Author: bugman
Date: Thu Jan 22 15:45:02 2009
New Revision: 8593
URL: http://svn.gna.org/viewcvs/relax?rev=8593&view=rev
Log:
A large number of fixes for the write_pdb() method.
It can now handle the new structural data design.
Modified:
branches/multi_structure/generic_fns/structure/internal.py
Modified: branches/multi_structure/generic_fns/structure/internal.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_structure/generic_fns/structure/internal.py?rev=8593&r1=8592&r2=8593&view=diff
==============================================================================
--- branches/multi_structure/generic_fns/structure/internal.py (original)
+++ branches/multi_structure/generic_fns/structure/internal.py Thu Jan 22
15:45:02 2009
@@ -632,7 +632,7 @@
return True
- def write_pdb(self, file, struct_index=None):
+ def write_pdb(self, file, model_num=None):
"""Method for the creation of a PDB file from the structural data.
A number of PDB records including HET, HETNAM, FORMUL, HETATM, TER,
CONECT, MASTER, and END
@@ -650,9 +650,9 @@
@param file: The PDB file object. This object must be
writable.
@type file: file object
- @param struct_index: The index of the structural container to
write. If None, all
- structures will be written.
- @type struct_index: int
+ @keyword model_num: The model to place into the PDB file. If not
supplied, then all
+ models will be placed into the file.
+ @type model_num: None or int
"""
# Validate the structural data.
@@ -673,6 +673,11 @@
file.write("REMARK 40 CREATED BY RELAX (HTTP://NMR-RELAX.COM)\n")
num_remark = 2
+ # Determine if model records will be created.
+ model_records = False
+ if model_num == None and self.num_models() > 1:
+ model_records = True
+
####################
# Hetrogen section #
@@ -682,31 +687,25 @@
het_data = []
het_data_coll = []
- # Loop over the structures.
- for index in xrange(self.num):
- # Skip non-matching structures.
- if struct_index != None and struct_index != index:
- continue
-
- # Alias the structure container.
- struct = self.structural_data[index]
-
+ # Loop over the molecules of the first model.
+ index = 0
+ for mol in self.structural_data[0].mol:
# Check the validity of the data.
- self.__validate_data_arrays(struct)
-
- # Append an empty array for this structure.
+ self.__validate_data_arrays(mol)
+
+ # Append an empty array for this molecule.
het_data.append([])
# Collect the non-standard residue info.
- for i in xrange(len(struct.atom_name)):
+ for i in xrange(len(mol.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:
+ if mol.pdb_record[i] != 'HETATM' or mol.res_name[i] == None:
continue
# 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[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, []])
+ if not het_data[index] or not mol.res_num[i] ==
het_data[index][-1][0]:
+ het_data[index].append([mol.res_num[i], mol.res_name[i],
mol.chain_id[i], 0, []])
# Catch missing chain_ids.
if het_data[index][-1][2] == None:
@@ -718,16 +717,16 @@
# Find if the atom has already a count entry.
entry = False
for j in xrange(len(het_data[index][-1][4])):
- if struct.element[i] == het_data[index][-1][4][j][0]:
+ if mol.element[i] == het_data[index][-1][4][j][0]:
entry = True
# Create a new specific atom count entry.
if not entry:
- het_data[index][-1][4].append([struct.element[i], 0])
+ het_data[index][-1][4].append([mol.element[i], 0])
# Increment the specific atom count.
for j in xrange(len(het_data[index][-1][4])):
- if struct.element[i] == het_data[index][-1][4][j][0]:
+ if mol.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.
@@ -757,6 +756,9 @@
if not found:
het_data_coll.append(het_data[index][i])
+ # Increment the molecule index.
+ index = index + 1
+
# The HET records.
##################
@@ -823,86 +825,84 @@
# Coordinate section #
######################
- # Loop over the structures.
- for index in xrange(self.num):
- # Skip non-matching structures.
- if struct_index != None and struct_index != index:
+ # Loop over the models.
+ for model in self.structural_data:
+ # Single model.
+ if model_num and model_num != model.num:
continue
- # Alias the structure container.
- struct = self.structural_data[index]
-
-
- # MODEL record, for multiple structures.
- ########################################
-
- if not struct_index and len(self.structural_data) > 1:
+ # MODEL record, for multiple models.
+ ####################################
+
+ if model_records:
# Print out.
- print "\nMODEL " + `index+1`
+ print "\nMODEL %s" % model.num
# Write the model record.
- file.write("%-6s %4i\n" % ('MODEL', index+1))
+ file.write("%-6s %4i\n" % ('MODEL', model.num))
# Add the atomic coordinate records (ATOM, HETATM, and TER).
############################################################
- # Print out.
- print "ATOM, HETATM, TER"
-
- # Loop over the atomic data.
- for i in xrange(len(struct.atom_name)):
- # Aliases.
- 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:
- atom_name = ''
- if res_name == None:
- res_name = ''
- if chain_id == None:
- chain_id = ''
- if res_num == None:
- res_num = ''
- if x == None:
- x = ''
- if y == None:
- y = ''
- if z == None:
- z = ''
- if seg_id == None:
- seg_id = ''
- if element == None:
- element = ''
-
- # Write the ATOM record.
- if struct.pdb_record[i] == 'ATOM':
- 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', atom_num, atom_name, '',
res_name, chain_id, res_num, '', x, y, z, 1.0, 0, seg_id, element, ''))
- num_atom = num_atom + 1
-
- # Write the HETATM record.
- if struct.pdb_record[i] == 'HETATM':
- file.write("%-6s%5s %4s%1s%3s %1s%4s%1s
%8.3f%8.3f%8.3f%6.2f%6.2f %4s%2s%2s\n" % ('HETATM', atom_num, atom_name,
'', res_name, chain_id, res_num, '', x, y, z, 1.0, 0, seg_id, element, ''))
- num_hetatm = num_hetatm + 1
-
- # Finish off with the TER record.
- file.write("%-6s%5s %3s %1s%4s%1s\n" % ('TER', atom_num+1,
res_name, chain_id, res_num, ''))
- num_ter = num_ter + 1
+ # Loop over the molecules.
+ for mol in model.mol:
+ # Print out.
+ print "ATOM, HETATM, TER"
+
+ # Loop over the atomic data.
+ for i in xrange(len(mol.atom_name)):
+ # Aliases.
+ atom_num = mol.atom_num[i]
+ atom_name = mol.atom_name[i]
+ res_name = mol.res_name[i]
+ chain_id = mol.chain_id[i]
+ res_num = mol.res_num[i]
+ x = mol.x[i]
+ y = mol.y[i]
+ z = mol.z[i]
+ seg_id = mol.seg_id[i]
+ element = mol.element[i]
+
+ # Replace None with ''.
+ if atom_name == None:
+ atom_name = ''
+ if res_name == None:
+ res_name = ''
+ if chain_id == None:
+ chain_id = ''
+ if res_num == None:
+ res_num = ''
+ if x == None:
+ x = ''
+ if y == None:
+ y = ''
+ if z == None:
+ z = ''
+ if seg_id == None:
+ seg_id = ''
+ if element == None:
+ element = ''
+
+ # Write the ATOM record.
+ if mol.pdb_record[i] == 'ATOM':
+ 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', atom_num, atom_name, '',
res_name, chain_id, res_num, '', x, y, z, 1.0, 0, seg_id, element, ''))
+ num_atom = num_atom + 1
+
+ # Write the HETATM record.
+ if mol.pdb_record[i] == 'HETATM':
+ file.write("%-6s%5s %4s%1s%3s %1s%4s%1s
%8.3f%8.3f%8.3f%6.2f%6.2f %4s%2s%2s\n" % ('HETATM', atom_num, atom_name,
'', res_name, chain_id, res_num, '', x, y, z, 1.0, 0, seg_id, element, ''))
+ num_hetatm = num_hetatm + 1
+
+ # Finish off with the TER record.
+ file.write("%-6s%5s %3s %1s%4s%1s\n" % ('TER',
atom_num+1, res_name, chain_id, res_num, ''))
+ num_ter = num_ter + 1
# ENDMDL record, for multiple structures.
########################################
- if not struct_index and len(self.structural_data) > 1:
+ if model_records:
# Print out.
print "ENDMDL"
@@ -910,15 +910,18 @@
file.write("%-6s\n" % 'ENDMDL')
- # Create the CONECT records.
- ############################
-
- # Print out.
- print "CONECT"
-
- for i in xrange(len(struct.atom_name)):
+ # Create the CONECT records.
+ ############################
+
+ # Print out.
+ print "CONECT"
+
+ # Loop over the molecules of the first model.
+ for mol in self.structural_data[0].mol:
+ # Loop over the atoms.
+ for i in xrange(len(mol.atom_name)):
# No bonded atoms, hence no CONECT record is required.
- if not len(struct.bonded[i]):
+ if not len(mol.bonded[i]):
continue
# Initialise some data structures.
@@ -927,9 +930,9 @@
bonded = ['', '', '', '']
# Loop over the bonded atoms.
- for j in xrange(len(struct.bonded[i])):
+ for j in xrange(len(mol.bonded[i])):
# End of the array, hence create the CONECT record in this
iteration.
- if j == len(struct.bonded[i])-1:
+ if j == len(mol.bonded[i])-1:
flush = True
# Only four covalently bonded atoms allowed in one CONECT
record.
@@ -937,7 +940,7 @@
flush = True
# Get the bonded atom index.
- bonded[bonded_index] = struct.bonded[i][j]
+ bonded[bonded_index] = mol.bonded[i][j]
# Increment the bonded_index value.
bonded_index = bonded_index + 1
@@ -947,7 +950,7 @@
# Convert the atom indices to atom numbers.
for k in range(4):
if bonded[k] != '':
- bonded[k] = struct.atom_num[bonded[k]]
+ bonded[k] = mol.atom_num[bonded[k]]
# Write the CONECT record.
file.write("%-6s%5s%5s%5s%5s%5s%5s%5s%5s%5s%5s%5s\n" %
('CONECT', i+1, bonded[0], bonded[1], bonded[2], bonded[3], '', '', '', '', '',
''))
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