def test_align_file(self):
pdbin1 = os.path.join(self.testfiles_dir, '1D7M.pdb')
pdbin2 = os.path.join(self.testfiles_dir, '1GU8.pdb')
pdbin3 = os.path.join(self.testfiles_dir, '2UUI.pdb')
s1 = sequence_util.Sequence(pdb=pdbin1)
s1 += sequence_util.Sequence(pdb=pdbin2)
s1 += sequence_util.Sequence(pdb=pdbin3)
ref = ">1D7M.pdb" + os.linesep
ref += "EMANRLAGLENSLESEKVSREQLIKQKDQLNSLLASLESEGAEREKRLRELEAKLDETLKNLELEKLARMELEARLAKTE" + os.linesep
ref += "KDRAILELKLAEAIDEKSKLE" + os.linesep
ref += os.linesep
ref += ">1D7M.pdb" + os.linesep
ref += "EMANRLAGLENSLESEKVSREQLIKQKDQLNSLLASLESEGAEREKRLRELEAKLDETLKNLELEKLARMELEARLAKTE" + os.linesep
ref += "KDRAILELKLAEAIDEKSKLE" + os.linesep
ref += os.linesep
ref += ">1GU8.pdb" + os.linesep
ref += "VGLTTLFWLGAIGMLVGTLAFAWAGRDAGSGERRYYVTLVGISGIAAVAYVVMALGVGWVPVAERTVFAPRYIDWILTTP" + os.linesep
ref += "LIVYFLGLLAGLDSREFGIVITLNTVVMLAGFAGAMVPGIERYALFGMGAVAFLGLVYYLVGPMTESASQRSSGIKSLYV" + os.linesep
ref += "RLRNLTVILWAIYPFIWLLGPPGVALLTPTVDVALIVYLDLVTKVGFGFIALDAAATL" + os.linesep
ref += os.linesep
ref += ">2UUI.pdb" + os.linesep
ref += "MHHHHHHKDEVALLAAVTLLGVLLQAYFSLQVISARRAFRVSPPLTTGPPEFERVYRAQVNCSEYFPLFLATLWVAGIFF" + os.linesep
ref += "HEGAAALCGLVYLFARLRYFQGYARSAQLRLAPLYASARALWLLVALAALGLLAHFLPAALRAALLGRLRTLLPWA" + os.linesep
ref += os.linesep
self.assertEqual(s1.fasta_str(pdbname=True), ref)
def alignment_file(self, models, alignment_file=None):
"""Create an alignment file for the models - this is based on the assumption they are all the same length
but may have different residues"""
if not alignment_file:
alignment_file = os.path.join(self.work_dir, 'homologs.fasta')
all_seq = sequence_util.Sequence(pdb=models[0])
for model in models[1:]:
all_seq += sequence_util.Sequence(pdb=model)
if not all(map(lambda x: x == len(all_seq.sequences[0]), [len(s) for s in all_seq.sequences])):
raise RuntimeError('PDB files are not all of the same length!\n{0}'.format(models))
all_seq.write_fasta(alignment_file, pdbname=True)
return alignment_file
def test_add(self):
s1 = sequence_util.Sequence(
pdb=os.path.join(self.testfiles_dir, '1GU8.pdb'))
s2 = sequence_util.Sequence(
fasta=os.path.join(self.testfiles_dir, '2uui.fasta'))
s1 += s2
self.assertTrue(len(s1.sequences), 2)
self.assertTrue(len(s1.resseqs), 2)
self.assertTrue(len(s1.headers), 2)
self.assertTrue(len(s1.pdbs), 2)
self.assertTrue(len(s1.chains), 2)
self.assertTrue(len(s1.fasta_files), 2)
def test__parse_fasta_2(self):
fasta = [">foo"]
fasta += ["AAAAA AA"]
s = sequence_util.Sequence()
s._parse_fasta(fasta)
self.assertListEqual(s.headers, [">foo"])
self.assertListEqual(s.sequences, ["AAAAAAA"])
def model_core_from_theseus(models, alignment_file, var_by_res, work_dir=None):
"""
Only residues from the first protein are listed in the theseus output, but then not even all of them
We assume the output is based on the original alignment so that where each residue in the first protein
lines up with either another residue in one of the other proteins or a gap
SO - we need to go through the theseus data and for each residue that is core find the corresponding residues
in the other proteins
We use the resSeq numbers to match the residues across the alignment
"""
if not os.path.isdir(work_dir):
os.mkdir(work_dir)
seqalign = sequence_util.Sequence(fasta=alignment_file)
# We now need to add the list of pdbs, chains and resSeqs of the other models to the Sequence object
for m in models:
seqalign.add_pdb_data(m)
# Sanity check that the names of the pdb files match those from the fasta header
# Format is expected to be: '>1ujb.pdb(A)'
names = [h[1:].split('(')[0] for h in seqalign.headers]
if not seqalign.pdbs == names:
raise RuntimeError(
"headers and names of pdb files do not match!\n{0}\n{1}".format(
seqalign.pdbs, names))
# Get the name of the first pdb that the alignment is based on
first = seqalign.pdbs[0]
# Dictionary mapping model pdb to resSeqs that are core
model2core = {}
for p in seqalign.pdbs:
model2core[p] = [] # initialise
# Get list of core resSeqs in the first sequence
model2core[first] = [x.resSeq for x in var_by_res if x.core]
# Now go through the first sequence and get the resSeqs of the corresponding core for the other models
pointer = 0 # Tracks where we are in the first sequence
for i, resSeq in enumerate(seqalign.resseqs[0]):
if model2core[first][pointer] == resSeq:
# Core residue in first sequence so append the corresponding resSeqs for the other proteins
for j, pdb in enumerate(seqalign.pdbs[1:]):
model2core[pdb].append(seqalign.resseqs[j + 1][i])
pointer += 1
if pointer >= len(model2core[first]):
break
core_models = []
for m in models:
name = os.path.basename(m)
pdbout = ample_util.filename_append(m, astr='core', directory=work_dir)
pdb_edit.select_residues(m, pdbout, tokeep=model2core[name])
core_models.append(pdbout)
return core_models
def test_resseq(self):
pdbin = os.path.join(self.testfiles_dir, '1D7M.pdb')
s1 = sequence_util.Sequence(pdb=pdbin)
self.assertTrue(len(s1.sequences), 2)
self.assertTrue(len(s1.headers), 2)
self.assertTrue(len(s1.pdbs), 2)
self.assertEqual(s1.pdbs[0], os.path.basename(pdbin))
self.assertTrue(s1.resseqs[0][-1], 343)
def test_fail_char(self):
fp = sequence_util.Sequence()
# Test case 1 - expected to work
fp.sequences = ["YFLVKGMGVSDPDAKKFYAITTLVYAIAFTMYLSMLLGYGLTMVP"]
try:
fp.canonicalise()
except RuntimeError as msg:
self.assertTrue(False, msg)
# Test case 2 - expected to fail
fp.sequences = ["YFLVKGMGVSDPDAKKFYAITTLVXAIAFTMYLSMLLGYGLTMVP"]
self.assertRaises(RuntimeError, fp.canonicalise)
def test_from_pdb(self):
s1 = sequence_util.Sequence(
pdb=os.path.join(self.testfiles_dir, '4DZN.pdb'))
self.assertEqual(s1.name, '4DZN')
self.assertEqual(s1.pdbs, ['4DZN.pdb', '4DZN.pdb', '4DZN.pdb'])
self.assertEqual(s1.chains, ['A', 'B', 'C'])
outfasta = ">From pdb: 4DZN.pdb chain=A length=31" + os.linesep
outfasta += "GEIAALKQEIAALKKEIAALKEIAALKQGYY" + os.linesep
outfasta += os.linesep
outfasta += ">From pdb: 4DZN.pdb chain=B length=31" + os.linesep
outfasta += "GEIAALKQEIAALKKEIAALKEIAALKQGYY" + os.linesep
outfasta += os.linesep
outfasta += ">From pdb: 4DZN.pdb chain=C length=31" + os.linesep
outfasta += "GEIAALKQEIAALKKEIAALKEIAALKQGYY" + os.linesep
outfasta += os.linesep
self.assertEqual(outfasta, "".join(s1.fasta_str()))
def test_OK(self):
infasta = ">3HAP:A|PDBID|CHAIN|SEQUENCE" + os.linesep
infasta += "QAQITGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAI" + os.linesep
infasta += "TTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLV" + os.linesep
infasta += "DADQGTILAAVGADGIMIGTGLVGALTKVYSYRFVWWAISTAA" + os.linesep
infasta += "MLYILYVLFFGFTSKAESMRPEVASTFKVL" + os.linesep
infasta += "RNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILL" + os.linesep
infasta += "RSRAIFGEAEAPEPSAGDGAAATSD"
fp = sequence_util.Sequence()
fp._parse_fasta(infasta.split(os.linesep))
outfasta = ">3HAP:A|PDBID|CHAIN|SEQUENCE" + os.linesep
outfasta += "QAQITGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYW" + os.linesep
outfasta += "ARYADWLFTTPLLLLDLALLVDADQGTILAAVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKA" + os.linesep
outfasta += "ESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFGEAEAPEPSA" + os.linesep
outfasta += "GDGAAATSD" + os.linesep
outfasta += os.linesep
self.assertEqual(outfasta, "".join(fp.fasta_str()))
self.assertEqual(fp.length(), 249)
# Get full paths to all files
args.input_file = os.path.abspath(args.input_file)
if not os.path.isfile(args.input_file):
raise RuntimeError("Cannot find input file: {}".format(
args.input_file))
if args.output_file:
args.output_file = os.path.abspath(args.output_file)
else:
n = os.path.splitext(os.path.basename(args.input_file))[0]
args.output_file = n + "_std.pdb"
if args.ren:
renumber_residues(args.input_file, args.output_file, start=1)
elif args.std:
standardise(args.input_file,
args.output_file,
del_hetatm=True,
chain=args.chain)
elif args.seq:
logging.debug(sequence_util.Sequence(pdb=args.input_file).fasta_str())
elif args.split_models:
logging.debug(split_pdb(args.input_file))
elif args.split_chains:
logging.debug(split_into_chains(args.input_file, chain=args.chain))
elif args.chain:
logging.debug(
extract_chain(args.input_file,
args.output_file,
chainID=args.chain))
def test_canonicalise_4(self):
fp = sequence_util.Sequence()
fp.sequences = ["YFLVKGMGVSDPDAKKFYAITTLVXAIAFTMYLSMLLGYGLTMVP*"]
with self.assertRaises(RuntimeError):
fp.canonicalise()
def test_canonicalise_1(self):
fp = sequence_util.Sequence()
fp.sequences = ["YFLVKGMGVSDPDAKKFYAITTLVYAIAFTMYLSMLLGYGLTMVP"]
fp.canonicalise()
self.assertTrue(True)
def test_addPdb_data(self):
fasta1 = os.path.join(self.testfiles_dir, '1ujb_2a6pA_3c7tA.afasta')
pdbin1 = os.path.join(self.ample_share, 'examples', 'homologs',
'input', '1ujbA.pdb')
pdbin2 = os.path.join(self.ample_share, 'examples', 'homologs',
'input', '2a6pA.pdb')
pdbin3 = os.path.join(self.ample_share, 'examples', 'homologs',
'input', '3c7tA.pdb')
s1 = sequence_util.Sequence(fasta=fasta1)
s1.add_pdb_data(pdbin1)
s1.add_pdb_data(pdbin2)
s1.add_pdb_data(pdbin3)
self.assertEqual(s1.pdbs[0], os.path.basename(pdbin1))
self.assertEqual(s1.chains[0], 'A')
self.assertEqual(s1.pdbs[1], os.path.basename(pdbin2))
self.assertEqual(s1.chains[1], 'A')
self.assertEqual(s1.pdbs[2], os.path.basename(pdbin3))
self.assertEqual(s1.chains[2], 'A')
p1r = [
None,
None,
1,
2,
3,
4,
5,
6,
7,
8,
9,
10,
11,
12,
13,
14,
15,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
16,
17,
18,
19,
20,
21,
22,
23,
24,
25,
26,
27,
28,
29,
30,
31,
32,
33,
34,
35,
36,
37,
38,
39,
40,
41,
42,
43,
44,
None,
45,
46,
47,
48,
49,
50,
51,
52,
53,
54,
55,
56,
57,
58,
59,
60,
61,
62,
63,
64,
65,
66,
67,
68,
69,
None,
None,
70,
71,
72,
73,
74,
75,
76,
77,
78,
79,
80,
81,
82,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
83,
None,
None,
84,
85,
86,
87,
88,
89,
90,
91,
None,
92,
93,
94,
95,
96,
97,
98,
99,
100,
101,
102,
103,
104,
105,
106,
107,
108,
109,
110,
111,
112,
113,
114,
115,
116,
117,
118,
119,
120,
None,
None,
None,
None,
None,
None,
None,
None,
121,
122,
123,
None,
None,
None,
124,
125,
None,
None,
126,
None,
None,
127,
128,
129,
130,
131,
132,
133,
134,
135,
136,
137,
138,
None,
None,
139,
140,
141,
142,
143,
144,
145,
146,
147,
148,
149,
None,
None,
150,
151,
None,
152,
153,
154,
155,
156,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
]
p2r = [
4,
5,
6,
7,
8,
9,
10,
11,
12,
13,
14,
15,
16,
17,
18,
19,
20,
21,
22,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
23,
24,
25,
26,
27,
28,
None,
29,
30,
31,
32,
33,
34,
35,
36,
37,
38,
39,
40,
41,
42,
43,
44,
45,
46,
47,
48,
49,
50,
None,
51,
52,
53,
54,
55,
56,
57,
58,
59,
60,
61,
62,
63,
64,
65,
66,
67,
68,
69,
70,
71,
72,
73,
None,
None,
None,
None,
74,
None,
None,
75,
None,
76,
77,
78,
79,
80,
81,
82,
83,
84,
85,
86,
87,
88,
89,
90,
91,
92,
93,
94,
95,
96,
97,
98,
99,
100,
101,
102,
103,
104,
None,
None,
None,
None,
None,
None,
None,
None,
105,
106,
107,
108,
109,
110,
111,
112,
113,
114,
115,
116,
117,
118,
119,
120,
121,
122,
123,
124,
125,
126,
127,
128,
129,
130,
131,
132,
None,
133,
134,
135,
136,
137,
None,
None,
138,
139,
140,
141,
142,
143,
144,
145,
146,
147,
148,
149,
150,
151,
152,
153,
154,
155,
156,
157,
158,
159,
None,
None,
None,
None,
None,
None,
None,
None,
160,
161,
162,
163,
None,
164,
165,
166,
167,
168,
169,
None,
None,
170,
171,
172,
173,
174,
175,
176,
177,
178,
179,
180,
181,
182,
183,
184,
None,
None,
None,
185,
186,
187,
188,
189,
190,
191,
192,
None,
193,
194,
195,
196,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
None,
]
p3r = [
None,
72,
73,
74,
75,
76,
77,
78,
79,
80,
81,
82,
83,
84,
85,
86,
87,
88,
89,
90,
91,
92,
93,
94,
95,
96,
97,
98,
99,
100,
101,
102,
103,
104,
105,
106,
107,
108,
109,
110,
111,
112,
113,
114,
115,
116,
117,
118,
119,
120,
121,
122,
123,
124,
None,
125,
126,
127,
128,
129,
130,
131,
132,
133,
134,
135,
136,
137,
138,
139,
140,
141,
142,
143,
144,
145,
146,
147,
148,
149,
None,
150,
151,
152,
153,
154,
155,
156,
157,
158,
159,
160,
161,
162,
163,
164,
165,
166,
167,
168,
169,
170,
171,
172,
173,
174,
175,
176,
177,
178,
179,
180,
181,
182,
183,
184,
185,
186,
187,
188,
189,
190,
191,
192,
193,
194,
195,
196,
197,
198,
199,
200,
201,
202,
203,
204,
205,
206,
207,
208,
209,
210,
211,
212,
213,
214,
215,
216,
217,
218,
219,
220,
221,
222,
223,
224,
225,
226,
227,
228,
229,
230,
231,
232,
233,
234,
235,
236,
237,
238,
239,
240,
241,
242,
243,
244,
245,
246,
247,
248,
249,
250,
None,
251,
252,
253,
254,
255,
256,
257,
258,
259,
260,
261,
262,
263,
264,
265,
266,
267,
268,
269,
270,
271,
272,
273,
274,
275,
276,
277,
278,
279,
280,
281,
282,
283,
284,
285,
286,
287,
288,
None,
None,
289,
290,
291,
292,
293,
294,
295,
296,
297,
298,
299,
300,
301,
302,
303,
None,
None,
304,
None,
None,
None,
305,
306,
307,
308,
309,
310,
311,
312,
313,
314,
315,
None,
316,
317,
318,
319,
320,
321,
322,
323,
324,
325,
326,
327,
328,
329,
330,
]
self.assertEqual(s1.resseqs[0], p1r)
self.assertEqual(s1.resseqs[1], p2r)
self.assertEqual(s1.resseqs[2], p3r)
def model_core_from_fasta(models,
alignment_file,
work_dir=None,
case_sensitive=False):
if not os.path.isdir(work_dir):
os.mkdir(work_dir)
# Read in alignment to get
align_seq = sequence_util.Sequence(fasta=alignment_file)
# Check all alignments the same length
# Get pdb names from alignment headers
seq_names = [h[1:].strip() for h in align_seq.headers]
# Need to check if the alignment file is from gesamt, in which case, the names have the
# chain names in brackets appended
for i, s in enumerate(seq_names):
x = re.search("\([a-zA-Z]*\)$", s)
if x:
seq_names[i] = s.replace(x.group(0), "")
# Get array specifying which positions are core. If the positions all align, then there
# will be a capital letter for the residue. Gaps are signified by "-" and non-structurally-
# aligned residues by lower-case letters
GAP = '-'
# Can't use below as Theseus ignores lower-case letters in the alignment
if case_sensitive:
core = [
all([x in ample_util.one2three.keys() for x in t])
for t in zip(*align_seq.sequences)
]
else:
core = [all([x != GAP for x in t]) for t in zip(*align_seq.sequences)]
if not any(core):
raise RuntimeError(
"Cannot generate core for models: {0}".format(models))
# For each sequence, get a list of which positions are core
core_positions = []
for seq in align_seq.sequences:
p = []
count = 0
for i, pos in enumerate(seq):
if pos != GAP:
if core[i]:
p.append(count)
count += 1
core_positions.append(p)
# Should check lengths of sequences match the length of the aa in the pdbs
# Create dict mapping seq_names to core positions
core_dict = dict((s, core_positions[i]) for i, s in enumerate(seq_names))
# Cut the models down to core
core_models = []
for m in models:
name = os.path.basename(m)
pdbout = ample_util.filename_append(m, astr='core', directory=work_dir)
pdb_edit.select_residues(m, pdbout, tokeep_idx=core_dict[name])
core_models.append(pdbout)
return core_models
