Author: bugman
Date: Wed Feb 20 14:17:40 2013
New Revision: 18524
URL: http://svn.gna.org/viewcvs/relax?rev=18524&view=rev
Log:
Implemented the PDB HELIX record writing function
generic_fns.structure.pdb_write.helix().
Modified:
trunk/generic_fns/structure/pdb_write.py
Modified: trunk/generic_fns/structure/pdb_write.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/structure/pdb_write.py?rev=18524&r1=18523&r2=18524&view=diff
==============================================================================
--- trunk/generic_fns/structure/pdb_write.py (original)
+++ trunk/generic_fns/structure/pdb_write.py Wed Feb 20 14:17:40 2013
@@ -27,6 +27,23 @@
# Python module imports.
from textwrap import wrap
+
+
+def _handle_none(value):
+ """Auxiliary function for handling values of None.
+
+ @param value: The value to convert.
+ @type value: anything
+ @return: If the value is None, then an empty string. Otherwise
the original value is returned.
+ @rtype: anything
+ """
+
+ # Handle None.
+ if value == None:
+ return ''
+
+ # Normal value.
+ return value
def atom(file, serial='', name='', alt_loc='', res_name='', chain_id='',
res_seq='', icode='', x='', y='', z='', occupancy='', temp_factor='',
element='', charge=''):
@@ -507,6 +524,142 @@
file.write("%-6s %2s %3s %2s%1s%-51s\n" % ('FORMUL', comp_num, het_id,
continuation, asterisk, text))
+def helix(file, ser_num='', helix_id='', init_res_name='', init_chain_id='',
init_seq_id='', init_icode='', end_res_name='', end_chain_id='',
end_seq_num='', end_icode='', helix_class='', comment='', length=''):
+ """Generate 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 file: The file to write the record to.
+ @type file: file object
+ @keyword ser_num: The helix serial number
+ @type ser_num: int
+ @keyword helix_id: The helix identifier
+ @type helix_id: str
+ @keyword init_res_name: The name of the initial residue
+ @type init_res_name: str
+ @keyword init_chain_id: The chain identifier
+ @type init_chain_id: str
+ @keyword init_seq_id: The sequence number of the initial residue
+ @type init_seq_id: int
+ @keyword init_icode: The insertion code of the initial residue
+ @type init_icode: str
+ @keyword end_res_name: The name of the terminal residue
+ @type end_res_name: str
+ @keyword end_chain_id: The chain identifier
+ @type end_chain_id: str
+ @keyword end_seq_num: The sequence number of the terminal residue
+ @type end_seq_num: int
+ @keyword end_icode: The insertion code of the terminal residue
+ @type end_icode: str
+ @keyword helix_class: The helix class
+ @type helix_class: int
+ @keyword comment: The comment
+ @type comment: str
+ @keyword length: The helix length.
+ @type length: int
+ """
+
+ # The formatted record.
+ text = "%-6s %3s %3s %3s %1s %4s%1s %3s %s %4s%1s%2s%30s %5s " % (
+ 'HELIX',
+ _handle_none(ser_num),
+ _handle_none(helix_id),
+ _handle_none(init_res_name),
+ _handle_none(init_chain_id),
+ _handle_none(init_seq_id),
+ _handle_none(init_icode),
+ _handle_none(end_res_name),
+ _handle_none(end_chain_id),
+ _handle_none(end_seq_num),
+ _handle_none(end_icode),
+ _handle_none(helix_class),
+ _handle_none(comment),
+ _handle_none(length)
+ )
+
+ # Write out the formatted record.
+ file.write(text)
+ file.write('\n')
+
+
def het(file, het_id='', chain_id='', seq_num='', icode='',
num_het_atoms='', text=''):
"""Generate the HET record.
r18524 - /trunk/generic_fns/structure/pdb_write.py