pub_soft/apbs
3
0
Fork 0
mirror of https://github.com/Electrostatics/apbs.git synced 2026-06-04 12:44:23 +08:00
Code Issues Packages Projects Releases Wiki Activity

merged

Browse Source
This commit is contained in:
Leighton W. Wilson
2020-11-10 18:40:03 -05:00
parent 4d693819f8 30acba88ef
commit 72cf0b31bc
102 changed files with 1324 additions and 566 deletions
Download Patch File Download Diff File Expand all files Collapse all files

121
.build.sh
View File

@@ -1,43 +1,92 @@
#!/bin/bash
#export CC=clang
#export CXX=clang
#export CMAKE_C_COMPILER=clang
#export CMAKE_CXX_COMPILER=clang
#export CMAKE_C_LINK_EXECUTABLE=clang
#export CMAKE_CXX_LINK_EXECUTABLE=clang
export BUILD_DIR=build
export CC=gcc
export CXX=g++
#export CMAKE_C_COMPILER=$CC
#export CMAKE_CXX_COMPILER=$CXX
#export CMAKE_C_LINK_EXECUTABLE=$CC
#export CMAKE_CXX_LINK_EXECUTABLE=$CXX
export SRC_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
export COVERAGE="-g -O0 -fprofile-arcs -ftest-coverage"
export COVERAGE=""
export BUILD_DIR="$SRC_DIR/build"
export INSTALL_DIR=$HOME/apbs
export PATH=$INSTALL_DIR:$PATH
export RELEASE_TYPE=Debug
export RELEASE_TYPE=Release
rm -rf $INSTALL_DIR || exit 1
mkdir -p $INSTALL_DIR || exit 1
rm -rf $BUILD_DIR || exit 1
mkdir $BUILD_DIR || exit 1
cd $BUILD_DIR || exit 1
#cmake -S .. -B $BUILD_DIR --trace-source=../CMakeLists.txt --trace-expand \
cmake \
-DCMAKE_INSTALL_PREFIX=$INSTALL_DIR \
-DCMAKE_BUILD_TYPE=$RELEASE_TYPE \
-DENABLE_GEOFLOW=ON \
-DENABLE_BEM=ON \
-DENABLE_FETK=ON \
-DENABLE_OPENMP=ON \
-DENABLE_PBAM=ON \
-DENABLE_PBSAM=ON \
-DENABLE_PYTHON=ON \
-DENABLE_TESTS=ON \
-DENABLE_TINKER=OFF \
-DBUILD_SHARED_LIBS=ON \
-DBUILD_DOC=OFF \
.. || exit 1
# -DCMAKE_C_FLAGS="-fPIC" \
# -DCMAKE_C_FLAGS="--coverage" \
# -DCMAKE_CXX_FLAGS="--coverage" \
VERBOSE=1 make -j 1 || exit 1
VERBOSE=1 make -j 1 install || exit 1
export PATH="$INSTALL_DIR/bin:$PATH"
ctest -C Release --output-on-failure # || exit 1
cpack -C Release -G ZIP || exit
echo "==================================== WHERE AM I ==================================== "
pwd
echo "==================================== VERSIONS: ==================================== "
echo "==================================== PYTHON VERSION"
python -c "import sys; print(sys.version)"
echo "==================================== CMAKE VERSION"
cmake --version
echo "==================================== C Compiler VERSION"
$CMAKE_C_COMPILER --version
echo "==================================== C++ Compiler VERSION"
$CMAKE_CXX_COMPILER --version
echo "==================================== SWIG VERSION"
swig -version
echo "==================================== Install Python requirements ==================================== "
pip3 install -U pip
pip3 install -U pytest
pip3 install -U virtualenv
pip3 install -U numpy
pip3 install -r requirements.txt
# Just build APBS for now
echo "==================================== PWD FOR TOP DIR ==================================== "
pwd
echo "==================================== Get External SubModules ==================================== "
git submodule init
git submodule update
echo "==================================== BUILD =============================================== "
rm -rf $BUILD_DIR || exit 1
rm -rf $INSTALL_DIR || exit 1
mkdir -p $BUILD_DIR || exit 1
mkdir -p $INSTALL_DIR || exit 1
# Build pybind11
pushd $(pwd)/externals/pybind11
[ -d build ] || mkdir -p build
[ -d install ] || mkdir -p install
pushd build
cmake \
-DDOWNLOAD_CATCH=ON \
-DPYBIND11_TEST=OFF \
-DCMAKE_INSTALL_PREFIX=$(python3 -c "import os,sys; print(os.path.realpath(sys.argv[1]))" ../install) \
..
make -j install
popd
export pybind11_DIR=$(python3 -c "import os,sys; print(os.path.realpath(sys.argv[1]))" ./install)
popd
cd $BUILD_DIR || exit 1
#cmake -S .. -B $BUILD_DIR --trace-source=../CMakeLists.txt --trace-expand \
cmake \
-DBUILD_DOC=OFF \
-DBUILD_SHARED_LIBS=OFF \
-DCMAKE_C_FLAGS="${CMAKE_C_FLAGS} ${COVERAGE}" \
-DCMAKE_CXX_FLAGS="${CMAKE_CXX_FLAGS} ${COVERAGE}" \
-DCMAKE_BUILD_TYPE=$RELEASE_TYPE \
-DCMAKE_INSTALL_PREFIX=$INSTALL_DIR \
-DENABLE_BEM=ON \
-DENABLE_GEOFLOW=ON \
-DENABLE_FETK=ON \
-DENABLE_OPENMP=ON \
-DENABLE_PBAM=ON \
-DENABLE_PBSAM=ON \
-DENABLE_PYTHON=OFF \
-DENABLE_TESTS=ON \
-DENABLE_TINKER=OFF \
.. || exit 1
VERBOSE=1 make -j 1 || exit 1
VERBOSE=1 make -j 1 install #|| exit 1
export PATH="$INSTALL_DIR/bin:$PATH"
# Run a single test if it fails using the following:
# ctest -VV -R pbam_test
ctest -C Release --output-on-failure #|| exit 1
cpack -C Release -G ZIP || exit 1
unzip -l APBS*.zip

29
.github/workflows/build.yml vendored
View File

@@ -10,6 +10,7 @@ jobs:
runs-on: ${{ matrix.os }}
if: "!contains(github.event.head_commit.message, 'noci')"
strategy:
fail-fast: false
matrix:
# os: [ubuntu-latest]
# os: [macOS-latest]
@@ -34,33 +35,7 @@ jobs:
apt-get: bison flex swig libreadline-dev
- name: Build and Install
run: |
echo "==================================== WHERE AM I ==================================== "
pwd
echo "==================================== VERSIONS: ==================================== "
echo "==================================== PYTHON VERSION"
python -c "import sys; print(sys.version)"
echo "==================================== CMAKE VERSION"
cmake --version
echo "==================================== Gcc VERSION"
gcc --version
echo "==================================== G++ VERSION"
g++ --version
echo "==================================== SWIG VERSION"
swig -version
echo "==================================== Install Python requirements ==================================== "
pip3 install -U pip
pip3 install -U pytest
pip3 install -U virtualenv
pip3 install -U numpy
pip3 install -r requirements.txt
# Just build APBS for now
echo "==================================== PWD FOR TOP DIR ==================================== "
pwd
echo "==================================== Get External SubModules ==================================== "
git submodule init
git submodule update
echo "==================================== BUILD =============================================== "
./.build.sh
env:
# https://codecov.io/gh/Electrostatics/apbs-pdb2pqr
# https://codecov.io/gh/Electrostatics/apbs
CODECOV_TOKEN: "e3a1e24c-5598-4f47-9353-7fa0ac57f98e"

3
.gitignore vendored
View File

@@ -152,3 +152,6 @@ examples
# Output files
*.out
# Personal notes
NOTES.txt

7
.gitmodules vendored
View File

@@ -11,6 +11,7 @@
[submodule "externals/bem"]
path = externals/bem
url = https://github.com/Treecodes/TABI-PB.git
[submodule "externals/pb_solvers"]
path = externals/pb_solvers
url = https://github.com/Electrostatics/pb_solvers
[submodule "externals/pybind11"]
path = externals/pybind11
url = https://github.com/pybind/pybind11
ignore = all

41
CMakeLists.txt
View File

@@ -57,10 +57,13 @@ OPTION(BUILD_SHARED_LIBS "Build shared libraries." OFF)
################################################################################
message(STATUS "Setting project paths")
set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fPIC")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Werror -fpermissive -fPIC")
set(CMAKE_CXX_STANDARD 17)
if(WIN32)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -W4")
set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} /STACK:100000000")
else()
set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fPIC")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wpedantic -fpermissive -fPIC")
endif()
if(APPLE AND BUILD_SHARED_LIBS)
set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -undefined dynamic_lookup")
@@ -122,8 +125,7 @@ set(SYS_LIBPATHS /usr/lib64)
################################################################################
# Debian/Ubuntu hack for #
# https://github.com/Electrostatics/apbs-pdb2pqr/issues/364 #
# Debian/Ubuntu hack #
################################################################################
if(EXISTS "/etc/debian_version" AND
"${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
@@ -301,6 +303,13 @@ if(ENABLE_MPI)
endif()
endif()
################################################################################
# Handle the finite element solver dependencies #
################################################################################
option(ENABLE_FETK "Enable the finite element solver" OFF)
################################################################################
# Deal with MALOC #
# Note that we depend exclusively on the MALOC that is in our external FETK #
@@ -316,16 +325,10 @@ if(NOT ENABLE_FETK)
${EXTERNALS_PATH}/fetk/maloc/src/psh)
list(APPEND APBS_LIB_DIRS ${EXTERNALS_PATH}/fetk/maloc/lib)
list(APPEND APBS_LIBS maloc)
endif()
################################################################################
# Handle the finite element solver dependencies #
################################################################################
option(ENABLE_FETK "Enable the finite element solver" OFF)
if(ENABLE_FETK)
if (WIN32)
list(APPEND MALOC_LIBS wsock32 WS2_32)
endif()
else()
if(WIN32)
message(FATAL_ERROR "FETK will not built on Windows because it uses autotools!")
else()
@@ -392,8 +395,7 @@ if(ENABLE_FETK)
vf2c
tetgen
triangle
readline
termcap)
readline)
if(BUILD_SHARED_LIBS)
install(DIRECTORY ${install_dir}/lib/
@@ -469,6 +471,9 @@ if(ENABLE_PBAM)
ExternalProject_Get_Property(pbam binary_dir)
add_definitions(-DENABLE_PBAM)
list(APPEND APBS_LIB_DIRS "${binary_dir}/pbam/src")
if (WIN32)
list(APPEND APBS_LIB_DIRS "${binary_dir}/pbam/src/${CMAKE_BUILD_TYPE}")
endif()
list(APPEND APBS_LIBS PBAMLib)
include_directories(${EXTERNALS_PATH}/pb_s_am/pbam/src)
include_directories(${EXTERNALS_PATH}/pb_s_am/pb_shared/src)
@@ -709,7 +714,7 @@ if(CYGWIN)
endif()
if(NOT CYGWIN AND NOT MINGW AND WIN32)
list(APPEND APBS_LIBS wsock32)
list(APPEND APBS_LIBS wsock32 WS2_32)
ADD_DEFINITIONS("/D _CRT_SECURE_NO_WARNINGS")
endif()
@@ -828,7 +833,7 @@ set(CPACK_PACKAGE_VERSION_PATCH "${CMAKE_MICRO_VERSION}")
# NOTE: The following is tempting but does not work!
# set(FULL_PACKAGE_NAME "${PACKAGE_NAME}-${MAJOR_VERSION}.${MINOR_VERSION}.${MICRO_VERSION}")
set(CPACK_PACKAGE_VENDOR "PNNL")
set(CPACK_PACKAGE_CONTACT "APBS - https://github.com/Electrostatics/apbs-pdb2pqr")
set(CPACK_PACKAGE_CONTACT "APBS - https://github.com/Electrostatics/apbs")
set(CPACK_PACKAGE_FILE_NAME "${PACKAGE_NAME}-${APBS_VERSION}.${CMAKE_HOST_SYSTEM_NAME}")
set(CPACK_STRIP_FILES True)

101
apbs/chemistry/atom.py
View File

@@ -1,4 +1,4 @@
from typing import List, Union
from typing import Union
import numpy as np
from apbs.geometry import Coordinate
@@ -16,40 +16,87 @@ class Atom:
name (str): Atom name from PDB/PDR file
"""
def __init__(self, *vals: List[float]):
if len(vals) > 0:
self.position = Coordinate(*vals)
else:
self.position = Coordinate()
self.radius: float = 0.0
self.charge: float = 0.0
self.partID: float = 0.0
self.epsilon: float = 0.0
self.id: int = 0
self.res_name: str = ""
self.name: str = ""
def __init__(self, *args, **kwargs):
"""
Arguments:
:param int id: A unique identifier for this Atom
:param str field_name: Specifies the type of PQR entry and should either
be ATOM or HETATM in order to be parsed by APBS.
:param int atom_number: The atom index.
:param str atom_name: The atom name.
:param str residue_name: The residue name.
:param str chain_id: An optional value which provides the chain ID of
the atom. NOTE: that chain ID support is a new
feature of APBS 0.5.0 and later versions.
:param int residue_number: The residue index.
:param str ins_code: An optional value which provides the PDB insertion code.
:param float x: The X atomic coordinate in angstroms
:param float y: The Y atomic coordinate in angstroms
:param float z: The Z atomic coordinate in angstroms
:param float charge: The atomic charge (in electrons).
:param float radius: The atomic radius (in angstroms).
:Example:
atom = Atom(
id=42,
field_name=ATOM,
atom_number=39,
atom_name=O3PB,
residue_name=ADP,
chain_id=None,
residue_number=1,
ins_code=None,
x=-16.362,
y=-6.763,
z=26.980,
charge=-0.900,
radius=1.700
)
"""
if len(args) > 0:
self.position = Coordinate(args[0], args[1], args[2])
self.field_name: str = kwargs.get("field_name", None)
self.atom_number: int = int(kwargs.get("atom_number", 0))
self.atom_name: str = kwargs.get("atom_name", None)
self.residue_name: str = kwargs.get("residue_name", None)
self.chain_id: str = kwargs.get("chain_id", None)
self.residue_number: int = int(kwargs.get("residue_number", 0))
self.ins_code: str = kwargs.get("ins_code", None)
if "x" in kwargs and "y" in kwargs and "z" in kwargs:
self.position = Coordinate(
float(kwargs.get("x")),
float(kwargs.get("y")),
float(kwargs.get("z")),
)
self.charge: float = float(kwargs.get("charge", 0.0))
self.radius: float = float(kwargs.get("radius", 0.0))
self.epsilon: float = float(kwargs.get("epsilon", 0.0))
self.id: int = int(kwargs.get("id", 0))
if "id" not in kwargs:
raise ValueError("The Atom id must be set to non-zero value")
def __str__(self):
return "Atom< name< %s >, %s, radius< %s >, charge< %s >>" % (
self.name,
self.position,
self.radius,
self.charge,
)
return f"Atom< name< {self.field_name} >, {self.position}, radius< {self.radius} >, charge< {self.charge} > >"
def __repr__(self):
return "Atom< name< %s >, %s radius< %s >, charge< %s >>" % (
self.name,
self.position,
self.radius,
self.charge,
)
return f"Atom< name< {self.field_name} >, {self.position}, radius< {self.radius} >, charge< {self.charge} > >"
def euclidian_dist2(
self, other: Union["Atom", Coordinate, np.ndarray]
) -> float:
"""
Euclidian distance without the square root
:param other: Another Atom, Coordinate, or np.ndarray to calculate
the euclidian distance from this Atom (without taking
the square root)
:type other: Atom, Coordinate, or np.ndarray
:return: The euclidian distance between two X,Y,Z coordinates
:rtype: float
"""
if isinstance(other, Atom):
return np.sum((self.position._data - other.position._data) ** 2)
@@ -60,9 +107,7 @@ class Atom:
# https://numpy.org/doc/stable/reference/generated/numpy.dot.html
return np.sum((self.position._data - other) ** 2)
else:
raise RuntimeError(
"Incorrect data type passed into euclidian_dist2"
)
raise TypeError
@property
def x(self) -> float:

33
apbs/chemistry/atom_complex_calc.py
View File

@@ -1,4 +1,4 @@
import math
import numpy as np
import sys # noqa
from apbs.geometry import (
@@ -15,9 +15,7 @@ from . import (
class AtomComplexCalc:
"""
Port of Vacc
"""
"""Port of Vacc."""
def __init__(
self, alist: AtomList, clist: CellList, surface_density: float
@@ -34,8 +32,8 @@ class AtomComplexCalc:
self.alist = alist
self.surface_density = surface_density
max_radius = alist.max_radius + clist.max_radius
max_area = 4.0 * (max_radius ** 2) * math.pi
nsphere = math.ceil(max_area * surface_density)
max_area = 4.0 * (max_radius ** 2) * np.pi
nsphere = np.ceil(max_area * surface_density)
# TODO: calculate reference shpere (see VaccSurf_refSphere)
@@ -43,7 +41,7 @@ class AtomComplexCalc:
def stride(self) -> Coordinate:
return self.clist.stride
def accessable_outside_inflated_venderwalls(
def accessible_outside_inflated_vdw_radius(
self, center: Coordinate, radius: float, atom_id_to_ignore: int
) -> bool:
"""
@@ -58,8 +56,7 @@ class AtomComplexCalc:
"""
if radius > self.clist.max_radius:
raise RuntimeError(
"Got radius %f greater than max radius %f from"
" cell list." % (radius, self.clist.max_radius)
f"Got radius {radius} greater than max radius {self.clist.max_radius} from cell list."
)
c = (center - self.lower_corner) / self.stride
@@ -84,8 +81,11 @@ class AtomComplexCalc:
"""Create a new surface from the points that do fall on the reference
surface.
:param atom: Atom from which surface will be constructed.
:param Atom atom: Atom from which surface will be constructed.
:param Surface ref: The reference surface.
:param float prad: The previous radius
:return: Returns surface generated from the atom.
:rtype: Surface
.. note:: Although this seems like a candidate for a static method, the
`accessable_outside_inflated_venderwalls_rad` method of this class
@@ -95,7 +95,7 @@ class AtomComplexCalc:
arad = atom.radius
apos = atom.position
atomID = atom.id
atom_id = atom.id
surf: Surface
if arad < Constants.very_small_eps:
@@ -112,9 +112,7 @@ class AtomComplexCalc:
pos.z = rad(ref.zs[i]) + apos.z
# need to implement
if self.accessable_outside_inflated_venderwalls_rad(
pos, prad, atomID
):
if self.accessible_outside_inflated_vdw_radius(pos, prad, atom_id):
npoints += 1
ref.is_on_surf[i] = True
else:
@@ -127,12 +125,7 @@ class AtomComplexCalc:
surf.coords[-1].is_on_surf = True
surf.area = (
4.0
* math.pi
* rad
* rad
* float(surf.npoints)
/ float(ref.npoints)
4.0 * np.pi * rad * rad * float(surf.npoints) / float(ref.npoints)
)
return surf

66
apbs/chemistry/atom_list.py
View File

@@ -1,4 +1,5 @@
from math import inf
import numpy as np
from typing import List
from . import Atom
from apbs.geometry import Coordinate
from typing import Tuple
@@ -6,43 +7,53 @@ from typing import Tuple
class AtomList:
"""
Thin abstraction over a container of atoms
Thin abstraction over a container of atoms.
Attributes:
dp (dict): dict for dynamic programming of values that may not need to
be re-calculated
"""
def __init__(self, filename: str = None, atoms=None):
def __init__(self, atoms: List = None):
"""
Construct a list of Atoms.
:param List atoms: A list of Atoms
"""
self._atoms: Tuple[Atom] = atoms if atoms is not None else []
self.charge: float = None
self.maxrad: float = None
self._center = Coordinate()
self._mincrd = Coordinate()
self._maxcrd = Coordinate()
self._min_coord = Coordinate()
self._max_coord = Coordinate()
self._dp = dict()
if filename is not None:
self.read_pdb(filename)
def center(self) -> Coordinate:
"""Molecule center
note: not the median molecule, but the average of the max values int
the x, y, and z coordinates
:return: The center Coordinate
:rtype: Coordinate
"""
if "center" not in self._dp.keys():
ma = self.maxcrd()
mi = self.mincrd()
ma = self.max_coord()
mi = self.min_coord()
self._dp["center"] = Coordinate(
(ma.x + mi.x) * 0.5, (ma.y + mi.y) * 0.5, (ma.z + mi.z) * 0.5,
(ma.x + mi.x) * 0.5,
(ma.y + mi.y) * 0.5,
(ma.z + mi.z) * 0.5,
)
return self._dp["center"]
def mincrd(self) -> Coordinate:
def min_coord(self) -> Coordinate:
"""Minimum coordinates
:return: The minimum Coordinate
:rtype: Coordinate
"""
if "min" not in self._dp.keys():
x, y, z = inf, inf, inf
x, y, z = np.inf, np.inf, np.inf
for a in self._atoms:
x = min(x, a.x)
y = min(y, a.y)
@@ -51,8 +62,10 @@ class AtomList:
return self._dp["min"]
def maxcrd(self) -> Coordinate:
def max_coord(self) -> Coordinate:
"""Maximum coordinates
:return: The maximum Coordinate
:rtype: Coordinate
"""
if "max" not in self._dp.keys():
x, y, z = 0.0, 0.0, 0.0
@@ -81,30 +94,3 @@ class AtomList:
@property
def atoms(self) -> Tuple[Atom]:
return self._atoms
def read_pdb(self, fn: str):
"""
Read serialized atoms in the PBD format from a file
"""
with open(fn, "r") as f:
lines = f.readlines()
idx = 0
for line in lines:
fields = [
idx.lower() for idx in line.strip().split(" ") if idx != ""
]
if fields[0] in ("atom", "hetatm"):
a = Atom()
a.name = fields[2].upper()
a.res_name = fields[3].upper()
a.position = Atom(
float(fields[5]), float(fields[6]), float(fields[7]),
)
a.id = idx
if len(fields) == 10:
a.charge = float(fields[8])
a.radius = float(fields[9])
self._atoms.append(a)
idx += 1

24
apbs/geometry/sphere.py
View File

@@ -1,4 +1,4 @@
import math
import numpy as np
from . import Surface, SurfacePoint
@@ -16,32 +16,32 @@ class Sphere:
s: Surface
frac = npoints / 4.0
ntheta = math.ceil(math.sqrt(math.pi * frac))
dtheta = math.pi / float(ntheta)
ntheta = np.ceil(np.sqrt(np.pi * frac))
dtheta = np.pi / float(ntheta)
nphimax = 2 * ntheta
# Count number of points to be used
nactual: int = 0
for i in range(ntheta):
theta = dtheta * float(i)
sintheta = math.sin(theta)
costheta = math.cos(theta)
nphi = math.ceil(sintheta * nphimax)
sintheta = np.sin(theta)
costheta = np.cos(theta)
nphi = np.ceil(sintheta * nphimax)
nactual += nphi
s = Surface(1.0, nactual)
nactual = 0
for i in range(ntheta):
theta = dtheta * float(i)
sintheta = math.sin(theta)
costheta = math.cos(theta)
nphi = math.ceil(sintheta * nphimax)
sintheta = np.sin(theta)
costheta = np.cos(theta)
nphi = np.ceil(sintheta * nphimax)
if nphi != 0:
dphi = 2 * math.pi / float(nphi)
dphi = 2 * np.pi / float(nphi)
for j in range(nphi):
phi = dphi * float(j)
sinphi = math.sin(phi)
cosphi = math.cos(phi)
sinphi = np.sin(phi)
cosphi = np.cos(phi)
s[nactual] = SurfacePoint(
cosphi * sintheta,
sinphi * sintheta,

26
apbs/grid/grid.py
View File

@@ -1,11 +1,10 @@
from typing import List, Optional
from apbs.geometry import Coordinate, Constants
import math
import numpy as np
class CurvatureFlag:
"""Enum class to replace curvature flags in original source
"""
"""Enum class to replace curvature flags in original source"""
ReducedMaximalCurvature = 0
MeanCurvature = 1
@@ -70,12 +69,12 @@ class Grid:
)
hi = Coordinate(
int(math.ceil(tmp.x)), int(math.ceil(tmp.y)), int(math.ceil(tmp.z))
int(np.ceil(tmp.x)), int(np.ceil(tmp.y)), int(np.ceil(tmp.z))
)
lo = Coordinate(
int(math.floor(tmp.x)),
int(math.floor(tmp.y)),
int(math.floor(tmp.z)),
int(np.floor(tmp.x)),
int(np.floor(tmp.y)),
int(np.floor(tmp.z)),
)
hi.x = (
@@ -137,7 +136,7 @@ class Grid:
ret_value = sum(ret_value)
if ret_value == math.nan:
if ret_value == np.nan:
# TODO: Add a more descriptive error
raise RuntimeError(
"Value routine failed to converge with the following "
@@ -169,24 +168,21 @@ class Grid:
...
def integrate(self) -> float:
"""Get the integral of the data
"""
"""Get the integral of the data"""
...
def norml1(self) -> float:
r"""Get the \f$L_1\f$ norm of the data. This returns the integral:
\f[ \| u \|_{L_1} = \int_\Omega | u(x) | dx \f]
\f[ \| u \|_{L_1} = \int_\Omega | u(x) | dx \f]
"""
...
def norml2(self) -> float:
r"""Computes the \f$L_2\f$ norm of the data.
"""
r"""Computes the \f$L_2\f$ norm of the data."""
...
def norml_inf(self) -> float:
r"""Computes the \f$L_\infty\f$ norm of the data.
"""
r"""Computes the \f$L_\infty\f$ norm of the data."""
...
def seminormH1(self) -> float:

7
apbs/multigrid/multigrid.py
View File

@@ -22,4 +22,11 @@ class MultiGrid:
def set_part(
self, lower_corner: Coordinate, upper_corner: Coordinate
) -> None:
"""
:param lower_corner: The X,Y,Z coordinates in angstroms
:type lower_corner: Coordinate
:param upper_corner: The X,Y,Z coordinates in angstroms
:type upper_corner: Coordinate
"""
# TODO: This needs to be implemented
pass

1
apbs/pqr/__init__.py Normal file
View File

@@ -0,0 +1 @@
from .reader import PQRReader # noqa F401

89
apbs/pqr/reader.py Normal file
View File

@@ -0,0 +1,89 @@
from pyparsing import Group, Literal, Word, ZeroOrMore, alphas, alphanums, nums
from apbs.chemistry import Atom, AtomList
class PQRReader:
"""A grammar/parser for PQR formatted data and files."""
def __init__(self):
"""Define the grammar for an ATOM/HETATM in PQR format."""
identifier = Word(alphas, alphanums + "_")
integer_val = Word(nums + "-")
float_val = Word(nums + "-" + ".")
keyword_val = Literal("ATOM") | Literal("HETATM")
atom_value = Group(
keyword_val("field_name")
+ integer_val("atom_number")
+ identifier("atom_name")
+ identifier("residue_name")
+ ZeroOrMore(identifier("chain_id"))
+ integer_val("residue_number")
+ ZeroOrMore(identifier("ins_code"))
+ float_val("x")
+ float_val("y")
+ float_val("z")
+ float_val("charge")
+ float_val("radius")
)
self.atom = atom_value + ZeroOrMore(atom_value)
def loads(self, pqr_string: str) -> AtomList:
"""
Find instances of atoms ignoring other syntax.
:param str pqr_string: One or more ATOM/HETATM
:return: the list of Atoms in the pqr_string
:rtype: AtomList
"""
atoms = []
idx: int = 1
for item, _start, _stop in self.atom.scanString(pqr_string):
for match in item:
atom = Atom(
field_name=match.field_name,
atom_number=int(match.atom_number),
atom_name=match.atom_name,
residue_name=match.residue_name,
chain_id=match.chain_id,
residue_number=int(match.residue_number),
ins_code=match.ins_code,
x=float(match.x),
y=float(match.y),
z=float(match.z),
charge=float(match.charge),
radius=float(match.radius),
id=int(idx),
)
atoms.append(atom)
idx += 1
return AtomList(atoms)
def load(self, filename: str) -> AtomList:
"""
Read Atoms from a file in PQR format
:param str filename: The path/filename to the PQR file
:return: the list of Atoms in the pqr file
:rtype: AtomList
"""
with open(filename, "r") as fp:
data = fp.read().replace("\n", "")
return self.loads(data)
if __name__ == "__main__":
# execute only if run as a script
sample = r"""
REMARK This is just test data and values may have been modified for testing
ATOM 5226 HD1 TYR 337 -24.642 -2.718 30.187 0.115 1.358
ATOM 7 CD LYS D 1 44.946 37.289 9.712 -0.0608 1.9080
ATOM 39 O3PB ADP 1 -16.362 -6.763 26.980 -0.900 1.700
REMARK This is just a comment hiding in the data
HETATM 39 O3PB ADP 1 -16.362 -6.763 26.980 -0.900 1.700
ATOM 39 O3PB ADP 1 D -16.362 -6.763 26.980 -0.900 1.700
"""
reader = PQRReader()
atoms = []
atoms = reader.loads(sample)
print(atoms)

17
apbs/test/test_chemistry/test_atom.py
View File

@@ -6,11 +6,16 @@ import pytest
class TestAtom:
def test_ctor(self):
sut = Atom(0, 0, 0)
sut = Atom(id=1, x=0, y=0, z=0)
assert (sut.position._data == np.array((0, 0, 0))).all()
def test_atom_exception(self):
"""test that exception is raised for invalid atoms"""
with pytest.raises(ValueError):
assert Atom(0, 0, 0)
def test_property_get(self):
sut = Atom(1, 2, 3)
sut = Atom(id=1, x=1, y=2, z=3)
assert sut.x == 1
assert sut.y == 2
assert sut.z == 3
@@ -25,8 +30,8 @@ class TestAtom:
)
def test_euclidian_distance_atom(self, params1, params2):
expect = np.sum((np.array(params1) - np.array(params2)) ** 2)
a = Atom(*params1)
b = Atom(*params2)
a = Atom(id=1, *params1)
b = Atom(id=2, *params2)
assert a.euclidian_dist2(b) == expect
@pytest.mark.parametrize(
@@ -39,7 +44,7 @@ class TestAtom:
)
def test_euclidian_distance_array(self, params1, params2):
expect = np.sum((np.array(params1) - np.array(params2)) ** 2)
a = Atom(*params1)
a = Atom(id=1, *params1)
assert a.euclidian_dist2(np.array(params2)) == expect
@pytest.mark.parametrize(
@@ -52,6 +57,6 @@ class TestAtom:
)
def test_euclidian_distance_array2(self, params1, params2):
expect = np.sum((np.array(params1) - np.array(params2)) ** 2)
a = Atom(*params1)
a = Atom(id=1, *params1)
b = Coordinate(*params2)
assert a.euclidian_dist2(b) == expect

82
apbs/test/test_chemistry/test_atom_list.py
View File

@@ -1,14 +1,16 @@
from apbs.geometry import Coordinate
from apbs.chemistry import AtomList, CellList
import pytest
from apbs.chemistry import Atom, AtomList
from apbs.pqr import PQRReader
from pytest import approx, fixture
@pytest.fixture()
def pdb_file(tmp_path):
@fixture
def get_atom_list(tmp_path) -> AtomList:
"""Return the AtomList from the file generated."""
fp = tmp_path / "atom.pdb"
fqpn = tmp_path / "atom.pdb"
with open(fp, "w") as f:
with open(fqpn, "w") as f:
f.write(
"HETATM 1 C ALK 1 "
"1.000 4.000 7.000 0.000 1.000\n"
@@ -21,51 +23,51 @@ def pdb_file(tmp_path):
"HETATM 1 C ALK 1 "
"3.000 6.000 9.000 0.000 3.000\n"
)
return fp
reader = PQRReader()
return reader.load(fqpn)
class TestAtomList:
def test_read_pdb(self, pdb_file: str):
def test_atom_list(get_atom_list: AtomList):
sut = AtomList(pdb_file)
assert len(sut._atoms) == 3
sut = get_atom_list
assert sut.count == 3
a = sut._atoms[0]
assert a.name == "C"
assert a.res_name == "ALK"
assert a.position.x == 1.0
assert a.position.y == 4.0
assert a.position.z == 7.0
assert a.charge == 0.0
assert a.radius == 1.0
a: Atom = sut._atoms[0]
assert a.atom_name == "C"
assert a.residue_name == "ALK"
assert a.x == 1.0
assert a.y == 4.0
assert a.z == 7.0
assert 0.0 == approx(a.charge)
assert 1.0 == approx(a.radius)
def test_min(self, pdb_file: str):
sut = AtomList(pdb_file)
def test_min(get_atom_list: AtomList):
lo: Coordinate = sut.mincrd()
assert lo.x == 1.0
assert lo.y == 4.0
assert lo.z == 7.0
sut = get_atom_list
def test_max(self, pdb_file: str):
lo: Coordinate = sut.min_coord()
assert lo.x == approx(1.0)
assert lo.y == approx(4.0)
assert lo.z == approx(7.0)
sut = AtomList(pdb_file)
hi: Coordinate = sut.maxcrd()
assert hi.x == 3.0
assert hi.y == 6.0
assert hi.z == 9.0
def test_max(get_atom_list: AtomList):
def test_center(self, pdb_file: str):
sut = get_atom_list
sut = AtomList(pdb_file)
hi: Coordinate = sut.max_coord()
assert hi.x == 3.0
assert hi.y == 6.0
assert hi.z == 9.0
mi: Coordinate = sut.center()
assert mi.x == 2.0
assert mi.y == 5.0
assert mi.z == 8.0
def test_max_radius(self, pdb_file: str):
sut = CellList(pdb_file)
assert sut.max_radius == 3.0
def test_center(get_atom_list: AtomList):
sut = get_atom_list
mi: Coordinate = sut.center()
assert mi.x == 2.0
assert mi.y == 5.0
assert mi.z == 8.0

11
apbs/test/test_chemistry/test_cell_list.py
View File

@@ -1,9 +1,10 @@
from apbs.chemistry import CellList
from apbs.test.test_chemistry.test_atom_list import TestAtomList, pdb_file
# from apbs.test.test_chemistry.test_atom_list import TestAtomList
import pytest
class TestCellList(TestAtomList):
@pytest.mark.skip(reason="Needs test")
def test_cell_list_method(self):
pass
# class TestCellList(TestAtomList):
# @pytest.mark.skip(reason="Needs test")
# def test_cell_list_method(self):
# pass

1
apbs/test/test_geometry/test_sphere.py
View File

@@ -1,4 +1,5 @@
from apbs.geometry import Sphere
from apbs.geometry import Surface
import pytest

1
apbs/test/test_pqr/__init__.py Normal file
View File

@@ -0,0 +1 @@
from apbs.test.test_pqr.test_pqrreader import * # noqa F401

31
apbs/test/test_pqr/test_pqrreader.py Normal file
View File

@@ -0,0 +1,31 @@
import pathlib
from apbs.chemistry.atom_list import AtomList
from apbs.pqr import PQRReader
class TestPQRReader:
def test_ctor(self):
sut = PQRReader()
sample = r"""
ATOM 5226 HD1 TYR 337 -24.642 -2.718 30.187 0.115 1.358
ATOM 7 CD LYS D 1 44.946 37.289 9.712 -0.0608 1.9080
REMARK This is just a comment hiding in the data
HETATM 39 O3PB ADP 1 -16.362 -6.763 26.980 -0.900 1.700
ATOM 39 O3PB ADP 1 D -16.362 -6.763 26.980 -0.900 1.700
REMARK The next line is incorrect on purpose (e.g. ATAM instead of ATOM)
ATAM 39 O3PB ADP 1 D -16.362 -6.763 26.980 -0.900 1.700
"""
atomlist: AtomList = sut.loads(sample)
for idx in range(1):
assert abs(atomlist.atoms[idx].x - -24.642) < 0.001
assert int(atomlist.atoms[idx].x) == -24
print(atomlist.atoms)
def test_load(self):
sut = PQRReader()
pqr_imput = (
pathlib.Path(__file__).parent.parent.parent.parent.absolute()
/ "examples/actin-dimer/mol1.pqr"
)
atomlist: AtomList = sut.load(pqr_imput)
assert len(atomlist.atoms) == 5861

122
appveyor.yml
View File

@@ -9,11 +9,16 @@ image:
clone_folder: c:\projects\source
clone_depth: 5
clone_depth: 2
environment:
PYTHON: "C:\\Python37-x64"
APPVEYOR_RDP_PASSWORD: "RedRum666!"
artifacts:
- path: '**\APBS*.zip'
name: APBS.zip
matrix:
fast_finish: false
@@ -21,24 +26,31 @@ matrix:
# - C:\ProgramData\chocolatey\bin -> appveyor.yml # swig.exe
# - C:\ProgramData\chocolatey\lib -> appveyor.yml # supporting swig Lib files.
# For interactive debugging using Remote Desktop, you need the init, on_finish, and APPVEYOR_RDP_PASSWORD
# - https://www.appveyor.com/docs/how-to/rdp-to-build-worker/
# init:
# - ps: iex ((new-object net.webclient).DownloadString('https://raw.githubusercontent.com/appveyor/ci/master/scripts/enable-rdp.ps1'))
# on_finish:
# - ps: $blockRdp = $true; iex ((new-object net.webclient).DownloadString('https://raw.githubusercontent.com/appveyor/ci/master/scripts/enable-rdp.ps1'))
install:
# Install non-python dependencies using chocolatey package manager
# - choco install tools\windows\swig.4.0.0.nupkg --yes --limit-output
- IF NOT EXIST C:\ProgramData\chocolatey\bin\swig.exe choco install --ignorechecksum -f -r -y swig --version=4.0.0
# - type C:\ProgramData\chocolatey\logs\chocolatey.log
# - type C:\ProgramData\chocolatey\logs\chocolatey.log
- where /r C:\ProgramData\chocolatey swig.swg
- SET SWIG_DIR=C:\ProgramData\chocolatey\lib\swig\tools\install
- SET SWIG_EXECUTABLE=C:\ProgramData\chocolatey\lib\swig\tools\install\swig.exe
- "SET PATH=%PYTHON%;%PYTHON%\\Scripts;C:\\Program Files (x86)\\CMake\\bin;%PATH%;C:\\projects\\source\\build\\bin;C:\\ProgramData\\chocolatey\\lib\\swig\\tools\\install;C:\\ProgramData\\chocolatey\\bin;%PATH%"
# - swig -swiglib
- "SET SWIG_DIR=C:\\ProgramData\\chocolatey\\lib\\swig\\tools\\install"
- "SET SWIG_EXECUTABLE=C:\\ProgramData\\chocolatey\\lib\\swig\\tools\\install\\swig.exe"
# Add SWIG, Python, and CMake to PATH
- SET PATH=%PYTHON%;%PYTHON%\Scripts;C:\Program Files (x86)\CMake\bin;C:\projects\source\build\bin;C:\ProgramData\chocolatey\lib\swig\tools\install;C:\ProgramData\chocolatey\bin;%PATH%
- echo %PATH%
# Check that we have the expected version and architecture for Python
- where /r C:\Python37-x64 python.exe
- python --version
- python -m pip install --upgrade pip
# Install the build dependencies of the project. If some dependencies contain
@@ -47,27 +59,91 @@ install:
# target Python version and architecture
- pip.exe install -r c:\projects\source\requirements.txt
build_script:
- cmd: >-
# Setup Visual Studio Environment for compiling, linking, and logging
- set MSBuildLogger="C:\Program Files\AppVeyor\BuildAgent\Appveyor.MSBuildLogger.dll"
- call "C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\Common7\Tools\vsdevcmd\core\vsdevcmd_start.bat"
- call "C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Auxiliary\Build\vcvars64.bat"
git submodule init
# set
# REM set VSDIR="C:\Program Files (x86)\Microsoft Visual Studio"
# set VSDIR="C:\"
# FOR /F "tokens=* USEBACKQ" %F IN (`where /r %VSDIR% vsdevcmd_start.bat`) DO (SET vsdevcmd="%F")
# REM Should be something like C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\Common7\Tools\vsdevcmd\core\vsdevcmd_start.bat"
# ECHO "VS DEV CMD BAT FILE = %vsdevcmd%"
# call %vsdevcmd%
# FOR /F "tokens=* USEBACKQ" %F IN (`where /r %VSDIR% vsvars64.bat`) DO (SET vsdevcmd="%F")
# REM Should be something like "C:\Program Files (x86)\Microsoft Visual Studio\2017\Community\VC\Auxiliary\Build\vcvars64.bat"
# ECHO "VS VARS FILE = %vsdevcmd%"
# call %vsdevcmd%
git submodule update
# Get the external projects configured
- cd c:\projects\source
- git submodule init
- git submodule update
cd c:\projects\source
- echo "*****************************************************************************"
- echo PYBIND11_BUILD
- echo "*****************************************************************************"
- set pybind11_DIR=C:\projects\source\externals\pybind11\install
- cd externals/pybind11
- mkdir build
- mkdir install
- cd build
mkdir build
- echo "*****************************************************************************"
- echo PYBIND11_CONFIGURE
- echo "*****************************************************************************"
- cmake .. -DCMAKE_INSTALL_PREFIX=%pybind11_DIR% -DDOWNLOAD_CATCH=ON
cd build
- echo "*****************************************************************************"
- echo PYBIND11_MAKE_INSTALL
- echo "*****************************************************************************"
# cmake --build . --config Release --parallel 1 --target install -- /m:1 /v:diag /logger:%MSBuildLogger%
- cmake --build . --config Release --parallel 1 --target install -- /m:1 /logger:%MSBuildLogger%
cmake -DCMAKE_BUILD_TYPE=Release -DBUILD_TESTING=ON -DBUILD_TOOLS=ON -DCHECK_EPSILON=ON -DENABLE_BEM=ON -DENABLE_GEOFLOW=ON -DENABLE_INLINE=ON -DENABLE_PBAM=OFF -DENABLE_PYTHON=ON -DENABLE_TESTS=ON -DENABLE_VERBOSE_DEBUG=ON -DGET_NanoShaper=ON -G "Visual Studio 16 2019" -A x64 c:\projects\source
- set pybind11_DIR=C:\projects\source\externals\pybind11\install\share\cmake\pybind11
- cd ..
- cd c:\projects\source
- mkdir build
- cd build
cat c:\projects\source\build\CMakeFiles\CMakeError.log
- echo "*****************************************************************************"
- echo APBS_CONFIG
- echo "*****************************************************************************"
- cmake --config Release -DPYBIND11_DIR=%pybind11_DIR% -DCMAKE_BUILD_TYPE=Release -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DBUILD_TESTING=ON -DBUILD_TOOLS=ON -DCHECK_EPSILON=ON -DENABLE_FETK=OFF -DENABLE_BEM=ON -DENABLE_GEOFLOW=ON -DENABLE_INLINE=ON -DENABLE_PBAM=ON -DENABLE_PYTHON=OFF -DENABLE_TESTS=ON -DBUILD_SHARED_LIBS=OFF -DENABLE_VERBOSE_DEBUG=ON -DGET_NanoShaper=ON -G "Visual Studio 16 2019" -A x64 c:\projects\source
cmake --build . --config "Release"
- echo "*****************************************************************************"
- echo APBS_CMAKE_OUTPUT
- echo "*****************************************************************************"
- if exist c:\projects\source\build\CMakeFiles\CMakeOutput.log type c:\projects\source\build\CMakeFiles\CMakeOutput.log
ctest -C Release --verbose --output-on-failure
- echo "*****************************************************************************"
- echo APBS_CMAKE_ERROR
- echo "*****************************************************************************"
- if exist c:\projects\source\build\CMakeFiles\CMakeError.log type c:\projects\source\build\CMakeFiles\CMakeError.log
cpack -C Release -G ZIP
- echo "*****************************************************************************"
- echo APBS_MAKE_INSTALL
- echo "*****************************************************************************"
- cmake --build . --config Release --parallel 1 --target install -- /m:1 /logger:%MSBuildLogger%
unzip -l APBS*.zip
- echo "*****************************************************************************"
- echo APBS_TEST
- echo "*****************************************************************************"
- ctest -C Release --verbose --output-on-failure
- echo "*****************************************************************************"
- echo APBS_PACKAGE
- echo "*****************************************************************************"
- cpack -C Release -G ZIP
- unzip -l APBS*.zip
- echo "*****************************************************************************"
- echo APBS_DONE
- echo "*****************************************************************************"
on_failure:
- if exist c:\projects\source\build\CMakeFiles\CMakeOutput.log type c:\projects\source\build\CMakeFiles\CMakeOutput.log
- if exist c:\projects\source\build\CMakeFiles\CMakeError.log type c:\projects\source\build\CMakeFiles\CMakeError.log

8
docs/getting/source.rst
View File

@@ -180,6 +180,14 @@ Building the code - advanced
# NOTE: In case you need to debug the source code:
# export RELEASE_TYPE=Debug
export RELEASE_TYPE=Release
# NOTE: If cmake or make fail, save yourself and make sure your remove
# everything including the build directory. This code base uses
# many older autoconf based projects that do not know how to save
# state or recover from partial builds. If cmake or make fail, you
# should figure out how to fix it and then remove everything and
# try again.
rmdir $APBS_BUILD_DIR
mkdir -p $APBS_BUILD_DIR
cd $APBS_BUILD_DIR
# NOTE: In case you need to debug cmake, use verbose debug/trace mode:
# cmake -S .. -B $BUILD_DIR --trace-source=../CMakeLists.txt --trace-expand \

7
docs/help.rst
View File

@@ -17,13 +17,6 @@ Announcements
Announcements about updates to the APBS-PDB2PQR software and related news are available through our `mailing list <http://us11.campaign-archive1.com/home/?u=a5808042b2b3ea90ee3603cd8&id=28701e36f0>`_; please `register for updates <http://eepurl.com/by4eQr>`_.
-----------------
Old mailing lists
-----------------
We continue to monitor the `pdb2pqr-users <https://sourceforge.net/p/pdb2pqr/mailman/pdb2pqr-users/>`_ and `apbs-users <https://sourceforge.net/p/apbs/mailman/apbs-users/>`_ mailing lists.
However, we are in the process of phasing out these mailing lists (due to high spam content) in favor of user support through `GitHub issues`_.
----------------------
Contacting the authors
----------------------

3
docs/requirements.txt Normal file
View File

@@ -0,0 +1,3 @@
sphinx
sphinx_rtd_theme
sphinx_sitemap

6
examples/FKBP/1d7h-dmso-mol.in
View File

@@ -1,9 +1,5 @@
##########################################################################
### 1D7H/DMSO BINDING ENERGY
### $Id$
###
### Please see APBS documentation (http://apbs.sourceforge.net/doc/) for
### syntax help.
# 1D7H/DMSO BINDING ENERGY
##########################################################################
read

6
examples/FKBP/1d7h-dmso-smol.in
View File

@@ -1,9 +1,5 @@
##########################################################################
### 1D7H/DMSO BINDING ENERGY
### $Id$
###
### Please see APBS documentation (http://apbs.sourceforge.net/doc/) for
### syntax help.
# 1D7H/DMSO BINDING ENERGY
##########################################################################
read

6
examples/FKBP/1d7i-dss-mol.in
View File

@@ -1,9 +1,5 @@
##########################################################################
### 1D7I/DSS BINDING ENERGY
### $Id$
###
### Please see APBS documentation (http://apbs.sourceforge.net/doc/) for
### syntax help.
# 1D7I/DSS BINDING ENERGY
##########################################################################
read

6
examples/FKBP/1d7i-dss-smol.in
View File

@@ -1,9 +1,5 @@
##########################################################################
### 1D7I/DSS BINDING ENERGY
### $Id$
###
### Please see APBS documentation (http://apbs.sourceforge.net/doc/) for
### syntax help.
# 1D7I/DSS BINDING ENERGY
##########################################################################
read

6
examples/actin-dimer/apbs-mol-auto.in
View File

@@ -1,9 +1,5 @@
##########################################################################
### ACTIN DIMER BINDING ENERGY
### $Id$
###
### Please see APBS documentation (http://apbs.sourceforge.net/doc/) for
### syntax help.
# ACTIN DIMER BINDING ENERGY
##########################################################################
read

6
examples/actin-dimer/apbs-mol-parallel.in
View File

@@ -1,9 +1,5 @@
#########################################################################/smo
### ACTIN DIMER BINDING ENERGY
### $Id$
###
### Please see APBS documentation (http://apbs.sourceforge.net/doc/) for
### syntax help.
# ACTIN DIMER BINDING ENERGY
##########################################################################
read

6
examples/actin-dimer/apbs-smol-auto.in
View File

@@ -1,9 +1,5 @@
##########################################################################
### ACTIN DIMER BINDING ENERGY
### $Id$
###
### Please see APBS documentation (http://apbs.sourceforge.net/doc/) for
### syntax help.
# ACTIN DIMER BINDING ENERGY
##########################################################################
read

6
examples/actin-dimer/apbs-smol-parallel.in
View File

@@ -1,9 +1,5 @@
##########################################################################
### ACTIN DIMER BINDING ENERGY
### $Id$
###
### Please see APBS documentation (http://apbs.sourceforge.net/doc/) for
### syntax help.
# ACTIN DIMER BINDING ENERGY
##########################################################################
read

4
examples/bem-binding-energy/1d30.in
View File

@@ -14,14 +14,14 @@ elec name comp_solv # Solvated complex
pdie 1.0 # Solute dielectric
sdie 80.00 # Solvent dielectric
srad 1.4 # Solvent probe radius
sdens 5 # NO. of Elements per A^2
sdens 1.76 # NO. of Elements per A^2
temp 298.00 # Temperature
tree_order 3 # taylor expansion order
tree_n0 500 # maxium particle per leaf
mac 0.8 # multipole acceptance criterion
mesh skin # mesh options: ses, skin. Options ses and skin require nonoshaper.
mesh ses # mesh options: ses, skin. Options ses and skin require nonoshaper.
outdata 0 # outdata (0 - dat file, 1 - dat and VTK file)
end

4
examples/bem-binding-energy/1d30_monomer1.in
View File

@@ -14,14 +14,14 @@ elec name comp_solv # Solvated complex
pdie 1.0 # Solute dielectric
sdie 80.00 # Solvent dielectric
srad 1.4 # Solvent probe radius
sdens 5 # NO. of Elements per A^2
sdens 1.76 # NO. of Elements per A^2
temp 298.00 # Temperature
tree_order 3 # taylor expansion order
tree_n0 500 # maxium particle per leaf
mac 0.8 # multipole acceptance criterion
mesh skin # mesh options: ses, skin. Options ses and skin require nonoshaper.
mesh ses # mesh options: ses, skin. Options ses and skin require nonoshaper.
outdata 0 # outdata (0 - dat file, 1 - dat and VTK file)
end

4
examples/bem-binding-energy/1d30_monomer2.in
View File

@@ -14,14 +14,14 @@ elec name comp_solv # Solvated complex
pdie 1.0 # Solute dielectric
sdie 80.00 # Solvent dielectric
srad 1.4 # Solvent probe radius
sdens 5 # NO. of Elements per A^2
sdens 1.76 # NO. of Elements per A^2
temp 298.00 # Temperature
tree_order 3 # taylor expansion order
tree_n0 500 # maxium particle per leaf
mac 0.8 # multipole acceptance criterion
mesh skin # mesh options: ses, skin. Options ses and skin require nonoshaper.
mesh ses # mesh options: ses, skin. Options ses and skin require nonoshaper.
outdata 0 # outdata (0 - dat file, 1 - dat and VTK file)
end

9
examples/bem-binding-energy/README.md
View File

@@ -16,9 +16,6 @@ More details are available on the APBS website contributions section.
Input File| APBS Version| Result (kJ/mol)| Expected (kJ/mol)
---|---|---|---
[1d30.in](1d30.in)| **3.0**| **-21961.965**| **-21961.946**
| | 1.5| -21961.983|
[1d30_monomer1.in](1d30_monomer1.in)| **3.0**| **-26075.345**| **-26075.316**
| | 1.5| -26075.357|
[1d30_monomer2.in](1d30_monomer2.in)| **3.0**| **-762.105**| **-762.103**
| | 1.5| -762.103|
[1d30.in](1d30.in)| **3.0**| **-22113.098**| **-22113.098**
[1d30_monomer1.in](1d30_monomer1.in)| **3.0**| **-26225.275**| **-26225.275**
[1d30_monomer2.in](1d30_monomer2.in)| **3.0**| **-779.948**| **-779.948**

4
examples/bem-pKa/2LZT-ASH66.in
View File

@@ -14,14 +14,14 @@ elec name comp_solv # Solvated complex
pdie 20.0 # Solute dielectric
sdie 78.54 # Solvent dielectric
srad 1.4 # Solvent probe radius
sdens 10 # NO. of Elements per A^2
sdens 2.47 # NO. of Elements per A^2
temp 298.00 # Temperature
tree_order 3 # taylor expansion order
tree_n0 500 # maxium particle per leaf
mac 0.8 # multipole acceptance criterion
mesh skin # mesh options: ses, skin. Options ses and skin require nonoshaper.
mesh ses # mesh options: ses, skin. Options ses and skin require nonoshaper.
outdata 0 # outdata (0 - dat file, 1 - dat and VTK file)
end

4
examples/bem-pKa/2LZT-ASP66.in
View File

@@ -14,14 +14,14 @@ elec name comp_solv # Solvated complex
pdie 20.0 # Solute dielectric
sdie 78.54 # Solvent dielectric
srad 1.4 # Solvent probe radius
sdens 10 # NO. of Elements per A^2
sdens 2.47 # NO. of Elements per A^2
temp 298.00 # Temperature
tree_order 3 # taylor expansion order
tree_n0 500 # maxium particle per leaf
mac 0.8 # multipole acceptance criterion
mesh skin # mesh options: ses, skin. Options ses and skin require nonoshaper.
mesh ses # mesh options: ses, skin. Options ses and skin require nonoshaper.
outdata 0 # outdata (0 - dat file, 1 - dat and VTK file)
end

4
examples/bem-pKa/2LZT-noASH66.in
View File

@@ -14,14 +14,14 @@ elec name comp_solv # Solvated complex
pdie 20.0 # Solute dielectric
sdie 78.54 # Solvent dielectric
srad 1.4 # Solvent probe radius
sdens 10 # NO. of Elements per A^2
sdens 2.47 # NO. of Elements per A^2
temp 298.00 # Temperature
tree_order 3 # taylor expansion order
tree_n0 500 # maxium particle per leaf
mac 0.8 # multipole acceptance criterion
mesh skin # mesh options: ses, skin. Options ses and skin require nonoshaper.
mesh ses # mesh options: ses, skin. Options ses and skin require nonoshaper.
outdata 0 # outdata (0 - dat file, 1 - dat and VTK file)
end

4
examples/bem-pKa/2LZT-noASP66.in
View File

@@ -14,14 +14,14 @@ elec name comp_solv # Solvated complex
pdie 20.0 # Solute dielectric
sdie 78.54 # Solvent dielectric
srad 1.4 # Solvent probe radius
sdens 10 # NO. of Elements per A^2
sdens 2.47 # NO. of Elements per A^2
temp 298.00 # Temperature
tree_order 3 # taylor expansion order
tree_n0 500 # maxium particle per leaf
mac 0.8 # multipole acceptance criterion
mesh skin # mesh options: ses, skin. Options ses and skin require nonoshaper.
mesh ses # mesh options: ses, skin. Options ses and skin require nonoshaper.
outdata 0 # outdata (0 - dat file, 1 - dat and VTK file)
end

4
examples/bem-pKa/ASH66.in
View File

@@ -14,14 +14,14 @@ elec name comp_solv # Solvated complex
pdie 20.0 # Solute dielectric
sdie 78.54 # Solvent dielectric
srad 1.4 # Solvent probe radius
sdens 10 # NO. of Elements per A^2
sdens 10 # NO. of Elements per A^2
temp 298.00 # Temperature
tree_order 3 # taylor expansion order
tree_n0 500 # maxium particle per leaf
mac 0.8 # multipole acceptance criterion
mesh skin # mesh (1 - NanoShaper SES, 2 - NanoShaper Skin)
mesh ses # mesh options: ses, skin. Options ses and skin require nonoshaper.
outdata 0 # outdata (0 - dat file, 1 - dat and VTK file)
end

4
examples/bem-pKa/ASP66.in
View File

@@ -14,14 +14,14 @@ elec name comp_solv # Solvated complex
pdie 20.0 # Solute dielectric
sdie 78.54 # Solvent dielectric
srad 1.4 # Solvent probe radius
sdens 10 # NO. of Elements per A^2
sdens 10 # NO. of Elements per A^2
temp 298.00 # Temperature
tree_order 3 # taylor expansion order
tree_n0 500 # maxium particle per leaf
mac 0.8 # multipole acceptance criterion
mesh 2 # mesh (1 - NanoShaper SES, 2 - NanoShaper Skin)
mesh ses # mesh options: ses, skin. Options ses and skin require nonoshaper.
outdata 0 # outdata (0 - dat file, 1 - dat and VTK file)
end

9
examples/bem-pKa/README.md
View File

@@ -19,9 +19,6 @@ http://www.poissonboltzmann.org/examples/Lysozyme_pKa_example/
File Input| APBS Version| Result (kJ/mol)| Expected (kJ/mol)
---|---|---|---
[ASH66.in](ASH66.in)| **3.0**| **-4.165**| **-4.165**
| 1.5| -4.165|
[2LTZ-ASH66.in](2LTZ-ASH66.in)| **3.0**| **-360.665**| **-360.665**
| 1.5| -360.665|
[2LTZ-noASH66.in](2LTZ-noASH66.in)| **3.0**| **-359.870**| **-359.870**
| 1.5| -359.870|
[ASH66.in](ASH66.in)| **3.0**| **-4.026**| **-4.026**
[2LTZ-ASH66.in](2LTZ-ASH66.in)| **3.0**| **-369.020**| **-369.020**
[2LTZ-noASH66.in](2LTZ-noASH66.in)| **3.0**| **-367.795**| **-367.795**

2
examples/bem/1a63_msms.in
View File

@@ -21,7 +21,7 @@ elec name comp_solv # Solvated complex
tree_n0 500 # maxium particle per leaf
mac 0.8 # multipole acceptance criterion
mesh skin # mesh options: ses, skin. Options ses and skin require nonoshaper.
mesh ses # mesh options: ses, skin. Options ses and skin require nonoshaper.
outdata 1 # outdata (0 - dat file, 1 - dat and VTK file)
end

11
examples/bem/README.md
View File

@@ -6,12 +6,11 @@ TABI-PB to solve the PBE. BEMs have the characteristic that only the boundary of
domain has to be discretized. This is particularly useful for problems in which the data
of interest is at the boundary of the solution.
This directory contains five example .in files.
This directory contains four example .in files.
Three examples calculate surface potentials for 1a63 in a 0.15 M salt solution:
1. 1a63_msms.in uses MSMS to create a solvent excluded surface (SES) triangulation.
2. 1a63_NanoShaper_SES.in uses NanoShaper to create an SES triangulation.
3. 1a63_NanoShaper_Skin.in uses NanoShaper to create a Skin surface triangulation.
Two examples calculate surface potentials for 1a63 in a 0.15 M salt solution:
1. 1a63_NanoShaper_SES.in uses NanoShaper to create an SES triangulation.
2. 1a63_NanoShaper_Skin.in uses NanoShaper to create a Skin surface triangulation.
Two examples calculate surface potentials for 451c in a 0.15 M salt solution:
1. 451c_order1.in uses a 1st order Taylor series expansion for the treecode.
@@ -22,7 +21,7 @@ More details on TABI-PB are available on the APBS website contributions section.
Input File| APBS Version| Result (kJ/mol) | Expected (kJ/mol)
---|---|---|---
[451c_order1.in](451c_order1.in)| **3.0**| **-4907.470**| -4907.443
[451c_order1.in](451c_order1.in)| **3.0**| **-4907.441**| -4907.443
| | 1.5| -4907.455|
[451c_order5.in](451c_order5.in)| **3.0**| **-4920.112**| -4920.133
| | 1.5| -4920.091|

6
examples/born/apbs-apolar.in
View File

@@ -1,9 +1,5 @@
#############################################################################
### BORN ION SOLVATION ENERGY
### $Id: apbs.in 996 2006-11-27 19:21:40Z sdg0919 $
###
### Please see APBS documentation (http://apbs.sourceforge.net/doc/) for
### input file syntax.
# BORN ION SOLVATION ENERGY
#############################################################################
# READ IN MOLECULES

6
examples/born/apbs-forces.in
View File

@@ -1,9 +1,5 @@
#############################################################################
### BORN ION SOLVATION ENERGY
### $Id: apbs-mol-auto.in 1119 2007-07-23 13:52:03Z sobolevnrm $
###
### Please see APBS documentation (http://apbs.sourceforge.net/doc/) for
### input file sytax.
# BORN ION SOLVATION ENERGY
#############################################################################
# READ IN MOLECULES

6
examples/born/apbs-mol-auto.in
View File

@@ -1,9 +1,5 @@
#############################################################################
### BORN ION SOLVATION ENERGY
### $Id$
###
### Please see APBS documentation (http://apbs.sourceforge.net/doc/) for
### input file sytax.
# BORN ION SOLVATION ENERGY
#############################################################################
# READ IN MOLECULES

6
examples/born/apbs-mol-fem-extmesh.in
View File

@@ -1,9 +1,5 @@
#############################################################################
### BORN ION SOLVATION ENERGY -- FE method
### $Id: apbs-mol-fem.in 1026 2006-12-29 16:02:16Z sobolevnrm $
###
### Please see APBS documentation (http://apbs.sourceforge.net/doc/) for
### input file sytax.
# BORN ION SOLVATION ENERGY -- FE method
#############################################################################
read
mol pqr ion.pqr

6
examples/born/apbs-mol-fem.in
View File

@@ -1,9 +1,5 @@
#############################################################################
### BORN ION SOLVATION ENERGY -- FE method
### $Id$
###
### Please see APBS documentation (http://apbs.sourceforge.net/doc/) for
### input file sytax.
# BORN ION SOLVATION ENERGY -- FE method
#############################################################################
read
mol pqr ion.pqr

6
examples/born/apbs-mol-parallel.in
View File

@@ -1,9 +1,5 @@
#############################################################################
### BORN ION SOLVATION ENERGY
### $Id$
###
### Please see APBS documentation (http://apbs.sourceforge.net/doc/) for
### input file sytax.
# BORN ION SOLVATION ENERGY
#############################################################################
# READ IN MOLECULES

6
examples/born/apbs-smol-auto.in
View File

@@ -1,9 +1,5 @@
#############################################################################
### BORN ION SOLVATION ENERGY
### $Id$
###
### Please see APBS documentation (http://apbs.sourceforge.net/doc/) for
### input file sytax.
# BORN ION SOLVATION ENERGY
#############################################################################
# READ IN MOLECULES

6
examples/born/apbs-smol-fem.in
View File

@@ -1,9 +1,5 @@
#############################################################################
### BORN ION SOLVATION ENERGY -- FE method
### $Id$
###
### Please see APBS documentation (http://apbs.sourceforge.net/doc/) for
### input file sytax.
# BORN ION SOLVATION ENERGY -- FE method
#############################################################################
read
mol pqr ion.pqr

6
examples/born/apbs-smol-parallel.in
View File

@@ -1,9 +1,5 @@
#############################################################################
### BORN ION SOLVATION ENERGY
### $Id: apbs-smol-parallel.in 1346 2009-02-10 21:11:14Z sdg0919 $
###
### Please see APBS documentation (http://apbs.sourceforge.net/doc/) for
### input file sytax.
# BORN ION SOLVATION ENERGY
#############################################################################
# READ IN MOLECULES

6
examples/hca-bind/apbs-mol.in
View File

@@ -1,9 +1,5 @@
##########################################################################
### HCA/ACETAZOLAMIDE BINDING
### $Id$
###
### Please see APBS documentation (http://apbs.sourceforge.net/doc/) for
### syntax help.
# HCA/ACETAZOLAMIDE BINDING
##########################################################################
read

6
examples/hca-bind/apbs-smol.in
View File

@@ -1,9 +1,5 @@
##########################################################################
### HCA/ACETAZOLAMIDE BINDING
### $Id$
###
### Please see APBS documentation (http://apbs.sourceforge.net/doc/) for
### syntax help.
# HCA/ACETAZOLAMIDE BINDING
##########################################################################
read

6
examples/helix/Apbs_dummy-TEMPLATE.in
View File

@@ -1,9 +1,5 @@
#############################################################################
### TM SOLVATION ENERGY
### : apbs.in 998 2006-11-28 21:24:40Z sobolevnrm $
###
### Please see APBS documentation (http://apbs.sourceforge.net/doc/) for
### input file sytax.
# TM SOLVATION ENERGY
#############################################################################
# READ IN MOLECULES
read

6
examples/helix/Apbs_dummy.in
View File

@@ -1,9 +1,5 @@
#############################################################################
### TM SOLVATION ENERGY
### : apbs.in 998 2006-11-28 21:24:40Z sobolevnrm $
###
### Please see APBS documentation (http://apbs.sourceforge.net/doc/) for
### input file sytax.
# TM SOLVATION ENERGY
#############################################################################
# READ IN MOLECULES
read

4
examples/helix/Apbs_solv-TEMPLATE.in
View File

@@ -1,7 +1,5 @@
#############################################################################
### TM SOLVATION ENERGY
### Please see APBS documentation (http://apbs.sourceforge.net/doc/) for
### input file sytax.
# TM SOLVATION ENERGY
#############################################################################
# READ IN MOLECULES
read

6
examples/ion-pmf/complex.in
View File

@@ -1,9 +1,5 @@
##########################################################################
### ION-ION PMF
### $Id$
###
### Please see APBS documentation (http://apbs.sourceforge.net/doc/) for
### syntax help.
# ION-ION PMF
##########################################################################
read

6
examples/ion-pmf/ion-pmf.in
View File

@@ -1,9 +1,5 @@
##########################################################################
### ION-ION PMF
### $Id$
###
### Please see APBS documentation (http://apbs.sourceforge.net/doc/) for
### syntax help.
# ION-ION PMF
##########################################################################
read

6
examples/ion-protein/apbs-mol-pdiel12.in
View File

@@ -1,9 +1,5 @@
##########################################################################
### ION-PROTEIN BINDING ENERGY
### $Id$
###
### Please see APBS documentation (http://apbs.sourceforge.net/doc/) for
### syntax help.
# ION-PROTEIN BINDING ENERGY
##########################################################################
read

6
examples/ion-protein/apbs-mol-pdiel2.in
View File

@@ -1,9 +1,5 @@
##########################################################################
### ION-PROTEIN BINDING ENERGY
### $Id$
###
### Please see APBS documentation (http://apbs.sourceforge.net/doc/) for
### syntax help.
# ION-PROTEIN BINDING ENERGY
##########################################################################
read

6
examples/ion-protein/apbs-smol-pdiel12.in
View File

@@ -1,9 +1,5 @@
##########################################################################
### ION-PROTEIN BINDING ENERGY
### $Id$
###
### Please see APBS documentation (http://apbs.sourceforge.net/doc/) for
### syntax help.
# ION-PROTEIN BINDING ENERGY
##########################################################################
read

6
examples/ion-protein/apbs-smol-pdiel2.in
View File

@@ -1,9 +1,5 @@
##########################################################################
### ION-PROTEIN BINDING ENERGY
### $Id$
###
### Please see APBS documentation (http://apbs.sourceforge.net/doc/) for
### syntax help.
# ION-PROTEIN BINDING ENERGY
##########################################################################
read

6
examples/misc/apbs-PDB.in
View File

@@ -1,9 +1,5 @@
##########################################################################
### POTENTIAL CALCULATION FROM PDB FILE
### $Id$
###
### Please see APBS documentation (http://apbs.sourceforge.net/doc/) for
### syntax help.
# POTENTIAL CALCULATION FROM PDB FILE
##########################################################################
read

6
examples/misc/apbs.in
View File

@@ -1,9 +1,5 @@
##########################################################################
### POTENTIAL CALCULATION EXAMPLE
### $Id$
###
### Please see APBS documentation (http://apbs.sourceforge.net/doc/) for
### syntax help.
# POTENTIAL CALCULATION EXAMPLE
##########################################################################

6
examples/opal/actin-dimer-para.in
View File

@@ -1,9 +1,5 @@
#########################################################################
### ACTIN DIMER BINDING ENERGY
### $Id: apbs-mol-parallel.in 1258 2008-04-10 17:50:16Z sdg0919 $
###
### Please see APBS documentation (http://apbs.sourceforge.net/doc/) for
### syntax help.
# ACTIN DIMER BINDING ENERGY
##########################################################################
read

6
examples/opal/actin-dimer.in
View File

@@ -1,9 +1,5 @@
##########################################################################
### ACTIN DIMER BINDING ENERGY
### $Id: apbs-mol-auto.in 1258 2008-04-10 17:50:16Z sdg0919 $
###
### Please see APBS documentation (http://apbs.sourceforge.net/doc/) for
### syntax help.
# ACTIN DIMER BINDING ENERGY
##########################################################################
read

6
examples/pka-lig/apbs-mol-surf.in
View File

@@ -1,9 +1,5 @@
##########################################################################
### PROTEIN KINASE INHIBITOR BINDING ENERGY -- MOLECULAR SURFACE
### $Id$
###
### Please see APBS documentation (http://apbs.sourceforge.net/doc/) for
### syntax help.
# PROTEIN KINASE INHIBITOR BINDING ENERGY -- MOLECULAR SURFACE
##########################################################################
read

6
examples/pka-lig/apbs-mol-vdw.in
View File

@@ -1,9 +1,5 @@
##########################################################################
### PROTEIN KINASE BINDING ENERGY -- VAN DER WAALS SURFACE
### $Id$
###
### Please see APBS documentation (http://apbs.sourceforge.net/doc/) for
### syntax help.
# PROTEIN KINASE BINDING ENERGY -- VAN DER WAALS SURFACE
##########################################################################
read

6
examples/pka-lig/apbs-smol-surf.in
View File

@@ -1,9 +1,5 @@
##########################################################################
### PROTEIN KINASE INHIBITOR BINDING ENERGY -- MOLECULAR SURFACE
### $Id$
###
### Please see APBS documentation (http://apbs.sourceforge.net/doc/) for
### syntax help.
# PROTEIN KINASE INHIBITOR BINDING ENERGY -- MOLECULAR SURFACE
##########################################################################
read

6
examples/pka-lig/apbs-smol-vdw.in
View File

@@ -1,9 +1,5 @@
##########################################################################
### PROTEIN KINASE BINDING ENERGY -- VAN DER WAALS SURFACE
### $Id$
###
### Please see APBS documentation (http://apbs.sourceforge.net/doc/) for
### syntax help.
# PROTEIN KINASE BINDING ENERGY -- VAN DER WAALS SURFACE
##########################################################################
read

6
examples/point-pmf/apbs.in
View File

@@ -1,9 +1,5 @@
##########################################################################
### POINT CHARGE POTENTIAL OF MEAN FORCE
### $Id$
###
### Please see APBS documentation (http://apbs.sourceforge.net/doc/) for
### syntax help.
# POINT CHARGE POTENTIAL OF MEAN FORCE
##########################################################################
read

6
examples/point-pmf/complex-0_1.in
View File

@@ -1,9 +1,5 @@
##########################################################################
### POINT CHARGE POTENTIAL OF MEAN FORCE
### $Id$
###
### Please see APBS documentation (http://apbs.sourceforge.net/doc/) for
### syntax help.
# POINT CHARGE POTENTIAL OF MEAN FORCE
##########################################################################
read

6
examples/point-pmf/complex-0_2.in
View File

@@ -1,9 +1,5 @@
##########################################################################
### POINT CHARGE POTENTIAL OF MEAN FORCE
### $Id$
###
### Please see APBS documentation (http://apbs.sourceforge.net/doc/) for
### syntax help.
# POINT CHARGE POTENTIAL OF MEAN FORCE
##########################################################################
read

6
examples/point-pmf/complex-0_3.in
View File

@@ -1,9 +1,5 @@
##########################################################################
### POINT CHARGE POTENTIAL OF MEAN FORCE
### $Id$
###
### Please see APBS documentation (http://apbs.sourceforge.net/doc/) for
### syntax help.
# POINT CHARGE POTENTIAL OF MEAN FORCE
##########################################################################
read

6
examples/point-pmf/complex-0_4.in
View File

@@ -1,9 +1,5 @@
##########################################################################
### POINT CHARGE POTENTIAL OF MEAN FORCE
### $Id$
###
### Please see APBS documentation (http://apbs.sourceforge.net/doc/) for
### syntax help.
# POINT CHARGE POTENTIAL OF MEAN FORCE
##########################################################################
read

6
examples/point-pmf/point-pmf-0.in
View File

@@ -1,9 +1,5 @@
##########################################################################
### POINT CHARGE POTENTIAL OF MEAN FORCE
### $Id$
###
### Please see APBS documentation (http://apbs.sourceforge.net/doc/) for
### syntax help.
# POINT CHARGE POTENTIAL OF MEAN FORCE
##########################################################################
read

6
examples/solv/apbs-mol.in
View File

@@ -1,9 +1,5 @@
##########################################################################
### ELECTROSTATIC ENERGY FOR METHANOL -> METHOXIDE IONIZATION
### $Id$
###
### Please see APBS documentation (http://apbs.sourceforge.net/doc/) for
### syntax help.
# ELECTROSTATIC ENERGY FOR METHANOL -> METHOXIDE IONIZATION
##########################################################################
read

6
examples/solv/apbs-smol.in
View File

@@ -1,9 +1,5 @@
##########################################################################
### ELECTROSTATIC ENERGY FOR METHANOL -> METHOXIDE IONIZATION
### $Id$
###
### Please see APBS documentation (http://apbs.sourceforge.net/doc/) for
### syntax help.
# ELECTROSTATIC ENERGY FOR METHANOL -> METHOXIDE IONIZATION
##########################################################################
read

1
externals/pb_solvers vendored

Submodule externals/pb_solvers deleted from 168a83ed57

1
externals/pybind11 vendored Submodule

Submodule externals/pybind11 added at fbc7563623

5
requirements.txt
View File

@@ -1,3 +1,2 @@
sphinx>=3.1
sphinx_rtd_theme
sphinx_sitemap
python-dev-tools
pybind11

9
src/main.c
View File

@@ -82,6 +82,14 @@ int main(
char **argv /**< Argument strings */
)
{
// Dump compile-time options
for (int i=0; i<argc; i++) {
if (strcmp(argv[i],"--config")==0) {
dump_options();
return 0;
}
}
// PCE: Adding below variables temporarily
clock_t ts, te;
// End PCE
@@ -238,6 +246,7 @@ int main(
for type are either \"xml\" or \"flat\".\n\
--help Display this help information.\n\
--version Display the current APBS version.\n\
--config Display configuration options APBS was built with.\n\
----------------------------------------------------------------------\n\n"};
/* ************** CHECK PARALLEL STATUS *************** */

2
src/mg/vgrid.c
View File

@@ -748,7 +748,7 @@ VPUBLIC int Vgrid_readDX(Vgrid *thee,
VJMPERR1(!strcmp(tok, "items"));
/* Get # */
VJMPERR2(1 == Vio_scanf(sock, "%s", tok));
VJMPERR1(1 == sscanf(tok, "%lu", &itmp));
VJMPERR1(1 == sscanf(tok, "%zu", &itmp));
u = (size_t)thee->nx * thee->ny * thee->nz;
VJMPERR1(u == itmp);
/* Get "data" */

2
src/pmgc/buildGd.c
View File

@@ -229,7 +229,7 @@ VPUBLIC void VbuildG_1(int *nxf, int *nyf, int *nzf,
for(jj=2; jj<=*ny-1; jj++) {
j = 2 * jj - 1;
for(ii=2; ii<=*nx-1; i++) {
for(ii=2; ii<=*nx-1; ii++) {
i = 2 * ii - 1;
// Index computations

139
src/routines.c
View File

@@ -5522,3 +5522,142 @@ VPUBLIC int solvePBSAM( Valist* molecules[NOSH_MAXMOL],
}
#endif
/**
* Dump compile-time options
*/
VPUBLIC void dump_options()
{
puts("Apbs configuration:");
printf("PACKAGE_STRING:%s",PACKAGE_STRING);
printf("APBS_FAST:");
#ifdef APBS_FAST
puts("1");
#else
puts("0");
#endif
printf("DEBUG:");
#ifdef DEBUG
puts("1");
#else
puts("0");
#endif
printf("VERBOSE_DEBUG:");
#ifdef VERBOSE_DEBUG
puts("1");
#else
puts("0");
#endif
printf("VAPBSQUIET:");
#ifdef VAPBSQUIET
puts("1");
#else
puts("0");
#endif
printf("HAVE_TIME_FUNC:");
#ifdef HAVE_TIME_FUNC
puts("1");
#else
puts("0");
#endif
printf("HAVE_RAND_FUNC:");
#ifdef HAVE_RAND_FUNC
puts("1");
#else
puts("0");
#endif
printf("HAVE_SRAND_FUNC:");
#ifdef HAVE_SRAND_FUNC
puts("1");
#else
puts("0");
#endif
printf("HAVE_LIBREADLINE:");
#ifdef HAVE_LIBREADLINE
puts("1");
#else
puts("0");
#endif
printf("APBS_NOINLINE:");
#ifdef APBS_NOINLINE
puts("1");
#else
puts("0");
#endif
printf("HAVE_EMBED:");
#ifdef HAVE_EMBED
puts("1");
#else
puts("0");
#endif
printf("HAVE_ZLIB:");
#ifdef HAVE_ZLIB
puts("1");
#else
puts("0");
#endif
printf("WITH_TINKER:");
#ifdef WITH_TINKER
puts("1");
#else
puts("0");
#endif
printf("FETK_ENABLED:");
#ifdef FETK_ENABLED
printf("1");
#else
puts("0");
#endif
printf("HAVE_PUNC_H:");
#ifdef HAVE_PUNC_H
puts("1");
#else
printf("0");
#endif
printf("HAVE_MCX_H:");
#ifdef HAVE_MCX_H
puts("1");
#else
puts("0");
#endif
printf("HAVE_MC_H:");
#ifdef HAVE_MC_H
printf("1");
#else
puts("0");
#endif
printf("HAVE_BIOM_H:");
#ifdef HAVE_BIOM_H
puts("1");
#else
printf("0");
#endif
printf("HAVE_MPI_H:");
#ifdef HAVE_MPI_H
puts("1");
#else
puts("0");
#endif
printf("FLOAT_EPSILON:%f\n",FLOAT_EPSILON);
printf("DOUBLE_EPSILON:%f\n",DOUBLE_EPSILON);
}

6
src/routines.h
View File

@@ -868,3 +868,9 @@ VEXTERNC int solvePBSAM(
PBSAMparm *samparm
);
#endif
/**
* @brief Dump compile-time options to I/O
* @ingroup Frontend
*/
VEXTERNC void dump_options();

17
tests/test_cases.cfg
View File

@@ -82,21 +82,20 @@ imidazole : -1.030222099963E+01 5.417419E-01
[bem]
input_dir : ../examples/bem
451c_order1 : -1.172906546441e+03
451c_order5 : -1.175936034727E+03
451c_order1 : -4.907440990309e+03
451c_order5 : -4.920116369298e+03
[bem-pKa]
input_dir : ../examples/bem-pKa
ASH66 : -9.954199102140E-01
# 2LZT-ASH66 : -8.620097356247E+01
# 2LZT-noASH66 : -8.601110775968E+01
ASH66 : -4.025681443841E+00
2LZT-ASH66 : -3.690203872934E+02
2LZT-noASH66 : -3.677953304674E+02
[bem-binding-energy]
input_dir : ../examples/bem-binding-energy
1d30 : -5.249027161163E+03
1d30_monomer1 : -6.232145066905E+03
1d30_monomer2 : -1.821470879387E+02
1d30 : -2.211309768995E+04
1d30_monomer1 : -2.622527466533E+04
1d30_monomer2 : -7.799475420336E+02
[pbam]

1
tools/CMakeLists.txt
View File

@@ -5,5 +5,6 @@ add_subdirectory(manip)
if(ENABLE_PYTHON)
add_subdirectory(python)
add_subdirectory(python-pybind)
endif(ENABLE_PYTHON)

8
tools/matlab/solver/Examples/Meth/meth.in
View File

@@ -1,9 +1,5 @@
##########################################################################
### ELECTROSTATIC ENERGY FOR METHANOL -> METHOXIDE IONIZATION
### $Id: apbs-mol.in 1346 2009-02-10 21:11:14Z sdg0919 $
###
### Please see APBS documentation (http://apbs.sourceforge.net/doc/) for
### syntax help.
# ELECTROSTATIC ENERGY FOR METHANOL -> METHOXIDE IONIZATION
##########################################################################
read
@@ -138,4 +134,4 @@ print elecEnergy methoxide-solv - methoxide-ref end
# Solvation energy difference
print elecEnergy methoxide-solv - methoxide-ref - methanol-solv + methanol-ref end
quit
quit

6
tools/matlab/solver/Examples/born-ion/born.in
View File

@@ -1,9 +1,5 @@
#############################################################################
### BORN ION SOLVATION ENERGY
### $Id: apbs-mol-auto.in 1119 2007-07-23 13:52:03Z sobolevnrm $
###
### Please see APBS documentation (http://apbs.sourceforge.net/doc/) for
### input file sytax.
# BORN ION SOLVATION ENERGY
#############################################################################
# READ IN MOLECULES

6
tools/matlab/solver/Examples/pka/apbs-smol-vdw.in
View File

@@ -1,9 +1,5 @@
##########################################################################
### PROTEIN KINASE BINDING ENERGY -- VAN DER WAALS SURFACE
### $Id: apbs-smol-vdw.in 1346 2009-02-10 21:11:14Z sdg0919 $
###
### Please see APBS documentation (http://apbs.sourceforge.net/doc/) for
### syntax help.
# PROTEIN KINASE BINDING ENERGY -- VAN DER WAALS SURFACE
##########################################################################
read

28
tools/python-pybind/CMakeLists.txt Normal file
View File

@@ -0,0 +1,28 @@
find_package(pybind11 REQUIRED)
add_library(apbs_pybind
MODULE
module.cpp
bind_nosh.cpp
bind_vatom.cpp
bind_valist.cpp
)
set_target_properties(apbs_pybind
PROPERTIES
PREFIX "${PYTHON_MODULE_PREFIX}"
SUFFIX "${PYTHON_MODULE_EXTENSION}"
OUTPUT_NAME "apbs"
)
message(STATUS "LIBS ${APBS_LIBS}")
message(STATUS "INTERNAL_LIBS ${APBS_INTERNAL_LIBS}")
target_link_libraries(
apbs_pybind
PRIVATE
pybind11::module
${APBS_LIBS}
${APBS_INTERNAL_LIBS}
)
install(TARGETS apbs_pybind LIBRARY DESTINATION lib)

22
tools/python-pybind/bind_constants.hpp Normal file
View File

@@ -0,0 +1,22 @@
#pragma once
/**
* @file tools/python-pybind/bind_constants.hpp
* @author Asher Mancinelli <asher.mancinelli@pnnl.gov>
* @brief Contains bindings for exported constants.
*
* @note The constants exported here were simply the same ones exported by the
* original SWIG python interface.
*
* @see tools/python/apbslib.c
*/
inline void bind_constants(py::module& m)
{
m.attr("NPT_ENERGY") = py::int_(static_cast<int>(NPT_ENERGY));
m.attr("NPT_FORCE") = py::int_(static_cast<int>(NPT_FORCE));
m.attr("NPT_ELECENERGY") = py::int_(static_cast<int>(NPT_ELECENERGY));
m.attr("NPT_ELECFORCE") = py::int_(static_cast<int>(NPT_ELECFORCE));
m.attr("NPT_APOLENERGY") = py::int_(static_cast<int>(NPT_APOLENERGY));
m.attr("NPT_APOLFORCE") = py::int_(static_cast<int>(NPT_APOLFORCE));
}

121
tools/python-pybind/bind_nosh.cpp Normal file
View File

@@ -0,0 +1,121 @@
#include "bind_nosh.hpp"
#include "bind_valist.hpp"
int parseInputFromString(NOsh *nosh, std::string str)
{
int ret, bufsize;
Vio *sock;
startVio();
VASSERT( bufsize <= VMAX_BUFSIZE );
sock = Vio_ctor("BUFF","ASC",VNULL,"0","r");
Vio_bufTake(sock, const_cast<char*>(str.c_str()), str.size());
ret = NOsh_parseInput(nosh, sock);
sock->VIObuffer = VNULL;
Vio_dtor(&sock);
return ret;
}
void bind_nosh(py::module& m)
{
m.def("getPotentials", &getPotentials<double>);
py::enum_<NOsh_MolFormat>(m, "NOsh_MolFormat").export_values();
py::enum_<NOsh_CalcType>(m, "NOsh_CalcType").export_values();
py::enum_<NOsh_ParmFormat>(m, "NOsh_ParmFormat").export_values();
py::enum_<NOsh_PrintType>(m, "NOsh_PrintType").export_values();
py::class_<NOsh_calc>(m, "NOsh_calc")
.def(py::init(
[] (NOsh_CalcType calcType)
{
return std::unique_ptr<NOsh_calc>(NOsh_calc_ctor(calcType));
}))
.def("NOsh_calc_mgparm_set",
[] (NOsh_calc& nosh, MGparm& mgparm)
{
nosh.mgparm = &mgparm;
})
.def("__del__",
[] (NOsh_calc* self)
{
NOsh_calc_dtor(&self);
})
.def_readwrite("mgparm", &NOsh_calc::mgparm)
.def_readwrite("femparm", &NOsh_calc::femparm)
.def_readwrite("bemparm", &NOsh_calc::bemparm)
.def_readwrite("geoflowparm", &NOsh_calc::geoflowparm)
.def_readwrite("pbamparm", &NOsh_calc::pbamparm)
.def_readwrite("pbsamparm", &NOsh_calc::pbsamparm)
.def_readwrite("pbeparm", &NOsh_calc::pbeparm)
.def_readwrite("apolparm", &sNOsh_calc::apolparm)
.def_readwrite("calctype", &sNOsh_calc::calctype);
py::class_<NOsh>(m, "NOsh")
.def(py::init<>())
.def("parseInputFromString",
[] (NOsh& self, std::string str) -> int
{
int ret, bufsize;
Vio *sock;
startVio();
VASSERT( bufsize <= VMAX_BUFSIZE );
sock = Vio_ctor("BUFF","ASC",VNULL,"0","r");
Vio_bufTake(sock, const_cast<char*>(str.c_str()), str.size());
ret = NOsh_parseInput(&self, sock);
sock->VIObuffer = VNULL;
Vio_dtor(&sock);
return ret;
})
.def("__del__",
[] (NOsh* self)
{
NOsh_dtor(&self);
})
.def("getMolpath" , [] (NOsh& thee, int imol)
{ return std::string(NOsh_getMolpath(&thee, imol)); })
.def("getDielXpath" , [] (NOsh& thee, int imap)
{ return std::string(NOsh_getDielXpath(&thee, imap)); })
.def("getDielYpath" , [] (NOsh& thee, int imap)
{ return std::string(NOsh_getDielYpath(&thee, imap)); })
.def("getDielZpath" , [] (NOsh& thee, int imap)
{ return std::string(NOsh_getDielZpath(&thee, imap)); })
.def("getKappapath" , [] (NOsh& thee, int imap)
{ return std::string(NOsh_getKappapath(&thee, imap)); })
.def("getPotpath" , [] (NOsh& thee, int imap)
{ return std::string(NOsh_getPotpath(&thee, imap)); })
.def("getChargepath" , [] (NOsh& thee, int imap)
{ return std::string(NOsh_getChargepath(&thee, imap)); })
.def("elecname" , [] (NOsh& thee, int ielec)
{ return std::string(NOsh_elecname(&thee, ielec)); })
.def("getDielfmt" , &NOsh_getDielfmt)
.def("getKappafmt" , &NOsh_getKappafmt)
.def("getPotfmt" , &NOsh_getPotfmt)
.def("getChargefmt" , &NOsh_getChargefmt)
.def("elec2calc" , &NOsh_elec2calc)
.def("apol2calc" , &NOsh_apol2calc)
.def("printNarg" , &NOsh_printNarg)
.def("printOp" , &NOsh_printOp)
.def("printCalc" , &NOsh_printCalc)
.def("getCalc" , &NOsh_getCalc)
.def("printWhat" , &NOsh_printWhat)
.def("parseInput" , &NOsh_parseInput)
.def("parseInputFile", &NOsh_parseInputFile)
// These two are wrappers to use std::vector for easier conversion
// between python lists and C arrays
.def("setupElecCalc" , [] (NOsh& thee, std::vector<Valist*> alist)
{
NOsh_setupElecCalc(&thee, alist.data());
})
.def("setupApolCalc" , [] (NOsh& thee, std::vector<Valist*> alist)
{
NOsh_setupApolCalc(&thee, alist.data());
});
}

77
tools/python-pybind/bind_nosh.hpp Normal file
View File

@@ -0,0 +1,77 @@
#pragma once
#include <string>
#include <vector>
#include <optional>
#include <stdexcept>
#include <pybind11/pybind11.h>
#include <pybind11/stl.h>
namespace py = pybind11;
#ifdef __GNUC__
#pragma GCC diagnostic ignored "-Wunused-function"
#endif
extern "C"
{
#include "apbscfg.h"
#include "routines.h"
#include "generic/nosh.h"
}
/**
* @file tools/python-pybind/bind_nosh.hpp
* @author Asher Mancinelli <asher.mancinelli@pnnl.gov>
* @brief Contains bindings for nosh-related functions.
*
* @note keep all implementations in the impl unless templated.
* @note contains bindings for nosh and all classes encapsulated by this struct
* within the source.
*
* @see src/generic/nosh.h:195
*/
/**
* @todo request help documenting
*/
template<typename T>
std::vector<T> getPotentials(NOsh *nosh, PBEparm *pbeparm, Vpmg *pmg, Valist *alist)
{
Vgrid *grid;
Vatom *atom;
int i, nx, ny, nz;
double hx, hy, hzed, xcent, ycent, zcent, xmin, ymin, zmin;
double value;
double *position;
std::vector<T> values;
nx = pmg->pmgp->nx;
ny = pmg->pmgp->ny;
nz = pmg->pmgp->nz;
hx = pmg->pmgp->hx;
hy = pmg->pmgp->hy;
hzed = pmg->pmgp->hzed;
xcent = pmg->pmgp->xcent;
ycent = pmg->pmgp->ycent;
zcent = pmg->pmgp->zcent;
xmin = xcent - 0.5*(nx-1)*hx;
ymin = ycent - 0.5*(ny-1)*hy;
zmin = zcent - 0.5*(nz-1)*hzed;
Vpmg_fillArray(pmg, pmg->rwork, VDT_POT, 0.0, pbeparm->pbetype, pbeparm);
grid = Vgrid_ctor(nx, ny, nz, hx, hy, hzed, xmin, ymin, zmin,
pmg->rwork);
for (i=0;i<Valist_getNumberAtoms(alist);i++){
atom = Valist_getAtom(alist, i);
position = Vatom_getPosition(atom);
Vgrid_value(grid, position, &value);
values[i] = value;
}
Vgrid_dtor(&grid);
return values;
}
/**
* @brief Perform binding to module
*/
void bind_nosh(py::module& m);

97
tools/python-pybind/bind_valist.cpp Normal file
View File

@@ -0,0 +1,97 @@
#include "bind_valist.hpp"
void Valist_load(Valist *self,
int size,
std::vector<double> x,
std::vector<double> y,
std::vector<double> z,
std::vector<double> chg,
std::vector<double> rad)
{
int i, j;
double pos[3];
Vatom *atom;
VASSERT(self != VNULL);
self->atoms = static_cast<Vatom*>(Vmem_malloc(self->vmem, size, sizeof(Vatom)));
self->number = size;
for (i = 0; i < size; i++) {
pos[0] = x[i];
pos[1] = y[i];
pos[2] = z[i];
Vatom_setCharge(&(self->atoms[i]), chg[i]);
Vatom_setRadius(&(self->atoms[i]), rad[i]);
Vatom_setPosition(&(self->atoms[i]), pos);
Vatom_setAtomID(&(self->atoms[i]), i);
}
self->center[0] = 0.0;
self->center[1] = 0.0;
self->center[2] = 0.0;
self->maxrad = 0.0;
self->charge = 0.0;
/* Reset stat variables */
atom = &(self->atoms[0]);
for (i = 0; i < 3; i++) {
self->maxcrd[i] = self->mincrd[i] = atom->position[i];
}
self->maxrad = atom->radius;
for (i = 0; i < self->number; i++) {
atom = &(self->atoms[i]);
for (j = 0; j < 3; j++) {
if (atom->position[j] < self->mincrd[j])
self->mincrd[j] = atom->position[j];
if (atom->position[j] > self->maxcrd[j])
self->maxcrd[j] = atom->position[j];
}
if (atom->radius > self->maxrad) self->maxrad = atom->radius;
self->charge = self->charge + atom->charge;
}
self->center[0] = 0.5 * (self->maxcrd[0] + self->mincrd[0]);
self->center[1] = 0.5 * (self->maxcrd[1] + self->mincrd[1]);
self->center[2] = 0.5 * (self->maxcrd[2] + self->mincrd[2]);
}
/**
* @brief Class to bind sValist to C++ STL types for better interfacing
* with python.
*/
struct Valist_glue : public Valist
{
std::array<double, 3> center; /**< Molecule center (xmin - xmax)/2, etc.*/
std::array<double, 3> mincrd; /**< Minimum coordinates */
std::array<double, 3> maxcrd; /**< Maximum coordinates */
std::vector<Vatom> vatoms; /**< Atom list */
};
void bind_valist(py::module &m)
{
py::class_<Valist_glue>(m, "Valist")
.def(py::init<>())
.def("__del__", [](Valist* self) { Valist_dtor(&self); })
.def("load", &Valist_load)
.def("getAtomList" , &Valist_getAtomList)
.def("getCenterX" , &Valist_getCenterX)
.def("getCenterY" , &Valist_getCenterY)
.def("getCenterZ" , &Valist_getCenterZ)
.def("getNumberAtoms" , &Valist_getNumberAtoms)
.def("getAtom" , &Valist_getAtom)
.def("memChk" , &Valist_memChk)
.def("readPQR" , &Valist_readPQR)
.def("readPDB" , &Valist_readPDB)
.def("readXML" , &Valist_readXML)
.def_readwrite("number" , &Valist::number)
.def_readwrite("center" , &Valist_glue::center)
.def_readwrite("mincrd" , &Valist_glue::mincrd)
.def_readwrite("maxcrd" , &Valist_glue::maxcrd)
.def_readwrite("maxrad" , &Valist::maxrad)
.def_readwrite("charge" , &Valist::charge)
.def_readwrite("vatoms" , &Valist_glue::vatoms)
.def_readwrite("vmem" , &Valist::vmem);
}

44
tools/python-pybind/bind_valist.hpp Normal file
View File

@@ -0,0 +1,44 @@
#pragma once
#include <vector>
#include <pybind11/pybind11.h>
#include <pybind11/stl.h>
namespace py = pybind11;
#ifdef __GNUC__
#pragma GCC diagnostic ignored "-Wunused-function"
#endif
extern "C"
{
#include "apbscfg.h"
#include "generic/valist.h"
}
/**
* @file tools/python-pybind/bind_valist.hpp
* @author Asher Mancinelli <asher.mancinelli@pnnl.gov>
* @brief Contains bindings for Valist-related functions.
*
* @note keep all implementations in the impl unless templated.
* @note contains bindings for nosh and all classes encapsulated by this struct
* within the source.
*
* @see src/generic/valist.h:195
*/
/**
* @todo request documentation for this
*/
void Valist_load(Valist *self,
int size,
std::vector<double> x,
std::vector<double> y,
std::vector<double> z,
std::vector<double> chg,
std::vector<double> rad);
/**
* @brief Perform binding to module
*/
void bind_valist(py::module& m);

64
tools/python-pybind/bind_vatom.cpp Normal file
View File

@@ -0,0 +1,64 @@
#include "bind_vatom.hpp"
#include <cstdio>
#include <pybind11/stl.h>
#include <pybind11/numpy.h>
void bind_vatom(py::module& m)
{
py::class_<sVatom>(m, "Vatom")
.def(py::init<>())
#ifdef WITH_TINKER
.def("setInducedDipole" , &Vatom_setInducedDipole)
.def("setNLInducedDipole", &Vatom_setNLInducedDipole)
.def("setDipole" , &Vatom_setDipole)
.def("setQuadrupole" , &Vatom_setQuadrupole)
.def("getDipole" , &Vatom_getDipole)
.def("getQuadrupole" , &Vatom_getQuadrupole)
.def("getInducedDipole" , &Vatom_getInducedDipole)
.def("getNLInducedDipole", &Vatom_getNLInducedDipole)
.def_readwrite("dipole" , &sVatom::dipole) /**< Permanent dipole */
.def_readwrite("quadrupole" , &sVatom::quadrupole) /**< Permanent quadrupole */
.def_readwrite("inducedDipole" , &sVatom::inducedDipole) /**< Induced dipole */
.def_readwrite("nlInducedDipole" , &sVatom::nlInducedDipole) /**< Non-local induced dipole */
#endif
.def("copyTo" , &Vatom_copyTo)
.def("copyFrom" , &Vatom_copyFrom)
.def_readwrite("radius" , &sVatom::radius)
.def_readwrite("charge" , &sVatom::charge)
.def_readwrite("partID" , &sVatom::partID)
.def_readwrite("epsilon" , &sVatom::epsilon)
.def_readwrite("id" , &sVatom::id)
.def_property("position",
[] (sVatom& self)
{
return std::vector<double>(self.position, self.position+3);
},
[] (sVatom& self, py::array_t<double> other)
{
py::buffer_info buf = other.request();
assert(buf.ndim == 1 && "Vatom::position is 1D!");
assert(other.size() == 3 && "Vatom::position has length 3!");
auto* ptr = static_cast<double*>(buf.ptr);
for(int i=0;i<3;i++) self.position[i] = ptr[i];
})
.def_property("atomName",
&Vatom_getAtomName,
[] (sVatom& self, std::string other)
{
for(int i=0;i<VMAX_RECLEN;i++)
{
if(other.c_str()[i]=='\0') break;
self.atomName[i] = other.c_str()[i];
}
})
.def_property("resName",
&Vatom_getResName,
[] (sVatom& self, std::string other)
{
for(int i=0;i<VMAX_RECLEN;i++)
{
if(other.c_str()[i]=='\0') break;
self.resName[i] = other.c_str()[i];
}
});
}

Some files were not shown because too many files have changed in this diff Show More