Commit 291525d0 authored by Berk Onat's avatar Berk Onat
Browse files

Initial attenpt to add cmake setup

parent 9d450070
cmake_minimum_required(VERSION 2.8.12)
if(NOT DEFINED CMAKE_MACOSX_RPATH)
set(CMAKE_MACOSX_RPATH 0)
endif()
project(molfile)
# Set source directory
set(SOURCE_DIR "molfile")
# Tell CMake that headers are also in SOURCE_DIR
include_directories(${SOURCE_DIR}, "./vmd_molfile_plugin/molfile_plugin/include", "./vmd_molfile_plugin/molfile_plugin/lib")
include_directories(${SOURCE_DIR} "${SOURCE_DIR}/vmd_molfile_plugin/molfile_plugin/include" "${SOURCE_DIR}/vmd_molfile_plugin/molfile_plugin/lib")
set(SOURCES "${SOURCE_DIR}/libpymolfile_wrap.cxx", "${SOURCE_DIR}/pymolfile.c")
set(SOURCES "${SOURCE_DIR}/libpymolfile_wrap.cxx" "${SOURCE_DIR}/pymolfile.c" "${SOURCE_DIR}/lib/libmolfile_plugin.a")
find_package (EXPAT)
find_package (NetCDF)
# Set source directory
set(SOURCE_DIR "molfile")
# Tell CMake that headers are also in SOURCE_DIR
include_directories(${SOURCE_DIR} "${SOURCE_DIR}/vmd_molfile_plugin/molfile_plugin/include" "${SOURCE_DIR}/vmd_molfile_plugin/molfile_plugin/lib")
set(SOURCES "${SOURCE_DIR}/libpymolfile_wrap.cxx" "${SOURCE_DIR}/pymolfile.c" "${SOURCE_DIR}/lib/libmolfile_plugin.a")
#!/usr/bin/env python
import sys
from setuptools import setup, Extension, find_packages
try:
from setuptools.command.build_ext import build_ext
from setuptools import setup, Extension, Command, find_packages
except:
from distutils.command.build_ext import build_ext
from distutils import setup, Extension, Command, find_packages
VERSION = "0.0.1"
......@@ -91,6 +96,37 @@ largefile_macros = [
]
if __name__ == '__main__':
libpymolfile_module = Extension(
'pymolfile/molfile/_libpymolfile',
sources=[
'pymolfile/molfile/libpymolfile.i' ,
'pymolfile/molfile/pymolfile.c'
],
swig_opts=['-py3 -c++ -python'],
library_dirs=[
'/usr/lib',
'lib/'
],
libraries=['libmolfile_plugin.a'],
include_dirs = [
get_numpy_include,
'/usr/include',
'pymolfile/molfile',
'pymolfile/molfile/lib/'
'pymolfile/molfile/include/',
'pymolfile/molfile/include/molfile_plugin/include',
'pymolfile/molfile/lib/molfile_plugin/lib',
'pymolfile/molfile/include/plugin_src/include',
'pymolfile/molfile/include/netcdf/include',
'pymolfile/molfile/include/expat/include',
'pymolfile/molfile/include/tng/include',
],
extra_compile_args = [
'-DNDEBUG', '-DUNIX', '-D__UNIX', '-m64',
'-fPIC', '-O2', '-w', '-fmessage-length=0'
]
)
setup(
name = "pymolfile",
author = "Berk Onat",
......@@ -103,34 +139,36 @@ if __name__ == '__main__':
zip_safe = False,
packages = find_packages(),
ext_modules = [
LibpymolfileExtension(cmake_compile
),
NumpyExtension(
"pymolfile/molfile._libpymolfile",
sources = [
"pymolfile/molfile/libpymolfile_wrap.cxx",
"pymolfile/molfile/pymolfile.c",
"pymolfile/molfile/lib/libmolfile_plugin.a",
],
include_dirs = [
get_numpy_include,
"pymolfile/molfile/include/",
"pymolfile/molfile/include/molfile_plugin/include",
"pymolfile/molfile/lib/molfile_plugin/lib",
"pymolfile/molfile/include/plugin_src/include",
"pymolfile/molfile/include/netcdf/include",
"pymolfile/molfile/include/expat/include",
"pymolfile/molfile/include/tng/include",
],
define_macros = largefile_macros
),
#libmolfile_plugin_compile(cmake_libmolfile_plugin_compile),
libpymolfile_module,
# NumpyExtension(
# "pymolfile/molfile/_libpymolfile",
# "pymolfile"
# sources = [
# "pymolfile/molfile/libpymolfile_wrap.cxx",
# "pymolfile/molfile/pymolfile.c",
# "pymolfile/molfile/lib/libmolfile_plugin.a",
# ],
# include_dirs = [
# get_numpy_include,
# "pymolfile/molfile/include/",
# "pymolfile/molfile/include/molfile_plugin/include",
# "pymolfile/molfile/lib/molfile_plugin/lib",
# "pymolfile/molfile/include/plugin_src/include",
# "pymolfile/molfile/include/netcdf/include",
# "pymolfile/molfile/include/expat/include",
# "pymolfile/molfile/include/tng/include",
# ],
# define_macros = largefile_macros
# ),
],
py_modules=["pymolfile"],
requires = [ "numpy" ],
setup_requires = [ "numpy" ],
install_requires = [ "numpy" ],
extras_require = {
"netcdf": [ "netCDF Library" ],
"tng_io": [ "TNG Library" ],
"expat": [ "Expat XML Library" ]
#?do we need this? "netcdf": [ "netCDF Library" ],
#?and this? "tng_io": [ "TNG Library" ],
#?and this? "expat": [ "Expat XML Library" ]
}
)
......@@ -24,10 +24,14 @@ path="./test/"
#sfname = path + "betaGal.mrc"
#sfname = path + "adrenalin.mol2"
#sfname = path + "adrenalin.sdf"
#sfname = path + "1CRN.cif"
#sfname = path + "esp.dx"
#sfname = path + "md_ascii_trj.gro"
sfname = path + "md_ascii_trj.pdb"
#sfname = path + "3pqr.pqr"
#cfname = path + "3pqr_validation.xml"
#sfname = path + "3pqr-pot.dxbin"
#sfname = path + "3pqr.cns"
#sfname = path + "1cnr.ply"
print("Reading file...")
moltopo = pym.OpenMolfile(sfname, silent=True)
......
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<?xml version="1.0" ?>
<wwPDB-validation-information xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="http://wwpdb.org/validation/schema/wwpdb_validation_v002.xsd">
<Entry B_factor_type="FULL" CCP4version="6.5.0" DCC_R="0.22" DCC_Rfree="0.25" DCC_refinement_program="REFMAC" DataAnisotropy="0.114" DataCompleteness="99.03" EDS_R="0.22" EDS_resolution="2.85" EDS_resolution_low="34.86" Fo_Fc_correlation="0.910" IoverSigma="2.87(2.85A)" PDB-R="0.22" PDB-Rfree="0.25" PDB-deposition-date="2010-11-26" PDB-resolution="2.85" PDB-resolution-low="34.86" PDB-revision-date="2011-04-06" PDB-revision-number="3" RefmacVersion="5.8.0135" RestypesNotcheckedForBondAngleGeometry="BMA,NAG,TRE,RET,SO4,ACT,PLM,BOG,MAN" TransNCS="The largest off-origin peak in the Patterson function is 4.75% of the height of the origin peak. No significant pseudotranslation is detected." TwinL="0.497" TwinL2="0.330" WilsonBaniso="[67.476,67.476,60.050,-0.000,0.000,0.000]" WilsonBestimate="64.712" XMLcreationDate="Feb 13, 2017 -- 03:35 am GMT" absolute-percentile-DCC_Rfree="38.0" absolute-percentile-clashscore="27.4" absolute-percentile-percent-RSRZ-outliers="39.9" absolute-percentile-percent-rama-outliers="28.2" absolute-percentile-percent-rota-outliers="54.2" acentric_outliers="0" angles_rmsz="0.52" attemptedValidationSteps="mogul,molprobity,validation-pack,xtriage,eds,percentiles,writexml,writepdf" babinet_b="10.000" babinet_k="0.010" bonds_rmsz="0.46" bulk_solvent_b="67.276" bulk_solvent_k="0.314" centric_outliers="0" clashscore="11.29" high-resol-relative-percentile-DCC_Rfree="2.82" high-resol-relative-percentile-clashscore="2.82" high-resol-relative-percentile-percent-RSRZ-outliers="2.82" high-resol-relative-percentile-percent-rama-outliers="2.82" high-resol-relative-percentile-percent-rota-outliers="2.82" low-resol-relative-percentile-DCC_Rfree="2.9" low-resol-relative-percentile-clashscore="2.9" low-resol-relative-percentile-percent-RSRZ-outliers="2.9" low-resol-relative-percentile-percent-rama-outliers="2.9" low-resol-relative-percentile-percent-rota-outliers="2.9" num-H-reduce="2872" num-free-reflections="1420" numMillerIndices="28421" numPDBids-absolute-percentile-DCC_Rfree="100719" numPDBids-absolute-percentile-clashscore="112137" numPDBids-absolute-percentile-percent-RSRZ-outliers="101464" numPDBids-absolute-percentile-percent-rama-outliers="110173" numPDBids-absolute-percentile-percent-rota-outliers="110143" numPDBids-relative-percentile-DCC_Rfree="2469" numPDBids-relative-percentile-clashscore="2749" numPDBids-relative-percentile-percent-RSRZ-outliers="2487" numPDBids-relative-percentile-percent-rama-outliers="2687" numPDBids-relative-percentile-percent-rota-outliers="2690" num_angles_rmsz="3795" num_bonds_rmsz="2788" pdbid="3PQR" percent-RSRZ-outliers="3.86" percent-free-reflections="5.27" percent-rama-outliers="0.60" percent-rota-outliers="2.43" percentilebins="all,2.85,xray" protein-DNA-RNA-entities="1,2" relative-percentile-DCC_Rfree="73.5" relative-percentile-clashscore="53.9" relative-percentile-percent-RSRZ-outliers="33.9" relative-percentile-percent-rama-outliers="59.9" relative-percentile-percent-rota-outliers="82.0" xtriage_input_columns="F_meas_au,F_meas_sigma_au"/>
<ModelledSubgroup NatomsEDS="8" altcode=" " avgoccu="1.000" chain="A" ent="1" icode=" " model="1" num-H-reduce="11" owab="101.050" resname="MET" resnum="1" rota="mtp" rscc="0.853" rsr="0.376" rsrz="2.344" said="A" seq="1"/>
<ModelledSubgroup NatomsEDS="8" altcode=" " avgoccu="1.000" chain="A" ent="1" icode=" " model="1" num-H-reduce="4" owab="90.530" phi="-147.4" psi="6.1" rama="Allowed" resname="ASN" resnum="2" rota="p30" rscc="0.833" rsr="0.214" rsrz="0.318" said="A" seq="2"/>
<ModelledSubgroup NatomsEDS="4" altcode=" " avgoccu="1.000" chain="A" ent="1" icode=" " model="1" num-H-reduce="3" owab="63.440" phi="-118.2" psi="-176.3" rama="Favored" resname="GLY" resnum="3" rscc="0.970" rsr="0.139" rsrz="-0.403" said="A" seq="3"/>
<ModelledSubgroup NatomsEDS="7" altcode=" " avgoccu="1.000" chain="A" ent="1" icode=" " lig_rsrz_nbr_id="0" model="1" num-H-reduce="7" owab="48.370" phi="-144.3" psi="113.5" rama="Favored" resname="THR" resnum="4" rota="m" rscc="0.986" rsr="0.167" rsrz="-0.227" said="A" seq="4"/>
<ModelledSubgroup NatomsEDS="9" altcode=" " avgoccu="1.000" chain="A" ent="1" icode=" " lig_rsrz_nbr_id="0" model="1" num-H-reduce="6" owab="60.170" phi="-88.5" psi="153.5" rama="Favored" resname="GLU" resnum="5" rota="mt-10" rscc="0.971" rsr="0.199" rsrz="-0.282" said="A" seq="5"/>
<ModelledSubgroup NatomsEDS="4" altcode=" " avgoccu="1.000" chain="A" ent="1" icode=" " lig_rsrz_nbr_id="0" model="1" num-H-reduce="3" owab="51.680" phi="-148.2" psi="167.9" rama="Favored" resname="GLY" resnum="6" rscc="0.958" rsr="0.128" rsrz="-0.532" said="A" seq="6">
<clash atom="HA3" cid="14" clashmag="0.60" dist="2.37"/>
</ModelledSubgroup>
<ModelledSubgroup NatomsEDS="7" altcode=" " avgoccu="1.000" chain="A" ent="1" icode=" " lig_rsrz_nbr_id="0" model="1" num-H-reduce="7" owab="58.600" phi="-44.3" psi="-53.5" rama="Favored" resname="PRO" resnum="7" rota="Cg_exo" rscc="0.942" rsr="0.237" rsrz="0.682" said="A" seq="7"/>
<ModelledSubgroup NatomsEDS="8" altcode=" " avgoccu="1.000" chain="A" ent="1" icode=" " model="1" num-H-reduce="6" owab="57.090" phi="-137.2" psi="63.8" rama="Allowed" resname="ASN" resnum="8" rota="p30" rscc="0.932" rsr="0.185" rsrz="-0.063" said="A" seq="8"/>
<ModelledSubgroup NatomsEDS="11" altcode=" " avgoccu="1.000" chain="A" ent="1" icode=" " lig_rsrz_nbr_id="0" model="1" num-H-reduce="9" owab="49.570" phi="-170.0" psi="165.5" rama="Favored" resname="PHE" resnum="9" rota="p90" rscc="0.988" rsr="0.162" rsrz="-0.560" said="A" seq="9">
<clash atom="C" cid="44" clashmag="0.45" dist="2.90"/>
<clash atom="CD1" cid="44" clashmag="0.45" dist="2.90"/>
<clash atom="CZ" cid="14" clashmag="0.60" dist="2.37"/>
</ModelledSubgroup>
<ModelledSubgroup NatomsEDS="12" altcode=" " avgoccu="1.000" chain="A" ent="1" icode=" " model="1" num-H-reduce="9" owab="56.830" phi="-142.6" psi="91.2" rama="Favored" resname="TYR" resnum="10" rota="t80" rscc="0.967" rsr="0.156" rsrz="-0.556" said="A" seq="10"/>
<ModelledSubgroup NatomsEDS="7" altcode=" " avgoccu="1.000" chain="A" ent="1" icode=" " model="1" num-H-reduce="9" owab="50.060" phi="-70.9" psi="120.1" rama="Favored" resname="VAL" resnum="11" rota="t" rscc="0.976" rsr="0.173" rsrz="-0.370" said="A" seq="11"/>
<ModelledSubgroup NatomsEDS="7" altcode=" " avgoccu="1.000" chain="A" ent="1" icode=" " model="1" num-H-reduce="7" owab="55.030" phi="-76.7" psi="54.8" rama="Favored" resname="PRO" resnum="12" rota="Cg_endo" rscc="0.987" rsr="0.112" rsrz="-0.918" said="A" seq="12"/>
<ModelledSubgroup NatomsEDS="11" altcode=" " avgoccu="1.000" chain="A" ent="1" icode=" " model="1" num-H-reduce="9" owab="52.200" phi="-151.5" psi="138.1" rama="Favored" resname="PHE" resnum="13" rota="t80" rscc="0.970" rsr="0.193" rsrz="-0.189" said="A" seq="13"/>
<ModelledSubgroup NatomsEDS="6" altcode=" " avgoccu="1.000" chain="A" ent="1" icode=" " model="1" num-H-reduce="5" owab="57.080" phi="-74.5" psi="137.1" rama="Favored" resname="SER" resnum="14" rota="OUTLIER" rscc="0.993" rsr="0.142" rsrz="-0.475" said="A" seq="14"/>
<ModelledSubgroup NatomsEDS="8" altcode=" " avgoccu="1.000" chain="A" ent="1" icode=" " lig_rsrz_nbr_id="0" model="1" num-H-reduce="5" owab="53.090" phi="-90.5" psi="16.2" rama="Favored" resname="ASN" resnum="15" rota="t30" rscc="0.980" rsr="0.108" rsrz="-1.075" said="A" seq="15"/>
<ModelledSubgroup NatomsEDS="9" altcode=" " avgoccu="1.000" chain="A" ent="1" icode=" " model="1" num-H-reduce="13" owab="71.370" phi="-54.4" psi="-24.9" rama="Favored" resname="LYS" resnum="16" rota="ptpt" rscc="0.952" rsr="0.235" rsrz="-0.086" said="A" seq="16">
<clash atom="HB3" cid="57" clashmag="0.41" dist="1.84"/>
<clash atom="HE2" cid="57" clashmag="0.41" dist="1.84"/>
</ModelledSubgroup>
<ModelledSubgroup NatomsEDS="7" altcode=" " avgoccu="1.000" chain="A" ent="1" icode=" " model="1" num-H-reduce="7" owab="57.650" phi="-98.7" psi="1.8" rama="Favored" resname="THR" resnum="17" rota="p" rscc="0.967" rsr="0.117" rsrz="-0.907" said="A" seq="17"/>
<ModelledSubgroup NatomsEDS="4" altcode=" " avgoccu="1.000" chain="A" ent="1" icode=" " lig_rsrz_nbr_id="0" model="1" num-H-reduce="3" owab="57.880" phi="76.1" psi="3.5" rama="Favored" resname="GLY" resnum="18" rscc="0.980" rsr="0.105" rsrz="-0.801" said="A" seq="18"/>
<ModelledSubgroup NatomsEDS="7" altcode=" " avgoccu="1.000" chain="A" ent="1" icode=" " lig_rsrz_nbr_id="0" model="1" num-H-reduce="9" owab="52.360" phi="-79.0" psi="-18.7" rama="Favored" resname="VAL" resnum="19" rota="m" rscc="0.968" rsr="0.151" rsrz="-0.641" said="A" seq="19"/>
<ModelledSubgroup NatomsEDS="7" altcode=" " avgoccu="1.000" chain="A" ent="1" icode=" " lig_rsrz_nbr_id="0" model="1" num-H-reduce="9" owab="50.080" phi="-64.3" psi="128.9" rama="Favored" resname="VAL" resnum="20" rota="t" rscc="0.990" rsr="0.133" rsrz="-0.862" said="A" seq="20">
<clash atom="HA" cid="61" clashmag="0.41" dist="2.56"/>
</ModelledSubgroup>
<ModelledSubgroup NatomsEDS="11" altcode=" " avgoccu="1.000" chain="A" ent="1" icode=" " lig_rsrz_nbr_id="0" model="1" num-H-reduce="13" owab="57.230" phi="-116.2" psi="154.7" rama="Favored" resname="ARG" resnum="21" rota="mmt-85" rscc="0.953" rsr="0.213" rsrz="-0.139" said="A" seq="21"/>
<ModelledSubgroup NatomsEDS="6" altcode=" " avgoccu="1.000" chain="A" ent="1" icode=" " lig_rsrz_nbr_id="0" model="1" num-H-reduce="5" owab="54.220" phi="-48.6" psi="131.3" rama="Favored" resname="SER" resnum="22" rota="t" rscc="0.950" rsr="0.154" rsrz="-0.315" said="A" seq="22"/>
<ModelledSubgroup NatomsEDS="7" altcode=" " avgoccu="1.000" chain="A" ent="1" icode=" " model="1" num-H-reduce="7" owab="56.620" phi="-66.8" psi="-10.6" rama="Favored" resname="PRO" resnum="23" rota="Cg_endo" rscc="0.985" rsr="0.126" rsrz="-0.739" said="A" seq="23">
<clash atom="HB3" cid="55" clashmag="0.41" dist="2.02"/>
</ModelledSubgroup>
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<ModelledSubgroup NatomsEDS="5" altcode=" " avgoccu="1.000" chain="A" ent="1" icode=" " model="1" num-H-reduce="5" owab="49.570" phi="-154.1" psi="157.8" rama="Favored" resname="ALA" resnum="26" rscc="0.990" rsr="0.166" rsrz="-0.219" said="A" seq="26"/>
<ModelledSubgroup NatomsEDS="7" altcode=" " avgoccu="1.000" chain="A" ent="1" icode=" " lig_rsrz_nbr_id="6" model="1" num-H-reduce="7" owab="51.100" phi="-54.0" psi="151.1" rama="Favored" resname="PRO" resnum="27" rota="Cg_exo" rscc="0.981" rsr="0.122" rsrz="-0.790" said="A" seq="27">
<clash atom="HB3" cid="49" clashmag="0.44" dist="2.53"/>
</ModelledSubgroup>
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<clash atom="NE2" cid="25" clashmag="0.52" dist="2.43"/>
</ModelledSubgroup>
<ModelledSubgroup NatomsEDS="12" altcode=" " avgoccu="1.000" chain="A" ent="1" icode=" " lig_rsrz_nbr_id="6" model="1" num-H-reduce="9" owab="54.410" phi="-68.8" psi="1.9" rama="Favored" resname="TYR" resnum="29" rota="m-85" rscc="0.964" rsr="0.124" rsrz="-0.974" said="A" seq="29">
<clash atom="CE2" cid="49" clashmag="0.44" dist="2.53"/>
</ModelledSubgroup>
<ModelledSubgroup NatomsEDS="12" altcode=" " avgoccu="1.000" chain="A" ent="1" icode=" " model="1" num-H-reduce="9" owab="47.090" phi="-91.9" psi="-15.9" rama="Favored" resname="TYR" resnum="30" rota="p90" rscc="0.984" rsr="0.125" rsrz="-0.961" said="A" seq="30">
<clash atom="CZ" cid="61" clashmag="0.41" dist="2.56"/>
<clash atom="OH" cid="25" clashmag="0.52" dist="2.43"/>
</ModelledSubgroup>
<ModelledSubgroup NatomsEDS="8" altcode=" " avgoccu="1.000" chain="A" ent="1" icode=" " lig_rsrz_nbr_id="3" model="1" num-H-reduce="11" owab="54.020" phi="-105.2" psi="4.5" rama="Favored" resname="LEU" resnum="31" rota="OUTLIER" rscc="0.943" rsr="0.145" rsrz="-0.851" said="A" seq="31">
<clash atom="HB2" cid="28" clashmag="0.50" dist="1.93"/>
<clash atom="C" cid="27" clashmag="0.51" dist="2.30"/>
<clash atom="C" cid="59" clashmag="0.41" dist="2.89"/>
<clash atom="CD1" cid="59" clashmag="0.41" dist="2.89"/>
<clash atom="HD12" cid="27" clashmag="0.51" dist="2.30"/>
</ModelledSubgroup>
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