Resolving merging conflict.

apbs/CMakeLists.txt

@@ -59,6 +59,9 @@ message(STATUS "Setting project paths")
 
 set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fPIC")
 set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Werror -fpermissive -fPIC")
+if(WIN32)
+    set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} /STACK:100000000")
+endif()
 if(APPLE AND BUILD_SHARED_LIBS)
   set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -undefined dynamic_lookup")
 endif()

pdb2pqr/pdb2pqr/__main__.py

@@ -0,0 +1,23 @@
+"""PDB2PQR
+
+This package takes a PDB file as input and performs optimizations before
+yielding a new PDB-style file as output.
+
+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
+
+
+_LOGGER = logging.getLogger(__name__)
+logging.captureWarnings(True)
+
+
+if __name__ == "__main__":
+    logging.basicConfig(level=logging.DEBUG)
+    logging.captureWarnings(True)
+    parser = build_parser()
+    args = parser.parse_args()
+    main(args)

pdb2pqr/pdb2pqr/config.py

@@ -45,19 +45,19 @@ FILTER_WARNINGS = ["Skipped atom during water optimization",
 FILTER_WARNINGS_LIMIT = 20
 
 # Expected location for topology definition file
-TOPOLOGY_DEF_PATH = "dat/TOPOLOGY.xml"
+TOPOLOGY_DEF_PATH = "TOPOLOGY.xml"
 
 # Expected location for amino acid topology definition file
-AA_DEF_PATH = "dat/AA.xml"
+AA_DEF_PATH = "AA.xml"
 
 # Expected location for nucleic acid topology definition file
-NA_DEF_PATH = "dat/NA.xml"
+NA_DEF_PATH = "NA.xml"
 
 # Expected location for hydrogens topology definition file
-HYD_DEF_PATH = "dat/HYDROGENS.xml"
+HYD_DEF_PATH = "HYDROGENS.xml"
 
 # Expected location for topology patch definition file
-PATCH_DEF_PATH = "dat/PATCHES.xml"
+PATCH_DEF_PATH = "PATCHES.xml"
 
 # Number of angle steps to scan when debumping
 DEBUMP_ANGLE_STEPS = 72

pdb2pqr/pdb2pqr/input_output.py

@@ -233,9 +233,13 @@ def test_for_file(name, type_):
     test_names = [name, name.upper(), name.lower()]
     test_suffixes = ["", ".%s" % type_.upper(), ".%s" % type_.lower()]
 
+<<<<<<< HEAD
     dat_dir = Path.joinpath(Path(__file__).parents[1], "dat")
     test_dirs = sys_path + [dat_dir, "."]
 
+=======
+    test_dirs = [Path(p).joinpath("pdb2pqr", "dat") for p in sys_path + [Path.cwd()]]
+>>>>>>> setup_branc
     if name.lower() in FORCE_FIELDS:
         name = name.upper()
 
@@ -272,6 +276,16 @@ def test_dat_file(name):
     """
     return test_for_file(name, "DAT")
 
+def test_xml_file(name):
+    """Test for the existence of the forcefield file with a few name permutations.
+
+    Args:
+        name of the xml file
+    Returns:
+        filename or empty string
+    """
+    return test_for_file(name, "xml")
+
 
 def get_pdb_file(name):
     """Obtain a PDB file.

pdb2pqr/pdb2pqr/main.py

@@ -537,3 +537,4 @@ def main(args):
     if args.apbs_input:
         raise NotImplementedError("Missing argument for APBS input file.")
         io.dump_apbs(args.output_pqr)
+

pdb2pqr/setup.py

@@ -0,0 +1,57 @@
+#!/usr/bin/python3
+
+"""
+The use of continuum solvation methods such as APBS requires accurate and complete structural data as well as force field parameters such as atomic charges and radii. 
+Unfortunately, the limiting step in continuum electrostatics calculations is often the addition of missing atomic coordinates to molecular structures from the Protein 
+Data Bank and the assignment of parameters to these structures. To adds this problem, we have developed PDB2PQR. This software 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. These tasks include:
+
+* Adding a limited number of missing heavy (non-hydrogen) atoms to biomolecular structures.
+* Estimating titration states and protonating biomolecules in a manner consistent with favorable hydrogen bonding.
+* Assigning charge and radius parameters from a variety of force fields.
+* Generating "PQR" output compatible with several popular computational modeling and analysis packages.
+
+This service is intended to facilitate the setup and execution of electrostatics calculations for both experts and non-experts and thereby broaden the accessibility of 
+biomolecular solvation and electrostatics analyses to the biomedical community. 
+"""
+
+import sys
+import setuptools
+
+if sys.version_info[:2] < (3,6):
+    raise RuntimeError("Python version >= 3.6 is required.")
+
+with open("README.md", "r") as f:
+    long_description = f.read()
+
+MAJOR = 3
+MINOR = 0
+MICRO = 0
+VERSION = "%d.%d.%d" % (MAJOR, MINOR, MICRO)
+
+setuptools.setup(
+    name = "pdb2pqr",
+    version = VERSION,
+    author = "Baker, Nathan A. et al.",
+    author_email = "nathan.baker@pnnl.gov",
+    description = "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.",
+    long_description = long_description,
+    install_requires = ["propka >= 3.2", "pandas >= 1.0"],
+    url = " https://github.com/Electrostatics/apbs-pdb2pqr/tree/master/pdb2pqr",
+    packages = setuptools.find_packages(exclude = ["pdb2pka", "*.pdb2pka", "pdb2pka.*", "*.pdb2pka.*"]),
+    package_data = {
+        "pdb2pqr": ["dat/*.xml", "dat/*.DAT", "dat/*.names"]
+    },
+    license = "BSD",
+    classifiers = [
+        "Programming Language :: Python :: 3",
+        "License :: BSD",
+        "Operating System :: Microsoft :: Windows",
+        "Operating System :: MacOS",
+        "Operating System :: Linux",
+        "Topic :: Scientific/Engineering :: Bio-Informatics",
+        "Topic :: Scientific/Engineering :: Chemestry"
+    ],
+    keywords = "science chemestry modelcular biology",
+    entry_points = {"console_scripts": "pdb2pqr30 = pdb2pqr.main:main"}
+)

pdb2pqr/tests/propka_test.py

@@ -0,0 +1,26 @@
+"""Tests for PROPKA functionality."""
+import logging
+from pathlib import Path
+import pytest
+import common
+
+
+_LOGGER = logging.getLogger(__name__)
+
+
+@pytest.mark.parametrize("input_pdb", ["1K1I", "1AFS", "1FAS", "5DV8", "5D8V"], ids=str)
+def test_propka_apo(input_pdb, tmp_path):
+    """PROPKA non-regression tests on proteins without ligands."""
+    args = "--log-level=INFO --ff=AMBER --drop-water --titration-state-method=propka"
+    output_pqr = Path(input_pdb).stem + ".pqr"
+    common.run_pdb2pqr(args=args, input_pdb=input_pdb, output_pqr=output_pqr,
+                        tmp_path=tmp_path)
+
+
+# @pytest.mark.parametrize("input_pdb", ["1K1I", "1FAS"], ids=str)
+# def test_propka_apo(input_pdb, tmp_path):
+#     """PROPKA titration of proteins without ligands."""
+#     args = "--log-level=INFO --ff=AMBER --drop-water --titration-state-method=propka"
+#     output_pqr = Path(input_pdb).stem + ".pqr"
+#     run_pdb2pqr(args, input_pdb, output_pqr, tmp_path)
+

pdb2pqr/tests/short_basic_test.py

@@ -8,10 +8,9 @@ import common
 _LOGGER = logging.getLogger(__name__)
 
 
-_LOGGER.error("Need functional and regression test coverage for --userff")
-_LOGGER.error("Need functional and regression test coverage for --usernames")
-_LOGGER.error("Need functional and regression test coverage for --ligand")
-_LOGGER.error("Need functional and regression test coverage for --apbs-input")
+_LOGGER.warning("Need functional and regression test coverage for --userff")
+_LOGGER.warning("Need functional and regression test coverage for --usernames")
+_LOGGER.warning("Need functional and regression test coverage for --apbs-input")
 
 
 @pytest.mark.parametrize("input_pdb", ["1K1I", "1AFS", "1FAS", "5DV8", "5D8V"], ids=str)
@@ -21,53 +20,3 @@ def test_basic_apo(input_pdb, tmp_path):
     output_pqr = Path(input_pdb).stem + ".pqr"
     common.run_pdb2pqr(args=args, input_pdb=input_pdb, output_pqr=output_pqr,
                         tmp_path=tmp_path)
-
-
-@pytest.mark.parametrize("input_pdb", ["1K1I", "1AFS", "1FAS", "5DV8", "5D8V"], ids=str)
-def test_propka_apo(input_pdb, tmp_path):
-    """PROPKA non-regression tests on proteins without ligands."""
-    args = "--log-level=INFO --ff=AMBER --drop-water --titration-state-method=propka"
-    output_pqr = Path(input_pdb).stem + ".pqr"
-    common.run_pdb2pqr(args=args, input_pdb=input_pdb, output_pqr=output_pqr,
-                        tmp_path=tmp_path)
-
-
-# @pytest.mark.parametrize("input_pdb", ["1K1I", "1FAS"], ids=str)
-# def test_propka_apo(input_pdb, tmp_path):
-#     """PROPKA titration of proteins without ligands."""
-#     args = "--log-level=INFO --ff=AMBER --drop-water --titration-state-method=propka"
-#     output_pqr = Path(input_pdb).stem + ".pqr"
-#     run_pdb2pqr(args, input_pdb, output_pqr, tmp_path)
-
-
-# @pytest.mark.parametrize(
-#     "args, input_pdb, input_mol2, output_pqr",
-#     [
-#         pytest.param(
-#             "--log-level=INFO --ff=AMBER",
-#             "1HPX",
-#             common.DATA_DIR / "1HPX-ligand.mol2",
-#             "output.pqr",
-#             id="1HPX-ligand AMBER"
-#         ),
-#         pytest.param(
-#             "--log-level=INFO --ff=AMBER",
-#             common.DATA_DIR / "1QBS.pdb",
-#             common.DATA_DIR / "1QBS-ligand.mol2",
-#             "output.pqr",
-#             id="1QBS-ligand AMBER"
-#         ),
-#         pytest.param(
-#             "--log-level=INFO --ff=AMBER",
-#             common.DATA_DIR / "1US0.pdb",
-#             common.DATA_DIR / "1US0-ligand.mol2",
-#             "output.pqr",
-#             id="1US0-ligand AMBER"
-#         ),
-#     ]
-# )
-# def test_ligand(args, input_pdb, input_mol2, output_pqr, tmp_path):
-#     """Test ligand handling."""
-#     args_ = "{args} --ligand={ligand}".format(args=args, ligand=input_mol2)
-#     run_pdb2pqr(args_, input_pdb, output_pqr, tmp_path)
-#     _LOGGER.warning("This test needs better checking to avoid silent failure.")