Coverage for /home/pedror/MMS@FCUL/pypka/pypka/titsite.py : 79%

Hot-keys on this page
r m x p toggle line displays
j k next/prev highlighted chunk
0 (zero) top of page
1 (one) first highlighted chunk
"""Titrable Site with more than one Tautomer""" """ Args: res_number (int): number of the site in the .pdb and .sites file molecule (TitratingMolecule): molecule to which the Site belongs
# Site Details self._res_name (str): residue name self._type (str): site type ('c' or 'a') 'c' if site is cationic 'a' if site is anionic self._center (list) : Site focus center if dimension is 0, then center is defined in cent file elif dimension is 2, then center (z) is defined in cent file and center (x, y) are defined in boxsize variable self._center_original (list): Site geometric center on cent file when dimension is 2
# Site Tautomers self._tautomers (dict): tautomers of Site (except reference tautomer) key is tautomer name value is tautomer instance self._ref_tautomer (Tautomer): reference tautomer instance
# Site Atoms self._atoms (dict): existing atoms in site key is atom id name value is atom id number """
# Set Methods """Adds Tautomers from res_tauts to self._tautomers
Args: res_tauts (list): tautomers from sites file """ for tautomer in res_tauts: self._res_name = tautomer[:3] correct_number = str(int(tautomer[-1]) - 1) tautomer = tautomer[:2] + correct_number
tID = Tautomer(tautomer, self, self._molecule) self._tautomers[tautomer] = tID
"""Adds Tautomers from res_tauts to self._tautomers
Args: res_tauts (list): tautomers from sites file """
"""Gets last tautomer from .sites file adds one and saves it as the reference tautomer"""
"""Stores the charge set of each existing tautomer for the present Site""" self._ref_tautomer)
""" Args: aname (str): atom name anumb (int): atom id number """
raise Exception('ERROR: The original center is only ' 'needed for 2-dimensional calculation')
# Get Methods
"""Returns list of all tautomers instances except the tautomers of reference""" return self._tautomers.values()
return self._atoms.keys()
return self._ref_tautomer
return self._molecule
if config.params['pbc_dim'] != 2: raise Exception('ERROR: The original center is only ' 'needed for 2-dimensional calculation') return self._center_original
return self._center
# Iter Methods for i in self._tautomers.values(): yield i
# Print Methods tautomers = ' '.join(sorted(self._tautomers.keys())) natoms = len(self._atoms) center = [ round(i, 2) for i in self._center ] out = 'Site Number -> {0:5} '\ 'Tautomers -> {1:30} '\ 'Reference -> {2:5} '\ 'NAtoms -> {3:6} '\ 'Center -> {4}'.format(self._res_number,tautomers, self._ref_tautomer.getName(), natoms, center) return out
|