Author: bugman
Date: Wed Feb 20 14:37:40 2013
New Revision: 18525
URL: http://svn.gna.org/viewcvs/relax?rev=18525&view=rev
Log:
Improved PDB writing capabilities.
The functions of the generic_fns.structure.pdb_write module now all use the
_handle_none() function
to avoid the text "None" from appearing in the PDB file and
_record_validate() to be sure the record
has not been corrupted with bad input causing it to be either less or greater
than 80 characters.
Modified:
trunk/generic_fns/structure/pdb_write.py
Modified: trunk/generic_fns/structure/pdb_write.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/structure/pdb_write.py?rev=18525&r1=18524&r2=18525&view=diff
==============================================================================
--- trunk/generic_fns/structure/pdb_write.py (original)
+++ trunk/generic_fns/structure/pdb_write.py Wed Feb 20 14:37:40 2013
@@ -28,6 +28,9 @@
# Python module imports.
from textwrap import wrap
+# relax module imports.
+from relax_errors import RelaxError
+
def _handle_none(value):
"""Auxiliary function for handling values of None.
@@ -44,6 +47,22 @@
# Normal value.
return value
+
+
+def _record_validate(record):
+ """Check that the record is ok.
+
+ @param record: The PDB record as text.
+ @type record: str
+ @raises RelaxError: If the record is not exactly 80 characters long.
+ """
+
+ # Check the length.
+ if len(record) != 80:
+ if len(record) < 80:
+ raise RelaxError("The PDB record '%s' is too short." % record)
+ else:
+ raise RelaxError("The PDB record '%s' is too long." % record)
def atom(file, serial='', name='', alt_loc='', res_name='', chain_id='',
res_seq='', icode='', x='', y='', z='', occupancy='', temp_factor='',
element='', charge=''):
@@ -205,8 +224,31 @@
@type charge: int
"""
+ # The formatted record.
+ text = "%-6s%5s %-4s%1s%3s %1s%4s%1s %8.3f%8.3f%8.3f%6.2f%6.2f
%2s%2s" % (
+ 'ATOM',
+ _handle_none(serial),
+ _handle_none(name),
+ _handle_none(alt_loc),
+ _handle_none(res_name),
+ _handle_none(chain_id),
+ _handle_none(res_seq),
+ _handle_none(icode),
+ _handle_none(x),
+ _handle_none(y),
+ _handle_none(z),
+ _handle_none(occupancy),
+ _handle_none(temp_factor),
+ _handle_none(element),
+ _handle_none(charge)
+ )
+
+ # Validate.
+ _record_validate(text)
+
# Write out the formatted record.
- file.write("%-6s%5s %-4s%1s%3s %1s%4s%1s %8.3f%8.3f%8.3f%6.2f%6.2f
%2s%2s\n" % ('ATOM', serial, name, alt_loc, res_name, chain_id, res_seq,
icode, x, y, z, occupancy, temp_factor, element, charge))
+ file.write(text)
+ file.write('\n')
def conect(file, serial='', bonded1='', bonded2='', bonded3='', bonded4=''):
@@ -299,8 +341,22 @@
@type bonded4: int
"""
+ # The formatted record.
+ text = "%-6s%5s%5s%5s%5s%5s \n" % (
+ 'CONECT',
+ _handle_none(serial),
+ _handle_none(bonded1),
+ _handle_none(bonded2),
+ _handle_none(bonded3),
+ _handle_none(bonded4)
+ )
+
+ # Validate.
+ _record_validate(text)
+
# Write out the formatted record.
- file.write("%-6s%5s%5s%5s%5s%5s \n" %
('CONECT', serial, bonded1, bonded2, bonded3, bonded4))
+ file.write(text)
+ file.write('\n')
def end(file):
@@ -356,8 +412,15 @@
@type file: file object
"""
+ # The formatted record.
+ text = "END" + ' '*77
+
+ # Validate.
+ _record_validate(text)
+
# Write out the formatted record.
- file.write("END\n")
+ file.write(text)
+ file.write('\n')
def endmdl(file):
@@ -432,8 +495,15 @@
@type file: file object
"""
+ # The formatted record.
+ text = 'ENDMDL' + ' '*74
+
+ # Validate.
+ _record_validate(text)
+
# Write out the formatted record.
- file.write("%-6s\n" % 'ENDMDL')
+ file.write(text)
+ file.write('\n')
def formul(file, comp_num='', het_id='', continuation='', asterisk='',
text=''):
@@ -520,8 +590,22 @@
@type text: str
"""
+ # The formatted record.
+ text = "%-6s %2s %3s %2s%1s%-51s\n" % (
+ 'FORMUL',
+ _handle_none(comp_num),
+ _handle_none(het_id),
+ _handle_none(continuation),
+ _handle_none(asterisk),
+ _handle_none(text)
+ )
+
+ # Validate.
+ _record_validate(text)
+
# Write out the formatted record.
- file.write("%-6s %2s %3s %2s%1s%-51s\n" % ('FORMUL', comp_num, het_id,
continuation, asterisk, text))
+ file.write(text)
+ file.write('\n')
def helix(file, ser_num='', helix_id='', init_res_name='', init_chain_id='',
init_seq_id='', init_icode='', end_res_name='', end_chain_id='',
end_seq_num='', end_icode='', helix_class='', comment='', length=''):
@@ -655,6 +739,9 @@
_handle_none(length)
)
+ # Validate.
+ _record_validate(text)
+
# Write out the formatted record.
file.write(text)
file.write('\n')
@@ -754,8 +841,23 @@
@type text: str
"""
+ # The formatted record.
+ text = "%-6s %3s %1s%4s%1s %5s %-40s" % (
+ 'HET',
+ _handle_none(het_id),
+ _handle_none(chain_id),
+ _handle_none(seq_num),
+ _handle_none(icode),
+ _handle_none(num_het_atoms),
+ _handle_none(text)
+ )
+
+ # Validate.
+ _record_validate(text)
+
# Write out the formatted record.
- file.write("%-6s %3s %1s%4s%1s %5s %-40s\n" % ('HET', het_id,
chain_id, seq_num, icode, num_het_atoms, text))
+ file.write(text)
+ file.write('\n')
def hetatm(file, serial='', name='', alt_loc='', res_name='', chain_id='',
res_seq='', icode='', x='', y='', z='', occupancy='', temp_factor='',
element='', charge=''):
@@ -867,8 +969,31 @@
@type charge: int
"""
+ # The formatted record.
+ text = "%-6s%5s %4s%1s%3s %1s%4s%1s %8.3f%8.3f%8.3f%6.2f%6.2f
%2s%2s" % (
+ 'HETATM',
+ _handle_none(serial),
+ _handle_none(name),
+ _handle_none(alt_loc),
+ _handle_none(res_name),
+ _handle_none(chain_id),
+ _handle_none(res_seq),
+ _handle_none(icode),
+ _handle_none(x),
+ _handle_none(y),
+ _handle_none(z),
+ _handle_none(occupancy),
+ _handle_none(temp_factor),
+ _handle_none(element),
+ _handle_none(charge)
+ )
+
+ # Validate.
+ _record_validate(text)
+
# Write out the formatted record.
- file.write("%-6s%5s %4s%1s%3s %1s%4s%1s %8.3f%8.3f%8.3f%6.2f%6.2f
%2s%2s\n" % ('HETATM', serial, name, alt_loc, res_name, chain_id,
res_seq, icode, x, y, z, occupancy, temp_factor, element, charge))
+ file.write(text)
+ file.write('\n')
def hetnam(file, continuation='', het_id='', text=''):
@@ -951,8 +1076,20 @@
@type text: str
"""
+ # The formatted record.
+ text = "%-6s %2s %3s %-55s\n" % (
+ 'HETNAM',
+ _handle_none(continuation),
+ _handle_none(het_id),
+ _handle_none(text)
+ )
+
+ # Validate.
+ _record_validate(text)
+
# Write out the formatted record.
- file.write("%-6s %2s %3s %-55s\n" % ('HETNAM', continuation, het_id,
text))
+ file.write(text)
+ file.write('\n')
def master(file, num_remark=0, num_het=0, num_helix=0, num_sheet=0,
num_turn=0, num_site=0, num_xform=0, num_coord=0, num_ter=0, num_conect=0,
num_seq=0):
@@ -1044,8 +1181,29 @@
@type num_seq int
"""
+ # The formatted record.
+ text = "%-6s %5s%5s%5s%5s%5s%5s%5s%5s%5s%5s%5s%5s" % (
+ 'MASTER',
+ _handle_none(num_remark),
+ 0,
+ _handle_none(num_het),
+ _handle_none(num_helix),
+ _handle_none(num_sheet),
+ _handle_none(num_turn),
+ _handle_none(num_site),
+ _handle_none(num_xform),
+ _handle_none(num_coord),
+ _handle_none(num_ter),
+ _handle_none(num_conect),
+ _handle_none(num_seq)
+ )
+
+ # Validate.
+ _record_validate(text)
+
# Write out the formatted record.
- file.write("%-6s %5s%5s%5s%5s%5s%5s%5s%5s%5s%5s%5s%5s\n" % ('MASTER',
num_remark, 0, num_het, num_helix, num_sheet, num_turn, num_site, num_xform,
num_coord, num_ter, num_conect, num_seq))
+ file.write(text)
+ file.write('\n')
def model(file, serial=''):
@@ -1153,8 +1311,19 @@
@type serial: int
"""
+ # The formatted record.
+ text = "%-6s %4i%65s" % (
+ 'MODEL',
+ _handle_none(serial),
+ ''
+ )
+
+ # Validate.
+ _record_validate(text)
+
# Write out the formatted record.
- file.write("%-6s %4i\n" % ('MODEL', serial))
+ file.write(text)
+ file.write('\n')
def remark(file, num='', remark=''):
@@ -1190,9 +1359,17 @@
@type remark: str
"""
- # Write out the formatted record, splitting across lines if needed.
+ # The formatted record, splitting across lines if needed.
for line in wrap(remark, 68):
- file.write("%-6s %3s %-68s \n" % ("REMARK", num, line.upper()))
+ # The text.
+ text = "%-6s %3s %-68s " % ("REMARK", num, line.upper())
+
+ # Validate.
+ _record_validate(text)
+
+ # Write out the formatted record.
+ file.write(text)
+ file.write('\n')
def ter(file, serial='', res_name='', chain_id='', res_seq='', icode=''):
@@ -1287,4 +1464,18 @@
"""
# Write out the formatted record.
- file.write("%-6s%5s %3s %1s%4s%1s\n" % ('TER', serial, res_name,
chain_id, res_seq, icode))
+ text = "%-6s%5s %3s %1s%4s%1s" % (
+ 'TER',
+ _handle_none(serial),
+ _handle_none(res_name),
+ _handle_none(chain_id),
+ _handle_none(res_seq),
+ _handle_none(icode)
+ )
+
+ # Validate.
+ _record_validate(text)
+
+ # Write out the formatted record.
+ file.write(text)
+ file.write('\n')
r18525 - /trunk/generic_fns/structure/pdb_write.py