Folks,
Decided with prejudice to resolve this as
https://github.com/cctbx/cctbx_project/commit/8268c807a9063ecd59c052ddbe0cff...
Hope this is OK
Cheers Graeme
-----Original Message-----
From: [email protected] [mailto:[email protected]] On Behalf Of [email protected]
Sent: 16 June 2017 08:56
To: [email protected]
Subject: [cctbxbb] Fwd: [git/cctbx] master: Making cif behavior exactly the same as pdb (throwing away SCALE records if crystal_symmetry is supplied to obtain xray_structure). With test. (bdf35cf1c)
Please could people refrain from making cctbx tests dependent on phenix tools?
E.g. not
easy_run.call("phenix.cif_as_pdb %s.cif > junk.out"%prefix)
Obliged in anticipation
Cheers Graeme
Begin forwarded message:
From: CCTBX Commit via DLS Jenkins mailto:[email protected]>
Subject: [git/cctbx] master: Making cif behavior exactly the same as pdb (throwing away SCALE records if crystal_symmetry is supplied to obtain xray_structure). With test. (bdf35cf1c)
Date: 15 June 2017 at 19:43:57 BST
To: mailto:[email protected]>
Reply-To: mailto:[email protected]>
Repository : ssh://g18-sc-serv-04.diamond.ac.uk/cctbx
On branch : master
________________________________
commit bdf35cf1c69d235d2578d915836aad2a739c1c15
Author: Oleg Sobolev mailto:[email protected]>
Date: Thu Jun 15 11:43:52 2017 -0700
Making cif behavior exactly the same as pdb (throwing away SCALE records if crystal_symmetry is supplied to obtain xray_structure). With test.
________________________________
bdf35cf1c69d235d2578d915836aad2a739c1c15
iotbx/pdb/mmcif.py | 24 +++++-----
iotbx/regression/tst_xray_scale.py | 93 ++++++++++++++++++++++++++++++++++++++
iotbx/run_tests.py | 1 +
3 files changed, 107 insertions(+), 11 deletions(-)
diff --git a/iotbx/pdb/mmcif.py b/iotbx/pdb/mmcif.py index 6a5221a6a..2b79df99a 100644
--- a/iotbx/pdb/mmcif.py
+++ b/iotbx/pdb/mmcif.py
@@ -508,17 +508,19 @@ class cif_input(iotbx.pdb.pdb_input_mixin):
return extract_tls_from_cif_block(self.cif_block, hierarchy)
def scale_matrix(self):
- fractionalization_matrix = [
- self.cif_block.get('_atom_sites.fract_transf_matrix[%s][%s]' %(i, j))
- for i,j in ('11', '12', '13', '21', '22', '23', '31','32', '33')]
- if fractionalization_matrix.count(None) == 9:
- return None
- assert fractionalization_matrix.count(None) == 0
- fractionalization_vector = [
- self.cif_block.get('_atom_sites.fract_transf_vector[%s]' %i) for i in '123']
- assert fractionalization_matrix.count(None) == 0
- return [[float(i) for i in fractionalization_matrix],
- [float(i) for i in fractionalization_vector]]
+ if (not hasattr(self, "_scale_matrix")):
+ fractionalization_matrix = [
+ self.cif_block.get('_atom_sites.fract_transf_matrix[%s][%s]' %(i, j))
+ for i,j in ('11', '12', '13', '21', '22', '23', '31','32', '33')]
+ if fractionalization_matrix.count(None) == 9:
+ return None
+ assert fractionalization_matrix.count(None) == 0
+ fractionalization_vector = [
+ self.cif_block.get('_atom_sites.fract_transf_vector[%s]' %i) for i in '123']
+ assert fractionalization_matrix.count(None) == 0
+ self._scale_matrix = [[float(i) for i in fractionalization_matrix],
+ [float(i) for i in fractionalization_vector]]
+ return self._scale_matrix
def model_ids(self):
return flex.std_string([model.id for model in self.hierarchy.models()]) diff --git a/iotbx/regression/tst_xray_scale.py b/iotbx/regression/tst_xray_scale.py
new file mode 100644
index 000000000..e1a4ec9f3
--- /dev/null
+++ b/iotbx/regression/tst_xray_scale.py
@@ -0,0 +1,93 @@
+from __future__ import division
+from libtbx import easy_run
+import iotbx.pdb
+from cctbx import crystal
+from libtbx.test_utils import approx_equal
+
+cif_str="""
+data_5JUP
+#
+_atom_sites.entry_id 5JUP
+_atom_sites.fract_transf_matrix[1][1] 1.000000
+_atom_sites.fract_transf_matrix[1][2] 0.000000
+_atom_sites.fract_transf_matrix[1][3] 0.000000
+_atom_sites.fract_transf_matrix[2][1] 0.000000
+_atom_sites.fract_transf_matrix[2][2] 1.000000
+_atom_sites.fract_transf_matrix[2][3] 0.000000
+_atom_sites.fract_transf_matrix[3][1] 0.000000
+_atom_sites.fract_transf_matrix[3][2] 0.000000
+_atom_sites.fract_transf_matrix[3][3] 1.000000
+_atom_sites.fract_transf_vector[1] 0.00000
+_atom_sites.fract_transf_vector[2] 0.00000
+_atom_sites.fract_transf_vector[3] 0.00000
+#
+loop_
+_atom_type.symbol
+C
+MG
+N
+O
+P
+S
+#
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_entity_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.B_iso_or_equiv
+_atom_site.auth_seq_id
+_atom_site.auth_comp_id
+_atom_site.auth_asym_id
+_atom_site.auth_atom_id
+_atom_site.pdbx_PDB_model_num
+ATOM 9 C "C3'" . U A 1 1 ? 175.229 258.091 229.127 1.00 113.67 1 U A "C3'" 1
+ATOM 7 C "C4'" . U A 1 1 ? 175.388 257.913 227.616 1.00 113.21 1 U A "C4'" 1
+ATOM 6 C "C5'" . U A 1 1 ? 174.124 257.916 226.769 1.00 114.11 1 U A "C5'" 1
+ATOM 10 O "O3'" . U A 1 1 ? 176.253 257.344 229.761 1.00 112.89 1 U A "O3'" 1
+ATOM 8 O "O4'" . U A 1 1 ? 176.291 258.974 227.185 1.00 112.70 1 U A "O4'" 1
+ATOM 5 O "O5'" . U A 1 1 ? 173.735 259.270 226.430 1.00 115.09 1 U A "O5'" 1
+ATOM 3 O OP1 . U A 1 1 ? 174.056 259.302 223.918 1.00 117.16 1 U A OP1 1
+ATOM 4 O OP2 . U A 1 1 ? 172.661 261.090 225.058 1.00 104.87 1 U A OP2 1
+ATOM 1 O OP3 . U A 1 1 ? 171.796 258.709 224.899 1.00 116.23 1 U A OP3 1
+ATOM 2 P P . U A 1 1 ? 173.022 259.610 224.994 1.00 116.34 1 U A P 1
+#
+"""
+
+def run(prefix="iotbx_tst_xray_scale"):
+ """
+ Exercise obtaining exactly the same xray structure from pdb and cif.
+ Caveate is SCALE records (fract_transf_matrix). In pdb they
+explicitly
+ suppressed when crystal_symmetry is supplied, see
+ iotbx/pdb/__init__.py:939 (def xray_structure_simple):
+ if(crystal_symmetry is not None): self._scale_matrix = None
+ """
+ fo = open("%s.cif" % prefix,"w")
+ print >> fo, cif_str
+ fo.close()
+ # crystal symmetry from map
+ cs = crystal.symmetry((419., 419., 419., 90.0, 90.0, 90.0), 1)
+ # xrs from mmCIF
+ cif_inp = iotbx.pdb.input(file_name="%s.cif" % prefix)
+ # print "======== doing xrs from cif =============="
+ xrs_cif = cif_inp.xray_structure_simple(crystal_symmetry = cs)
+ # xrs from PDB
+ easy_run.call("phenix.cif_as_pdb %s.cif > junk.out"%prefix)
+ pdb_inp = iotbx.pdb.input(file_name="%s.pdb" % prefix)
+ # print "======== doing xrs from pdb =============="
+ xrs_pdb = pdb_inp.xray_structure_simple(crystal_symmetry = cs)
+ #
+ assert approx_equal(xrs_cif.sites_cart()[0], xrs_pdb.sites_cart()[0])
+
+if (__name__ == "__main__"):
+ run()
diff --git a/iotbx/run_tests.py b/iotbx/run_tests.py index 52eb3d2e4..9f3e50a98 100644
--- a/iotbx/run_tests.py
+++ b/iotbx/run_tests.py
@@ -93,6 +93,7 @@ tst_list = (
"$D/regression/tst_show_systematic_absences.py",
"$D/regression/tst_miller_sort_asu.py",
"$D/regression/tst_reflection_file_reader.py",
+ "$D/regression/tst_xray_scale.py",
)
def run():
--
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