molSimplify 1.7.4__py3-none-any.whl

molSimplify/Classes/helpers.py

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+#  @file helpers.py
+#  Contains some useful helper functions for classes.
+#
+#  Written by HJK Group
+#
+#  Dpt of Chemical Engineering, MIT
+
+from molSimplify.Classes.monomer3D import monomer3D
+from molSimplify.Classes.mol3D import mol3D
+from molSimplify.Classes.atom3D import atom3D
+
+
+def read_atom(line):
+    """ Reads a line of a pdb into an atom dictionary.
+
+    Parameters
+    ----------
+        line : str
+            a line of a pdb file
+
+    Returns
+    -------
+        atom_dict : dictionary
+            dictionary containing attributes of atom when reading the pdb
+    """
+
+    labels = ['Type', 'SerialNum', 'Name', 'AltLoc', 'ResName', 'ChainID',
+              'ResSeq', 'ICode', 'X', 'Y', 'Z', 'Occupancy', 'TempFactor',
+              'Element', 'Charge']
+    data = [line[0:6].strip(), int(line[6:11]), line[12:16].strip(),
+            line[16:17].strip(), line[17:20].strip(), line[21:22].strip(),
+            int(line[22:26]), line[26:27].strip(), float(line[30:38]),
+            float(line[38:46]), float(line[46:54]), float(line[54:60]),
+            float(line[60:66]), line[70:78].strip(), line[78:80].strip()]
+    atom_dict = dict(zip(labels, data))
+    atom_dict['Element'] = atom_dict['Element'][0] + atom_dict['Element'][1:].lower()
+    atom_dict["Line"] = line
+    return atom_dict
+
+
+def makeMol(a_dict, mols, conf, chains, prev_a_dict, bonds, aa=True):
+    """ Creates an monomer3D from a_dicts and adds it to the appropriate places.
+
+    Parameters
+    ----------
+        a_dict : dictionary
+            created from the read_atom method
+        mols : dictionary
+            keyed by chain and location, valued by monomer3Ds or mol3Ds
+        conf : list
+            contains amino acid conformations
+        chains : dictionary
+            contains amino acid chains
+        prev_a_dict : dictionary
+            the a_dict from the previous run
+        bonds : dictionary
+            contains bonding info
+        aa : boolean
+            True if mols consists of monomer3Ds, False if consists of mol3Ds
+
+    Returns
+    -------
+        mols, conf, chains, prev_a_dict as updated
+    """
+    loc = a_dict['AltLoc']
+    ploc = prev_a_dict["AltLoc"]
+    hack = False
+    hack2 = False
+    m = 0
+    key = (a_dict['ChainID'], a_dict['ResSeq'])
+    if key not in mols.keys():
+        if aa:
+            m = monomer3D(a_dict['ResName'], a_dict['ChainID'], a_dict['ResSeq'],
+                     a_dict['Occupancy'], loc)
+        else:
+            m = mol3D(a_dict['ResName'], loc)
+        mols[key] = [m]
+    elif loc != '' and ploc != '':
+        li = ord(ploc)
+        if loc > chr(li) and len(mols[key]) <= li-64:
+            if aa:
+                m = monomer3D(a_dict['ResName'], a_dict['ChainID'],
+                         a_dict['ResSeq'], a_dict['Occupancy'], loc)
+                m.temp_list = mols[key][-1].temp_list
+            else:
+                m = mol3D(a_dict['ResName'], loc)
+                m.temp_list = mols[key][-1].temp_list
+            if mols[key][-1].loc != loc:
+                mols[key].append(m)
+        else:
+            weirdo = True
+            for mol in mols[key]:
+                if mol.loc == loc:
+                    weirdo = False
+            if weirdo:
+                if aa:
+                    m = monomer3D(a_dict['ResName'], a_dict['ChainID'],
+                             a_dict['ResSeq'], a_dict['Occupancy'], loc)
+                    m.temp_list = mols[key][-1].temp_list
+                else:
+                    m = mol3D(a_dict['ResName'], loc)
+                    m.temp_list = mols[key][-1].temp_list
+                if mols[key][-1].loc != loc:
+                    mols[key].append(m)
+    elif loc == '':
+        # atom must be added to multiple conformations
+        hack = True
+    elif key in mols.keys() and ploc == '' and len(mols[key]) == 1:
+        hack2 = True
+        mols[key][0].setLoc(loc)
+        mols[key][0].temp_list = mols[key][0].atoms.copy()
+    prev_a_dict = a_dict
+    if a_dict['ChainID'] not in chains.keys():
+        chains[a_dict['ChainID']] = []  # initialize key of chain dictionary
+    if m != 0 and key not in conf and loc != '' and float(a_dict['Occupancy']) < 1:
+        conf.append(key)
+    if m != 0 and m not in chains[a_dict['ChainID']] and key not in conf:
+        chains[a_dict['ChainID']].append(m)
+    if loc == '' or ploc == '':
+        m = mols[key][0]
+    else:
+        for i in mols[key]:
+            if i.loc == loc:
+                m = i
+    atom = atom3D(Sym=a_dict['Element'], xyz=[a_dict['X'], a_dict['Y'],
+                                              a_dict['Z']],
+                  Tfactor=a_dict['TempFactor'], occup=a_dict['Occupancy'],
+                  greek=a_dict['Name'], line=a_dict['Line'])
+    if not hack2:
+        for a in m.temp_list:
+            if type(a) == tuple:
+                m.addAtom(a[1], a[0])
+            else:
+                m.addAtom(a)
+        m.temp_list = []
+    if hack:
+        for i in mols[key]:
+            i.addAtom(atom, a_dict['SerialNum'])
+    else:
+        m.addAtom(atom, a_dict['SerialNum'])  # terminal Os may be missing
+        if aa:
+            if atom.greek == "C":
+                m.c.append(atom)
+            if atom.greek == "N":
+                m.n.append(atom)
+    if key in conf and chains[a_dict['ChainID']] != []:
+        chains[a_dict['ChainID']] = []
+    if aa:
+        m.setBonds()
+        bonds.update(m.bonds)
+        if m.prev is None and (a_dict['ChainID'], a_dict['ResSeq'] - 1) in mols.keys():
+            m.setPrev(mols[(a_dict['ChainID'], a_dict['ResSeq'] - 1)][0])
+        prev_mol = m.prev
+        if prev_mol is not None:
+            if prev_mol.next is None:
+                prev_mol.setNext(m)
+            for n in m.n:
+                for c in prev_mol.c:
+                    bonds[n].add(c)
+                    bonds[c].add(n)
+    return atom, mols, conf, chains, prev_a_dict, bonds