Author: bugman
Date: Fri Jul 4 18:51:35 2008
New Revision: 6682
URL: http://svn.gna.org/viewcvs/relax?rev=6682&view=rev
Log:
Modified the __parse_pdb_record() method to parse CONECT records.
Modified:
branches/rdc_analysis/generic_fns/structure/internal.py
Modified: branches/rdc_analysis/generic_fns/structure/internal.py
URL:
http://svn.gna.org/viewcvs/relax/branches/rdc_analysis/generic_fns/structure/internal.py?rev=6682&r1=6681&r2=6682&view=diff
==============================================================================
--- branches/rdc_analysis/generic_fns/structure/internal.py (original)
+++ branches/rdc_analysis/generic_fns/structure/internal.py Fri Jul 4
18:51:35 2008
@@ -225,6 +225,27 @@
|_________|______________|______________|________________________________________________|
+ The format of the CONECT record is::
+
__________________________________________________________________________________________
+ | | | |
|
+ | Columns | Data type | Field | Definition
|
+
|_________|______________|______________|________________________________________________|
+ | | | |
|
+ | 1 - 6 | Record name | "CONECT" |
|
+ | 7 - 11 | Integer | serial | Atom serial number
|
+ | 12 - 16 | Integer | serial | Serial number of bonded
atom |
+ | 17 - 21 | Integer | serial | Serial number of bonded
atom |
+ | 22 - 26 | Integer | serial | Serial number of bonded
atom |
+ | 27 - 31 | Integer | serial | Serial number of bonded
atom |
+ | 32 - 36 | Integer | serial | Serial number of hydrogen
bonded atom |
+ | 37 - 41 | Integer | serial | Serial number of hydrogen
bonded atom |
+ | 42 - 46 | Integer | serial | Serial number of salt
bridged atom |
+ | 47 - 51 | Integer | serial | Serial number of hydrogen
bonded atom |
+ | 52 - 56 | Integer | serial | Serial number of hydrogen
bonded atom |
+ | 57 - 61 | Integer | serial | Serial number of salt
bridged atom |
+
|_________|______________|______________|________________________________________________|
+
+
@param record: The single line PDB record.
@type record: str
@return: The list of atomic information, each element
corresponding to the PDB fields
@@ -280,6 +301,35 @@
fields[11] = float(fields[11])
if fields[12]:
fields[12] = float(fields[12])
+
+ # CONECT records.
+ if search('^CONECT', record):
+ # Split up the record.
+ fields.append(record[0:6])
+ fields.append(record[6:11])
+ fields.append(record[11:16])
+ fields.append(record[16:21])
+ fields.append(record[21:26])
+ fields.append(record[26:31])
+
+ # 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[2]:
+ fields[2] = int(fields[2])
+ if fields[3]:
+ fields[3] = int(fields[3])
+ if fields[4]:
+ fields[4] = int(fields[4])
# Return the atomic info.
return fields
r6682 - /branches/rdc_analysis/generic_fns/structure/internal.py