diff --git a/modules/bindings/pymod/clustalw.py b/modules/bindings/pymod/clustalw.py
index 2a98eca077216f9e128600e4ce9f23e3a05fd356..f61d4f24f3f074badf749ae01f29b6893364dd87 100644
--- a/modules/bindings/pymod/clustalw.py
+++ b/modules/bindings/pymod/clustalw.py
@@ -3,7 +3,7 @@ from ost import settings, io, seq, LogError
import os
import subprocess
-def ClustalW(seq1, seq2=None, clustalw=None, keep_files=False, clustalw_option_string=False):
+def ClustalW(seq1, seq2=None, clustalw=None, keep_files=False):
clustalw_path=settings.Locate(('clustalw', 'clustalw2'),
explicit_file_name=clustalw)
@@ -32,10 +32,6 @@ def ClustalW(seq1, seq2=None, clustalw=None, keep_files=False, clustalw_option_s
command='%s -infile="%s" -output=fasta -outfile="%s"' % (clustalw_path,
temp_dir.files[0],
out)
- if clustalw_option_string!=False:
- command=command+" "+clustalw_option_string #see useful flags: http://toolkit.tuebingen.mpg.de/clustalw/help_params
-
-
ps=subprocess.Popen(command, shell=True, stdout=subprocess.PIPE)
ps.stdout.readlines()
aln=io.LoadAlignment(out)
diff --git a/modules/bindings/tests/test_clustalw.py b/modules/bindings/tests/test_clustalw.py
index 33d3868947506464222c04102b8042a0ea3ed305..fc93a19b6d4c270d46f1c79a3554077e8295f908 100644
--- a/modules/bindings/tests/test_clustalw.py
+++ b/modules/bindings/tests/test_clustalw.py
@@ -14,10 +14,6 @@ class TestClustalWBindings(unittest.TestCase):
self.multseq = io.LoadSequenceList("testfiles/multiple.fasta")
self.pw_alignment = io.LoadAlignment("testfiles/pairwise_aln.fasta")
self.mult_alignment = io.LoadAlignment("testfiles/multiple_aln.fasta")
- self.seq1 = io.LoadSequence("testfiles/seq1.fasta")
- self.seq2 = io.LoadSequence("testfiles/seq2.fasta")
- self.seq1_seq2_alignment = io.LoadAlignment("testfiles/seq1_seq2_aln.fasta")
- self.seq1_seq2_alignment_options_changed = io.LoadAlignment("testfiles/seq1_seq2_aln_options_changed.fasta")
def testPairwiseClustalW(self):
aln=clustalw.ClustalW(self.targetseq, self.templseq)
@@ -34,15 +30,6 @@ class TestClustalWBindings(unittest.TestCase):
assert self.mult_alignment.ToString(80) == aln.ToString(80), \
"Multiple alignment differs from precomputed one"
- def testPairwiseClustalWChangedOptions(self):
- # five residues removed two positions before the end of seq2
- aln=clustalw.ClustalW(self.seq1,self.seq2)
- assert self.seq1_seq2_alignment.ToString(80) == aln.ToString(80), \
- "Pairwise alignment with default gap penalties differs from precomputed one"
- aln=clustalw.ClustalW(self.seq1,self.seq2,clustalw_option_string="-GAPOPEN=2 -GAPEXT=0")
- assert self.seq1_seq2_alignment_options_changed.ToString(80) == aln.ToString(80), \
- "Pairwise alignment with modified gap penalties differs from precomputed one"
-
if __name__ == "__main__":
# test if clustalw package is available on system, otherwise ignore tests
diff --git a/modules/bindings/tests/testfiles/seq1.fasta b/modules/bindings/tests/testfiles/seq1.fasta
deleted file mode 100644
index 7aa326305015b25f0416e416fe14afe19984e29a..0000000000000000000000000000000000000000
--- a/modules/bindings/tests/testfiles/seq1.fasta
+++ /dev/null
@@ -1,2 +0,0 @@
->target
-MAETLIKVDLNQSPYDNPQVHNRWHPDIPMAVWVEPGAEFKLETYDWTGGAIKNDDSAEDVRDVDLSTVHFLSGPVGVKGAEPGDLLVVDLLDIGARDDSLWGFNGFFSKQNGGGFLDEHFPLAQKSIWDFHGMFTKSRHIPGVNFAGLIHPGLIGCLPDPKMLASWNERETGLIATDPDRIPGLANPPNATTAHMGQMQGEARDKAAAEGARTVPPREHGGNCDIKDLSRGSRVFFPVYVDGAGLSVGDLHFSQGDGEITFCGAIEMAGWVHMKVSLIKGGMAKYGIKNPIFKPSPMTPNYKDYLIFEGISVDEKGKQHYLDVTVAYRQACLNAIEYLKKFGYSGAQAYSLLGTAPVQGHISGVVDVPNACATLWLPTEIFDFDINPTAEGPQKIITGGVDLPIAQDK
\ No newline at end of file
diff --git a/modules/bindings/tests/testfiles/seq1_seq2_aln.fasta b/modules/bindings/tests/testfiles/seq1_seq2_aln.fasta
deleted file mode 100644
index e735762a95916b563ad735f89eaa3c22376fd505..0000000000000000000000000000000000000000
--- a/modules/bindings/tests/testfiles/seq1_seq2_aln.fasta
+++ /dev/null
@@ -1,4 +0,0 @@
->target
-MAETLIKVDLNQSPYDNPQVHNRWHPDIPMAVWVEPGAEFKLETYDWTGGAIKNDDSAEDVRDVDLSTVHFLSGPVGVKGAEPGDLLVVDLLDIGARDDSLWGFNGFFSKQNGGGFLDEHFPLAQKSIWDFHGMFTKSRHIPGVNFAGLIHPGLIGCLPDPKMLASWNERETGLIATDPDRIPGLANPPNATTAHMGQMQGEARDKAAAEGARTVPPREHGGNCDIKDLSRGSRVFFPVYVDGAGLSVGDLHFSQGDGEITFCGAIEMAGWVHMKVSLIKGGMAKYGIKNPIFKPSPMTPNYKDYLIFEGISVDEKGKQHYLDVTVAYRQACLNAIEYLKKFGYSGAQAYSLLGTAPVQGHISGVVDVPNACATLWLPTEIFDFDINPTAEGPQKIITGGVDLPIAQDK
->model
----------------------------------VEPGAEFKLETYDWTGGAIKNDDSAEDVRDVDLSTVHFLSGPVGVKGAEPGDLLVVDLLDIGARDDSLWGFNGFFSKQNGGGFLDEHFPLAQKSIWDFHGMFTKSRHIPGVNFAGLIHPGLIGCLPDPKMLASWNERETGLIATDPDRIPGLANPPNATTAHMGQMQGEARDKAAAEGARTVPPREHGGNCDIKDLSRGSRVFFPVYVDGAGLSVGDLHFSQGDGEITFCGAIEMAGWVIK---------------------------------------------------------------------------------------------------------------------------------------
\ No newline at end of file
diff --git a/modules/bindings/tests/testfiles/seq1_seq2_aln_options_changed.fasta b/modules/bindings/tests/testfiles/seq1_seq2_aln_options_changed.fasta
deleted file mode 100644
index 3efdc6cd889b07a900a1f63e6d5e8f1d13552af9..0000000000000000000000000000000000000000
--- a/modules/bindings/tests/testfiles/seq1_seq2_aln_options_changed.fasta
+++ /dev/null
@@ -1,4 +0,0 @@
->target
-MAETLIKVDLNQSPYDNPQVHNRWHPDIPMAVWVEPGAEFKLETYDWTGGAIKNDDSAEDVRDVDLSTVHFLSGPVGVKGAEPGDLLVVDLLDIGARDDSLWGFNGFFSKQNGGGFLDEHFPLAQKSIWDFHGMFTKSRHIPGVNFAGLIHPGLIGCLPDPKMLASWNERETGLIATDPDRIPGLANPPNATTAHMGQMQGEARDKAAAEGARTVPPREHGGNCDIKDLSRGSRVFFPVYVDGAGLSVGDLHFSQGDGEITFCGAIEMAGWVHMKVSLIKGGMAKYGIKNPIFKPSPMTPNYKDYLIFEGISVDEKGKQHYLDVTVAYRQACLNAIEYLKKFGYSGAQAYSLLGTAPVQGHISGVVDVPNACATLWLPTEIFDFDINPTAEGPQKIITGGVDLPIAQDK
->model
----------------------------------VEPGAEFKLETYDWTGGAIKNDDSAEDVRDVDLSTVHFLSGPVGVKGAEPGDLLVVDLLDIGARDDSLWGFNGFFSKQNGGGFLDEHFPLAQKSIWDFHGMFTKSRHIPGVNFAGLIHPGLIGCLPDPKMLASWNERETGLIATDPDRIPGLANPPNATTAHMGQMQGEARDKAAAEGARTVPPREHGGNCDIKDLSRGSRVFFPVYVDGAGLSVGDLHFSQGDGEITFCGAIEMAGWV------IK---------------------------------------------------------------------------------------------------------------------------------
\ No newline at end of file
diff --git a/modules/bindings/tests/testfiles/seq2.fasta b/modules/bindings/tests/testfiles/seq2.fasta
deleted file mode 100644
index 72a58bd2acab10c6be354a59e75b28eea045a906..0000000000000000000000000000000000000000
--- a/modules/bindings/tests/testfiles/seq2.fasta
+++ /dev/null
@@ -1,2 +0,0 @@
->model
-VEPGAEFKLETYDWTGGAIKNDDSAEDVRDVDLSTVHFLSGPVGVKGAEPGDLLVVDLLDIGARDDSLWGFNGFFSKQNGGGFLDEHFPLAQKSIWDFHGMFTKSRHIPGVNFAGLIHPGLIGCLPDPKMLASWNERETGLIATDPDRIPGLANPPNATTAHMGQMQGEARDKAAAEGARTVPPREHGGNCDIKDLSRGSRVFFPVYVDGAGLSVGDLHFSQGDGEITFCGAIEMAGWVIK
\ No newline at end of file
diff --git a/modules/io/src/mol/pdb_writer.cc b/modules/io/src/mol/pdb_writer.cc
index 94a6e856493bdff7cd1999faab939d85d8e2a9a4..8b16c2cce992fd7bf61675d315a00ca30178d581 100644
--- a/modules/io/src/mol/pdb_writer.cc
+++ b/modules/io/src/mol/pdb_writer.cc
@@ -136,8 +136,7 @@ void write_atom(std::ostream& ostr, FormattedLine& line,
} else {
for (std::vector<String>::const_iterator
i=names.begin(), e=names.end(); i!=e; ++i) {
- geom::Mat4 tf=atom.GetEntity().GetTransformationMatrix();
- p=geom::Vec3(tf*geom::Vec4(atom.GetAltPos(*i)));
+ p=atom.GetAltPos(*i);
line(30, 50).Clear();
if (i->size()>1) {
diff --git a/modules/io/tests/test_io_pdb.cc b/modules/io/tests/test_io_pdb.cc
index 5d78e69846fa17b84633279b314b847453675b14..df8ff5295dc686bbcf12c281b649a66a7218ff0c 100644
--- a/modules/io/tests/test_io_pdb.cc
+++ b/modules/io/tests/test_io_pdb.cc
@@ -364,31 +364,6 @@ BOOST_AUTO_TEST_CASE(write_conect)
"testfiles/pdb/conect-out.pdb"));
}
-BOOST_AUTO_TEST_CASE(alt_loc_tf)
-{
- String fname("testfiles/pdb/alt-loc.pdb");
- // this scope is required to force the writer stream to be closed before
- // opening the file again in compare_files. Avoids a race condition.
- mol::EntityHandle ent=mol::CreateEntity();
- PDBReader reader(fname);
- reader.Import(ent);
- String out_name("testfiles/pdb/alt-loc-tf-out.pdb");
- {
- PDBWriter writer(out_name);
- geom::Mat4 shift;
- shift.PasteTranslation(geom::Vec3(10,20,30));
- ent.RequestXCSEditor().ApplyTransform(shift);
- writer.Write(ent);
- }
- PDBReader r2(out_name);
- mol::EntityHandle ent2=mol::CreateEntity();
- r2.Import(ent2);
- mol::ResidueHandle res1=ent2.FindResidue("A", mol::ResNum(1));
- mol::AtomHandle a1=res1.FindAtom("N");
- BOOST_CHECK_EQUAL(res1.GetAltAtomPos(a1, "A"), geom::Vec3(26,84,30));
- BOOST_CHECK_EQUAL(res1.GetAltAtomPos(a1, "B"), geom::Vec3(18,-108,30));
-}
-
BOOST_AUTO_TEST_CASE(res_name_too_long)
{
std::stringstream out;
diff --git a/modules/seq/alg/pymod/renumber.py b/modules/seq/alg/pymod/renumber.py
index 9701d7ad7c2348bb9c47efe2437d00b1b58f4e05..39ea9fb489949845fb65681ac1cbb6f000f4e56e 100644
--- a/modules/seq/alg/pymod/renumber.py
+++ b/modules/seq/alg/pymod/renumber.py
@@ -1,11 +1,11 @@
from ost import io, seq, mol, conop
-from ost import *
+import ost
-def Renumber(seq_handle, sequence_number_with_attached_view=1):
+def Renumber(seq_handle):
"""
Function to renumber an entity according to an alignment between the model sequence
- and the full-length target sequence. The aligned model sequence or the alignment itself
- with an attached view needs to be provided. Upon succcess, the renumbered entity is returned.
+ and the full-length target sequence. The aligned model sequence with an attached
+ view needs to be provided. Upon succcess, the renumbered entity is returned.
.. code-block:: python
@@ -16,69 +16,35 @@ def Renumber(seq_handle, sequence_number_with_attached_view=1):
pdb_seq=seq.SequenceFromChain("model", ent.chains[0])
aln=ClustalW(s,pdb_seq)
aln.AttachView(1,ent.chains[0].Select(""))
- e=Renumber(aln.GetSequence(sequence_number_with_attached_view))
+ e=Renumber(aln.GetSequence(1))
io.SavePDB(e, "renum.pdb")
"""
- if isinstance(seq_handle, seq.SequenceHandle):
- if seq_handle.HasAttachedView()==False:
- raise RuntimeError, "Sequence Handle has no attached view"
- changed_residue_count=0
- renumberingFlag = False
- ent_n=mol.CreateEntity()
- ed=ent_n.RequestXCSEditor()
- c=ed.InsertChain(" ")
- for pos in range(len(seq_handle)):
- if seq_handle[pos]!='-':
- r=seq_handle.GetResidue(pos)
- if r.IsValid():
- #print seq_handle[pos],r.number.num,pos+1
- if r.number.num!=pos+1:
- changed_residue_count+=1
- renumberingFlag = True
- r_n=ed.AppendResidue(c,r.name, mol.ResNum(pos+1))
- for atom in r.atoms:
- ed.InsertAtom(r_n,atom.name,atom.pos,atom.prop)
- else:
- err='Error: renumbering failed at position %s' %pos
- raise RuntimeError, err
- if renumberingFlag == True:
- err = 'Warning: %s residues have been renumbered!' %changed_residue_count
- LogInfo(err)
- conop.ConnectAll(ent_n)
- return ent_n
+ if seq_handle.HasAttachedView()==False:
+ raise RuntimeError, "Sequence Handle has no attached view"
+ changed_residue_count=0
+ renumberingFlag = False
+ ent_n=mol.CreateEntity()
+ ed=ent_n.RequestXCSEditor()
+ c=ed.InsertChain(" ")
+ for pos in range(len(seq_handle)):
+ if seq_handle[pos]!='-':
+ r=seq_handle.GetResidue(pos)
+ if r.IsValid():
+ #print seq_handle[pos],r.number.num,pos+1
+ if r.number.num!=pos+1:
+ changed_residue_count+=1
+ renumberingFlag = True
+ r_n=ed.AppendResidue(c,r.name, mol.ResNum(pos+1))
+ for atom in r.atoms:
+ ed.InsertAtom(r_n,atom.name,atom.pos,atom.prop)
+ else:
+ err='Error: renumbering failed at position %s' %pos
+ raise RuntimeError, err
+ if renumberingFlag == True:
+ err = 'Warning: %s residues have been renumbered!' %changed_residue_count
+ ost.LogMessage(err)
+ conop.ConnectAll(ent_n)
+ return ent_n
- elif isinstance(seq_handle, seq.AlignmentHandle):
- if seq_handle.GetSequence(sequence_number_with_attached_view).HasAttachedView()==False:
- raise RuntimeError, "Sequence Handle has no attached view"
- dir(seq_handle)
- counter=0
- changed_residue_count=0
- renumberingFlag = False
- ent_n=mol.CreateEntity()
- ed=ent_n.RequestXCSEditor()
- c=ed.InsertChain(seq_handle.GetSequence(sequence_number_with_attached_view).GetAttachedView().chains[0].name)
- for col in seq_handle:
- if col[0]!='-' and col[1]!='-':
- if col[0]==col[1]:
- rnum=seq_handle.GetSequence(sequence_number_with_attached_view).GetResidueIndex(counter)
- r=seq_handle.GetSequence(sequence_number_with_attached_view).GetResidue(counter)
- if r.IsValid():
- if r.number.num!=counter+1:
- changed_residue_count+=1
- renumberingFlag = True
- r_n=ed.AppendResidue(c,r.name, mol.ResNum(counter+1))
- for atom in r.atoms:
- ed.InsertAtom(r_n,atom.name,atom.pos,atom.prop)
-
- else:
- raise RuntimeError("invalide residue at postion %s (renumbering failed)" %(counter))
- else:
- raise RuntimeError("residue mismatch at position %d (%s vs %s) (renumbering failed)"%(counter, col[0],col[1]))
- counter+=1
- if renumberingFlag == True:
- err = 'Warning: %s residues have been renumbered!' %changed_residue_count
- LogInfo(err)
- conop.ConnectAll(ent_n)
- return ent_n
diff --git a/modules/seq/alg/tests/CMakeLists.txt b/modules/seq/alg/tests/CMakeLists.txt
index aafdabc4b723b7ee0ac6b978eb28cf34f95b5c23..37969a869b14c0f740f2b8e221509120f1cd1a6e 100644
--- a/modules/seq/alg/tests/CMakeLists.txt
+++ b/modules/seq/alg/tests/CMakeLists.txt
@@ -2,7 +2,6 @@ set(OST_SEQ_ALG_UNIT_TESTS
test_merge_pairwise_alignments.cc
test_sequence_identity.cc
tests.cc
- test_renumber.py
)
ost_unittest(seq_alg "${OST_SEQ_ALG_UNIT_TESTS}")
diff --git a/modules/seq/alg/tests/test_renumber.py b/modules/seq/alg/tests/test_renumber.py
deleted file mode 100644
index 498c42c863f5fc564af954adb3ea4cd8c5319459..0000000000000000000000000000000000000000
--- a/modules/seq/alg/tests/test_renumber.py
+++ /dev/null
@@ -1,118 +0,0 @@
-import unittest
-from ost import *
-from ost import settings
-from ost import seq
-from ost.bindings.clustalw import *
-from ost.seq.alg import renumber
-
-class TestRenumber(unittest.TestCase):
-
- def setUp(self):
- self.target_seq = io.LoadSequence("testfiles/peptide.fasta")
- self.peptide_original = io.LoadEntity("testfiles/peptide_original.pdb")
- self.peptide_plus_5 = io.LoadEntity("testfiles/peptide_plus_5.pdb")
- self.peptide_random = io.LoadEntity("testfiles/peptide_random.pdb")
- self.peptide_del_1_2 = io.LoadEntity("testfiles/peptide_del_1_2.pdb")
- self.peptide_del_4 = io.LoadEntity("testfiles/peptide_del_4.pdb")
- self.peptide_mutation_3 = io.LoadEntity("testfiles/peptide_mutation_3.pdb")
-
-
- def testPeptidePlusFive(self):
- """
- All residue numbers shifted by 5.
- Check whether internal atom order changes while renumbering
- (a new entity is generated in the edit_mode)
- TODO: add more basic tests: are all properties preserved?
- """
- model_seq=seq.SequenceFromChain(" ", self.peptide_plus_5.chains[0])
- model_seq.name="model"
- aln=ClustalW(self.target_seq,model_seq)
- aln.AttachView(1,self.peptide_plus_5.Select(""))
- ent_n=renumber.Renumber(aln)
-
- for r_counter in range(len(self.peptide_original.residues)):
- assert self.peptide_original.residues[r_counter].qualified_name == ent_n.residues[r_counter].qualified_name, \
- "Renumbering failed on residue level: restoring from ResNum+5"
- for atom_nr in range(len(self.peptide_original.residues[r_counter].atoms)):
- assert self.peptide_original.residues[r_counter].atoms[atom_nr].name==ent_n.residues[r_counter].atoms[atom_nr].name, \
- "Renumbering failed on atom level: restoring from ResNum+5"
-
-
- def testPeptideRandom(self):
- """
- Change residue names in random order
- """
- model_seq=seq.SequenceFromChain(" ", self.peptide_random.chains[0])
- model_seq.name="model"
- aln=ClustalW(self.target_seq,model_seq)
- aln.AttachView(1,self.peptide_random.Select(""))
- ent_n=renumber.Renumber(aln)
-
- for r_counter in range(len(self.peptide_original.residues)):
- assert self.peptide_original.residues[r_counter].qualified_name == ent_n.residues[r_counter].qualified_name, \
- "Renumbering failed on residue level: restoring from random residue numbers"
- for atom_nr in range(len(self.peptide_original.residues[r_counter].atoms)):
- assert self.peptide_original.residues[r_counter].atoms[atom_nr].name==ent_n.residues[r_counter].atoms[atom_nr].name, \
- "Renumbering failed on atom level: restoring from random residue numbers"
-
-
- def testPeptideDel_1_2(self):
- """
- First two residues were removed
- """
- model_seq=seq.SequenceFromChain(" ", self.peptide_del_1_2.chains[0])
- model_seq.name="model"
- aln=ClustalW(self.target_seq,model_seq)
- aln.AttachView(1,self.peptide_del_1_2.Select(""))
- ent_n=renumber.Renumber(aln)
-
- for r_counter in range(len(self.peptide_original.residues)):
- if r_counter==0 or r_counter==1:
- continue
- assert self.peptide_original.residues[r_counter].qualified_name == ent_n.residues[r_counter-2].qualified_name, \
- "Renumbering failed on residue level: restoring from random residue numbers"
- for atom_nr in range(len(self.peptide_original.residues[r_counter].atoms)):
- assert self.peptide_original.residues[r_counter].atoms[atom_nr].name==ent_n.residues[r_counter-2].atoms[atom_nr].name, \
- "Renumbering failed on atom level: restoring from random residue numbers"
-
-
- def testPeptideDel_4(self):
- """
- Residues in the middle (position 4) was removed
- """
- model_seq=seq.SequenceFromChain(" ", self.peptide_del_4.chains[0])
- model_seq.name="model"
- aln=ClustalW(self.target_seq,model_seq)
- aln.AttachView(1,self.peptide_del_4.Select(""))
- ent_n=renumber.Renumber(aln)
-
- flag=0
- for r_counter in range(len(self.peptide_original.residues)):
- if r_counter==3:
- flag=1
- continue
- assert self.peptide_original.residues[r_counter].qualified_name == ent_n.residues[r_counter-flag].qualified_name, \
- "Renumbering failed on residue level: restoring from random residue numbers"
- for atom_nr in range(len(self.peptide_original.residues[r_counter].atoms)):
- assert self.peptide_original.residues[r_counter].atoms[atom_nr].name==ent_n.residues[r_counter-flag].atoms[atom_nr].name, \
- "Renumbering failed on atom level: restoring from random residue numbers"
-
-
- def testPeptideMutation_3(self):
- """
- Mutation to GLY at postion 3
- """
- model_seq=seq.SequenceFromChain(" ", self.peptide_mutation_3.chains[0])
- model_seq.name="model"
- aln=ClustalW(self.target_seq,model_seq)
- aln.AttachView(1,self.peptide_mutation_3.Select(""))
- self.assertRaises(RuntimeError, renumber.Renumber, aln)
-
-
-
-if __name__ == "__main__":
- # test renumbering
- try:
- unittest.main()
- except Exception, e:
- print e
\ No newline at end of file
diff --git a/modules/seq/alg/tests/testfiles/peptide.fasta b/modules/seq/alg/tests/testfiles/peptide.fasta
deleted file mode 100644
index 8366b04ca04fb059f3d15348e964b9bdf8f4490e..0000000000000000000000000000000000000000
--- a/modules/seq/alg/tests/testfiles/peptide.fasta
+++ /dev/null
@@ -1,2 +0,0 @@
->peptide
-MPTNA
\ No newline at end of file
diff --git a/modules/seq/alg/tests/testfiles/peptide_del_1_2.pdb b/modules/seq/alg/tests/testfiles/peptide_del_1_2.pdb
deleted file mode 100644
index 06fc7e30a5bd50f197a3db75a8cda18ba1b5361f..0000000000000000000000000000000000000000
--- a/modules/seq/alg/tests/testfiles/peptide_del_1_2.pdb
+++ /dev/null
@@ -1,20 +0,0 @@
-ATOM 16 N THR 1 -26.565 -9.309 10.007 1.00 0.00 N
-ATOM 17 CA THR 1 -26.102 -8.194 9.247 1.00 0.00 C
-ATOM 18 C THR 1 -25.296 -7.372 10.186 1.00 0.00 C
-ATOM 19 O THR 1 -24.295 -6.768 9.810 1.00 0.00 O
-ATOM 20 CB THR 1 -27.274 -7.369 8.683 1.00 0.00 C
-ATOM 21 OG1 THR 1 -28.080 -6.880 9.762 1.00 0.00 O
-ATOM 22 CG2 THR 1 -28.139 -8.227 7.772 1.00 0.00 C
-ATOM 23 N ASN 2 -25.736 -7.349 11.452 1.00 0.00 N
-ATOM 24 CA ASN 2 -25.104 -6.609 12.495 1.00 0.00 C
-ATOM 25 C ASN 2 -23.742 -7.171 12.684 1.00 0.00 C
-ATOM 26 O ASN 2 -22.806 -6.454 13.030 1.00 0.00 O
-ATOM 27 CB ASN 2 -25.901 -6.728 13.795 1.00 0.00 C
-ATOM 28 CG ASN 2 -27.189 -5.929 13.764 1.00 0.00 C
-ATOM 29 OD1 ASN 2 -27.340 -5.007 12.963 1.00 0.00 O
-ATOM 30 ND2 ASN 2 -28.124 -6.282 14.639 1.00 0.00 N
-ATOM 31 N ALA 3 -16.677 -4.828 10.806 1.00 0.00 N
-ATOM 32 CA ALA 3 -15.984 -3.708 10.241 1.00 0.00 C
-ATOM 33 C ALA 3 -15.498 -2.863 11.363 1.00 0.00 C
-ATOM 34 O ALA 3 -14.369 -2.378 11.344 1.00 0.00 O
-ATOM 35 CB ALA 3 -16.917 -2.901 9.352 1.00 0.00 C
\ No newline at end of file
diff --git a/modules/seq/alg/tests/testfiles/peptide_del_4.pdb b/modules/seq/alg/tests/testfiles/peptide_del_4.pdb
deleted file mode 100644
index 183ce9c57a125cc1bd0a16c7125b1fb13154de5d..0000000000000000000000000000000000000000
--- a/modules/seq/alg/tests/testfiles/peptide_del_4.pdb
+++ /dev/null
@@ -1,27 +0,0 @@
-ATOM 1 N MET 1 -29.037 -8.783 14.347 1.00 0.00 N
-ATOM 2 CA MET 1 -28.985 -9.502 13.056 1.00 0.00 C
-ATOM 3 C MET 1 -27.597 -9.852 12.665 1.00 0.00 C
-ATOM 4 O MET 1 -26.614 -9.275 13.129 1.00 0.00 O
-ATOM 5 CB MET 1 -29.575 -8.640 11.938 1.00 0.00 C
-ATOM 6 CG MET 1 -31.084 -8.470 12.016 1.00 0.00 C
-ATOM 7 SD MET 1 -31.752 -7.534 10.628 1.00 0.00 S
-ATOM 8 CE MET 1 -33.497 -7.530 11.030 1.00 0.00 C
-ATOM 9 N PRO 2 -27.533 -10.838 11.828 1.00 0.00 N
-ATOM 10 CA PRO 2 -26.273 -11.293 11.337 1.00 0.00 C
-ATOM 11 C PRO 2 -25.709 -10.233 10.478 1.00 0.00 C
-ATOM 12 O PRO 2 -24.518 -10.265 10.186 1.00 0.00 O
-ATOM 13 CB PRO 2 -26.616 -12.565 10.559 1.00 0.00 C
-ATOM 14 CG PRO 2 -28.043 -12.386 10.161 1.00 0.00 C
-ATOM 15 CD PRO 2 -28.699 -11.637 11.286 1.00 0.00 C
-ATOM 16 N THR 3 -26.565 -9.309 10.007 1.00 0.00 N
-ATOM 17 CA THR 3 -26.102 -8.194 9.247 1.00 0.00 C
-ATOM 18 C THR 3 -25.296 -7.372 10.186 1.00 0.00 C
-ATOM 19 O THR 3 -24.295 -6.768 9.810 1.00 0.00 O
-ATOM 20 CB THR 3 -27.274 -7.369 8.683 1.00 0.00 C
-ATOM 21 OG1 THR 3 -28.080 -6.880 9.762 1.00 0.00 O
-ATOM 22 CG2 THR 3 -28.139 -8.227 7.772 1.00 0.00 C
-ATOM 31 N ALA 4 -16.677 -4.828 10.806 1.00 0.00 N
-ATOM 32 CA ALA 4 -15.984 -3.708 10.241 1.00 0.00 C
-ATOM 33 C ALA 4 -15.498 -2.863 11.363 1.00 0.00 C
-ATOM 34 O ALA 4 -14.369 -2.378 11.344 1.00 0.00 O
-ATOM 35 CB ALA 4 -16.917 -2.901 9.352 1.00 0.00 C
\ No newline at end of file
diff --git a/modules/seq/alg/tests/testfiles/peptide_mutation_3.pdb b/modules/seq/alg/tests/testfiles/peptide_mutation_3.pdb
deleted file mode 100644
index be9fa82c7d15a43b2a9d906466c33c74d0293fca..0000000000000000000000000000000000000000
--- a/modules/seq/alg/tests/testfiles/peptide_mutation_3.pdb
+++ /dev/null
@@ -1,32 +0,0 @@
-ATOM 1 N MET 1 -29.037 -8.783 14.347 1.00 0.00 N
-ATOM 2 CA MET 1 -28.985 -9.502 13.056 1.00 0.00 C
-ATOM 3 C MET 1 -27.597 -9.852 12.665 1.00 0.00 C
-ATOM 4 O MET 1 -26.614 -9.275 13.129 1.00 0.00 O
-ATOM 5 CB MET 1 -29.575 -8.640 11.938 1.00 0.00 C
-ATOM 6 CG MET 1 -31.084 -8.470 12.016 1.00 0.00 C
-ATOM 7 SD MET 1 -31.752 -7.534 10.628 1.00 0.00 S
-ATOM 8 CE MET 1 -33.497 -7.530 11.030 1.00 0.00 C
-ATOM 9 N PRO 2 -27.533 -10.838 11.828 1.00 0.00 N
-ATOM 10 CA PRO 2 -26.273 -11.293 11.337 1.00 0.00 C
-ATOM 11 C PRO 2 -25.709 -10.233 10.478 1.00 0.00 C
-ATOM 12 O PRO 2 -24.518 -10.265 10.186 1.00 0.00 O
-ATOM 13 CB PRO 2 -26.616 -12.565 10.559 1.00 0.00 C
-ATOM 14 CG PRO 2 -28.043 -12.386 10.161 1.00 0.00 C
-ATOM 15 CD PRO 2 -28.699 -11.637 11.286 1.00 0.00 C
-ATOM 16 N GLY 3 -26.565 -9.309 10.007 1.00 0.00 N
-ATOM 17 CA GLY 3 -26.102 -8.194 9.247 1.00 0.00 C
-ATOM 18 C GLY 3 -25.296 -7.372 10.186 1.00 0.00 C
-ATOM 19 O GLY 3 -24.295 -6.768 9.810 1.00 0.00 O
-ATOM 23 N ASN 4 -25.736 -7.349 11.452 1.00 0.00 N
-ATOM 24 CA ASN 4 -25.104 -6.609 12.495 1.00 0.00 C
-ATOM 25 C ASN 4 -23.742 -7.171 12.684 1.00 0.00 C
-ATOM 26 O ASN 4 -22.806 -6.454 13.030 1.00 0.00 O
-ATOM 27 CB ASN 4 -25.901 -6.728 13.795 1.00 0.00 C
-ATOM 28 CG ASN 4 -27.189 -5.929 13.764 1.00 0.00 C
-ATOM 29 OD1 ASN 4 -27.340 -5.007 12.963 1.00 0.00 O
-ATOM 30 ND2 ASN 4 -28.124 -6.282 14.639 1.00 0.00 N
-ATOM 31 N ALA 5 -16.677 -4.828 10.806 1.00 0.00 N
-ATOM 32 CA ALA 5 -15.984 -3.708 10.241 1.00 0.00 C
-ATOM 33 C ALA 5 -15.498 -2.863 11.363 1.00 0.00 C
-ATOM 34 O ALA 5 -14.369 -2.378 11.344 1.00 0.00 O
-ATOM 35 CB ALA 5 -16.917 -2.901 9.352 1.00 0.00 C
\ No newline at end of file
diff --git a/modules/seq/alg/tests/testfiles/peptide_original.pdb b/modules/seq/alg/tests/testfiles/peptide_original.pdb
deleted file mode 100644
index 8068ae46b1353f2c52556919ef5cf89c2d5e5a1f..0000000000000000000000000000000000000000
--- a/modules/seq/alg/tests/testfiles/peptide_original.pdb
+++ /dev/null
@@ -1,35 +0,0 @@
-ATOM 1 N MET 1 -29.037 -8.783 14.347 1.00 0.00 N
-ATOM 2 CA MET 1 -28.985 -9.502 13.056 1.00 0.00 C
-ATOM 3 C MET 1 -27.597 -9.852 12.665 1.00 0.00 C
-ATOM 4 O MET 1 -26.614 -9.275 13.129 1.00 0.00 O
-ATOM 5 CB MET 1 -29.575 -8.640 11.938 1.00 0.00 C
-ATOM 6 CG MET 1 -31.084 -8.470 12.016 1.00 0.00 C
-ATOM 7 SD MET 1 -31.752 -7.534 10.628 1.00 0.00 S
-ATOM 8 CE MET 1 -33.497 -7.530 11.030 1.00 0.00 C
-ATOM 9 N PRO 2 -27.533 -10.838 11.828 1.00 0.00 N
-ATOM 10 CA PRO 2 -26.273 -11.293 11.337 1.00 0.00 C
-ATOM 11 C PRO 2 -25.709 -10.233 10.478 1.00 0.00 C
-ATOM 12 O PRO 2 -24.518 -10.265 10.186 1.00 0.00 O
-ATOM 13 CB PRO 2 -26.616 -12.565 10.559 1.00 0.00 C
-ATOM 14 CG PRO 2 -28.043 -12.386 10.161 1.00 0.00 C
-ATOM 15 CD PRO 2 -28.699 -11.637 11.286 1.00 0.00 C
-ATOM 16 N THR 3 -26.565 -9.309 10.007 1.00 0.00 N
-ATOM 17 CA THR 3 -26.102 -8.194 9.247 1.00 0.00 C
-ATOM 18 C THR 3 -25.296 -7.372 10.186 1.00 0.00 C
-ATOM 19 O THR 3 -24.295 -6.768 9.810 1.00 0.00 O
-ATOM 20 CB THR 3 -27.274 -7.369 8.683 1.00 0.00 C
-ATOM 21 OG1 THR 3 -28.080 -6.880 9.762 1.00 0.00 O
-ATOM 22 CG2 THR 3 -28.139 -8.227 7.772 1.00 0.00 C
-ATOM 23 N ASN 4 -25.736 -7.349 11.452 1.00 0.00 N
-ATOM 24 CA ASN 4 -25.104 -6.609 12.495 1.00 0.00 C
-ATOM 25 C ASN 4 -23.742 -7.171 12.684 1.00 0.00 C
-ATOM 26 O ASN 4 -22.806 -6.454 13.030 1.00 0.00 O
-ATOM 27 CB ASN 4 -25.901 -6.728 13.795 1.00 0.00 C
-ATOM 28 CG ASN 4 -27.189 -5.929 13.764 1.00 0.00 C
-ATOM 29 OD1 ASN 4 -27.340 -5.007 12.963 1.00 0.00 O
-ATOM 30 ND2 ASN 4 -28.124 -6.282 14.639 1.00 0.00 N
-ATOM 31 N ALA 5 -16.677 -4.828 10.806 1.00 0.00 N
-ATOM 32 CA ALA 5 -15.984 -3.708 10.241 1.00 0.00 C
-ATOM 33 C ALA 5 -15.498 -2.863 11.363 1.00 0.00 C
-ATOM 34 O ALA 5 -14.369 -2.378 11.344 1.00 0.00 O
-ATOM 35 CB ALA 5 -16.917 -2.901 9.352 1.00 0.00 C
\ No newline at end of file
diff --git a/modules/seq/alg/tests/testfiles/peptide_plus_5.pdb b/modules/seq/alg/tests/testfiles/peptide_plus_5.pdb
deleted file mode 100644
index c64a572640047c0f784ecf3ccd733b4756f39f92..0000000000000000000000000000000000000000
--- a/modules/seq/alg/tests/testfiles/peptide_plus_5.pdb
+++ /dev/null
@@ -1,35 +0,0 @@
-ATOM 1 N MET 6 -29.037 -8.783 14.347 1.00 0.00 N
-ATOM 2 CA MET 6 -28.985 -9.502 13.056 1.00 0.00 C
-ATOM 3 C MET 6 -27.597 -9.852 12.665 1.00 0.00 C
-ATOM 4 O MET 6 -26.614 -9.275 13.129 1.00 0.00 O
-ATOM 5 CB MET 6 -29.575 -8.640 11.938 1.00 0.00 C
-ATOM 6 CG MET 6 -31.084 -8.470 12.016 1.00 0.00 C
-ATOM 7 SD MET 6 -31.752 -7.534 10.628 1.00 0.00 S
-ATOM 8 CE MET 6 -33.497 -7.530 11.030 1.00 0.00 C
-ATOM 9 N PRO 7 -27.533 -10.838 11.828 1.00 0.00 N
-ATOM 10 CA PRO 7 -26.273 -11.293 11.337 1.00 0.00 C
-ATOM 11 C PRO 7 -25.709 -10.233 10.478 1.00 0.00 C
-ATOM 12 O PRO 7 -24.518 -10.265 10.186 1.00 0.00 O
-ATOM 13 CB PRO 7 -26.616 -12.565 10.559 1.00 0.00 C
-ATOM 14 CG PRO 7 -28.043 -12.386 10.161 1.00 0.00 C
-ATOM 15 CD PRO 7 -28.699 -11.637 11.286 1.00 0.00 C
-ATOM 16 N THR 8 -26.565 -9.309 10.007 1.00 0.00 N
-ATOM 17 CA THR 8 -26.102 -8.194 9.247 1.00 0.00 C
-ATOM 18 C THR 8 -25.296 -7.372 10.186 1.00 0.00 C
-ATOM 19 O THR 8 -24.295 -6.768 9.810 1.00 0.00 O
-ATOM 20 CB THR 8 -27.274 -7.369 8.683 1.00 0.00 C
-ATOM 21 OG1 THR 8 -28.080 -6.880 9.762 1.00 0.00 O
-ATOM 22 CG2 THR 8 -28.139 -8.227 7.772 1.00 0.00 C
-ATOM 23 N ASN 9 -25.736 -7.349 11.452 1.00 0.00 N
-ATOM 24 CA ASN 9 -25.104 -6.609 12.495 1.00 0.00 C
-ATOM 25 C ASN 9 -23.742 -7.171 12.684 1.00 0.00 C
-ATOM 26 O ASN 9 -22.806 -6.454 13.030 1.00 0.00 O
-ATOM 27 CB ASN 9 -25.901 -6.728 13.795 1.00 0.00 C
-ATOM 28 CG ASN 9 -27.189 -5.929 13.764 1.00 0.00 C
-ATOM 29 OD1 ASN 9 -27.340 -5.007 12.963 1.00 0.00 O
-ATOM 30 ND2 ASN 9 -28.124 -6.282 14.639 1.00 0.00 N
-ATOM 31 N ALA 10 -16.677 -4.828 10.806 1.00 0.00 N
-ATOM 32 CA ALA 10 -15.984 -3.708 10.241 1.00 0.00 C
-ATOM 33 C ALA 10 -15.498 -2.863 11.363 1.00 0.00 C
-ATOM 34 O ALA 10 -14.369 -2.378 11.344 1.00 0.00 O
-ATOM 35 CB ALA 10 -16.917 -2.901 9.352 1.00 0.00 C
\ No newline at end of file
diff --git a/modules/seq/alg/tests/testfiles/peptide_random.pdb b/modules/seq/alg/tests/testfiles/peptide_random.pdb
deleted file mode 100644
index 74597e72bf51d7f8f0f6fcacb198dd14d16f7e3f..0000000000000000000000000000000000000000
--- a/modules/seq/alg/tests/testfiles/peptide_random.pdb
+++ /dev/null
@@ -1,35 +0,0 @@
-ATOM 1 N MET 6 -29.037 -8.783 14.347 1.00 0.00 N
-ATOM 2 CA MET 6 -28.985 -9.502 13.056 1.00 0.00 C
-ATOM 3 C MET 6 -27.597 -9.852 12.665 1.00 0.00 C
-ATOM 4 O MET 6 -26.614 -9.275 13.129 1.00 0.00 O
-ATOM 5 CB MET 6 -29.575 -8.640 11.938 1.00 0.00 C
-ATOM 6 CG MET 6 -31.084 -8.470 12.016 1.00 0.00 C
-ATOM 7 SD MET 6 -31.752 -7.534 10.628 1.00 0.00 S
-ATOM 8 CE MET 6 -33.497 -7.530 11.030 1.00 0.00 C
-ATOM 9 N PRO 1 -27.533 -10.838 11.828 1.00 0.00 N
-ATOM 10 CA PRO 1 -26.273 -11.293 11.337 1.00 0.00 C
-ATOM 11 C PRO 1 -25.709 -10.233 10.478 1.00 0.00 C
-ATOM 12 O PRO 1 -24.518 -10.265 10.186 1.00 0.00 O
-ATOM 13 CB PRO 1 -26.616 -12.565 10.559 1.00 0.00 C
-ATOM 14 CG PRO 1 -28.043 -12.386 10.161 1.00 0.00 C
-ATOM 15 CD PRO 1 -28.699 -11.637 11.286 1.00 0.00 C
-ATOM 16 N THR 7 -26.565 -9.309 10.007 1.00 0.00 N
-ATOM 17 CA THR 7 -26.102 -8.194 9.247 1.00 0.00 C
-ATOM 18 C THR 7 -25.296 -7.372 10.186 1.00 0.00 C
-ATOM 19 O THR 7 -24.295 -6.768 9.810 1.00 0.00 O
-ATOM 20 CB THR 7 -27.274 -7.369 8.683 1.00 0.00 C
-ATOM 21 OG1 THR 7 -28.080 -6.880 9.762 1.00 0.00 O
-ATOM 22 CG2 THR 7 -28.139 -8.227 7.772 1.00 0.00 C
-ATOM 23 N ASN 4 -25.736 -7.349 11.452 1.00 0.00 N
-ATOM 24 CA ASN 4 -25.104 -6.609 12.495 1.00 0.00 C
-ATOM 25 C ASN 4 -23.742 -7.171 12.684 1.00 0.00 C
-ATOM 26 O ASN 4 -22.806 -6.454 13.030 1.00 0.00 O
-ATOM 27 CB ASN 4 -25.901 -6.728 13.795 1.00 0.00 C
-ATOM 28 CG ASN 4 -27.189 -5.929 13.764 1.00 0.00 C
-ATOM 29 OD1 ASN 4 -27.340 -5.007 12.963 1.00 0.00 O
-ATOM 30 ND2 ASN 4 -28.124 -6.282 14.639 1.00 0.00 N
-ATOM 31 N ALA 2 -16.677 -4.828 10.806 1.00 0.00 N
-ATOM 32 CA ALA 2 -15.984 -3.708 10.241 1.00 0.00 C
-ATOM 33 C ALA 2 -15.498 -2.863 11.363 1.00 0.00 C
-ATOM 34 O ALA 2 -14.369 -2.378 11.344 1.00 0.00 O
-ATOM 35 CB ALA 2 -16.917 -2.901 9.352 1.00 0.00 C
\ No newline at end of file