Author: bugman
Date: Fri Feb 20 11:26:56 2015
New Revision: 27692
URL: http://svn.gna.org/viewcvs/relax?rev=27692&view=rev
Log:
Fixes for all of the PDB documentation HTML links in the docstrings.
The PDB have shifted their documentation from
http://www.wwpdb.org/documentation/format33/v3.3.html
to http://www.wwpdb.org/documentation/file-format/format33/v3.3.html,
stupidly without redirects.
This will create dead links in the relax API documentation at
http://www.nmr-relax.com/api/3.3/, as
well as the older API documentation (http://www.nmr-relax.com/api/2.2/,
http://www.nmr-relax.com/api/3.0/, http://www.nmr-relax.com/api/3.1/,
http://www.nmr-relax.com/api/3.2/).
Modified:
trunk/lib/structure/internal/object.py
trunk/lib/structure/pdb_read.py
trunk/lib/structure/pdb_write.py
Modified: trunk/lib/structure/internal/object.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/structure/internal/object.py?rev=27692&r1=27691&r2=27692&view=diff
==============================================================================
--- trunk/lib/structure/internal/object.py (original)
+++ trunk/lib/structure/internal/object.py Fri Feb 20 11:26:56 2015
@@ -303,7 +303,7 @@
def _parse_pdb_connectivity_annotation(self, lines):
"""Loop over and parse the PDB connectivity annotation records.
- These are the records identified in the U{PDB version 3.30
documentation<http://www.wwpdb.org/documentation/format33/sect6.html>}.
+ These are the records identified in the U{PDB version 3.30
documentation<http://www.wwpdb.org/documentation/file-format/format33/sect6.html>}.
@param lines: The lines of the PDB file excluding the sections
prior to the connectivity annotation section.
@@ -332,7 +332,7 @@
def _parse_pdb_coord(self, lines):
"""Generator function for looping over the models in the PDB file.
- These are the records identified in the PDB version 3.30
documentation at U{http://www.wwpdb.org/documentation/format33/sect9.html}.
+ These are the records identified in the PDB version 3.30
documentation at
U{http://www.wwpdb.org/documentation/file-format/format33/sect9.html}.
@param lines: The lines of the coordinate section.
@@ -380,7 +380,7 @@
def _parse_pdb_hetrogen(self, lines):
"""Loop over and parse the PDB hetrogen records.
- These are the records identified in the PDB version 3.30
documentation at U{http://www.wwpdb.org/documentation/format33/sect4.html}.
+ These are the records identified in the PDB version 3.30
documentation at
U{http://www.wwpdb.org/documentation/file-format/format33/sect4.html}.
@param lines: The lines of the PDB file excluding the sections
prior to the hetrogen section.
@@ -410,7 +410,7 @@
def _parse_pdb_misc(self, lines):
"""Loop over and parse the PDB miscellaneous records.
- These are the records identified in the PDB version 3.30
documentation at U{http://www.wwpdb.org/documentation/format33/sect7.html}.
+ These are the records identified in the PDB version 3.30
documentation at
U{http://www.wwpdb.org/documentation/file-format/format33/sect7.html}.
@param lines: The lines of the PDB file excluding the sections
prior to the miscellaneous section.
@@ -437,7 +437,7 @@
def _parse_pdb_prim_struct(self, lines):
"""Loop over and parse the PDB primary structure records.
- These are the records identified in the PDB version 3.30
documentation at U{http://www.wwpdb.org/documentation/format33/sect3.html}.
+ These are the records identified in the PDB version 3.30
documentation at
U{http://www.wwpdb.org/documentation/file-format/format33/sect3.html}.
@param lines: The lines of the PDB file excluding the title
section.
@@ -469,7 +469,7 @@
def _parse_pdb_ss(self, lines, read_mol=None):
"""Loop over and parse the PDB secondary structure records.
- These are the records identified in the PDB version 3.30
documentation at U{http://www.wwpdb.org/documentation/format33/sect5.html}.
+ These are the records identified in the PDB version 3.30
documentation at
U{http://www.wwpdb.org/documentation/file-format/format33/sect5.html}.
@param lines: The lines of the PDB file excluding the sections
prior to the secondary structure section.
@@ -562,7 +562,7 @@
def _parse_pdb_title(self, lines):
"""Loop over and parse the PDB title records.
- These are the records identified in the PDB version 3.30
documentation at U{http://www.wwpdb.org/documentation/format33/sect2.html}.
+ These are the records identified in the PDB version 3.30
documentation at
U{http://www.wwpdb.org/documentation/file-format/format33/sect2.html}.
@param lines: All lines of the PDB file.
@@ -604,7 +604,7 @@
def _parse_pdb_transform(self, lines):
"""Loop over and parse the PDB transform records.
- These are the records identified in the PDB version 3.30
documentation at U{http://www.wwpdb.org/documentation/format33/sect8.html}.
+ These are the records identified in the PDB version 3.30
documentation at
U{http://www.wwpdb.org/documentation/file-format/format33/sect8.html}.
@param lines: The lines of the PDB file excluding the sections
prior to the transform section.
Modified: trunk/lib/structure/pdb_read.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/structure/pdb_read.py?rev=27692&r1=27691&r2=27692&view=diff
==============================================================================
--- trunk/lib/structure/pdb_read.py (original)
+++ trunk/lib/structure/pdb_read.py Fri Feb 20 11:26:56 2015
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2013 Edward d'Auvergne
#
+# Copyright (C) 2013-2015 Edward d'Auvergne
#
#
#
# This file is part of the program relax (http://www.nmr-relax.com).
#
#
#
@@ -22,7 +22,7 @@
# Module docstring.
"""Module for parsing PDB records.
-This module currently used the PDB format version 3.30 from July, 2011
U{http://www.wwpdb.org/documentation/format33/v3.3.html}.
+This module currently used the PDB format version 3.30 from July, 2011
U{http://www.wwpdb.org/documentation/file-format/format33/v3.3.html}.
"""
# relax module imports.
@@ -32,7 +32,7 @@
def atom(record):
"""Parse the ATOM record.
- The following is the PDB v3.3 documentation
U{http://www.wwpdb.org/documentation/format33/sect9.html#ATOM}.
+ The following is the PDB v3.3 documentation
U{http://www.wwpdb.org/documentation/file-format/format33/sect9.html#ATOM}.
ATOM
====
@@ -235,7 +235,7 @@
def conect(record):
"""Parse the CONECT record.
- The following is the PDB v3.3 documentation
U{http://www.wwpdb.org/documentation/format33/sect10.html#CONECT}.
+ The following is the PDB v3.3 documentation
U{http://www.wwpdb.org/documentation/file-format/format33/sect10.html#CONECT}.
CONECT
======
@@ -366,7 +366,7 @@
def formul(record):
"""Parse the FORMUL record.
- The following is the PDB v3.3 documentation
U{http://www.wwpdb.org/documentation/format33/sect4.html#FORMUL}.
+ The following is the PDB v3.3 documentation
U{http://www.wwpdb.org/documentation/file-format/format33/sect4.html#FORMUL}.
FORMUL
======
@@ -454,7 +454,7 @@
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}.
+ The following is the PDB v3.3 documentation
U{http://www.wwpdb.org/documentation/file-format/format33/sect5.html#HELIX}.
HELIX
=====
@@ -596,7 +596,7 @@
def het(record):
"""Parse the HET record.
- The following is the PDB v3.3 documentation
U{http://www.wwpdb.org/documentation/format33/sect4.html#HET}.
+ The following is the PDB v3.3 documentation
U{http://www.wwpdb.org/documentation/file-format/format33/sect4.html#HET}.
HET
===
@@ -693,7 +693,7 @@
def hetatm(record):
"""Parse the HETATM record.
- The following is the PDB v3.3 documentation
U{http://www.wwpdb.org/documentation/format33/sect9.html#HETATM}.
+ The following is the PDB v3.3 documentation
U{http://www.wwpdb.org/documentation/file-format/format33/sect9.html#HETATM}.
HETATM
======
@@ -836,7 +836,7 @@
def hetnam(record):
"""Parse the HETNAM record.
- The following is the PDB v3.3 documentation
U{http://www.wwpdb.org/documentation/format33/sect4.html#HETNAM}.
+ The following is the PDB v3.3 documentation
U{http://www.wwpdb.org/documentation/file-format/format33/sect4.html#HETNAM}.
HETNAM
======
@@ -925,7 +925,7 @@
def model(record):
"""Parse the MODEL record.
- The following is the PDB v3.3 documentation
U{http://www.wwpdb.org/documentation/format33/sect9.html#MODEL}.
+ The following is the PDB v3.3 documentation
U{http://www.wwpdb.org/documentation/file-format/format33/sect9.html#MODEL}.
MODEL
=====
@@ -1047,7 +1047,7 @@
def remark(record):
"""Parse the REMARK record.
- The following is the PDB v3.3 documentation
U{http://www.wwpdb.org/documentation/format33/remarks.html}.
+ The following is the PDB v3.3 documentation
U{http://www.wwpdb.org/documentation/file-format/format33/remarks.html}.
REMARK
======
@@ -1084,7 +1084,7 @@
def sheet(record):
"""Parse the SHEET record.
- The following is the PDB v3.3 documentation
U{http://www.wwpdb.org/documentation/format33/sect5.html#SHEET}.
+ The following is the PDB v3.3 documentation
U{http://www.wwpdb.org/documentation/file-format/format33/sect5.html#SHEET}.
SHEET
=====
@@ -1259,7 +1259,7 @@
def ter(record):
"""Parse the TER record.
- The following is the PDB v3.3 documentation
U{http://www.wwpdb.org/documentation/format33/sect9.html#TER}.
+ The following is the PDB v3.3 documentation
U{http://www.wwpdb.org/documentation/file-format/format33/sect9.html#TER}.
TER
===
Modified: trunk/lib/structure/pdb_write.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/structure/pdb_write.py?rev=27692&r1=27691&r2=27692&view=diff
==============================================================================
--- trunk/lib/structure/pdb_write.py (original)
+++ trunk/lib/structure/pdb_write.py Fri Feb 20 11:26:56 2015
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2013-2014 Edward d'Auvergne
#
+# Copyright (C) 2013-2015 Edward d'Auvergne
#
#
#
# This file is part of the program relax (http://www.nmr-relax.com).
#
#
#
@@ -22,7 +22,7 @@
# Module docstring.
"""Module for creating PDB records.
-This module currently used the PDB format version 3.30 from July, 2011
U{http://www.wwpdb.org/documentation/format33/v3.3.html}.
+This module currently used the PDB format version 3.30 from July, 2011
U{http://www.wwpdb.org/documentation/file-format/format33/v3.3.html}.
"""
# Python module imports.
@@ -92,7 +92,7 @@
def atom(file, serial='', name='', alt_loc='', res_name='', chain_id='',
res_seq='', icode='', x='', y='', z='', occupancy=1.0, temp_factor=0.0,
element='', charge=''):
"""Generate the ATOM record.
- The following is the PDB v3.3 documentation
U{http://www.wwpdb.org/documentation/format33/sect9.html#ATOM}.
+ The following is the PDB v3.3 documentation
U{http://www.wwpdb.org/documentation/file-format/format33/sect9.html#ATOM}.
ATOM
====
@@ -309,7 +309,7 @@
def conect(file, serial='', bonded1='', bonded2='', bonded3='', bonded4=''):
"""Generate the CONECT record.
- The following is the PDB v3.3 documentation
U{http://www.wwpdb.org/documentation/format33/sect10.html#CONECT}.
+ The following is the PDB v3.3 documentation
U{http://www.wwpdb.org/documentation/file-format/format33/sect10.html#CONECT}.
CONECT
======
@@ -431,7 +431,7 @@
def end(file):
"""Generate the END record.
- The following is the PDB v3.3 documentation
U{http://www.wwpdb.org/documentation/format33/sect11.html#END}.
+ The following is the PDB v3.3 documentation
U{http://www.wwpdb.org/documentation/file-format/format33/sect11.html#END}.
END
===
@@ -501,7 +501,7 @@
def endmdl(file):
"""Generate the ENDMDL record.
- The following is the PDB v3.3 documentation
U{http://www.wwpdb.org/documentation/format33/v3.3.html}.
+ The following is the PDB v3.3 documentation
U{http://www.wwpdb.org/documentation/file-format/format33/v3.3.html}.
ENDMDL
======
@@ -591,7 +591,7 @@
def formul(file, comp_num='', het_id='', continuation='', asterisk='',
text=''):
"""Generate the FORMUL record.
- The following is the PDB v3.3 documentation
U{http://www.wwpdb.org/documentation/format33/sect4.html#FORMUL}.
+ The following is the PDB v3.3 documentation
U{http://www.wwpdb.org/documentation/file-format/format33/sect4.html#FORMUL}.
FORMUL
======
@@ -703,7 +703,7 @@
def helix(file, ser_num='', helix_id='', init_res_name='', init_chain_id='',
init_seq_num='', 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}.
+ The following is the PDB v3.3 documentation
U{http://www.wwpdb.org/documentation/file-format/format33/sect5.html#HELIX}.
HELIX
=====
@@ -851,7 +851,7 @@
def het(file, het_id='', chain_id='', seq_num='', icode='',
num_het_atoms='', text=''):
"""Generate the HET record.
- The following is the PDB v3.3 documentation
U{http://www.wwpdb.org/documentation/format33/sect4.html#HET}.
+ The following is the PDB v3.3 documentation
U{http://www.wwpdb.org/documentation/file-format/format33/sect4.html#HET}.
HET
===
@@ -975,7 +975,7 @@
def hetatm(file, serial='', name='', alt_loc='', res_name='', chain_id='',
res_seq='', icode='', x='', y='', z='', occupancy=1.0, temp_factor=0.0,
element='', charge=''):
"""Generate the HETATM record.
- The following is the PDB v3.3 documentation
U{http://www.wwpdb.org/documentation/format33/sect9.html#HETATM}.
+ The following is the PDB v3.3 documentation
U{http://www.wwpdb.org/documentation/file-format/format33/sect9.html#HETATM}.
HETATM
======
@@ -1132,7 +1132,7 @@
def hetnam(file, continuation='', het_id='', text=''):
"""Generate the HETNAM record.
- The following is the PDB v3.3 documentation
U{http://www.wwpdb.org/documentation/format33/sect4.html#HETNAM}.
+ The following is the PDB v3.3 documentation
U{http://www.wwpdb.org/documentation/file-format/format33/sect4.html#HETNAM}.
HETNAM
======
@@ -1239,7 +1239,7 @@
def master(file, num_remark=0, num_het=0, num_helix=0, num_sheet=0,
num_turn=0, num_site=0, num_xform=0, num_coord=0, num_ter=0, num_conect=0,
num_seq=0):
"""Generate the MASTER record.
- The following is the PDB v3.3 documentation
U{http://www.wwpdb.org/documentation/format33/sect11.html#MASTER}.
+ The following is the PDB v3.3 documentation
U{http://www.wwpdb.org/documentation/file-format/format33/sect11.html#MASTER}.
MASTER
======
@@ -1361,7 +1361,7 @@
def model(file, serial=''):
"""Generate the MODEL record.
- The following is the PDB v3.3 documentation
U{http://www.wwpdb.org/documentation/format33/sect9.html#MODEL}.
+ The following is the PDB v3.3 documentation
U{http://www.wwpdb.org/documentation/file-format/format33/sect9.html#MODEL}.
MODEL
=====
@@ -1495,7 +1495,7 @@
def remark(file, num='', remark=''):
"""Generate the REMARK record.
- The following is the PDB v3.3 documentation
U{http://www.wwpdb.org/documentation/format33/remarks.html}.
+ The following is the PDB v3.3 documentation
U{http://www.wwpdb.org/documentation/file-format/format33/remarks.html}.
REMARK
======
@@ -1553,7 +1553,7 @@
def sheet(file, strand='', sheet_id='', num_strands='', init_res_name='',
init_chain_id='', init_seq_num='', init_icode='', end_res_name='',
end_chain_id='', end_seq_num='', end_icode='', sense='', cur_atom='',
cur_res_name='', cur_chain_id='', cur_res_seq='', cur_icode='', prev_atom='',
prev_res_name='', prev_chain_id='', prev_res_seq='', prev_icode=''):
"""Generate the SHEET record.
- The following is the PDB v3.3 documentation
U{http://www.wwpdb.org/documentation/format33/sect5.html#SHEET}.
+ The following is the PDB v3.3 documentation
U{http://www.wwpdb.org/documentation/file-format/format33/sect5.html#SHEET}.
SHEET
=====
@@ -1749,7 +1749,7 @@
def ter(file, serial='', res_name='', chain_id='', res_seq='', icode=''):
"""Generate the TER record.
- The following is the PDB v3.3 documentation
U{http://www.wwpdb.org/documentation/format33/sect9.html#TER}.
+ The following is the PDB v3.3 documentation
U{http://www.wwpdb.org/documentation/file-format/format33/sect9.html#TER}.
TER
===
r27692 - in /trunk/lib/structure: internal/object.py pdb_read.py pdb_write.py