Author: bugman
Date: Fri Oct 28 16:10:16 2011
New Revision: 14940
URL: http://svn.gna.org/viewcvs/relax?rev=14940&view=rev
Log:
Created the structure.add_atom user function.
This simply exposes some of the functionality of the structural API to the
user. The get_molecule()
API method has also been added to return molecule containers.
Modified:
1.3/generic_fns/structure/api_base.py
1.3/generic_fns/structure/internal.py
1.3/generic_fns/structure/main.py
1.3/prompt/structure.py
Modified: 1.3/generic_fns/structure/api_base.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/api_base.py?rev=14940&r1=14939&r2=14940&view=diff
==============================================================================
--- 1.3/generic_fns/structure/api_base.py (original)
+++ 1.3/generic_fns/structure/api_base.py Fri Oct 28 16:10:16 2011
@@ -248,6 +248,21 @@
model_cont = self.structural_data[-1]
+ def get_molecule(self, molecule, model=None):
+ """Return the molecule.
+
+ @param molecule: The molecule name.
+ @type molecule: int or None
+ @keyword model: The model number.
+ @type model: int or None
+ @return: The MolContainer corresponding to the molecule
name and model number.
+ @rtype: MolContainer instance or None
+ """
+
+ # Raise the error.
+ raise RelaxImplementError
+
+
def load_pdb(self, file_path, read_mol=None, set_mol_name=None,
read_model=None, set_model_num=None, verbosity=False):
"""Prototype method stub for loading structures from a PDB file.
Modified: 1.3/generic_fns/structure/internal.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/internal.py?rev=14940&r1=14939&r2=14940&view=diff
==============================================================================
--- 1.3/generic_fns/structure/internal.py (original)
+++ 1.3/generic_fns/structure/internal.py Fri Oct 28 16:10:16 2011
@@ -341,7 +341,7 @@
# Init.
total_atom = 0
- model = 0
+ model = 0
records = []
# Loop over the data.
@@ -565,23 +565,64 @@
# None values.
if data == None:
data = ''
-
+
# Force convert to string.
if not isinstance(data, str):
data = repr(data)
-
+
# Conversion to float.
if format == 'float':
# None values.
if data == None:
data = 0.0
-
+
# Force convert to float.
if not isinstance(data, float):
data = float(data)
# Return the converted data.
return data
+
+
+ def add_atom(self, mol_name=None, atom_name=None, res_name=None,
res_num=None, pos=[None, None, None], element=None, atom_num=None,
chain_id=None, segment_id=None, pdb_record=None):
+ """Add a new atom to the structural data object.
+
+ @keyword mol_name: The name of the molecule.
+ @type mol_name: str
+ @keyword atom_name: The atom name, e.g. 'H1'.
+ @type atom_name: str or None
+ @keyword res_name: The residue name.
+ @type res_name: str or None
+ @keyword res_num: The residue number.
+ @type res_num: int or None
+ @keyword pos: The position vector of coordinates.
+ @type pos: list (length = 3)
+ @keyword element: The element symbol.
+ @type element: str or None
+ @keyword atom_num: The atom number.
+ @type atom_num: int or None
+ @keyword chain_id: The chain identifier.
+ @type chain_id: str or None
+ @keyword segment_id: The segment identifier.
+ @type segment_id: str or None
+ @keyword pdb_record: The optional PDB record name, e.g. 'ATOM' or
'HETATM'.
+ @type pdb_record: str or None
+ """
+
+ # Test if the current data pipe exists.
+ pipes.test()
+
+ # Add the molecule, if it does not exist.
+ if cdp.structure.get_molecule(mol_name) == None:
+ cdp.structure.add_molecule(name=mol_name)
+
+ # Loop over each model.
+ for model in self.structural_data:
+ # Specific molecule.
+ mol = cdp.structure.get_molecule(mol_name)
+
+ # Add the atom.
+ mol.atom_add(atom_name=atom_name, res_name=res_name,
res_num=res_num, pos=pos, element=element, atom_num=atom_num,
chain_id=chain_id, segment_id=segment_id, pdb_record=pdb_record)
def atom_loop(self, atom_id=None, str_id=None, model_num=None,
model_num_flag=False, mol_name_flag=False, res_num_flag=False,
res_name_flag=False, atom_num_flag=False, atom_name_flag=False,
element_flag=False, pos_flag=False, ave=False):
@@ -755,7 +796,7 @@
if index != None:
# Get the atom bonded to this
model/molecule/residue/atom.
bonded_num, bonded_name, element, pos, attached_name,
warnings = self.__bonded_atom(attached_atom, index, mol)
-
+
# No bonded atom.
if (bonded_num, bonded_name, element) == (None, None,
None):
continue
@@ -793,6 +834,38 @@
# Initialise the empty model list.
self.structural_data = ModelList()
+
+
+ def get_molecule(self, molecule, model=None):
+ """Return the molecule.
+
+ Only one model can be specified.
+
+
+ @param molecule: The molecule name.
+ @type molecule: int or None
+ @keyword model: The model number.
+ @type model: int or None
+ @raises RelaxError: If the model is not specified and there is more
than one model loaded.
+ @return: The MolContainer corresponding to the molecule
name and model number.
+ @rtype: MolContainer instance or None
+ """
+
+ # Check if the target is a single molecule.
+ if model == None and self.num_models() > 1:
+ raise RelaxError("The target molecule cannot be determined as
there are %s models already present." % self.num_modes())
+
+ # No models.
+ if not len(self.structural_data):
+ return
+
+ # Loop over the models.
+ for model_cont in self.model_loop(model):
+ # Loop over the molecules.
+ for mol in model_cont.mol:
+ # Return the matching molecule.
+ if mol.mol_name == molecule:
+ return mol
def load_pdb(self, file_path, read_mol=None, set_mol_name=None,
read_model=None, set_model_num=None, verbosity=False):
@@ -967,7 +1040,7 @@
for model_records in self.__parse_models_xyz(file_path):
# Increment the xyz_model_increment
xyz_model_increment = xyz_model_increment +1
-
+
# Only load the desired model.
if read_model and xyz_model_increment not in read_model:
continue
@@ -1012,7 +1085,7 @@
# Loading worked.
return True
-
+
def rotate(self, R=None, origin=None, model=None):
"""Rotate the structural information about the given origin.
@@ -1150,7 +1223,7 @@
# Find if the atom has already a count entry.
entry = False
- for j in xrange(len(het_data[index][-1][4])):
+ for j in xrange(len(het_data[index][-1][4])):
if mol.element[i] == het_data[index][-1][4][j][0]:
entry = True
@@ -1159,7 +1232,7 @@
het_data[index][-1][4].append([mol.element[i], 0])
# Increment the specific atom count.
- for j in xrange(len(het_data[index][-1][4])):
+ for j in xrange(len(het_data[index][-1][4])):
if mol.element[i] == het_data[index][-1][4][j][0]:
het_data[index][-1][4][j][1] =
het_data[index][-1][4][j][1] + 1
@@ -1716,35 +1789,35 @@
fields[2] = float(fields[2])
if fields[3]:
fields[3] = float(fields[3])
-
+
# Return the atomic info.
return fields
- def atom_add(self, pdb_record=None, atom_num=None, atom_name=None,
res_name=None, chain_id=None, res_num=None, pos=[None, None, None],
segment_id=None, element=None):
+ def atom_add(self, atom_name=None, res_name=None, res_num=None,
pos=[None, None, None], element=None, atom_num=None, chain_id=None,
segment_id=None, pdb_record=None):
"""Method for adding an atom to the structural data object.
This method will create the key-value pair for the given atom.
- @keyword pdb_record: The optional PDB record name, e.g. 'ATOM' or
'HETATM'.
- @type pdb_record: str or None
- @keyword atom_num: The atom number.
- @type atom_num: int or None
@keyword atom_name: The atom name, e.g. 'H1'.
@type atom_name: str or None
@keyword res_name: The residue name.
@type res_name: str or None
- @keyword chain_id: The chain identifier.
- @type chain_id: str or None
@keyword res_num: The residue number.
@type res_num: int or None
@keyword pos: The position vector of coordinates.
@type pos: list (length = 3)
+ @keyword element: The element symbol.
+ @type element: str or None
+ @keyword atom_num: The atom number.
+ @type atom_num: int or None
+ @keyword chain_id: The chain identifier.
+ @type chain_id: str or None
@keyword segment_id: The segment identifier.
@type segment_id: str or None
- @keyword element: The element symbol.
- @type element: str or None
+ @keyword pdb_record: The optional PDB record name, e.g. 'ATOM' or
'HETATM'.
+ @type pdb_record: str or None
"""
# Append to all the arrays.
@@ -1773,7 +1846,7 @@
@keyword index2: The index of the second atom.
@type index2: int
"""
-
+
# Update the bonded array structure, if necessary.
if index2 not in self.bonded[index1]:
self.bonded[index1].append(index2)
@@ -1828,7 +1901,7 @@
# initialisation for atom number
atom_number = 1
-
+
# Loop over the records.
for record in records:
# Parse the record.
Modified: 1.3/generic_fns/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/main.py?rev=14940&r1=14939&r2=14940&view=diff
==============================================================================
--- 1.3/generic_fns/structure/main.py (original)
+++ 1.3/generic_fns/structure/main.py Fri Oct 28 16:10:16 2011
@@ -42,6 +42,41 @@
from relax_io import get_file_path, open_write_file, write_spin_data
from relax_warnings import RelaxWarning, RelaxNoPDBFileWarning,
RelaxZeroVectorWarning
+
+def add_atom(mol_name=None, atom_name=None, res_name=None, res_num=None,
pos=[None, None, None], element=None, atom_num=None, chain_id=None,
segment_id=None, pdb_record=None):
+ """Add a new atom to the structural data object.
+
+ @keyword mol_name: The name of the molecule.
+ @type mol_name: str
+ @keyword atom_name: The atom name, e.g. 'H1'.
+ @type atom_name: str or None
+ @keyword res_name: The residue name.
+ @type res_name: str or None
+ @keyword res_num: The residue number.
+ @type res_num: int or None
+ @keyword pos: The position vector of coordinates.
+ @type pos: list (length = 3)
+ @keyword element: The element symbol.
+ @type element: str or None
+ @keyword atom_num: The atom number.
+ @type atom_num: int or None
+ @keyword chain_id: The chain identifier.
+ @type chain_id: str or None
+ @keyword segment_id: The segment identifier.
+ @type segment_id: str or None
+ @keyword pdb_record: The optional PDB record name, e.g. 'ATOM' or
'HETATM'.
+ @type pdb_record: str or None
+ """
+
+ # Test if the current data pipe exists.
+ pipes.test()
+
+ # Place the structural object into the relax data store if needed.
+ if not hasattr(cdp, 'structure'):
+ cdp.structure = Internal()
+
+ # Add the atoms.
+ cdp.structure.add_atom(mol_name=mol_name, atom_name=atom_name,
res_name=res_name, res_num=res_num, pos=pos, element=element,
atom_num=atom_num, chain_id=chain_id, segment_id=segment_id,
pdb_record=pdb_record)
def delete():
Modified: 1.3/prompt/structure.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/structure.py?rev=14940&r1=14939&r2=14940&view=diff
==============================================================================
--- 1.3/prompt/structure.py (original)
+++ 1.3/prompt/structure.py Fri Oct 28 16:10:16 2011
@@ -34,6 +34,55 @@
class Structure(User_fn_class):
"""Class containing the structural related functions."""
+ def add_atom(self, atom_name=None, res_name=None, res_num=None,
pos=[None, None, None], element=None, atom_num=None, chain_id=None,
segment_id=None, pdb_record=None):
+ # Function intro text.
+ if self._exec_info.intro:
+ text = self._exec_info.ps3 + "structure.add_atom("
+ text = text + "atom_name=" + repr(atom_name)
+ text = text + ", res_name=" + repr(res_name)
+ text = text + ", res_num=" + repr(res_num)
+ text = text + ", pos=" + repr(pos)
+ text = text + ", element=" + repr(element)
+ text = text + ", atom_num=" + repr(atom_num)
+ text = text + ", chain_id=" + repr(chain_id)
+ text = text + ", segment_id=" + repr(segment_id)
+ text = text + ", pdb_record=" + repr(pdb_record) + ")"
+ print(text)
+
+ # The argument checks.
+ arg_check.is_str(atom_name, 'atom name')
+ arg_check.is_str(res_name, 'residue name')
+ arg_check.is_int(res_num, 'residue number')
+ arg_check.is_float_array(pos, 'atomic position', size=3)
+ arg_check.is_str(element, 'element', can_be_none=True)
+ arg_check.is_int(atom_num, 'atom number', can_be_none=True)
+ arg_check.is_str(chain_id, 'chain ID', can_be_none=True)
+ arg_check.is_str(segment_id, 'segment_id', can_be_none=True)
+ arg_check.is_str(pdb_record, 'pdb_record', can_be_none=True)
+
+ # Execute the functional code.
+ generic_fns.structure.main.add_atom(atom_name=atom_name,
res_name=res_name, res_num=res_num, pos=pos, element=element,
atom_num=atom_num, chain_id=chain_id, segment_id=segment_id,
pdb_record=pdb_record)
+
+ # The function doc info.
+ add_atom._doc_title = "Add an atom."
+ add_atom._doc_title_short = "Atom creation."
+ add_atom._doc_args = [
+ ["atom_name", "The atom name."],
+ ["res_name", "The residue name."],
+ ["res_num", "The residue number."],
+ ["pos", "The atomic coordinates."],
+ ["element", "The element name."],
+ ["atom_num", "The optional atom number."],
+ ["chain_id", "The optional chain ID string."],
+ ["segment_id", "The optional segment ID string."],
+ ["pdb_record", "The optional PDB record name, e.g. 'ATOM' or
'HETATM'."]
+ ]
+ add_atom._doc_desc = """
+ This allows
+ """
+ _build_doc(add_atom)
+
+
def create_diff_tensor_pdb(self, scale=1.8e-6, file='tensor.pdb',
dir=None, force=False):
# Function intro text.
if self._exec_info.intro:
r14940 - in /1.3: generic_fns/structure/ prompt/