diff options
Diffstat (limited to 'sci-chemistry/ambertools/files/ambertools-15-update.1.patch')
| -rw-r--r-- | sci-chemistry/ambertools/files/ambertools-15-update.1.patch | 118 |
1 files changed, 118 insertions, 0 deletions
diff --git a/sci-chemistry/ambertools/files/ambertools-15-update.1.patch b/sci-chemistry/ambertools/files/ambertools-15-update.1.patch new file mode 100644 index 000000000..28d25e590 --- /dev/null +++ b/sci-chemistry/ambertools/files/ambertools-15-update.1.patch @@ -0,0 +1,118 @@ +*******> update.1 + +Author: Jason Swails + +Date: June 1, 2015 + +Programs: MMPBSA.py, ParmEd, cpptraj + +Description: This fixes a number of small issues: + 1) Fix Python 2.4 and Python 2.5 support for ParmEd and MMPBSA.py + 2) Fix the MMPBSA.py Python API + 3) Scale charges correctly for LIE action in cpptraj with non-unity + dielectric constant + +-------------------------------------------------------------------------------- + + AmberTools/src/cpptraj/src/Action_LIE.cpp | 2 +- + AmberTools/src/mmpbsa_py/MMPBSA_mods/API.py | 3 ++- + AmberTools/src/mmpbsa_py/MMPBSA_mods/infofile.py | 1 + + AmberTools/src/parmed/chemistry/__init__.py | 6 +++++- + .../test/mmpbsa_py/07_Comprehensive/Run.comprehensive | 18 ++++++++++++++++++ + 5 files changed, 27 insertions(+), 3 deletions(-) + +diff --git AmberTools/src/cpptraj/src/Action_LIE.cpp AmberTools/src/cpptraj/src/Action_LIE.cpp +index 25825c1..716a04f 100644 +--- AmberTools/src/cpptraj/src/Action_LIE.cpp ++++ AmberTools/src/cpptraj/src/Action_LIE.cpp +@@ -132,7 +132,7 @@ int Action_LIE::SetupParms(Topology const& ParmIn) { + atom_charge_.reserve( ParmIn.Natom() ); + for (Topology::atom_iterator atom = ParmIn.begin(); + atom != ParmIn.end(); ++atom) +- atom_charge_.push_back( atom->Charge() * Constants::ELECTOAMBER / dielc_ ); ++ atom_charge_.push_back( atom->Charge() * Constants::ELECTOAMBER / sqrt(dielc_) ); + return 0; + } + +diff --git AmberTools/src/mmpbsa_py/MMPBSA_mods/API.py AmberTools/src/mmpbsa_py/MMPBSA_mods/API.py +index e6c4fe9..d7cc7ec 100644 +--- AmberTools/src/mmpbsa_py/MMPBSA_mods/API.py ++++ AmberTools/src/mmpbsa_py/MMPBSA_mods/API.py +@@ -63,7 +63,7 @@ class mmpbsa_data(dict): + self.stability = app.stability + # Now load the data + for key in app.calc_types: +- if key == 'mutant': ++ if key == 'mutant' or key =='qh': + has_mutant = True + continue + self[key] = {} +@@ -86,6 +86,7 @@ class mmpbsa_data(dict): + if has_mutant: + self.mutant = {} + for key in app.calc_types['mutant']: ++ if key == 'qh': continue + self.mutant[key] = {} + tmpdict = {} + for dkey in app.calc_types['mutant'][key]['complex'].data: +diff --git AmberTools/src/mmpbsa_py/MMPBSA_mods/infofile.py AmberTools/src/mmpbsa_py/MMPBSA_mods/infofile.py +index ecdc2f2..ecaa6c1 100644 +--- AmberTools/src/mmpbsa_py/MMPBSA_mods/infofile.py ++++ AmberTools/src/mmpbsa_py/MMPBSA_mods/infofile.py +@@ -80,6 +80,7 @@ class InfoFile(object): + outfile.write('numframes = %d\n' % self.app.numframes) + outfile.write('numframes_nmode = %d\n' % self.app.numframes_nmode) + outfile.write("mut_str = '%s'\n" % self.app.mut_str) ++ outfile.write('using_chamber = %s\n' % self.app.using_chamber) + outfile.write(self.app.input_file_text) + + def read_info(self, name=None): +diff --git AmberTools/src/parmed/chemistry/__init__.py AmberTools/src/parmed/chemistry/__init__.py +index 52f5245..544e016 100644 +--- AmberTools/src/parmed/chemistry/__init__.py ++++ AmberTools/src/parmed/chemistry/__init__.py +@@ -11,10 +11,14 @@ from chemistry.structure import Structure + from chemistry.topologyobjects import * + from chemistry import unit + from chemistry.residue import * +-from chemistry import amber, charmm, tinker, openmm ++from chemistry import amber, charmm, tinker + from chemistry import formats + load_file = formats.load_file + read_PDB = formats.PDBFile.parse + read_CIF = formats.CIFFile.parse + write_PDB = formats.PDBFile.write + write_CIF = formats.CIFFile.write ++try: ++ from chemistry import openmm ++except ImportError: ++ pass +diff --git AmberTools/test/mmpbsa_py/07_Comprehensive/Run.comprehensive AmberTools/test/mmpbsa_py/07_Comprehensive/Run.comprehensive +index 268515e..aa7d9df 100755 +--- AmberTools/test/mmpbsa_py/07_Comprehensive/Run.comprehensive ++++ AmberTools/test/mmpbsa_py/07_Comprehensive/Run.comprehensive +@@ -108,6 +108,24 @@ if [ -z "$DO_PARALLEL" ]; then + ../../dacdif -a 6.0 FINAL_RESULTS_MMPBSA_2.dat.save FINAL_RESULTS_MMPBSA_2.dat + fi + ++# Check the API ++python << EOF ++from __future__ import division ++import MMPBSA_mods.API as API ++ ++print('Checking the API') ++try: ++ stuff = API.load_mmpbsa_info('_MMPBSA_info') ++ total_data = stuff['gb']['complex']['TOTAL'] ++ if abs((sum(total_data) / len(total_data)) + 466.7565) > 0.0002: ++ print('possible FAILURE') ++ else: ++ print('PASSED') ++except: ++ print('Program error') ++print('==============================================================') ++EOF ++ + $EXE --clean 2>&1 > /dev/null + + rm -f mmpbsa.in mmpbsa.out FINAL_DECOMP_MMPBSA_2.csv-e FINAL_DECOMP_MMPBSA.dat |