<pre style='margin:0'>
Renee Otten (reneeotten) pushed a commit to branch master
in repository macports-ports.
</pre>
<p><a href="https://github.com/macports/macports-ports/commit/71420c65c9fbc47eba5825aeca8561d8105b7c47">https://github.com/macports/macports-ports/commit/71420c65c9fbc47eba5825aeca8561d8105b7c47</a></p>
<pre style="white-space: pre; background: #F8F8F8">The following commit(s) were added to refs/heads/master by this push:
<span style='display:block; white-space:pre;color:#404040;'> new 71420c65c9f pymol: Update to 2.5.0 as well as remove X11 and python27 variants
</span>71420c65c9f is described below
<span style='display:block; white-space:pre;color:#808000;'>commit 71420c65c9fbc47eba5825aeca8561d8105b7c47
</span>Author: jwhowarth <howarth.mailing.lists@gmail.com>
AuthorDate: Thu May 27 11:22:18 2021 -0400
<span style='display:block; white-space:pre;color:#404040;'> pymol: Update to 2.5.0 as well as remove X11 and python27 variants
</span><span style='display:block; white-space:pre;color:#404040;'>
</span><span style='display:block; white-space:pre;color:#404040;'> pymol: Update to 2.5.0 and remove X11 and python27 variants. Drop unused patches.
</span>---
science/pymol/Portfile | 73 +---
science/pymol/files/apbs-psize.patch | 11 -
science/pymol/files/patch-devel-setup.py.diff | 11 -
science/pymol/files/pdb2pqr.patch | 13 -
science/pymol/files/pmg_tk_platform.patch | 51 ---
science/pymol/files/python_string_split.patch | 580 --------------------------
science/pymol/files/setup.py.diff | 10 +-
7 files changed, 15 insertions(+), 734 deletions(-)
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/pymol/Portfile b/science/pymol/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 4bf755919de..009ee5cf5d0 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/science/pymol/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/science/pymol/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -2,13 +2,11 @@
</span>
PortSystem 1.0
PortGroup python 1.0
<span style='display:block; white-space:pre;background:#ffe0e0;'>-PortGroup active_variants 1.1
</span> PortGroup github 1.0
<span style='display:block; white-space:pre;background:#ffe0e0;'>-github.setup schrodinger pymol-open-source 2.4.0 v
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+github.setup schrodinger pymol-open-source 2.5.0 v
</span> name pymol
conflicts pymol-devel
<span style='display:block; white-space:pre;background:#ffe0e0;'>-revision 2
</span>
categories science chemistry
platforms darwin
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -23,9 +21,9 @@ long_description PyMOL is a molecular graphics system with an embedded Python
</span>
homepage https://www.pymol.org/
<span style='display:block; white-space:pre;background:#ffe0e0;'>-checksums rmd160 e7a962473732172b370e6c7a880384e7a1ffa62e \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- sha256 b0af15082c44c92c285cab341506da50407619f5dee09d98fdf2802e356219fd \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- size 10552074
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+checksums rmd160 6432d47616aee1e5d9d40cc2a74425b33159d7a0 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ sha256 67c5aa944ce9ac2e3babd42e7e2b78ed11719283a2c0a063e100cfe24665c0d3 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ size 10471287
</span>
subport pymol-devel {
github.setup schrodinger pymol-open-source 4a3c72ace1f8e39e80db4026d45222f8b7a44169
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -38,31 +36,20 @@ subport pymol-devel {
</span> size 10469954
}
<span style='display:block; white-space:pre;background:#ffe0e0;'>-variant python27 conflicts python36 python37 python38 python39 description {Use Python 2.7} {}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-variant python36 conflicts python27 python37 python38 python39 description {Use Python 3.6} {}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-variant python37 conflicts python27 python36 python38 python39 description {Use Python 3.7} {}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-variant python38 conflicts python27 python36 python37 python39 description {Use Python 3.8} {}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-variant python39 conflicts python27 python36 python37 python38 description {Use Python 3.9} {}
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+variant python36 conflicts python37 python38 python39 description {Use Python 3.6} {}
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+variant python37 conflicts python36 python38 python39 description {Use Python 3.7} {}
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+variant python38 conflicts python36 python37 python39 description {Use Python 3.8} {}
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+variant python39 conflicts python36 python37 python38 description {Use Python 3.9} {}
</span>
<span style='display:block; white-space:pre;background:#ffe0e0;'>-if {[variant_isset python27]} {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- python.default_version 27
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-} elseif {[variant_isset python36]} {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+if {[variant_isset python36]} {
</span> python.default_version 36
} elseif {[variant_isset python37]} {
python.default_version 37
} elseif {[variant_isset python38]} {
python.default_version 38
<span style='display:block; white-space:pre;background:#ffe0e0;'>-} elseif {[variant_isset python39]} {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- python.default_version 39
</span> } else {
<span style='display:block; white-space:pre;background:#ffe0e0;'>- if {[variant_isset x11]} {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- # The APBS Tools plugin requires pdb2pqr, which can't be run under python3 yet
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- default_variants +python27
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- python.default_version 27
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- } else {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- default_variants +python39
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- python.default_version 39
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- }
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ default_variants +python39
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ python.default_version 39
</span> }
python.link_binaries no
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -80,44 +67,11 @@ depends_lib-append port:freetype \
</span> port:py${python.version}-numpy \
port:py${python.version}-pyqt5
<span style='display:block; white-space:pre;background:#ffe0e0;'>-variant x11 {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- depends_lib-delete port:py${python.version}-pyqt5
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- depends_lib-append port:freeglut \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- port:mesa \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- port:py${python.version}-pmw \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- port:py${python.version}-tkinter \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- port:tcl \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- port:tk
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- require_active_variants tcl "" corefoundation
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- require_active_variants tk "" quartz
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- build.args-append --glut --no-osx-frameworks
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span> patchfiles pymol_shell.diff \
<span style='display:block; white-space:pre;background:#ffe0e0;'>- pmg_tk_platform.patch \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- apbs-psize.patch \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- python_string_split.patch \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- pdb2pqr.patch \
</span> setup.py.diff
<span style='display:block; white-space:pre;background:#ffe0e0;'>-if {${subport} eq "pymol-devel"} {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- patchfiles-delete \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- apbs-psize.patch \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- python_string_split.patch \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- pdb2pqr.patch \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- patchfiles-replace \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- setup.py.diff \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- patch-devel-setup.py.diff
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span> post-patch {
reinplace "s|@PREFIX@|${prefix}|g" ${worksrcpath}/setup.py
<span style='display:block; white-space:pre;background:#ffe0e0;'>- if { [ file exists ${worksrcpath}/modules/pmg_tk/startup/apbs_tools.py ] } {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- reinplace "s|@PREFIX@|${prefix}|g" ${worksrcpath}/modules/pmg_tk/startup/apbs_tools.py
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- }
</span> reinplace "s|@@PYTHON_PKGDIR@@|${python.pkgd}|g" ${worksrcpath}/setup/pymol_macports
reinplace "s|@@PYTHON_BINARY@@|${python.bin}|g" ${worksrcpath}/setup/pymol_macports
reinplace "s|cxx + ' ' + cxxflags|'${configure.cxx} ' + cxxflags|g" ${worksrcpath}/monkeypatch_distutils.py
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -127,11 +81,6 @@ post-patch {
</span> post-destroot {
file copy ${worksrcpath}/setup/pymol_macports ${destroot}${prefix}/bin/pymol
file attributes ${destroot}${prefix}/bin/pymol -permissions a+x
<span style='display:block; white-space:pre;background:#ffe0e0;'>- if {![variant_isset x11]} {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- file delete ${destroot}${python.pkgd}/pmg_tk/startup/apbs_tools.py
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- } else {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- reinplace {s|options\.gui = 'pmg_qt'|options.gui = 'pmg_tk'|g} ${destroot}${python.pkgd}/pymol/invocation.py
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- }
</span> }
test.run yes
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/pymol/files/apbs-psize.patch b/science/pymol/files/apbs-psize.patch
</span>deleted file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index 22585f0258c..00000000000
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/science/pymol/files/apbs-psize.patch
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ /dev/null
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -1,11 +0,0 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- modules/pmg_tk/startup/apbs_tools.py.orig
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ modules/pmg_tk/startup/apbs_tools.py
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -888,7 +888,7 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- pass
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if not psize_location:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- psize_location = get_default_location('psize.py')
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ psize_location = get_default_location('apbs-psize.py')
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if not apbs_location:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- apbs_location = get_default_location('apbs.exe')
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if not apbs_location:
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/pymol/files/patch-devel-setup.py.diff b/science/pymol/files/patch-devel-setup.py.diff
</span>deleted file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index 18fc0d90ff8..00000000000
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/science/pymol/files/patch-devel-setup.py.diff
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ /dev/null
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -1,11 +0,0 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- setup.py.orig 2020-07-06 11:00:54.000000000 -0400
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ setup.py 2020-07-06 11:01:23.000000000 -0400
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -86,7 +86,7 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- X11 = ['/usr/X11'] * (not options.osx_frameworks)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if sys.platform == 'darwin':
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- for prefix in ['/sw', '/opt/local', '/usr/local']:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ for prefix in ['@@PREFIX@@', '/usr/local']:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if sys.base_prefix.startswith(prefix):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- return [prefix] + X11
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/pymol/files/pdb2pqr.patch b/science/pymol/files/pdb2pqr.patch
</span>deleted file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index 840186af1a9..00000000000
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/science/pymol/files/pdb2pqr.patch
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ /dev/null
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -1,13 +0,0 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-Index: modules/pmg_tk/startup/apbs_tools.py
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-===================================================================
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- modules/pmg_tk/startup/apbs_tools.py (revision 4187)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ modules/pmg_tk/startup/apbs_tools.py (working copy)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -169,7 +169,7 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- APBS_BINARY_LOCATION = None # corresponding environment variable: APBS_BINARY_DIR
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- APBS_WEB_LOCATION = None # corresponding environment variable: APBS_WEB_DIR
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- APBS_PSIZE_LOCATION = None # corresponding environment variable: APBS_PSIZE_DIR
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--APBS_PDB2PQR_LOCATION = None # corresponding environment variable: APBS_PDB2PQR_DIR
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+APBS_PDB2PQR_LOCATION = '@PREFIX@/share/pdb2pqr/' # corresponding environment variable: APBS_PDB2PQR_DIR
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- TEMPORARY_FILE_DIR = tempfile.gettempdir() # corresponding environment variable: TEMP
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- apbs_plea = ("IMPORTANT REQUEST: If you have not already done so, please register\n"
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/pymol/files/pmg_tk_platform.patch b/science/pymol/files/pmg_tk_platform.patch
</span>deleted file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index d51b488508b..00000000000
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/science/pymol/files/pmg_tk_platform.patch
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ /dev/null
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -1,51 +0,0 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-Index: modules/pmg_tk/PMGApp.py
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-===================================================================
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- modules/pmg_tk/PMGApp.py (revision 4187)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ modules/pmg_tk/PMGApp.py (working copy)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -229,7 +229,7 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- self.fifo.put(cmmd)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- def my_show(self,win,center=1):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- if sys.platform!='linux2':
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ if (sys.platform!='linux2') and (sys.platform!='darwin'):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- win.show()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- else: # autocenter, deiconify, and run mainloop
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- # this is a workaround for a bug in the
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -247,7 +247,7 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- win.deiconify()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- def my_withdraw(self,win):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- if sys.platform!='linux2':
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ if (sys.platform!='linux2') or (sys.platform!='darwin'):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- win.withdraw()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- else:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- win.destroy()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-Index: modules/pmg_tk/skins/normal/__init__.py
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-===================================================================
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- modules/pmg_tk/skins/normal/__init__.py (revision 4187)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ modules/pmg_tk/skins/normal/__init__.py (working copy)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -345,13 +345,13 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- win.show()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- def my_withdraw(self,win):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- if sys.platform!='linux2':
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ if (sys.platform!='linux2') and (sys.platform!='darwin'):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- win.withdraw()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- else:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- win.destroy()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- def my_activate(self,win,center=1,focus=None):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- if sys.platform!='linux2':
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ if (sys.platform!='linux2') and (sys.platform!='darwin'):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- win.activate()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- else: # autocenter, deiconify, and run mainloop
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- # this is a workaround for a bug in the
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -372,7 +372,7 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- win.mainloop()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- def my_deactivate(self,win):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- if sys.platform!='linux2':
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ if (sys.platform!='linux2') and (sys.platform!='darwin'):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- win.deactivate()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- else: # autocenter, deiconify, and run mainloop
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- win.destroy()
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/pymol/files/python_string_split.patch b/science/pymol/files/python_string_split.patch
</span>deleted file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index e6f7c284b60..00000000000
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/science/pymol/files/python_string_split.patch
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ /dev/null
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -1,580 +0,0 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-From aa0645e90fb6aab6180cca726e3f2a2453cde829 Mon Sep 17 00:00:00 2001
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-From: Thomas Holder <thomas.holder@schrodinger.com>
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-Date: Fri, 22 May 2020 08:45:20 +0200
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-Subject: [PATCH] Fix #101 `string.split()` usage in apbs_tools.py
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-Patch by @jwhowarth
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>----
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- modules/pmg_tk/startup/apbs_tools.py | 3 +--
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- 1 file changed, 1 insertion(+), 2 deletions(-)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-diff --git modules/pmg_tk/startup/apbs_tools.py modules/pmg_tk/startup/apbs_tools.py
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-index 75f06f22..473379bc 100644
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- modules/pmg_tk/startup/apbs_tools.py
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ modules/pmg_tk/startup/apbs_tools.py
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -145,7 +145,6 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- import tempfile
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- import os,math,re
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--import string
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- import sys
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if sys.version_info[0] < 3:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -269,7 +268,7 @@ def verify(name,f):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- searchDirs.append(os.path.join("/sw", "share", "apbs-mpi-lammpi", "tools", "manip"))
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- searchDirs.append(os.path.join("/usr", "local", "share", "tools", "manip"))
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- searchDirs.extend(string.split(os.environ["PATH"], ":"))
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ searchDirs.extend(os.environ["PATH"].split(":"))
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- searchDirs.append(os.path.join("/usr", "local", "bin"))
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- searchDirs.append(os.path.join("/opt", "local", "bin"))
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- searchDirs.append(os.path.join("/sw", "bin"))
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-From e1122b078e43fb7e503a32ed5c6176e8d36ec4ea Mon Sep 17 00:00:00 2001
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-From: Thomas Holder <thomas.holder@schrodinger.com>
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-Date: Fri, 22 May 2020 08:52:37 +0200
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-Subject: [PATCH] Fix remaining `string` module uses
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>----
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- examples/devel/importing.py | 3 +-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- examples/devel/syncmol.py | 2 +-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- modules/chempy/cc1.py | 8 +--
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- modules/chempy/mmd.py | 15 +++--
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- modules/chempy/mol.py | 11 ++--
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- modules/chempy/pdb.py | 15 +++--
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- modules/chempy/sdf.py | 7 +--
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- modules/chempy/tinker/amber.py | 101 ++++++++++++++++-----------------
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- modules/chempy/tinker/state.py | 9 ++-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- 9 files changed, 81 insertions(+), 90 deletions(-)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-diff --git examples/devel/importing.py examples/devel/importing.py
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-index f704356f..2daadf58 100644
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- examples/devel/importing.py
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ examples/devel/importing.py
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -12,13 +12,12 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- # sleep a second after importing.
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--import string
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- import __main__
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- # note that passing in a "-z" option would keep the window hidden
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- # until you called pymol.cmd.window("show").
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--__main__.pymol_argv= string.split("pymol -qxiF -X 300 -Y 100 -H 400 -W 400")
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+__main__.pymol_argv= "pymol -qxiF -X 300 -Y 100 -H 400 -W 400".split()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- import pymol
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- # give PyMOL enough time to initialize (we need to find a safe and
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-diff --git examples/devel/syncmol.py examples/devel/syncmol.py
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-index ef55cd24..bbce8926 100644
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- examples/devel/syncmol.py
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ examples/devel/syncmol.py
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -195,7 +195,7 @@ def handle(self):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- _stdin_reader_thread.setDaemon(1)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- _stdin_reader_thread.start()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- elif tok == 'send':
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- addr = string.split(sys.argv.pop(),':')
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ addr = sys.argv.pop().split(':')
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if len(addr)==1:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- host = 'localhost'
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- port = int(addr[0])
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-diff --git modules/chempy/cc1.py modules/chempy/cc1.py
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-index 199fff4a..2328c988 100644
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- modules/chempy/cc1.py
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ modules/chempy/cc1.py
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -15,8 +15,6 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- from chempy.models import Indexed
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- from chempy import Storage,Atom,Bond
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--import string
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- class CC1(Storage): # ChemDraw3D 5.0 std., cartesian coordinates
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- def fromList(self,molList):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -33,12 +31,12 @@ def fromList(self,molList):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- for a in range(nAtom):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- at = Atom()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- at.index = cnt
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- id_dict[string.strip(molList[irec][3:8])] = at.index
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ id_dict[molList[irec][3:8].strip()] = at.index
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- at.coord = [float(molList[irec][8:20]),
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- float(molList[irec][20:32]),float(molList[irec][32:44])]
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- at.symbol = string.strip(molList[irec][0:3])
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ at.symbol = molList[irec][0:3].strip()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- at.numeric_type = int(molList[irec][44:49])
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- lst = string.split(string.strip(molList[irec][49:]))
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ lst = molList[irec][49:].split()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- at.bonds = lst
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- irec = irec + 1
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- cnt = cnt + 1
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-diff --git modules/chempy/mmd.py modules/chempy/mmd.py
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-index ef8e16fe..a93262c3 100644
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- modules/chempy/mmd.py
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ modules/chempy/mmd.py
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -17,7 +17,6 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- from chempy.models import Indexed,Connected
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- from chempy import Storage,Atom,Bond
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--import string
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- import copy
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- class MMD(Storage):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -29,7 +28,7 @@ def fromList(self,MMODList):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- # get header information
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- nAtom = int(MMODList[0][1:6])
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- model.molecule.title = string.strip(MMODList[0][8:])
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ model.molecule.title = MMODList[0][8:].strip()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- irec = 1
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- # loop through atoms
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -42,7 +41,7 @@ def fromList(self,MMODList):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- at.numeric_type = int(MMODList[irec][1:4])
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- # extract connectivity information
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- tokens = string.splitfields(MMODList[irec][5:52])
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ tokens = MMODList[irec][5:52].split()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- at.neighbor = []
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- at.bondorder = []
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -61,20 +60,20 @@ def fromList(self,MMODList):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- # extract other information
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- at.coord = [float(MMODList[irec][53:64]),
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- float(MMODList[irec][65:76]), float(MMODList[irec][77:88])]
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- at.resi = string.strip(MMODList[irec][89:94])
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ at.resi = MMODList[irec][89:94].strip()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- at.resi_number = int(at.resi)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- resn_code = string.strip(MMODList[irec][94:95])
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ resn_code = MMODList[irec][94:95].strip()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if len(resn_code): at.resn_code = resn_code
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- color_code = string.strip(MMODList[irec][96:100])
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ color_code = MMODList[irec][96:100].strip()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if color_code!='':
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- at.color_code = int(color_code)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- else:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- at.color_code = 0
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- chain = string.strip(MMODList[irec][95:96])
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ chain = MMODList[irec][95:96].strip()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if len(chain): at.chain = chain
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- at.partial_charge = float(MMODList[irec][100:109])
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- at.resn = MMODList[irec][119:123]
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- name = string.strip(MMODList[irec][124:128])
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ name = MMODList[irec][124:128].strip()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if len(name): at.name = name
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- model.atom.append(at)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- irec = irec + 1
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-diff --git modules/chempy/mol.py modules/chempy/mol.py
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-index 175a248f..748a0aed 100644
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- modules/chempy/mol.py
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ modules/chempy/mol.py
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -20,7 +20,6 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- except ImportError:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- CmdException = Exception
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--import string
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- class MOL(Storage):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -29,9 +28,9 @@ def fromList(self,molList):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- model = Indexed()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- # read header information
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- model.molecule.title = string.strip(molList[0])
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- model.molecule.dim_code = string.strip(molList[1][20:22])
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- model.molecule.comments = string.strip(molList[2])
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ model.molecule.title = molList[0].strip()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ model.molecule.dim_code = molList[1][20:22].strip()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ model.molecule.comments = molList[2].strip()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- try:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- model.molecule.chiral = int(molList[3][12:15])
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- except:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -48,7 +47,7 @@ def fromList(self,molList):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- at.index = cnt
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- at.coord = [float(molList[irec][0:10]),
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- float(molList[irec][10:20]),float(molList[irec][20:30])]
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- at.symbol = string.strip(molList[irec][31:33])
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ at.symbol = molList[irec][31:33].strip()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- try:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- at.stereo = int(molList[irec][39:42])
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- except:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -75,7 +74,7 @@ def fromList(self,molList):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- # obtain formal charges from M CHG record
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- while molList[irec][0:6]!='M END':
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if molList[irec][0:6]=='M CHG':
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- cl = string.split(string.strip(molList[irec][6:]))
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ cl = molList[irec][6:].split()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- cll = int(cl[0])*2
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- a=1
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- while a<=cll:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-diff --git modules/chempy/pdb.py modules/chempy/pdb.py
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-index 505731e2..0d061be3 100644
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- modules/chempy/pdb.py
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ modules/chempy/pdb.py
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -14,7 +14,6 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- from chempy import Storage,Atom
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- from chempy.models import Indexed
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--import string
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- class PDB(Storage):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -31,11 +30,11 @@ def fromList(self,list): # currently no handling of conect records
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- at = Atom()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if rec[0]=='A': at.hetatm=0 # default is 1
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- at.index = cnt
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- at.name = string.strip(rec[12:16])
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- at.alt = string.strip(rec[16:17])
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- at.resn = string.strip(rec[17:20])
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- at.chain = string.strip(rec[21:22])
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- at.resi = string.strip(rec[22:27]) # note: insertion is part of resi
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ at.name = rec[12:16].strip()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ at.alt = rec[16:17].strip()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ at.resn = rec[17:20].strip()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ at.chain = rec[21:22].strip()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ at.resi = rec[22:27].strip() # note: insertion is part of resi
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- at.resi_number = int(rec[22:26])
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- at.coord = [float(rec[30:38]),
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- float(rec[38:46]),
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -48,8 +47,8 @@ def fromList(self,list): # currently no handling of conect records
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- at.b = float(rec[60:66])
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- except ValueError:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- at.b = 0.0
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- at.segi = string.strip(rec[72:76])
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- at.symbol = string.strip(rec[76:78])
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ at.segi = rec[72:76].strip()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ at.symbol = rec[76:78].strip()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if not len(at.symbol):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- at.symbol = at.name[0:1]
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if at.symbol in '012345678':
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-diff --git modules/chempy/sdf.py modules/chempy/sdf.py
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-index a36cd8d3..78e462f8 100644
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- modules/chempy/sdf.py
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ modules/chempy/sdf.py
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -14,7 +14,6 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- from __future__ import print_function
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--import string
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- import re
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- import copy
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -66,7 +65,7 @@ def __init__(self,sdflist):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- sd = self.data[kee]
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- l = l + 1
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- while l<ll:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- if len(string.strip(sdflist[l]))!=0:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ if sdflist[l].strip():
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- sd.append(sdflist[l])
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- l = l + 1
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- else:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -98,7 +97,7 @@ def get_single(self,kee): # automatic stripping
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if kee in self.data:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- sdk = self.data[kee]
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if len(sdk):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- return string.strip(sdk[0])
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ return sdk[0].strip()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- else:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- return None
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- else:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -142,7 +141,7 @@ def __init__(*args):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- return None
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if mode=='pf': # pseudofile
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- self.file = fname
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- elif (mode[0:1]=='r') and (string.find(fname,':')>1):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ elif mode[0:1] == 'r' and '://' in fname:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- # does this look like a URL? (but not a DOS path)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- try:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- from urllib import urlopen
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-diff --git modules/chempy/tinker/amber.py modules/chempy/tinker/amber.py
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-index 7ded34b2..1f4deec0 100644
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- modules/chempy/tinker/amber.py
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ modules/chempy/tinker/amber.py
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -16,7 +16,6 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- from chempy import feedback
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--import string
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- import copy
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- default_extra = { # atomic number, and normal valency (for tinker)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -126,33 +125,33 @@ def __init__(self,fname):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- self.type = []
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- self.mw = {}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- while 1:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- l = string.strip(f.readline())
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ l = f.readline().strip()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if not len(l): break
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- a2 = string.strip(l[0:2])
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ a2 = l[0:2].strip()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- self.type.append(a2)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- self.mw[a2] = [float(l[3:13]),string.strip(l[34:])]
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ self.mw[a2] = [float(l[3:13]),l[34:].strip()]
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- # skip 1
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- l = f.readline()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- # read bonds
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- self.bond = {}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- while 1:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- l = string.strip(f.readline())
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ l = f.readline().strip()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if not len(l): break
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- a5 = l[0:5]
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- self.bond[a5] = [float(l[5:12]),float(l[12:22]),
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- string.strip(l[22:])]
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ l[22:].strip()]
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- # read angles
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- self.angle = {}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- while 1:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- l = string.strip(f.readline())
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ l = f.readline().strip()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if not len(l): break
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- a5 = l[0:8]
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- self.angle[a5] = [float(l[8:16]),float(l[16:28]),
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- string.strip(l[28:])]
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ l[28:].strip()]
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- # read torsion
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- self.torsion = {}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- while 1:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- l = string.strip(f.readline())
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ l = f.readline().strip()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if not len(l): break
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- a5 = l[0:11]
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if a5 in self.torsion:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -161,49 +160,49 @@ def __init__(self,fname):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- float(l[15:27]),
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- float(l[27:36]),
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- abs(int(float(l[40:52]))),
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- string.strip(l[52:])])
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ l[52:].strip()])
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- else:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- self.torsion[a5] = [int(l[11:15]),
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- float(l[15:27]),
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- float(l[27:36]),
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- abs(int(float(l[40:52]))),
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- string.strip(l[52:])]
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ l[52:].strip()]
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- # read impropers
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- self.improper = {}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- while 1:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- l = string.strip(f.readline())
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ l = f.readline().strip()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if not len(l): break
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- a5 = l[0:11]
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- self.improper[a5] = [float(l[15:27]),
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- float(l[27:40]),
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- abs(int(float(l[40:51]))),
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- string.strip(l[51:])]
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ l[51:].strip()]
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- # skip
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- while 1:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- l = string.strip(f.readline())
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ l = f.readline().strip()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if not len(l): break
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- # read vdw equivalents
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- self.vdw_eq = {}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- while 1:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- l = string.strip(f.readline())
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ l = f.readline().strip()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if not len(l): break
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- a4 = string.strip(l[0:4])
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ a4 = l[0:4].strip()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- l = l[4:]
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- while len(l):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- self.vdw_eq[string.strip(l[0:4])] = a4
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ self.vdw_eq[l[0:4].strip()] = a4
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- l = l[4:]
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- # skip
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- l = string.strip(f.readline())
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ l = f.readline().strip()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- # read vdw parameters
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- self.vdw = {}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- while 1:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- l = string.strip(f.readline())
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ l = f.readline().strip()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if not len(l): break
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- l = ' ' + l
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- a4 = string.strip(l[0:4])
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ a4 = l[0:4].strip()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- self.vdw[a4] = [float(l[4:20]),
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- float(l[20:37]),
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- string.strip(l[37:])]
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ l[37:].strip()]
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- # read extra tinker information if present
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- self.extra = {}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -211,7 +210,7 @@ def __init__(self,fname):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- l = f.readline()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if not l: break
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if l[0:6] == 'TINKER':
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- self.extra[string.strip(l[6:12])] = [
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ self.extra[l[6:12].strip()] = [
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- int(l[12:18]),
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- int(l[18:24])]
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if not self.extra:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -757,7 +756,7 @@ def write_tinker_prm(self,fname,proofread=None,smooth=None):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- # bonds
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bond = {}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- for a in list(self.bond.keys()):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- kee = (map[string.strip(a[0:2])],map[string.strip(a[3:5])])
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ kee = (map[a[0:2].strip()],map[a[3:5].strip()])
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bond[kee] = a
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- kees = list(bond.keys())
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- kees.sort()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -768,9 +767,9 @@ def write_tinker_prm(self,fname,proofread=None,smooth=None):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- # angles
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- angle = {}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- for a in list(self.angle.keys()):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- kee = (map[string.strip(a[0:2])],
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- map[string.strip(a[3:5])],
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- map[string.strip(a[6:8])],
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ kee = (map[a[0:2].strip()],
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ map[a[3:5].strip()],
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ map[a[6:8].strip()],
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- )
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- angle[kee] = a
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- kees = list(angle.keys())
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -783,10 +782,10 @@ def write_tinker_prm(self,fname,proofread=None,smooth=None):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if not smooth:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- improper = {}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- for a in self.improper.keys():
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- kee = (map[string.strip(a[0:2])],
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- map[string.strip(a[3:5])],
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- map[string.strip(a[6:8])],
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- map[string.strip(a[9:11])],
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ kee = (map[a[0:2].strip()],
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ map[a[3:5].strip()],
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ map[a[6:8].strip()],
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ map[a[9:11].strip()],
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- )
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- improper[kee] = a
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- kees = list(improper.keys())
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -799,10 +798,10 @@ def write_tinker_prm(self,fname,proofread=None,smooth=None):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- else:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- improper = {}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- for a in self.improper.keys():
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- kee = (map[string.strip(a[0:2])],
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- map[string.strip(a[3:5])],
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- map[string.strip(a[6:8])],
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- map[string.strip(a[9:11])],
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ kee = (map[a[0:2].strip()],
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ map[a[3:5].strip()],
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ map[a[6:8].strip()],
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ map[a[9:11].strip()],
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- )
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- improper[kee] = a
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- kees = list(improper.keys())
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -814,10 +813,10 @@ def write_tinker_prm(self,fname,proofread=None,smooth=None):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- # torsions
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- torsion = {}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- for a in self.torsion.keys():
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- kee = (map[string.strip(a[0:2])],
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- map[string.strip(a[3:5])],
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- map[string.strip(a[6:8])],
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- map[string.strip(a[9:11])],
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ kee = (map[a[0:2].strip()],
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ map[a[3:5].strip()],
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ map[a[6:8].strip()],
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ map[a[9:11].strip()],
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- )
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- torsion[kee] = a
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- kees = list(torsion.keys())
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -834,7 +833,7 @@ def write_tinker_prm(self,fname,proofread=None,smooth=None):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- lst[0]/div,lst[1],lst[2])
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- lst = lst[5:]
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- while len(st)>79:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- st = string.replace(st,' ',' ')
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ st = st.replace(' ',' ')
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- f.write(st+"\n")
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- # null charge records
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- for c in range(len(self.present)):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -876,7 +875,7 @@ def get_list(self):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bnd_list = []
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bond = {}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- for a in list(self.bond.keys()):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- kee = (map[string.strip(a[0:2])],map[string.strip(a[3:5])])
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ kee = (map[a[0:2].strip()],map[a[3:5].strip()])
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bond[kee] = a
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- kees = list(bond.keys())
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- kees.sort()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -888,9 +887,9 @@ def get_list(self):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- ang_list = []
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- angle = {}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- for a in self.angle.keys():
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- kee = (map[string.strip(a[0:2])],
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- map[string.strip(a[3:5])],
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- map[string.strip(a[6:8])],
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ kee = (map[a[0:2].strip()],
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ map[a[3:5].strip()],
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ map[a[6:8].strip()],
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- )
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- angle[kee] = a
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- kees = list(angle.keys())
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -903,10 +902,10 @@ def get_list(self):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- imp_list = []
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- improper = {}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- for a in self.improper.keys():
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- kee = (map[string.strip(a[0:2])],
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- map[string.strip(a[3:5])],
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- map[string.strip(a[6:8])],
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- map[string.strip(a[9:11])],
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ kee = (map[a[0:2].strip()],
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ map[a[3:5].strip()],
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ map[a[6:8].strip()],
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ map[a[9:11].strip()],
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- )
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- improper[kee] = a
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- kees = list(improper.keys())
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -920,10 +919,10 @@ def get_list(self):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- tor_list = []
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- torsion = {}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- for a in self.torsion.keys():
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- kee = (map[string.strip(a[0:2])],
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- map[string.strip(a[3:5])],
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- map[string.strip(a[6:8])],
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- map[string.strip(a[9:11])],
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ kee = (map[a[0:2].strip()],
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ map[a[3:5].strip()],
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ map[a[6:8].strip()],
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ map[a[9:11].strip()],
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- )
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- torsion[kee] = a
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- kees = list(torsion.keys())
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-diff --git modules/chempy/tinker/state.py modules/chempy/tinker/state.py
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-index 93e3f286..2df7187e 100644
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- modules/chempy/tinker/state.py
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ modules/chempy/tinker/state.py
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -17,7 +17,6 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- from chempy import tinker,io,feedback
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- from chempy.tinker import keyword
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- import copy
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--import string
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- class State:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -81,15 +80,15 @@ def analyze(self,kw=None,summary=1):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if not flag:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if lin[0:25]==' Total Potential Energy :':
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- self.summary.append([
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- string.strip(lin[0:23]),
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ lin[0:23].strip(),
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- float(lin[25:49])])
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- flag = 1
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- else:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- tok = string.split(string.strip(lin))
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ tok = lin.split()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if len(tok):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if(tok[0]!='Energy'):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- self.summary.append([
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- string.strip(lin[0:23]),
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ lin[0:23].strip(),
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- float(lin[25:49]),
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- int(lin[49:64])])
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- f.close()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -150,7 +149,7 @@ def minimize(self,gradient=0.1,max_iter=100,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- float(lin[41:51]),
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- float(lin[51:60]),
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- int(lin[60:67]),
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- string.strip(lin[67:])])
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ lin[67:].strip()])
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- except ValueError:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- pass
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- f.close()
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/pymol/files/setup.py.diff b/science/pymol/files/setup.py.diff
</span><span style='display:block; white-space:pre;color:#808080;'>index 060ec74dff1..9a9b3b23277 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/science/pymol/files/setup.py.diff
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/science/pymol/files/setup.py.diff
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -1,13 +1,11 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-Index: setup.py
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-===================================================================
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- setup.py (revision 4187)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ setup.py (working copy)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -87,7 +87,7 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- setup.py.orig 2021-05-10 14:38:37.000000000 -0400
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ setup.py 2021-05-14 11:35:43.000000000 -0400
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -92,7 +92,7 @@
</span> X11 = ['/usr/X11'] * (not options.osx_frameworks)
if sys.platform == 'darwin':
- for prefix in ['/sw', '/opt/local', '/usr/local']:
+ for prefix in ['@PREFIX@', '/usr/local']:
<span style='display:block; white-space:pre;background:#ffe0e0;'>- if sys.executable.startswith(prefix):
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ if sys.base_prefix.startswith(prefix):
</span> return [prefix] + X11
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