Author: bugman
Date: Tue Mar 19 15:40:02 2013
New Revision: 18882
URL: http://svn.gna.org/viewcvs/relax?rev=18882&view=rev
Log:
Implemented the internal structural object _trim_helix() method.
This is used when the structure.delete user function is called to trim and
remove the helix
metadata. For this to work, the additional method _residue_data() was
written to create a
dictionary with residue numbers as keys and the residue names as numbers.
This dictionary is used
by _trim_helix() to change the residue names in the helix metadata.
Modified:
trunk/generic_fns/structure/internal.py
Modified: trunk/generic_fns/structure/internal.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/structure/internal.py?rev=18882&r1=18881&r2=18882&view=diff
==============================================================================
--- trunk/generic_fns/structure/internal.py (original)
+++ trunk/generic_fns/structure/internal.py Tue Mar 19 15:40:02 2013
@@ -23,6 +23,7 @@
"""Module containing the internal relax structural object."""
# Python module imports.
+from copy import deepcopy
from numpy import array, dot, float64, linalg, zeros
import os
from os import F_OK, access
@@ -682,6 +683,33 @@
return mol_index
+ def _residue_data(self, res_nums=None, res_names=None):
+ """Convert the residue info into a dictionary of unique residues
with numbers as keys.
+
+ @keyword res_nums: The list of residue numbers.
+ @type res_nums: list of int
+ @keyword res_names: The list of residue names matching the numbers.
+ @type res_names: list of str
+ @return: The dictionary of residue names with residue
numbers as keys.
+ @rtype: dict of str
+ """
+
+ # Initialise.
+ data = {}
+
+ # Loop over the data.
+ for i in range(len(res_nums)):
+ # The residue data already exists.
+ if res_nums[i] in data:
+ continue
+
+ # Add the data.
+ data[res_nums[i]] = res_names[i]
+
+ # Return the dictionary.
+ return data
+
+
def _validate_data_arrays(self, struct):
"""Check the validity of the data arrays in the given structure
object.
@@ -826,6 +854,68 @@
# Return the converted data.
return data
+
+
+ def _trim_helix(self, helix=None, trim_res_list=[], res_data=None):
+ """Trim the given helix based on the list of deleted residue numbers.
+
+ @keyword helix: The single helix metadata structure.
+ @type helix: list
+ @keyword trim_res_list: The list of residue numbers which no longer
exist.
+ @type trim_res_list: list of int
+ @keyword res_data: The dictionary of residue names with residue
numbers as keys.
+ @type res_data: dict of str
+ @return: The trimmed helix metadata structure, or
None if the whole helix is to be deleted.
+ @rtype: list or None
+ """
+
+ # Unpack the helix residue numbers.
+ start_res = helix[4]
+ end_res = helix[8]
+
+ # The reverse residue list.
+ trim_res_list_rev = deepcopy(trim_res_list)
+ trim_res_list_rev.reverse()
+
+ # The helix residues.
+ helix_res = list(range(start_res, end_res+1))
+
+ # Trim forwards.
+ for res_num in trim_res_list:
+ if res_num == start_res:
+ # Remove the residue.
+ helix_res.pop(0)
+
+ # No helix left.
+ if len(helix_res) == 0:
+ break
+
+ # Realias the starting residue.
+ start_res = helix_res[0]
+
+ # No helix left.
+ if len(helix_res) == 0:
+ return None
+
+ # Trim backwards.
+ for res_num in trim_res_list_rev:
+ if res_num == end_res:
+ helix_res.pop(-1)
+ end_res = helix_res[-1]
+
+ # Replace the starting and ending residues.
+ if start_res != helix[4]:
+ helix[4] = start_res
+ helix[2] = res_data[start_res]
+ if end_res != helix[8]:
+ helix[8] = end_res
+ helix[6] = res_data[end_res]
+
+ # The helix length.
+ helix[-1] = len(helix_res)
+
+ # Return the modified helix.
+ return helix
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):
@@ -1255,6 +1345,7 @@
sel_obj = Selection(atom_id)
# Loop over the models.
+ del_res_nums = []
for model in self.model_loop():
# Loop over the molecules.
for mol_index in range(len(model.mol)):
@@ -1268,6 +1359,9 @@
indices = []
for i in self.atom_loop(atom_id=atom_id,
model_num=model.num, index_flag=True):
indices.append(i)
+
+ # Generate a residue data dictionary for the metadata
trimming (prior to atom deletion).
+ res_data = self._residue_data(res_nums=mol.res_num,
res_names=mol.res_name)
# Loop over the reverse indices and pop out the data.
indices.reverse()
@@ -1279,11 +1373,34 @@
mol.element.pop(i)
mol.pdb_record.pop(i)
mol.res_name.pop(i)
- mol.res_num.pop(i)
+ del_res_nums.append(mol.res_num.pop(i))
mol.seg_id.pop(i)
mol.x.pop(i)
mol.y.pop(i)
mol.z.pop(i)
+
+ # Nothing more to do.
+ if not len(del_res_nums):
+ return
+
+ # Handle the helix metadata.
+ del_helix_indices = []
+ for i in range(len(self.helices)):
+ # Trim the helix.
+ helix = self._trim_helix(helix=self.helices[i],
trim_res_list=del_res_nums, res_data=res_data)
+
+ # Trimmed helix.
+ if helix != None:
+ self.helices[i] = helix
+
+ # No helix left.
+ else:
+ del_helix_indices.append(i)
+
+ # Loop over the reverse helix indices and pop out the data.
+ del_helix_indices.reverse()
+ for i in del_helix_indices:
+ self.helices.pop(i)
def get_molecule(self, molecule, model=None):
r18882 - /trunk/generic_fns/structure/internal.py