Author: bugman
Date: Thu Dec 7 04:53:27 2006
New Revision: 2921
URL: http://svn.gna.org/viewcvs/relax?rev=2921&view=rev
Log:
Added the ability to create ATOM PDB records within the
'self.write_pdb_file()' method.
Modified:
1.3/generic_fns/structure.py
Modified: 1.3/generic_fns/structure.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure.py?rev=2921&r1=2920&r2=2921&view=diff
==============================================================================
--- 1.3/generic_fns/structure.py (original)
+++ 1.3/generic_fns/structure.py Thu Dec 7 04:53:27 2006
@@ -544,10 +544,10 @@
H_id = data.proton + end
# Add the central X atom.
- self.atom_add(atom_id=X_id, record_name='ATM',
atom_name=data.heteronuc, res_name=data.name, chain_id='A', res_num=data.num,
pos=R, element=data.heteronuc)
+ self.atom_add(atom_id=X_id, record_name='ATOM',
atom_name=data.heteronuc, res_name=data.name, chain_id='A', res_num=data.num,
pos=R, element=data.heteronuc)
# Add the H atom.
- self.atom_add(atom_id=H_id, record_name='ATM',
atom_name=data.proton, res_name=data.name, chain_id='A', res_num=data.num,
pos=vector, element=data.proton)
+ self.atom_add(atom_id=H_id, record_name='ATOM',
atom_name=data.proton, res_name=data.name, chain_id='A', res_num=data.num,
pos=vector, element=data.proton)
# Connect the two atoms.
self.atom_connect(atom_id=X_id, bonded_id=H_id)
@@ -1139,6 +1139,35 @@
|_________|______________|______________|________________________________________________|
+ ATOM record
+ -----------
+
+ The ATOM record contains the atomic coordinates for atoms belonging
to standard residues.
+ The format is of the record is:
+
__________________________________________________________________________________________
+ | | | |
|
+ | Columns | Data type | Field | Definition
|
+
|_________|______________|______________|________________________________________________|
+ | | | |
|
+ | 1 - 6 | Record name | "ATOM" |
|
+ | 7 - 11 | Integer | serial | Atom serial number.
|
+ | 13 - 16 | Atom | name | Atom name.
|
+ | 17 | Character | altLoc | Alternate location
indicator. |
+ | 18 - 20 | Residue name | resName | Residue name.
|
+ | 22 | Character | chainID | Chain identifier.
|
+ | 23 - 26 | Integer | resSeq | Residue sequence number.
|
+ | 27 | AChar | iCode | Code for insertion of
residues. |
+ | 31 - 38 | Real(8.3) | x | Orthogonal coordinates for
X in Angstroms. |
+ | 39 - 46 | Real(8.3) | y | Orthogonal coordinates for
Y in Angstroms. |
+ | 47 - 54 | Real(8.3) | z | Orthogonal coordinates for
Z in Angstroms. |
+ | 55 - 60 | Real(6.2) | occupancy | Occupancy.
|
+ | 61 - 66 | Real(6.2) | tempFactor | Temperature factor.
|
+ | 73 - 76 | LString(4) | segID | Segment identifier,
left-justified. |
+ | 77 - 78 | LString(2) | element | Element symbol,
right-justified. |
+ | 79 - 80 | LString(2) | charge | Charge on the atom.
|
+
|_________|______________|______________|________________________________________________|
+
+
HETATM record
-------------
@@ -1399,7 +1428,7 @@
for array in atomic_arrays:
# Write the ATOM record.
if array[1] == 'ATOM':
- raise RelaxError, 'Not coded yet.'
+ 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':
r2921 - /1.3/generic_fns/structure.py