Author: bugman
Date: Sat Jul 5 04:19:04 2008
New Revision: 6725
URL: http://svn.gna.org/viewcvs/relax?rev=6725&view=rev
Log:
Fixes for the hetrogen section.
These records are now correctly created, independent of the number of loaded
structures.
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=6725&r1=6724&r2=6725&view=diff
==============================================================================
--- branches/rdc_analysis/generic_fns/structure/internal.py (original)
+++ branches/rdc_analysis/generic_fns/structure/internal.py Sat Jul 5
04:19:04 2008
@@ -703,8 +703,13 @@
num_remark = 2
- # Hetrogen section.
- ###################
+ ####################
+ # Hetrogen section #
+ ####################
+
+ # Initialise the hetrogen info array.
+ het_data = []
+ het_data_coll = []
# Loop over the structures.
for index in xrange(len(self.structural_data)):
@@ -718,16 +723,10 @@
# Check the validity of the data.
self.__validate_data_arrays(struct)
+ # Append an empty array for this structure.
+ het_data.append([])
# Collect the non-standard residue info.
- ########################################
-
- # Initialise some data.
- H_count = 0
- C_count = 0
- het_data = []
-
- # Loop over the atomic data.
for i in xrange(len(struct.atom_name)):
# Skip non-HETATM records and HETATM records with no residue
info.
if struct.pdb_record[i] != 'HETATM' or struct.res_name[i] ==
None:
@@ -735,95 +734,123 @@
# If the residue is not already stored initialise a new
het_data element.
# (residue number, residue name, chain ID, number of atoms,
atom count array).
- 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, []])
+ if not het_data[index] or not struct.res_num[i] ==
het_data[index][-1][0]:
+ het_data[index].append([struct.res_num[i],
struct.res_name[i], struct.chain_id[i], 0, []])
# Catch missing chain_ids.
- if het_data[-1][2] == None:
- het_data[-1][2] = ''
+ if het_data[index][-1][2] == None:
+ het_data[index][-1][2] = ''
# Total atom count.
- het_data[-1][3] = het_data[-1][3] + 1
+ het_data[index][-1][3] = het_data[index][-1][3] + 1
# Find if the atom has already a count entry.
entry = False
- for j in xrange(len(het_data[-1][4])):
- if struct.element[i] == het_data[-1][4][j][0]:
+ for j in xrange(len(het_data[index][-1][4])):
+ if struct.element[i] == het_data[index][-1][4][j][0]:
entry = True
# Create a new specific atom count entry.
if not entry:
- het_data[-1][4].append([struct.element[i], 0])
+ het_data[index][-1][4].append([struct.element[i], 0])
# Increment the specific atom count.
- for j in xrange(len(het_data[-1][4])):
- if struct.element[i] == het_data[-1][4][j][0]:
- het_data[-1][4][j][1] = het_data[-1][4][j][1] + 1
-
-
- # The HET records.
- ##################
-
- # Print out.
- print "Creating the HET records."
-
- # Write the HET records.
- for het in het_data:
- file.write("%-6s %3s %1s%4s%1s %5s %-40s\n" % ('HET',
het[2], het[1], het[0], '', het[3], ''))
-
-
- # The HETNAM records.
- #####################
-
- # Print out.
- print "Creating the HETNAM records."
-
- # Loop over the non-standard residues.
- residues = []
- for het in het_data:
- # Test if the residue HETNAM record as already been written
(otherwise store its name).
- if het[1] in residues:
- continue
- else:
- residues.append(het[1])
-
- # Get the chemical name.
- chemical_name = self.__get_chemical_name(het[1])
- if not chemical_name:
- chemical_name = 'Unknown'
-
- # Write the HETNAM records.
- file.write("%-6s %2s %3s %-55s\n" % ('HETNAM', '', het[1],
chemical_name))
-
-
- # The FORMUL records.
- #####################
-
- # Print out.
- print "Creating the FORMUL records."
-
- # Loop over the non-standard residues and generate and write the
chemical formula.
- residues = []
- for het in het_data:
- # Test if the residue HETNAM record as already been written
(otherwise store its name).
- if het[1] in residues:
- continue
- else:
- residues.append(het[1])
-
- # Initialise the chemical formula.
- formula = ''
-
- # Loop over the atoms.
- for atom_count in het[4]:
- formula = formula + atom_count[0] + `atom_count[1]`
-
- # The FORMUL record (chemical formula).
- file.write("%-6s %2s %3s %2s%1s%-51s\n" % ('FORMUL',
het[0], het[1], '', '', formula))
-
-
- # Coordinate section.
+ for j in xrange(len(het_data[index][-1][4])):
+ if struct.element[i] == het_data[index][-1][4][j][0]:
+ het_data[index][-1][4][j][1] =
het_data[index][-1][4][j][1] + 1
+
+ # Create the collective hetrogen info data structure.
+ for i in xrange(len(het_data[index])):
+ # Find the entry in the collective structure.
+ found = False
+ for j in xrange(len(het_data_coll)):
+ # Matching residue numbers.
+ if het_data[index][i][0] == het_data_coll[j][0]:
+ # Change the flag.
+ found = True
+
+ # The checks.
+ if het_data_coll[i][1] != het_data[index][i][1]:
+ raise RelaxError, "The " +
`het_data[index][i][1]` + " residue name of hetrogen " +
`het_data[index][i][0]` + " " + het_data[index][i][1] + " of structure " +
`index` + " does not match the " + `het_data_coll[j][1]` + " name of the
previous structures."
+
+ elif het_data_coll[i][2] != het_data[index][i][2]:
+ raise RelaxError, "The hetrogen chain id " +
`het_data[index][i][2]` + " does not match " + `het_data_coll[j][2]` + " of
residue " + `het_data_coll[j][0]` + " " + het_data_coll[j][1] + " of the
previous structures."
+
+ elif het_data_coll[i][3] != het_data[index][i][3]:
+ raise RelaxError, "The " +
`het_data[index][i][3]` + " atoms of hetrogen " + `het_data_coll[j][0]` + " "
+ het_data_coll[j][1] + " of structure " + `index` + " does not match the " +
`het_data_coll[j][3]` + " of the previous structures."
+
+ elif het_data_coll[i][4] != het_data[index][i][4]:
+ raise RelaxError, "The atom counts " +
`het_data[index][i][4]` + " for the hetrogen residue " +
`het_data_coll[j][0]` + " " + het_data_coll[j][1] + " of structure " +
`index` + " do not match the counts " + `het_data_coll[j][4]` + " of the
previous structures."
+
+ # If there is no match, add the new residue to the
collective.
+ if not found:
+ het_data_coll.append(het_data[index][i])
+
+
+ # The HET records.
+ ##################
+
+ # Print out.
+ print "Creating the HET records."
+
+ # Write the HET records.
+ for het in het_data_coll:
+ file.write("%-6s %3s %1s%4s%1s %5s %-40s\n" % ('HET',
het[2], het[1], het[0], '', het[3], ''))
+
+
+ # The HETNAM records.
#####################
+
+ # Print out.
+ print "Creating the HETNAM records."
+
+ # Loop over the non-standard residues.
+ residues = []
+ for het in het_data_coll:
+ # Test if the residue HETNAM record as already been written
(otherwise store its name).
+ if het[1] in residues:
+ continue
+ else:
+ residues.append(het[1])
+
+ # Get the chemical name.
+ chemical_name = self.__get_chemical_name(het[1])
+ if not chemical_name:
+ chemical_name = 'Unknown'
+
+ # Write the HETNAM records.
+ file.write("%-6s %2s %3s %-55s\n" % ('HETNAM', '', het[1],
chemical_name))
+
+
+ # The FORMUL records.
+ #####################
+
+ # Print out.
+ print "Creating the FORMUL records."
+
+ # Loop over the non-standard residues and generate and write the
chemical formula.
+ residues = []
+ for het in het_data_coll:
+ # Test if the residue HETNAM record as already been written
(otherwise store its name).
+ if het[1] in residues:
+ continue
+ else:
+ residues.append(het[1])
+
+ # Initialise the chemical formula.
+ formula = ''
+
+ # Loop over the atoms.
+ for atom_count in het[4]:
+ formula = formula + atom_count[0] + `atom_count[1]`
+
+ # The FORMUL record (chemical formula).
+ file.write("%-6s %2s %3s %2s%1s%-51s\n" % ('FORMUL', het[0],
het[1], '', '', formula))
+
+
+ ######################
+ # Coordinate section #
+ ######################
# Loop over the structures.
for index in xrange(len(self.structural_data)):
r6725 - /branches/rdc_analysis/generic_fns/structure/internal.py