From: <nat...@us...> - 2012-03-01 23:55:35
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Revision: 14988 http://cctbx.svn.sourceforge.net/cctbx/?rev=14988&view=rev Author: natechols Date: 2012-03-01 23:55:27 +0000 (Thu, 01 Mar 2012) Log Message: ----------- revert r14971 Revision Links: -------------- http://cctbx.svn.sourceforge.net/cctbx/?rev=14971&view=rev Modified Paths: -------------- trunk/mmtbx/kinemage/validation.py trunk/mmtbx/secondary_structure/base_pairing.py trunk/mmtbx/validation/clashscore.py Modified: trunk/mmtbx/kinemage/validation.py =================================================================== --- trunk/mmtbx/kinemage/validation.py 2012-03-01 23:19:37 UTC (rev 14987) +++ trunk/mmtbx/kinemage/validation.py 2012-03-01 23:55:27 UTC (rev 14988) @@ -212,14 +212,10 @@ end_xyz[2]) def make_probe_dots(hierarchy, keep_hydrogens=False): - assert (libtbx.env.has_module(name="reduce") and - libtbx.env.has_module(name="probe")) - reduce_path = libtbx.env.under_build("bin/phenix.reduce") - probe_path = libtbx.env.under_build("bin/phenix.probe") - probe = probe_path + \ - ' -4H -quiet -noticks -nogroup -dotmaster -mc -self "ALL" -' - trim = reduce_path + " -quiet -trim -" - build = reduce_path + " -oh -his -flip -pen9999 -keep -allalt -" + probe = \ + 'phenix.probe -4H -quiet -noticks -nogroup -dotmaster -mc -self "ALL" -' + trim = "phenix.reduce -quiet -trim -" + build = "phenix.reduce -oh -his -flip -pen9999 -keep -allalt -" probe_return = "" for i,m in enumerate(hierarchy.models()): r = pdb.hierarchy.root() Modified: trunk/mmtbx/secondary_structure/base_pairing.py =================================================================== --- trunk/mmtbx/secondary_structure/base_pairing.py 2012-03-01 23:19:37 UTC (rev 14987) +++ trunk/mmtbx/secondary_structure/base_pairing.py 2012-03-01 23:55:27 UTC (rev 14988) @@ -240,8 +240,7 @@ reverted_reduce_output += line+'\n' else: reverted_reduce_output = reduce_output - probe_path = libtbx.env.under_build("bin/phenix.probe") - cmd = probe_path + " " + flags + " -" + cmd = "phenix.probe " + flags + " -" probe_output = easy_run.fully_buffered(cmd, stdin_lines=reverted_reduce_output) return probe_output @@ -267,10 +266,8 @@ def run_reduce(hierarchy, remove_hydrogens=True): #log = sys.stderr - assert (libtbx.env.has_module(name="reduce")) - reduce_path = libtbx.env.under_build("bin/phenix.reduce") - trim = "%s -quiet -trim -" % reduce_path - build = "%s -quiet -build -allalt -" % reduce_path + trim = "phenix.reduce -quiet -trim -" + build = "phenix.reduce -quiet -build -allalt -" input_str = "" pdb_string = hierarchy.as_pdb_string() clean_lines = [] Modified: trunk/mmtbx/validation/clashscore.py =================================================================== --- trunk/mmtbx/validation/clashscore.py 2012-03-01 23:19:37 UTC (rev 14987) +++ trunk/mmtbx/validation/clashscore.py 2012-03-01 23:55:27 UTC (rev 14988) @@ -211,16 +211,12 @@ keep_hydrogens=False): assert (libtbx.env.has_module(name="reduce") and libtbx.env.has_module(name="probe")) - reduce_path = libtbx.env.under_build("bin/phenix.reduce") - probe_path = libtbx.env.under_build("bin/phenix.probe") - self.trim = \ - "%s -quiet -trim -" % reduce_path - self.build = \ - "%s -oh -his -flip -pen9999 -keep -allalt -" % reduce_path + self.trim = "phenix.reduce -quiet -trim -" + self.build = "phenix.reduce -oh -his -flip -pen9999 -keep -allalt -" self.probe_txt = \ - '%s -u -q -mc -het -once "ogt33 not water" "ogt33" -' % probe_path + 'phenix.probe -u -q -mc -het -once "ogt33 not water" "ogt33" -' self.probe_atom_txt = \ - '%s -q -mc -het -dumpatominfo "ogt33 not water" -' % probe_path + 'phenix.probe -q -mc -het -dumpatominfo "ogt33 not water" -' if not keep_hydrogens: h_pdb_string = self.run_reduce(pdb_string) else: This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |