Author: bugman
Date: Sat Jul 5 00:35:54 2008
New Revision: 6704
URL: http://svn.gna.org/viewcvs/relax?rev=6704&view=rev
Log:
Fixes for the write_pdb() method for handling multiple structures better.
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=6704&r1=6703&r2=6704&view=diff
==============================================================================
--- branches/rdc_analysis/generic_fns/structure/internal.py (original)
+++ branches/rdc_analysis/generic_fns/structure/internal.py Sat Jul 5
00:35:54 2008
@@ -713,34 +713,34 @@
het_data = []
# Loop over the atomic data.
- for i in xrange(len(self.structural_data.atom_names)):
+ for i in xrange(len(struct.atom_name)):
# Catch the HETATM records.
- if self.structural_data.pdb_record[i] != 'HETATM':
+ if struct.pdb_record[i] != 'HETATM':
continue
# If the residue is not already stored initialise a new
het_data element.
# (residue number, residue name, chain ID, number of atoms,
number of H, number of C, number of N).
- if not het_data or not self.structural_data.res_num[i] ==
het_data[-1][0]:
- het_data.append([self.structural_data.res_num[i],
self.structural_data.res_name[i], self.structural_data.chain_id[i], 0, 0, 0,
0])
+ if not het_data or not struct.res_num[i] == het_data[-1][0]:
+ het_data.append([struct.res_num[i], struct.res_name[i],
struct.chain_id[i], 0, 0, 0, 0])
# Total atom count.
het_data[-1][3] = het_data[-1][3] + 1
# Proton count.
- if self.structural_data.element[i] == 'H':
+ if struct.element[i] == 'H':
het_data[-1][4] = het_data[-1][4] + 1
# Carbon count.
- elif self.structural_data.element[i] == 'C':
+ elif struct.element[i] == 'C':
het_data[-1][5] = het_data[-1][5] + 1
# Nitrogen count.
- elif self.structural_data.element[i] == 'N':
+ elif struct.element[i] == 'N':
het_data[-1][6] = het_data[-1][6] + 1
# Unsupported element type.
else:
- raise RelaxError, "The element " +
`self.structural_data.element[i]` + " was expected to be one of ['H', 'C',
'N']."
+ raise RelaxError, "The element " + `struct.element[i]` +
" was expected to be one of ['H', 'C', 'N']."
# The HET records.
@@ -823,18 +823,18 @@
print "Creating the atomic coordinate records (ATOM, HETATM, and
TER)."
# Loop over the atomic data.
- for i in xrange(len(self.structural_data.atom_names)):
+ for i in xrange(len(struct.atom_names)):
# Aliases.
- atom_num = self.structural_data.atom_num[i]
- atom_name = self.structural_data.atom_name[i]
- res_name = self.structural_data.res_name[i]
- chain_id = self.structural_data.chain_id[i]
- res_num = self.structural_data.res_num[i]
- x = self.structural_data.x[i]
- y = self.structural_data.y[i]
- z = self.structural_data.z[i]
- seg_id = self.structural_data.seg_id[i]
- element = self.structural_data.element[i]
+ atom_num = struct.atom_num[i]
+ atom_name = struct.atom_name[i]
+ res_name = struct.res_name[i]
+ chain_id = struct.chain_id[i]
+ res_num = struct.res_num[i]
+ x = struct.x[i]
+ y = struct.y[i]
+ z = struct.z[i]
+ seg_id = struct.seg_id[i]
+ element = struct.element[i]
# Replace None with ''.
if atom_name == None:
@@ -876,9 +876,9 @@
print "Creating the CONECT records."
connect_count = 0
- for i in xrange(len(self.structural_data.atom_names)):
+ for i in xrange(len(struct.atom_names)):
# No bonded atoms, hence no CONECT record is required.
- if not len(self.structural_data.bonded[i]):
+ if not len(struct.bonded[i]):
continue
# Initialise some data structures.
@@ -887,9 +887,9 @@
bonded = ['', '', '', '']
# Loop over the bonded atoms.
- for j in xrange(len(self.structural_data.bonded[i])):
+ for j in xrange(len(struct.bonded[i])):
# End of the array, hence create the CONECT record in
this iteration.
- if j == len(self.structural_data.bonded[i])-1:
+ if j == len(struct.bonded[i])-1:
flush = 1
# Only four covalently bonded atoms allowed in one
CONECT record.
@@ -897,7 +897,7 @@
flush = 1
# Get the bonded atom index.
- bonded[bonded_index] = self.structural_data.bonded[i][j]
+ bonded[bonded_index] = struct.bonded[i][j]
# Increment the bonded_index value.
bonded_index = bonded_index + 1
@@ -923,7 +923,7 @@
print "Creating the MASTER record."
# Write the MASTER record.
- file.write("%-6s %5s%5s%5s%5s%5s%5s%5s%5s%5s%5s%5s%5s\n" %
('MASTER', 0, 0, len(het_data), 0, 0, 0, 0, 0, len(self.structural_data), 1,
connect_count, 0))
+ file.write("%-6s %5s%5s%5s%5s%5s%5s%5s%5s%5s%5s%5s%5s\n" %
('MASTER', 0, 0, len(het_data), 0, 0, 0, 0, 0, len(struct), 1, connect_count,
0))
# END.
r6704 - /branches/rdc_analysis/generic_fns/structure/internal.py