Author: bugman
Date: Tue Nov 7 06:25:38 2006
New Revision: 2755
URL: http://svn.gna.org/viewcvs/relax?rev=2755&view=rev
Log:
Using the new 'self.atomic_data' data structure, the tensor PDB file is now
created correctly.
The centre of mass atom, diffusion tensor representative atoms, and the atoms
representing the axes
now belong to separate residues, COM, TNS, and AXS respectively. A large
number of changes were
necessary to fix the breakages introduced by the change in 'self.atomic_data'.
The atom number in 'self.atomic_data' was one out.
The atom name for the tensor atoms was being set to the 'atom_id' string.
This was incorrect as the
protons should have been named H1, H2, H3, etc. The 'atom_id' string was too
long for the HETATM
record.
In the 'self.write_pdb_file()' function, the elements of the 'het_data'
structure used for
non-standard residues has been documented in the docstring. This structure
is now created prior to
the creation of the HET, HETNAM, and FORMUL records.
All the other records (HETATM, TER, CONECT, MASTER, END) are now correctly
created.
Modified:
branches/tensor_pdb/generic_fns/pdb.py
Modified: branches/tensor_pdb/generic_fns/pdb.py
URL:
http://svn.gna.org/viewcvs/relax/branches/tensor_pdb/generic_fns/pdb.py?rev=2755&r1=2754&r2=2755&view=diff
==============================================================================
--- branches/tensor_pdb/generic_fns/pdb.py (original)
+++ branches/tensor_pdb/generic_fns/pdb.py Tue Nov 7 06:25:38 2006
@@ -81,7 +81,7 @@
self.atomic_data[atom_id] = []
# Fill the positions.
- self.atomic_data[atom_id].append(len(self.atomic_data) + 1)
+ self.atomic_data[atom_id].append(len(self.atomic_data))
self.atomic_data[atom_id].append(atom_name)
self.atomic_data[atom_id].append(res_name)
self.atomic_data[atom_id].append(chain_id)
@@ -288,8 +288,9 @@
# Print out.
print "\nGenerating the geometric object."
- # Increment value.
+ # Increment value and initial atom number.
inc = 20
+ atom_num = 1
# Get the uniform vector distribution.
print " Creating the uniform vector distribution."
@@ -318,7 +319,7 @@
pos = R + vector
# Add the vector as a H atom of the TNS residue.
- self.atom_add(atom_id=atom_id, atom_name=atom_id,
res_name='TNS', chain_id=chain_id, res_num=res_num, pos=pos, element='H')
+ self.atom_add(atom_id=atom_id, atom_name='H'+`atom_num`,
res_name='TNS', chain_id=chain_id, res_num=res_num, pos=pos, element='H')
# Connect to the previous atom (to generate the longitudinal
lines).
if j != 0:
@@ -334,6 +335,9 @@
if i == inc-1:
neighbour_id = 'T' + `0` + 'P' + `j`
self.atom_connect(atom_id=atom_id,
bonded_id=neighbour_id)
+
+ # Increment the atom number.
+ atom_num = atom_num + 1
# Increment the residue number.
res_num = res_num + 1
@@ -470,7 +474,7 @@
# Unknown hetID.
raise RelaxError, "The residue ID (hetID) " + `hetID` + " is not
recognised."
-
+
def load_structures(self):
"""Function for loading the structures from the PDB file."""
@@ -881,7 +885,16 @@
============
A number of PDB records including HET, HETNAM, FORMUL, HETATM, TER,
CONECT, MASTER, and END
- are created.
+ are created. To create the non-standard residue records HET,
HETNAM, and FORMUL, the data
+ structure 'het_data' is created. It is an array of arrays where the
first dimension
+ corresponds to a different residue and the second dimension has the
elements:
+
+ 0: Residue number.
+ 1: Residue name.
+ 2: Chain ID.
+ 3: Total number of atoms in the residue.
+ 4: Number of H atoms in the residue.
+ 5: Number of C atoms in the residue.
The PDB records
@@ -978,7 +991,14 @@
TER record
----------
- The end of the ATOM and HETATM records. The format is of the record
is:
+ The end of the ATOM and HETATM records. According to the draft
atomic coordinate entry
+ format description:
+
+ "The TER record has the same residue name, chain identifier,
sequence number and insertion
+ code as the terminal residue. The serial number of the TER record is
one number greater than
+ the serial number of the ATOM/HETATM preceding the TER."
+
+ The format is of the record is:
__________________________________________________________________________________________
| | | |
|
| Columns | Data type | Field | Definition
|
@@ -1065,92 +1085,133 @@
@return: None
"""
- # The HET records.
- ##################
-
- # Get the data for the HET record.
- het_data = []
- for key in self.atomic_data:
- # The residue number.
- res_num = self.atomic_data[key][4]
-
- # If the residue is already stored, increment the number of
HETATM records and go to the next atom.
- exists = 0
- for i in xrange(len(het_data)):
- if res_num == het_data[i][2]:
- het_data[i][3] = het_data[i][3] + 1
- exists = 1
- if exists:
- continue
-
- # Add the data (residue name, chain ID, residue number, number
of atoms).
- het_data.append([self.atomic_data[key][2],
self.atomic_data[key][3], self.atomic_data[key][4], 1])
-
- # Write the HET record.
- for het in het_data:
- file.write("%-6s %3s %1s%4s%1s %5s %-40s\n" % ('HET',
het[0], het[1], het[2], '', het[3], ''))
-
-
- # The HETNAM records.
- #####################
-
- file.write("%-6s %2s %3s %-55s\n" % ('HETNAM', '', res_name,
chemical_name))
-
- # Count the elements.
+ # Sort the atoms.
+ #################
+
+ # Convert the self.atomic_data structure from a dictionary of arrays
to an array of arrays and sort it by atom number.
+ atomic_arrays = self.atomic_data.values()
+ atomic_arrays.sort()
+
+
+ # Collect the non-standard residue info.
+ ########################################
+
+ # Initialise some data.
H_count = 0
C_count = 0
- for key in self.atomic_data:
- # The element.
- element = self.atomic_data[key][1]
-
- # Protons.
+ het_data = []
+
+ # Loop over the atomic data.
+ for array in atomic_arrays:
+ # The residue number and element.
+ res_num = array[4]
+ element = array[9]
+
+ # 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).
+ if not het_data or not res_num == het_data[-1][0]:
+ het_data.append([array[4], array[2], array[3], 0, 0, 0])
+
+ # Total atom count.
+ het_data[-1][3] = het_data[-1][3] + 1
+
+ # Proton count.
if element == 'H':
- H_count = H_count + 1
-
- # Carbons.
+ het_data[-1][4] = het_data[-1][4] + 1
+
+ # Carbon count.
elif element == 'C':
- C_count = C_count + 1
+ het_data[-1][5] = het_data[-1][5] + 1
# Unsupported element type.
else:
raise RelaxError, "The element " + `element` + " was
expected to be one of ['H', 'C']."
- # Chemical formula.
- formula = ''
- if H_count:
- if formula:
- formula = formula + ' '
- formula = formula + 'H' + `H_count`
- if C_count:
- if formula:
- formula = formula + ' '
- formula = formula + 'C' + `C_count`
-
- # The FORMUL record (chemical formula).
- file.write("%-6s %2s %3s %2s%1s%-51s\n" % ('FORMUL', 1, res_name,
'', '', formula))
-
- # Convert the self.atomic_data structure from a dictionary of arrays
to an array of arrays and sort it by atom number.
- atomic_arrays = self.atomic_data.values()
- atomic_arrays.sort()
+ # Sort by residue number.
+ het_data.sort()
+
+
+ # 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.
+ for het in het_data:
+ # 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.
+ for het in het_data:
+ # Chemical formula.
+ formula = ''
+ if het[4]:
+ if formula:
+ formula = formula + ' '
+ formula = formula + 'H' + `het[4]`
+ if het[5]:
+ if formula:
+ formula = formula + ' '
+ formula = formula + 'C' + `het[5]`
+
+ # The FORMUL record (chemical formula).
+ file.write("%-6s %2s %3s %2s%1s%-51s\n" % ('FORMUL', het[0],
het[1], '', '', formula))
+
# Add the HETATM records.
+ #########################
+
+ # Print out.
+ print "Creating the HETATM records."
+
for array in atomic_arrays:
# Write the HETATM record.
- 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', array[0],
array[1]+`array[0]`, '', res_name, chain_id, res_num, '', array[2], array[3],
array[4], occupancy, 0, '', array[1], ''))
-
- # Terminate (TER record).
- file.write("%-6s%5s %3s %1s%4s%1s\n" % ('TER',
len(self.atomic_data)+1, res_name, chain_id, '', ''))
+ 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', array[0], array[1],
'', array[2], array[3], array[4], '', array[5], array[6], array[7],
occupancy, 0, array[8], array[9], ''))
+
+
+ # Terminate the chain - TER record.
+ ###################################
+
+ # Write the TER record.
+ file.write("%-6s%5s %3s %1s%4s%1s\n" % ('TER',
len(self.atomic_data)+1, array[2], array[3], array[4], ''))
+
# Create the CONECT records.
+ ############################
+
+ # Print out.
+ print "Creating the CONECT records."
+
connect_count = 0
for array in atomic_arrays:
# No bonded atoms, hence no CONECT record is required.
- if len(array) == 4:
+ if len(array) == 10:
continue
# The atom number.
atom_num = array[0]
-
# Initialise some data structures.
flush = 0
@@ -1158,9 +1219,9 @@
bonded = ['', '', '', '']
# Loop over the bonded atoms.
- for i in xrange(len(array[5:])):
+ for i in xrange(len(array[10:])):
# End of the array, hence create the CONECT record in this
iteration.
- if i == len(array[5:])-1:
+ if i == len(array[10:])-1:
flush = 1
# Only four covalently bonded atoms allowed in one CONECT
record.
@@ -1168,7 +1229,7 @@
flush = 1
# Get the bonded atom name.
- bonded[bonded_index] = array[i+5]
+ bonded[bonded_index] = array[i+10]
# Increment the bonded_index value.
bonded_index = bonded_index + 1
@@ -1188,7 +1249,20 @@
# MASTER record.
- file.write("%-6s %5s%5s%5s%5s%5s%5s%5s%5s%5s%5s%5s%5s\n" %
('MASTER', 0, 0, 1, 0, 0, 0, 0, 0, len(self.atomic_data), 1, connect_count,
0))
+ ################
+
+ # 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.atomic_data), 1,
connect_count, 0))
+
# END.
+ ######
+
+ # Print out.
+ print "Creating the END record."
+
+ # Write the END record.
file.write("END\n")
r2755 - /branches/tensor_pdb/generic_fns/pdb.py