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| author | Viktor Drobot | 2021-01-27 20:11:47 +0300 |
|---|---|---|
| committer | Viktor Drobot | 2021-01-27 20:11:47 +0300 |
| commit | 9f18cc64cb379622f8fbc8c11e1ff118f2b6e385 (patch) | |
| tree | 060b42c6250fa90bb171e32db0ee75e256e10826 | |
| parent | 6324f0d79939fbb7f148786e47bd8650da2e1e29 (diff) | |
| download | aur-9f18cc64cb379622f8fbc8c11e1ff118f2b6e385.tar.gz | |
Update 3.1.0
| -rw-r--r-- | .SRCINFO | 13 | ||||
| -rw-r--r-- | PKGBUILD | 19 | ||||
| -rw-r--r-- | fix_entrypoint.patch | 74 | ||||
| -rw-r--r-- | fix_matchedatoms.patch | 34 |
4 files changed, 8 insertions, 132 deletions
@@ -1,22 +1,17 @@ pkgbase = python-pdb2pqr pkgdesc = Automates many of the common tasks of preparing structures for continuum solvation calculations as well as many other types of biomolecular structure modeling, analysis, and simulation. - pkgver = 3.0.1 - pkgrel = 3 + pkgver = 3.1.0 + pkgrel = 1 url = http://pypi.python.org/pypi/pdb2pqr arch = any license = BSD - makedepends = patch depends = python>=3.5 depends = python-propka>=3.2 depends = python-pandas>=1.0 depends = python-pytest>=5.4.1 options = !emptydirs - source = https://files.pythonhosted.org/packages/source/p/pdb2pqr/pdb2pqr-3.0.1.tar.gz - source = fix_entrypoint.patch - source = fix_matchedatoms.patch - sha256sums = 15ac0ce77dc17fb459092aca12cc7c2c070904f77914f1197282e28f418b6bd0 - sha256sums = bb177e8fb9a31f2486e5682ae97139ebf87948fb4dc33dc892e90ff606df7211 - sha256sums = 8708438980e5dda5036d2c4fa404d1817104ebbf0443f7798a2698b75a38fe9c + source = https://files.pythonhosted.org/packages/source/p/pdb2pqr/pdb2pqr-3.1.0.tar.gz + sha256sums = a6f5e2eefbd8bd2a072a89ee4026977de02dadd56e921095afac88d596b63820 pkgname = python-pdb2pqr @@ -2,28 +2,17 @@ pkgname=python-pdb2pqr _name=${pkgname#python-} -pkgver=3.0.1 -pkgrel=3 +pkgver=3.1.0 +pkgrel=1 pkgdesc="Automates many of the common tasks of preparing structures for continuum solvation calculations as well as many other types of biomolecular structure modeling, analysis, and simulation." arch=(any) url="http://pypi.python.org/pypi/${_name}" license=(BSD) depends=('python>=3.5' 'python-propka>=3.2' 'python-pandas>=1.0' 'python-pytest>=5.4.1') -makedepends=(patch) -source=("https://files.pythonhosted.org/packages/source/${_name::1}/${_name}/${_name}-${pkgver}.tar.gz" - "fix_entrypoint.patch" - "fix_matchedatoms.patch") -sha256sums=('15ac0ce77dc17fb459092aca12cc7c2c070904f77914f1197282e28f418b6bd0' - 'bb177e8fb9a31f2486e5682ae97139ebf87948fb4dc33dc892e90ff606df7211' - '8708438980e5dda5036d2c4fa404d1817104ebbf0443f7798a2698b75a38fe9c') +source=("https://files.pythonhosted.org/packages/source/${_name::1}/${_name}/${_name}-${pkgver}.tar.gz") +sha256sums=('a6f5e2eefbd8bd2a072a89ee4026977de02dadd56e921095afac88d596b63820') options=(!emptydirs) -prepare() { - cd "${srcdir}/${_name}-${pkgver}" - patch -Np0 -i "${srcdir}/fix_entrypoint.patch" - patch -Np0 -i "${srcdir}/fix_matchedatoms.patch" -} - build() { cd "${srcdir}/${_name}-${pkgver}" python setup.py build diff --git a/fix_entrypoint.patch b/fix_entrypoint.patch deleted file mode 100644 index cb004817eb72..000000000000 --- a/fix_entrypoint.patch +++ /dev/null @@ -1,74 +0,0 @@ ---- pdb2pqr/__init__.py 2020-07-03 20:02:43.000000000 +0300 -+++ pdb2pqr/__init__.py 2020-08-25 20:48:59.940600307 +0300 -@@ -6,11 +6,11 @@ - For more information, see http://www.poissonboltzmann.org/
- """
- import logging
- from sys import version_info
- assert version_info >= (3, 5)
--from .main import main, build_parser
-+from .main import main_driver, build_parser
-
-
- _LOGGER = logging.getLogger(__name__)
- logging.captureWarnings(True)
-
-@@ -18,6 +18,6 @@ - if __name__ == "__main__":
- logging.basicConfig(level=logging.DEBUG)
- logging.captureWarnings(True)
- parser = build_parser()
- args = parser.parse_args()
-- main(args)
-+ main_driver(args)
---- pdb2pqr/__main__.py 2020-07-03 20:02:43.000000000 +0300 -+++ pdb2pqr/__main__.py 2020-08-25 20:49:15.213902523 +0300 -@@ -6,11 +6,11 @@ - For more information, see http://www.poissonboltzmann.org/
- """
- import logging
- from sys import version_info
- assert version_info >= (3, 5)
--from pdb2pqr.main import main, build_parser
-+from pdb2pqr.main import main_driver, build_parser
-
-
- _LOGGER = logging.getLogger(__name__)
- logging.captureWarnings(True)
-
-@@ -18,6 +18,6 @@ - if __name__ == "__main__":
- logging.basicConfig(level=logging.DEBUG)
- logging.captureWarnings(True)
- parser = build_parser()
- args = parser.parse_args()
-- main(args)
-+ main_driver(args)
---- pdb2pqr/main.py 2020-07-03 20:02:43.000000000 +0300 -+++ pdb2pqr/main.py 2020-08-25 20:50:27.673754924 +0300 -@@ -533,11 +533,11 @@ - lines = io.print_protein_atoms(matched_atoms, args.keep_chain)
-
- return {"lines": lines, "header": header, "missed_residues": missing_atoms}
-
-
--def main(args):
-+def main_driver(args):
- """Main driver for running program from the command line.
-
- Validate inputs, launch PDB2PQR, handle output.
-
- Args:
-@@ -581,5 +581,12 @@ - missing_lines=results["missed_residues"], is_cif=is_cif)
-
- if args.apbs_input:
- raise NotImplementedError("Missing argument for APBS input file.")
- io.dump_apbs(args.output_pqr)
-+
-+
-+def main():
-+ """Hook for command-line usage."""
-+ parser = build_parser()
-+ args = parser.parse_args()
-+ main_driver(args)
diff --git a/fix_matchedatoms.patch b/fix_matchedatoms.patch deleted file mode 100644 index ce1b64135cf0..000000000000 --- a/fix_matchedatoms.patch +++ /dev/null @@ -1,34 +0,0 @@ ---- pdb2pqr/main.py 2020-08-25 20:53:35.000000000 +0300 -+++ pdb2pqr/main.py 2020-08-25 21:15:39.017396736 +0300 -@@ -470,17 +470,16 @@ - hydrogen_routines.optimize_hydrogens()
- hydrogen_routines.cleanup()
-
- _LOGGER.info("Applying force field to biomolecule states.")
- protein.set_states()
-- hitlist, misslist = protein.apply_force_field(forcefield_)
-+ matched_atoms, missing_atoms = protein.apply_force_field(forcefield_)
-
- if args.ligand is not None:
- _LOGGER.info("Processing ligand.")
- _LOGGER.warning("Using ZAP9 forcefield for ligand radii.")
- ligand.assign_parameters()
-- missing_atoms = []
- lig_atoms = []
- for residue in protein.residues:
- tot_charge = 0
- for pdb_atom in residue.atoms:
- # Only check residues with HETATM
-@@ -497,11 +496,11 @@ - "Can't find HETATM {r.name} {r.res_seq} {a.name} "
- "in MOL2 file").format(r=residue, a=pdb_atom)
- _LOGGER.warning(err)
- missing_atoms.append(pdb_atom)
-
-- matched_atoms = hitlist + lig_atoms
-+ matched_atoms += lig_atoms
-
- for residue in protein.residues:
- if not isclose(
- residue.charge, int(residue.charge), abs_tol=CHARGE_ERROR):
- err = (
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