Removed obsoletet ligand test

meld/tests/test_addligands.py

-'''
-SWISS-MODEL 2.0
-
-doc at: "firefox file:///import/bc2/home/schwede/gallo/swissmodel/doc/build/html/index.html"
-
-use: ./TESTS --verbose meld
-'''
-import os, sys, math
-import shutil
-from ost import *
-from sm.core.test import *
-from sm.core import *
-from sm.meld import *
-from sm import smtl, config, tplsearch
-from sm.pipeline import project
-from sm.pipeline.model import HomologyModel
-from sm.pipeline.addligands import *
-
-class TestAddLigands(unittest.TestCase):
-  def setUp(self):
-    if os.path.exists('data/ligands/SMTL'):
-      shutil.rmtree('data/ligands/SMTL')
-    if os.path.exists('data/ligands/test.sm'):
-      shutil.rmtree('data/ligands/test.sm')
-
-  def tearDown(self):
-    # using the same path for each test SMTL, we have to clear the cache
-    smtl.SMTL.LOADED_SMTLS = {}
-    if os.path.exists('data/ligands/SMTL'):
-      shutil.rmtree('data/ligands/SMTL')
-    if os.path.exists('data/ligands/test.sm'):
-      shutil.rmtree('data/ligands/test.sm')
-
-  def fastIsLigandInContact(self):
-    in_contact = []
-    bound = IsLigandInContact(in_contact)
-    self.assertEqual(bound, False)
-    in_contact = ['_.12','-.2']
-    bound = IsLigandInContact(in_contact)
-    self.assertEqual(bound, False)
-    in_contact = ['_.12', 'T.1']
-    bound = IsLigandInContact(in_contact)
-    self.assertEqual(bound, False)
-    in_contact = ['_.12', 'T.1','S.2']
-    bound = IsLigandInContact(in_contact)
-    self.assertEqual(bound, True)
-
-  def fastIsLigandBound(self):
-    target_seq = io.LoadSequence('data/ligands/3G04C.fasta')
-    seq1 = io.LoadSequence('data/ligands/3G04C.fasta')
-    templates = tplsearch.TemplateList()
-    tem = tplsearch.Template.Create('3G04',1,'A',seq.CreateAlignment(target_seq, seq1))
-    templates.append(tem)
-    lib = smtl.SMTL.Create('data/ligands/SMTL')
-    lib.Update(add=('3G04', ), mmcif_dir='data/ligands/', calc_profiles=False)
-    prj = project.Project.Create('test', target_seq, lib, output_dir='./data/ligands',
-                                 pdb_storage='external', split=False)
-    prj.ImportTemplates(templates, lib, pdb_storage='default', tolerant=False, found_by=None)
-    model = io.LoadPDB('data/ligands/3G04_model_no_lig.pdb')
-    bio_unit = prj.smtl.Get(tem.pdb_id,tem.assembly_id)
-    lig = bio_unit.ligands[0].chains[0]
-    is_bound = IsLigandBound(lig, model)
-    self.assertEqual(is_bound,False)
-    lig = bio_unit.ligands[0].chains[1]
-    is_bound = IsLigandBound(lig, model)
-    self.assertEqual(is_bound,True)
-    lig = bio_unit.ligands[0].chains[2]
-    is_bound = IsLigandBound(lig, model)
-    self.assertEqual(is_bound,True)
-    lig = bio_unit.ligands[0].chains[3]
-    is_bound = IsLigandBound(lig, model)
-    self.assertEqual(is_bound,True)
-    lig = bio_unit.ligands[0].chains[4]
-    is_bound = IsLigandBound(lig, model)
-    self.assertEqual(is_bound,True)
-    lig = bio_unit.ligands[0].chains[5]
-    is_bound = IsLigandBound(lig, model)
-    self.assertEqual(is_bound,True)
-    lig = bio_unit.ligands[1].chains[0]
-    is_bound = IsLigandBound(lig, model)
-    self.assertEqual(is_bound,False)
-
-    lig = bio_unit.ligands[1].chains[1]
-    is_bound = IsLigandBound(lig, model)
-    self.assertEqual(is_bound,False)
-    lig = bio_unit.ligands[1].chains[2]
-    is_bound = IsLigandBound(lig, model)
-    self.assertEqual(is_bound,True)
-    lig = bio_unit.ligands[1].chains[3]
-    is_bound = IsLigandBound(lig, model)
-    self.assertEqual(is_bound,True)
-    lig = bio_unit.ligands[1].chains[4]
-    is_bound = IsLigandBound(lig, model)
-    self.assertEqual(is_bound,True)
-
-  def fastAssignResiduesConservation(self):
-    # perfect aln
-    mod_seq = seq.CreateSequence('M', 'AAAAA')
-    tem_seq = seq.CreateSequence('T', 'AAAAA')
-    aln = seq.CreateAlignment(mod_seq, tem_seq)
-    in_contact = ['_.12', 'T.1','T.3','T.4','C.23']
-    is_cons = AssignResiduesConservation(in_contact, aln)
-    self.assertEqual(is_cons, True)
-    # bad aln
-    mod_seq = seq.CreateSequence('M', 'TA--A')
-    tem_seq = seq.CreateSequence('T', 'TSAAS')
-    aln = seq.CreateAlignment(mod_seq, tem_seq)
-    in_contact = ['_.12', 'T.1','T.3','T.4','C.23']
-    is_cons = AssignResiduesConservation(in_contact, aln)
-    self.assertEqual(is_cons, False)
-
-  def fastCopyLigand(self):
-    tem = io.LoadPDB('data/ligands/3IIJ.pdb')
-    ligand = tem.Select('rname=ADP')
-    model = io.LoadPDB('data/ligands/3IIJ_no_ligands.pdb')
-    add_lig, no_overlaps, new_model = CopyLigand(ligand, model)
-    self.assertEqual(add_lig, True)
-    self.assertEqual(no_overlaps, True)
-    adp = new_model.Select('rname=ADP')
-    self.assertEqual(adp.residues[0].name, 'ADP')
-    ligands = new_model.Select('protein=false and water=false')
-    self.assertEqual(ligands.residue_count, 1)
-
-  def fastRunAddLigands(self):
-    mod_seq = io.LoadSequence('data/ligands/3IIJ.fasta')
-    tem_seq = io.LoadSequence('data/ligands/3IIJ.fasta')
-    aln = seq.CreateAlignment(mod_seq, tem_seq)
-    tem = tplsearch.Template.Create('3iij', 1, 'A', aln)
-    model = io.LoadPDB('data/ligands/3IIJ_no_ligands.pdb')
-    lib = smtl.SMTL.Create('data/ligands/SMTL')
-    lib.Update(add=('3IIJ', ), mmcif_dir='data/ligands/', calc_profiles=False)
-    bio_unit = lib.Get(tem.pdb_id,tem.assembly_id)
-    chain = bio_unit.GetChainByName(tem.chain_name)
-    new_aln = chain.ToAtomSeqAlignment(tem.alignment)
-    rep, new_model = RunAddLigands(bio_unit, model, aln)
-    lig_rep = rep[0]
-    self.assertEqual(lig_rep['description'], "ADENOSINE-5'-DIPHOSPHATE")
-    self.assertEqual(lig_rep['name'][0], 'ADP')
-    self.assertEqual(lig_rep['number'], '1')
-    self.assertEqual(lig_rep['included'], True)
-    self.assertEqual(lig_rep['reason']['bound'], True)
-    self.assertEqual(lig_rep['reason']['relevant'], True)
-    self.assertEqual(lig_rep['reason']['conserved_residues'], True)
-    self.assertEqual(lig_rep['reason']['sterically_valid'], True)
-    lig_rep = rep[1]
-#    self.assertEqual(lig_rep['description'], "SULFATE ION")
-#    self.assertEqual(lig_rep['name'][0], 'SO4')
-#    self.assertEqual(lig_rep['number'], '2')
-#    self.assertEqual(lig_rep['included'], False)
-#    self.assertEqual(lig_rep['reason']['bound'], True)
-#    self.assertEqual(lig_rep['reason']['relevant'], False)
-#    self.assertEqual(len(rep), 5)
-#    ligands = new_model.Select('protein=false and water=false')
-#    self.assertEqual(ligands.residues[0].name, 'ADP')
-#    self.assertEqual(ligands.residue_count, 1)
-
-if __name__ == "__main__":
-  run()