Author: bugman
Date: Sun Nov 5 08:56:07 2006
New Revision: 2747
URL: http://svn.gna.org/viewcvs/relax?rev=2747&view=rev
Log:
Rewrote the docstring of the 'self.write_pdb_file()' function to include PDB
record descriptions.
Desriptions of the PDB records HET, HETNAM, FORMUL, HETATM, TER, CONECT,
MASTER, and END including
tables of columns, data type, field, and definition have been added. This
info comes from the
"Protein Data Bank Contents Guide: Atomic Coordinate Entry Format
Description" version 2.1 (draft),
October 25, 1996.
Modified:
branches/tensor_pdb/generic_fns/pdb.py
Modified: branches/tensor_pdb/generic_fns/pdb.py
URL:
http://svn.gna.org/viewcvs/relax/branches/tensor_pdb/generic_fns/pdb.py?rev=2747&r1=2746&r2=2747&view=diff
==============================================================================
--- branches/tensor_pdb/generic_fns/pdb.py (original)
+++ branches/tensor_pdb/generic_fns/pdb.py Sun Nov 5 08:56:07 2006
@@ -801,7 +801,195 @@
def write_pdb_file(self, file, chain_id, res_num, res_name,
chemical_name, occupancy):
- """Function for creating a PDB file from the given data."""
+ """Function for creating a PDB file from the given data.
+
+ Introduction
+ ============
+
+ A number of PDB records including HET, HETNAM, FORMUL, HETATM, TER,
CONECT, MASTER, and END
+ are created.
+
+
+ The PDB records
+ ===============
+
+ The following information about the PDB records has been taken from
the "Protein Data Bank
+ Contents Guide: Atomic Coordinate Entry Format Description" version
2.1 (draft), October 25
+ 1996.
+
+ HET record
+ ----------
+
+ The HET record describes non-standard residues. The format is of
the record is:
+
__________________________________________________________________________________________
+ | | | |
|
+ | Columns | Data type | Field | Definition
|
+
|_________|______________|______________|________________________________________________|
+ | | | |
|
+ | 1 - 6 | Record name | "HET " |
|
+ | 8 - 10 | LString(3) | hetID | Het identifier,
right-justified. |
+ | 13 | Character | ChainID | Chain identifier.
|
+ | 14 - 17 | Integer | seqNum | Sequence number.
|
+ | 18 | AChar | iCode | Insertion code.
|
+ | 21 - 25 | Integer | numHetAtoms | Number of HETATM records
for the group present |
+ | | | | in the entry.
|
+ | 31 - 70 | String | text | Text describing Het group.
|
+
|_________|______________|______________|________________________________________________|
+
+
+ HETNAM record
+ -------------
+
+ The HETNAM associates a chemical name with the hetID from the HET
record. The format is of
+ the record is:
+
__________________________________________________________________________________________
+ | | | |
|
+ | Columns | Data type | Field | Definition
|
+
|_________|______________|______________|________________________________________________|
+ | | | |
|
+ | 1 - 6 | Record name | "HETNAM" |
|
+ | 9 - 10 | Continuation | continuation | Allows concatenation of
multiple records. |
+ | 12 - 14 | LString(3) | hetID | Het identifier,
right-justified. |
+ | 16 - 70 | String | text | Chemical name.
|
+
|_________|______________|______________|________________________________________________|
+
+
+ FORMUL record
+ -------------
+
+ The chemical formula for non-standard groups. The format is of the
record is:
+
__________________________________________________________________________________________
+ | | | |
|
+ | Columns | Data type | Field | Definition
|
+
|_________|______________|______________|________________________________________________|
+ | | | |
|
+ | 1 - 6 | Record name | "FORMUL" |
|
+ | 9 - 10 | Integer | compNum | Component number.
|
+ | 13 - 15 | LString(3) | hetID | Het identifier.
|
+ | 17 - 18 | Integer | continuation | Continuation number.
|
+ | 19 | Character | asterisk | "*" for water.
|
+ | 20 - 70 | String | text | Chemical formula.
|
+
|_________|______________|______________|________________________________________________|
+
+
+ HETATM record
+ -------------
+
+ The HETATM record contains the atomic coordinates for atoms
belonging to non-standard
+ groups. The format is of the record is:
+
__________________________________________________________________________________________
+ | | | |
|
+ | Columns | Data type | Field | Definition
|
+
|_________|______________|______________|________________________________________________|
+ | | | |
|
+ | 1 - 6 | Record name | "HETATM" |
|
+ | 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. |
+ | 39 - 46 | Real(8.3) | y | Orthogonal coordinates for
Y. |
+ | 47 - 54 | Real(8.3) | z | Orthogonal coordinates for
Z. |
+ | 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.
|
+
|_________|______________|______________|________________________________________________|
+
+
+ TER record
+ ----------
+
+ The end of the ATOM and HETATM records. The format is of the record
is:
+
__________________________________________________________________________________________
+ | | | |
|
+ | Columns | Data type | Field | Definition
|
+
|_________|______________|______________|________________________________________________|
+ | | | |
|
+ | 1 - 6 | Record name | "TER " |
|
+ | 7 - 11 | Integer | serial | Serial number.
|
+ | 18 - 20 | Residue name | resName | Residue name.
|
+ | 22 | Character | chainID | Chain identifier.
|
+ | 23 - 26 | Integer | resSeq | Residue sequence number.
|
+ | 27 | AChar | iCode | Insertion code.
|
+
|_________|______________|______________|________________________________________________|
+
+
+ CONECT record
+ -------------
+
+ The connectivity between atoms. This is required for all HET groups
and for non-standard
+ bonds. The format is of the 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 |
+
|_________|______________|______________|________________________________________________|
+
+
+ MASTER record
+ -------------
+
+ The control record for bookkeeping. The format is of the record is:
+
__________________________________________________________________________________________
+ | | | |
|
+ | Columns | Data type | Field | Definition
|
+
|_________|______________|______________|________________________________________________|
+ | | | |
|
+ | 1 - 6 | Record name | "MASTER" |
|
+ | 11 - 15 | Integer | numRemark | Number of REMARK records
|
+ | 16 - 20 | Integer | "0" |
|
+ | 21 - 25 | Integer | numHet | Number of HET records
|
+ | 26 - 30 | Integer | numHelix | Number of HELIX records
|
+ | 31 - 35 | Integer | numSheet | Number of SHEET records
|
+ | 36 - 40 | Integer | numTurn | Number of TURN records
|
+ | 41 - 45 | Integer | numSite | Number of SITE records
|
+ | 46 - 50 | Integer | numXform | Number of coordinate
transformation records |
+ | | | | (ORIGX+SCALE+MTRIX)
|
+ | 51 - 55 | Integer | numCoord | Number of atomic
coordinate records |
+ | | | | (ATOM+HETATM)
|
+ | 56 - 60 | Integer | numTer | Number of TER records
|
+ | 61 - 65 | Integer | numConect | Number of CONECT records
|
+ | 66 - 70 | Integer | numSeq | Number of SEQRES records
|
+
|_________|______________|______________|________________________________________________|
+
+
+ END record
+ ----------
+
+ The end of the PDB file. The format is of the record is:
+
__________________________________________________________________________________________
+ | | | |
|
+ | Columns | Data type | Field | Definition
|
+
|_________|______________|______________|________________________________________________|
+ | | | |
|
+ | 1 - 6 | Record name | "END " |
|
+
|_________|______________|______________|________________________________________________|
+
+
+
+
+ @type file: string
+ @param file: The PDB file name.
+ @return: None
+ """
# The HET record.
file.write("%-6s %3s %1s%4s%1s %5s %-40s\n" % ('HET',
res_name, chain_id, res_num, '', len(self.atomic_data), ''))
r2747 - /branches/tensor_pdb/generic_fns/pdb.py