From e531a2334f05d7cab1f61be01630220052d76942 Mon Sep 17 00:00:00 2001
From: "Brett T. Hannigan" <bhannigan@palenque.degrado>
Date: Thu, 19 Sep 2013 09:49:43 -0700
Subject: [PATCH] Deleting ligand stuff for now.

---
 src/suns_ligand.py | 109 ---------------------------------------------
 1 file changed, 109 deletions(-)
 delete mode 100644 src/suns_ligand.py

diff --git a/src/suns_ligand.py b/src/suns_ligand.py
deleted file mode 100644
index 19667ce..0000000
--- a/src/suns_ligand.py
+++ /dev/null
@@ -1,109 +0,0 @@
-import pybel
-
-LIGAND_DEFINITIONS = {'phosphate': 'OP(=O)(O)O',
-                      'sulfate': 'S(=O)(=O)(O)O',
-                      'nitrate': 'N(=O)(=O)O',
-                      'selmet': 'C[Se]C',
-                      'acetate': 'C(=O)(O)C',
-                      'adamantane': 'N[C@@]12C[C@H]3C[C@@H](C1)C[C@@H](C2)C3',
-                     }
-                     
-LIGAND_SELECTION = '_SUNS_LIGAND'
-
-def find_atom_index(frp, ap):
-    '''This function will loop through the atom lines in frp
-       looking for a line which has the substring given in ap.
-       Substring because the getPdbString function of pymol renumbers
-       the atom numbers starting at 1, so two selections may have the
-       same atoms with different atom numbers.'''
-    for i, atom in enumerate(frp):
-        if(atom.find(ap) >= 0):
-            return i
-    return -1
-        
-
-def find_atom_indices(fullResiduePdbstr, atomPdbstr):
-    '''This function will take a pdb string, and look 
-       for which lines each of the given atom strings 
-       appear on.'''
-    frp = fullResiduePdbstr.split('\n')
-    indices = []
-    for ap in atomPdbstr:
-        index = find_atom_index(frp, ap)
-        if(index >= 0):
-            indices += [index]
-    return indices
-
-def get_pdb_string(fullResiduePdbstr, match):
-    '''This function will simply extract the proper
-       lines from a PDB string for the atoms that
-       matched a motif.'''
-    frp = fullResiduePdbstr.split('\n')
-    subStr = [frp[i-1] for i in match]
-    return '\n'.join(subStr)
-
-def get_atom_names_statement(pdbstr):
-    '''This function will generate a list of atom names
-       from the given pdb string.'''
-    atomNames = ''   
-    for l in pdbstr.split('\n'):
-        if( (l[0:6] == 'HETATM') or (l[0:4] == 'ATOM') ):
-            atomNames += l[12:16].strip() + '+'
-
-    # Remove the final # sign
-    return atomNames[0:-1]
-    
-def look_for_ligand(fullResiduePdbstr, atomPdbstr):
-    '''This function will look for the defined ligand
-       motifs in this ligand residue.'''
-    atomIndices = find_atom_indices(fullResiduePdbstr, atomPdbstr)
-    if(len(atomIndices) != 2):
-        return
-    mol = pybel.readstring('pdb', fullResiduePdbstr)
-    for ligand in LIGAND_DEFINITIONS:
-        smarts = pybel.Smarts(LIGAND_DEFINITIONS[ligand])
-        matches = smarts.findall(mol)
-        for match in matches:
-            # The Smarts search appears to use 1 based indexing.
-            if(((atomIndices[0]+1) in match) and ((atomIndices[1]+1) in match)):
-                retVal = {}
-                retVal['motif'] = ligand
-                retVal['pdbstr'] = get_pdb_string(fullResiduePdbstr, match)
-                retVal['atomNames'] = get_atom_names_statement(retVal['pdbstr'])
-                return retVal
-    
-    return {}
-
-def find_ligand_word(cmd, obj, bondAtoms):
-    '''This function will take the pymol cmd object, the name
-       of the object selected, and the two bonded atoms selected,
-       will get the pdb text of the full residue, look for any
-       defined ligand motifs and return the first motif found that
-       includes the two atoms in question.'''
-    # Get the pdb string of the full residue.
-    selectStatement = obj + ' and model ' + bondAtoms[0]['model'] + ' and chain ' + bondAtoms[0]['chain'] + ' and resn ' + bondAtoms[0]['resn'] + ' and resi ' + bondAtoms[0]['resi']
-    if(bondAtoms[0]['segi'].strip() != ''):
-        selectStatement += ' and segi ' + bondAtoms[0][1]
-    cmd.select(LIGAND_SELECTION, selectStatement)
-    fullResiduePdbstr = cmd.get_pdbstr(LIGAND_SELECTION)
-    
-    # Get the pdb string of the first atom
-    selectStatement2 = selectStatement + ' and name ' + bondAtoms[0]['name']
-    cmd.select(LIGAND_SELECTION, selectStatement2)
-    atomPdbstr = [cmd.get_pdbstr(LIGAND_SELECTION).split('\n')[0][13:]]
-    
-    # Get the pdb string of the second atom
-    selectStatement2 = selectStatement + ' and name ' + bondAtoms[1]['name']
-    cmd.select(LIGAND_SELECTION, selectStatement2)
-    atomPdbstr += [cmd.get_pdbstr(LIGAND_SELECTION).split('\n')[0][13:]]
-    
-    ligandMatch = look_for_ligand(fullResiduePdbstr, atomPdbstr)
-    key = None
-    if(ligandMatch != {}):
-        selectStatement = '(' + selectStatement + ' and name ' + ligandMatch['atomNames'] + ')'
-        key = (obj, bondAtoms[0]['model'], bondAtoms[0]['segi'], bondAtoms[0]['chain'], bondAtoms[0]['resn'], bondAtoms[0]['resi'], ligandMatch['motif'])
-    else:
-        selectStatement = None
-                
-    return (selectStatement, key)
-    
\ No newline at end of file