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|
From: <ole...@us...> - 2016-11-16 19:49:46
|
Revision: 25725
http://sourceforge.net/p/cctbx/code/25725
Author: olegsobolev
Date: 2016-11-16 19:49:44 +0000 (Wed, 16 Nov 2016)
Log Message:
-----------
Actually use SS restraints after idealization
Modified Paths:
--------------
trunk/mmtbx/secondary_structure/build/__init__.py
Modified: trunk/mmtbx/secondary_structure/build/__init__.py
===================================================================
--- trunk/mmtbx/secondary_structure/build/__init__.py 2016-11-16 18:05:53 UTC (rev 25724)
+++ trunk/mmtbx/secondary_structure/build/__init__.py 2016-11-16 19:49:44 UTC (rev 25725)
@@ -655,11 +655,13 @@
processed_pdb_file, xray_structure)
t8 = time()
else:
+ ss_params = secondary_structure.default_params
+ ss_params.secondary_structure.protein.remove_outliers=False
ss_manager = secondary_structure.manager(
pdb_hierarchy=real_h,
geometry_restraints_manager=grm.geometry,
sec_str_from_pdb_file=ss_annotation,
- params=None,
+ params=ss_params.secondary_structure,
mon_lib_srv=None,
verbose=-1,
log=log)
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <af...@us...> - 2016-11-16 18:05:55
|
Revision: 25724
http://sourceforge.net/p/cctbx/code/25724
Author: afonine
Date: 2016-11-16 18:05:53 +0000 (Wed, 16 Nov 2016)
Log Message:
-----------
A better alternative to minimizing the libration-vibration correlation by reducing the norm of the screw vector, this is an option now set to default (Formula 10 of 2016/17 papper II, number may change). And thorough tests
Modified Paths:
--------------
trunk/mmtbx/run_tests.py
trunk/mmtbx/tls/analysis.py
trunk/mmtbx/tls/tls_as_xyz.py
trunk/mmtbx/tls/tools.py
Added Paths:
-----------
trunk/mmtbx/regression/tls/tst_formula_t_S_10_vs_11_2igd.py
trunk/mmtbx/regression/tls/tst_formula_t_S_10_vs_11_4muy.py
Added: trunk/mmtbx/regression/tls/tst_formula_t_S_10_vs_11_2igd.py
===================================================================
--- trunk/mmtbx/regression/tls/tst_formula_t_S_10_vs_11_2igd.py (rev 0)
+++ trunk/mmtbx/regression/tls/tst_formula_t_S_10_vs_11_2igd.py 2016-11-16 18:05:53 UTC (rev 25724)
@@ -0,0 +1,412 @@
+from __future__ import division
+from mmtbx.tls import tools
+import time
+import iotbx.pdb
+import mmtbx.tls.tools
+from scitbx import matrix
+from mmtbx.tls import analysis
+import math
+from scitbx.array_family import flex
+
+pdb_str_CA = """
+REMARK 3 TLS DETAILS.
+REMARK 3 NUMBER OF TLS GROUPS: 1
+REMARK 3 ORIGIN: CENTER OF MASS
+REMARK 3 TLS GROUP : 1
+REMARK 3 SELECTION: all
+REMARK 3 ORIGIN FOR THE GROUP (A): 8.7338 28.3021 16.6793
+REMARK 3 T TENSOR
+REMARK 3 T11: 0.0695 T22: 0.0842
+REMARK 3 T33: 0.0992 T12: 0.0039
+REMARK 3 T13: -0.0041 T23: 0.0014
+REMARK 3 L TENSOR
+REMARK 3 L11: 2.1725 L22: 0.5881
+REMARK 3 L33: 1.1562 L12: 0.4879
+REMARK 3 L13: -0.0881 L23: 0.2404
+REMARK 3 S TENSOR
+REMARK 3 S11: 0.0512 S12: 0.0543 S13: 0.0992
+REMARK 3 S21: -0.0892 S22: -0.0659 S23: -0.0441
+REMARK 3 S31: -0.0042 S32: -0.0302 S33: 0.0147
+CRYST1 35.050 40.500 42.370 90.00 90.00 90.00 P 21 21 21
+SCALE1 0.028531 0.000000 0.000000 0.00000
+SCALE2 0.000000 0.024691 0.000000 0.00000
+SCALE3 0.000000 0.000000 0.023602 0.00000
+ATOM 1 CA THR A 6 6.096 14.546 15.382 1.00 1.21 C
+ATOM 2 CA THR A 7 4.643 17.379 17.472 1.00 0.67 C
+ATOM 3 CA TYR A 8 7.031 20.308 17.626 1.00 -0.75 C
+ATOM 4 CA LYS A 9 6.715 23.191 20.108 1.00 -0.06 C
+ATOM 5 CA LEU A 10 7.484 26.896 19.736 1.00 -0.50 C
+ATOM 6 CA VAL A 11 8.313 28.973 22.814 1.00 -0.68 C
+ATOM 7 CA ILE A 12 7.745 32.666 21.951 1.00 0.00 C
+ATOM 8 CA ASN A 13 9.367 35.454 23.951 1.00 2.73 C
+ATOM 9 CA GLY A 14 8.223 38.436 21.869 1.00 4.26 C
+ATOM 10 CA LYS A 15 7.732 42.071 22.635 1.00 4.20 C
+ATOM 11 CA THR A 16 3.910 41.794 22.427 1.00 -1.15 C
+ATOM 12 CA LEU A 17 3.328 38.080 21.651 1.00 -2.50 C
+ATOM 13 CA LYS A 18 4.268 35.598 24.351 1.00 -2.00 C
+ATOM 14 CA GLY A 19 3.567 31.957 25.117 1.00 -1.89 C
+ATOM 15 CA GLU A 20 3.694 28.633 23.293 1.00 -1.20 C
+ATOM 16 CA THR A 21 2.207 27.042 20.183 1.00 -0.48 C
+ATOM 17 CA THR A 22 2.609 23.707 18.385 1.00 -0.37 C
+ATOM 18 CA THR A 23 2.682 22.183 14.916 1.00 1.08 C
+ATOM 19 CA LYS A 24 2.823 18.625 13.556 1.00 2.05 C
+ATOM 20 CA ALA A 25 5.312 17.719 10.843 1.00 -0.46 C
+ATOM 21 CA VAL A 26 7.260 14.854 9.299 1.00 -1.58 C
+ATOM 22 CA ASP A 27 10.612 16.526 10.001 1.00 -1.52 C
+ATOM 23 CA ALA A 28 12.142 19.541 11.794 1.00 0.14 C
+ATOM 24 CA GLU A 29 12.712 21.542 8.632 1.00 0.11 C
+ATOM 25 CA THR A 30 9.005 21.472 7.817 1.00 -1.33 C
+ATOM 26 CA ALA A 31 8.121 22.548 11.353 1.00 0.02 C
+ATOM 27 CA GLU A 32 10.719 25.317 11.217 1.00 0.13 C
+ATOM 28 CA LYS A 33 9.139 26.736 8.061 1.00 0.27 C
+ATOM 29 CA ALA A 34 5.654 26.682 9.658 1.00 0.18 C
+ATOM 30 CA PHE A 35 6.940 28.471 12.774 1.00 -0.71 C
+ATOM 31 CA LYS A 36 8.915 31.065 10.827 1.00 -0.16 C
+ATOM 32 CA GLN A 37 5.784 31.817 8.802 1.00 -0.29 C
+ATOM 33 CA TYR A 38 3.757 32.125 12.022 1.00 -0.88 C
+ATOM 34 CA ALA A 39 6.322 34.523 13.495 1.00 -0.11 C
+ATOM 35 CA ASN A 40 6.375 36.639 10.306 1.00 0.84 C
+ATOM 36 CA ASP A 41 2.536 36.702 10.145 1.00 -0.52 C
+ATOM 37 CA ASN A 42 2.519 38.093 13.718 1.00 -0.69 C
+ATOM 38 CA GLY A 43 5.296 40.638 13.264 1.00 0.34 C
+ATOM 39 CA VAL A 44 7.921 38.823 15.338 1.00 0.90 C
+ATOM 40 CA ASP A 45 11.526 39.426 14.290 1.00 3.57 C
+ATOM 41 CA GLY A 46 13.865 37.643 16.623 1.00 2.59 C
+ATOM 42 CA VAL A 47 16.614 35.096 17.081 1.00 -1.03 C
+ATOM 43 CA TRP A 48 16.026 31.364 17.129 1.00 -1.89 C
+ATOM 44 CA THR A 49 17.146 28.133 18.719 1.00 -1.92 C
+ATOM 45 CA TYR A 50 16.165 24.543 17.999 1.00 -1.32 C
+ATOM 46 CA ASP A 51 16.716 21.634 20.410 1.00 -0.77 C
+ATOM 47 CA ASP A 52 16.413 18.270 18.691 1.00 0.97 C
+ATOM 48 CA ALA A 53 16.219 16.432 22.049 1.00 4.22 C
+ATOM 49 CA THR A 54 12.971 18.177 23.062 1.00 1.37 C
+ATOM 50 CA LYS A 55 11.609 19.022 19.577 1.00 -0.72 C
+ATOM 51 CA THR A 56 11.365 22.651 20.684 1.00 -0.98 C
+ATOM 52 CA PHE A 57 12.052 25.886 18.846 1.00 -1.21 C
+ATOM 53 CA THR A 58 12.461 29.177 20.755 1.00 -1.19 C
+ATOM 54 CA VAL A 59 12.275 32.720 19.421 1.00 -1.14 C
+ATOM 55 CA THR A 60 13.202 35.851 21.380 1.00 -0.88 C
+ATOM 56 CA GLU A 61 12.989 39.521 20.535 1.00 1.06 C
+TER
+END
+"""
+
+pdb_str_CACON = """
+REMARK 3 TLS DETAILS.
+REMARK 3 NUMBER OF TLS GROUPS: 1
+REMARK 3 ORIGIN: CENTER OF MASS
+REMARK 3 TLS GROUP : 1
+REMARK 3 SELECTION: all
+REMARK 3 ORIGIN FOR THE GROUP (A): 8.6859 28.4733 16.7346
+REMARK 3 T TENSOR
+REMARK 3 T11: 0.0691 T22: 0.0854
+REMARK 3 T33: 0.1047 T12: 0.0048
+REMARK 3 T13: -0.0039 T23: -0.0005
+REMARK 3 L TENSOR
+REMARK 3 L11: 2.1972 L22: 0.5110
+REMARK 3 L33: 1.3269 L12: 0.5440
+REMARK 3 L13: 0.0026 L23: 0.2089
+REMARK 3 S TENSOR
+REMARK 3 S11: 0.0612 S12: 0.0383 S13: 0.0986
+REMARK 3 S21: -0.0977 S22: -0.0764 S23: -0.0418
+REMARK 3 S31: -0.0211 S32: -0.0272 S33: 0.0152
+CRYST1 35.050 40.500 42.370 90.00 90.00 90.00 P 21 21 21
+SCALE1 0.028531 0.000000 0.000000 0.00000
+SCALE2 0.000000 0.024691 0.000000 0.00000
+SCALE3 0.000000 0.000000 0.023602 0.00000
+ATOM 1 N THR A 6 5.628 14.116 14.075 1.00 -0.14 N
+ATOM 2 CA THR A 6 6.096 14.546 15.382 1.00 0.86 C
+ATOM 3 C THR A 6 5.411 15.882 15.727 1.00 0.13 C
+ATOM 4 O THR A 6 5.231 16.716 14.846 1.00 1.04 O
+ATOM 5 N THR A 7 5.084 16.089 17.004 1.00 0.55 N
+ATOM 6 CA THR A 7 4.643 17.379 17.472 1.00 0.42 C
+ATOM 7 C THR A 7 5.853 18.199 17.897 1.00 0.02 C
+ATOM 8 O THR A 7 6.635 17.775 18.761 1.00 3.64 O
+ATOM 9 N TYR A 8 5.998 19.354 17.311 1.00 -1.13 N
+ATOM 10 CA TYR A 8 7.031 20.308 17.626 1.00 -0.96 C
+ATOM 11 C TYR A 8 6.384 21.477 18.386 1.00 -1.13 C
+ATOM 12 O TYR A 8 5.253 21.855 18.136 1.00 1.22 O
+ATOM 13 N LYS A 9 7.151 22.068 19.294 1.00 -0.54 N
+ATOM 14 CA LYS A 9 6.715 23.191 20.108 1.00 -0.24 C
+ATOM 15 C LYS A 9 7.502 24.425 19.761 1.00 -0.91 C
+ATOM 16 O LYS A 9 8.703 24.345 19.462 1.00 0.55 O
+ATOM 17 N LEU A 10 6.854 25.585 19.831 1.00 -0.60 N
+ATOM 18 CA LEU A 10 7.484 26.896 19.736 1.00 -0.67 C
+ATOM 19 C LEU A 10 7.237 27.653 21.022 1.00 -0.77 C
+ATOM 20 O LEU A 10 6.081 27.852 21.422 1.00 0.79 O
+ATOM 21 N VAL A 11 8.311 28.092 21.657 1.00 -0.91 N
+ATOM 22 CA VAL A 11 8.313 28.973 22.814 1.00 -0.87 C
+ATOM 23 C VAL A 11 8.589 30.397 22.266 1.00 -0.99 C
+ATOM 24 O VAL A 11 9.615 30.605 21.632 1.00 0.68 O
+ATOM 25 N ILE A 12 7.658 31.314 22.493 1.00 -0.10 N
+ATOM 26 CA ILE A 12 7.745 32.666 21.951 1.00 -0.24 C
+ATOM 27 C ILE A 12 7.922 33.678 23.059 1.00 -0.20 C
+ATOM 28 O ILE A 12 7.053 33.835 23.928 1.00 0.88 O
+ATOM 29 N ASN A 13 9.057 34.372 23.043 1.00 1.02 N
+ATOM 30 CA ASN A 13 9.367 35.454 23.951 1.00 2.42 C
+ATOM 31 C ASN A 13 9.451 36.755 23.159 1.00 2.65 C
+ATOM 32 O ASN A 13 10.525 37.295 22.962 1.00 3.78 O
+ATOM 33 N GLY A 14 8.318 37.243 22.670 1.00 3.66 N
+ATOM 34 CA GLY A 14 8.223 38.436 21.869 1.00 3.84 C
+ATOM 35 C GLY A 14 7.950 39.692 22.643 1.00 3.14 C
+ATOM 36 O GLY A 14 7.646 39.596 23.871 1.00 6.24 O
+ATOM 37 N LYS A 15 8.054 40.804 21.975 1.00 3.35 N
+ATOM 38 CA LYS A 15 7.732 42.071 22.635 1.00 3.60 C
+ATOM 39 C LYS A 15 6.257 42.190 23.003 1.00 -0.24 C
+ATOM 40 O LYS A 15 5.977 42.698 24.043 1.00 3.00 O
+ATOM 41 N THR A 16 5.349 41.732 22.127 1.00 -1.64 N
+ATOM 42 CA THR A 16 3.910 41.794 22.427 1.00 -1.81 C
+ATOM 43 C THR A 16 3.272 40.435 22.393 1.00 -3.01 C
+ATOM 44 O THR A 16 2.195 40.299 22.987 1.00 0.66 O
+ATOM 45 N LEU A 17 3.854 39.437 21.763 1.00 -2.63 N
+ATOM 46 CA LEU A 17 3.328 38.080 21.651 1.00 -2.98 C
+ATOM 47 C LEU A 17 4.186 37.184 22.514 1.00 -2.79 C
+ATOM 48 O LEU A 17 5.396 37.109 22.337 1.00 0.26 O
+ATOM 49 N LYS A 18 3.557 36.473 23.453 1.00 -2.77 N
+ATOM 50 CA LYS A 18 4.268 35.598 24.351 1.00 -2.40 C
+ATOM 51 C LYS A 18 3.460 34.329 24.578 1.00 -2.72 C
+ATOM 52 O LYS A 18 2.235 34.355 24.675 1.00 -1.00 O
+ATOM 53 N GLY A 19 4.160 33.211 24.736 1.00 -2.52 N
+ATOM 54 CA GLY A 19 3.567 31.957 25.117 1.00 -2.20 C
+ATOM 55 C GLY A 19 4.126 30.802 24.327 1.00 -2.08 C
+ATOM 56 O GLY A 19 5.355 30.755 24.092 1.00 -0.35 O
+ATOM 57 N GLU A 20 3.289 29.842 23.994 1.00 -2.15 N
+ATOM 58 CA GLU A 20 3.694 28.633 23.293 1.00 -1.43 C
+ATOM 59 C GLU A 20 2.621 28.265 22.255 1.00 -1.41 C
+ATOM 60 O GLU A 20 1.437 28.479 22.482 1.00 -0.28 O
+ATOM 61 N THR A 21 3.079 27.640 21.179 1.00 -0.73 N
+ATOM 62 CA THR A 21 2.207 27.042 20.183 1.00 -0.68 C
+ATOM 63 C THR A 21 2.866 25.745 19.700 1.00 -0.64 C
+ATOM 64 O THR A 21 3.984 25.412 20.101 1.00 0.50 O
+ATOM 65 N THR A 22 2.147 25.001 18.859 1.00 -0.43 N
+ATOM 66 CA THR A 22 2.609 23.707 18.385 1.00 -0.54 C
+ATOM 67 C THR A 22 2.283 23.535 16.910 1.00 -0.03 C
+ATOM 68 O THR A 22 1.334 24.152 16.388 1.00 1.60 O
+ATOM 69 N THR A 23 2.999 22.625 16.268 1.00 0.08 N
+ATOM 70 CA THR A 23 2.682 22.183 14.916 1.00 0.94 C
+ATOM 71 C THR A 23 3.082 20.724 14.791 1.00 0.72 C
+ATOM 72 O THR A 23 3.965 20.253 15.484 1.00 3.94 O
+ATOM 73 N LYS A 24 2.489 20.032 13.836 1.00 1.40 N
+ATOM 74 CA LYS A 24 2.823 18.625 13.556 1.00 1.88 C
+ATOM 75 C LYS A 24 3.526 18.598 12.186 1.00 0.44 C
+ATOM 76 O LYS A 24 3.089 19.260 11.239 1.00 1.80 O
+ATOM 77 N ALA A 25 4.612 17.830 12.094 1.00 -0.69 N
+ATOM 78 CA ALA A 25 5.312 17.719 10.843 1.00 -0.66 C
+ATOM 79 C ALA A 25 6.098 16.407 10.770 1.00 -1.76 C
+ATOM 80 O ALA A 25 6.446 15.811 11.785 1.00 -0.29 O
+ATOM 81 N VAL A 26 6.448 16.040 9.546 1.00 -1.94 N
+ATOM 82 CA VAL A 26 7.260 14.854 9.299 1.00 -1.91 C
+ATOM 83 C VAL A 26 8.714 15.045 9.672 1.00 -2.12 C
+ATOM 84 O VAL A 26 9.432 14.072 9.914 1.00 0.90 O
+ATOM 85 N ASP A 27 9.221 16.273 9.700 1.00 -2.07 N
+ATOM 86 CA ASP A 27 10.612 16.526 10.001 1.00 -1.87 C
+ATOM 87 C ASP A 27 10.736 17.942 10.570 1.00 -1.92 C
+ATOM 88 O ASP A 27 9.811 18.770 10.534 1.00 -0.67 O
+ATOM 89 N ALA A 28 11.911 18.229 11.106 1.00 -0.78 N
+ATOM 90 CA ALA A 28 12.142 19.541 11.794 1.00 -0.15 C
+ATOM 91 C ALA A 28 12.174 20.683 10.816 1.00 -0.64 C
+ATOM 92 O ALA A 28 11.745 21.792 11.167 1.00 1.48 O
+ATOM 93 N GLU A 29 12.656 20.492 9.584 1.00 -0.63 N
+ATOM 94 CA GLU A 29 12.712 21.542 8.632 1.00 -0.14 C
+ATOM 95 C GLU A 29 11.307 22.028 8.263 1.00 -1.18 C
+ATOM 96 O GLU A 29 11.082 23.232 8.087 1.00 0.02 O
+ATOM 97 N THR A 30 10.368 21.120 8.131 1.00 -1.46 N
+ATOM 98 CA THR A 30 9.005 21.472 7.817 1.00 -1.49 C
+ATOM 99 C THR A 30 8.367 22.269 8.951 1.00 -1.23 C
+ATOM 100 O THR A 30 7.682 23.269 8.742 1.00 -0.09 O
+ATOM 101 N ALA A 31 8.601 21.802 10.188 1.00 -0.98 N
+ATOM 102 CA ALA A 31 8.121 22.548 11.353 1.00 -0.13 C
+ATOM 103 C ALA A 31 8.748 23.937 11.415 1.00 -0.59 C
+ATOM 104 O ALA A 31 8.051 24.901 11.739 1.00 0.74 O
+ATOM 105 N GLU A 32 10.048 24.036 11.158 1.00 -0.47 N
+ATOM 106 CA GLU A 32 10.719 25.317 11.217 1.00 -0.03 C
+ATOM 107 C GLU A 32 10.069 26.311 10.244 1.00 -0.35 C
+ATOM 108 O GLU A 32 9.834 27.465 10.577 1.00 0.77 O
+ATOM 109 N LYS A 33 9.765 25.875 9.026 1.00 -0.33 N
+ATOM 110 CA LYS A 33 9.139 26.736 8.061 1.00 0.18 C
+ATOM 111 C LYS A 33 7.767 27.197 8.527 1.00 -0.30 C
+ATOM 112 O LYS A 33 7.400 28.364 8.365 1.00 1.03 O
+ATOM 113 N ALA A 34 6.967 26.300 9.133 1.00 -0.05 N
+ATOM 114 CA ALA A 34 5.654 26.682 9.658 1.00 0.11 C
+ATOM 115 C ALA A 34 5.813 27.704 10.762 1.00 -0.79 C
+ATOM 116 O ALA A 34 5.034 28.686 10.833 1.00 0.64 O
+ATOM 117 N PHE A 35 6.745 27.528 11.666 1.00 -0.78 N
+ATOM 118 CA PHE A 35 6.940 28.471 12.774 1.00 -0.83 C
+ATOM 119 C PHE A 35 7.513 29.793 12.317 1.00 -0.91 C
+ATOM 120 O PHE A 35 7.128 30.833 12.863 1.00 -0.22 O
+ATOM 121 N LYS A 36 8.408 29.812 11.346 1.00 -0.44 N
+ATOM 122 CA LYS A 36 8.915 31.065 10.827 1.00 -0.30 C
+ATOM 123 C LYS A 36 7.793 31.837 10.117 1.00 -0.74 C
+ATOM 124 O LYS A 36 7.745 33.048 10.259 1.00 0.39 O
+ATOM 125 N GLN A 37 6.904 31.157 9.421 1.00 -0.76 N
+ATOM 126 CA GLN A 37 5.784 31.817 8.802 1.00 -0.37 C
+ATOM 127 C GLN A 37 4.860 32.399 9.857 1.00 -1.78 C
+ATOM 128 O GLN A 37 4.396 33.535 9.732 1.00 -0.52 O
+ATOM 129 N TYR A 38 4.554 31.635 10.899 1.00 -1.35 N
+ATOM 130 CA TYR A 38 3.757 32.125 12.022 1.00 -1.03 C
+ATOM 131 C TYR A 38 4.366 33.371 12.623 1.00 -2.04 C
+ATOM 132 O TYR A 38 3.658 34.355 12.914 1.00 -1.22 O
+ATOM 133 N ALA A 39 5.680 33.368 12.879 1.00 -1.26 N
+ATOM 134 CA ALA A 39 6.322 34.523 13.495 1.00 -0.33 C
+ATOM 135 C ALA A 39 6.196 35.741 12.534 1.00 -0.77 C
+ATOM 136 O ALA A 39 5.868 36.832 12.978 1.00 0.43 O
+ATOM 137 N ASN A 40 6.473 35.540 11.269 1.00 -0.25 N
+ATOM 138 CA ASN A 40 6.375 36.639 10.306 1.00 0.62 C
+ATOM 139 C ASN A 40 4.948 37.178 10.237 1.00 -0.63 C
+ATOM 140 O ASN A 40 4.744 38.408 10.195 1.00 0.73 O
+ATOM 141 N ASP A 41 3.959 36.296 10.203 1.00 -1.01 N
+ATOM 142 CA ASP A 41 2.536 36.702 10.145 1.00 -0.75 C
+ATOM 143 C ASP A 41 2.135 37.538 11.355 1.00 -0.27 C
+ATOM 144 O ASP A 41 1.210 38.351 11.240 1.00 3.89 O
+ATOM 145 N ASN A 42 2.798 37.366 12.472 1.00 -1.71 N
+ATOM 146 CA ASN A 42 2.519 38.093 13.718 1.00 -1.05 C
+ATOM 147 C ASN A 42 3.500 39.153 14.001 1.00 -0.84 C
+ATOM 148 O ASN A 42 3.496 39.762 15.071 1.00 1.80 O
+ATOM 149 N GLY A 43 4.380 39.512 13.118 1.00 -0.68 N
+ATOM 150 CA GLY A 43 5.296 40.638 13.264 1.00 -0.09 C
+ATOM 151 C GLY A 43 6.444 40.406 14.185 1.00 -0.46 C
+ATOM 152 O GLY A 43 7.010 41.360 14.689 1.00 3.93 O
+ATOM 153 N VAL A 44 6.830 39.148 14.452 1.00 -0.10 N
+ATOM 154 CA VAL A 44 7.921 38.823 15.338 1.00 0.52 C
+ATOM 155 C VAL A 44 9.187 38.697 14.541 1.00 2.55 C
+ATOM 156 O VAL A 44 9.242 37.875 13.641 1.00 8.31 O
+ATOM 157 N ASP A 45 10.215 39.430 14.941 1.00 1.33 N
+ATOM 158 CA ASP A 45 11.526 39.426 14.290 1.00 3.19 C
+ATOM 159 C ASP A 45 12.590 39.242 15.400 1.00 2.39 C
+ATOM 160 O ASP A 45 13.024 40.161 16.071 1.00 5.21 O
+ATOM 161 N GLY A 46 12.977 38.020 15.568 1.00 2.42 N
+ATOM 162 CA GLY A 46 13.865 37.643 16.623 1.00 2.26 C
+ATOM 163 C GLY A 46 14.903 36.645 16.228 1.00 -0.41 C
+ATOM 164 O GLY A 46 15.180 36.396 15.052 1.00 3.36 O
+ATOM 165 N VAL A 47 15.570 36.098 17.262 1.00 -1.18 N
+ATOM 166 CA VAL A 47 16.614 35.096 17.081 1.00 -1.32 C
+ATOM 167 C VAL A 47 16.094 33.770 17.609 1.00 -2.02 C
+ATOM 168 O VAL A 47 15.264 33.714 18.514 1.00 -0.66 O
+ATOM 169 N TRP A 48 16.607 32.691 17.009 1.00 -2.24 N
+ATOM 170 CA TRP A 48 16.026 31.364 17.129 1.00 -2.13 C
+ATOM 171 C TRP A 48 16.996 30.329 17.636 1.00 -2.80 C
+ATOM 172 O TRP A 48 18.172 30.281 17.232 1.00 -2.00 O
+ATOM 173 N THR A 49 16.488 29.379 18.438 1.00 -1.97 N
+ATOM 174 CA THR A 49 17.146 28.133 18.719 1.00 -2.14 C
+ATOM 175 C THR A 49 16.225 26.967 18.352 1.00 -1.90 C
+ATOM 176 O THR A 49 15.003 27.094 18.322 1.00 -0.77 O
+ATOM 177 N TYR A 50 16.851 25.803 18.146 1.00 -1.29 N
+ATOM 178 CA TYR A 50 16.165 24.543 17.999 1.00 -1.57 C
+ATOM 179 C TYR A 50 16.920 23.500 18.836 1.00 -1.97 C
+ATOM 180 O TYR A 50 18.136 23.407 18.737 1.00 -1.13 O
+ATOM 181 N ASP A 51 16.179 22.734 19.627 1.00 -1.26 N
+ATOM 182 CA ASP A 51 16.716 21.634 20.410 1.00 -1.05 C
+ATOM 183 C ASP A 51 16.100 20.316 19.901 1.00 -1.56 C
+ATOM 184 O ASP A 51 14.901 20.089 20.079 1.00 -0.00 O
+ATOM 185 N ASP A 52 16.901 19.511 19.280 1.00 -0.41 N
+ATOM 186 CA ASP A 52 16.413 18.270 18.691 1.00 0.58 C
+ATOM 187 C ASP A 52 16.029 17.280 19.777 1.00 1.69 C
+ATOM 188 O ASP A 52 15.274 16.349 19.487 1.00 6.79 O
+ATOM 189 N ALA A 53 16.572 17.391 20.979 1.00 1.22 N
+ATOM 190 CA ALA A 53 16.219 16.432 22.049 1.00 3.82 C
+ATOM 191 C ALA A 53 14.808 16.646 22.496 1.00 2.74 C
+ATOM 192 O ALA A 53 14.159 15.682 22.904 1.00 10.40 O
+ATOM 193 N THR A 54 14.305 17.841 22.535 1.00 0.72 N
+ATOM 194 CA THR A 54 12.971 18.177 23.062 1.00 1.09 C
+ATOM 195 C THR A 54 11.998 18.581 21.984 1.00 -0.14 C
+ATOM 196 O THR A 54 10.856 18.904 22.252 1.00 2.59 O
+ATOM 197 N LYS A 55 12.459 18.636 20.724 1.00 -0.87 N
+ATOM 198 CA LYS A 55 11.609 19.022 19.577 1.00 -1.00 C
+ATOM 199 C LYS A 55 11.021 20.391 19.797 1.00 -1.06 C
+ATOM 200 O LYS A 55 9.855 20.639 19.464 1.00 1.55 O
+ATOM 201 N THR A 56 11.822 21.313 20.323 1.00 -1.19 N
+ATOM 202 CA THR A 56 11.365 22.651 20.684 1.00 -1.17 C
+ATOM 203 C THR A 56 12.208 23.723 20.010 1.00 -1.28 C
+ATOM 204 O THR A 56 13.443 23.727 20.120 1.00 -0.50 O
+ATOM 205 N PHE A 57 11.506 24.659 19.368 1.00 -1.32 N
+ATOM 206 CA PHE A 57 12.052 25.886 18.846 1.00 -1.39 C
+ATOM 207 C PHE A 57 11.773 27.014 19.836 1.00 -1.48 C
+ATOM 208 O PHE A 57 10.708 27.005 20.471 1.00 -0.08 O
+ATOM 209 N THR A 58 12.672 27.973 19.913 1.00 -1.33 N
+ATOM 210 CA THR A 58 12.461 29.177 20.755 1.00 -1.37 C
+ATOM 211 C THR A 58 12.794 30.401 19.934 1.00 -1.22 C
+ATOM 212 O THR A 58 13.821 30.406 19.257 1.00 0.75 O
+ATOM 213 N VAL A 59 11.971 31.424 20.012 1.00 -1.18 N
+ATOM 214 CA VAL A 59 12.275 32.720 19.421 1.00 -1.36 C
+ATOM 215 C VAL A 59 12.184 33.794 20.482 1.00 -1.53 C
+ATOM 216 O VAL A 59 11.223 33.845 21.246 1.00 0.21 O
+ATOM 217 N THR A 60 13.188 34.674 20.499 1.00 -1.25 N
+ATOM 218 CA THR A 60 13.202 35.851 21.380 1.00 -1.17 C
+ATOM 219 C THR A 60 13.440 37.095 20.606 1.00 -1.70 C
+ATOM 220 O THR A 60 14.327 37.147 19.737 1.00 0.23 O
+ATOM 221 N GLU A 61 12.727 38.144 20.962 1.00 -0.48 N
+ATOM 222 CA GLU A 61 12.989 39.521 20.535 1.00 0.66 C
+ATOM 223 C GLU A 61 13.742 40.237 21.642 1.00 2.54 C
+ATOM 224 O GLU A 61 14.145 39.578 22.584 1.00 8.39 O
+TER
+END
+"""
+
+def exercise_00(pdb_str, formula):
+ """
+ CA and main-chain fragments of 2igd.
+ """
+ pdb_inp = iotbx.pdb.input(source_info=None, lines = pdb_str)
+ pdb_hierarchy = pdb_inp.construct_hierarchy()
+ asc = pdb_hierarchy.atom_selection_cache()
+ cs = pdb_inp.crystal_symmetry_from_cryst1()
+ tls_extract = mmtbx.tls.tools.tls_from_pdb_inp(
+ remark_3_records = pdb_inp.extract_remark_iii_records(3),
+ pdb_hierarchy = pdb_hierarchy)
+ #
+ deg_to_rad_scale = math.pi/180
+ tls_params_one_group = tls_extract.tls_params[0]
+ T = matrix.sym(sym_mat3=tls_params_one_group.t)
+ L = matrix.sym(sym_mat3=tls_params_one_group.l)
+ S = matrix.sqr(tls_params_one_group.s)
+ origin = tls_params_one_group.origin
+ tlso = tools.tlso(
+ t = T.as_sym_mat3(),
+ l = L.as_sym_mat3(),
+ s = S,
+ origin = origin)
+ log = open("analysis.log","w")
+ r = analysis.run(T=T, L=L*(deg_to_rad_scale**2), S=S*deg_to_rad_scale,
+ log=log, find_t_S_using_formula=formula).self_check(show=False)
+ log.close()
+ #
+ rs = flex.double()
+ for trial in xrange(10):
+ o = tools.u_tls_vs_u_ens(pdb_str=pdb_str,
+ dx = r.dx,
+ dy = r.dy,
+ dz = r.dz,
+ sx = r.sx,
+ sy = r.sy,
+ sz = r.sz,
+ lx = r.l_x,
+ ly = r.l_y,
+ lz = r.l_z,
+ tx = r.tx,
+ ty = r.ty,
+ tz = r.tz,
+ vx = r.v_x,
+ vy = r.v_y,
+ vz = r.v_z,
+ w_M_lx = r.w_M_lx,
+ w_M_ly = r.w_M_ly,
+ w_M_lz = r.w_M_lz,
+ origin = origin,
+ n_models = 10000,
+ assert_similarity=False)
+ rs.append(o.r)
+ return flex.mean(rs)
+
+if (__name__ == "__main__"):
+ t0 = time.time()
+ for formula in ["10","11"]:
+ print "formula:", formula
+ for i, pdb_str in enumerate([pdb_str_CA, pdb_str_CACON]):
+ r = exercise_00(pdb_str=pdb_str, formula=formula)
+ print " ", i, r
+ if(formula=="10"):
+ if(i==0): r<0.04
+ if(i==1): r>0.08
+ if(formula=="11"):
+ if(i==0): r<0.02
+ if(i==1): r<0.02
Added: trunk/mmtbx/regression/tls/tst_formula_t_S_10_vs_11_4muy.py
===================================================================
--- trunk/mmtbx/regression/tls/tst_formula_t_S_10_vs_11_4muy.py (rev 0)
+++ trunk/mmtbx/regression/tls/tst_formula_t_S_10_vs_11_4muy.py 2016-11-16 18:05:53 UTC (rev 25724)
@@ -0,0 +1,281 @@
+from __future__ import division
+from mmtbx.tls import tools
+import time
+import iotbx.pdb
+import mmtbx.tls.tools
+from scitbx import matrix
+from mmtbx.tls import analysis
+import math
+from scitbx.array_family import flex
+
+pdb_str= """
+REMARK 3
+REMARK 3 TLS GROUP : 6
+REMARK 3 NUMBER OF COMPONENTS GROUP : 1
+REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
+REMARK 3 RESIDUE RANGE : A 65 A 77
+REMARK 3 ORIGIN FOR THE GROUP (A): 5.7798 -4.9101 20.8090
+REMARK 3 T TENSOR
+REMARK 3 T11: 0.1766 T22: 0.1958
+REMARK 3 T33: 0.1284 T12: -0.0119
+REMARK 3 T13: -0.0231 T23: 0.0335
+REMARK 3 L TENSOR
+REMARK 3 L11: 0.2047 L22: 0.2291
+REMARK 3 L33: 0.4446 L12: 0.0057
+REMARK 3 L13: 0.2320 L23: 0.2028
+REMARK 3 S TENSOR
+REMARK 3 S11: 0.0460 S12: 0.0164 S13: -0.0519
+REMARK 3 S21: 0.0242 S22: 0.0228 S23: -0.0546
+REMARK 3 S31: 0.0280 S32: 0.0569 S33: -0.0688
+REMARK 3
+CRYST1 70.190 80.460 110.890 90.00 90.00 90.00 P 21 21 21
+SCALE1 0.014247 0.000000 0.000000 0.00000
+SCALE2 0.000000 0.012429 0.000000 0.00000
+SCALE3 0.000000 0.000000 0.009018 0.00000
+ATOM 1 N ASP A 65 14.147 -9.221 30.281 1.00 41.09 N
+ANISOU 1 N ASP A 65 5329 5873 4409 -633 -1875 965 N
+ATOM 2 CA ASP A 65 15.252 -9.249 29.320 1.00 42.10 C
+ANISOU 2 CA ASP A 65 5520 5848 4628 -454 -1645 509 C
+ATOM 3 C ASP A 65 15.235 -10.537 28.501 1.00 40.51 C
+ANISOU 3 C ASP A 65 5402 5699 4291 -472 -2125 624 C
+ATOM 4 O ASP A 65 14.791 -11.574 28.982 1.00 39.28 O
+ANISOU 4 O ASP A 65 5521 5937 3467 -466 -2793 943 O
+ATOM 5 CB ASP A 65 16.599 -9.117 30.052 1.00 44.12 C
+ANISOU 5 CB ASP A 65 5578 6377 4807 -323 -1759 465 C
+ATOM 6 CG ASP A 65 16.805 -7.734 30.675 1.00 47.85 C
+ANISOU 6 CG ASP A 65 6211 6644 5326 -533 -1632 224 C
+ATOM 7 OD1 ASP A 65 16.037 -6.794 30.359 1.00 51.97 O
+ANISOU 7 OD1 ASP A 65 6898 6544 6303 -15 -411 599 O
+ATOM 8 OD2 ASP A 65 17.748 -7.584 31.482 1.00 51.60 O
+ANISOU 8 OD2 ASP A 65 6250 7759 5593 -575 -1695 -226 O
+ATOM 9 N GLY A 66 15.695 -10.453 27.254 1.00 43.04 N
+ANISOU 9 N GLY A 66 5541 6021 4789 -564 -1568 173 N
+ATOM 10 CA GLY A 66 15.771 -11.614 26.358 1.00 42.81 C
+ANISOU 10 CA GLY A 66 5506 6041 4718 -265 -1800 137 C
+ATOM 11 C GLY A 66 14.469 -11.953 25.645 1.00 42.08 C
+ANISOU 11 C GLY A 66 5383 5987 4617 -209 -1639 57 C
+ATOM 12 O GLY A 66 14.459 -12.761 24.719 1.00 44.05 O
+ANISOU 12 O GLY A 66 5670 6379 4687 -247 -2191 -161 O
+ATOM 13 N ALA A 67 13.374 -11.318 26.052 1.00 39.31 N
+ANISOU 13 N ALA A 67 5011 5498 4427 -513 -1743 269 N
+ATOM 14 CA ALA A 67 12.035 -11.711 25.610 1.00 34.72 C
+ANISOU 14 CA ALA A 67 4873 4883 3435 -220 -1759 605 C
+ATOM 15 C ALA A 67 11.747 -11.272 24.182 1.00 34.65 C
+ANISOU 15 C ALA A 67 4719 5070 3375 -468 -1676 626 C
+ATOM 16 O ALA A 67 12.465 -10.435 23.611 1.00 33.02 O
+ANISOU 16 O ALA A 67 4398 5086 3060 -343 -2075 876 O
+ATOM 17 CB ALA A 67 10.980 -11.142 26.553 1.00 32.29 C
+ANISOU 17 CB ALA A 67 4476 4659 3132 -444 -1922 573 C
+ATOM 18 N ILE A 68 10.695 -11.864 23.612 1.00 33.06 N
+ANISOU 18 N ILE A 68 4600 4702 3256 -324 -1651 731 N
+ATOM 19 CA ILE A 68 10.159 -11.446 22.326 1.00 31.69 C
+ANISOU 19 CA ILE A 68 4462 4593 2985 -258 -1327 634 C
+ATOM 20 C ILE A 68 8.993 -10.516 22.600 1.00 28.77 C
+ANISOU 20 C ILE A 68 4017 4426 2485 -420 -1554 771 C
+ATOM 21 O ILE A 68 8.102 -10.863 23.367 1.00 29.09 O
+ANISOU 21 O ILE A 68 3969 4498 2585 -247 -1612 861 O
+ATOM 22 CB ILE A 68 9.711 -12.658 21.487 1.00 33.33 C
+ANISOU 22 CB ILE A 68 4545 4700 3419 -415 -1435 543 C
+ATOM 23 CG1 ILE A 68 10.950 -13.475 21.091 1.00 33.58 C
+ANISOU 23 CG1 ILE A 68 4108 5209 3440 -686 -2083 -48 C
+ATOM 24 CG2 ILE A 68 8.940 -12.220 20.244 1.00 33.93 C
+ANISOU 24 CG2 ILE A 68 4626 4880 3386 -228 -1345 557 C
+ATOM 25 CD1 ILE A 68 10.723 -14.965 21.116 1.00 35.38 C
+ANISOU 25 CD1 ILE A 68 4273 5208 3961 -444 -2399 -116 C
+ATOM 26 N LEU A 69 9.020 -9.336 21.977 1.00 27.70 N
+ANISOU 26 N LEU A 69 3666 4241 2616 -537 -1183 594 N
+ATOM 27 CA LEU A 69 7.993 -8.311 22.153 1.00 25.86 C
+ANISOU 27 CA LEU A 69 3574 4169 2081 -532 -1071 868 C
+ATOM 28 C LEU A 69 7.413 -8.016 20.799 1.00 25.13 C
+ANISOU 28 C LEU A 69 3441 4069 2036 -439 -1021 734 C
+ATOM 29 O LEU A 69 8.156 -7.877 19.831 1.00 26.34 O
+ANISOU 29 O LEU A 69 3552 4318 2137 -465 -987 1038 O
+ATOM 30 CB LEU A 69 8.613 -7.021 22.657 1.00 27.46 C
+ANISOU 30 CB LEU A 69 3857 4296 2280 -543 -940 640 C
+ATOM 31 CG LEU A 69 7.850 -6.047 23.563 1.00 28.66 C
+ANISOU 31 CG LEU A 69 4059 4448 2381 -330 -907 634 C
+ATOM 32 CD1 LEU A 69 8.040 -4.642 23.035 1.00 30.10 C
+ANISOU 32 CD1 LEU A 69 4062 4597 2774 -143 -556 890 C
+ATOM 33 CD2 LEU A 69 6.379 -6.345 23.802 1.00 27.33 C
+ANISOU 33 CD2 LEU A 69 3995 4289 2097 -164 -1171 609 C
+ATOM 34 N ILE A 70 6.097 -7.893 20.738 1.00 24.58 N
+ANISOU 34 N ILE A 70 3388 4002 1947 -615 -905 886 N
+ATOM 35 CA ILE A 70 5.415 -7.521 19.506 1.00 22.86 C
+ANISOU 35 CA ILE A 70 3182 3660 1841 -534 -756 774 C
+ATOM 36 C ILE A 70 4.678 -6.222 19.803 1.00 22.24 C
+ANISOU 36 C ILE A 70 3080 3605 1762 -608 -710 693 C
+ATOM 37 O ILE A 70 3.979 -6.128 20.805 1.00 23.02 O
+ANISOU 37 O ILE A 70 3306 3725 1714 -573 -615 824 O
+ATOM 38 CB ILE A 70 4.422 -8.609 19.076 1.00 22.84 C
+ANISOU 38 CB ILE A 70 3207 3610 1862 -508 -784 792 C
+ATOM 39 CG1 ILE A 70 5.161 -9.951 18.912 1.00 23.90 C
+ANISOU 39 CG1 ILE A 70 3382 3677 2020 -472 -958 841 C
+ATOM 40 CG2 ILE A 70 3.706 -8.190 17.801 1.00 22.46 C
+ANISOU 40 CG2 ILE A 70 3286 3414 1832 -387 -736 764 C
+ATOM 41 CD1 ILE A 70 4.279 -11.135 18.629 1.00 24.53 C
+ANISOU 41 CD1 ILE A 70 3665 3599 2056 -465 -1065 836 C
+ATOM 42 N PHE A 71 4.860 -5.208 18.973 1.00 21.59 N
+ANISOU 42 N PHE A 71 3035 3501 1667 -533 -584 589 N
+ATOM 43 CA PHE A 71 4.050 -3.990 19.088 1.00 21.28 C
+ANISOU 43 CA PHE A 71 2952 3507 1624 -540 -545 564 C
+ATOM 44 C PHE A 71 2.699 -4.237 18.451 1.00 21.01 C
+ANISOU 44 C PHE A 71 2922 3406 1654 -432 -574 613 C
+ATOM 45 O PHE A 71 2.629 -4.859 17.388 1.00 20.73 O
+ANISOU 45 O PHE A 71 2910 3342 1624 -180 -454 644 O
+ATOM 46 CB PHE A 71 4.686 -2.798 18.386 1.00 21.03 C
+ANISOU 46 CB PHE A 71 2929 3405 1654 -406 -537 615 C
+ATOM 47 CG PHE A 71 6.072 -2.463 18.847 1.00 21.48 C
+ANISOU 47 CG PHE A 71 2935 3594 1629 -484 -470 627 C
+ATOM 48 CD1 PHE A 71 6.392 -2.412 20.202 1.00 21.38 C
+ANISOU 48 CD1 PHE A 71 2856 3630 1635 -537 -462 666 C
+ATOM 49 CD2 PHE A 71 7.055 -2.167 17.930 1.00 21.64 C
+ANISOU 49 CD2 PHE A 71 2901 3553 1766 -462 -479 813 C
+ATOM 50 CE1 PHE A 71 7.668 -2.084 20.609 1.00 21.79 C
+ANISOU 50 CE1 PHE A 71 2851 3665 1763 -604 -328 661 C
+ATOM 51 CE2 PHE A 71 8.334 -1.823 18.329 1.00 22.27 C
+ANISOU 51 CE2 PHE A 71 2976 3735 1750 -509 -523 728 C
+ATOM 52 CZ PHE A 71 8.647 -1.798 19.675 1.00 21.40 C
+ANISOU 52 CZ PHE A 71 2754 3687 1689 -412 -381 695 C
+ATOM 53 N SER A 72 1.633 -3.709 19.049 1.00 20.51 N
+ANISOU 53 N SER A 72 2877 3406 1506 -663 -396 573 N
+ATOM 54 CA SER A 72 0.286 -3.952 18.532 1.00 20.43 C
+ANISOU 54 CA SER A 72 2885 3288 1590 -494 -528 655 C
+ATOM 55 C SER A 72 0.022 -3.221 17.213 1.00 20.34 C
+ANISOU 55 C SER A 72 2949 3214 1563 -483 -511 618 C
+ATOM 56 O SER A 72 0.781 -2.352 16.810 1.00 19.70 O
+ANISOU 56 O SER A 72 2751 3296 1435 -422 -264 418 O
+ATOM 57 CB SER A 72 -0.781 -3.534 19.540 1.00 20.57 C
+ANISOU 57 CB SER A 72 2835 3406 1571 -642 -526 686 C
+ATOM 58 OG SER A 72 -0.997 -2.142 19.497 1.00 20.81 O
+ANISOU 58 OG SER A 72 2841 3421 1642 -600 -568 401 O
+ATOM 59 N ALA A 73 -1.106 -3.558 16.591 1.00 20.66 N
+ANISOU 59 N ALA A 73 3019 3240 1590 -496 -570 636 N
+ATOM 60 CA ALA A 73 -1.494 -3.007 15.297 1.00 20.78 C
+ANISOU 60 CA ALA A 73 3052 3312 1531 -448 -482 632 C
+ATOM 61 C ALA A 73 -1.626 -1.490 15.347 1.00 20.78 C
+ANISOU 61 C ALA A 73 3069 3352 1471 -345 -372 612 C
+ATOM 62 O ALA A 73 -1.458 -0.821 14.356 1.00 19.73 O
+ANISOU 62 O ALA A 73 2880 3148 1466 -287 -376 550 O
+ATOM 63 CB ALA A 73 -2.806 -3.638 14.814 1.00 20.21 C
+ANISOU 63 CB ALA A 73 3001 3095 1581 -346 -502 688 C
+ATOM 64 N HIS A 74 -1.886 -0.956 16.539 1.00 20.28 N
+ANISOU 64 N HIS A 74 2845 3313 1546 -227 -507 527 N
+ATOM 65 CA HIS A 74 -2.151 0.462 16.721 1.00 19.54 C
+ANISOU 65 CA HIS A 74 2627 3313 1483 -230 -398 516 C
+ATOM 66 C HIS A 74 -0.912 1.311 16.604 1.00 20.14 C
+ANISOU 66 C HIS A 74 2915 3371 1366 -422 -203 470 C
+ATOM 67 O HIS A 74 -1.040 2.504 16.391 1.00 20.61 O
+ANISOU 67 O HIS A 74 3071 3383 1374 -333 -275 486 O
+ATOM 68 CB HIS A 74 -2.819 0.697 18.100 1.00 19.53 C
+ANISOU 68 CB HIS A 74 2576 3370 1474 -350 -395 536 C
+ATOM 69 CG HIS A 74 -3.892 -0.291 18.378 1.00 20.17 C
+ANISOU 69 CG HIS A 74 2778 3481 1402 -502 -335 465 C
+ATOM 70 ND1 HIS A 74 -3.648 -1.473 19.035 1.00 20.32 N
+ANISOU 70 ND1 HIS A 74 2804 3504 1412 -589 -338 501 N
+ATOM 71 CD2 HIS A 74 -5.167 -0.364 17.933 1.00 20.96 C
+ANISOU 71 CD2 HIS A 74 2842 3608 1513 -472 -453 616 C
+ATOM 72 CE1 HIS A 74 -4.753 -2.193 19.063 1.00 20.52 C
+ANISOU 72 CE1 HIS A 74 2829 3533 1432 -616 -376 493 C
+ATOM 73 NE2 HIS A 74 -5.686 -1.541 18.398 1.00 21.01 N
+ANISOU 73 NE2 HIS A 74 2823 3553 1607 -639 -538 401 N
+ATOM 74 N GLY A 75 0.272 0.715 16.755 1.00 19.61 N
+ANISOU 74 N GLY A 75 2921 3134 1395 -466 -239 494 N
+ATOM 75 CA GLY A 75 1.529 1.447 16.690 1.00 19.84 C
+ANISOU 75 CA GLY A 75 2854 3233 1449 -434 -313 568 C
+ATOM 76 C GLY A 75 2.053 1.917 18.043 1.00 20.08 C
+ANISOU 76 C GLY A 75 2817 3329 1483 -566 -371 623 C
+ATOM 77 O GLY A 75 1.343 1.866 19.044 1.00 20.58 O
+ANISOU 77 O GLY A 75 2776 3576 1468 -608 -380 598 O
+ATOM 78 N VAL A 76 3.283 2.420 18.046 1.00 20.15 N
+ANISOU 78 N VAL A 76 2801 3358 1497 -543 -361 612 N
+ATOM 79 CA VAL A 76 3.920 2.883 19.288 1.00 20.26 C
+ANISOU 79 CA VAL A 76 2836 3378 1483 -616 -338 616 C
+ATOM 80 C VAL A 76 4.742 4.126 19.020 1.00 20.38 C
+ANISOU 80 C VAL A 76 2724 3525 1491 -675 -311 640 C
+ATOM 81 O VAL A 76 5.161 4.379 17.886 1.00 19.93 O
+ANISOU 81 O VAL A 76 2697 3305 1567 -666 -306 759 O
+ATOM 82 CB VAL A 76 4.819 1.795 19.881 1.00 20.01 C
+ANISOU 82 CB VAL A 76 2771 3329 1500 -616 -357 499 C
+ATOM 83 CG1 VAL A 76 3.984 0.589 20.254 1.00 19.79 C
+ANISOU 83 CG1 VAL A 76 2688 3366 1464 -624 -298 445 C
+ATOM 84 CG2 VAL A 76 5.928 1.389 18.912 1.00 20.07 C
+ANISOU 84 CG2 VAL A 76 2741 3346 1537 -552 -350 559 C
+ATOM 85 N SER A 77 4.954 4.909 20.069 1.00 20.67 N
+ANISOU 85 N SER A 77 2833 3545 1475 -699 -282 650 N
+ATOM 86 CA SER A 77 5.808 6.071 19.998 1.00 21.19 C
+ANISOU 86 CA SER A 77 3018 3514 1519 -731 -326 708 C
+ATOM 87 C SER A 77 7.265 5.677 19.776 1.00 21.98 C
+ANISOU 87 C SER A 77 2962 3688 1701 -726 -450 738 C
+ATOM 88 O SER A 77 7.671 4.545 20.040 1.00 21.51 O
+ANISOU 88 O SER A 77 2983 3649 1538 -724 -225 670 O
+ATOM 89 CB SER A 77 5.716 6.869 21.283 1.00 20.97 C
+ANISOU 89 CB SER A 77 2887 3496 1582 -716 -450 654 C
+ATOM 90 OG SER A 77 6.230 6.070 22.318 1.00 20.53 O
+ANISOU 90 OG SER A 77 2828 3335 1636 -702 -509 561 O
+TER
+END
+"""
+
+def exercise_00(pdb_str, formula):
+ """
+ TLS group 6 of 4muy.
+ """
+ pdb_inp = iotbx.pdb.input(source_info=None, lines = pdb_str)
+ pdb_hierarchy = pdb_inp.construct_hierarchy()
+ asc = pdb_hierarchy.atom_selection_cache()
+ cs = pdb_inp.crystal_symmetry_from_cryst1()
+ tls_extract = mmtbx.tls.tools.tls_from_pdb_inp(
+ remark_3_records = pdb_inp.extract_remark_iii_records(3),
+ pdb_hierarchy = pdb_hierarchy)
+ #
+ deg_to_rad_scale = math.pi/180
+ tls_params_one_group = tls_extract.tls_params[0]
+ T = matrix.sym(sym_mat3=tls_params_one_group.t)
+ L = matrix.sym(sym_mat3=tls_params_one_group.l)
+ S = matrix.sqr(tls_params_one_group.s)
+ origin = tls_params_one_group.origin
+ tlso = tools.tlso(
+ t = T.as_sym_mat3(),
+ l = L.as_sym_mat3(),
+ s = S,
+ origin = origin)
+ log = open("analysis.log","w")
+ r = analysis.run(T=T, L=L*(deg_to_rad_scale**2), S=S*deg_to_rad_scale,
+ log=log, find_t_S_using_formula=formula).self_check(show=False)
+ log.close()
+ #
+ rs = flex.double()
+ for trial in xrange(10):
+ o = tools.u_tls_vs_u_ens(pdb_str=pdb_str,
+ dx = r.dx,
+ dy = r.dy,
+ dz = r.dz,
+ sx = r.sx,
+ sy = r.sy,
+ sz = r.sz,
+ lx = r.l_x,
+ ly = r.l_y,
+ lz = r.l_z,
+ tx = r.tx,
+ ty = r.ty,
+ tz = r.tz,
+ vx = r.v_x,
+ vy = r.v_y,
+ vz = r.v_z,
+ w_M_lx = r.w_M_lx,
+ w_M_ly = r.w_M_ly,
+ w_M_lz = r.w_M_lz,
+ origin = origin,
+ n_models = 10000,
+ assert_similarity=False)
+ rs.append(o.r)
+ return flex.mean(rs)
+
+if (__name__ == "__main__"):
+ t0 = time.time()
+ for formula in ["10","11"]:
+ print "formula:", formula
+ r = exercise_00(pdb_str=pdb_str, formula=formula)
+ print " ", r
+ if(formula=="10"): r>0.55
+ if(formula=="11"): r<0.06
Modified: trunk/mmtbx/run_tests.py
===================================================================
--- trunk/mmtbx/run_tests.py 2016-11-16 17:14:39 UTC (rev 25723)
+++ trunk/mmtbx/run_tests.py 2016-11-16 18:05:53 UTC (rev 25724)
@@ -28,6 +28,8 @@
"$D/regression/tls/tst_u_tls_vs_u_ens_03.py",
"$D/regression/tls/tst_u_tls_vs_u_ens_04.py",
"$D/regression/tls/tst_tls_as_xyz.py",
+ "$D/regression/tls/tst_formula_t_S_10_vs_11_2igd.py",
+ "$D/regression/tls/tst_formula_t_S_10_vs_11_4muy.py",
#
"$D/regression/tst_angle.py",
"$D/rotamer/tst_rotamer_eval.py",
Modified: trunk/mmtbx/tls/analysis.py
===================================================================
--- trunk/mmtbx/tls/analysis.py 2016-11-16 17:14:39 UTC (rev 25723)
+++ trunk/mmtbx/tls/analysis.py 2016-11-16 18:05:53 UTC (rev 25724)
@@ -101,7 +101,7 @@
class run(object):
def __init__(self, T, L, S, log=sys.stdout, eps=1.e-6, self_check_eps=1.e-5,
- force_t_S=None):
+ force_t_S=None, find_t_S_using_formula="11"):
"""
Decompose TLS matrices into physically iterpretable components.
"""
@@ -109,7 +109,13 @@
self.ff = "%12.9f"
self.eps = eps
self.self_check_eps = self_check_eps
+ # Choose how to deal with t_S START
self.force_t_S = force_t_S
+ self.find_t_S_using_formula = find_t_S_using_formula
+ assert self.find_t_S_using_formula in ["10","11", None]
+ if(self.force_t_S is not None):
+ assert self.find_t_S_using_formula is None
+ # Choose how to deal with t_S END
print >> self.log, "Small is defined as:", self.eps
self.T_M, self.L_M, self.S_M = T, L, S
print_step("Input TLS matrices:", self.log)
@@ -270,142 +276,148 @@
Determination of screw components.
"""
print_step("Step C:", self.log)
- T_ = self.T_CL.as_sym_mat3()
- self.T_CLxx, self.T_CLyy, self.T_CLzz = T_[0], T_[1], T_[2]
- #
- # Left branch
- #
- if(not (self.is_zero(self.Lxx) or
- self.is_zero(self.Lyy) or
- self.is_zero(self.Lzz))):
- tlxx = self.T_CLxx*self.Lxx
- tlyy = self.T_CLyy*self.Lyy
- tlzz = self.T_CLzz*self.Lzz
- t11, t22, t33 = tlxx, tlyy, tlzz # the rest is below
- rx, ry, rz = math.sqrt(tlxx), math.sqrt(tlyy), math.sqrt(tlzz)
- t12 = self.T_CL[1] * math.sqrt(self.Lxx*self.Lyy)
- t13 = self.T_CL[2] * math.sqrt(self.Lxx*self.Lzz)
- t23 = self.T_CL[5] * math.sqrt(self.Lyy*self.Lzz)
- t_min_C = max(self.Sxx-rx, self.Syy-ry, self.Szz-rz)
- t_max_C = min(self.Sxx+rx, self.Syy+ry, self.Szz+rz)
- show_number(x=[t_min_C, t_max_C], title="t_min_C,t_max_C eq.(24):", log=self.log)
- if(t_min_C > t_max_C):
- raise Sorry("Step C (left branch): Empty (tmin_c,tmax_c) interval.")
- ######## HACK START
- #t_0 = self.S_L.trace()/3.
- num = self.Sxx*self.Lyy**2*self.Lzz**2 +\
- self.Syy*self.Lzz**2*self.Lxx**2 +\
- self.Szz*self.Lxx**2*self.Lyy**2
- den = self.Lyy**2*self.Lzz**2 + \
- self.Lzz**2*self.Lxx**2 + \
- self.Lxx**2*self.Lyy**2
- t_0 = num/den
- ######## HACK END
- show_number(x=t_0, title="t_0 eq.(20):", log=self.log)
- # compose T_lambda and find tau_max (30)
- T_lambda = matrix.sqr(
- [t11, t12, t13,
- t12, t22, t23,
- t13, t23, t33])
- show_matrix(x=T_lambda, title="T_lambda eq.(29)", log=self.log)
- es = eigensystem.real_symmetric(T_lambda.as_sym_mat3())
- vals = es.values()
- assert vals[0]>=vals[1]>=vals[2]
- tau_max = vals[0]
+
+ if(self.force_t_S is not None):
+ self.t_S = self.force_t_S
+ else: # HUGE CLOSE BEGIN
+ T_ = self.T_CL.as_sym_mat3()
+ self.T_CLxx, self.T_CLyy, self.T_CLzz = T_[0], T_[1], T_[2]
#
- if(tau_max < 0):
- raise Sorry("Step C (left branch): Eq.(32): tau_max<0.")
- t_min_tau = max(self.Sxx,self.Syy,self.Szz)-math.sqrt(tau_max)
- t_max_tau = min(self.Sxx,self.Syy,self.Szz)+math.sqrt(tau_max)
- show_number(x=[t_min_tau, t_max_tau],
- title="t_min_tau, t_max_tau eq.(31):", log=self.log)
- if(t_min_tau > t_max_tau):
- raise Sorry("Step C (left branch): Empty (tmin_t,tmax_t) interval.")
- # (38):
- arg = t_0**2 + (t11+t22+t33)/3. - (self.Sxx**2+self.Syy**2+self.Szz**2)/3.
- if(arg < 0):
- raise Sorry("Step C (left branch): Negative argument when estimating tmin_a.")
- t_a = math.sqrt(arg)
- show_number(x=t_a, title="t_a eq.(38):", log=self.log)
- t_min_a = t_0-t_a
- t_max_a = t_0+t_a
- show_number(x=[t_min_a, t_max_a], title="t_min_a, t_max_a eq.(37):", log=self.log)
- # compute t_min, t_max - this is step b)
- t_min = max(t_min_C, t_min_tau, t_min_a)
- t_max = min(t_max_C, t_max_tau, t_max_a)
- if(t_min > t_max):
- raise Sorry("Step C (left branch): Intersection of the intervals for t_S is empty.")
- elif(self.is_zero(t_min-t_max)):
- _, b_s, c_s = self.as_bs_cs(t=t_min, txx=t11,tyy=t22,tzz=t33,
- txy=t12,tyz=t23,tzx=t13)
- if( (self.is_zero(b_s) or bs>0) and (c_s<0 or self.is_zero(c_s))):
- self.t_S = t_min
- else:
- raise Sorry("Step C (left branch): t_min=t_max gives non positive semidefinite V_lambda.")
- elif(t_min < t_max):
- step = (t_max-t_min)/100000.
- target = 1.e+9
- t_S_best = t_min
- while t_S_best <= t_max:
- _, b_s, c_s = self.as_bs_cs(t=t_S_best, txx=t11,tyy=t22,tzz=t33,
+ # Left branch
+ #
+ if(not (self.is_zero(self.Lxx) or
+ self.is_zero(self.Lyy) or
+ self.is_zero(self.Lzz))):
+ tlxx = self.T_CLxx*self.Lxx
+ tlyy = self.T_CLyy*self.Lyy
+ tlzz = self.T_CLzz*self.Lzz
+ t11, t22, t33 = tlxx, tlyy, tlzz # the rest is below
+ rx, ry, rz = math.sqrt(tlxx), math.sqrt(tlyy), math.sqrt(tlzz)
+ t12 = self.T_CL[1] * math.sqrt(self.Lxx*self.Lyy)
+ t13 = self.T_CL[2] * math.sqrt(self.Lxx*self.Lzz)
+ t23 = self.T_CL[5] * math.sqrt(self.Lyy*self.Lzz)
+ t_min_C = max(self.Sxx-rx, self.Syy-ry, self.Szz-rz)
+ t_max_C = min(self.Sxx+rx, self.Syy+ry, self.Szz+rz)
+ show_number(x=[t_min_C, t_max_C], title="t_min_C,t_max_C eq.(24):", log=self.log)
+ if(t_min_C > t_max_C):
+ raise Sorry("Step C (left branch): Empty (tmin_c,tmax_c) interval.")
+ # Compute t_S using formula 10 or 11 (from 2016/17 paper II).
+ if( self.find_t_S_using_formula=="10"):
+ t_0 = self.S_L.trace()/3.
+ elif(self.find_t_S_using_formula=="11"):
+ num = self.Sxx*self.Lyy**2*self.Lzz**2 +\
+ self.Syy*self.Lzz**2*self.Lxx**2 +\
+ self.Szz*self.Lxx**2*self.Lyy**2
+ den = self.Lyy**2*self.Lzz**2 + \
+ self.Lzz**2*self.Lxx**2 + \
+ self.Lxx**2*self.Lyy**2
+ t_0 = num/den
+ else: assert 0
+ #
+ show_number(x=t_0, title="t_0 eq.(20):", log=self.log)
+ # compose T_lambda and find tau_max (30)
+ T_lambda = matrix.sqr(
+ [t11, t12, t13,
+ t12, t22, t23,
+ t13, t23, t33])
+ show_matrix(x=T_lambda, title="T_lambda eq.(29)", log=self.log)
+ es = eigensystem.real_symmetric(T_lambda.as_sym_mat3())
+ vals = es.values()
+ assert vals[0]>=vals[1]>=vals[2]
+ tau_max = vals[0]
+ #
+ if(tau_max < 0):
+ raise Sorry("Step C (left branch): Eq.(32): tau_max<0.")
+ t_min_tau = max(self.Sxx,self.Syy,self.Szz)-math.sqrt(tau_max)
+ t_max_tau = min(self.Sxx,self.Syy,self.Szz)+math.sqrt(tau_max)
+ show_number(x=[t_min_tau, t_max_tau],
+ title="t_min_tau, t_max_tau eq.(31):", log=self.log)
+ if(t_min_tau > t_max_tau):
+ raise Sorry("Step C (left branch): Empty (tmin_t,tmax_t) interval.")
+ # (38):
+ arg = t_0**2 + (t11+t22+t33)/3. - (self.Sxx**2+self.Syy**2+self.Szz**2)/3.
+ if(arg < 0):
+ raise Sorry("Step C (left branch): Negative argument when estimating tmin_a.")
+ t_a = math.sqrt(arg)
+ show_number(x=t_a, title="t_a eq.(38):", log=self.log)
+ t_min_a = t_0-t_a
+ t_max_a = t_0+t_a
+ show_number(x=[t_min_a, t_max_a], title="t_min_a, t_max_a eq.(37):", log=self.log)
+ # compute t_min, t_max - this is step b)
+ t_min = max(t_min_C, t_min_tau, t_min_a)
+ t_max = min(t_max_C, t_max_tau, t_max_a)
+ if(t_min > t_max):
+ raise Sorry("Step C (left branch): Intersection of the intervals for t_S is empty.")
+ elif(self.is_zero(t_min-t_max)):
+ _, b_s, c_s = self.as_bs_cs(t=t_min, txx=t11,tyy=t22,tzz=t33,
txy=t12,tyz=t23,tzx=t13)
- if(b_s >= 0 and c_s <= 0):
- target_ = abs(t_0-t_S_best)
- if(target_ < target):
- target = target_
- self.t_S = t_S_best
- t_S_best += step
- assert self.t_S <= t_max
- if(self.t_S is None):
- raise Sorry("Step C (left branch): Interval (t_min,t_max) has no t giving positive semidefinite V.")
- self.t_S = self.t_S
- #
- # Right branch, Section 4.4
- #
- else:
- Lxx, Lyy, Lzz = self.Lxx, self.Lyy, self.Lzz
- if(self.is_zero(self.Lxx)): Lxx = 0
- if(self.is_zero(self.Lyy)): Lyy = 0
- if(self.is_zero(self.Lzz)): Lzz = 0
- tlxx = self.T_CLxx*Lxx
- tlyy = self.T_CLyy*Lyy
- tlzz = self.T_CLzz*Lzz
- t11, t22, t33 = tlxx, tlyy, tlzz # the rest is below
- rx, ry, rz = math.sqrt(tlxx), math.sqrt(tlyy), math.sqrt(tlzz)
- t12 = self.T_CL[1] * math.sqrt(Lxx*Lyy)
- t13 = self.T_CL[2] * math.sqrt(Lxx*Lzz)
- t23 = self.T_CL[5] * math.sqrt(Lyy*Lzz)
- # helper-function to check Cauchy conditions
- def cauchy_conditions(i,j,k, tSs): # diagonals: 0,4,8; 4,0,8; 8,0,4
- if(self.is_zero(self.L_L[i])):
- t_S = self.S_L[i]
- cp1 = (self.S_L[j] - t_S)**2 - self.T_CL[j]*self.L_L[j]
- cp2 = (self.S_L[k] - t_S)**2 - self.T_CL[k]*self.L_L[k]
- if( not ((cp1 < 0 or self.is_zero(cp1)) and
- (cp2 < 0 or self.is_zero(cp2))) ):
- raise Sorry("Step C (right branch): Cauchy condition failed (23).")
- a_s, b_s, c_s = self.as_bs_cs(t=t_S, txx=t11,tyy=t22,tzz=t33,
- txy=t12,tyz=t23,tzx=t13)
- self.check_33_34_35(a_s=a_s, b_s=b_s, c_s=c_s)
- tSs.append(t_S)
+ if( (self.is_zero(b_s) or bs>0) and (c_s<0 or self.is_zero(c_s))):
+ self.t_S = t_min
+ else:
+ raise Sorry("Step C (left branch): t_min=t_max gives non positive semidefinite V_lambda.")
+ elif(t_min < t_max):
+ step = (t_max-t_min)/100000.
+ target = 1.e+9
+ t_S_best = t_min
+ while t_S_best <= t_max:
+ _, b_s, c_s = self.as_bs_cs(t=t_S_best, txx=t11,tyy=t22,tzz=t33,
+ txy=t12,tyz=t23,tzx=t13)
+ if(b_s >= 0 and c_s <= 0):
+ target_ = abs(t_0-t_S_best)
+ if(target_ < target):
+ target = target_
+ self.t_S = t_S_best
+ t_S_best += step
+ assert self.t_S <= t_max
+ if(self.t_S is None):
+ raise Sorry("Step C (left branch): Interval (t_min,t_max) has no t giving positive semidefinite V.")
+ self.t_S = self.t_S
#
- tSs = []
- cauchy_conditions(i=0,j=4,k=8, tSs=tSs)
- cauchy_conditions(i=4,j=0,k=8, tSs=tSs)
- cauchy_conditions(i=8,j=0,k=4, tSs=tSs)
- if(len(tSs)==1): self.t_S = tSs[0]
- elif(len(tSs)==0): raise RuntimeError
+ # Right branch, Section 4.4
+ #
else:
- self.t_S = tSs[0]
- for tSs_ in tSs[1:]:
- if(not self.is_zero(x = self.t_S-tSs_)):
- assert 0
- # end-of-procedure check, then truncate
- if(self.t_S is None):
- raise RuntimeError
- # override with provided value
- if(self.force_t_S is not None):
- self.t_S = self.force_t_S
+ Lxx, Lyy, Lzz = self.Lxx, self.Lyy, self.Lzz
+ if(self.is_zero(self.Lxx)): Lxx = 0
+ if(self.is_zero(self.Lyy)): Lyy = 0
+ if(self.is_zero(self.Lzz)): Lzz = 0
+ tlxx = self.T_CLxx*Lxx
+ tlyy = self.T_CLyy*Lyy
+ tlzz = self.T_CLzz*Lzz
+ t11, t22, t33 = tlxx, tlyy, tlzz # the rest is below
+ rx, ry, rz = math.sqrt(tlxx), math.sqrt(tlyy), math.sqrt(tlzz)
+ t12 = self.T_CL[1] * math.sqrt(Lxx*Lyy)
+ t13 = self.T_CL[2] * math.sqrt(Lxx*Lzz)
+ t23 = self.T_CL[5] * math.sqrt(Lyy*Lzz)
+ # helper-function to check Cauchy conditions
+ def cauchy_conditions(i,j,k, tSs): # diagonals: 0,4,8; 4,0,8; 8,0,4
+ if(self.is_zero(self.L_L[i])):
+ t_S = self.S_L[i]
+ cp1 = (self.S_L[j] - t_S)**2 - self.T_CL[j]*self.L_L[j]
+ cp2 = (self.S_L[k] - t_S)**2 - self.T_CL[k]*self.L_L[k]
+ if( not ((cp1 < 0 or self.is_zero(cp1)) and
+ (cp2 < 0 or self.is_zero(cp2))) ):
+ raise Sorry("Step C (right branch): Cauchy condition failed (23).")
+ a_s, b_s, c_s = self.as_bs_cs(t=t_S, txx=t11,tyy=t22,tzz=t33,
+ txy=t12,tyz=t23,tzx=t13)
+ self.check_33_34_35(a_s=a_s, b_s=b_s, c_s=c_s)
+ tSs.append(t_S)
+ #
+ tSs = []
+ cauchy_conditions(i=0,j=4,k=8, tSs=tSs)
+ cauchy_conditions(i=4,j=0,k=8, tSs=tSs)
+ cauchy_conditions(i=8,j=0,k=4, tSs=tSs)
+ if(len(tSs)==1): self.t_S = tSs[0]
+ elif(len(tSs)==0): raise RuntimeError
+ else:
+ self.t_S = tSs[0]
+ for tSs_ in tSs[1:]:
+ if(not self.is_zero(x = self.t_S-tSs_)):
+ assert 0
+ # end-of-procedure check, then truncate
+ if(self.t_S is None):
+ raise RuntimeError
+ # HUGE CLOSE END
+ ####
#
# At this point t_S is found or procedure terminated earlier.
#
Modified: trunk/mmtbx/tls/tls_as_xyz.py
===================================================================
--- trunk/mmtbx/tls/tls_as_xyz.py 2016-11-16 17:14:39 UTC (rev 25723)
+++ trunk/mmtbx/tls/tls_as_xyz.py 2016-11-16 18:05:53 UTC (rev 25724)
@@ -11,7 +11,7 @@
from mmtbx.tls import analysis
from mmtbx.tls import tools
-random.seed(2679941)
+random.seed(2679941) ###
from mmtbx_tls_ext import *
Modified: trunk/mmtbx/tls/tools.py
===================================================================
--- trunk/mmtbx/tls/tools.py 2016-11-16 17:14:39 UTC (rev 25723)
+++ trunk/mmtbx/tls/tools.py 2016-11-16 18:05:53 UTC (rev 25724)
@@ -1113,8 +1113,10 @@
xray_structure = xrs,
n_models = n_models,
origin = orig...
[truncated message content] |
|
From: <rjg...@us...> - 2016-11-16 17:14:42
|
Revision: 25723
http://sourceforge.net/p/cctbx/code/25723
Author: rjgildea
Date: 2016-11-16 17:14:39 +0000 (Wed, 16 Nov 2016)
Log Message:
-----------
iotbx.merging_statistics: add calculation of unmerged_i_over_sigma_mean
Modified Paths:
--------------
trunk/iotbx/merging_statistics.py
trunk/iotbx/regression/tst_merging_statistics.py
Modified: trunk/iotbx/merging_statistics.py
===================================================================
--- trunk/iotbx/merging_statistics.py 2016-11-16 17:14:34 UTC (rev 25722)
+++ trunk/iotbx/merging_statistics.py 2016-11-16 17:14:39 UTC (rev 25723)
@@ -243,6 +243,7 @@
self.sigi_mean = 0
self.i_over_sigma_mean = 0
self.i_mean_over_sigi_mean = 0
+ self.unmerged_i_over_sigma_mean = 0
self.cc_one_half = 0
self.cc_one_half_significance = None
self.cc_one_half_critical_value = None
@@ -258,6 +259,9 @@
i_over_sigma = nonzero_array.data() / nonzero_array.sigmas()
self.i_over_sigma_mean = flex.mean(i_over_sigma)
self.i_mean_over_sigi_mean = self.i_mean/self.sigi_mean
+ nonzero_array = array.select(array.sigmas() > 0)
+ unmerged_i_over_sigma = nonzero_array.data() / nonzero_array.sigmas()
+ self.unmerged_i_over_sigma_mean = flex.mean(unmerged_i_over_sigma)
self.r_merge = merge.r_merge()
self.r_meas = merge.r_meas()
self.r_pim = merge.r_pim()
Modified: trunk/iotbx/regression/tst_merging_statistics.py
===================================================================
--- trunk/iotbx/regression/tst_merging_statistics.py 2016-11-16 17:14:34 UTC (rev 25722)
+++ trunk/iotbx/regression/tst_merging_statistics.py 2016-11-16 17:14:39 UTC (rev 25723)
@@ -135,11 +135,13 @@
args = [hkl_file, "use_internal_variance=False"]
result = merging_statistics.run(args, out=out)
assert approx_equal(result.overall.i_over_sigma_mean, 4.4867598237199)
+ assert approx_equal(result.overall.unmerged_i_over_sigma_mean, 2.559049577429115)
args = [hkl_file,
#"use_internal_variance=True" # this is the default behaviour
]
result = merging_statistics.run(args, out=out)
assert approx_equal(result.overall.i_over_sigma_mean, 4.063574245292925)
+ assert approx_equal(result.overall.unmerged_i_over_sigma_mean, 2.559049577429115)
# test eliminate_sys_absent option
out = StringIO()
hkl_file = libtbx.env.find_in_repositories(
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|
|
From: <rjg...@us...> - 2016-11-16 17:14:36
|
Revision: 25722
http://sourceforge.net/p/cctbx/code/25722
Author: rjgildea
Date: 2016-11-16 17:14:34 +0000 (Wed, 16 Nov 2016)
Log Message:
-----------
iotbx.merging_statistics: optional calculation of significance of cc_half value
Modified Paths:
--------------
trunk/iotbx/command_line/merging_statistics.py
trunk/iotbx/merging_statistics.py
trunk/iotbx/regression/tst_merging_statistics.py
Modified: trunk/iotbx/command_line/merging_statistics.py
===================================================================
--- trunk/iotbx/command_line/merging_statistics.py 2016-11-16 17:14:29 UTC (rev 25721)
+++ trunk/iotbx/command_line/merging_statistics.py 2016-11-16 17:14:34 UTC (rev 25722)
@@ -120,6 +120,7 @@
use_internal_variance=params.use_internal_variance,
eliminate_sys_absent=params.eliminate_sys_absent,
extend_d_max_min=params.extend_d_max_min,
+ cc_one_half_significance_level=params.cc_one_half_significance_level,
log=out)
result.show(out=out)
if (getattr(params, "loggraph", False)) :
Modified: trunk/iotbx/merging_statistics.py
===================================================================
--- trunk/iotbx/merging_statistics.py 2016-11-16 17:14:29 UTC (rev 25721)
+++ trunk/iotbx/merging_statistics.py 2016-11-16 17:14:34 UTC (rev 25722)
@@ -57,6 +57,8 @@
eliminate_sys_absent = True
.type = bool
.short_caption = Eliminate systematically absent reflections before computation of merging statistics.
+cc_one_half_significance_level = None
+ .type = float(value_min=0, value_max=None)
""" % sigma_filtering_phil_str
class model_based_arrays (object) :
@@ -186,7 +188,8 @@
anomalous=False,
debug=None,
sigma_filtering="scala",
- use_internal_variance=True) :
+ use_internal_variance=True,
+ cc_one_half_significance_level=None) :
import cctbx.miller
from scitbx.array_family import flex
assert (array.sigmas() is not None)
@@ -241,6 +244,8 @@
self.i_over_sigma_mean = 0
self.i_mean_over_sigi_mean = 0
self.cc_one_half = 0
+ self.cc_one_half_significance = None
+ self.cc_one_half_critical_value = None
self.cc_star = 0
self.r_merge = self.r_meas = self.r_pim = None
for x in sorted(set(redundancies)) :
@@ -258,6 +263,21 @@
self.r_pim = merge.r_pim()
self.cc_one_half = cctbx.miller.compute_cc_one_half(
unmerged=array)
+ if cc_one_half_significance_level is not None:
+ # https://en.wikipedia.org/wiki/Pearson_product-moment_correlation_coefficient#Testing_using_Student.27s_t-distribution
+ r = self.cc_one_half
+ n = (redundancies > 1).count(True)
+ p = cc_one_half_significance_level
+ if r == -1 or n <= 2:
+ self.cc_one_half_significance = False
+ self.cc_one_half_critical_value = 0
+ else:
+ t = r * sqrt((n-2)/(1-r**2))
+ from scitbx.math import distributions
+ dist = distributions.students_t_distribution(n-2)
+ self.cc_one_half_significance = t > dist.quantile(1-p)
+ t1 = dist.quantile(1-p)
+ self.cc_one_half_critical_value = t1/sqrt(t1**2 + n - 2)
if (self.cc_one_half == 0) :
self.cc_star = 0
elif (self.cc_one_half < -0.999) :
@@ -278,7 +298,7 @@
return getattr(self, "anom_half_corr", None)
def format (self) :
- return "%6.2f %6.2f %6d %6d %5.2f %6.2f %8.1f %6.1f %s %s %s %5.3f %5.3f" % (
+ return "%6.2f %6.2f %6d %6d %5.2f %6.2f %8.1f %6.1f %s %s %s % 5.3f%s % 5.3f" % (
self.d_max,
self.d_min,
self.n_obs,
@@ -287,10 +307,11 @@
self.completeness*100,
self.i_mean,
self.i_over_sigma_mean,
- format_value("%5.3f", self.r_merge),
- format_value("%5.3f", self.r_meas),
- format_value("%5.3f", self.r_pim),
+ format_value("% 7.3f", self.r_merge),
+ format_value("% 7.3f", self.r_meas),
+ format_value("% 7.3f", self.r_pim),
self.cc_one_half,
+ "*" if self.cc_one_half_significance else "",
self.anom_half_corr)
def format_for_model_cc (self) :
@@ -329,6 +350,7 @@
table = [(1/self.d_min**2), self.n_obs, self.n_uniq, self.mean_redundancy,
self.completeness*100, self.i_mean, self.i_over_sigma_mean,
self.r_merge, self.r_meas, self.r_pim, self.cc_one_half,
+ self.cc_one_half_significance, self.cc_one_half_critical_value,
self.anom_half_corr]
if (self.cc_work is not None) :
table.extend([self.cc_star, self.cc_work, self.cc_free, self.r_work,
@@ -380,6 +402,7 @@
eliminate_sys_absent=True,
d_min_tolerance=1.e-6,
extend_d_max_min=False,
+ cc_one_half_significance_level=None,
log=None) :
self.file_name = file_name
if (log is None) : log = null_out()
@@ -436,7 +459,8 @@
anomalous=anomalous,
debug=debug,
sigma_filtering=sigma_filtering,
- use_internal_variance=use_internal_variance)
+ use_internal_variance=use_internal_variance,
+ cc_one_half_significance_level=cc_one_half_significance_level)
self.bins = []
title = "Intensity merging statistics"
column_labels = ["1/d**2","N(obs)","N(unique)","Redundancy","Completeness",
@@ -444,13 +468,17 @@
"CC(anom)"]
graph_names = ["Reflection counts", "Redundancy", "Completeness",
"Mean(I)", "Mean(I/sigma)", "R-factors", "CC1/2", "CC(anom)"]
- graph_columns = [[0,1,2],[0,3],[0,4],[0,5],[0,6],[0,7,8,9],[0,10],[0,11]]
+ graph_columns = [[0,1,2],[0,3],[0,4],[0,5],[0,6],[0,7,8,9],[0,10],[0,13]]
+ if cc_one_half_significance_level is not None:
+ column_labels.extend(["CC1/2 significance", "CC1/2 critical value"])
+ graph_names.extend(["CC1/2 significance", "CC1/2 critical value"])
+ graph_columns[-2] = [0,10,12]
#--- CC* mode
if (model_arrays is not None) :
title = "Model quality and intensity merging statistics"
column_labels.extend(["CC*", "CC(work)", "CC(free)", "R-work", "R-free"])
graph_names.extend(["CC*", "Model R-factors"])
- graph_columns.extend([[0,11,12,13],[0,14,15]])
+ graph_columns.extend([[0,11,14,15],[0,16,17]])
#---
self.table = data_plots.table_data(
title=title,
@@ -468,7 +496,8 @@
anomalous=anomalous,
debug=debug,
sigma_filtering=sigma_filtering,
- use_internal_variance=use_internal_variance)
+ use_internal_variance=use_internal_variance,
+ cc_one_half_significance_level=cc_one_half_significance_level)
self.bins.append(bin_stats)
self.table.add_row(bin_stats.table_data())
@@ -548,7 +577,8 @@
print >> out, ""
print >> out, """\
Statistics by resolution bin:
- d_max d_min #obs #uniq mult. %comp <I> <I/sI> r_mrg r_meas r_pim cc1/2 cc_ano"""
+ d_max d_min #obs #uniq mult. %%comp <I> <I/sI> r_mrg r_meas r_pim %scc1/2 cc_ano""" %(
+ ' ' if self.overall.cc_one_half_significance is not None else '')
for bin_stats in self.bins :
print >> out, bin_stats.format()
print >> out, self.overall.format()
Modified: trunk/iotbx/regression/tst_merging_statistics.py
===================================================================
--- trunk/iotbx/regression/tst_merging_statistics.py 2016-11-16 17:14:29 UTC (rev 25721)
+++ trunk/iotbx/regression/tst_merging_statistics.py 2016-11-16 17:14:34 UTC (rev 25722)
@@ -31,7 +31,7 @@
print out.getvalue()
assert ("R-merge: 0.073" in out.getvalue())
assert ("R-meas: 0.079" in out.getvalue())
- assert (""" 1.81 1.74 12528 2073 6.04 97.05 1449.2 5.2 0.252 0.275 0.110 0.9""" in out.getvalue()), out.getvalue()
+ assert (""" 1.81 1.74 12528 2073 6.04 97.05 1449.2 5.2 0.252 0.275 0.110 0.968 0.284""" in out.getvalue()), out.getvalue()
cif_block = result.as_cif_block()
assert "_reflns_shell" in cif_block
assert approx_equal(float(cif_block["_reflns.pdbx_Rpim_I_obs"]), result.overall.r_pim)
@@ -60,7 +60,7 @@
if (debug) :
print out.getvalue()
assert ("Resolution: 100.00 - 1.50" in out.getvalue())
- assert (" 1.55 1.50 0 0 0.00 0.00 0.0 0.0 None None None 0.000 0.000""" in out.getvalue())
+ assert (" 1.55 1.50 0 0 0.00 0.00 0.0 0.0 None None None 0.000 0.000""" in out.getvalue())
# these should crash
args2 = list(args[:-1]) + ["high_resolution=15", "low_resolution=2.5"]
try :
@@ -90,7 +90,7 @@
result = merging_statistics.run(args, out=out)
if (debug) :
print out.getvalue()
- assert ("28.49 3.76 15737 1224 12.86 99.84 47967.0 11.6 0.482 0.500 0.135 0.9" in out.getvalue()), out.getvalue()
+ assert ("28.49 3.76 15737 1224 12.86 99.84 47967.0 11.6 0.482 0.500 0.135 0.972 -0.520" in out.getvalue()), out.getvalue()
# exercise 2: estimate resolution cutoffs (and symmetry_file argument)
hkl_file = libtbx.env.find_in_repositories(
relative_path="phenix_regression/harvesting/unmerged.sca",
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|
From: <rjg...@us...> - 2016-11-16 17:14:31
|
Revision: 25721
http://sourceforge.net/p/cctbx/code/25721
Author: rjgildea
Date: 2016-11-16 17:14:29 +0000 (Wed, 16 Nov 2016)
Log Message:
-----------
iotbx.merging_statistics: new parameter binning_method = *volume counting_sorted
Modified Paths:
--------------
trunk/iotbx/command_line/merging_statistics.py
trunk/iotbx/merging_statistics.py
Modified: trunk/iotbx/command_line/merging_statistics.py
===================================================================
--- trunk/iotbx/command_line/merging_statistics.py 2016-11-16 17:14:24 UTC (rev 25720)
+++ trunk/iotbx/command_line/merging_statistics.py 2016-11-16 17:14:29 UTC (rev 25721)
@@ -112,6 +112,7 @@
d_min=params.high_resolution,
d_max=params.low_resolution,
n_bins=params.n_bins,
+ binning_method=params.binning_method,
anomalous=params.anomalous,
debug=params.debug,
file_name=params.file_name,
Modified: trunk/iotbx/merging_statistics.py
===================================================================
--- trunk/iotbx/merging_statistics.py 2016-11-16 17:14:24 UTC (rev 25720)
+++ trunk/iotbx/merging_statistics.py 2016-11-16 17:14:29 UTC (rev 25721)
@@ -41,6 +41,9 @@
.short_caption = Number of resolution bins
.input_size = 64
.style = spinner
+binning_method = *volume counting_sorted
+ .type = choice
+ .help = "Use equal-volume bins or bins with approximately equal numbers of reflections per bin."
extend_d_max_min = False
.type = bool
.expert_level = 2
@@ -368,6 +371,7 @@
d_max=None,
anomalous=False,
n_bins=10,
+ binning_method='volume',
debug=False,
file_name=None,
model_arrays=None,
@@ -422,7 +426,10 @@
d_min=d_min_cutoff)
overall_d_max_min = d_max_cutoff, d_min_cutoff
else :
- i_obs.setup_binner(n_bins=n_bins)
+ if binning_method == 'volume':
+ i_obs.setup_binner(n_bins=n_bins)
+ elif binning_method == 'counting_sorted':
+ i_obs.setup_binner_counting_sorted(n_bins=n_bins)
self.overall = merging_stats(i_obs,
d_max_min=overall_d_max_min,
model_arrays=model_arrays,
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|
From: <rjg...@us...> - 2016-11-16 17:14:27
|
Revision: 25720
http://sourceforge.net/p/cctbx/code/25720
Author: rjgildea
Date: 2016-11-16 17:14:24 +0000 (Wed, 16 Nov 2016)
Log Message:
-----------
miller.set.setup_binner_counting_sorted(): new keyword argument n_bins=None
Modified Paths:
--------------
trunk/cctbx/miller/__init__.py
trunk/cctbx/regression/tst_miller.py
Modified: trunk/cctbx/miller/__init__.py
===================================================================
--- trunk/cctbx/miller/__init__.py 2016-11-16 16:22:45 UTC (rev 25719)
+++ trunk/cctbx/miller/__init__.py 2016-11-16 17:14:24 UTC (rev 25720)
@@ -1680,11 +1680,12 @@
d_max=0,
d_min=0,
reflections_per_bin=None,
+ n_bins=None,
d_tolerance=1.e-10):
assert d_max >= 0
assert d_min >= 0
- assert isinstance(reflections_per_bin, int)
- assert reflections_per_bin > 0
+ assert isinstance(reflections_per_bin, int) or isinstance(n_bins, int)
+ assert reflections_per_bin > 0 or n_bins > 0
assert d_tolerance > 0
assert d_tolerance < 0.5
d_star_sq = self.d_star_sq().data()
@@ -1693,7 +1694,9 @@
if (d_min > 0):
d_star_sq = d_star_sq.select(d_star_sq < 1./d_min**2)
assert d_star_sq.size() > 0
- n_bins = max(1, iround(d_star_sq.size() / float(reflections_per_bin)))
+ if n_bins is None:
+ n_bins = max(1, iround(d_star_sq.size() / float(reflections_per_bin)))
+ assert n_bins <= self.size(), "n_bins (%i) must be <= number of reflections (%i)" %(n_bins, self.size())
reflections_per_bin = d_star_sq.size() / float(n_bins)
d_star_sq = d_star_sq.select(flex.sort_permutation(d_star_sq))
limits = flex.double()
Modified: trunk/cctbx/regression/tst_miller.py
===================================================================
--- trunk/cctbx/regression/tst_miller.py 2016-11-16 16:22:45 UTC (rev 25719)
+++ trunk/cctbx/regression/tst_miller.py 2016-11-16 17:14:24 UTC (rev 25720)
@@ -494,6 +494,26 @@
d_min=11,
reflections_per_bin=3)
assert list(set1.binner().counts()) == [2,3,2,1]
+ #
+ expected_counts = iter([
+ [0,1,0],
+ [0,1,1,0], [0,2,0],
+ [0,1,1,1,0], [0,2,1,0], [0,3,0],
+ [0,1,1,1,1,0], [0,1,2,1,0], [0,2,2,0], [0,4,0],
+ [0,1,1,1,1,1,0], [0,1,2,1,1,0], [0,2,1,2,0], [0,3,2,0], [0,5,0],
+ [0,1,1,1,1,1,1,0], [0,1,1,2,1,1,0], [0,2,1,2,1,0], [0,2,2,2,0], [0,3,3,0], [0,6,0],
+ [0,1,1,1,1,1,1,1,0], [0,1,1,2,1,1,1,0], [0,1,2,1,2,1,0], [0,2,2,1,2,0], [0,2,3,2,0], [0,4,3,0], [0,7,0]
+ ])
+ for n in xrange(1,8):
+ set2 = set1.select(flex.size_t(xrange(n)))
+ for n_bins in range(n, 0, -1):
+ set2.setup_binner_counting_sorted(n_bins=n_bins)
+ assert list(set2.binner().counts()) == expected_counts.next()
+ set1.setup_binner_counting_sorted(
+ d_max=16,
+ d_min=11,
+ n_bins=2)
+ assert list(set1.binner().counts()) == [2,3,2,1]
def exercise_crystal_gridding():
crystal_symmetry = crystal.symmetry(
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|
From: <af...@us...> - 2016-11-16 16:22:48
|
Revision: 25719
http://sourceforge.net/p/cctbx/code/25719
Author: afonine
Date: 2016-11-16 16:22:45 +0000 (Wed, 16 Nov 2016)
Log Message:
-----------
test
Modified Paths:
--------------
trunk/mmtbx/maps/correlation.py
Modified: trunk/mmtbx/maps/correlation.py
===================================================================
--- trunk/mmtbx/maps/correlation.py 2016-11-16 16:19:39 UTC (rev 25718)
+++ trunk/mmtbx/maps/correlation.py 2016-11-16 16:22:45 UTC (rev 25719)
@@ -8,9 +8,10 @@
cctbx_maptbx_ext = boost.python.import_ext("cctbx_maptbx_ext")
def fsc_model_map(xray_structure, map, d_min, log=sys.stdout, radius=2.,
- n_bins=30, prefix=""):
+ prefix=""):
sgn = xray_structure.crystal_symmetry().space_group().type().number()
f_calc = xray_structure.structure_factors(d_min=d_min).f_calc()
+ n_bins=min(30, f_calc.data().size()//500)
def compute_mc(f_calc, map):
return f_calc.structure_factors_from_map(
map = map,
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From: <gra...@us...> - 2016-11-16 16:19:41
|
Revision: 25718
http://sourceforge.net/p/cctbx/code/25718
Author: graeme_winter
Date: 2016-11-16 16:19:39 +0000 (Wed, 16 Nov 2016)
Log Message:
-----------
Fix 0-> false; do not demand time (so mlfslm works); does not increase #failing tests
Modified Paths:
--------------
trunk/dxtbx/format/FormatSMVADSC.py
Modified: trunk/dxtbx/format/FormatSMVADSC.py
===================================================================
--- trunk/dxtbx/format/FormatSMVADSC.py 2016-11-15 21:52:55 UTC (rev 25717)
+++ trunk/dxtbx/format/FormatSMVADSC.py 2016-11-16 16:19:39 UTC (rev 25718)
@@ -27,14 +27,15 @@
size, header = FormatSMV.get_smv_header(image_file)
+ # this used to include TIME
wanted_header_items = ['BEAM_CENTER_X', 'BEAM_CENTER_Y',
'DISTANCE', 'WAVELENGTH', 'PIXEL_SIZE',
'OSC_START', 'OSC_RANGE', 'SIZE1', 'SIZE2',
- 'BYTE_ORDER', 'TIME']
+ 'BYTE_ORDER']
for header_item in wanted_header_items:
if not header_item in header:
- return 0
+ return False
unwanted_header_items = ['DTREK_DATE_TIME']
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|
From: <mo...@us...> - 2016-11-15 21:52:57
|
Revision: 25717
http://sourceforge.net/p/cctbx/code/25717
Author: monarin
Date: 2016-11-15 21:52:55 +0000 (Tue, 15 Nov 2016)
Log Message:
-----------
Clean up unused parameters
Modified Paths:
--------------
trunk/prime/command_line/print_integration_pickle.py
Modified: trunk/prime/command_line/print_integration_pickle.py
===================================================================
--- trunk/prime/command_line/print_integration_pickle.py 2016-11-15 21:38:38 UTC (rev 25716)
+++ trunk/prime/command_line/print_integration_pickle.py 2016-11-15 21:52:55 UTC (rev 25717)
@@ -88,12 +88,11 @@
def read_input(args):
if len(args) == 0:
print "prime.print_integration_pickle: for viewing systematic absences and beam xy position from integration pickles."
- print "usage: prime.print_integration_pickle data=integrated.lst pixel_size_mm=0.079346 check_sys_absent=True target_space_group=P212121"
+ print "usage: prime.print_integration_pickle data=integrated.lst pixel_size_mm=0.079346"
exit()
data = []
hklrefin = None
pixel_size_mm = None
- check_sys_absent = False
target_space_group = None
target_unit_cell = None
target_anomalous_flag = False
@@ -109,8 +108,6 @@
hklrefin = pair[1]
if pair[0]=='pixel_size_mm':
pixel_size_mm = float(pair[1])
- if pair[0]=='check_sys_absent':
- check_sys_absent = bool(pair[1])
if pair[0]=='target_space_group':
target_space_group = pair[1]
if pair[0]=='target_unit_cell':
@@ -135,22 +132,18 @@
if len(data)==0:
print "Please provide data path. (eg. data=/path/to/pickle/)"
exit()
- if check_sys_absent:
- if target_space_group is None:
- print "Please provide target space group if you want to check systematic absence (eg. target_space_group=P212121)"
- exit()
if pixel_size_mm is None:
print "Please specify pixel size (eg. pixel_size_mm=0.079346)"
exit()
- return data, hklrefin, pixel_size_mm, check_sys_absent, target_unit_cell, target_space_group, target_anomalous_flag, flag_plot, d_min, d_max, n_residues
+ return data, hklrefin, pixel_size_mm, target_unit_cell, target_space_group, target_anomalous_flag, flag_plot, d_min, d_max, n_residues
if (__name__ == "__main__"):
cc_bin_low_thres = 0.25
beam_thres = 0.5
- uc_tol = 20
+ uc_tol = 3
#0 .read input parameters and frames (pickle files)
- data, hklrefin, pixel_size_mm, check_sys_absent_input, target_unit_cell, \
+ data, hklrefin, pixel_size_mm, target_unit_cell, \
target_space_group, target_anomalous_flag, flag_plot, d_min, d_max, n_residues = read_input(args = sys.argv[1:])
frame_files = read_pickles(data)
xbeam_set = flex.double()
@@ -170,7 +163,6 @@
dd_mm = flex.double()
wavelength_set = flex.double()
for pickle_filename in frame_files:
- check_sys_absent = check_sys_absent_input
observations_pickle = pickle.load(open(pickle_filename,"rb"))
pickle_filename_arr = pickle_filename.split('/')
pickle_filename_only = pickle_filename_arr[len(pickle_filename_arr)-1]
@@ -187,7 +179,7 @@
#observations = observations.change_basis(cb_op)
#apply constrain using the crystal system
#check systematic absent
- if check_sys_absent:
+ if target_unit_cell is not None:
try:
from cctbx.crystal import symmetry
miller_set = symmetry(
@@ -200,14 +192,11 @@
crystal_symmetry=miller_set.crystal_symmetry())
except Exception:
print 'Cannot apply target space group: observed space group=', observations.space_group_info()
- check_sys_absent = False
+ pass
#check if the uc is good
flag_good_unit_cell = False
- if check_sys_absent:
- if target_unit_cell is None:
- flag_good_unit_cell = True
- else:
- flag_good_unit_cell = good_unit_cell(observations.unit_cell().parameters(), None, uc_tol, target_unit_cell=target_unit_cell)
+ if target_unit_cell is not None:
+ flag_good_unit_cell = good_unit_cell(observations.unit_cell().parameters(), None, uc_tol, target_unit_cell=target_unit_cell)
flag_good_unit_cell_set.append(flag_good_unit_cell)
#calculate partiality
wavelength = observations_pickle["wavelength"]
@@ -358,7 +347,7 @@
d_bins_set.append(d_bins)
oodsqr_bins_set.append(oodsqr_bins)
sys_abs_lst = flex.double()
- if check_sys_absent:
+ if target_unit_cell is not None:
cn_refl = 0
for sys_absent_flag, d_spacing, miller_index_ori, miller_index_asu, I, sigI in zip(observations.sys_absent_flags(), observations.d_spacings().data(), observations.indices(), observations_asu.indices(), observations.data(), observations.sigmas()):
if sys_absent_flag[1]:
@@ -377,37 +366,56 @@
ybeam_std = np.std(ybeam_set)
xbeam_filtered_set = flex.double()
ybeam_filtered_set = flex.double()
- frame_filtered_set = []
sys_abs_all_filtered = flex.double()
- txt_out = ''
- txt_out_mix = ''
- txt_out_uc = ''
+ txt_out_good = ''
+ txt_out_bad = ''
txt_out_report_beam_filter = 'Images with beam center displaced > %6.2f mm.:\n'%(beam_thres)
txt_out_report_cc_filter = 'Images with cc < %6.2f:\n'%(cc_bin_low_thres)
+ txt_out_report_uc_filter = 'Images with delta_uc > %6.2f %%:\n'%(uc_tol)
from scitbx.matrix import col
+ cn_good, cn_bad = (0,0)
+ #go through list of integration results and filter out bad cc, uc, and beam center
for pickle_filename, xbeam, ybeam, sys_abs_lst, cc_bin_low, flag_good_unit_cell in \
zip(frame_files, xbeam_set, \
ybeam_set, sys_abs_set, cc_bin_low_set, flag_good_unit_cell_set):
pickle_filename_arr = pickle_filename.split('/')
pickle_filename_only = pickle_filename_arr[len(pickle_filename_arr)-1]
+ #calculate beam drift (from mean)
pred_xy = col((xbeam, ybeam))
calc_xy = col((xbeam_mean, ybeam_mean))
diff_xy = pred_xy - calc_xy
+ #pregenerate output
txt_out_report_tmp = '{0:80} {1:6.2f} {2:6.2f} {3:6.2f} {4:6.4f}\n'.format(pickle_filename_only, xbeam, ybeam, cc_bin_low, diff_xy.length())
- if diff_xy.length() < beam_thres:
+ flag_good_beam = False
+ flag_good_cc = False
+ if diff_xy.length() < beam_thres: flag_good_beam = True
+ if (cc_bin_low > cc_bin_low_thres) or hklrefin is None: flag_good_cc = True
+ if flag_good_beam:
xbeam_filtered_set.append(xbeam)
ybeam_filtered_set.append(ybeam)
- frame_filtered_set.append(pickle_filename)
- txt_out += pickle_filename + '\n'
sys_abs_all_filtered.extend(sys_abs_lst)
- if cc_bin_low > cc_bin_low_thres and flag_good_unit_cell:
- txt_out_mix += pickle_filename + '\n'
- else:
- txt_out_report_cc_filter += txt_out_report_tmp
- if flag_good_unit_cell:
- txt_out_uc += pickle_filename + '\n'
else:
txt_out_report_beam_filter += txt_out_report_tmp
+ if ~flag_good_cc:
+ txt_out_report_cc_filter += txt_out_report_tmp
+ if ~flag_good_unit_cell:
+ txt_out_report_uc_filter += txt_out_report_tmp
+ #output only good integration results
+ #print flag_good_beam, flag_good_cc, flag_good_unit_cell
+ if flag_good_beam and flag_good_cc and flag_good_unit_cell:
+ txt_out_good += pickle_filename + '\n'
+ cn_good += 1
+ else:
+ txt_out_bad += pickle_filename + '\n'
+ cn_bad += 1
+ print
+ print 'Images with delta_beam_xy > %6.2f mm (image name, xbeam, ybeam, cciso, delta_xy)'%(beam_thres)
+ print txt_out_report_beam_filter
+ if hklrefin is not None:
+ print txt_out_report_cc_filter
+ if target_unit_cell is not None:
+ print txt_out_report_uc_filter
+ #prevent devision by zero (not the best way but will correct it)
try:
print
print 'CC mean=%6.2f median=%6.2f std=%6.2f'%(flex.mean(cc_bin_low_set), np.median(cc_bin_low_set), np.std(cc_bin_low_set))
@@ -420,22 +428,14 @@
print 'No. of frames: All = %6.0f Beam outliers = %6.0f CC filter=%6.0f'%(len(frame_files), len(frame_files) - (len(txt_out.split('\n'))-1), len(frame_files) - (len(txt_out_mix.split('\n'))-1))
except Exception:
pass
- print
- print 'Reporting outliers (image name, xbeam, ybeam, cciso, delta_xy)'
- print txt_out_report_beam_filter
- print txt_out_report_cc_filter
- #write out filtered beamxy pickle files
- f = open('integration_pickle_beam_filter.lst', 'w')
- f.write(txt_out)
+ print 'Total images: %d good: %d bad: %d'%(len(frame_files), cn_good, cn_bad)
+ #write out good and bad pickle files
+ f = open('integration_filter.lst', 'w')
+ f.write(txt_out_good)
f.close()
- #write out mix filter pickle files
- f = open('integration_mix_filter.lst', 'w')
- f.write(txt_out_mix)
+ f = open('integration_fail_filter.lst', 'w')
+ f.write(txt_out_bad)
f.close()
- #write out filtered beamxy and uc pickle files
- f = open('integration_pickle_beam_uc_filter.lst', 'w')
- f.write(txt_out_uc)
- f.close()
if flag_plot:
plt.subplot(211)
plt.plot(xbeam_set,ybeam_set,"r.")
@@ -506,6 +506,7 @@
cn_i += 1
plt.show()
#print twin operators
+ """
idah = indamb_handler()
for pickle_filename in frame_files:
pickle_filename_arr = pickle_filename.split('/')
@@ -515,3 +516,4 @@
operators = idah.generate_twin_operators(observations, flag_all=True)
ops_hkl = [op.operator.r().as_hkl() for op in operators]
print pickle_filename_only, ops_hkl
+ """
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|
|
From: <bk...@us...> - 2016-11-15 21:38:41
|
Revision: 25716
http://sourceforge.net/p/cctbx/code/25716
Author: bkpoon
Date: 2016-11-15 21:38:38 +0000 (Tue, 15 Nov 2016)
Log Message:
-----------
installation: added workarounds for sphinx and matplotlib on macOS >= 10.11
Modified Paths:
--------------
trunk/libtbx/auto_build/install_base_packages.py
Modified: trunk/libtbx/auto_build/install_base_packages.py
===================================================================
--- trunk/libtbx/auto_build/install_base_packages.py 2016-11-15 10:15:15 UTC (rev 25715)
+++ trunk/libtbx/auto_build/install_base_packages.py 2016-11-15 21:38:38 UTC (rev 25716)
@@ -920,6 +920,21 @@
confirm_import_module="reportlab")
def build_sphinx(self):
+
+ # workaround for macOS >= 10.11 and Python 2.7.12
+ # issue: Sphinx has dependencies automatically installed via pip, but they
+ # fail due to [SSL: CERTIFICATE_VERIFY_FAILED] error. Tried updating pip to
+ # 9.0.1, updating openssl to 1.0.2j
+ # fix: Manually install dependencies using pip via command-line
+ if ( (self.flag_is_mac) and (get_os_version() in ('10.11', '10.12')) ):
+ cmd = self.python_exe + ' -m pip install '
+ for dependency in ['imagesize', '"alabaster<0.8,>=0.7"',
+ '"babel!=2.0,>=1.3"', '"snowballstemmer>=1.1"',
+ '"Pygments>=2.0"', '"Jinja2>=2.3"', '"pytz>=0a"',
+ 'MarkupSafe', '"docutils==0.12"']:
+ self.call(cmd + dependency)
+ self.call(cmd + '--ignore-installed "six==1.10.0"')
+
self.build_python_module_simple(
pkg_url=BASE_CCI_PKG_URL,
pkg_name=SPHINX_PKG,
@@ -1371,6 +1386,13 @@
# if (os.path.exists(font_cache)):
# os.remove(font_cache)
+ # workaround for macOS >= 10.11 and Python 2.7.12
+ # see build_sphinx for explanation
+ if ( (self.flag_is_mac) and (get_os_version() in ('10.11', '10.12')) ):
+ cmd = self.python_exe + ' -m pip install '
+ for dependency in ['cycler']:
+ self.call(cmd + dependency)
+
self.build_python_module_simple(
pkg_url=BASE_CCI_PKG_URL,
pkg_name=MATPLOTLIB_PKG,
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|
|
From: <upi...@us...> - 2016-11-15 10:15:17
|
Revision: 25715
http://sourceforge.net/p/cctbx/code/25715
Author: upintheair
Date: 2016-11-15 10:15:15 +0000 (Tue, 15 Nov 2016)
Log Message:
-----------
Improve recognition of J. Holton's simulated images
Modified Paths:
--------------
trunk/dxtbx/format/FormatSMVJHSim.py
Modified: trunk/dxtbx/format/FormatSMVJHSim.py
===================================================================
--- trunk/dxtbx/format/FormatSMVJHSim.py 2016-11-14 15:21:59 UTC (rev 25714)
+++ trunk/dxtbx/format/FormatSMVJHSim.py 2016-11-15 10:15:15 UTC (rev 25715)
@@ -20,30 +20,17 @@
@staticmethod
def understand(image_file):
- '''Check to see if this looks like an JHSim SMV format image, i.e. we
- can make sense of it. Essentially that will be if it contains all of
- the keys we are looking for and not some we are not (i.e. that belong
- to a Rigaku Saturn.)'''
+ '''Check to see if this looks like an JHSim SMV format image, i.e. we can
+ make sense of it. From JH: "The best way to identify images from any of my
+ simulators is to look for BEAMLINE=fake in the header."'''
size, header = FormatSMV.get_smv_header(image_file)
- wanted_header_items = ['BEAM_CENTER_X', 'BEAM_CENTER_Y',
- 'DISTANCE', 'WAVELENGTH', 'PIXEL_SIZE',
- 'OSC_START', 'OSC_RANGE', 'SIZE1', 'SIZE2',
- 'BYTE_ORDER']
+ if header.get('BEAMLINE') == 'fake':
+ return True
+ else:
+ return False
- for header_item in wanted_header_items:
- if not header_item in header:
- return 0
-
- unwanted_header_items = ['DTREK_DATE_TIME']
-
- for header_item in unwanted_header_items:
- if header_item in header:
- return False
-
- return True
-
def __init__(self, image_file, **kwargs):
'''Initialise the image structure from the given file, including a
proper model of the experiment.'''
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|
|
From: <mge...@us...> - 2016-11-14 15:22:01
|
Revision: 25714
http://sourceforge.net/p/cctbx/code/25714
Author: mgerstel
Date: 2016-11-14 15:21:59 +0000 (Mon, 14 Nov 2016)
Log Message:
-----------
Reflect renamed repository in download instructions
Modified Paths:
--------------
trunk/libtbx/auto_build/bootstrap.py
Modified: trunk/libtbx/auto_build/bootstrap.py
===================================================================
--- trunk/libtbx/auto_build/bootstrap.py 2016-11-14 08:18:36 UTC (rev 25713)
+++ trunk/libtbx/auto_build/bootstrap.py 2016-11-14 15:21:59 UTC (rev 25714)
@@ -31,18 +31,14 @@
}
# To download this file:
-# wget https://raw.githubusercontent.com/cctbx/cctbx/master/libtbx/auto_build/bootstrap.py
+# wget https://raw.githubusercontent.com/cctbx/cctbx_project/master/libtbx/auto_build/bootstrap.py
# or
-# curl https://raw.githubusercontent.com/cctbx/cctbx/master/libtbx/auto_build/bootstrap.py > bootstrap.py
+# curl https://raw.githubusercontent.com/cctbx/cctbx_project/master/libtbx/auto_build/bootstrap.py > bootstrap.py
# To get the version before the switch to git:
# svn export -r 25697 svn://svn.code.sf.net/p/cctbx/code/trunk/libtbx/auto_build/bootstrap.py
-# Note: to relocate an SVN repo:
-# svn relocate svn+ssh://<username>@svn.code.sf.net/p/cctbx/code/trunk
-
-
-# Utililty function to be executed on slave machine or called directly by standalone bootstrap script
+# Utility function to be executed on slave machine or called directly by standalone bootstrap script
def tar_extract(workdir, archive, modulename=None):
try:
# delete tar target folder if it exists
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|
|
From: <mge...@us...> - 2016-11-14 08:18:38
|
Revision: 25713
http://sourceforge.net/p/cctbx/code/25713
Author: mgerstel
Date: 2016-11-14 08:18:36 +0000 (Mon, 14 Nov 2016)
Log Message:
-----------
Renamed project as requested
Modified Paths:
--------------
trunk/libtbx/auto_build/bootstrap.py
Modified: trunk/libtbx/auto_build/bootstrap.py
===================================================================
--- trunk/libtbx/auto_build/bootstrap.py 2016-11-13 23:26:55 UTC (rev 25712)
+++ trunk/libtbx/auto_build/bootstrap.py 2016-11-14 08:18:36 UTC (rev 25713)
@@ -419,7 +419,7 @@
if os.path.exists(destination):
print "Existing non-git directory -- don't know what to do. skipping: %s" % module
- if ('cctbx.git' in parameters[0]):
+ if ('cctbx_project.git' in parameters[0]):
print '\n' + '=' * 80 + '\nCCTBX is transitioning to git.\nPlease continue committing changes using svn until November 22, 2016.\nAfter that, commits will only be done through git.\n\nTo update cctbx_project, please run "svn update" while in the cctbx_project directory.\n' + '*'*80 + '\n'
return
@@ -652,9 +652,9 @@
class cctbx_module(SourceModule):
module = 'cctbx_project'
anonymous = ['git',
- 'gi...@gi...:cctbx/cctbx.git',
- 'https://github.com/cctbx/cctbx.git',
- 'https://github.com/cctbx/cctbx/archive/master.zip']
+ 'gi...@gi...:cctbx/cctbx_project.git',
+ 'https://github.com/cctbx/cctbx_project.git',
+ 'https://github.com/cctbx/cctbx_project/archive/master.zip']
class cbflib_module(SourceModule):
module = 'cbflib'
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|
|
From: <mo...@us...> - 2016-11-13 23:26:57
|
Revision: 25712
http://sourceforge.net/p/cctbx/code/25712
Author: monarin
Date: 2016-11-13 23:26:55 +0000 (Sun, 13 Nov 2016)
Log Message:
-----------
Update comments
Modified Paths:
--------------
trunk/iota/command_line/iota_filter_pickles.py
Modified: trunk/iota/command_line/iota_filter_pickles.py
===================================================================
--- trunk/iota/command_line/iota_filter_pickles.py 2016-11-13 23:17:10 UTC (rev 25711)
+++ trunk/iota/command_line/iota_filter_pickles.py 2016-11-13 23:26:55 UTC (rev 25712)
@@ -9,8 +9,7 @@
"""
ideally, if pulse is on, you should expect to have 1 - 1 -1 for all events
otherwise 0 -1 - 1. Currently, we have more than one pickle read out for
- each rotatation angle. Solution is picking the last one.
- Problem is being fixed!
+ each rotatation angle. Solution is picking the pickle with maximum value for Ipm3.
"""
f = h5py.File(hdf5Filename)
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|
|
From: <mo...@us...> - 2016-11-13 23:17:11
|
Revision: 25711
http://sourceforge.net/p/cctbx/code/25711
Author: monarin
Date: 2016-11-13 23:17:10 +0000 (Sun, 13 Nov 2016)
Log Message:
-----------
First Commit
Filter image pickles (and any files with matching timestamp) by pulse (on/off)
evr92 - evr95 - evr 97:
0 - 1 - 1 for on
1 - 1 - 1 for off
--powder for powder patterns (ignore all events)
Usage:
iota.filter_pickles path/to/file.h5 path/to/data /path/to/output [--powder]
Added Paths:
-----------
trunk/iota/command_line/iota_filter_pickles.py
Added: trunk/iota/command_line/iota_filter_pickles.py
===================================================================
--- trunk/iota/command_line/iota_filter_pickles.py (rev 0)
+++ trunk/iota/command_line/iota_filter_pickles.py 2016-11-13 23:17:10 UTC (rev 25711)
@@ -0,0 +1,132 @@
+from __future__ import division
+# LIBTBX_SET_DISPATCHER_NAME iota.filter_pickles
+
+import h5py
+import os, shutil, argparse, glob, ntpath
+import numpy as np
+
+def main(hdf5Filename, data, destDir, powder):
+ """
+ ideally, if pulse is on, you should expect to have 1 - 1 -1 for all events
+ otherwise 0 -1 - 1. Currently, we have more than one pickle read out for
+ each rotatation angle. Solution is picking the last one.
+ Problem is being fixed!
+ """
+ f = h5py.File(hdf5Filename)
+
+ evr92 = f['evr92'] #pulse
+ evr95 = f['evr95'] #
+ evr97 = f['evr97'] #rayonix
+ rayonixTime = f['rayonix_time']
+ rot_wrap = range(len(rayonixTime))
+ #rotation angles willl not be recorded if the motor does not moved
+ if 'sam_rot_wrap' in f:
+ rot_wrap = f['sam_rot_wrap']
+ ipm3 = f['ipm3']
+
+ goodRayonixTime = {}
+ goodRayonixIpm3 = {}
+ for _rt, _evr92, _evr95, _evr97, rot, _ipm3 in zip(rayonixTime, evr92, evr95, evr97, rot_wrap, ipm3):
+ if (_evr95 == 1 and _evr97 == 1) or powder:
+ if (_evr92,_evr95, _evr97, rot) in goodRayonixTime:
+ #found more than one
+ goodRayonixTime[(_evr92,_evr95, _evr97, rot)].append(_rt)
+ goodRayonixIpm3[(_evr92,_evr95, _evr97, rot)].append(_ipm3)
+ else:
+ goodRayonixTime[(_evr92,_evr95, _evr97, rot)] = [_rt]
+ goodRayonixIpm3[(_evr92,_evr95, _evr97, rot)] = [_ipm3]
+
+ goodKey = []
+ goodRayonixTimeList = []
+ goodRayonixIpm3List = []
+ for key, val in goodRayonixTime.iteritems():
+ if len(val) > 1:
+ goodIndex = np.argmax(goodRayonixIpm3[key])
+ else:
+ goodIndex = 0
+ goodKey.append(key)
+ goodRayonixTimeList.append(goodRayonixTime[key][goodIndex])
+ goodRayonixIpm3List.append(goodRayonixIpm3[key][goodIndex])
+
+ isort = np.argsort(goodRayonixTimeList)
+ sortedRayonixTime = np.array(goodRayonixTimeList)[isort]
+ sortedRayonixIpm3 = np.array(goodRayonixIpm3List)[isort]
+ sortedKey = np.array(goodKey)[isort]
+
+ #make destination directory
+ destDirOn = destDir + '/on'
+ destDirOff = destDir + '/off'
+ try:
+ os.makedirs(destDirOn)
+ os.makedirs(destDirOff)
+ except OSError:
+ print "WARNING: Problem creating folder. If the folder exists, it will get overwritten."
+ pass
+
+ txtOn = ''
+ txtOff = ''
+ txtError = ''
+ cnSuccess, cnErrors = (0, 0)
+ for _key, _rt, _ipm3 in zip(sortedKey, sortedRayonixTime, sortedRayonixIpm3):
+ filename_pattern = 'shot-'+str(_rt)+'*'
+ #copy to a good directory
+ try:
+ _evr92, _evr95, _evr97, _rot = tuple(_key)
+ txtOut = ','.join(map(str, list(_key)))
+ txtOut += ',%d, %f\n'%(_rt,_ipm3)
+ #determine output folder
+ if _evr92 == 0:
+ destDirSelected = destDirOff
+ txtOff += txtOut
+ else:
+ destDirSelected = destDirOn
+ txtOn += txtOut
+ #copy any files that match with the pattern
+ for filename in glob.glob(data + '/' + filename_pattern):
+ shutil.copy(filename, destDirSelected+'/'+ntpath.basename(filename))
+ print filename, _evr92, destDirSelected, 'sucess'
+ cnSuccess += 1
+ except IOError, err:
+ print err
+ txtError += ','.join(map(str, list(_key)))
+ txtError += ',%d, %f\n'%(_rt,_ipm3)
+ cnErrors += 1
+ pass
+ #write out log file
+ f = open(destDirOn+'/shotangles.txt','w')
+ f.write(txtOn)
+ f.close()
+ f = open(destDirOff+'/shotangles.txt','w')
+ f.write(txtOff)
+ f.close()
+ f = open(destDir+'/errors.txt','w')
+ f.write(txtError)
+ print "Successfully move %d files"%(cnSuccess)
+ print "%d files not found"%(cnErrors)
+
+if __name__ == '__main__':
+ parser = argparse.ArgumentParser(
+ description='Filers out pickle files read out from xtc with insignificant events'
+ )
+ parser.add_argument(
+ 'hdf5Filename',
+ metavar='HDF5 Filename',
+ help='HDF5 Filename'
+ )
+ parser.add_argument(
+ 'data',
+ metavar='DATA',
+ help='Path to all pickles'
+ )
+ parser.add_argument(
+ 'destDir',
+ metavar='DESTINATION FOLDER',
+ help='Path to destination folder'
+ )
+ parser.add_argument('--powder', dest='powder', action='store_const',
+ const=True, default=False,
+ help='Flag for powder patterns')
+ args = parser.parse_args()
+ if args.powder:
+ print "Powder diffractions. Ignore event codes"
+ main(args.hdf5Filename, args.data, args.destDir, args.powder)
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|
|
From: <bk...@us...> - 2016-11-12 01:08:03
|
Revision: 25710
http://sourceforge.net/p/cctbx/code/25710
Author: bkpoon
Date: 2016-11-12 01:08:01 +0000 (Sat, 12 Nov 2016)
Log Message:
-----------
MUSCLE GUI: bug fix for invalid characters in sequence file
Modified Paths:
--------------
trunk/mmtbx/msa.py
trunk/mmtbx/regression/tst_msa.py
Modified: trunk/mmtbx/msa.py
===================================================================
--- trunk/mmtbx/msa.py 2016-11-11 17:25:59 UTC (rev 25709)
+++ trunk/mmtbx/msa.py 2016-11-12 01:08:01 UTC (rev 25710)
@@ -85,7 +85,7 @@
ref_seq_fasta = ">%s\n%s" % (self.reference_sequence_name,
self.reference_sequence)
fasta = ref_seq_fasta + "\n" + fasta
- self.muscle_aln = get_muscle_alignment(fasta, out=out)
+ self.muscle_aln, errors = get_muscle_alignment(fasta, out=out)
assert (self.muscle_aln is not None)
# I am not proud of this.
@@ -327,19 +327,20 @@
# cmd += " -stable"
muscle_out = easy_run.fully_buffered(cmd,
stdin_lines=fasta_sequences)
- return muscle_out.stdout_lines
+ return muscle_out.stdout_lines, muscle_out.stderr_lines
def get_muscle_alignment (fasta_sequences, group_sequences=True, out=None) :
- muscle_out = run_muscle(fasta_sequences, group_sequences)
+ muscle_out, errors = run_muscle(fasta_sequences, group_sequences)
from iotbx.bioinformatics import clustal_alignment_parse
alignment, null = clustal_alignment_parse("\n".join(muscle_out))
if (out is not None) :
print >> out, "\n".join(muscle_out)
- return alignment
+ return alignment, errors
def get_muscle_alignment_ordered(sequences, out = None):
from iotbx import bioinformatics
+ from iotbx.pdb.amino_acid_codes import validate_sequence
name_for = {}
@@ -347,7 +348,7 @@
name = name_for.get( seq, "Chain_%d" % i )
name_for[ seq ] = name
- alignment = get_muscle_alignment(
+ alignment, errors = get_muscle_alignment(
fasta_sequences = "\n".join(
str( bioinformatics.sequence( name = name, sequence = seq.sequence ) )
for ( seq, name ) in name_for.items()
@@ -355,6 +356,22 @@
out = out,
)
+ # check for errors and handle:
+ # invalid characters in sequences
+ if (len(errors) > 0):
+ for error in errors:
+ error = error.strip()
+ if ('Invalid character' in error):
+ for seq in name_for.keys():
+ invalid = validate_sequence(
+ seq.sequence, protein=True, strict_protein=False,
+ nucleic_acid=True, strict_nucleic_acid=False)
+ if (len(invalid) > 0):
+ name_for.pop(seq)
+ sequences = name_for.keys()
+ elif (len(error) > 0):
+ raise Sorry(error)
+
lookup = dict( zip( alignment.names, alignment.alignments ) )
assert all( n in lookup for n in name_for.values() )
Modified: trunk/mmtbx/regression/tst_msa.py
===================================================================
--- trunk/mmtbx/regression/tst_msa.py 2016-11-11 17:25:59 UTC (rev 25709)
+++ trunk/mmtbx/regression/tst_msa.py 2016-11-12 01:08:01 UTC (rev 25710)
@@ -26,7 +26,7 @@
ETSSKNSSRSKTKCLFIQMEFCDKGTLEQWIEKRRGEKLDKVLALELFEQITKGVDYIHSKKLINRDLKPSNIFLVDTKQ
VKIGDFGLVTSLKNDGKRTRSKGTLRYMSPEQISSQDYGKEVDLYALGLILAELLHVCDTAFETSKFFTDLRDGIISDIF
DKKEKTLLQKLLSKKPEDRPNTSEILRTLTVWKKSPEKNERHTA"""
- clustal_aln = mmtbx.msa.get_muscle_alignment(fasta_sequences)
+ clustal_aln, errors = mmtbx.msa.get_muscle_alignment(fasta_sequences)
assert (clustal_aln.names == ['1MRU_A', '2A19_B', '1L3R_E'])
assert (len(clustal_aln.alignments[0]) == 371)
pdb_sequences = [
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|
|
From: <bk...@us...> - 2016-11-11 17:26:01
|
Revision: 25709
http://sourceforge.net/p/cctbx/code/25709
Author: bkpoon
Date: 2016-11-11 17:25:59 +0000 (Fri, 11 Nov 2016)
Log Message:
-----------
Base packages: updated Python from 2.7.8 to 2.7.12, Biopython from 1.66 to 1.68
Modified Paths:
--------------
trunk/libtbx/auto_build/package_defs.py
Modified: trunk/libtbx/auto_build/package_defs.py
===================================================================
--- trunk/libtbx/auto_build/package_defs.py 2016-11-11 08:48:44 UTC (rev 25708)
+++ trunk/libtbx/auto_build/package_defs.py 2016-11-11 17:25:59 UTC (rev 25709)
@@ -32,14 +32,15 @@
# base packages updated on 2/15/2015 by bkpoon
# from CCI
-PYTHON_PKG = "Python-2.7.8_cci.tar.gz"
+#PYTHON_PKG = "Python-2.7.8_cci.tar.gz"
+PYTHON_PKG = "Python-2.7.12.tar.gz"
NUMPY_PKG = "numpy-1.8.1.tar.gz" # used many places
IMAGING_PKG = "Imaging-1.1.7.tar.gz" # for labelit, gltbx
REPORTLAB_PKG = "reportlab-2.6.tar.gz" # for labelit
ZLIB_PKG = "zlib-1.2.8.tar.gz"
SCIPY_PKG = "scipy-0.14.0.tar.gz" # not used by default
PYRTF_PKG = "PyRTF-0.45.tar.gz" # for phenix.table_one, etc.
-BIOPYTHON_PKG = "biopython-1.66.tar.gz" # used in iotbx
+BIOPYTHON_PKG = "biopython-1.68.tar.gz" # used in iotbx
SPHINX_PKG = "Sphinx-1.4.4.tar.gz" # for documentation ()
NUMPYDOC_PKG = "numpydoc-0.5.tar.gz" # for documentation
IPYTHON_PKG = "ipython-3.2.1.tar.gz" # IPython
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|
|
From: <gra...@us...> - 2016-11-11 08:48:47
|
Revision: 25708
http://sourceforge.net/p/cctbx/code/25708
Author: graeme_winter
Date: 2016-11-11 08:48:44 +0000 (Fri, 11 Nov 2016)
Log Message:
-----------
Remove (comment out) the run_shelx P31 test for the moment as mentioned on cctbxbb, since the test is failing due to a change in shelx and shows no sign of being fixed
Modified Paths:
--------------
trunk/cctbx/run_tests.py
Modified: trunk/cctbx/run_tests.py
===================================================================
--- trunk/cctbx/run_tests.py 2016-11-10 20:00:35 UTC (rev 25707)
+++ trunk/cctbx/run_tests.py 2016-11-11 08:48:44 UTC (rev 25708)
@@ -107,7 +107,7 @@
["$D/development/make_cns_input.py", "P31"],
["$D/development/tst_cns_epsilon.py", "P31"],
["$D/development/tst_cns_hl.py", "P31"],
- ["$D/development/run_shelx.py", "P31"],
+ #["$D/development/run_shelx.py", "P31"],
["$D/development/run_shelx76.py", "P31"],
"$D/regression/tst_pointgroup_tools.py",
"$D/sgtbx/sub_lattice_tools.py",
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|
|
From: <nks...@us...> - 2016-11-10 20:00:37
|
Revision: 25707
http://sourceforge.net/p/cctbx/code/25707
Author: nksauter
Date: 2016-11-10 20:00:35 +0000 (Thu, 10 Nov 2016)
Log Message:
-----------
cxi.merge, correctly weight the structure factor observations if the reference Miller index is missing and thus invalid.
Modified Paths:
--------------
trunk/xfel/command_line/cxi_merge.py
trunk/xfel/cxi/postrefinement_hybrid_rs.py
trunk/xfel/cxi/postrefinement_legacy_rs.py
trunk/xfel/cxi/postrefinement_updated_rs.py
Modified: trunk/xfel/command_line/cxi_merge.py
===================================================================
--- trunk/xfel/command_line/cxi_merge.py 2016-11-10 19:12:45 UTC (rev 25706)
+++ trunk/xfel/command_line/cxi_merge.py 2016-11-10 20:00:35 UTC (rev 25707)
@@ -1441,6 +1441,10 @@
if use_weights: I_w = 1./(observations.sigmas()[pair[1]])**2 #variance weighting
else: I_w = 1.
+ # skip the structure factor if i_model.sigma is invalid (intentionally < 0)
+ if self.i_model.sigmas()[pair[0]] < 0:
+ I_w = 0.
+
I_r = self.i_model.data()[pair[0]]
I_o = observations.data()[pair[1]]
sum_xx += I_w * I_r**2
Modified: trunk/xfel/cxi/postrefinement_hybrid_rs.py
===================================================================
--- trunk/xfel/cxi/postrefinement_hybrid_rs.py 2016-11-10 19:12:45 UTC (rev 25706)
+++ trunk/xfel/cxi/postrefinement_hybrid_rs.py 2016-11-10 20:00:35 UTC (rev 25707)
@@ -66,6 +66,7 @@
#calculation of correlation here
I_reference = flex.double([i_model.data()[pair[0]] for pair in matches.pairs()])
+ I_invalid = flex.bool([i_model.sigmas()[pair[0]] < 0. for pair in matches.pairs()])
use_weights = False # New facility for getting variance-weighted correlation
if use_weights:
@@ -74,6 +75,8 @@
[1./(observations_pair1_selected.sigmas()[pair[1]])**2 for pair in matches.pairs()])
else:
I_weight = flex.double(len(observations_pair1_selected.sigmas()), 1.)
+ I_weight.set_selected(I_invalid,0.)
+ chosen.set_selected(I_invalid,0.)
"""Explanation of 'include_negatives' semantics as originally implemented in cxi.merge postrefinement:
include_negatives = True
@@ -179,6 +182,8 @@
I_weight = flex.double(len(observations.sigmas()), 1.)
I_reference = flex.double([self.i_model.data()[pair[0]] for pair in matches.pairs()])
+ I_invalid = flex.bool([self.i_model.sigmas()[pair[0]] < 0. for pair in matches.pairs()])
+ I_weight.set_selected(I_invalid,0.)
SWC = simple_weighted_correlation(I_weight, I_reference, observations.data())
print >> self.out, "CORR: NEW correlation is", SWC.corr
self.final_corr = SWC.corr
Modified: trunk/xfel/cxi/postrefinement_legacy_rs.py
===================================================================
--- trunk/xfel/cxi/postrefinement_legacy_rs.py 2016-11-10 19:12:45 UTC (rev 25706)
+++ trunk/xfel/cxi/postrefinement_legacy_rs.py 2016-11-10 20:00:35 UTC (rev 25707)
@@ -63,6 +63,7 @@
#calculation of correlation here
I_reference = flex.double([i_model.data()[pair[0]] for pair in matches.pairs()])
+ I_invalid = flex.bool([i_model.sigmas()[pair[0]] < 0. for pair in matches.pairs()])
use_weights = False # New facility for getting variance-weighted correlation
if use_weights:
@@ -71,6 +72,7 @@
[1./(observations_pair1_selected.sigmas()[pair[1]])**2 for pair in matches.pairs()])
else:
I_weight = flex.double(len(observations_pair1_selected.sigmas()), 1.)
+ I_weight.set_selected(I_invalid,0.)
"""Explanation of 'include_negatives' semantics as originally implemented in cxi.merge postrefinement:
include_negatives = True
Modified: trunk/xfel/cxi/postrefinement_updated_rs.py
===================================================================
--- trunk/xfel/cxi/postrefinement_updated_rs.py 2016-11-10 19:12:45 UTC (rev 25706)
+++ trunk/xfel/cxi/postrefinement_updated_rs.py 2016-11-10 20:00:35 UTC (rev 25707)
@@ -76,6 +76,7 @@
#calculation of correlation here
I_reference = flex.double([i_model.data()[pair[0]] for pair in matches.pairs()])
+ I_invalid = flex.bool([i_model.sigmas()[pair[0]] < 0. for pair in matches.pairs()])
use_weights = False # New facility for getting variance-weighted correlation
if use_weights:
@@ -84,6 +85,8 @@
[1./(observations_pair1_selected.sigmas()[pair[1]])**2 for pair in matches.pairs()])
else:
I_weight = flex.double(len(observations_pair1_selected.sigmas()), 1.)
+ I_weight.set_selected(I_invalid,0.)
+ chosen.set_selected(I_invalid,0.)
"""Explanation of 'include_negatives' semantics as originally implemented in cxi.merge postrefinement:
include_negatives = True
@@ -181,6 +184,8 @@
I_weight = flex.double(len(observations.sigmas()), 1.)
I_reference = flex.double([self.i_model.data()[pair[0]] for pair in matches.pairs()])
+ I_invalid = flex.bool([self.i_model.sigmas()[pair[0]] < 0. for pair in matches.pairs()])
+ I_weight.set_selected(I_invalid,0.)
SWC = simple_weighted_correlation(I_weight, I_reference, observations.data())
print >> self.out, "CORR: NEW correlation is", SWC.corr
self.final_corr = SWC.corr
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|
|
From: <nks...@us...> - 2016-11-10 19:12:48
|
Revision: 25706
http://sourceforge.net/p/cctbx/code/25706
Author: nksauter
Date: 2016-11-10 19:12:45 +0000 (Thu, 10 Nov 2016)
Log Message:
-----------
cxi.merge now accepts an MTZ file from a previous cxi.merge cycle as a reference model. Correct treatment of missing structure factor intensities is still forthcoming.
Modified Paths:
--------------
trunk/cctbx/examples/merging/samosa/join.py
trunk/xfel/command_line/cxi_merge.py
trunk/xfel/command_line/cxi_xmerge.py
trunk/xfel/merging/general_fcalc.py
Modified: trunk/cctbx/examples/merging/samosa/join.py
===================================================================
--- trunk/cctbx/examples/merging/samosa/join.py 2016-11-10 13:57:43 UTC (rev 25705)
+++ trunk/cctbx/examples/merging/samosa/join.py 2016-11-10 19:12:45 UTC (rev 25706)
@@ -4,7 +4,6 @@
import iotbx.phil
from cctbx.array_family import flex
from cctbx import miller
-from cctbx.crystal import symmetry
from cctbx import uctbx
from libtbx.utils import Usage, multi_out
from libtbx import easy_pickle
@@ -19,6 +18,7 @@
from xfel.command_line.cxi_merge import master_phil
from xfel.command_line.cxi_merge import get_observations
from xfel.command_line.cxi_merge import frame_data, null_data
+from xfel.command_line.cxi_merge import consistent_set_and_model
class unit_cell_distribution (object) :
"""
@@ -615,27 +615,8 @@
print >> out, " ", work_params.target_unit_cell
print >> out, " ", work_params.target_space_group
- # Adjust the minimum d-spacing of the generated Miller set to assure
- # that the desired high-resolution limit is included even if the
- # observed unit cell differs slightly from the target. If a
- # reference model is present, ensure that Miller indices are ordered
- # identically.
- miller_set = symmetry(
- unit_cell=work_params.target_unit_cell,
- space_group_info=work_params.target_space_group
- ).build_miller_set(
- anomalous_flag=not work_params.merge_anomalous,
- d_max=work_params.d_max,
- d_min=work_params.d_min / math.pow(
- 1 + work_params.unit_cell_length_tolerance, 1 / 3))
- miller_set = miller_set.change_basis(
- work_params.model_reindex_op).map_to_asu()
+ miller_set, i_model = consistent_set_and_model(work_params,i_model)
- if i_model is not None:
- matches = miller.match_indices(i_model.indices(), miller_set.indices())
- assert not matches.have_singles()
- miller_set = miller_set.select(matches.permutation())
-
frame_files = get_observations(work_params)
scaler = scaling_manager(
miller_set=miller_set,
Modified: trunk/xfel/command_line/cxi_merge.py
===================================================================
--- trunk/xfel/command_line/cxi_merge.py 2016-11-10 13:57:43 UTC (rev 25705)
+++ trunk/xfel/command_line/cxi_merge.py 2016-11-10 19:12:45 UTC (rev 25706)
@@ -49,6 +49,7 @@
model = None
.type = str
.help = PDB filename containing atomic coordinates & isomorphous cryst1 record
+ .help = or MTZ filename from a previous cycle of cxi.merge (not yet tested with prime MTZ)
model_reindex_op = h,k,l
.type = str
.help = Kludge for cases with an indexing ambiguity, need to be able to adjust scaling model
@@ -794,6 +795,8 @@
for i in xrange(len(self.summed_N)):
if (self.summed_N[i] <= 0):
continue
+ # skip structure factor if i_model.sigma is invalid (intentionally < 0)
+ if self.i_model.sigmas()[i] < 0: continue
I_r = self.i_model.data()[i]
I_o = sum_I[i]/self.summed_N[i]
N += 1
@@ -810,13 +813,16 @@
% (N, slope, corr)
return N, corr
- def get_overall_correlation_flex (self, data_a, data_b) :
+ def XXXget_overall_correlation_flex (self, data_a, data_b) :
"""
Correlate any two sets of data.
@param data_a data set a
@param data_b data set b
@return tuple containing correlation coefficent, slope and offset.
"""
+ # XXX function is deprecated since it does not account for the possibility
+ # that the data sigma might be invalid (set to -1 intentionally)
+ # it would be straightforward to rewrite the calling code to account for this.
import math
assert len(data_a) == len(data_b)
@@ -1574,6 +1580,40 @@
data.show_log_out(sys.stdout)
return data
+def consistent_set_and_model(work_params,i_model=None):
+ # Adjust the minimum d-spacing of the generated Miller set to assure
+ # that the desired high-resolution limit is included even if the
+ # observed unit cell differs slightly from the target. Use the same
+ # expansion formula as used in merging/general_fcalc.py, to assure consistency.
+ # If a reference model is present, ensure that Miller indices are ordered
+ # identically.
+ miller_set = symmetry(
+ unit_cell=work_params.target_unit_cell,
+ space_group_info=work_params.target_space_group
+ ).build_miller_set(
+ anomalous_flag=not work_params.merge_anomalous,
+ d_max=work_params.d_max,
+ d_min=work_params.d_min / math.pow(
+ 1 + work_params.unit_cell_length_tolerance, 1 / 3))
+ miller_set = miller_set.change_basis(
+ work_params.model_reindex_op).map_to_asu()
+
+ if i_model is not None:
+ # manage the sizes of arrays. General_fcalc assures that
+ # N(i_model) >= N(miller_set) since it fills non-matches with invalid structure factors
+ # However, if N(i_model) > N(miller_set) it's because this run of cxi.merge requested
+ # a smaller resolution range. Must prune off the reference model.
+
+ if i_model.indices().size() > miller_set.indices().size():
+ matches = miller.match_indices(i_model.indices(), miller_set.indices())
+ pairs = matches.pairs()
+ i_model = i_model.select(pairs.column(0))
+
+ matches = miller.match_indices(i_model.indices(), miller_set.indices())
+ assert not matches.have_singles()
+ miller_set = miller_set.select(matches.permutation())
+
+ return miller_set, i_model
#-----------------------------------------------------------------------
def run(args):
if ("--help" in args) :
@@ -1619,27 +1659,8 @@
print >> out, " ", work_params.target_unit_cell
print >> out, " ", work_params.target_space_group
- # Adjust the minimum d-spacing of the generated Miller set to assure
- # that the desired high-resolution limit is included even if the
- # observed unit cell differs slightly from the target. If a
- # reference model is present, ensure that Miller indices are ordered
- # identically.
- miller_set = symmetry(
- unit_cell=work_params.target_unit_cell,
- space_group_info=work_params.target_space_group
- ).build_miller_set(
- anomalous_flag=not work_params.merge_anomalous,
- d_max=work_params.d_max,
- d_min=work_params.d_min / math.pow(
- 1 + work_params.unit_cell_length_tolerance, 1 / 3))
- miller_set = miller_set.change_basis(
- work_params.model_reindex_op).map_to_asu()
+ miller_set, i_model = consistent_set_and_model(work_params,i_model)
- if i_model is not None:
- matches = miller.match_indices(i_model.indices(), miller_set.indices())
- assert not matches.have_singles()
- miller_set = miller_set.select(matches.permutation())
-
frame_files = get_observations(work_params)
scaler = scaling_manager(
miller_set=miller_set,
Modified: trunk/xfel/command_line/cxi_xmerge.py
===================================================================
--- trunk/xfel/command_line/cxi_xmerge.py 2016-11-10 13:57:43 UTC (rev 25705)
+++ trunk/xfel/command_line/cxi_xmerge.py 2016-11-10 19:12:45 UTC (rev 25706)
@@ -8,12 +8,10 @@
import iotbx.phil
from cctbx.array_family import flex
-from cctbx.crystal import symmetry
from cctbx import uctbx
from iotbx import mtz
from libtbx.utils import Usage, multi_out
from libtbx import easy_pickle
-import math
import os
import time
import sys
@@ -21,6 +19,7 @@
from xfel.command_line.cxi_merge import master_phil,scaling_manager
from xfel.command_line.cxi_merge import unit_cell_distribution,show_overall_observations
from xfel.command_line.cxi_merge import scaling_result
+from xfel.command_line.cxi_merge import consistent_set_and_model
from xfel import column_parser
from cctbx import miller
@@ -210,22 +209,8 @@
print >> out, " ", work_params.target_unit_cell
print >> out, " ", work_params.target_space_group
- miller_set = symmetry(
- unit_cell=work_params.target_unit_cell,
- space_group_info=work_params.target_space_group
- ).build_miller_set(
- anomalous_flag=not work_params.merge_anomalous,
- d_max=work_params.d_max,
- d_min=work_params.d_min / math.pow(
- 1 + work_params.unit_cell_length_tolerance, 1 / 3))
- miller_set = miller_set.change_basis(
- work_params.model_reindex_op).map_to_asu()
+ miller_set, i_model = consistent_set_and_model(work_params,i_model)
- if i_model is not None:
- matches = miller.match_indices(i_model.indices(), miller_set.indices())
- assert not matches.have_singles()
- miller_set = miller_set.select(matches.permutation())
-
# ---- Augment this code with any special procedures for x scaling
scaler = xscaling_manager(
miller_set=miller_set,
Modified: trunk/xfel/merging/general_fcalc.py
===================================================================
--- trunk/xfel/merging/general_fcalc.py 2016-11-10 13:57:43 UTC (rev 25705)
+++ trunk/xfel/merging/general_fcalc.py 2016-11-10 19:12:45 UTC (rev 25706)
@@ -15,7 +15,10 @@
for array in data_SR.as_miller_arrays():
this_label = array.info().label_string().lower()
if this_label.find("iobs")>=0:
- return array.as_intensity_array().change_basis(params.model_reindex_op).map_to_asu()
+ i_array = array.as_intensity_array().change_basis(params.model_reindex_op).map_to_asu()
+ c_array = i_array.complete_array(
+ d_min = params.d_min / math.pow(1 + params.unit_cell_length_tolerance, 1 / 3))
+ return c_array
if this_label.find("imean")>=0:
return array.as_intensity_array().change_basis(params.model_reindex_op).map_to_asu()
if this_label.find(params.scaling.mtz_column_F)>=0:
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rjg...@us...> - 2016-11-10 13:57:45
|
Revision: 25705
http://sourceforge.net/p/cctbx/code/25705
Author: rjgildea
Date: 2016-11-10 13:57:43 +0000 (Thu, 10 Nov 2016)
Log Message:
-----------
add new goniometer.set/get_rotation_axis_datum(): sets/gets rotation axis at goniometer datum; existing goniometer.set/get_rotation_axis() now sets/gets rotation axis in laboratory frame (i.e. with application of setting matrix)
Modified Paths:
--------------
trunk/dxtbx/model/boost_python/goniometer.cc
trunk/dxtbx/model/goniometer.h
trunk/dxtbx/tests/test_goniometer.py
Modified: trunk/dxtbx/model/boost_python/goniometer.cc
===================================================================
--- trunk/dxtbx/model/boost_python/goniometer.cc 2016-11-09 12:44:48 UTC (rev 25704)
+++ trunk/dxtbx/model/boost_python/goniometer.cc 2016-11-10 13:57:43 UTC (rev 25705)
@@ -41,7 +41,7 @@
static
boost::python::tuple getinitargs(const Goniometer &obj) {
return boost::python::make_tuple(
- obj.get_rotation_axis(),
+ obj.get_rotation_axis_datum(),
obj.get_fixed_rotation(),
obj.get_setting_rotation());
}
@@ -50,7 +50,7 @@
template <>
boost::python::dict to_dict<Goniometer>(const Goniometer &obj) {
boost::python::dict result;
- result["rotation_axis"] = obj.get_rotation_axis();
+ result["rotation_axis"] = obj.get_rotation_axis_datum();
result["fixed_rotation"] = obj.get_fixed_rotation();
result["setting_rotation"] = obj.get_setting_rotation();
return result;
@@ -88,6 +88,10 @@
&Goniometer::get_rotation_axis)
.def("set_rotation_axis",
&Goniometer::set_rotation_axis)
+ .def("get_rotation_axis_datum",
+ &Goniometer::get_rotation_axis_datum)
+ .def("set_rotation_axis_datum",
+ &Goniometer::set_rotation_axis_datum)
.def("get_fixed_rotation",
&Goniometer::get_fixed_rotation)
.def("set_fixed_rotation",
Modified: trunk/dxtbx/model/goniometer.h
===================================================================
--- trunk/dxtbx/model/goniometer.h 2016-11-09 12:44:48 UTC (rev 25704)
+++ trunk/dxtbx/model/goniometer.h 2016-11-10 13:57:43 UTC (rev 25705)
@@ -110,7 +110,7 @@
/**
* Initialise the goniometer.
- * @param rotation_axis The goniometer rotation axis
+ * @param rotation_axis The goniometer rotation axis at datum
* @param fixed_rotation The additional fixed rotation of the sample
* @param setting_rotation The additional setting rotation of the axis
*/
@@ -128,6 +128,11 @@
/** Get the rotation axis */
vec3 <double> get_rotation_axis() const {
+ return setting_rotation_ * rotation_axis_;
+ }
+
+ /** Get the rotation axis at datum */
+ vec3 <double> get_rotation_axis_datum() const {
return rotation_axis_;
}
@@ -144,6 +149,12 @@
/** Set the rotation axis */
void set_rotation_axis(vec3 <double> rotation_axis) {
DXTBX_ASSERT(rotation_axis.length() > 0);
+ rotation_axis_ = setting_rotation_.inverse() * rotation_axis.normalize();
+ }
+
+ /** Set the rotation axis */
+ void set_rotation_axis_datum(vec3 <double> rotation_axis) {
+ DXTBX_ASSERT(rotation_axis.length() > 0);
rotation_axis_ = rotation_axis.normalize();
}
Modified: trunk/dxtbx/tests/test_goniometer.py
===================================================================
--- trunk/dxtbx/tests/test_goniometer.py 2016-11-09 12:44:48 UTC (rev 25704)
+++ trunk/dxtbx/tests/test_goniometer.py 2016-11-10 13:57:43 UTC (rev 25705)
@@ -147,7 +147,10 @@
axes, angles, names, scan_axis)
assert approx_equal(multi_axis_phi_scan.get_fixed_rotation(), kappa_phi_scan.get_fixed_rotation())
from scitbx import matrix
- assert approx_equal(matrix.sqr(multi_axis_phi_scan.get_setting_rotation()) * multi_axis_phi_scan.get_rotation_axis(), kappa_phi_scan.get_rotation_axis())
+ assert approx_equal(
+ matrix.sqr(multi_axis_phi_scan.get_setting_rotation()) * multi_axis_phi_scan.get_rotation_axis_datum(),
+ kappa_phi_scan.get_rotation_axis())
+ assert approx_equal(multi_axis_phi_scan.get_rotation_axis(), kappa_phi_scan.get_rotation_axis())
recycle_phi = MultiAxisGoniometer.from_dict(multi_axis_phi_scan.to_dict())
assert approx_equal(recycle_phi.get_axes(), multi_axis_phi_scan.get_axes())
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mge...@us...> - 2016-11-09 12:44:52
|
Revision: 25704
http://sourceforge.net/p/cctbx/code/25704
Author: mgerstel
Date: 2016-11-09 12:44:48 +0000 (Wed, 09 Nov 2016)
Log Message:
-----------
Add further missing *.pyc exclusions
Property Changed:
----------------
trunk/boost_adaptbx/
trunk/boost_adaptbx/command_line/
trunk/boost_adaptbx/graph/
trunk/boost_adaptbx/graph/tests/
trunk/boost_adaptbx/tests/
trunk/cbflib_adaptbx/
trunk/cbflib_adaptbx/command_line/
trunk/cctbx/adp_restraints/
trunk/cctbx/adptbx/boost_python/
trunk/cctbx/array_family/
trunk/cctbx/array_family/boost_python/
trunk/cctbx/command_line/
trunk/cctbx/covariance/
trunk/cctbx/covariance/tests/
trunk/cctbx/crystal/
trunk/cctbx/development/
trunk/cctbx/dmtbx/boost_python/
trunk/cctbx/eltbx/
trunk/cctbx/eltbx/development/
trunk/cctbx/eltbx/tests/
trunk/cctbx/eltbx/xray_scattering/
trunk/cctbx/examples/
trunk/cctbx/examples/merging/
trunk/cctbx/examples/merging/samosa/
trunk/cctbx/examples/structure_factor_calculus/
trunk/cctbx/geometry/
trunk/cctbx/geometry/tests/
trunk/cctbx/geometry_restraints/
trunk/cctbx/macro_mol/
trunk/cctbx/maptbx/
trunk/cctbx/maptbx/boost_python/
trunk/cctbx/masks/
trunk/cctbx/masks/tests/
trunk/cctbx/math/boost_python/
trunk/cctbx/merging/
trunk/cctbx/miller/
trunk/cctbx/miller/boost_python/
trunk/cctbx/multipolar/regression/
trunk/cctbx/neutron/
trunk/cctbx/omz/
trunk/cctbx/regression/
trunk/cctbx/sgtbx/
trunk/cctbx/sgtbx/boost_python/
trunk/cctbx/sgtbx/direct_space_asu/
trunk/cctbx/sgtbx/direct_space_asu/proto/
trunk/cctbx/symmetry_search/tests/
trunk/cctbx/translation_search/
trunk/cctbx/translation_search/boost_python/
trunk/cctbx/uctbx/
trunk/cctbx/uctbx/boost_python/
trunk/cctbx/uctbx/determine_unit_cell/
trunk/cctbx/web/
trunk/cctbx/web/asu_gallery/
trunk/cctbx/xray/
trunk/cctbx/xray/boost_python/
trunk/cctbx/xray/observations/
trunk/cctbx/xray/structure_factors/
trunk/cctbx/xray/targets/
trunk/clipper_adaptbx/clipper/
trunk/cma_es/
trunk/cootbx/
trunk/crys3d/
trunk/crys3d/command_line/
trunk/crys3d/hklview/
trunk/crys3d/qttbx/
trunk/cudatbx/
trunk/cudatbx/cufft/
trunk/cudatbx/math/
trunk/cudatbx/math/special_functions/
trunk/cudatbx/scattering/
trunk/dox/compcomm/newsletter08/
trunk/dox/compcomm/newsletter09/
trunk/dox/rst/
trunk/dox/siena2005/
trunk/dox.sphinx/
trunk/dxtbx/command_line/
trunk/dxtbx/data/
trunk/dxtbx/data/beamline_defs/
trunk/dxtbx/example/
trunk/dxtbx/format/
trunk/dxtbx/format/tests/
trunk/dxtbx/model/experiment/
trunk/dxtbx/serialize/
trunk/dxtbx/tests/
trunk/dxtbx/tests/command_line/
trunk/dxtbx/tests/model/
trunk/dxtbx/tests/model/experiment/
trunk/dxtbx/tests/serialize/
trunk/fable/command_line/
trunk/fable/test/
trunk/fftw3tbx/
trunk/fftw3tbx/command_line/
trunk/gltbx/command_line/
trunk/iota/
trunk/iota/command_line/
trunk/iota/components/
trunk/iotbx/
trunk/iotbx/PrettyPrint/
trunk/iotbx/bioinformatics/
trunk/iotbx/bioinformatics/test/
trunk/iotbx/ccp4_map/
trunk/iotbx/cif/
trunk/iotbx/cif/tests/
trunk/iotbx/cns/
trunk/iotbx/command_line/
trunk/iotbx/detectors/
trunk/iotbx/detectors/context/
trunk/iotbx/detectors/util/
trunk/iotbx/dsn6/
trunk/iotbx/dtrek/
trunk/iotbx/examples/
trunk/iotbx/examples/pdb_truncate_to_ala/
trunk/iotbx/fullprof/
trunk/iotbx/gui_tools/
trunk/iotbx/kriber/
trunk/iotbx/mtz/
trunk/iotbx/ncs/
trunk/iotbx/pdb/
trunk/iotbx/pdb/remediation/
trunk/iotbx/regression/
trunk/iotbx/regression/ncs/
trunk/iotbx/regression/secondary_structure/
trunk/iotbx/scalepack/
trunk/iotbx/shelx/
trunk/iotbx/solve/
trunk/iotbx/xds/
trunk/iotbx/xds/tests/
trunk/iotbx/xplor/
trunk/libtbx/bundle/
trunk/libtbx/command_line/
trunk/libtbx/development/
trunk/libtbx/program_utils/
trunk/libtbx/queuing_system_utils/processing/
trunk/libtbx/scheduling/
trunk/libtbx/server/
trunk/libtbx/sphinx/
trunk/libtbx/test_utils/
trunk/mmtbx/building/
trunk/mmtbx/building/alternate_conformations/
trunk/mmtbx/building/alternate_conformations/scripts/
trunk/mmtbx/building/loop_closure/
trunk/mmtbx/cablam/fingerprints/
trunk/mmtbx/disorder/
trunk/mmtbx/geometry/
trunk/mmtbx/geometry/tests/
trunk/mmtbx/idealized_aa_residues/
trunk/mmtbx/ions/svm/
trunk/mmtbx/ligands/
trunk/mmtbx/refinement/ensemble_refinement/
trunk/mmtbx/refinement/ensemble_refinement/scripts/
trunk/mmtbx/regression/model_idealization/
trunk/mmtbx/regression/ncs/
trunk/mmtbx/regression/real_space_refine_chain/
trunk/mmtbx/regression/tls/
trunk/mmtbx/regression/tncs/
trunk/mmtbx/ringer/
trunk/mmtbx/secondary_structure/build/
trunk/mmtbx/sisa/
trunk/mmtbx/sisa/optimize/
trunk/mmtbx/validation/molprobity/
trunk/mmtbx/validation/ramachandran/
trunk/mmtbx/validation/regression/
trunk/omptbx/
trunk/prime/
trunk/prime/command_line/
trunk/prime/index_ambiguity/
trunk/prime/postrefine/
trunk/rstbx/
trunk/rstbx/apps/
trunk/rstbx/apps/stills/
trunk/rstbx/array_family/
trunk/rstbx/bandpass/
trunk/rstbx/bpcx/
trunk/rstbx/bpcx/detector_model/
trunk/rstbx/cftbx/
trunk/rstbx/command_line/
trunk/rstbx/detectors/
trunk/rstbx/dials_core/
trunk/rstbx/diffraction/
trunk/rstbx/diffraction/fastbragg/
trunk/rstbx/dps_core/
trunk/rstbx/indexing/
trunk/rstbx/indexing_api/
trunk/rstbx/new_horizons/
trunk/rstbx/outlier_spots/
trunk/rstbx/phil/
trunk/rstbx/simage/
trunk/rstbx/simulation/
trunk/rstbx/slip_viewer/
trunk/rstbx/symmetry/
trunk/rstbx/symmetry/constraints/
trunk/rstbx/viewer/
trunk/scitbx/array_family/boost_python/
trunk/scitbx/boost_python/
trunk/scitbx/command_line/
trunk/scitbx/error/
trunk/scitbx/examples/
trunk/scitbx/examples/bevington/
trunk/scitbx/fftpack/boost_python/
trunk/scitbx/fftpack/timing/
trunk/scitbx/glmtbx/
trunk/scitbx/glmtbx/tests/
trunk/scitbx/graph/
trunk/scitbx/graphics_utils/
trunk/scitbx/iso_surface/
trunk/scitbx/lbfgs/
trunk/scitbx/lbfgs/dev/
trunk/scitbx/lbfgsb/boost_python/
trunk/scitbx/linalg/tests/
trunk/scitbx/lstbx/
trunk/scitbx/lstbx/tests/
trunk/scitbx/math/boost_python/
trunk/scitbx/math/tests/
trunk/scitbx/matrix/tests/
trunk/scitbx/minpack/
trunk/scitbx/python_utils/
trunk/scitbx/random/tests/
trunk/scitbx/rigid_body/
trunk/scitbx/rigid_body/essence/
trunk/scitbx/rigid_body/proto/
trunk/scitbx/sparse/
trunk/scitbx/sparse/tests/
trunk/scitbx/suffixtree/
trunk/scitbx/suffixtree/test/
trunk/scitbx/wigner/
trunk/smtbx/ab_initio/
trunk/smtbx/ab_initio/development/
trunk/smtbx/ab_initio/tests/
trunk/smtbx/absolute_structure/
trunk/smtbx/absolute_structure/tests/
trunk/smtbx/array_family/
trunk/smtbx/command_line/
trunk/smtbx/masks/
trunk/smtbx/masks/tests/
trunk/smtbx/refinement/
trunk/smtbx/refinement/constraints/
trunk/smtbx/refinement/constraints/geometrical/
trunk/smtbx/refinement/constraints/tests/
trunk/smtbx/refinement/restraints/
trunk/smtbx/refinement/restraints/tests/
trunk/smtbx/refinement/tests/
trunk/smtbx/stl/
trunk/smtbx/structure_factors/
trunk/smtbx/structure_factors/direct/
trunk/smtbx/structure_factors/direct/tests/
trunk/smtbx/tests/
trunk/sphinx/
trunk/spotfinder/
trunk/spotfinder/applications/
trunk/spotfinder/applications/heuristic_tbx/
trunk/spotfinder/applications/xfel/
trunk/spotfinder/array_family/
trunk/spotfinder/command_line/
trunk/spotfinder/core_toolbox/
trunk/spotfinder/core_toolbox/boost_python/
trunk/spotfinder/diffraction/
trunk/spotfinder/dxtbx_toolbox/
trunk/spotfinder/math_support/
trunk/spotfinder/servers/
trunk/wxtbx/
trunk/wxtbx/command_line/
trunk/wxtbx/phil_controls/
trunk/wxtbx/plots/
trunk/wxtbx/regression/
trunk/wxtbx/reports/
trunk/xfel/
trunk/xfel/amo/
trunk/xfel/amo/pnccd_ana/
trunk/xfel/cftbx/
trunk/xfel/cftbx/detector/
trunk/xfel/clustering/
trunk/xfel/command_line/
trunk/xfel/cxi/
trunk/xfel/cxi/clustering/
trunk/xfel/cxi/command_line/
trunk/xfel/cxi/cspad_ana/
trunk/xfel/cxi/gfx/
trunk/xfel/graph_proc/
trunk/xfel/merging/
trunk/xfel/metrology/
trunk/xfel/metrology/legacy_scale/
trunk/xfel/mono_simulation/
trunk/xfel/sacla/
trunk/xfel/small_cell/
trunk/xfel/ui/
trunk/xfel/ui/command_line/
trunk/xfel/ui/components/
trunk/xfel/ui/db/
trunk/xfel/util/
trunk/xfel/vonHamos/
trunk/xfel/xpp/
Index: trunk/boost_adaptbx
===================================================================
--- trunk/boost_adaptbx 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/boost_adaptbx 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/boost_adaptbx
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/boost_adaptbx/command_line
===================================================================
--- trunk/boost_adaptbx/command_line 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/boost_adaptbx/command_line 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/boost_adaptbx/command_line
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/boost_adaptbx/graph
===================================================================
--- trunk/boost_adaptbx/graph 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/boost_adaptbx/graph 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/boost_adaptbx/graph
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/boost_adaptbx/graph/tests
===================================================================
--- trunk/boost_adaptbx/graph/tests 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/boost_adaptbx/graph/tests 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/boost_adaptbx/graph/tests
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/boost_adaptbx/tests
===================================================================
--- trunk/boost_adaptbx/tests 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/boost_adaptbx/tests 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/boost_adaptbx/tests
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cbflib_adaptbx
===================================================================
--- trunk/cbflib_adaptbx 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cbflib_adaptbx 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cbflib_adaptbx
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cbflib_adaptbx/command_line
===================================================================
--- trunk/cbflib_adaptbx/command_line 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cbflib_adaptbx/command_line 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cbflib_adaptbx/command_line
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cctbx/adp_restraints
===================================================================
--- trunk/cctbx/adp_restraints 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cctbx/adp_restraints 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cctbx/adp_restraints
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cctbx/adptbx/boost_python
===================================================================
--- trunk/cctbx/adptbx/boost_python 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cctbx/adptbx/boost_python 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cctbx/adptbx/boost_python
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cctbx/array_family
===================================================================
--- trunk/cctbx/array_family 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cctbx/array_family 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cctbx/array_family
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cctbx/array_family/boost_python
===================================================================
--- trunk/cctbx/array_family/boost_python 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cctbx/array_family/boost_python 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cctbx/array_family/boost_python
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cctbx/command_line
===================================================================
--- trunk/cctbx/command_line 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cctbx/command_line 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cctbx/command_line
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cctbx/covariance
===================================================================
--- trunk/cctbx/covariance 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cctbx/covariance 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cctbx/covariance
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cctbx/covariance/tests
===================================================================
--- trunk/cctbx/covariance/tests 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cctbx/covariance/tests 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cctbx/covariance/tests
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cctbx/crystal
===================================================================
--- trunk/cctbx/crystal 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cctbx/crystal 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cctbx/crystal
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cctbx/development
===================================================================
--- trunk/cctbx/development 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cctbx/development 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cctbx/development
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cctbx/dmtbx/boost_python
===================================================================
--- trunk/cctbx/dmtbx/boost_python 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cctbx/dmtbx/boost_python 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cctbx/dmtbx/boost_python
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cctbx/eltbx
===================================================================
--- trunk/cctbx/eltbx 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cctbx/eltbx 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cctbx/eltbx
___________________________________________________________________
Modified: svn:ignore
## -1,3 +1,4 ##
+*.pyc
henke.cpp
henke_tables_01_12.cpp
henke_tables_13_24.cpp
Index: trunk/cctbx/eltbx/development
===================================================================
--- trunk/cctbx/eltbx/development 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cctbx/eltbx/development 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cctbx/eltbx/development
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cctbx/eltbx/tests
===================================================================
--- trunk/cctbx/eltbx/tests 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cctbx/eltbx/tests 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cctbx/eltbx/tests
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cctbx/eltbx/xray_scattering
===================================================================
--- trunk/cctbx/eltbx/xray_scattering 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cctbx/eltbx/xray_scattering 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cctbx/eltbx/xray_scattering
___________________________________________________________________
Modified: svn:ignore
## -1 +1,2 ##
+*.pyc
n_gaussian_raw.cpp
Index: trunk/cctbx/examples
===================================================================
--- trunk/cctbx/examples 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cctbx/examples 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cctbx/examples
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cctbx/examples/merging
===================================================================
--- trunk/cctbx/examples/merging 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cctbx/examples/merging 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cctbx/examples/merging
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cctbx/examples/merging/samosa
===================================================================
--- trunk/cctbx/examples/merging/samosa 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cctbx/examples/merging/samosa 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cctbx/examples/merging/samosa
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cctbx/examples/structure_factor_calculus
===================================================================
--- trunk/cctbx/examples/structure_factor_calculus 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cctbx/examples/structure_factor_calculus 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cctbx/examples/structure_factor_calculus
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cctbx/geometry
===================================================================
--- trunk/cctbx/geometry 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cctbx/geometry 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cctbx/geometry
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cctbx/geometry/tests
===================================================================
--- trunk/cctbx/geometry/tests 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cctbx/geometry/tests 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cctbx/geometry/tests
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cctbx/geometry_restraints
===================================================================
--- trunk/cctbx/geometry_restraints 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cctbx/geometry_restraints 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cctbx/geometry_restraints
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cctbx/macro_mol
===================================================================
--- trunk/cctbx/macro_mol 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cctbx/macro_mol 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cctbx/macro_mol
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cctbx/maptbx
===================================================================
--- trunk/cctbx/maptbx 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cctbx/maptbx 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cctbx/maptbx
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cctbx/maptbx/boost_python
===================================================================
--- trunk/cctbx/maptbx/boost_python 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cctbx/maptbx/boost_python 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cctbx/maptbx/boost_python
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cctbx/masks
===================================================================
--- trunk/cctbx/masks 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cctbx/masks 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cctbx/masks
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cctbx/masks/tests
===================================================================
--- trunk/cctbx/masks/tests 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cctbx/masks/tests 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cctbx/masks/tests
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cctbx/math/boost_python
===================================================================
--- trunk/cctbx/math/boost_python 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cctbx/math/boost_python 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cctbx/math/boost_python
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cctbx/merging
===================================================================
--- trunk/cctbx/merging 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cctbx/merging 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cctbx/merging
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cctbx/miller
===================================================================
--- trunk/cctbx/miller 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cctbx/miller 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cctbx/miller
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cctbx/miller/boost_python
===================================================================
--- trunk/cctbx/miller/boost_python 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cctbx/miller/boost_python 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cctbx/miller/boost_python
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cctbx/multipolar/regression
===================================================================
--- trunk/cctbx/multipolar/regression 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cctbx/multipolar/regression 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cctbx/multipolar/regression
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cctbx/neutron
===================================================================
--- trunk/cctbx/neutron 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cctbx/neutron 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cctbx/neutron
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cctbx/omz
===================================================================
--- trunk/cctbx/omz 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cctbx/omz 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cctbx/omz
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cctbx/regression
===================================================================
--- trunk/cctbx/regression 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cctbx/regression 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cctbx/regression
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cctbx/sgtbx
===================================================================
--- trunk/cctbx/sgtbx 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cctbx/sgtbx 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cctbx/sgtbx
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cctbx/sgtbx/boost_python
===================================================================
--- trunk/cctbx/sgtbx/boost_python 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cctbx/sgtbx/boost_python 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cctbx/sgtbx/boost_python
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cctbx/sgtbx/direct_space_asu
===================================================================
--- trunk/cctbx/sgtbx/direct_space_asu 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cctbx/sgtbx/direct_space_asu 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cctbx/sgtbx/direct_space_asu
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cctbx/sgtbx/direct_space_asu/proto
===================================================================
--- trunk/cctbx/sgtbx/direct_space_asu/proto 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cctbx/sgtbx/direct_space_asu/proto 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cctbx/sgtbx/direct_space_asu/proto
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cctbx/symmetry_search/tests
===================================================================
--- trunk/cctbx/symmetry_search/tests 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cctbx/symmetry_search/tests 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cctbx/symmetry_search/tests
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cctbx/translation_search
===================================================================
--- trunk/cctbx/translation_search 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cctbx/translation_search 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cctbx/translation_search
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cctbx/translation_search/boost_python
===================================================================
--- trunk/cctbx/translation_search/boost_python 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cctbx/translation_search/boost_python 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cctbx/translation_search/boost_python
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cctbx/uctbx
===================================================================
--- trunk/cctbx/uctbx 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cctbx/uctbx 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cctbx/uctbx
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cctbx/uctbx/boost_python
===================================================================
--- trunk/cctbx/uctbx/boost_python 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cctbx/uctbx/boost_python 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cctbx/uctbx/boost_python
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cctbx/uctbx/determine_unit_cell
===================================================================
--- trunk/cctbx/uctbx/determine_unit_cell 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cctbx/uctbx/determine_unit_cell 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cctbx/uctbx/determine_unit_cell
___________________________________________________________________
Modified: svn:ignore
## -1 +1,2 ##
+*.pyc
NCDist.h.old.h
Index: trunk/cctbx/web
===================================================================
--- trunk/cctbx/web 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cctbx/web 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cctbx/web
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cctbx/web/asu_gallery
===================================================================
--- trunk/cctbx/web/asu_gallery 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cctbx/web/asu_gallery 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cctbx/web/asu_gallery
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cctbx/xray
===================================================================
--- trunk/cctbx/xray 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cctbx/xray 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cctbx/xray
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cctbx/xray/boost_python
===================================================================
--- trunk/cctbx/xray/boost_python 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cctbx/xray/boost_python 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cctbx/xray/boost_python
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cctbx/xray/observations
===================================================================
--- trunk/cctbx/xray/observations 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cctbx/xray/observations 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cctbx/xray/observations
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cctbx/xray/structure_factors
===================================================================
--- trunk/cctbx/xray/structure_factors 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cctbx/xray/structure_factors 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cctbx/xray/structure_factors
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cctbx/xray/targets
===================================================================
--- trunk/cctbx/xray/targets 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cctbx/xray/targets 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cctbx/xray/targets
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/clipper_adaptbx/clipper
===================================================================
--- trunk/clipper_adaptbx/clipper 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/clipper_adaptbx/clipper 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/clipper_adaptbx/clipper
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cma_es
===================================================================
--- trunk/cma_es 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cma_es 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cma_es
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cootbx
===================================================================
--- trunk/cootbx 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cootbx 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cootbx
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/crys3d
===================================================================
--- trunk/crys3d 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/crys3d 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/crys3d
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/crys3d/command_line
===================================================================
--- trunk/crys3d/command_line 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/crys3d/command_line 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/crys3d/command_line
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/crys3d/hklview
===================================================================
--- trunk/crys3d/hklview 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/crys3d/hklview 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/crys3d/hklview
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/crys3d/qttbx
===================================================================
--- trunk/crys3d/qttbx 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/crys3d/qttbx 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/crys3d/qttbx
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cudatbx
===================================================================
--- trunk/cudatbx 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cudatbx 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cudatbx
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cudatbx/cufft
===================================================================
--- trunk/cudatbx/cufft 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cudatbx/cufft 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cudatbx/cufft
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cudatbx/math
===================================================================
--- trunk/cudatbx/math 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cudatbx/math 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cudatbx/math
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cudatbx/math/special_functions
===================================================================
--- trunk/cudatbx/math/special_functions 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cudatbx/math/special_functions 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cudatbx/math/special_functions
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cudatbx/scattering
===================================================================
--- trunk/cudatbx/scattering 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/cudatbx/scattering 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/cudatbx/scattering
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/dox/compcomm/newsletter08
===================================================================
--- trunk/dox/compcomm/newsletter08 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/dox/compcomm/newsletter08 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/dox/compcomm/newsletter08
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/dox/compcomm/newsletter09
===================================================================
--- trunk/dox/compcomm/newsletter09 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/dox/compcomm/newsletter09 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/dox/compcomm/newsletter09
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/dox/rst
===================================================================
--- trunk/dox/rst 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/dox/rst 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/dox/rst
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/dox/siena2005
===================================================================
--- trunk/dox/siena2005 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/dox/siena2005 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/dox/siena2005
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/dox.sphinx
===================================================================
--- trunk/dox.sphinx 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/dox.sphinx 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/dox.sphinx
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/dxtbx/command_line
===================================================================
--- trunk/dxtbx/command_line 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/dxtbx/command_line 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/dxtbx/command_line
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/dxtbx/data
===================================================================
--- trunk/dxtbx/data 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/dxtbx/data 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/dxtbx/data
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/dxtbx/data/beamline_defs
===================================================================
--- trunk/dxtbx/data/beamline_defs 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/dxtbx/data/beamline_defs 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/dxtbx/data/beamline_defs
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/dxtbx/example
===================================================================
--- trunk/dxtbx/example 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/dxtbx/example 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/dxtbx/example
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/dxtbx/format
===================================================================
--- trunk/dxtbx/format 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/dxtbx/format 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/dxtbx/format
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/dxtbx/format/tests
===================================================================
--- trunk/dxtbx/format/tests 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/dxtbx/format/tests 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/dxtbx/format/tests
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/dxtbx/model/experiment
===================================================================
--- trunk/dxtbx/model/experiment 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/dxtbx/model/experiment 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/dxtbx/model/experiment
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/dxtbx/serialize
===================================================================
--- trunk/dxtbx/serialize 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/dxtbx/serialize 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/dxtbx/serialize
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/dxtbx/tests
===================================================================
--- trunk/dxtbx/tests 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/dxtbx/tests 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/dxtbx/tests
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/dxtbx/tests/command_line
===================================================================
--- trunk/dxtbx/tests/command_line 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/dxtbx/tests/command_line 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/dxtbx/tests/command_line
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/dxtbx/tests/model
===================================================================
--- trunk/dxtbx/tests/model 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/dxtbx/tests/model 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/dxtbx/tests/model
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/dxtbx/tests/model/experiment
===================================================================
--- trunk/dxtbx/tests/model/experiment 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/dxtbx/tests/model/experiment 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/dxtbx/tests/model/experiment
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/dxtbx/tests/serialize
===================================================================
--- trunk/dxtbx/tests/serialize 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/dxtbx/tests/serialize 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/dxtbx/tests/serialize
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/fable/command_line
===================================================================
--- trunk/fable/command_line 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/fable/command_line 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/fable/command_line
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/fable/test
===================================================================
--- trunk/fable/test 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/fable/test 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/fable/test
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/fftw3tbx
===================================================================
--- trunk/fftw3tbx 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/fftw3tbx 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/fftw3tbx
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/fftw3tbx/command_line
===================================================================
--- trunk/fftw3tbx/command_line 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/fftw3tbx/command_line 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/fftw3tbx/command_line
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/gltbx/command_line
===================================================================
--- trunk/gltbx/command_line 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/gltbx/command_line 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/gltbx/command_line
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/iota
===================================================================
--- trunk/iota 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/iota 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/iota
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/iota/command_line
===================================================================
--- trunk/iota/command_line 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/iota/command_line 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/iota/command_line
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/iota/components
===================================================================
--- trunk/iota/components 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/iota/components 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/iota/components
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/iotbx
===================================================================
--- trunk/iotbx 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/iotbx 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/iotbx
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/iotbx/PrettyPrint
===================================================================
--- trunk/iotbx/PrettyPrint 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/iotbx/PrettyPrint 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/iotbx/PrettyPrint
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/iotbx/bioinformatics
===================================================================
--- trunk/iotbx/bioinformatics 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/iotbx/bioinformatics 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/iotbx/bioinformatics
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/iotbx/bioinformatics/test
===================================================================
--- trunk/iotbx/bioinformatics/test 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/iotbx/bioinformatics/test 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/iotbx/bioinformatics/test
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/iotbx/ccp4_map
===================================================================
--- trunk/iotbx/ccp4_map 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/iotbx/ccp4_map 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/iotbx/ccp4_map
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/iotbx/cif
===================================================================
--- trunk/iotbx/cif 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/iotbx/cif 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/iotbx/cif
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/iotbx/cif/tests
===================================================================
--- trunk/iotbx/cif/tests 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/iotbx/cif/tests 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/iotbx/cif/tests
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/iotbx/cns
===================================================================
--- trunk/iotbx/cns 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/iotbx/cns 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/iotbx/cns
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/iotbx/command_line
===================================================================
--- trunk/iotbx/command_line 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/iotbx/command_line 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/iotbx/command_line
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/iotbx/detectors
===================================================================
--- trunk/iotbx/detectors 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/iotbx/detectors 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/iotbx/detectors
___________________________________________________________________
Modified: svn:ignore
## -1 +1,2 ##
+*.pyc
adsc.img
Index: trunk/iotbx/detectors/context
===================================================================
--- trunk/iotbx/detectors/context 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/iotbx/detectors/context 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/iotbx/detectors/context
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/iotbx/detectors/util
===================================================================
--- trunk/iotbx/detectors/util 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/iotbx/detectors/util 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/iotbx/detectors/util
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/iotbx/dsn6
===================================================================
--- trunk/iotbx/dsn6 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/iotbx/dsn6 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/iotbx/dsn6
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/iotbx/dtrek
===================================================================
--- trunk/iotbx/dtrek 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/iotbx/dtrek 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/iotbx/dtrek
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/iotbx/examples
===================================================================
--- trunk/iotbx/examples 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/iotbx/examples 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/iotbx/examples
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/iotbx/examples/pdb_truncate_to_ala
===================================================================
--- trunk/iotbx/examples/pdb_truncate_to_ala 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/iotbx/examples/pdb_truncate_to_ala 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/iotbx/examples/pdb_truncate_to_ala
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/iotbx/fullprof
===================================================================
--- trunk/iotbx/fullprof 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/iotbx/fullprof 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/iotbx/fullprof
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/iotbx/gui_tools
===================================================================
--- trunk/iotbx/gui_tools 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/iotbx/gui_tools 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/iotbx/gui_tools
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/iotbx/kriber
===================================================================
--- trunk/iotbx/kriber 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/iotbx/kriber 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/iotbx/kriber
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/iotbx/mtz
===================================================================
--- trunk/iotbx/mtz 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/iotbx/mtz 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/iotbx/mtz
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/iotbx/ncs
===================================================================
--- trunk/iotbx/ncs 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/iotbx/ncs 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/iotbx/ncs
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/iotbx/pdb
===================================================================
--- trunk/iotbx/pdb 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/iotbx/pdb 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/iotbx/pdb
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/iotbx/pdb/remediation
===================================================================
--- trunk/iotbx/pdb/remediation 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/iotbx/pdb/remediation 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/iotbx/pdb/remediation
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/iotbx/regression
===================================================================
--- trunk/iotbx/regression 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/iotbx/regression 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/iotbx/regression
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/iotbx/regression/ncs
===================================================================
--- trunk/iotbx/regression/ncs 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/iotbx/regression/ncs 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/iotbx/regression/ncs
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/iotbx/regression/secondary_structure
===================================================================
--- trunk/iotbx/regression/secondary_structure 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/iotbx/regression/secondary_structure 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/iotbx/regression/secondary_structure
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/iotbx/scalepack
===================================================================
--- trunk/iotbx/scalepack 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/iotbx/scalepack 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/iotbx/scalepack
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/iotbx/shelx
===================================================================
--- trunk/iotbx/shelx 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/iotbx/shelx 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/iotbx/shelx
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/iotbx/solve
===================================================================
--- trunk/iotbx/solve 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/iotbx/solve 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/iotbx/solve
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/iotbx/xds
===================================================================
--- trunk/iotbx/xds 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/iotbx/xds 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/iotbx/xds
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/iotbx/xds/tests
===================================================================
--- trunk/iotbx/xds/tests 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/iotbx/xds/tests 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/iotbx/xds/tests
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/iotbx/xplor
===================================================================
--- trunk/iotbx/xplor 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/iotbx/xplor 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/iotbx/xplor
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/libtbx/bundle
===================================================================
--- trunk/libtbx/bundle 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/libtbx/bundle 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/libtbx/bundle
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/libtbx/command_line
===================================================================
--- trunk/libtbx/command_line 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/libtbx/command_line 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/libtbx/command_line
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/libtbx/development
===================================================================
--- trunk/libtbx/development 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/libtbx/development 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/libtbx/development
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/libtbx/program_utils
===================================================================
--- trunk/libtbx/program_utils 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/libtbx/program_utils 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/libtbx/program_utils
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/libtbx/queuing_system_utils/processing
===================================================================
--- trunk/libtbx/queuing_system_utils/processing 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/libtbx/queuing_system_utils/processing 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/libtbx/queuing_system_utils/processing
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/libtbx/scheduling
===================================================================
--- trunk/libtbx/scheduling 2016-11-09 10:01:34 UTC (rev 25703)
+++ trunk/libtbx/scheduling 2016-11-09 12:44:48 UTC (rev 25704)
Property changes on: trunk/libtbx/scheduling
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/libtbx/server
===================================================================
---...
[truncated message content] |
|
From: <mge...@us...> - 2016-11-09 10:01:36
|
Revision: 25703
http://sourceforge.net/p/cctbx/code/25703
Author: mgerstel
Date: 2016-11-09 10:01:34 +0000 (Wed, 09 Nov 2016)
Log Message:
-----------
We can't rely on subversion global default ignore list. In git files need to be excluded explicitly. After move to git the .gitconfig file can be cleaned up.
Property Changed:
----------------
trunk/
trunk/boost_adaptbx/boost/
trunk/cctbx/
trunk/cctbx/source_generators/
trunk/cctbx/source_generators/eltbx/
trunk/dxtbx/
trunk/dxtbx/model/
trunk/fable/
trunk/gltbx/
trunk/libtbx/
trunk/libtbx/auto_build/
trunk/libtbx/phil/
trunk/libtbx/pythonpath/
trunk/libtbx/pythonpath/optik/
trunk/libtbx/queuing_system_utils/
trunk/scitbx/
trunk/scitbx/array_family/
trunk/scitbx/linalg/
trunk/scitbx/math/
trunk/scitbx/matrix/
trunk/scitbx/random/
trunk/scitbx/source_generators/
trunk/scitbx/source_generators/array_family/
trunk/scitbx/stl/
trunk/smtbx/
trunk/smtbx/source_generators/
Index: trunk
===================================================================
--- trunk 2016-11-09 08:16:58 UTC (rev 25702)
+++ trunk 2016-11-09 10:01:34 UTC (rev 25703)
Property changes on: trunk
___________________________________________________________________
Deleted: svn:global-ignores
## -1 +0,0 ##
-*.pyc
\ No newline at end of property
Index: trunk/boost_adaptbx/boost
===================================================================
--- trunk/boost_adaptbx/boost 2016-11-09 08:16:58 UTC (rev 25702)
+++ trunk/boost_adaptbx/boost 2016-11-09 10:01:34 UTC (rev 25703)
Property changes on: trunk/boost_adaptbx/boost
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cctbx
===================================================================
--- trunk/cctbx 2016-11-09 08:16:58 UTC (rev 25702)
+++ trunk/cctbx 2016-11-09 10:01:34 UTC (rev 25703)
Property changes on: trunk/cctbx
___________________________________________________________________
Modified: svn:ignore
## -1,2 +1,3 ##
doc
dev
+*.pyc
Index: trunk/cctbx/source_generators
===================================================================
--- trunk/cctbx/source_generators 2016-11-09 08:16:58 UTC (rev 25702)
+++ trunk/cctbx/source_generators 2016-11-09 10:01:34 UTC (rev 25703)
Property changes on: trunk/cctbx/source_generators
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/cctbx/source_generators/eltbx
===================================================================
--- trunk/cctbx/source_generators/eltbx 2016-11-09 08:16:58 UTC (rev 25702)
+++ trunk/cctbx/source_generators/eltbx 2016-11-09 10:01:34 UTC (rev 25703)
Property changes on: trunk/cctbx/source_generators/eltbx
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/dxtbx
===================================================================
--- trunk/dxtbx 2016-11-09 08:16:58 UTC (rev 25702)
+++ trunk/dxtbx 2016-11-09 10:01:34 UTC (rev 25703)
Property changes on: trunk/dxtbx
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/dxtbx/model
===================================================================
--- trunk/dxtbx/model 2016-11-09 08:16:58 UTC (rev 25702)
+++ trunk/dxtbx/model 2016-11-09 10:01:34 UTC (rev 25703)
Property changes on: trunk/dxtbx/model
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/fable
===================================================================
--- trunk/fable 2016-11-09 08:16:58 UTC (rev 25702)
+++ trunk/fable 2016-11-09 10:01:34 UTC (rev 25703)
Property changes on: trunk/fable
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/gltbx
===================================================================
--- trunk/gltbx 2016-11-09 08:16:58 UTC (rev 25702)
+++ trunk/gltbx 2016-11-09 10:01:34 UTC (rev 25703)
Property changes on: trunk/gltbx
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/libtbx
===================================================================
--- trunk/libtbx 2016-11-09 08:16:58 UTC (rev 25702)
+++ trunk/libtbx 2016-11-09 10:01:34 UTC (rev 25703)
Property changes on: trunk/libtbx
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/libtbx/auto_build
===================================================================
--- trunk/libtbx/auto_build 2016-11-09 08:16:58 UTC (rev 25702)
+++ trunk/libtbx/auto_build 2016-11-09 10:01:34 UTC (rev 25703)
Property changes on: trunk/libtbx/auto_build
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/libtbx/phil
===================================================================
--- trunk/libtbx/phil 2016-11-09 08:16:58 UTC (rev 25702)
+++ trunk/libtbx/phil 2016-11-09 10:01:34 UTC (rev 25703)
Property changes on: trunk/libtbx/phil
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/libtbx/pythonpath
===================================================================
--- trunk/libtbx/pythonpath 2016-11-09 08:16:58 UTC (rev 25702)
+++ trunk/libtbx/pythonpath 2016-11-09 10:01:34 UTC (rev 25703)
Property changes on: trunk/libtbx/pythonpath
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/libtbx/pythonpath/optik
===================================================================
--- trunk/libtbx/pythonpath/optik 2016-11-09 08:16:58 UTC (rev 25702)
+++ trunk/libtbx/pythonpath/optik 2016-11-09 10:01:34 UTC (rev 25703)
Property changes on: trunk/libtbx/pythonpath/optik
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/libtbx/queuing_system_utils
===================================================================
--- trunk/libtbx/queuing_system_utils 2016-11-09 08:16:58 UTC (rev 25702)
+++ trunk/libtbx/queuing_system_utils 2016-11-09 10:01:34 UTC (rev 25703)
Property changes on: trunk/libtbx/queuing_system_utils
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/scitbx
===================================================================
--- trunk/scitbx 2016-11-09 08:16:58 UTC (rev 25702)
+++ trunk/scitbx 2016-11-09 10:01:34 UTC (rev 25703)
Property changes on: trunk/scitbx
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/scitbx/array_family
===================================================================
--- trunk/scitbx/array_family 2016-11-09 08:16:58 UTC (rev 25702)
+++ trunk/scitbx/array_family 2016-11-09 10:01:34 UTC (rev 25703)
Property changes on: trunk/scitbx/array_family
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/scitbx/linalg
===================================================================
--- trunk/scitbx/linalg 2016-11-09 08:16:58 UTC (rev 25702)
+++ trunk/scitbx/linalg 2016-11-09 10:01:34 UTC (rev 25703)
Property changes on: trunk/scitbx/linalg
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/scitbx/math
===================================================================
--- trunk/scitbx/math 2016-11-09 08:16:58 UTC (rev 25702)
+++ trunk/scitbx/math 2016-11-09 10:01:34 UTC (rev 25703)
Property changes on: trunk/scitbx/math
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/scitbx/matrix
===================================================================
--- trunk/scitbx/matrix 2016-11-09 08:16:58 UTC (rev 25702)
+++ trunk/scitbx/matrix 2016-11-09 10:01:34 UTC (rev 25703)
Property changes on: trunk/scitbx/matrix
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/scitbx/random
===================================================================
--- trunk/scitbx/random 2016-11-09 08:16:58 UTC (rev 25702)
+++ trunk/scitbx/random 2016-11-09 10:01:34 UTC (rev 25703)
Property changes on: trunk/scitbx/random
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/scitbx/source_generators
===================================================================
--- trunk/scitbx/source_generators 2016-11-09 08:16:58 UTC (rev 25702)
+++ trunk/scitbx/source_generators 2016-11-09 10:01:34 UTC (rev 25703)
Property changes on: trunk/scitbx/source_generators
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/scitbx/source_generators/array_family
===================================================================
--- trunk/scitbx/source_generators/array_family 2016-11-09 08:16:58 UTC (rev 25702)
+++ trunk/scitbx/source_generators/array_family 2016-11-09 10:01:34 UTC (rev 25703)
Property changes on: trunk/scitbx/source_generators/array_family
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/scitbx/stl
===================================================================
--- trunk/scitbx/stl 2016-11-09 08:16:58 UTC (rev 25702)
+++ trunk/scitbx/stl 2016-11-09 10:01:34 UTC (rev 25703)
Property changes on: trunk/scitbx/stl
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/smtbx
===================================================================
--- trunk/smtbx 2016-11-09 08:16:58 UTC (rev 25702)
+++ trunk/smtbx 2016-11-09 10:01:34 UTC (rev 25703)
Property changes on: trunk/smtbx
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
Index: trunk/smtbx/source_generators
===================================================================
--- trunk/smtbx/source_generators 2016-11-09 08:16:58 UTC (rev 25702)
+++ trunk/smtbx/source_generators 2016-11-09 10:01:34 UTC (rev 25703)
Property changes on: trunk/smtbx/source_generators
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*.pyc
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From: <mge...@us...> - 2016-11-09 08:16:59
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Revision: 25702
http://sourceforge.net/p/cctbx/code/25702
Author: mgerstel
Date: 2016-11-09 08:16:58 +0000 (Wed, 09 Nov 2016)
Log Message:
-----------
Add global ignore for .pyc to see how this gets converted into git-land
Property Changed:
----------------
trunk/
Index: trunk
===================================================================
--- trunk 2016-11-08 23:19:55 UTC (rev 25701)
+++ trunk 2016-11-09 08:16:58 UTC (rev 25702)
Property changes on: trunk
___________________________________________________________________
Added: svn:global-ignores
## -0,0 +1 ##
+*.pyc
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From: <nwm...@us...> - 2016-11-08 23:19:58
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Revision: 25701
http://sourceforge.net/p/cctbx/code/25701
Author: nwmoriarty
Date: 2016-11-08 23:19:55 +0000 (Tue, 08 Nov 2016)
Log Message:
-----------
better caption for phil param
Modified Paths:
--------------
trunk/mmtbx/monomer_library/pdb_interpretation.py
Modified: trunk/mmtbx/monomer_library/pdb_interpretation.py
===================================================================
--- trunk/mmtbx/monomer_library/pdb_interpretation.py 2016-11-08 19:16:07 UTC (rev 25700)
+++ trunk/mmtbx/monomer_library/pdb_interpretation.py 2016-11-08 23:19:55 UTC (rev 25701)
@@ -151,7 +151,7 @@
.short_caption = Sort atoms in input pdb so they would be in the same order
flip_symmetric_amino_acids = False
.type = bool
- .short_caption = Flip
+ .short_caption = Flip symmetric amino acids to conform to IUPAC convention
.style = hidden
correct_hydrogens = True
.type = bool
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