE J 402 5
6
+
+
+ @param record: The PDB HELIX record.
+ @type record: str
+ @return: The record name, helix serial number, helix
identifier, name of the initial residue, chain identifier, sequence number of
the initial residue, insertion code of the initial residue, name of the
terminal residue, chain identifier, sequence number of the terminal residue,
insertion code of the terminal residue, helix class, comment, helix length.
+ @rtype: tuple of str, int, str, str, str, int, str, str,
str, int, str, int, str, int
+ """
+
+ # Initialise.
+ fields = []
+
+ # Split up the record.
+ fields.append(record[0:6])
+ fields.append(record[7:10])
+ fields.append(record[11:14])
+ fields.append(record[15:18])
+ fields.append(record[19])
+ fields.append(record[21:25])
+ fields.append(record[25])
+ fields.append(record[27:30])
+ fields.append(record[31])
+ fields.append(record[33:37])
+ fields.append(record[37])
+ fields.append(record[38:40])
+ fields.append(record[40:70])
+ fields.append(record[71:76])
+
+ # 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[5]:
+ fields[5] = int(fields[5])
+ if fields[9]:
+ fields[9] = int(fields[9])
+ if fields[11]:
+ fields[11] = int(fields[11])
+ if fields[13]:
+ fields[13] = int(fields[13])
+
+ # Return the data.
+ return tuple(fields)
def het(record):
r18509 - /trunk/generic_fns/structure/pdb_read.py