Author: bugman
Date: Thu Dec 18 15:24:05 2008
New Revision: 8220
URL: http://svn.gna.org/viewcvs/relax?rev=8220&view=rev
Log:
Redesigned the structure.read_pdb() arguments and docstring.
Modified:
branches/multi_structure/prompt/structure.py
Modified: branches/multi_structure/prompt/structure.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_structure/prompt/structure.py?rev=8220&r1=8219&r2=8220&view=diff
==============================================================================
--- branches/multi_structure/prompt/structure.py (original)
+++ branches/multi_structure/prompt/structure.py Thu Dec 18 15:24:05 2008
@@ -31,7 +31,7 @@
import generic_fns.structure.geometric
import generic_fns.structure.main
import help
-from relax_errors import RelaxBinError, RelaxBoolError, RelaxFloatError,
RelaxIntError, RelaxNoneIntError, RelaxNoneStrError, RelaxNumError,
RelaxStrError
+from relax_errors import RelaxBinError, RelaxBoolError, RelaxFloatError,
RelaxIntError, RelaxNoneIntError, RelaxNoneIntListIntError,
RelaxNoneStrError, RelaxNoneStrListStrError, RelaxNumError, RelaxStrError
class Structure:
@@ -311,7 +311,7 @@
generic_fns.structure.main.load_spins(spin_id=spin_id,
combine_models=combine_models, ave_pos=ave_pos)
- def read_pdb(self, file=None, dir=None, read_mol=None,
set_mol_names=None, read_model=None, set_model_nums=None,
parser='scientific'):
+ def read_pdb(self, file=None, dir=None, read_mol=None,
set_mol_name=None, read_model=None, set_model_num=None, parser='internal'):
"""The PDB loading function.
Keyword Arguments
@@ -323,11 +323,11 @@
read_mol: If set, only the given molecule(s) will be read.
- set_mol_names: Set the names of the read molecules.
+ set_mol_name: Set the names of the read molecules.
read_model: If set, only the given model number(s) from the PDB
file will be read.
- set_model_nums: Set the model numbers of the read molecules.
+ set_model_num: Set the model numbers of the read molecules.
parser: The PDB parser used to read the file.
@@ -335,33 +335,73 @@
Description
~~~~~~~~~~~
- To load a specific model from the PDB file, set the read_model flag
to an integer i. The
- structures beginning with the line 'MODEL i' in the PDB file will be
loaded and the model
- number for these structures will be set to i. If this argument is
not set, all structures
- from all models will be read.
-
- A few different PDB parsers can be used to read the structural data.
These are selected by
+ The reading of PDB files into relax is quite a flexible procedure
allowing for both models,
+ defined as an ensemble of the same molecule but with different
atomic positions, and
+ different molecules within the same model. One of more molecules
can exist in one or more
+ models. The flexibility allows PDB models to be converted into
different molecules and
+ different PDB files loaded as the same molecule but as different
models. This flexibility
+ is controlled by the four keyword arguments 'read_mol',
'set_mol_name', 'read_model', and
+ 'set_model_num'.
+
+ A few different PDB parsers can be used to read the structural data.
The choice of which to
+ use depends on whether your PDB file is supported by that reader.
These are selected by
setting the 'parser' argument to one of:
'scientific' - the Scientific Python PDB parser.
'internal' - a lower quality and less reliable, although faster,
PDB parser built into
relax.
-
- Example
- ~~~~~~~
-
- To load all structures from the PDB file 'test.pdb' in the directory
'~/pdb', type one of:
+ In a PDB file, the models are specified by the MODEL PDB record.
All the supported PDB
+ readers in relax recognise this. The molecule level is quite
different between the
+ Scientific Python and internal readers. For how Scientific Python
defines molecules, please
+ see its documentation. The internal reader is far simpler as it
defines molecules using the
+ TER PDB record. In both cases, the molecules will be numbered
consecutively from 1.
+
+ The 'set_mol_name' argument is used to name the molecules within the
PDB (within one
+ model). If not set, then the molecules will be named after the file
name, with the molecule
+ number appended if more than one exists.
+
+ Note that relax will complain if it cannot work out what to do.
+
+
+ Examples
+ ~~~~~~~~
+
+ To load all structures from the PDB file 'test.pdb' in the directory
'~/pdb', including all
+ models and all molecules, type one of:
relax> structure.read_pdb('test.pdb', '~/pdb')
relax> structure.read_pdb(file='test.pdb', dir='pdb')
- To load the 10th model from the file 'test.pdb' using the internal
relax parser, use one of:
-
- relax> structure.read_pdb('test.pdb', model=10, parser='internal')
- relax> structure.read_pdb(file='test.pdb', model=10,
parser='internal')
-
+ To load the 10th model from the file 'test.pdb' using the Scientific
Python PDB parser and
+ naming it 'CaM', use one of:
+
+ relax> structure.read_pdb('test.pdb', read_model=10,
set_mol_name='CaM',
+ parser='scientific')
+ relax> structure.read_pdb(file='test.pdb', read_model=10,
set_mol_name='CaM',
+ parser='scientific')
+
+
+ To load models 1 and 5 from the file 'test.pdb' as two different
structures of the same
+ model, type one of:
+
+ relax> structure.read_pdb('test.pdb', read_model=[1, 5],
set_model_num=[1, 1])
+ relax> structure.read_pdb('test.pdb', set_mol_name=['CaM_1',
'CaM_2'], read_model=[1, 5],
+ set_model_num=[1, 1])
+
+ To load the files 'lactose_MCMM4_S1_1.pdb', 'lactose_MCMM4_S1_2.pdb',
+ 'lactose_MCMM4_S1_3.pdb' and 'lactose_MCMM4_S1_4.pdb' as models,
type the following sequence
+ of commands:
+
+ relax> structure.read_pdb('lactose_MCMM4_S1_1.pdb',
set_mol_name='lactose_MCMM4_S1',
+ set_model_num=1)
+ relax> structure.read_pdb('lactose_MCMM4_S1_2.pdb',
set_mol_name='lactose_MCMM4_S1',
+ set_model_num=2)
+ relax> structure.read_pdb('lactose_MCMM4_S1_3.pdb',
set_mol_name='lactose_MCMM4_S1',
+ set_model_num=3)
+ relax> structure.read_pdb('lactose_MCMM4_S1_4.pdb',
set_mol_name='lactose_MCMM4_S1',
+ set_model_num=4)
"""
# Function intro text.
@@ -369,7 +409,10 @@
text = sys.ps3 + "structure.read_pdb("
text = text + "file=" + `file`
text = text + ", dir=" + `dir`
- text = text + ", model=" + `model`
+ text = text + ", read_mol=" + `read_mol`
+ text = text + ", set_mol_name=" + `set_mol_name`
+ text = text + ", read_model=" + `read_model`
+ text = text + ", set_model_num=" + `set_model_num`
text = text + ", parser=" + `parser` + ")"
print text
@@ -381,16 +424,44 @@
if dir != None and type(dir) != str:
raise RelaxNoneStrError, ('directory name', dir)
- # The model argument.
- if model != None and type(model) != int:
- raise RelaxNoneIntError, ('model', model)
+ # The read_mol, read_models, and set_model_num arguments.
+ arg_list = [read_mol, read_model, set_model_num]
+ arg_desc = ['read molecule number', 'read model', 'set model
numbers']
+ for i in range(len(arg_list)):
+ # Basic type check.
+ if arg_list[i] != None and type(arg_list[i]) != int and
type(arg_list[i]) != list:
+ raise RelaxNoneIntListIntError, (arg_desc[i], arg_list[i])
+
+ # List check.
+ if type(arg_list[i]) == list:
+ # Zero size list.
+ if len(arg_list[i]) == 0:
+ raise RelaxNoneIntListIntError, (arg_desc[i],
arg_list[i])
+
+ # Element check.
+ for j in range(len(arg_list[i])):
+ if type(arg_list[i][j]) != int:
+ raise RelaxNoneIntListIntError, (arg_desc[i],
arg_list[i])
+
+ # The set_mol_name arguments.
+ if set_mol_name != None and type(set_mol_name) != str and
type(set_mol_name) != list:
+ raise RelaxNoneStrListStrError, ('set molecule names',
set_mol_name)
+ if type(set_mol_name) == list:
+ # Zero size list.
+ if len(set_mol_name) == 0:
+ raise RelaxNoneStrListStrError, ('set molecule names',
set_mol_name)
+
+ # Element check.
+ for i in range(len(set_mol_name)):
+ if type(set_mol_name[i]) != str:
+ raise RelaxNoneStrListStrError, ('set molecule names',
set_mol_name)
# PDB parser.
if type(parser) != str:
raise RelaxStrError, ('PDB parser', parser)
# Execute the functional code.
- generic_fns.structure.main.read_pdb(file=file, dir=dir, model=model,
parser=parser)
+ generic_fns.structure.main.read_pdb(file=file, dir=dir,
read_mol=read_mol, set_mol_name=set_mol_name, read_model=read_model,
set_model_num=set_model_num, parser=parser)
def vectors(self, attached='H', spin_id=None, struct_index=None,
verbosity=1, ave=True, unit=True):
r8220 - /branches/multi_structure/prompt/structure.py