Author: bugman
Date: Sun Oct 29 03:51:46 2006
New Revision: 2681
URL: http://svn.gna.org/viewcvs/relax?rev=2681&view=rev
Log:
A overhaul of the handling of the tensor PDB atomic data and how atoms are
added and connected.
A new data structure called 'self.atomic_data' has been created to store all
the atomic data. The
data structure is a dictionary of arrays. The key is a string corresponding
to the 'atom_id'. The
elements of the array are:
0: Atom number.
1: Element type.
2: The x coordinate of the atom.
3: The y coordinate of the atom.
4: The z coordinate of the atom.
5+: The bonded atom numbers.
Two new functions have been added to maintain the 'self.atomic_data'
structure. The first is
'self.atom_add()' which creates a key-value pair within the data structure
for the given atom adding
the atom number, element type, and coordinates of the atom.
The second function is 'self.atom_connect()'. Two arguments are expected,
the 'atom_id' and
'bonded_id' strings. The atom number corresponding to 'bonded_id' is added
to the 'atom_id' array
and vice versa.
The centre of mass atom is now added using the 'self.atom_add()' function.
The atom corresponding
to the unique axis of the spheroid ('Dpar_vect') is also added using this
function. These two atoms
are connected using 'self.atom_connect()'.
The 'self.write_pdb_file()' function has been modified accordingly.
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=2681&r1=2680&r2=2681&view=diff
==============================================================================
--- branches/tensor_pdb/generic_fns/pdb.py (original)
+++ branches/tensor_pdb/generic_fns/pdb.py Sun Oct 29 03:51:46 2006
@@ -37,6 +37,80 @@
self.print_flag = 1
+ def atom_add(self, atom_id, element, pos):
+ """Function for adding an atom to the self.atomic_data structure.
+
+ The self.atomic_data data structure is a dictionary of arrays. The
keys correspond to the
+ 'atom_id' strings. The elements of the array are:
+
+ 0: Atom number.
+
+ 1: Element type.
+
+ 2: The x coordinate of the atom.
+
+ 3: The y coordinate of the atom.
+
+ 4: The z coordinate of the atom.
+
+ 5 onwards: The bonded atom numbers.
+
+ This function will create the key-value pair for the atom.
+
+ """
+
+ # Create the key-value pair.
+ # The array elements added are:
+ # The atom number (length of the structure + 1).
+ # The element type.
+ # The coordinates.
+ self.atomic_data[atom_id] = [len(self.atomic_data) + 1, element,
pos[0], pos[1], pos[2]]
+
+
+ def atom_connect(self, atom_id, bonded_id):
+ """Function for connecting two atoms within the self.atomic_data
data structure.
+
+ The self.atomic_data data structure is a dictionary of arrays. The
keys correspond to the
+ 'atom_id' strings. The elements of the array are:
+
+ 0: Atom number.
+
+ 1: Element type.
+
+ 2: The x coordinate of the atom.
+
+ 3: The y coordinate of the atom.
+
+ 4: The z coordinate of the atom.
+
+ 5 onwards: The bonded atom numbers.
+
+ This function will find the atom number corresponding to both the
atom_id and bonded_id.
+ The bonded_id atom number will then be appended to the atom_id
array. Because the
+ connections work both ways in the PDB file, the atom_id atom number
will be appended to the
+ bonded_id atom array as well.
+
+ """
+
+ # Find the atom number corresponding to atom_id.
+ if self.atomic_data.has_key(atom_id):
+ atom_num = self.atomic_data[atom_id][0]
+ else:
+ raise RelaxError, "The atom corresponding to the atom_id " +
`atom_id` + " doesn't exist."
+
+ # Find the atom number corresponding to bonded_id.
+ if self.atomic_data.has_key(bonded_id):
+ bonded_num = self.atomic_data[bonded_id][0]
+ else:
+ raise RelaxError, "The atom corresponding to the bonded_id " +
`bonded_id` + " doesn't exist."
+
+ # Add the bonded_id to the atom_id array.
+ self.atomic_data[atom_id].append(bonded_num)
+
+ # Add the atom_id to the bonded_id array.
+ self.atomic_data[bonded_id].append(atom_num)
+
+
def atomic_mass(self, element=None):
"""Return the atomic mass of the given element."""
@@ -156,11 +230,10 @@
# Initialise the PDB data.
##########################
- # PDB HETATM and CONECT data.
- hetatm = []
- conect = []
-
- # Chain ID, residue number, residue name.
+ # The atom and atomic connections data structures.
+ self.atomic_data = {}
+
+ # Chain ID, residue number, residue name, chemical name, occupancy,
and default element.
chain_id = 'A'
res_num = 1
res_name = 'TNS'
@@ -176,7 +249,7 @@
R = self.center_of_mass()
# Add the central atom.
- hetatm.append([R, 'C'])
+ self.atom_add(atom_id='R', element='C', pos=R)
# Axes of the tensor.
@@ -196,8 +269,9 @@
# Position relative to the center of mass.
pos = R + Dpar_vect
- # Add the position as a HETATM.
- hetatm.append([pos, 'C'])
+ # Add the atom and connect it to the center of mass.
+ self.atom_add(atom_id='Dpar', element='C', pos=pos)
+ self.atom_connect(atom_id='Dpar', bonded_id='R')
# Print out.
print " Scaling factor: " + `scale`
@@ -207,13 +281,6 @@
print
- # Connectivities.
- #################
-
- conect.append(['1', '2'])
- conect.append(['2', '1'])
-
-
# Create the PDB file.
######################
@@ -221,7 +288,7 @@
tensor_pdb_file = self.relax.IO.open_write_file(self.file, self.dir,
force=self.force)
# Write the data.
- self.write_pdb_file(tensor_pdb_file, hetatm, conect, chain_id,
res_num, res_name, chemical_name, occupancy)
+ self.write_pdb_file(tensor_pdb_file, chain_id, res_num, res_name,
chemical_name, occupancy)
# Close the file.
tensor_pdb_file.close()
@@ -557,11 +624,11 @@
data.xh_vect = ave_vector / sqrt(dot(ave_vector, ave_vector))
- def write_pdb_file(self, file, hetatm, conect, chain_id, res_num,
res_name, chemical_name, occupancy):
+ def write_pdb_file(self, file, chain_id, res_num, res_name,
chemical_name, occupancy):
"""Function for creating a PDB file from the given data."""
# The HET record.
- file.write("%-6s %3s %1s%4s%1s %5s %-40s\n" % ('HET',
res_name, chain_id, res_num, '', len(hetatm), ''))
+ file.write("%-6s %3s %1s%4s%1s %5s %-40s\n" % ('HET',
res_name, chain_id, res_num, '', len(self.atomic_data), ''))
# The HETNAM record.
file.write("%-6s %2s %3s %-55s\n" % ('HETNAM', '', res_name,
chemical_name))
@@ -569,11 +636,19 @@
# Count the elements.
H_count = 0
C_count = 0
- for vector, element in hetatm:
+ for key in self.atomic_data:
+ # The element.
+ element = self.atomic_data[key][1]
+
+ # Protons.
if element == 'H':
H_count = H_count + 1
+
+ # Carbons.
elif element == 'C':
C_count = C_count + 1
+
+ # Unsupported element type.
else:
raise RelaxError, "The element " + `element` + " was
expected to be one of ['H', 'C']."
@@ -591,49 +666,54 @@
# The FORMUL record (chemical formula).
file.write("%-6s %2s %3s %2s%1s%-51s\n" % ('FORMUL', 1, res_name,
'', '', formula))
- # Loop over the HETATMs.
- serial_num = 1
- for vector, element in hetatm:
+ # Add the HETATM records.
+ for key in self.atomic_data:
# 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', serial_num,
element+`serial_num`, '', res_name, chain_id, res_num, '', vector[0],
vector[1], vector[2], occupancy, 0, '', element, ''))
-
- # Increment the atom number.
- serial_num = serial_num + 1
+ 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',
self.atomic_data[key][0],
self.atomic_data[key][1]+`self.atomic_data[key][0]`, '', res_name, chain_id,
res_num, '', self.atomic_data[key][2], self.atomic_data[key][3],
self.atomic_data[key][4], occupancy, 0, '', self.atomic_data[key][1], ''))
# Terminate (TER record).
- file.write("%-6s%5s %3s %1s%4s%1s\n" % ('TER', serial_num,
res_name, chain_id, '', ''))
-
- # Loop over the connections.
- for array in conect:
- # The atom.
- atom_serial_num = array[0]
+ file.write("%-6s%5s %3s %1s%4s%1s\n" % ('TER',
len(self.atomic_data)+1, res_name, chain_id, '', ''))
+
+ # Create the CONECT records.
+ connect_count = 0
+ for key in self.atomic_data:
+ # The atom number.
+ atom_num = self.atomic_data[key][0]
# First bonded atom.
- bonded1 = array[1]
+ if len(self.atomic_data[key]) > 5:
+ bonded1 = self.atomic_data[key][5]
+
+ # No CONECT record required!
+ else:
+ continue
# Second bonded atom.
- if len(array) > 2:
- bonded2 = array[2]
+ if len(self.atomic_data[key]) > 6:
+ bonded2 = self.atomic_data[key][6]
else:
bonded2 = ''
# Third bonded atom.
- if len(array) > 3:
- bonded3 = array[3]
+ if len(self.atomic_data[key]) > 7:
+ bonded3 = self.atomic_data[key][7]
else:
bonded3 = ''
# Forth bonded atom.
- if len(array) > 4:
- bonded4 = array[4]
+ if len(self.atomic_data[key]) > 8:
+ bonded4 = self.atomic_data[key][8]
else:
bonded4 = ''
# Write the CONECT record.
- file.write("%-6s%5s%5s%5s%5s%5s%5s%5s%5s%5s%5s%5s\n" %
('CONECT', atom_serial_num, bonded1, bonded2, bonded3, bonded4, '', '', '',
'', '', ''))
+ file.write("%-6s%5s%5s%5s%5s%5s%5s%5s%5s%5s%5s%5s\n" %
('CONECT', atom_num, bonded1, bonded2, bonded3, bonded4, '', '', '', '', '',
''))
+
+ # Increment the CONECT record count.
+ connect_count = connect_count + 1
# 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(hetatm), 1, len(conect), 0))
+ 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))
# END.
file.write("END\n")
r2681 - /branches/tensor_pdb/generic_fns/pdb.py