Edward,
I created a minfx-py fink package and a test package for
relax-py updated to the new 1.3.2 source. Unfortunately, I am
seeing a lot of failures in the testsuite on powerpc-apple-darwin9.
The results are appended below. I'll try i386-apple-darwin9 tonight.
This compares to 1.3.0 without minfx which showed no failures.
Jack
relax --test-suite
Function intros have been enabled.
#############################
# System / functional tests #
#############################
F....................FF.FFF..............E.................
======================================================================
ERROR: Test the reading of an NMRView peak list.
----------------------------------------------------------------------
relax> pipe.create(pipe_name='mf', pipe_type='mf')
relax> residue.create(res_num=70, res_name=None, mol_id=None)
relax> residue.create(res_num=72, res_name=None, mol_id=None)
relax> spin.name(spin_id=None, name='N')
relax> relax_fit.read(file='cNTnC.xpk',
dir='/sw/lib/relax-py25/test_suite/shared_data/peak_lists',
relax_time=0.017600000000000001, format='sparky', heteronuc='N', proton='HN',
int_col=None)
Sparky formatted data file.
Opening the file
'/sw/lib/relax-py25/test_suite/shared_data/peak_lists/cNTnC.xpk' for reading.
Number of header lines found: 2
Traceback (most recent call last):
File "/sw/lib/relax-py25/test_suite/system_tests/nmrview.py", line 60, in
test_read_peak_list
self.relax.interpreter._Relax_fit.read(file="cNTnC.xpk", dir=sys.path[-1]
+ "/test_suite/shared_data/peak_lists", relax_time=0.0176)
File "/sw/lib/relax-py25/prompt/relax_fit.py", line 193, in read
relax_fit_obj.read(file=file, dir=dir, relax_time=relax_time,
format=format, heteronuc=heteronuc, proton=proton, int_col=int_col)
File "/sw/lib/relax-py25/specific_fns/relax_fit.py", line 1034, in read
intensity.read(file=file, dir=dir, format=format, heteronuc=heteronuc,
proton=proton, int_col=int_col, assign_func=self.assign_function)
File "/sw/lib/relax-py25/generic_fns/intensity.py", line 284, in read
res_num, H_name, X_name, intensity = intensity_fn(file_data[i])
File "/sw/lib/relax-py25/generic_fns/intensity.py", line 95, in
intensity_sparky
raise RelaxError, "Improperly formatted Sparky file."
RelaxError: RelaxError: Improperly formatted Sparky file.
======================================================================
FAIL: The user function angles().
----------------------------------------------------------------------
relax> pipe.create(pipe_name='mf', pipe_type='mf')
relax> sequence.read(file='Ap4Aase.seq',
dir='/sw/lib/relax-py25/test_suite/shared_data', mol_name_col=None,
res_num_col=0, res_name_col=1, spin_num_col=None, spin_name_col=None,
sep=None)
Opening the file '/sw/lib/relax-py25/test_suite/shared_data/Ap4Aase.seq' for
reading.
Mol_name Res_num Res_name Spin_num Spin_name
None 1 GLY None None
None 2 PRO None None
None 3 LEU None None
None 4 GLY None None
None 5 SER None None
None 6 MET None None
None 7 ASP None None
None 8 SER None None
None 9 PRO None None
None 10 PRO None None
None 11 GLU None None
None 12 GLY None None
None 13 TYR None None
None 14 ARG None None
None 15 ARG None None
None 16 ASN None None
None 17 VAL None None
None 18 GLY None None
None 19 ILE None None
None 20 CYS None None
None 21 LEU None None
None 22 MET None None
None 23 ASN None None
None 24 ASN None None
None 25 ASP None None
None 26 LYS None None
None 27 LYS None None
None 28 ILE None None
None 29 PHE None None
None 30 ALA None None
None 31 ALA None None
None 32 SER None None
None 33 ARG None None
None 34 LEU None None
None 35 ASP None None
None 36 ILE None None
None 37 PRO None None
None 38 ASP None None
None 39 ALA None None
None 40 TRP None None
None 41 GLN None None
None 42 MET None None
None 43 PRO None None
None 44 GLN None None
None 45 GLY None None
None 46 GLY None None
None 47 ILE None None
None 48 ASP None None
None 49 GLU None None
None 50 GLY None None
None 51 GLU None None
None 52 ASP None None
None 53 PRO None None
None 54 ARG None None
None 55 ASN None None
None 56 ALA None None
None 57 ALA None None
None 58 ILE None None
None 59 ARG None None
None 60 GLU None None
None 61 LEU None None
None 62 ARG None None
None 63 GLU None None
None 64 GLU None None
None 65 THR None None
None 66 GLY None None
None 67 VAL None None
None 68 THR None None
None 69 SER None None
None 70 ALA None None
None 71 GLU None None
None 72 VAL None None
None 73 ILE None None
None 74 ALA None None
None 75 GLU None None
None 76 VAL None None
None 77 PRO None None
None 78 TYR None None
None 79 TRP None None
None 80 LEU None None
None 81 THR None None
None 82 TYR None None
None 83 ASP None None
None 84 PHE None None
None 85 PRO None None
None 86 PRO None None
None 87 LYS None None
None 88 VAL None None
None 89 ARG None None
None 90 GLU None None
None 91 LYS None None
None 92 LEU None None
None 93 ASN None None
None 94 ILE None None
None 95 GLN None None
None 96 TRP None None
None 97 GLY None None
None 98 SER None None
None 99 ASP None None
None 100 TRP None None
None 101 LYS None None
None 102 GLY None None
None 103 GLN None None
None 104 ALA None None
None 105 GLN None None
None 106 LYS None None
None 107 TRP None None
None 108 PHE None None
None 109 LEU None None
None 110 PHE None None
None 111 LYS None None
None 112 PHE None None
None 113 THR None None
None 114 GLY None None
None 115 GLN None None
None 116 ASP None None
None 117 GLN None None
None 118 GLU None None
None 119 ILE None None
None 120 ASN None None
None 121 LEU None None
None 122 LEU None None
None 123 GLY None None
None 124 ASP None None
None 125 GLY None None
None 126 SER None None
None 127 GLU None None
None 128 LYS None None
None 129 PRO None None
None 130 GLU None None
None 131 PHE None None
None 132 GLY None None
None 133 GLU None None
None 134 TRP None None
None 135 SER None None
None 136 TRP None None
None 137 VAL None None
None 138 THR None None
None 139 PRO None None
None 140 GLU None None
None 141 GLN None None
None 142 LEU None None
None 143 ILE None None
None 144 ASP None None
None 145 LEU None None
None 146 THR None None
None 147 VAL None None
None 148 GLU None None
None 149 PHE None None
None 150 LYS None None
None 151 LYS None None
None 152 PRO None None
None 153 VAL None None
None 154 TYR None None
None 155 LYS None None
None 156 GLU None None
None 157 VAL None None
None 158 LEU None None
None 159 SER None None
None 160 VAL None None
None 161 PHE None None
None 162 ALA None None
None 163 PRO None None
None 164 HIS None None
None 165 LEU None None
relax> structure.read_pdb(file='Ap4Aase_res1-12.pdb',
dir='/sw/lib/relax-py25/test_suite/shared_data/structures', model=1,
parser='scientific')
Scientific Python PDB parser.
Loading structure 1 from the PDB file.
Structure('/sw/lib/relax-py25/test_suite/shared_data/structures/Ap4Aase_res1-12.pdb',
model=1):
Peptide chain of length 12
relax> structure.load_spins(spin_id='@N', ave_pos=True)
Adding the following spins to the relax data store.
Mol_name Res_num Res_name Spin_num Spin_name
None 1 GLY 1 N
None 2 PRO 11 N
None 3 LEU 28 N
None 4 GLY 51 N
None 5 SER 59 N
None 6 MET 71 N
None 7 ASP 91 N
None 8 SER 104 N
None 9 PRO 116 N
None 10 PRO 133 N
None 11 GLU 150 N
None 12 GLY 167 N
relax> structure.vectors(attached='H', spin_id=None, struct_index=None,
verbosity=1, ave=True, unit=True)
Extracting vectors from the single structure.
Calculating the unit vectors.
The attached atom is a proton.
RelaxWarning: No attached atom could be found (atom ID ':1@1&@N').
RelaxWarning: No attached atom could be found (atom ID ':2@11&@N').
Extracted N-H vectors for ':3@28&@N'.
Extracted N-H vectors for ':4@51&@N'.
Extracted N-H vectors for ':5@59&@N'.
Extracted N-H vectors for ':6@71&@N'.
Extracted N-H vectors for ':7@91&@N'.
Extracted N-H vectors for ':8@104&@N'.
RelaxWarning: No attached atom could be found (atom ID ':9@116&@N').
RelaxWarning: No attached atom could be found (atom ID ':10@133&@N').
Extracted N-H vectors for ':11@150&@N'.
Extracted N-H vectors for ':12@167&@N'.
RelaxWarning: Either the spin number or name must be set for the spin ':13'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':14'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':15'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':16'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':17'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':18'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':19'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':20'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':21'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':22'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':23'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':24'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':25'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':26'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':27'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':28'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':29'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':30'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':31'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':32'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':33'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':34'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':35'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':36'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':37'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':38'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':39'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':40'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':41'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':42'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':43'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':44'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':45'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':46'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':47'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':48'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':49'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':50'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':51'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':52'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':53'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':54'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':55'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':56'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':57'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':58'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':59'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':60'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':61'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':62'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':63'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':64'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':65'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':66'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':67'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':68'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':69'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':70'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':71'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':72'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':73'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':74'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':75'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':76'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':77'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':78'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':79'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':80'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':81'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':82'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':83'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':84'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':85'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':86'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':87'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':88'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':89'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':90'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':91'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':92'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':93'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':94'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':95'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':96'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':97'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':98'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':99'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':100'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':101'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':102'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':103'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':104'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':105'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':106'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':107'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':108'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':109'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':110'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':111'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':112'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':113'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':114'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':115'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':116'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':117'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':118'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':119'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':120'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':121'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':122'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':123'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':124'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':125'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':126'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':127'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':128'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':129'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':130'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':131'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':132'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':133'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':134'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':135'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':136'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':137'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':138'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':139'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':140'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':141'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':142'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':143'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':144'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':145'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':146'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':147'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':148'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':149'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':150'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':151'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':152'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':153'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':154'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':155'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':156'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':157'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':158'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':159'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':160'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':161'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':162'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':163'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':164'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':165'
to identify the corresponding atom in the structure.
relax> diffusion_tensor.init(params=(16980000.0, 14170000.0,
67.174000000000007, -83.718000000000004), time_scale=1.0, d_scale=1.0,
angle_units='deg', param_types=3, spheroid_type=None, fixed=True)
relax> sequence.display(sep=None, mol_name_flag=True, res_num_flag=True,
res_name_flag=True, spin_num_flag=True, spin_name_flag=True)
Mol_name Res_num Res_name Spin_num Spin_name
None 1 GLY 1 N
None 2 PRO 11 N
None 3 LEU 28 N
None 4 GLY 51 N
None 5 SER 59 N
None 6 MET 71 N
None 7 ASP 91 N
None 8 SER 104 N
None 9 PRO 116 N
None 10 PRO 133 N
None 11 GLU 150 N
None 12 GLY 167 N
None 13 TYR None None
None 14 ARG None None
None 15 ARG None None
None 16 ASN None None
None 17 VAL None None
None 18 GLY None None
None 19 ILE None None
None 20 CYS None None
None 21 LEU None None
None 22 MET None None
None 23 ASN None None
None 24 ASN None None
None 25 ASP None None
None 26 LYS None None
None 27 LYS None None
None 28 ILE None None
None 29 PHE None None
None 30 ALA None None
None 31 ALA None None
None 32 SER None None
None 33 ARG None None
None 34 LEU None None
None 35 ASP None None
None 36 ILE None None
None 37 PRO None None
None 38 ASP None None
None 39 ALA None None
None 40 TRP None None
None 41 GLN None None
None 42 MET None None
None 43 PRO None None
None 44 GLN None None
None 45 GLY None None
None 46 GLY None None
None 47 ILE None None
None 48 ASP None None
None 49 GLU None None
None 50 GLY None None
None 51 GLU None None
None 52 ASP None None
None 53 PRO None None
None 54 ARG None None
None 55 ASN None None
None 56 ALA None None
None 57 ALA None None
None 58 ILE None None
None 59 ARG None None
None 60 GLU None None
None 61 LEU None None
None 62 ARG None None
None 63 GLU None None
None 64 GLU None None
None 65 THR None None
None 66 GLY None None
None 67 VAL None None
None 68 THR None None
None 69 SER None None
None 70 ALA None None
None 71 GLU None None
None 72 VAL None None
None 73 ILE None None
None 74 ALA None None
None 75 GLU None None
None 76 VAL None None
None 77 PRO None None
None 78 TYR None None
None 79 TRP None None
None 80 LEU None None
None 81 THR None None
None 82 TYR None None
None 83 ASP None None
None 84 PHE None None
None 85 PRO None None
None 86 PRO None None
None 87 LYS None None
None 88 VAL None None
None 89 ARG None None
None 90 GLU None None
None 91 LYS None None
None 92 LEU None None
None 93 ASN None None
None 94 ILE None None
None 95 GLN None None
None 96 TRP None None
None 97 GLY None None
None 98 SER None None
None 99 ASP None None
None 100 TRP None None
None 101 LYS None None
None 102 GLY None None
None 103 GLN None None
None 104 ALA None None
None 105 GLN None None
None 106 LYS None None
None 107 TRP None None
None 108 PHE None None
None 109 LEU None None
None 110 PHE None None
None 111 LYS None None
None 112 PHE None None
None 113 THR None None
None 114 GLY None None
None 115 GLN None None
None 116 ASP None None
None 117 GLN None None
None 118 GLU None None
None 119 ILE None None
None 120 ASN None None
None 121 LEU None None
None 122 LEU None None
None 123 GLY None None
None 124 ASP None None
None 125 GLY None None
None 126 SER None None
None 127 GLU None None
None 128 LYS None None
None 129 PRO None None
None 130 GLU None None
None 131 PHE None None
None 132 GLY None None
None 133 GLU None None
None 134 TRP None None
None 135 SER None None
None 136 TRP None None
None 137 VAL None None
None 138 THR None None
None 139 PRO None None
None 140 GLU None None
None 141 GLN None None
None 142 LEU None None
None 143 ILE None None
None 144 ASP None None
None 145 LEU None None
None 146 THR None None
None 147 VAL None None
None 148 GLU None None
None 149 PHE None None
None 150 LYS None None
None 151 LYS None None
None 152 PRO None None
None 153 VAL None None
None 154 TYR None None
None 155 LYS None None
None 156 GLU None None
None 157 VAL None None
None 158 LEU None None
None 159 SER None None
None 160 VAL None None
None 161 PHE None None
None 162 ALA None None
None 163 PRO None None
None 164 HIS None None
None 165 LEU None None
relax> angle_diff_frame()
RelaxWarning: No angles could be calculated for the spin ':1&:GLY@1&@N'.
RelaxWarning: No angles could be calculated for the spin ':2&:PRO@11&@N'.
RelaxWarning: No angles could be calculated for the spin ':9&:PRO@116&@N'.
RelaxWarning: No angles could be calculated for the spin ':10&:PRO@133&@N'.
RelaxWarning: No angles could be calculated for the spin ':13&:TYR'.
RelaxWarning: No angles could be calculated for the spin ':14&:ARG'.
RelaxWarning: No angles could be calculated for the spin ':15&:ARG'.
RelaxWarning: No angles could be calculated for the spin ':16&:ASN'.
RelaxWarning: No angles could be calculated for the spin ':17&:VAL'.
RelaxWarning: No angles could be calculated for the spin ':18&:GLY'.
RelaxWarning: No angles could be calculated for the spin ':19&:ILE'.
RelaxWarning: No angles could be calculated for the spin ':20&:CYS'.
RelaxWarning: No angles could be calculated for the spin ':21&:LEU'.
RelaxWarning: No angles could be calculated for the spin ':22&:MET'.
RelaxWarning: No angles could be calculated for the spin ':23&:ASN'.
RelaxWarning: No angles could be calculated for the spin ':24&:ASN'.
RelaxWarning: No angles could be calculated for the spin ':25&:ASP'.
RelaxWarning: No angles could be calculated for the spin ':26&:LYS'.
RelaxWarning: No angles could be calculated for the spin ':27&:LYS'.
RelaxWarning: No angles could be calculated for the spin ':28&:ILE'.
RelaxWarning: No angles could be calculated for the spin ':29&:PHE'.
RelaxWarning: No angles could be calculated for the spin ':30&:ALA'.
RelaxWarning: No angles could be calculated for the spin ':31&:ALA'.
RelaxWarning: No angles could be calculated for the spin ':32&:SER'.
RelaxWarning: No angles could be calculated for the spin ':33&:ARG'.
RelaxWarning: No angles could be calculated for the spin ':34&:LEU'.
RelaxWarning: No angles could be calculated for the spin ':35&:ASP'.
RelaxWarning: No angles could be calculated for the spin ':36&:ILE'.
RelaxWarning: No angles could be calculated for the spin ':37&:PRO'.
RelaxWarning: No angles could be calculated for the spin ':38&:ASP'.
RelaxWarning: No angles could be calculated for the spin ':39&:ALA'.
RelaxWarning: No angles could be calculated for the spin ':40&:TRP'.
RelaxWarning: No angles could be calculated for the spin ':41&:GLN'.
RelaxWarning: No angles could be calculated for the spin ':42&:MET'.
RelaxWarning: No angles could be calculated for the spin ':43&:PRO'.
RelaxWarning: No angles could be calculated for the spin ':44&:GLN'.
RelaxWarning: No angles could be calculated for the spin ':45&:GLY'.
RelaxWarning: No angles could be calculated for the spin ':46&:GLY'.
RelaxWarning: No angles could be calculated for the spin ':47&:ILE'.
RelaxWarning: No angles could be calculated for the spin ':48&:ASP'.
RelaxWarning: No angles could be calculated for the spin ':49&:GLU'.
RelaxWarning: No angles could be calculated for the spin ':50&:GLY'.
RelaxWarning: No angles could be calculated for the spin ':51&:GLU'.
RelaxWarning: No angles could be calculated for the spin ':52&:ASP'.
RelaxWarning: No angles could be calculated for the spin ':53&:PRO'.
RelaxWarning: No angles could be calculated for the spin ':54&:ARG'.
RelaxWarning: No angles could be calculated for the spin ':55&:ASN'.
RelaxWarning: No angles could be calculated for the spin ':56&:ALA'.
RelaxWarning: No angles could be calculated for the spin ':57&:ALA'.
RelaxWarning: No angles could be calculated for the spin ':58&:ILE'.
RelaxWarning: No angles could be calculated for the spin ':59&:ARG'.
RelaxWarning: No angles could be calculated for the spin ':60&:GLU'.
RelaxWarning: No angles could be calculated for the spin ':61&:LEU'.
RelaxWarning: No angles could be calculated for the spin ':62&:ARG'.
RelaxWarning: No angles could be calculated for the spin ':63&:GLU'.
RelaxWarning: No angles could be calculated for the spin ':64&:GLU'.
RelaxWarning: No angles could be calculated for the spin ':65&:THR'.
RelaxWarning: No angles could be calculated for the spin ':66&:GLY'.
RelaxWarning: No angles could be calculated for the spin ':67&:VAL'.
RelaxWarning: No angles could be calculated for the spin ':68&:THR'.
RelaxWarning: No angles could be calculated for the spin ':69&:SER'.
RelaxWarning: No angles could be calculated for the spin ':70&:ALA'.
RelaxWarning: No angles could be calculated for the spin ':71&:GLU'.
RelaxWarning: No angles could be calculated for the spin ':72&:VAL'.
RelaxWarning: No angles could be calculated for the spin ':73&:ILE'.
RelaxWarning: No angles could be calculated for the spin ':74&:ALA'.
RelaxWarning: No angles could be calculated for the spin ':75&:GLU'.
RelaxWarning: No angles could be calculated for the spin ':76&:VAL'.
RelaxWarning: No angles could be calculated for the spin ':77&:PRO'.
RelaxWarning: No angles could be calculated for the spin ':78&:TYR'.
RelaxWarning: No angles could be calculated for the spin ':79&:TRP'.
RelaxWarning: No angles could be calculated for the spin ':80&:LEU'.
RelaxWarning: No angles could be calculated for the spin ':81&:THR'.
RelaxWarning: No angles could be calculated for the spin ':82&:TYR'.
RelaxWarning: No angles could be calculated for the spin ':83&:ASP'.
RelaxWarning: No angles could be calculated for the spin ':84&:PHE'.
RelaxWarning: No angles could be calculated for the spin ':85&:PRO'.
RelaxWarning: No angles could be calculated for the spin ':86&:PRO'.
RelaxWarning: No angles could be calculated for the spin ':87&:LYS'.
RelaxWarning: No angles could be calculated for the spin ':88&:VAL'.
RelaxWarning: No angles could be calculated for the spin ':89&:ARG'.
RelaxWarning: No angles could be calculated for the spin ':90&:GLU'.
RelaxWarning: No angles could be calculated for the spin ':91&:LYS'.
RelaxWarning: No angles could be calculated for the spin ':92&:LEU'.
RelaxWarning: No angles could be calculated for the spin ':93&:ASN'.
RelaxWarning: No angles could be calculated for the spin ':94&:ILE'.
RelaxWarning: No angles could be calculated for the spin ':95&:GLN'.
RelaxWarning: No angles could be calculated for the spin ':96&:TRP'.
RelaxWarning: No angles could be calculated for the spin ':97&:GLY'.
RelaxWarning: No angles could be calculated for the spin ':98&:SER'.
RelaxWarning: No angles could be calculated for the spin ':99&:ASP'.
RelaxWarning: No angles could be calculated for the spin ':100&:TRP'.
RelaxWarning: No angles could be calculated for the spin ':101&:LYS'.
RelaxWarning: No angles could be calculated for the spin ':102&:GLY'.
RelaxWarning: No angles could be calculated for the spin ':103&:GLN'.
RelaxWarning: No angles could be calculated for the spin ':104&:ALA'.
RelaxWarning: No angles could be calculated for the spin ':105&:GLN'.
RelaxWarning: No angles could be calculated for the spin ':106&:LYS'.
RelaxWarning: No angles could be calculated for the spin ':107&:TRP'.
RelaxWarning: No angles could be calculated for the spin ':108&:PHE'.
RelaxWarning: No angles could be calculated for the spin ':109&:LEU'.
RelaxWarning: No angles could be calculated for the spin ':110&:PHE'.
RelaxWarning: No angles could be calculated for the spin ':111&:LYS'.
RelaxWarning: No angles could be calculated for the spin ':112&:PHE'.
RelaxWarning: No angles could be calculated for the spin ':113&:THR'.
RelaxWarning: No angles could be calculated for the spin ':114&:GLY'.
RelaxWarning: No angles could be calculated for the spin ':115&:GLN'.
RelaxWarning: No angles could be calculated for the spin ':116&:ASP'.
RelaxWarning: No angles could be calculated for the spin ':117&:GLN'.
RelaxWarning: No angles could be calculated for the spin ':118&:GLU'.
RelaxWarning: No angles could be calculated for the spin ':119&:ILE'.
RelaxWarning: No angles could be calculated for the spin ':120&:ASN'.
RelaxWarning: No angles could be calculated for the spin ':121&:LEU'.
RelaxWarning: No angles could be calculated for the spin ':122&:LEU'.
RelaxWarning: No angles could be calculated for the spin ':123&:GLY'.
RelaxWarning: No angles could be calculated for the spin ':124&:ASP'.
RelaxWarning: No angles could be calculated for the spin ':125&:GLY'.
RelaxWarning: No angles could be calculated for the spin ':126&:SER'.
RelaxWarning: No angles could be calculated for the spin ':127&:GLU'.
RelaxWarning: No angles could be calculated for the spin ':128&:LYS'.
RelaxWarning: No angles could be calculated for the spin ':129&:PRO'.
RelaxWarning: No angles could be calculated for the spin ':130&:GLU'.
RelaxWarning: No angles could be calculated for the spin ':131&:PHE'.
RelaxWarning: No angles could be calculated for the spin ':132&:GLY'.
RelaxWarning: No angles could be calculated for the spin ':133&:GLU'.
RelaxWarning: No angles could be calculated for the spin ':134&:TRP'.
RelaxWarning: No angles could be calculated for the spin ':135&:SER'.
RelaxWarning: No angles could be calculated for the spin ':136&:TRP'.
RelaxWarning: No angles could be calculated for the spin ':137&:VAL'.
RelaxWarning: No angles could be calculated for the spin ':138&:THR'.
RelaxWarning: No angles could be calculated for the spin ':139&:PRO'.
RelaxWarning: No angles could be calculated for the spin ':140&:GLU'.
RelaxWarning: No angles could be calculated for the spin ':141&:GLN'.
RelaxWarning: No angles could be calculated for the spin ':142&:LEU'.
RelaxWarning: No angles could be calculated for the spin ':143&:ILE'.
RelaxWarning: No angles could be calculated for the spin ':144&:ASP'.
RelaxWarning: No angles could be calculated for the spin ':145&:LEU'.
RelaxWarning: No angles could be calculated for the spin ':146&:THR'.
RelaxWarning: No angles could be calculated for the spin ':147&:VAL'.
RelaxWarning: No angles could be calculated for the spin ':148&:GLU'.
RelaxWarning: No angles could be calculated for the spin ':149&:PHE'.
RelaxWarning: No angles could be calculated for the spin ':150&:LYS'.
RelaxWarning: No angles could be calculated for the spin ':151&:LYS'.
RelaxWarning: No angles could be calculated for the spin ':152&:PRO'.
RelaxWarning: No angles could be calculated for the spin ':153&:VAL'.
RelaxWarning: No angles could be calculated for the spin ':154&:TYR'.
RelaxWarning: No angles could be calculated for the spin ':155&:LYS'.
RelaxWarning: No angles could be calculated for the spin ':156&:GLU'.
RelaxWarning: No angles could be calculated for the spin ':157&:VAL'.
RelaxWarning: No angles could be calculated for the spin ':158&:LEU'.
RelaxWarning: No angles could be calculated for the spin ':159&:SER'.
RelaxWarning: No angles could be calculated for the spin ':160&:VAL'.
RelaxWarning: No angles could be calculated for the spin ':161&:PHE'.
RelaxWarning: No angles could be calculated for the spin ':162&:ALA'.
RelaxWarning: No angles could be calculated for the spin ':163&:PRO'.
RelaxWarning: No angles could be calculated for the spin ':164&:HIS'.
RelaxWarning: No angles could be calculated for the spin ':165&:LEU'.
Class containing all the spin system specific data.
Objects:
element: 'N'
name: 'N'
num: 1
pos: array([ 8.442, 10.188, 6.302])
select: True
Class containing all the spin system specific data.
Objects:
element: 'N'
name: 'N'
num: 11
pos: array([ 5.613, 8.385, 7.943])
select: True
Class containing all the spin system specific data.
Objects:
alpha: 2.8102691247870468
attached_atom: 'H'
element: 'N'
name: 'N'
num: 28
pos: array([ 4.074, 6.099, 5.719])
select: True
xh_vect: array([ 0.40899187, -0.80574458, 0.42837054])
Traceback (most recent call last):
File "/sw/lib/relax-py25/test_suite/system_tests/angles.py", line 104, in
test_angles
self.assertAlmostEqual(cdp.mol[0].res[i].spin[0].xh_vect[j],
xh_vects[i][j])
AssertionError: 0.40899187042469931 != -1.6863286833629661e+272 within 7
places
======================================================================
FAIL: Constrained BFGS opt, backtracking line search {S2=0.970, te=2048,
Rex=0.149}
----------------------------------------------------------------------
relax> pipe.create(pipe_name='mf', pipe_type='mf')
relax> sequence.read(file='noe.500.out',
dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149',
mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None,
spin_name_col=None, sep=None)
Opening the file
'/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/noe.500.out'
for reading.
Mol_name Res_num Res_name Spin_num Spin_name
None 1 GLY None None
None 2 ALA None None
relax> relax_data.read(ri_label='R1', frq_label='600', frq=600000000.0,
file='r1.600.out',
dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149',
mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None,
spin_name_col=None, data_col=2, error_col=3, sep=None)
Opening the file
'/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/r1.600.out'
for reading.
relax> relax_data.read(ri_label='R2', frq_label='600', frq=600000000.0,
file='r2.600.out',
dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149',
mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None,
spin_name_col=None, data_col=2, error_col=3, sep=None)
Opening the file
'/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/r2.600.out'
for reading.
relax> relax_data.read(ri_label='NOE', frq_label='600', frq=600000000.0,
file='noe.600.out',
dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149',
mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None,
spin_name_col=None, data_col=2, error_col=3, sep=None)
Opening the file
'/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/noe.600.out'
for reading.
relax> relax_data.read(ri_label='R1', frq_label='500', frq=500000000.0,
file='r1.500.out',
dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149',
mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None,
spin_name_col=None, data_col=2, error_col=3, sep=None)
Opening the file
'/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/r1.500.out'
for reading.
relax> relax_data.read(ri_label='R2', frq_label='500', frq=500000000.0,
file='r2.500.out',
dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149',
mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None,
spin_name_col=None, data_col=2, error_col=3, sep=None)
Opening the file
'/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/r2.500.out'
for reading.
relax> relax_data.read(ri_label='NOE', frq_label='500', frq=500000000.0,
file='noe.500.out',
dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149',
mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None,
spin_name_col=None, data_col=2, error_col=3, sep=None)
Opening the file
'/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/noe.500.out'
for reading.
relax> diffusion_tensor.init(params=1e-08, time_scale=1.0, d_scale=1.0,
angle_units='deg', param_types=0, spheroid_type=None, fixed=True)
relax> value.set(val=1.0200000000000001e-10, param='bond_length',
spin_id=None)
relax> value.set(val=-0.00015999999999999999, param='csa', spin_id=None)
relax> value.set(val='15N', param='heteronucleus', spin_id=None)
relax> value.set(val='1H', param='proton', spin_id=None)
relax> model_free.select_model(model='m4', spin_id=None)
relax> value.set(val=[1.0, 0.0, 0.0], param=['S2', 'te', 'Rex'], spin_id=None)
relax> minimise(*args=('bfgs', 'back'), func_tol=1e-25,
max_iterations=10000000, constraints=True, scaling=True, verbosity=1)
Only the model-free parameters for single spins will be used.
Fitting to spin ':2&:ALA'
~~~~~~~~~~~~~~~~~~~~~~~~
Method of Multipliers
~~~~~~~~~~~~~~~~~~~~
k: 0 xk: array([ 1., 0., 0.])
fk: 3.9844117908982288
Entering sub-algorithm.
Quasi-Newton BFGS minimisation
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Line search: Backtracking line search.
k: 0 xk: array([ 1., 0., 0.])
fk: 3.9844117908982288
Parameter values: array([ 0.90905502, 74.36929555, 1.22310091])
Function value: -1447.7789206950388
Iterations: 37
Function calls: 93
Gradient calls: 38
Hessian calls: 0
Warning: None
k: 1 xk: array([ 0.90905502, 74.36929555, 1.22310091])
fk: 48.121412825285702
Entering sub-algorithm.
Quasi-Newton BFGS minimisation
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Line search: Backtracking line search.
k: 0 xk: array([ 0.90905502, 74.36929555, 1.22310091])
fk: 46.071579585447914
Parameter values: array([ 9.89561039e-01, 4.08922110e+02,
1.27899123e-01])
Function value: 1.5767185057428068
Iterations: 38
Function calls: 259
Gradient calls: 39
Hessian calls: 0
Warning: None
k: 2 xk: array([ 9.89561039e-01, 4.08922110e+02, 1.27899123e-01])
fk: 3.626551745580596
Entering sub-algorithm.
Quasi-Newton BFGS minimisation
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Line search: Backtracking line search.
k: 0 xk: array([ 9.89561039e-01, 4.08922110e+02,
1.27899123e-01]) fk: 3.626551745580596
Parameter values: array([ 9.74034731e-01, 8.37698106e+02,
1.23106917e-01])
Function value: 2.1800782005407622
Iterations: 31
Function calls: 201
Gradient calls: 32
Hessian calls: 0
Warning: None
k: 3 xk: array([ 9.74034731e-01, 8.37698106e+02, 1.23106917e-01])
fk: 2.1800782005407622
Entering sub-algorithm.
Quasi-Newton BFGS minimisation
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Line search: Backtracking line search.
k: 0 xk: array([ 9.74034731e-01, 8.37698106e+02,
1.23106917e-01]) fk: 2.1800782005407622
Parameter values: array([ 9.70000000e-01, 2.04800000e+03,
1.49000000e-01])
Function value: 7.5991121570503778e-22
Iterations: 42
Function calls: 98
Gradient calls: 43
Hessian calls: 0
Warning: None
k: 4 xk: array([ 9.70000000e-01, 2.04800000e+03, 1.49000000e-01])
fk: 7.5991121570503778e-22
Entering sub-algorithm.
Quasi-Newton BFGS minimisation
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Line search: Backtracking line search.
k: 0 xk: array([ 9.70000000e-01, 2.04800000e+03,
1.49000000e-01]) fk: 7.5991121570503778e-22
Parameter values: array([ 9.70000000e-01, 2.04800000e+03,
1.49000000e-01])
Function value: 1.9022883080402212e-24
Iterations: 6
Function calls: 26
Gradient calls: 7
Hessian calls: 0
Warning: None
k: 5 xk: array([ 9.70000000e-01, 2.04800000e+03, 1.49000000e-01])
fk: 1.9022883080402212e-24
Entering sub-algorithm.
Quasi-Newton BFGS minimisation
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Line search: Backtracking line search.
k: 0 xk: array([ 9.70000000e-01, 2.04800000e+03,
1.49000000e-01]) fk: 1.9022883080402212e-24
Parameter values: array([ 9.70000000e-01, 2.04800000e+03,
1.49000000e-01])
Function value: 1.8533903598853284e-24
Iterations: 2
Function calls: 18
Gradient calls: 3
Hessian calls: 0
Warning: None
Parameter values: array([ 9.70000000e-01, 2.04800000e+03,
1.49000000e-01])
Function value: 1.8533903598853284e-24
Iterations: 156
Function calls: 695
Gradient calls: 162
Hessian calls: 0
Warning: None
Traceback (most recent call last):
File "/sw/lib/relax-py25/test_suite/system_tests/model_free.py", line 301,
in test_opt_constr_bfgs_back_S2_0_970_te_2048_Rex_0_149
self.value_test(spin, select, s2, te, rex, chi2, iter, f_count, g_count,
h_count, warning)
File "/sw/lib/relax-py25/test_suite/system_tests/model_free.py", line 1046,
in value_test
self.assertEqual(spin.iter, iter, msg=mesg)
AssertionError: Optimisation failure.
System: Darwin
Release: 9.5.0
Version: Darwin Kernel Version 9.5.0: Wed Sep 3 11:31:44 PDT 2008;
root:xnu-1228.7.58~1/RELEASE_PPC
Win32 version:
Distribution:
Architecture: 32bit
Machine: Power Macintosh
Processor: powerpc
Python version: 2.5.2
numpy version: 1.1.1
s2: 0.9699999999999861
te: 2047.9999999978033
rex: 0.14900000000028032
chi2: 1.8533903598853284e-24
iter: 156
f_count: 695
g_count: 162
h_count: 0
warning: None
======================================================================
FAIL: Constrained BFGS opt, More and Thuente line search {S2=0.970, te=2048,
Rex=0.149}
----------------------------------------------------------------------
relax> pipe.create(pipe_name='mf', pipe_type='mf')
relax> sequence.read(file='noe.500.out',
dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149',
mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None,
spin_name_col=None, sep=None)
Opening the file
'/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/noe.500.out'
for reading.
Mol_name Res_num Res_name Spin_num Spin_name
None 1 GLY None None
None 2 ALA None None
relax> relax_data.read(ri_label='R1', frq_label='600', frq=600000000.0,
file='r1.600.out',
dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149',
mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None,
spin_name_col=None, data_col=2, error_col=3, sep=None)
Opening the file
'/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/r1.600.out'
for reading.
relax> relax_data.read(ri_label='R2', frq_label='600', frq=600000000.0,
file='r2.600.out',
dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149',
mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None,
spin_name_col=None, data_col=2, error_col=3, sep=None)
Opening the file
'/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/r2.600.out'
for reading.
relax> relax_data.read(ri_label='NOE', frq_label='600', frq=600000000.0,
file='noe.600.out',
dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149',
mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None,
spin_name_col=None, data_col=2, error_col=3, sep=None)
Opening the file
'/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/noe.600.out'
for reading.
relax> relax_data.read(ri_label='R1', frq_label='500', frq=500000000.0,
file='r1.500.out',
dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149',
mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None,
spin_name_col=None, data_col=2, error_col=3, sep=None)
Opening the file
'/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/r1.500.out'
for reading.
relax> relax_data.read(ri_label='R2', frq_label='500', frq=500000000.0,
file='r2.500.out',
dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149',
mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None,
spin_name_col=None, data_col=2, error_col=3, sep=None)
Opening the file
'/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/r2.500.out'
for reading.
relax> relax_data.read(ri_label='NOE', frq_label='500', frq=500000000.0,
file='noe.500.out',
dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149',
mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None,
spin_name_col=None, data_col=2, error_col=3, sep=None)
Opening the file
'/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/noe.500.out'
for reading.
relax> diffusion_tensor.init(params=1e-08, time_scale=1.0, d_scale=1.0,
angle_units='deg', param_types=0, spheroid_type=None, fixed=True)
relax> value.set(val=1.0200000000000001e-10, param='bond_length',
spin_id=None)
relax> value.set(val=-0.00015999999999999999, param='csa', spin_id=None)
relax> value.set(val='15N', param='heteronucleus', spin_id=None)
relax> value.set(val='1H', param='proton', spin_id=None)
relax> model_free.select_model(model='m4', spin_id=None)
relax> value.set(val=[1.0, 0.0, 0.0], param=['S2', 'te', 'Rex'], spin_id=None)
relax> minimise(*args=('bfgs', 'mt'), func_tol=1e-25,
max_iterations=10000000, constraints=True, scaling=True, verbosity=1)
Only the model-free parameters for single spins will be used.
Fitting to spin ':2&:ALA'
~~~~~~~~~~~~~~~~~~~~~~~~
Method of Multipliers
~~~~~~~~~~~~~~~~~~~~
k: 0 xk: array([ 1., 0., 0.])
fk: 3.9844117908982288
Entering sub-algorithm.
Quasi-Newton BFGS minimisation
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Line search: More and Thuente line search.
k: 0 xk: array([ 1., 0., 0.])
fk: 3.9844117908982288
Parameter values: array([ 0.90905506, 74.36943011, 1.22310156])
Function value: -1447.7789206948671
Iterations: 22
Function calls: 50
Gradient calls: 50
Hessian calls: 0
Warning: None
k: 1 xk: array([ 0.90905506, 74.36943011, 1.22310156])
fk: 48.121371716752257
Entering sub-algorithm.
Quasi-Newton BFGS minimisation
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Line search: More and Thuente line search.
k: 0 xk: array([ 0.90905506, 74.36943011, 1.22310156])
fk: 46.071517922561874
Parameter values: array([ 9.94936631e-01, 8.81385060e+01,
-3.79281070e-05])
Function value: 1.9644199905707935
Iterations: 38
Function calls: 128
Gradient calls: 128
Hessian calls: 0
Warning: The gradient at point 0 of this line search is
positive, ie p is not a descent direction and the line search will not work.
(fatal minimisation error).
k: 2 xk: array([ 9.94936631e-01, 8.81385060e+01, -3.79281070e-05])
fk: 144.63923664803443
Entering sub-algorithm.
Quasi-Newton BFGS minimisation
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Line search: More and Thuente line search.
k: 0 xk: array([ 9.94936631e-01, 8.81385060e+01,
-3.79281070e-05]) fk: 4.0147053471508878
Parameter values: array([ 9.70000000e-01, 2.04800000e+03,
1.49000000e-01])
Function value: -7.1927064951510456e-05
Iterations: 56
Function calls: 129
Gradient calls: 129
Hessian calls: 0
Warning: None
k: 3 xk: array([ 9.70000000e-01, 2.04800000e+03, 1.49000000e-01])
fk: 1.6264773549380294e-20
Entering sub-algorithm.
Quasi-Newton BFGS minimisation
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Line search: More and Thuente line search.
k: 0 xk: array([ 9.70000000e-01, 2.04800000e+03,
1.49000000e-01]) fk: 1.6264773549380294e-20
Parameter values: array([ 9.70000000e-01, 2.04800000e+03,
1.49000000e-01])
Function value: 2.6808864830250424e-21
Iterations: 1
Function calls: 4
Gradient calls: 4
Hessian calls: 0
Warning: None
k: 4 xk: array([ 9.70000000e-01, 2.04800000e+03, 1.49000000e-01])
fk: 2.6808864830250424e-21
Entering sub-algorithm.
Quasi-Newton BFGS minimisation
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Line search: More and Thuente line search.
k: 0 xk: array([ 9.70000000e-01, 2.04800000e+03,
1.49000000e-01]) fk: 2.6808864830250424e-21
Parameter values: array([ 9.70000000e-01, 2.04800000e+03,
1.49000000e-01])
Function value: 4.8056261450870388e-23
Iterations: 2
Function calls: 7
Gradient calls: 7
Hessian calls: 0
Warning: None
k: 5 xk: array([ 9.70000000e-01, 2.04800000e+03, 1.49000000e-01])
fk: 4.8056261450870388e-23
Entering sub-algorithm.
Quasi-Newton BFGS minimisation
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Line search: More and Thuente line search.
k: 0 xk: array([ 9.70000000e-01, 2.04800000e+03,
1.49000000e-01]) fk: 4.8056261450870388e-23
Parameter values: array([ 9.70000000e-01, 2.04800000e+03,
1.49000000e-01])
Function value: 4.8056261450870388e-23
Iterations: 1
Function calls: 59
Gradient calls: 59
Hessian calls: 0
Warning: None
Parameter values: array([ 9.70000000e-01, 2.04800000e+03,
1.49000000e-01])
Function value: 4.8056261450870388e-23
Iterations: 120
Function calls: 377
Gradient calls: 377
Hessian calls: 0
Warning: None
Traceback (most recent call last):
File "/sw/lib/relax-py25/test_suite/system_tests/model_free.py", line 355,
in test_opt_constr_bfgs_mt_S2_0_970_te_2048_Rex_0_149
self.value_test(spin, select, s2, te, rex, chi2, iter, f_count, g_count,
h_count, warning)
File "/sw/lib/relax-py25/test_suite/system_tests/model_free.py", line 1047,
in value_test
self.assertEqual(spin.f_count, f_count, msg=mesg)
AssertionError: Optimisation failure.
System: Darwin
Release: 9.5.0
Version: Darwin Kernel Version 9.5.0: Wed Sep 3 11:31:44 PDT 2008;
root:xnu-1228.7.58~1/RELEASE_PPC
Win32 version:
Distribution:
Architecture: 32bit
Machine: Power Macintosh
Processor: powerpc
Python version: 2.5.2
numpy version: 1.1.1
s2: 0.9700000000000607
te: 2048.0000000115510
rex: 0.14899999999885080
chi2: 4.8056261450870388e-23
iter: 120
f_count: 377
g_count: 377
h_count: 0
warning: None
======================================================================
FAIL: Constrained coordinate descent opt, More and Thuente line search
{S2=0.970, te=2048, Rex=0.149}
----------------------------------------------------------------------
relax> pipe.create(pipe_name='mf', pipe_type='mf')
relax> sequence.read(file='noe.500.out',
dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149',
mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None,
spin_name_col=None, sep=None)
Opening the file
'/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/noe.500.out'
for reading.
Mol_name Res_num Res_name Spin_num Spin_name
None 1 GLY None None
None 2 ALA None None
relax> relax_data.read(ri_label='R1', frq_label='600', frq=600000000.0,
file='r1.600.out',
dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149',
mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None,
spin_name_col=None, data_col=2, error_col=3, sep=None)
Opening the file
'/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/r1.600.out'
for reading.
relax> relax_data.read(ri_label='R2', frq_label='600', frq=600000000.0,
file='r2.600.out',
dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149',
mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None,
spin_name_col=None, data_col=2, error_col=3, sep=None)
Opening the file
'/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/r2.600.out'
for reading.
relax> relax_data.read(ri_label='NOE', frq_label='600', frq=600000000.0,
file='noe.600.out',
dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149',
mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None,
spin_name_col=None, data_col=2, error_col=3, sep=None)
Opening the file
'/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/noe.600.out'
for reading.
relax> relax_data.read(ri_label='R1', frq_label='500', frq=500000000.0,
file='r1.500.out',
dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149',
mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None,
spin_name_col=None, data_col=2, error_col=3, sep=None)
Opening the file
'/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/r1.500.out'
for reading.
relax> relax_data.read(ri_label='R2', frq_label='500', frq=500000000.0,
file='r2.500.out',
dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149',
mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None,
spin_name_col=None, data_col=2, error_col=3, sep=None)
Opening the file
'/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/r2.500.out'
for reading.
relax> relax_data.read(ri_label='NOE', frq_label='500', frq=500000000.0,
file='noe.500.out',
dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149',
mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None,
spin_name_col=None, data_col=2, error_col=3, sep=None)
Opening the file
'/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/noe.500.out'
for reading.
relax> diffusion_tensor.init(params=1e-08, time_scale=1.0, d_scale=1.0,
angle_units='deg', param_types=0, spheroid_type=None, fixed=True)
relax> value.set(val=1.0200000000000001e-10, param='bond_length',
spin_id=None)
relax> value.set(val=-0.00015999999999999999, param='csa', spin_id=None)
relax> value.set(val='15N', param='heteronucleus', spin_id=None)
relax> value.set(val='1H', param='proton', spin_id=None)
relax> model_free.select_model(model='m4', spin_id=None)
relax> value.set(val=[1.0, 0.0, 0.0], param=['S2', 'te', 'Rex'], spin_id=None)
relax> minimise(*args=('cd', 'mt'), func_tol=1e-25, max_iterations=10000000,
constraints=True, scaling=True, verbosity=1)
Only the model-free parameters for single spins will be used.
Fitting to spin ':2&:ALA'
~~~~~~~~~~~~~~~~~~~~~~~~
Method of Multipliers
~~~~~~~~~~~~~~~~~~~~
k: 0 xk: array([ 1., 0., 0.])
fk: 3.9844117908982288
Entering sub-algorithm.
Back-and-forth coordinate descent minimisation
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Line search: More and Thuente line search.
k: 0 xk: array([ 1., 0., 0.])
fk: 3.9844117908982288
Parameter values: array([ 0.90905609, 74.37463254, 1.22289922])
Function value: -1447.7789199590425
Iterations: 25
Function calls: 75
Gradient calls: 75
Hessian calls: 0
Warning: None
k: 1 xk: array([ 0.90905609, 74.37463254, 1.22289922])
fk: 48.120438129522014
Entering sub-algorithm.
Back-and-forth coordinate descent minimisation
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Line search: More and Thuente line search.
k: 0 xk: array([ 0.90905609, 74.37463254, 1.22289922])
fk: 46.070117173804164
Parameter values: array([ 9.70000218e-01, 2.04801529e+03,
1.48994731e-01])
Function value: -2.0503209554858945
Iterations: 89
Function calls: 284
Gradient calls: 284
Hessian calls: 0
Warning: None
k: 2 xk: array([ 9.70000218e-01, 2.04801529e+03, 1.48994731e-01])
fk: 2.3195995262977486e-10
Entering sub-algorithm.
Back-and-forth coordinate descent minimisation
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Line search: More and Thuente line search.
k: 0 xk: array([ 9.70000218e-01, 2.04801529e+03,
1.48994731e-01]) fk: 2.3195995262977486e-10
Parameter values: array([ 9.70000218e-01, 2.04800873e+03,
1.48997054e-01])
Function value: 1.2998777447179547e-10
Iterations: 18
Function calls: 136
Gradient calls: 136
Hessian calls: 0
Warning: None
k: 3 xk: array([ 9.70000218e-01, 2.04800873e+03, 1.48997054e-01])
fk: 1.2998777447179547e-10
Entering sub-algorithm.
Back-and-forth coordinate descent minimisation
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Line search: More and Thuente line search.
k: 0 xk: array([ 9.70000218e-01, 2.04800873e+03,
1.48997054e-01]) fk: 1.2998777447179547e-10
Parameter values: array([ 9.70000000e-01, 2.04800000e+03,
1.48999999e-01])
Function value: 2.3477234248531005e-18
Iterations: 65
Function calls: 184
Gradient calls: 184
Hessian calls: 0
Warning: None
k: 4 xk: array([ 9.70000000e-01, 2.04800000e+03, 1.48999999e-01])
fk: 2.3477234248531005e-18
Entering sub-algorithm.
Back-and-forth coordinate descent minimisation
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Line search: More and Thuente line search.
k: 0 xk: array([ 9.70000000e-01, 2.04800000e+03,
1.48999999e-01]) fk: 2.3477234248531005e-18
Parameter values: array([ 9.70000000e-01, 2.04800000e+03,
1.48999999e-01])
Function value: 2.3477234248531005e-18
Iterations: 1
Function calls: 78
Gradient calls: 78
Hessian calls: 0
Warning: None
Parameter values: array([ 9.70000000e-01, 2.04800000e+03,
1.48999999e-01])
Function value: 2.3477234248531005e-18
Iterations: 198
Function calls: 757
Gradient calls: 757
Hessian calls: 0
Warning: None
Traceback (most recent call last):
File "/sw/lib/relax-py25/test_suite/system_tests/model_free.py", line 452,
in test_opt_constr_cd_mt_S2_0_970_te_2048_Rex_0_149
self.value_test(spin, select, s2, te, rex, chi2, iter, f_count, g_count,
h_count, warning)
File "/sw/lib/relax-py25/test_suite/system_tests/model_free.py", line 1047,
in value_test
self.assertEqual(spin.f_count, f_count, msg=mesg)
AssertionError: Optimisation failure.
System: Darwin
Release: 9.5.0
Version: Darwin Kernel Version 9.5.0: Wed Sep 3 11:31:44 PDT 2008;
root:xnu-1228.7.58~1/RELEASE_PPC
Win32 version:
Distribution:
Architecture: 32bit
Machine: Power Macintosh
Processor: powerpc
Python version: 2.5.2
numpy version: 1.1.1
s2: 0.9700000000219674
te: 2048.0000015341870
rex: 0.14899999946977982
chi2: 2.3477234248531005e-18
iter: 198
f_count: 757
g_count: 757
h_count: 0
warning: None
======================================================================
FAIL: Constrained Newton opt, GMW Hessian mod, backtracking line search
{S2=0.970, te=2048, Rex=0.149}
----------------------------------------------------------------------
relax> pipe.create(pipe_name='mf', pipe_type='mf')
relax> sequence.read(file='noe.500.out',
dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149',
mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None,
spin_name_col=None, sep=None)
Opening the file
'/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/noe.500.out'
for reading.
Mol_name Res_num Res_name Spin_num Spin_name
None 1 GLY None None
None 2 ALA None None
relax> relax_data.read(ri_label='R1', frq_label='600', frq=600000000.0,
file='r1.600.out',
dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149',
mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None,
spin_name_col=None, data_col=2, error_col=3, sep=None)
Opening the file
'/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/r1.600.out'
for reading.
relax> relax_data.read(ri_label='R2', frq_label='600', frq=600000000.0,
file='r2.600.out',
dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149',
mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None,
spin_name_col=None, data_col=2, error_col=3, sep=None)
Opening the file
'/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/r2.600.out'
for reading.
relax> relax_data.read(ri_label='NOE', frq_label='600', frq=600000000.0,
file='noe.600.out',
dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149',
mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None,
spin_name_col=None, data_col=2, error_col=3, sep=None)
Opening the file
'/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/noe.600.out'
for reading.
relax> relax_data.read(ri_label='R1', frq_label='500', frq=500000000.0,
file='r1.500.out',
dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149',
mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None,
spin_name_col=None, data_col=2, error_col=3, sep=None)
Opening the file
'/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/r1.500.out'
for reading.
relax> relax_data.read(ri_label='R2', frq_label='500', frq=500000000.0,
file='r2.500.out',
dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149',
mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None,
spin_name_col=None, data_col=2, error_col=3, sep=None)
Opening the file
'/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/r2.500.out'
for reading.
relax> relax_data.read(ri_label='NOE', frq_label='500', frq=500000000.0,
file='noe.500.out',
dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149',
mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None,
spin_name_col=None, data_col=2, error_col=3, sep=None)
Opening the file
'/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/noe.500.out'
for reading.
relax> diffusion_tensor.init(params=1e-08, time_scale=1.0, d_scale=1.0,
angle_units='deg', param_types=0, spheroid_type=None, fixed=True)
relax> value.set(val=1.0200000000000001e-10, param='bond_length',
spin_id=None)
relax> value.set(val=-0.00015999999999999999, param='csa', spin_id=None)
relax> value.set(val='15N', param='heteronucleus', spin_id=None)
relax> value.set(val='1H', param='proton', spin_id=None)
relax> model_free.select_model(model='m4', spin_id=None)
relax> value.set(val=[1.0, 0.0, 0.0], param=['S2', 'te', 'Rex'], spin_id=None)
relax> minimise(*args=('newton', 'gmw', 'back'), func_tol=1e-25,
max_iterations=10000000, constraints=True, scaling=True, verbosity=1)
Only the model-free parameters for single spins will be used.
Fitting to spin ':2&:ALA'
~~~~~~~~~~~~~~~~~~~~~~~~
Method of Multipliers
~~~~~~~~~~~~~~~~~~~~
k: 0 xk: array([ 1., 0., 0.])
fk: 3.9844117908982288
Entering sub-algorithm.
Newton minimisation
~~~~~~~~~~~~~~~~~~~
Line search: Backtracking line search.
Hessian modification: The Gill, Murray, and Wright modified Cholesky
algorithm.
k: 0 xk: array([ 1., 0., 0.])
fk: 3.9844117908982288
Parameter values: array([ 0.90905499, 74.36909171, 1.22310096])
Function value: -1447.7789206948949
Iterations: 4
Function calls: 9
Gradient calls: 5
Hessian calls: 4
Warning: None
k: 1 xk: array([ 0.90905499, 74.36909171, 1.22310096])
fk: 48.121433050621448
Entering sub-algorithm.
Newton minimisation
~~~~~~~~~~~~~~~~~~~
Line search: Backtracking line search.
Hessian modification: The Gill, Murray, and Wright modified Cholesky
algorithm.
k: 0 xk: array([ 0.90905499, 74.36909171, 1.22310096])
fk: 46.071609923379611
Parameter values: array([ 9.69999986e-01, 2.04799695e+03,
1.49000257e-01])
Function value: -2.0498231272384211
Iterations: 11
Function calls: 37
Gradient calls: 12
Hessian calls: 11
Warning: None
k: 2 xk: array([ 9.69999986e-01, 2.04799695e+03, 1.49000257e-01])
fk: 3.414668279588586e-12
Entering sub-algorithm.
Newton minimisation
~~~~~~~~~~~~~~~~~~~
Line search: Backtracking line search.
Hessian modification: The Gill, Murray, and Wright modified Cholesky
algorithm.
k: 0 xk: array([ 9.69999986e-01, 2.04799695e+03,
1.49000257e-01]) fk: 3.414668279588586e-12
Parameter values: array([ 9.70000000e-01, 2.04800000e+03,
1.49000000e-01])
Function value: 1.2385186715645527e-22
Iterations: 1
Function calls: 3
Gradient calls: 2
Hessian calls: 1
Warning: None
k: 3 xk: array([ 9.70000000e-01, 2.04800000e+03, 1.49000000e-01])
fk: 1.2385186715645527e-22
Entering sub-algorithm.
Newton minimisation
~~~~~~~~~~~~~~~~~~~
Line search: Backtracking line search.
Hessian modification: The Gill, Murray, and Wright modified Cholesky
algorithm.
k: 0 xk: array([ 9.70000000e-01, 2.04800000e+03,
1.49000000e-01]) fk: 1.2385186715645527e-22
Parameter values: array([ 9.70000000e-01, 2.04800000e+03,
1.49000000e-01])
Function value: 5.7085251917483392e-28
Iterations: 1
Function calls: 3
Gradient calls: 2
Hessian calls: 1
Warning: None
k: 4 xk: array([ 9.70000000e-01, 2.04800000e+03, 1.49000000e-01])
fk: 5.7085251917483392e-28
Entering sub-algorithm.
Newton minimisation
~~~~~~~~~~~~~~~~~~~
Line search: Backtracking line search.
Hessian modification: The Gill, Murray, and Wright modified Cholesky
algorithm.
k: 0 xk: array([ 9.70000000e-01, 2.04800000e+03,
1.49000000e-01]) fk: 5.7085251917483392e-28
Parameter values: array([ 9.70000000e-01, 2.04800000e+03,
1.49000000e-01])
Function value: 5.7085251917483392e-28
Iterations: 1
Function calls: 42
Gradient calls: 2
Hessian calls: 1
Warning: None
Parameter values: array([ 9.70000000e-01, 2.04800000e+03,
1.49000000e-01])
Function value: 5.7085251917483392e-28
Iterations: 18
Function calls: 94
Gradient calls: 23
Hessian calls: 18
Warning: None
Traceback (most recent call last):
File "/sw/lib/relax-py25/test_suite/system_tests/model_free.py", line 499,
in test_opt_constr_newton_gmw_back_S2_0_970_te_2048_Rex_0_149
self.value_test(spin, select, s2, te, rex, chi2, iter, f_count, g_count,
h_count, warning)
File "/sw/lib/relax-py25/test_suite/system_tests/model_free.py", line 1047,
in value_test
self.assertEqual(spin.f_count, f_count, msg=mesg)
AssertionError: Optimisation failure.
System: Darwin
Release: 9.5.0
Version: Darwin Kernel Version 9.5.0: Wed Sep 3 11:31:44 PDT 2008;
root:xnu-1228.7.58~1/RELEASE_PPC
Win32 version:
Distribution:
Architecture: 32bit
Machine: Power Macintosh
Processor: powerpc
Python version: 2.5.2
numpy version: 1.1.1
s2: 0.9699999999999993
te: 2048.0000000000427
rex: 0.14900000000002098
chi2: 5.7085251917483392e-28
iter: 18
f_count: 94
g_count: 23
h_count: 18
warning: None
======================================================================
FAIL: Constrained Newton opt, GMW Hessian mod, More and Thuente line search
{S2=0.970, te=2048, Rex=0.149}
----------------------------------------------------------------------
relax> pipe.create(pipe_name='mf', pipe_type='mf')
relax> sequence.read(file='noe.500.out',
dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149',
mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None,
spin_name_col=None, sep=None)
Opening the file
'/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/noe.500.out'
for reading.
Mol_name Res_num Res_name Spin_num Spin_name
None 1 GLY None None
None 2 ALA None None
relax> relax_data.read(ri_label='R1', frq_label='600', frq=600000000.0,
file='r1.600.out',
dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149',
mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None,
spin_name_col=None, data_col=2, error_col=3, sep=None)
Opening the file
'/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/r1.600.out'
for reading.
relax> relax_data.read(ri_label='R2', frq_label='600', frq=600000000.0,
file='r2.600.out',
dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149',
mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None,
spin_name_col=None, data_col=2, error_col=3, sep=None)
Opening the file
'/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/r2.600.out'
for reading.
relax> relax_data.read(ri_label='NOE', frq_label='600', frq=600000000.0,
file='noe.600.out',
dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149',
mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None,
spin_name_col=None, data_col=2, error_col=3, sep=None)
Opening the file
'/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/noe.600.out'
for reading.
relax> relax_data.read(ri_label='R1', frq_label='500', frq=500000000.0,
file='r1.500.out',
dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149',
mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None,
spin_name_col=None, data_col=2, error_col=3, sep=None)
Opening the file
'/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/r1.500.out'
for reading.
relax> relax_data.read(ri_label='R2', frq_label='500', frq=500000000.0,
file='r2.500.out',
dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149',
mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None,
spin_name_col=None, data_col=2, error_col=3, sep=None)
Opening the file
'/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/r2.500.out'
for reading.
relax> relax_data.read(ri_label='NOE', frq_label='500', frq=500000000.0,
file='noe.500.out',
dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149',
mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None,
spin_name_col=None, data_col=2, error_col=3, sep=None)
Opening the file
'/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/noe.500.out'
for reading.
relax> diffusion_tensor.init(params=1e-08, time_scale=1.0, d_scale=1.0,
angle_units='deg', param_types=0, spheroid_type=None, fixed=True)
relax> value.set(val=1.0200000000000001e-10, param='bond_length',
spin_id=None)
relax> value.set(val=-0.00015999999999999999, param='csa', spin_id=None)
relax> value.set(val='15N', param='heteronucleus', spin_id=None)
relax> value.set(val='1H', param='proton', spin_id=None)
relax> model_free.select_model(model='m4', spin_id=None)
relax> value.set(val=[1.0, 0.0, 0.0], param=['S2', 'te', 'Rex'], spin_id=None)
relax> minimise(*args=('newton', 'gmw', 'mt'), func_tol=1e-25,
max_iterations=10000000, constraints=True, scaling=True, verbosity=1)
Only the model-free parameters for single spins will be used.
Fitting to spin ':2&:ALA'
~~~~~~~~~~~~~~~~~~~~~~~~
Method of Multipliers
~~~~~~~~~~~~~~~~~~~~
k: 0 xk: array([ 1., 0., 0.])
fk: 3.9844117908982288
Entering sub-algorithm.
Newton minimisation
~~~~~~~~~~~~~~~~~~~
Line search: More and Thuente line search.
Hessian modification: The Gill, Murray, and Wright modified Cholesky
algorithm.
k: 0 xk: array([ 1., 0., 0.])
fk: 3.9844117908982288
Parameter values: array([ 0.90905499, 74.36909171, 1.22310096])
Function value: -1447.7789206948949
Iterations: 4
Function calls: 9
Gradient calls: 9
Hessian calls: 4
Warning: None
k: 1 xk: array([ 0.90905499, 74.36909171, 1.22310096])
fk: 48.121433050621448
Entering sub-algorithm.
Newton minimisation
~~~~~~~~~~~~~~~~~~~
Line search: More and Thuente line search.
Hessian modification: The Gill, Murray, and Wright modified Cholesky
algorithm.
k: 0 xk: array([ 0.90905499, 74.36909171, 1.22310096])
fk: 46.071609923379611
Parameter values: array([ 9.69999996e-01, 2.04799919e+03,
1.49000073e-01])
Function value: -2.0498231272415968
Iterations: 15
Function calls: 73
Gradient calls: 73
Hessian calls: 15
Warning: None
k: 2 xk: array([ 9.69999996e-01, 2.04799919e+03, 1.49000073e-01])
fk: 2.3886846326646765e-13
Entering sub-algorithm.
Newton minimisation
~~~~~~~~~~~~~~~~~~~
Line search: More and Thuente line search.
Hessian modification: The Gill, Murray, and Wright modified Cholesky
algorithm.
k: 0 xk: array([ 9.69999996e-01, 2.04799919e+03,
1.49000073e-01]) fk: 2.3886846326646765e-13
Parameter values: array([ 9.70000000e-01, 2.04800000e+03,
1.49000000e-01])
Function value: 6.1070040854035286e-25
Iterations: 1
Function calls: 3
Gradient calls: 3
Hessian calls: 1
Warning: None
k: 3 xk: array([ 9.70000000e-01, 2.04800000e+03, 1.49000000e-01])
fk: 6.1070040854035286e-25
Entering sub-algorithm.
Newton minimisation
~~~~~~~~~~~~~~~~~~~
Line search: More and Thuente line search.
Hessian modification: The Gill, Murray, and Wright modified Cholesky
algorithm.
k: 0 xk: array([ 9.70000000e-01, 2.04800000e+03,
1.49000000e-01]) fk: 6.1070040854035286e-25
Parameter values: array([ 9.70000000e-01, 2.04800000e+03,
1.49000000e-01])
Function value: 6.8756889983348349e-28
Iterations: 1
Function calls: 3
Gradient calls: 3
Hessian calls: 1
Warning: None
k: 4 xk: array([ 9.70000000e-01, 2.04800000e+03, 1.49000000e-01])
fk: 6.8756889983348349e-28
Entering sub-algorithm.
Newton minimisation
~~~~~~~~~~~~~~~~~~~
Line search: More and Thuente line search.
Hessian modification: The Gill, Murray, and Wright modified Cholesky
algorithm.
k: 0 xk: array([ 9.70000000e-01, 2.04800000e+03,
1.49000000e-01]) fk: 6.8756889983348349e-28
Parameter values: array([ 9.70000000e-01, 2.04800000e+03,
1.49000000e-01])
Function value: 6.8756889983348349e-28
Iterations: 1
Function calls: 72
Gradient calls: 72
Hessian calls: 1
Warning: None
Parameter values: array([ 9.70000000e-01, 2.04800000e+03,
1.49000000e-01])
Function value: 6.8756889983348349e-28
Iterations: 22
Function calls: 160
Gradient calls: 160
Hessian calls: 22
Warning: None
Traceback (most recent call last):
File "/sw/lib/relax-py25/test_suite/system_tests/model_free.py", line 554,
in test_opt_constr_newton_gmw_mt_S2_0_970_te_2048_Rex_0_149
self.value_test(spin, select, s2, te, rex, chi2, iter, f_count, g_count,
h_count, warning)
File "/sw/lib/relax-py25/test_suite/system_tests/model_free.py", line 1047,
in value_test
self.assertEqual(spin.f_count, f_count, msg=mesg)
AssertionError: Optimisation failure.
System: Darwin
Release: 9.5.0
Version: Darwin Kernel Version 9.5.0: Wed Sep 3 11:31:44 PDT 2008;
root:xnu-1228.7.58~1/RELEASE_PPC
Win32 version:
Distribution:
Architecture: 32bit
Machine: Power Macintosh
Processor: powerpc
Python version: 2.5.2
numpy version: 1.1.1
s2: 0.9699999999999993
te: 2048.0000000000409
rex: 0.14900000000002178
chi2: 6.8756889983348349e-28
iter: 22
f_count: 160
g_count: 160
h_count: 22
warning: None
----------------------------------------------------------------------
Ran 59 tests in 154.110s
FAILED (failures=6, errors=1)
##############
# Unit tests #
##############
testing units...
----------------
/sw/lib/relax-py25/test_suite/unit_tests
..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................F............F..........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
======================================================================
FAIL: Test the Internal.atom_loop() method with the '@163' spin selection.
----------------------------------------------------------------------
Opening the file
'/sw/lib/relax-py25/test_suite/shared_data/structures/Ap4Aase_res1-12.pdb'
for reading.
Traceback (most recent call last):
File
"/sw/lib/relax-py25/test_suite/unit_tests/_generic_fns/_structure/test_internal.py",
line 197, in test_atom_loop_spin_selection2
self.assertEqual(pos.tostring(),
'\\\x8f\xc2\xf5(\x1c$@\xecQ\xb8\x1e\x85\xeb\x05\xc0\x89A`\xe5\xd0b*\xc0')
AssertionError:
'@$\x1c(\xf5\xc2\x8f\\\xc0\x05\xeb\x85\x1e\xb8Q\xec\xc0*b\xd0\xe5`A\x89' !=
'\\\x8f\xc2\xf5(\x1c$@\xecQ\xb8\x1e\x85\xeb\x05\xc0\x89A`\xe5\xd0b*\xc0'
======================================================================
FAIL: Test the Scientific_data.atom_loop() method with the '@163' spin
selection.
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/sw/lib/relax-py25/test_suite/unit_tests/_generic_fns/_structure/test_scientific.py",
line 297, in test_atom_loop_spin_selection2
self.assertEqual(pos.tostring(),
'\\\x8f\xc2\xf5(\x1c$@\xecQ\xb8\x1e\x85\xeb\x05\xc0\x89A`\xe5\xd0b*\xc0')
AssertionError:
'@$\x1c(\xf5\xc2\x8f\\\xc0\x05\xeb\x85\x1e\xb8Q\xec\xc0*b\xd0\xe5`A\x89' !=
'\\\x8f\xc2\xf5(\x1c$@\xecQ\xb8\x1e\x85\xeb\x05\xc0\x89A`\xe5\xd0b*\xc0'
----------------------------------------------------------------------
Ran 1046 tests in 27.144s
FAILED (failures=2)
###################################
# Summary of the relax test suite #
###################################
System/functional tests
............................................................. [ Failed ]
Unit tests
.......................................................................... [
Failed ]
Synopsis
............................................................................
[ Failed ]
relax 1.3.2 testsuite failures on darwin