Author: bugman
Date: Sat Jul 5 00:30:36 2008
New Revision: 6702
URL: http://svn.gna.org/viewcvs/relax?rev=6702&view=rev
Log:
Converted the write_pdb() function to loop over all 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=6702&r1=6701&r2=6702&view=diff
==============================================================================
--- branches/rdc_analysis/generic_fns/structure/internal.py (original)
+++ branches/rdc_analysis/generic_fns/structure/internal.py Sat Jul 5
00:30:36 2008
@@ -687,230 +687,239 @@
@type struct_index: int
"""
- # Check the validity of the data.
- self.__validate_data_arrays()
-
-
- # 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(self.structural_data.atom_names)):
- # Catch the HETATM records.
- if self.structural_data.pdb_record[i] != 'HETATM':
+ # Loop over the structures.
+ for i in xrange(len(self.structural_data)):
+ # Skip non-matching structures.
+ if struct_index != None and struct_index != i:
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])
-
- # Total atom count.
- het_data[-1][3] = het_data[-1][3] + 1
-
- # Proton count.
- if self.structural_data.element[i] == 'H':
- het_data[-1][4] = het_data[-1][4] + 1
-
- # Carbon count.
- elif self.structural_data.element[i] == 'C':
- het_data[-1][5] = het_data[-1][5] + 1
-
- # Nitrogen count.
- elif self.structural_data.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']."
-
-
- # 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])
-
- # 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 = ''
-
- # Protons.
- if het[4]:
- if formula:
- formula = formula + ' '
- formula = formula + 'H' + `het[4]`
-
- # Carbon.
- if het[5]:
- if formula:
- formula = formula + ' '
- formula = formula + 'C' + `het[5]`
-
- # Nitrogen
- if het[6]:
- if formula:
- formula = formula + ' '
- formula = formula + 'N' + `het[6]`
-
- # The FORMUL record (chemical formula).
- file.write("%-6s %2s %3s %2s%1s%-51s\n" % ('FORMUL', het[0],
het[1], '', '', formula))
-
-
- # Add the atomic coordinate records (ATOM, HETATM, and TER).
- ############################################################
-
- # Print out.
- 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)):
- # 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]
-
- # 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 array[1] == '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, ''))
-
- # Write the HETATM record.
- if array[1] == '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, ''))
-
- # Write the TER record.
- if array[1] == 'TER':
- file.write("%-6s%5s %3s %1s%4s%1s\n" % ('TER',
atom_num, res_name, chain_id, res_num, ''))
-
-
- # Create the CONECT records.
- ############################
-
- # Print out.
- print "Creating the CONECT records."
-
- connect_count = 0
- for i in xrange(len(self.structural_data.atom_names)):
- # No bonded atoms, hence no CONECT record is required.
- if not len(self.structural_data.bonded[i]):
- continue
-
- # Initialise some data structures.
- flush = 0
- bonded_index = 0
- bonded = ['', '', '', '']
-
- # Loop over the bonded atoms.
- for j in xrange(len(self.structural_data.bonded[i])):
- # End of the array, hence create the CONECT record in this
iteration.
- if j == len(self.structural_data.bonded[i])-1:
- flush = 1
-
- # Only four covalently bonded atoms allowed in one CONECT
record.
- if bonded_index == 3:
- flush = 1
-
- # Get the bonded atom index.
- bonded[bonded_index] = self.structural_data.bonded[i][j]
-
- # Increment the bonded_index value.
- bonded_index = bonded_index + 1
-
- # Generate the CONECT record and increment the counter.
- if flush:
- # 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], '', '', '', '',
'', ''))
-
- # Increment the CONECT record count.
- connect_count = connect_count + 1
-
- # Reset the flush flag, the bonded atom count, and the
bonded atom names.
- flush = 0
- bonded_index = 0
- bonded = ['', '', '', '']
-
-
- # MASTER record.
- ################
-
- # Print out.
- 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))
+ # Alias the structure container.
+ struct = self.structural_data[i]
+
+ # Check the validity of the data.
+ self.__validate_data_arrays(struct)
+
+
+ # 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(self.structural_data.atom_names)):
+ # Catch the HETATM records.
+ if self.structural_data.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])
+
+ # Total atom count.
+ het_data[-1][3] = het_data[-1][3] + 1
+
+ # Proton count.
+ if self.structural_data.element[i] == 'H':
+ het_data[-1][4] = het_data[-1][4] + 1
+
+ # Carbon count.
+ elif self.structural_data.element[i] == 'C':
+ het_data[-1][5] = het_data[-1][5] + 1
+
+ # Nitrogen count.
+ elif self.structural_data.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']."
+
+
+ # 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])
+
+ # 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 = ''
+
+ # Protons.
+ if het[4]:
+ if formula:
+ formula = formula + ' '
+ formula = formula + 'H' + `het[4]`
+
+ # Carbon.
+ if het[5]:
+ if formula:
+ formula = formula + ' '
+ formula = formula + 'C' + `het[5]`
+
+ # Nitrogen
+ if het[6]:
+ if formula:
+ formula = formula + ' '
+ formula = formula + 'N' + `het[6]`
+
+ # The FORMUL record (chemical formula).
+ file.write("%-6s %2s %3s %2s%1s%-51s\n" % ('FORMUL',
het[0], het[1], '', '', formula))
+
+
+ # Add the atomic coordinate records (ATOM, HETATM, and TER).
+ ############################################################
+
+ # Print out.
+ 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)):
+ # 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]
+
+ # 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 array[1] == '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, ''))
+
+ # Write the HETATM record.
+ if array[1] == '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, ''))
+
+ # Write the TER record.
+ if array[1] == 'TER':
+ file.write("%-6s%5s %3s %1s%4s%1s\n" % ('TER',
atom_num, res_name, chain_id, res_num, ''))
+
+
+ # Create the CONECT records.
+ ############################
+
+ # Print out.
+ print "Creating the CONECT records."
+
+ connect_count = 0
+ for i in xrange(len(self.structural_data.atom_names)):
+ # No bonded atoms, hence no CONECT record is required.
+ if not len(self.structural_data.bonded[i]):
+ continue
+
+ # Initialise some data structures.
+ flush = 0
+ bonded_index = 0
+ bonded = ['', '', '', '']
+
+ # Loop over the bonded atoms.
+ for j in xrange(len(self.structural_data.bonded[i])):
+ # End of the array, hence create the CONECT record in
this iteration.
+ if j == len(self.structural_data.bonded[i])-1:
+ flush = 1
+
+ # Only four covalently bonded atoms allowed in one
CONECT record.
+ if bonded_index == 3:
+ flush = 1
+
+ # Get the bonded atom index.
+ bonded[bonded_index] = self.structural_data.bonded[i][j]
+
+ # Increment the bonded_index value.
+ bonded_index = bonded_index + 1
+
+ # Generate the CONECT record and increment the counter.
+ if flush:
+ # 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], '', '', '', '',
'', ''))
+
+ # Increment the CONECT record count.
+ connect_count = connect_count + 1
+
+ # Reset the flush flag, the bonded atom count, and
the bonded atom names.
+ flush = 0
+ bonded_index = 0
+ bonded = ['', '', '', '']
+
+
+ # MASTER record.
+ ################
+
+ # Print out.
+ 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))
# END.
r6702 - /branches/rdc_analysis/generic_fns/structure/internal.py