diff --git a/meld/tests/test_addligands.py b/meld/tests/test_addligands.py
deleted file mode 100644
index 0e6ea7ba5f36b3fe93e569ce16153e7afa34c94c..0000000000000000000000000000000000000000
--- a/meld/tests/test_addligands.py
+++ /dev/null
@@ -1,158 +0,0 @@
-'''
-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()