Merge pull request #33 from Electrostatics/nathan/delint

De-lint atoms.py and part of bonds.py

propka/calculations.py

@@ -1,97 +1,52 @@
-
-from __future__ import division
-from __future__ import print_function
-
-import math, propka.protonate, propka.bonds,copy, sys
+"""PROPKA calculations."""
+import math
+import copy
+import sys
+import propka.protonate
+import propka.bonds
 from propka.lib import info, warning
 
 
-#
-# methods for setting up atom naming, bonding, and protonation
-#
-
 def setup_bonding_and_protonation(parameters, molecular_container):
+    """Set up bonding and protonation for a molecule.
+
+    Args:
+        molecular_container:  molecule container.
+    """
     # make bonds
     my_bond_maker = setup_bonding(parameters, molecular_container)
-
     # set up ligand atom names
     set_ligand_atom_names(molecular_container)
-
     # apply information on pi electrons
     my_bond_maker.add_pi_electron_information(molecular_container)
-
     # Protonate atoms
     if molecular_container.options.protonate_all:
         my_protonator = propka.protonate.Protonate(verbose=False)
         my_protonator.protonate(molecular_container)
 
 
-    return
-
-
-
 def setup_bonding(parameters, molecular_container):
-    # make bonds
-    my_bond_maker = propka.bonds.bondmaker()
-    my_bond_maker.find_bonds_for_molecules_using_boxes(molecular_container)
+    """Set up bonding for a molecular container.
 
+    Args:
+        molecular_container:  the molecular container in question
+    Returns:
+        BondMaker object
+    """
+    my_bond_maker = propka.bonds.BondMaker()
+    my_bond_maker.find_bonds_for_molecules_using_boxes(molecular_container)
     return my_bond_maker
 
 
 def set_ligand_atom_names(molecular_container):
-    for name in molecular_container.conformation_names:
-        molecular_container.conformations[name].set_ligand_atom_names()
-    return
-
-
-
-#
-# The following methods imitates propka3.0 protonation!
-#
-def setup_bonding_and_protonation_30_style(parameters, molecular_container):
-    # Protonate atoms
-    protonate_30_style(molecular_container)
+    """Set names for ligands in molecular container.
 
-    # make bonds
-    my_bond_maker = propka.bonds.bondmaker()
-    my_bond_maker.find_bonds_for_molecules_using_boxes(molecular_container)
-
-    return
-
-
-def protonate_30_style(molecular_container):
+    Args:
+        molecular_container:  molecular container for ligand names
+    """
     for name in molecular_container.conformation_names:
-        info('Now protonating', name)
-        # split atom into residues
-        curres = -1000000
-        residue = []
-        O=None
-        C=None
-        for atom in molecular_container.conformations[name].atoms:
-            if atom.resNumb != curres:
-                curres = atom.resNumb
-                if len(residue)>0:
-                    #backbone
-                    [O, C]= addBackBoneHydrogen(residue,O,C)
-                    #arginine
-                    if residue[0].resName == 'ARG':
-                        addArgHydrogen(residue)
-                    #histidine
-                    if residue[0].resName == 'HIS':
-                        addHisHydrogen(residue)
-                    #tryptophan
-                    if residue[0].resName == 'TRP':
-                        addTrpHydrogen(residue)
-                    #amides
-                    if residue[0].resName in ['GLN','ASN']:
-                        addAmdHydrogen(residue)
-
-
-                    residue = []
-            if atom.type=='atom':
-                residue.append(atom)
+        molecular_container.conformations[name].set_ligand_atom_names()
 
-    return
 
 def addArgHydrogen(residue):
     """
@@ -159,7 +114,7 @@ def addTrpHydrogen(residue):
         elif atom.name == "CE2":
             CE  = atom
     if CD == None or NE == None or CE == None:
-        str = "Did not find all atoms in %s%4d - in %s" % (self.resName, self.resNumb, "addTrpHydrogen()")
+        str = "Did not find all atoms in %s%4d - in %s" % (self.res_name, self.res_num, "addTrpHydrogen()")
         info(str)
         sys.exit(0)
 
@@ -176,15 +131,15 @@ def addAmdHydrogen(residue):
     O = None
     N = None
     for atom in residue:
-        if   (atom.resName == "GLN" and atom.name == "CD")  or (atom.resName == "ASN" and atom.name == "CG"):
+        if   (atom.res_name == "GLN" and atom.name == "CD")  or (atom.res_name == "ASN" and atom.name == "CG"):
             C = atom
-        elif (atom.resName == "GLN" and atom.name == "OE1") or (atom.resName == "ASN" and atom.name == "OD1"):
+        elif (atom.res_name == "GLN" and atom.name == "OE1") or (atom.res_name == "ASN" and atom.name == "OD1"):
             O = atom
-        elif (atom.resName == "GLN" and atom.name == "NE2") or (atom.resName == "ASN" and atom.name == "ND2"):
+        elif (atom.res_name == "GLN" and atom.name == "NE2") or (atom.res_name == "ASN" and atom.name == "ND2"):
             N = atom
 
     if C == None or O == None or N == None:
-        str = "Did not find N, C and/or O in %s%4d - in %s" % (atom.resName, atom.resNumb, "addAmdHydrogen()")
+        str = "Did not find N, C and/or O in %s%4d - in %s" % (atom.res_name, atom.res_num, "addAmdHydrogen()")
         info(str)
         sys.exit(0)
 
@@ -222,7 +177,7 @@ def addBackBoneHydrogen(residue, O, C):
         return [new_O,new_C]
 
 
-    if N.resName == "PRO":
+    if N.res_name == "PRO":
         """ PRO doesn't have an H-atom; do nothing """
     else:
         H = protonateDirection([N, O, C])
@@ -311,11 +266,11 @@ def protonateSP2(list):
 def make_new_H(atom, x,y,z):
 
     new_H = propka.atom.Atom()
-    new_H.setProperty(numb    = None,
+    new_H.set_property(numb    = None,
                       name    = 'H%s'%atom.name[1:],
-                      resName = atom.resName,
-                      chainID = atom.chainID,
-                      resNumb = atom.resNumb,
+                      res_name = atom.res_name,
+                      chain_id = atom.chain_id,
+                      res_num = atom.res_num,
                       x       = x,
                       y       = y,
                       z       = z,
@@ -329,7 +284,7 @@ def make_new_H(atom, x,y,z):
     new_H.steric_number = 0
     new_H.number_of_lone_pairs = 0
     new_H.number_of_protons_to_add = 0
-    new_H.number_of_pi_electrons_in_double_and_triple_bonds = 0
+    new_H.num_pi_elec_2_3_bonds = 0
 
     atom.bonded_atoms.append(new_H)
     atom.conformation_container.add_atom(new_H)
@@ -357,7 +312,7 @@ def radial_volume_desolvation(parameters, group):
 
     for atom in all_atoms:
         # ignore atoms in the same residue
-        if atom.resNumb == group.atom.resNumb and atom.chainID == group.atom.chainID:
+        if atom.res_num == group.atom.res_num and atom.chain_id == group.atom.chain_id:
             continue
 
         sq_dist = squared_distance(group, atom)
@@ -409,15 +364,15 @@ def contactDesolvation(parameters, group):
                     'N+': 4.5}
 
     all_atoms = group.atom.conformation_container.get_non_hydrogen_atoms()
-    if residue.resName in version.desolvationRadii:
-        local_cutoff = version.desolvationRadii[residue.resName]
+    if residue.res_name in version.desolvationRadii:
+        local_cutoff = version.desolvationRadii[residue.res_name]
     else:
         local_cutoff = 0.00
     residue.Nmass = 0
     residue.Nlocl = 0
 
     for atom in all_atoms:
-        if atom.resNumb != group.atom.resNumb or atom.chainID != group.atom.chainID:
+        if atom.res_num != group.atom.res_num or atom.chain_id != group.atom.chain_id:
             dX = atom.x - residue.x
             dY = atom.y - residue.y
             dZ = atom.z - residue.z

propka/conformation_container.py

@@ -158,7 +158,7 @@ def init_group(self, group):
         titrate_only = self.molecular_container.options.titrate_only
         if titrate_only is not None:
             at = group.atom
-            if not (at.chainID, at.resNumb, at.icode) in titrate_only:
+            if not (at.chain_id, at.res_num, at.icode) in titrate_only:
                 group.titratable = False
                 if group.residue_type == 'CYS':
                     group.exclude_cys_from_results = True
@@ -376,7 +376,7 @@ def get_heavy_ligand_atoms(self):
         return [atom for atom in self.atoms if atom.type=='hetatm' and atom.element != 'H']
 
     def get_chain(self,chain):
-        return [atom for atom in self.atoms if atom.chainID != chain]
+        return [atom for atom in self.atoms if atom.chain_id != chain]
 
 
     def add_atom(self, atom):
@@ -388,13 +388,13 @@ def add_atom(self, atom):
             atom.molecular_container = self.molecular_container
 
         # store chain id for bookkeeping
-        if not atom.chainID in self.chains:
-            self.chains.append(atom.chainID)
+        if not atom.chain_id in self.chains:
+            self.chains.append(atom.chain_id)
 
         return
 
     def copy_atom(self, atom):
-        new_atom  = atom.makeCopy()
+        new_atom  = atom.make_copy()
         self.atoms.append(new_atom)
         new_atom.conformation_container = self
 
@@ -443,8 +443,8 @@ def sort_atoms(self):
         return
 
     def sort_atoms_key(self, atom):
-        key = ord(atom.chainID)*1e7
-        key += atom.resNumb*1000
+        key = ord(atom.chain_id)*1e7
+        key += atom.res_num*1000
         if len(atom.name) > len(atom.element):
             key += ord(atom.name[len(atom.element)])
             #info(atom,ord(atom.name[len(atom.element)]), '|%s||%s|'%(atom.name,atom.element))

propka/determinants.py

@@ -54,7 +54,7 @@ def addDeterminants(group1, group2, distance, version):
 def addSidechainDeterminants(group1, group2, version=None):
     """
     adding side-chain determinants/perturbations
-    Note, resNumb1 > resNumb2
+    Note, res_num1 > res_num2
     """
 
     hbond_interaction = version.hydrogen_bond_interaction(group1, group2)

propka/group.py

@@ -111,22 +111,22 @@ def __init__(self, atom):
         self.common_charge_centre = False
 
 
-        self.residue_type = self.atom.resName
+        self.residue_type = self.atom.res_name
         if self.atom.terminal:
             self.residue_type = self.atom.terminal
 
         if self.atom.type=='atom':
-            self.label = '%-3s%4d%2s'%(self.residue_type, atom.resNumb, atom.chainID)
-        elif self.atom.resName in ['DA ','DC ','DG ','DT ']:
+            self.label = '%-3s%4d%2s'%(self.residue_type, atom.res_num, atom.chain_id)
+        elif self.atom.res_name in ['DA ','DC ','DG ','DT ']:
             self.label = '%1s%1s%1s%4d%2s'%(self.residue_type[1],
                                             atom.element,
                                             atom.name.replace('\'','')[-1],
-                                            atom.resNumb,
-                                            atom.chainID)
+                                            atom.res_num,
+                                            atom.chain_id)
 
-#            self.label = '%1s%1s%1s%4d%2s'%(self.residue_type[1], atom.element,atom.name[-1], atom.resNumb, atom.chainID)
+#            self.label = '%1s%1s%1s%4d%2s'%(self.residue_type[1], atom.element,atom.name[-1], atom.res_num, atom.chain_id)
         else:
-            self.label = '%-3s%4s%2s'%(self.residue_type, atom.name, atom.chainID)
+            self.label = '%-3s%4s%2s'%(self.residue_type, atom.name, atom.chain_id)
 
 
         # container for squared distances
@@ -253,7 +253,7 @@ def __eq__(self, other):
             return self.label==other.label
         else:
             # For heterogene atoms we also need to check the residue number
-            return self.label==other.label and self.atom.resNumb == other.atom.resNumb
+            return self.label==other.label and self.atom.res_num == other.atom.res_num
 
     def __hash__(self):
         """ Needed together with __eq__ - otherwise we can't make sets of groups """
@@ -361,7 +361,7 @@ def setup(self):
             if not self.model_pka_set:
                 self.model_pka = self.parameters.model_pkas[self.residue_type]
                 # check if we should apply a custom model pka
-                key = '%s-%s'%(self.atom.resName.strip(), self.atom.name.strip())
+                key = '%s-%s'%(self.atom.res_name.strip(), self.atom.name.strip())
                 if key in self.parameters.custom_model_pkas.keys():
                     self.model_pka = self.parameters.custom_model_pkas[key]
 
@@ -1122,7 +1122,7 @@ class Ion_group(Group):
     def __init__(self, atom):
         Group.__init__(self,atom)
         self.type = 'ION'
-        self.residue_type = atom.resName.strip()
+        self.residue_type = atom.res_name.strip()
         info('Found ion group:', atom)
         return
 
@@ -1201,15 +1201,15 @@ def is_protein_group(parameters,atom):
     ### Backbone
     if atom.type == 'atom' and atom.name == 'N':
         # ignore proline backbone nitrogens
-        if atom.resName != 'PRO':
+        if atom.res_name != 'PRO':
             return BBN_group(atom)
     if atom.type == 'atom' and atom.name == 'C':
         # ignore C- carboxyl
         if atom.count_bonded_elements('O') == 1:
             return BBC_group(atom)
 
     ### Filters for side chains based on PDB protein atom names
-    key = '%s-%s'%(atom.resName, atom.name)
+    key = '%s-%s'%(atom.res_name, atom.name)
 
     if key in parameters.protein_group_mapping.keys():
         return eval('%s_group(atom)'%parameters.protein_group_mapping[key])
@@ -1342,7 +1342,7 @@ def is_ligand_group_by_marvin_pkas(parameters, atom):
 
 def is_ion_group(parameters, atom):
 
-    if atom.resName.strip() in parameters.ions.keys():
+    if atom.res_name.strip() in parameters.ions.keys():
         return Ion_group(atom)
 
     return None

propka/hybrid36.py

@@ -1,3 +1,7 @@
+"""Provides an alternative PDB format that can transparently encode larger atom numbers.
+
+http://cci.lbl.gov/hybrid_36/
+"""
 import string
 
 _hybrid36_upper_chars = set(string.ascii_uppercase)