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authorje_fro <je_fro@32389bae-6d03-0410-99cf-db05cde120eb>2008-07-06 03:07:36 +0000
committerje_fro <je_fro@32389bae-6d03-0410-99cf-db05cde120eb>2008-07-06 03:07:36 +0000
commit1e308e619f99fdce7f6ea69691239102842abc8d (patch)
treef6cf3ff9353b3f5bc9013393b6070debc72d7cdc /sci-chemistry/pymol/files
parentImport for testing (diff)
downloadsci-1e308e619f99fdce7f6ea69691239102842abc8d.tar.gz
sci-1e308e619f99fdce7f6ea69691239102842abc8d.tar.bz2
sci-1e308e619f99fdce7f6ea69691239102842abc8d.zip
patches
git-svn-id: http://overlays.gentoo.org/svn/proj/science/overlay@1179 32389bae-6d03-0410-99cf-db05cde120eb
Diffstat (limited to 'sci-chemistry/pymol/files')
-rw-r--r--sci-chemistry/pymol/files/apbs-070604.patch1666
-rw-r--r--sci-chemistry/pymol/files/nosplash-gentoo.patch9
-rw-r--r--sci-chemistry/pymol/files/pymol-1.1-r1-data-path.patch51
-rw-r--r--sci-chemistry/pymol/files/pymol-1.1-r1-shaders.patch11
4 files changed, 1737 insertions, 0 deletions
diff --git a/sci-chemistry/pymol/files/apbs-070604.patch b/sci-chemistry/pymol/files/apbs-070604.patch
new file mode 100644
index 000000000..7f7caef73
--- /dev/null
+++ b/sci-chemistry/pymol/files/apbs-070604.patch
@@ -0,0 +1,1666 @@
+diff -Nu -Nu -uarN pymol-9999.orig/modules/pmg_tk/startup/apbs_tools.py pymol-9999/modules/pmg_tk/startup/apbs_tools.py
+--- pymol-9999.orig/modules/pmg_tk/startup/apbs_tools.py 2008-06-26 19:59:35.000000000 +0200
++++ pymol-9999/modules/pmg_tk/startup/apbs_tools.py 2008-06-26 20:00:32.000000000 +0200
+@@ -8,7 +8,7 @@
+ # notices.
+ #
+ # ----------------------------------------------------------------------
+-# APBS TOOLS is Copyright (C) 2005 by Michael G. Lerner
++# APBS TOOLS is Copyright (C) 2007 by Michael G. Lerner
+ #
+ # All Rights Reserved
+ #
+@@ -31,31 +31,245 @@
+ # ----------------------------------------------------------------------
+
+ """
++
++A NOTE TO OTHER DEVELOPERS:
++
++I understand that I'm giving this code away for Free, and that there's
++not a ton of great sample PyMOL plugin code out there, so feel free to
++use this as a template. However, please acknowledge me in some way if
++you do (somewhere in the comments if you only use a little bit of code
++or something more if you use a lot). In fact, if you just use the code
++as a skeleton for your interface and include most of it in your plugin
++without acknowledging me, then you're probably violating the copyright
++notice above.
++
++Thanks.
++
++-Michael
++
++TODO Before Release:
++
++ - Use 'acc' to calculate solvent-accessible surface areas. We'll use
++ the PyMOL 'standard' method and store this data as B-factors.
++
++ - Follow psize.py's memory calculation logic.
++
++ - Use getUnassignedAtomsFromPqr(...) on pdb2pqr-generated PQR files
++
+ Recent changes:
++
++Updates for XXXXXXX version
++ - Added second visualization pane. The previous interface for multiple
++ maps may not have been the most obvious one.
++
++ - Some of the APBS scripts (psize.py, etc.) are fail when columns run
++ together. Therefore, we remove information about chain, occupancy and
++ B-factor when writing out pdb and pqr files. We also round things to
++ three post-decimal digits of accuracy. That's not even quite enough,
++ so I added cleanupGeneratedPdbOrPqrFile() to fix things like coordinate lines
++ like 94.623-100.040 --> 94.62 -100.040
++ It just truncates the third post-decimal digit as necessary.
++
++ - updated memory checking requirements. Before, we used maxgridpoints.
++ Now, we're just trying something like gmemceil in APBS's psize.py.
++ That has two relevant lines:
++ nsmem = 200.0 * nsmall[0] * nsmall[1] * nsmall[2] / 1024 / 1024
++ if nsmem < self.constants["gmemceil"]:
++ and
++ gmem = 200.0 * n[0] * n[1] * n[2] / 1024 / 1024
++ if gmem > self.constants["gmemceil"]:
++ where n is finegridpoints.
++ We now do the same thing, and warn if we're truncating. For 400MB,
++ our old cutoff was
++ 400 = 200.0*maxgridpoints / 1024 / 1024
++ 400 * 1024 * 1024 / 200.0 = maxgridpoints
++ maxgridpoints = 2*1024*1024
++
++
++
++Updates for 04-06-2007 version
++ - Can now display multiple molecules with multiple maps at the same time.
++ - Ditto for iso surfaces.
++
++Updates for 03-12-2007 version
++ - Use regexp to check PDB2PQR generated PQR file, as per Todd Dolinsky's
++ suggestion.
++ - Added a little more on About Pane's splash screen.
++ - Switched About Pane's splash screen to include a scroll bar and let
++ you cut-n-paste from it, as per the Caver plugin
++ (http://loschmidt.chemi.muni.cz/caver/index.php).
++ - Removed warnings about spaces in directory names. The calls to
++ subprocess should take care of that now.
++
++Updates for the 03-08-2007 version
++ - Generalized default locations for programs, based on suggestions from
++ Warren DeLano, Nathan Baker and Luca Jovine.
++ - Made run(...) use os.system when subprocess does not exist.
++ - Now makes a feeble attempt to figure out what atoms PDB2PQR does not
++ understand, and warns user about them.
++ - Automatically refreshes and switches to the Visualization pane after
++ successfully running APBS.
++
++Updates for the 3-05-2007 version
++ - Switched everything over to the subprocess module.
++ - This allows us to deal with spaces in the directory name.
++ - It also allows better error reporting.
++ - I think this means we require python >= 2.4 as a backend.
++ - Subprocess output (apbs, pdb2pqr) now echoed to main PyMOL
++ window. Should make for way better debugging on Windows.
++ Also includes copyright notices, etc.
++
++Updates for the 3-01-2007 version
++ - Changes per Nathan Baker's email
++ - Changed 'Linear PB equation' to 'Linearized PB equation'
++ - Changed default APBS mode to 'Linearized PB equation'
++ - Removed 'focusing' from the list of boundary conditions
++ - Added 'Browse' feature as well as awareness of TEMP environment
++ variable for temporary file locations
++ - pdb2pqr location button no longer sets psize location (oops)
++ - Slightly better error reporting. Someday, should switch to
++ *spawn for messages that would actually be useful to the user.
++
++Updates for 2-23-2007 version
++ - Updates for APBS 0.5.0
++ - Added New Quintic b-spline as option for chgm.
++ - Added 7th-order polynomial as option for srfm
++ - Fixed bug (in my code, not APBS) where srfm was ignored
++ - Removed gamma line from ELEC section. It has been moved to the APOLAR
++ section in APBS now, and it is not relevant to our calculations. It was
++ only included because it was required before.
++ - Updated APBS url
++ - Updated copyright notice
++ - Updated text on About pane
++
++Update for new version
++ - Removed the test code. Nobody was using that code because nobody runs this
++ as a standalone app. Code rot avoided.
++ - Fixed typo in visualization pane: kT -> kT/e
++ - Changed defaults:
++ - interior_dielectric: 2.0 (unchanged)
++ - solvent_dielectric: 78.0 (was 80)
++ - ion_plus_one_conc: 0.15M (was 0)
++ - ion_minus_one_conc: 0.15M (was 0)
++ - ion_minus_one_rad: 1.8A (was 2.0)
++ - Made surface_solvent default to 1 (show solvent-accessible surface as
++ default)
++ - Changed "APBS Location" tab to "Program Locations"
++ - Added in ability to use pdb2pqr to generate pqr file.
++ NOTE: THE IMPLEMENTATION IS A SECURITY HOLE
++ because it calls directly through to os.system().
++ In most real-world cases, I doubt that actually matters, but people
++ should be aware of it.
++
+ Switched to new APBS input format
+ - changed sfrm 1 to srfm smol
+ - changed bcfl to use words instead of numbers
+ - changed chgm to use words instead of numbers
+ - added sdens parameter (default to APBS default of 10.0)
+- - tweaked 'max grid points' to give an acceptable number .. we assume nlev == 4. see comments in the source .. it's still possible to exceed max grid points by a little bit.
++ - tweaked 'max grid points' to give an acceptable number .. we assume
++ nlev == 4. see comments in the source .. it's still possible to exceed
++ max grid points by a little bit.
+ """
+
+
+ from __future__ import division
+ from __future__ import generators
+
+-import os,math
++import os,math,re
+ import Tkinter
+ from Tkinter import *
+ import Pmw
+ import distutils.spawn # used for find_executable
+ import traceback
++import pymol
+
+ #
+ # Global config variables
+ #
++
+ APBS_BINARY_LOCATION = None
+ APBS_PSIZE_LOCATION = None
++APBS_PDB2PQR_LOCATION = None
++TEMPORARY_FILE_DIR = None
++
++#
++# Default locations for programs are searched in this order:
++#
++# 1) the global config variables above
++# 2) environment variables
++# 3) something in the PATH
++# 4) known default locations, in order
++#
++# Typically, we will list the pymol-bundled locations last, so that
++# user-installed versions will override them. If the user doesn't
++# want their own version, they can feel free to uninstall it.
++#
++# These are defined in the tuples below, in that order.
++#
++default_locations = {'apbs_binary':(APBS_BINARY_LOCATION,
++ 'APBS_BINARY',
++ 'apbs',
++ '/usr/bin/apbs',
++ os.path.join(os.environ['PYMOL_PATH'],'ext/bin/apbs'),
++ ),
++ 'apbs_psize': (APBS_PSIZE_LOCATION,
++ 'APBS_PSIZE',
++ 'psize.py',
++ '/usr/share/apbs/tools/manip/psize.py',
++ os.path.join(os.environ['PYMOL_PATH'],'ext/bin/psize.py'),
++ ),
++ 'pdb2pqr': (APBS_PDB2PQR_LOCATION,
++ 'APBS_PDB2PQR',
++ 'pdb2pqr.py',
++ # Note: subprocess.call really doesn't like
++ # the way /sw/bin/pdb2pqr wraps pdb2pqr.py
++ #'/sw/bin/pdb2pqr',
++ '/usr/LIBANDPYTHON/site-packages/pdb2pqr/pdb2pqr.py',
++ os.path.join(os.environ['PYMOL_PATH'],'ext/bin/pdb2pqr'),
++ ),
++ 'temp': (TEMPORARY_FILE_DIR,
++ 'TEMP',
++ None, # None means don't look for an executable
++ os.path.abspath(os.path.curdir),
++ ),
++ }
++def get_default_location(name,fileordir='file'):
++ """
++ This searches through a tuple. In order, the elements of the tuple are
++ 1) A global config variable
++ 2) The name of an environment variable
++ 3) The name of an executable. We search PATH for it.
++ 3-whatever) known default locations, searched in order
++
++ If any of those are set to None, they'll be skipped. E.g. we set 3) to
++ None for the temporary file directory, as there's no executable
++ associated with it.
++
++ This isn't a perfectly elegant solution, but I don't think the problem
++ warrants anything more heavyweight than this.
++ """
++ verbose = True
++ global default_locations
++ choices = default_locations[name]
++ correct = {'file':os.path.isfile,
++ 'dir':os.path.isdir,}[fileordir]
++ if (choices[0] is not None) and correct(choices[0]):
++ if verbose: print "default location for",name,choices[0],"global var"
++ return choices[0]
++ elif (choices[1] in os.environ) and correct(choices[1]):
++ if verbose: print "default location for",name,os.environ[choices[1]],"environment var"
++ return os.environ[choices[1]]
++ elif choices[2] is not None:
++ result = distutils.spawn.find_executable(choices[2])
++ if (result is not None) and correct(result):
++ if verbose: print "default location for",name,result,"in path"
++ return result
++ for choice in choices[3:]:
++ if correct(choice):
++ if verbose: print "default location for",name,choice,"found default installation"
++ return choice
++ if verbose: print "default location for",name,"is not found"
++ return ''
+
+ # Python backward-compatibility...
+ try:
+@@ -66,352 +280,6 @@
+ False
+ except:
+ False = 0
+-#
+-# Cheap hack for testing purposes
+-#
+-try:
+- import pymol
+- REAL_PYMOL = True
+-except ImportError:
+- REAL_PYMOL = False
+- class pymol:
+- class cmd:
+- def load(self,name,sel=''):
+- pass
+- def get_names(self):
+- return ['mol1','mol2','map1','map2']
+- def get_type(self,thing):
+- if thing.startswith('mol'):
+- return 'object:molecule'
+- else:
+- return 'object:map'
+- def save(self,fname,selection):
+- f = file(fname,'w')
+- if fname.endswith('.pqr'):
+- f.write("""HEADER this is a header, kids
+-REMARK Format: x y z charge radius
+-ATOM 1 N MET 1 0.551 11.263 11.815 -0.300 1.8240
+-ATOM 2 CA MET 1 0.930 12.648 11.845 0.250 1.9643
+-ATOM 3 C MET 1 2.423 12.834 11.663 0.500 2.1046
+-ATOM 4 O MET 1 3.286 11.970 11.947 -0.500 1.6612
+-ATOM 5 CB MET 1 0.580 13.368 13.143 -0.120 1.9643
+-ATOM 6 CG MET 1 1.661 12.986 14.098 0.098 1.9643
+-ATOM 7 SD MET 1 1.441 13.562 15.776 -0.435 1.9924
+-ATOM 8 CE MET 1 2.528 12.285 16.478 0.037 1.9643
+-ATOM 9 N ILE 2 2.656 14.070 11.163 -0.500 1.8240
+-ATOM 10 CA ILE 2 3.942 14.570 10.821 0.140 1.9643
+-ATOM 11 C ILE 2 4.414 15.563 11.777 0.500 2.1046
+-ATOM 12 O ILE 2 3.666 16.500 12.106 -0.500 1.6612
+-ATOM 13 CB ILE 2 3.780 15.262 9.428 -0.060 1.9643
+-ATOM 14 CG1 ILE 2 3.485 14.180 8.372 -0.120 1.9643
+-ATOM 15 CG2 ILE 2 4.987 16.173 9.033 -0.180 1.9643
+-ATOM 16 CD ILE 2 2.969 14.795 7.082 -0.180 1.9643
+-ATOM 17 N SER 3 5.637 15.334 12.115 -0.500 1.8240
+-ATOM 18 CA SER 3 6.368 16.180 13.050 0.140 1.9643
+-ATOM 19 C SER 3 7.703 16.646 12.468 0.500 2.1046
+-ATOM 20 O SER 3 8.363 15.914 11.750 -0.500 1.6612
+-ATOM 21 CB SER 3 6.751 15.301 14.298 0.145 1.9643
+-ATOM 22 OG SER 3 5.544 14.967 14.987 -0.683 1.7510
+-ATOM 23 N LEU 4 8.112 17.862 12.816 -0.500 1.8240
+-ATOM 24 CA LEU 4 9.370 18.301 12.353 0.140 1.9643
+-ATOM 25 C LEU 4 10.283 18.416 13.583 0.500 2.1046
+-ATOM 26 O LEU 4 9.765 18.812 14.627 -0.500 1.6612
+-ATOM 27 CB LEU 4 9.230 19.754 11.875 -0.120 1.9643
+-ATOM 28 CG LEU 4 8.684 19.996 10.452 -0.060 1.9643
+-ATOM 29 CD1 LEU 4 7.569 19.115 9.957 -0.180 1.9643
+-ATOM 30 CD2 LEU 4 8.477 21.499 10.173 -0.180 1.9643
+-ATOM 31 N ILE 5 11.555 18.104 13.495 -0.500 1.8240
+-ATOM 32 CA ILE 5 12.465 18.230 14.624 0.140 1.9643
+-ATOM 33 C ILE 5 13.636 19.013 14.159 0.500 2.1046
+-ATOM 34 O ILE 5 14.222 18.681 13.116 -0.500 1.6612
+-ATOM 35 CB ILE 5 12.811 16.919 15.273 -0.060 1.9643
+-ATOM 36 CG1 ILE 5 13.886 17.156 16.315 -0.120 1.9643
+-ATOM 37 CG2 ILE 5 13.298 15.880 14.184 -0.180 1.9643
+-ATOM 38 CD ILE 5 13.981 15.939 17.251 -0.180 1.9643
+-ATOM 39 N ALA 6 14.012 20.093 14.895 -0.500 1.8240
+-ATOM 40 CA ALA 6 15.137 20.934 14.463 0.140 1.9643
+-ATOM 41 C ALA 6 15.851 21.640 15.619 0.500 2.1046
+-ATOM 42 O ALA 6 15.235 21.839 16.668 -0.500 1.6612
+-ATOM 43 CB ALA 6 14.449 22.032 13.594 -0.180 1.9643
+-ATOM 44 N ALA 7 17.119 21.996 15.415 -0.500 1.8240
+-ATOM 45 CA ALA 7 17.962 22.700 16.346 0.140 1.9643
+-ATOM 46 C ALA 7 18.099 24.081 15.714 0.500 2.1046
+-ATOM 47 O ALA 7 18.503 24.190 14.577 -0.500 1.6612
+-ATOM 48 CB ALA 7 19.279 22.022 16.626 -0.180 1.9643
+-ATOM 49 N LEU 8 17.738 25.159 16.435 -0.500 1.8240
+-ATOM 50 CA LEU 8 17.767 26.510 15.918 0.140 1.9643
+-ATOM 51 C LEU 8 18.542 27.441 16.789 0.500 2.1046
+-ATOM 52 O LEU 8 18.344 27.380 17.993 -0.500 1.6612
+-ATOM 53 CB LEU 8 16.306 27.133 16.150 -0.120 1.9643
+-ATOM 54 CG LEU 8 15.245 26.745 15.191 -0.060 1.9643
+-ATOM 55 CD1 LEU 8 14.714 25.361 15.532 -0.180 1.9643
+-ATOM 56 CD2 LEU 8 14.133 27.753 15.245 -0.180 1.9643
+-ATOM 57 N ALA 9 19.354 28.324 16.136 -0.500 1.8240
+-ATOM 58 CA ALA 9 20.109 29.322 16.859 0.140 1.9643
+-ATOM 59 C ALA 9 19.268 30.562 16.781 0.500 2.1046
+-ATOM 60 O ALA 9 18.052 30.512 16.395 -0.500 1.6612
+-ATOM 61 CB ALA 9 21.496 29.499 16.312 -0.180 1.9643
+-ATOM 62 N VAL 10 19.908 31.695 17.172 -0.500 1.8240
+-ATOM 63 CA VAL 10 19.182 32.944 17.121 0.140 1.9643
+-ATOM 64 C VAL 10 18.853 33.270 15.681 0.500 2.1046
+-ATOM 65 O VAL 10 19.589 32.940 14.704 -0.500 1.6612
+-ATOM 66 CB VAL 10 19.896 34.147 17.775 -0.060 1.9643
+-ATOM 67 CG1 VAL 10 20.668 33.742 19.022 -0.180 1.9643
+-ATOM 68 CG2 VAL 10 20.692 34.984 16.815 -0.180 1.9643
+-ATOM 69 N ASP 11 17.742 33.900 15.528 -0.500 1.8240
+-ATOM 70 CA ASP 11 17.367 34.231 14.199 0.140 1.9643
+-ATOM 71 C ASP 11 16.970 33.019 13.371 0.500 2.1046
+-ATOM 72 O ASP 11 16.959 33.131 12.206 -0.500 1.6612
+-ATOM 73 CB ASP 11 18.378 35.124 13.467 -0.220 1.9643
+-ATOM 74 CG ASP 11 18.356 36.564 14.035 0.700 2.1046
+-ATOM 75 OD1 ASP 11 17.333 37.176 14.327 -0.800 1.6612
+-ATOM 76 OD2 ASP 11 19.538 37.099 14.146 -0.800 1.6612
+-ATOM 77 N ARG 12 16.634 31.897 13.959 -0.500 1.8240
+-ATOM 78 CA ARG 12 16.193 30.711 13.247 0.140 1.9643
+-ATOM 79 C ARG 12 17.224 30.074 12.351 0.500 2.1046
+-ATOM 80 O ARG 12 16.841 29.226 11.518 -0.500 1.6612
+-ATOM 81 CB ARG 12 14.891 30.911 12.489 -0.120 1.9643
+-ATOM 82 CG ARG 12 13.770 31.437 13.345 -0.050 1.9643
+-ATOM 83 CD ARG 12 12.435 31.161 12.721 0.190 1.9643
+-ATOM 84 NE ARG 12 12.462 31.677 11.381 -0.700 1.8240
+-ATOM 85 CZ ARG 12 12.456 32.954 11.069 0.640 1.2628
+-ATOM 86 NH1 ARG 12 12.421 33.916 11.940 -0.800 1.8240
+-ATOM 87 NH2 ARG 12 12.494 33.278 9.801 -0.800 1.8240
+-ATOM 88 N VAL 13 18.498 30.450 12.518 -0.500 1.8240
+-ATOM 89 CA VAL 13 19.531 29.853 11.712 0.140 1.9643
+-ATOM 90 C VAL 13 19.672 28.345 12.064 0.500 2.1046
+-ATOM 91 O VAL 13 19.821 27.968 13.233 -0.500 1.6612
+-ATOM 92 CB VAL 13 20.863 30.533 11.990 -0.060 1.9643
+-ATOM 93 CG1 VAL 13 22.042 29.742 11.406 -0.180 1.9643
+-ATOM 94 CG2 VAL 13 20.797 31.998 11.467 -0.180 1.9643
+-ATOM 95 N ILE 14 19.629 27.482 11.056 -0.500 1.8240
+-ATOM 96 CA ILE 14 19.767 26.011 11.271 0.140 1.9643
+-ATOM 97 C ILE 14 20.995 25.409 10.552 0.500 2.1046
+-ATOM 98 O ILE 14 21.399 24.278 10.747 -0.500 1.6612
+-ATOM 99 CB ILE 14 18.506 25.235 10.843 -0.060 1.9643
+-ATOM 100 CG1 ILE 14 18.151 25.494 9.365 -0.120 1.9643
+-ATOM 101 CG2 ILE 14 17.307 25.571 11.723 -0.180 1.9643
+-ATOM 102 CD ILE 14 16.862 24.785 8.834 -0.180 1.9643
+-ATOM 103 N GLY 15 21.623 26.185 9.656 -0.500 1.8240
+-ATOM 104 CA GLY 15 22.773 25.644 8.908 0.080 1.9643
+-ATOM 105 C GLY 15 23.579 26.679 8.113 0.500 2.1046
+-ATOM 106 O GLY 15 23.216 27.824 8.023 -0.500 1.6612
+-ATOM 107 N MET 16 24.685 26.243 7.585 -0.500 1.8240
+-ATOM 108 CA MET 16 25.630 27.043 6.835 0.140 1.9643
+-ATOM 109 C MET 16 26.562 26.064 6.140 0.500 2.1046
+-ATOM 110 O MET 16 26.419 24.841 6.284 -0.500 1.6612
+-ATOM 111 CB MET 16 26.454 27.903 7.783 -0.120 1.9643
+-ATOM 112 CG MET 16 27.215 27.034 8.748 0.098 1.9643
+-ATOM 113 SD MET 16 28.614 27.916 9.432 -0.435 1.9924
+-ATOM 114 CE MET 16 29.524 27.955 7.874 0.037 1.9643
+-ATOM 115 N GLU 17 27.509 26.591 5.380 -0.500 1.8240
+-ATOM 116 CA GLU 17 28.375 25.714 4.685 0.140 1.9643
+-ATOM 117 C GLU 17 29.197 24.820 5.561 0.500 2.1046
+-ATOM 118 O GLU 17 29.293 23.610 5.320 -0.500 1.6612
+-ATOM 119 CB GLU 17 29.332 26.532 3.738 -0.120 1.9643
+-ATOM 120 CG GLU 17 28.646 27.132 2.520 -0.220 1.9643
+-ATOM 121 CD GLU 17 28.159 26.083 1.541 0.700 2.1046
+-ATOM 122 OE1 GLU 17 28.336 24.880 1.823 -0.800 1.6612
+-ATOM 123 OE2 GLU 17 27.599 26.466 0.492 -0.800 1.6612
+-ATOM 124 N ASN 18 29.817 25.419 6.557 -0.500 1.8240
+-ATOM 125 CA ASN 18 30.671 24.623 7.428 0.140 1.9643
+-ATOM 126 C ASN 18 29.968 24.072 8.644 0.500 2.1046
+-ATOM 127 O ASN 18 28.800 24.344 8.861 -0.500 1.6612
+-ATOM 128 CB ASN 18 31.891 25.429 7.870 -0.120 1.9643
+-ATOM 129 CG ASN 18 32.673 26.009 6.672 0.500 2.1046
+-ATOM 130 ND2 ASN 18 32.793 25.192 5.612 -0.760 1.8240
+-ATOM 131 OD1 ASN 18 33.131 27.181 6.693 -0.500 1.6612
+-ATOM 132 N ALA 19 30.721 23.301 9.419 -0.500 1.8240
+-ATOM 133 CA ALA 19 30.158 22.732 10.649 0.140 1.9643
+-ATOM 134 C ALA 19 29.808 23.892 11.608 0.500 2.1046
+-ATOM 135 O ALA 19 30.553 24.855 11.718 -0.500 1.6612
+-ATOM 136 CB ALA 19 31.208 21.851 11.326 -0.180 1.9643
+-ATOM 137 N MET 20 28.661 23.767 12.282 -0.500 1.8240
+-ATOM 138 CA MET 20 28.173 24.753 13.256 0.140 1.9643
+-ATOM 139 C MET 20 29.215 24.880 14.367 0.500 2.1046
+-ATOM 140 O MET 20 29.858 23.879 14.759 -0.500 1.6612
+-ATOM 141 CB MET 20 26.859 24.207 13.808 -0.120 1.9643
+-ATOM 142 CG MET 20 25.790 24.287 12.739 0.098 1.9643
+-ATOM 143 SD MET 20 25.744 25.961 12.033 -0.435 1.9924
+-ATOM 144 CE MET 20 24.199 26.587 12.680 0.037 1.9643
+-ATOM 1257 N ARG 21 -2.365 24.238 17.120 -0.500 1.8240
+-ATOM 1258 CA ARG 21 -3.722 24.429 17.637 0.040 1.9643
+-ATOM 1259 C ARG 21 -4.816 24.158 16.587 0.700 2.1046
+-ATOM 1260 O1 ARG 21 -4.718 24.783 15.486 -0.800 1.6612
+-ATOM 1261 CB ARG 21 -3.918 25.826 18.162 -0.120 1.9643
+-ATOM 1262 CG ARG 21 -3.019 26.176 19.341 -0.050 1.9643
+-ATOM 1263 CD ARG 21 -3.363 27.548 19.971 0.190 1.9643
+-ATOM 1264 NE ARG 21 -2.493 27.864 21.095 -0.700 1.8240
+-ATOM 1265 CZ ARG 21 -2.590 28.986 21.801 0.640 1.2628
+-ATOM 1266 NH1 ARG 21 -3.514 29.885 21.492 -0.800 1.8240
+-ATOM 1267 NH2 ARG 21 -1.762 29.206 22.813 -0.800 1.8240
+-ATOM 1268 O2 ARG 21 -5.807 23.410 16.918 -0.800 1.6612
+-END
+-
+-""")
+-
+- elif fname.endswith('.pdb'):
+- f.write("""ATOM 1 N MET 1 0.551 11.263 11.815 1.00 32.15 N
+-ATOM 2 CA MET 1 0.930 12.648 11.845 1.00 25.55 C
+-ATOM 3 C MET 1 2.423 12.834 11.663 1.00 20.72 C
+-ATOM 4 O MET 1 3.286 11.970 11.947 1.00 24.07 O
+-ATOM 5 CB MET 1 0.580 13.368 13.143 1.00 31.39 C
+-ATOM 6 CG MET 1 1.661 12.986 14.098 1.00 46.81 C
+-ATOM 7 SD MET 1 1.441 13.562 15.776 1.00 59.99 S
+-ATOM 8 CE MET 1 2.528 12.285 16.478 1.00 57.80 C
+-ATOM 9 N ILE 2 2.656 14.070 11.163 1.00 20.22 N
+-ATOM 10 CA ILE 2 3.942 14.570 10.821 1.00 20.46 C
+-ATOM 11 C ILE 2 4.414 15.563 11.777 1.00 11.61 C
+-ATOM 12 O ILE 2 3.666 16.500 12.106 1.00 16.02 O
+-ATOM 13 CB ILE 2 3.780 15.262 9.428 1.00 27.69 C
+-ATOM 14 CG1 ILE 2 3.485 14.180 8.372 1.00 27.14 C
+-ATOM 15 CG2 ILE 2 4.987 16.173 9.033 1.00 21.01 C
+-ATOM 16 CD1 ILE 2 2.969 14.795 7.082 1.00 28.78 C
+-ATOM 17 N SER 3 5.637 15.334 12.115 1.00 13.62 N
+-ATOM 18 CA SER 3 6.368 16.180 13.050 1.00 19.09 C
+-ATOM 19 C SER 3 7.703 16.646 12.468 1.00 17.57 C
+-ATOM 20 O SER 3 8.363 15.914 11.750 1.00 15.93 O
+-ATOM 21 CB SER 3 6.751 15.301 14.298 1.00 14.43 C
+-ATOM 22 OG SER 3 5.544 14.967 14.987 1.00 15.13 O
+-ATOM 23 N LEU 4 8.112 17.862 12.816 1.00 10.24 N
+-ATOM 24 CA LEU 4 9.370 18.301 12.353 1.00 11.22 C
+-ATOM 25 C LEU 4 10.283 18.416 13.583 1.00 12.15 C
+-ATOM 26 O LEU 4 9.765 18.812 14.627 1.00 19.68 O
+-ATOM 27 CB LEU 4 9.230 19.754 11.875 1.00 18.64 C
+-ATOM 28 CG LEU 4 8.684 19.996 10.452 1.00 19.41 C
+-ATOM 29 CD1 LEU 4 7.569 19.115 9.957 1.00 16.26 C
+-ATOM 30 CD2 LEU 4 8.477 21.499 10.173 1.00 17.49 C
+-ATOM 31 N ILE 5 11.555 18.104 13.495 1.00 11.49 N
+-ATOM 32 CA ILE 5 12.465 18.230 14.624 1.00 9.79 C
+-ATOM 33 C ILE 5 13.636 19.013 14.159 1.00 15.10 C
+-ATOM 34 O ILE 5 14.222 18.681 13.116 1.00 17.21 O
+-ATOM 35 CB ILE 5 12.811 16.919 15.273 1.00 13.29 C
+-ATOM 36 CG1 ILE 5 13.886 17.156 16.315 1.00 11.26 C
+-ATOM 37 CG2 ILE 5 13.298 15.880 14.184 1.00 16.94 C
+-ATOM 38 CD1 ILE 5 13.981 15.939 17.251 1.00 11.88 C
+-ATOM 39 N ALA 6 14.012 20.093 14.895 1.00 10.27 N
+-ATOM 40 CA ALA 6 15.137 20.934 14.463 1.00 11.73 C
+-ATOM 41 C ALA 6 15.851 21.640 15.619 1.00 17.85 C
+-ATOM 42 O ALA 6 15.235 21.839 16.668 1.00 16.34 O
+-ATOM 43 CB ALA 6 14.449 22.032 13.594 1.00 11.92 C
+-ATOM 44 N ALA 7 17.119 21.996 15.415 1.00 12.95 N
+-ATOM 45 CA ALA 7 17.962 22.700 16.346 1.00 11.97 C
+-ATOM 46 C ALA 7 18.099 24.081 15.714 1.00 26.40 C
+-ATOM 47 O ALA 7 18.503 24.190 14.577 1.00 16.56 O
+-ATOM 48 CB ALA 7 19.279 22.022 16.626 1.00 13.38 C
+-ATOM 49 N LEU 8 17.738 25.159 16.435 1.00 13.46 N
+-ATOM 50 CA LEU 8 17.767 26.510 15.918 1.00 11.94 C
+-ATOM 51 C LEU 8 18.542 27.441 16.789 1.00 23.46 C
+-ATOM 52 O LEU 8 18.344 27.380 17.993 1.00 15.97 O
+-ATOM 53 CB LEU 8 16.306 27.133 16.150 1.00 17.43 C
+-ATOM 54 CG LEU 8 15.245 26.745 15.191 1.00 26.42 C
+-ATOM 55 CD1 LEU 8 14.714 25.361 15.532 1.00 35.76 C
+-ATOM 56 CD2 LEU 8 14.133 27.753 15.245 1.00 21.53 C
+-ATOM 57 N ALA 9 19.354 28.324 16.136 1.00 16.75 N
+-ATOM 58 CA ALA 9 20.109 29.322 16.859 1.00 11.74 C
+-ATOM 59 C ALA 9 19.268 30.562 16.781 1.00 14.87 C
+-ATOM 60 O ALA 9 18.052 30.512 16.395 1.00 16.15 O
+-ATOM 61 CB ALA 9 21.496 29.499 16.312 1.00 18.58 C
+-ATOM 62 N VAL 10 19.908 31.695 17.172 1.00 19.77 N
+-ATOM 63 CA VAL 10 19.182 32.944 17.121 1.00 28.89 C
+-ATOM 64 C VAL 10 18.853 33.270 15.681 1.00 24.80 C
+-ATOM 65 O VAL 10 19.589 32.940 14.704 1.00 24.85 O
+-ATOM 66 CB VAL 10 19.896 34.147 17.775 1.00 35.16 C
+-ATOM 67 CG1 VAL 10 20.668 33.742 19.022 1.00 30.41 C
+-ATOM 68 CG2 VAL 10 20.692 34.984 16.815 1.00 35.93 C
+-ATOM 69 N ASP 11 17.742 33.900 15.528 1.00 25.72 N
+-ATOM 70 CA ASP 11 17.367 34.231 14.199 1.00 31.44 C
+-ATOM 71 C ASP 11 16.970 33.019 13.371 1.00 28.60 C
+-ATOM 72 O ASP 11 16.959 33.131 12.206 1.00 26.55 O
+-ATOM 73 CB ASP 11 18.378 35.124 13.467 1.00 29.36 C
+-ATOM 74 CG ASP 11 18.356 36.564 14.035 1.00 33.87 C
+-ATOM 75 OD1 ASP 11 17.333 37.176 14.327 1.00 36.53 O
+-ATOM 76 OD2 ASP 11 19.538 37.099 14.146 1.00 34.31 O
+-ATOM 77 N ARG 12 16.634 31.897 13.959 1.00 15.13 N
+-ATOM 78 CA ARG 12 16.193 30.711 13.247 1.00 13.52 C
+-ATOM 79 C ARG 12 17.224 30.074 12.351 1.00 15.81 C
+-ATOM 80 O ARG 12 16.841 29.226 11.518 1.00 19.91 O
+-ATOM 81 CB ARG 12 14.891 30.911 12.489 1.00 14.72 C
+-ATOM 82 CG ARG 12 13.770 31.437 13.345 1.00 24.78 C
+-ATOM 83 CD ARG 12 12.435 31.161 12.721 1.00 27.21 C
+-ATOM 84 NE ARG 12 12.462 31.677 11.381 1.00 36.54 N
+-ATOM 85 CZ ARG 12 12.456 32.954 11.069 1.00 37.11 C
+-ATOM 86 NH1 ARG 12 12.421 33.916 11.940 1.00 36.05 N
+-ATOM 87 NH2 ARG 12 12.494 33.278 9.801 1.00 46.75 N
+-ATOM 88 N VAL 13 18.498 30.450 12.518 1.00 14.21 N
+-ATOM 89 CA VAL 13 19.531 29.853 11.712 1.00 12.04 C
+-ATOM 90 C VAL 13 19.672 28.345 12.064 1.00 22.54 C
+-ATOM 91 O VAL 13 19.821 27.968 13.233 1.00 14.87 O
+-ATOM 92 CB VAL 13 20.863 30.533 11.990 1.00 16.62 C
+-ATOM 93 CG1 VAL 13 22.042 29.742 11.406 1.00 14.11 C
+-ATOM 94 CG2 VAL 13 20.797 31.998 11.467 1.00 16.15 C
+-ATOM 95 N ILE 14 19.629 27.482 11.056 1.00 14.13 N
+-ATOM 96 CA ILE 14 19.767 26.011 11.271 1.00 14.28 C
+-ATOM 97 C ILE 14 20.995 25.409 10.552 1.00 17.38 C
+-ATOM 98 O ILE 14 21.399 24.278 10.747 1.00 16.61 O
+-ATOM 99 CB ILE 14 18.506 25.235 10.843 1.00 19.53 C
+-ATOM 100 CG1 ILE 14 18.151 25.494 9.365 1.00 22.73 C
+-ATOM 101 CG2 ILE 14 17.307 25.571 11.723 1.00 14.60 C
+-ATOM 102 CD1 ILE 14 16.862 24.785 8.834 1.00 17.31 C
+-ATOM 103 N GLY 15 21.623 26.185 9.656 1.00 21.60 N
+-ATOM 104 CA GLY 15 22.773 25.644 8.908 1.00 17.53 C
+-ATOM 105 C GLY 15 23.579 26.679 8.113 1.00 18.53 C
+-ATOM 106 O GLY 15 23.216 27.824 8.023 1.00 16.92 O
+-ATOM 107 N MET 16 24.685 26.243 7.585 1.00 22.71 N
+-ATOM 108 CA MET 16 25.630 27.043 6.835 1.00 23.71 C
+-ATOM 109 C MET 16 26.562 26.064 6.140 1.00 28.63 C
+-ATOM 110 O MET 16 26.419 24.841 6.284 1.00 19.96 O
+-ATOM 111 CB MET 16 26.454 27.903 7.783 1.00 28.96 C
+-ATOM 112 CG MET 16 27.215 27.034 8.748 1.00 39.22 C
+-ATOM 113 SD MET 16 28.614 27.916 9.432 1.00 47.53 S
+-ATOM 114 CE MET 16 29.524 27.955 7.874 1.00 33.80 C
+-ATOM 115 N GLU 17 27.509 26.591 5.380 1.00 28.41 N
+-ATOM 116 CA GLU 17 28.375 25.714 4.685 1.00 29.16 C
+-ATOM 117 C GLU 17 29.197 24.820 5.561 1.00 24.40 C
+-ATOM 118 O GLU 17 29.293 23.610 5.320 1.00 25.76 O
+-ATOM 119 CB GLU 17 29.332 26.532 3.738 0.00 20.00 C
+-ATOM 120 CG GLU 17 28.646 27.132 2.520 0.00 20.00 C
+-ATOM 121 CD GLU 17 28.159 26.083 1.541 0.00 20.00 C
+-ATOM 122 OE1 GLU 17 28.336 24.880 1.823 0.00 20.00 O
+-ATOM 123 OE2 GLU 17 27.599 26.466 0.492 0.00 20.00 O
+-ATOM 124 N ASN 18 29.817 25.419 6.557 1.00 20.87 N
+-ATOM 125 CA ASN 18 30.671 24.623 7.428 1.00 18.24 C
+-ATOM 126 C ASN 18 29.968 24.072 8.644 1.00 25.72 C
+-ATOM 127 O ASN 18 28.800 24.344 8.861 1.00 22.25 O
+-ATOM 128 CB ASN 18 31.891 25.429 7.870 1.00 24.80 C
+-ATOM 129 CG ASN 18 32.673 26.009 6.672 1.00 35.68 C
+-ATOM 130 ND2 ASN 18 32.793 25.192 5.612 1.00 21.02 N
+-ATOM 131 OD1 ASN 18 33.131 27.181 6.693 1.00 43.36 O
+-ATOM 132 N ALA 19 30.721 23.301 9.419 1.00 24.77 N
+-ATOM 133 CA ALA 19 30.158 22.732 10.649 1.00 23.26 C
+-ATOM 134 C ALA 19 29.808 23.892 11.608 1.00 16.44 C
+-ATOM 135 O ALA 19 30.553 24.855 11.718 1.00 19.16 O
+-ATOM 136 CB ALA 19 31.208 21.851 11.326 1.00 17.26 C
+-ATOM 137 N MET 20 28.661 23.767 12.282 1.00 22.16 N
+-ATOM 138 CA MET 20 28.173 24.753 13.256 1.00 27.06 C
+-ATOM 139 C MET 20 29.215 24.880 14.367 1.00 16.21 C
+-ATOM 140 O MET 20 29.858 23.879 14.759 1.00 20.00 O
+-ATOM 141 CB MET 20 26.859 24.207 13.808 1.00 25.41 C
+-ATOM 142 CG MET 20 25.790 24.287 12.739 1.00 29.82 C
+-ATOM 143 SD MET 20 25.744 25.961 12.033 1.00 41.04 S
+-ATOM 144 CE MET 20 24.199 26.587 12.680 1.00 55.69 C
+-ATOM 1257 N ARG 21 -2.365 24.238 17.120 1.00 26.07 N
+-ATOM 1258 CA ARG 21 -3.722 24.429 17.637 1.00 38.04 C
+-ATOM 1259 C ARG 21 -4.816 24.158 16.587 1.00 52.67 C
+-ATOM 1260 O ARG 21 -4.718 24.783 15.486 1.00 56.66 O
+-ATOM 1261 CB ARG 21 -3.918 25.826 18.162 1.00 35.05 C
+-ATOM 1262 CG ARG 21 -3.019 26.176 19.341 1.00 32.34 C
+-ATOM 1263 CD ARG 21 -3.363 27.548 19.971 1.00 27.62 C
+-ATOM 1264 NE ARG 21 -2.493 27.864 21.095 0.00 20.00 N
+-ATOM 1265 CZ ARG 21 -2.590 28.986 21.801 0.00 20.00 C
+-ATOM 1266 NH1 ARG 21 -3.514 29.885 21.492 0.00 20.00 N
+-ATOM 1267 NH2 ARG 21 -1.762 29.206 22.813 0.00 20.00 N
+-ATOM 1268 OXT ARG 21 -5.807 23.410 16.918 1.00 51.94 O
+-END
+-""")
+- f.close()
+- cmd = cmd()
+- pymol = pymol()
+
+ def __init__(self):
+ if 0:
+@@ -439,28 +307,84 @@
+
+ defaults = {
+ "interior_dielectric" : 2.0,# ###
+- "solvent_dielectric" : 80.0,# ###
++ "solvent_dielectric" : 78.0,# ###
+ "solvent_radius" : 1.4,# ###
+ "system_temp" : 310.0,# ###
+- "apbs_mode" : 'Nonlinear Poisson-Boltzmann Equation',# ###
+- "ion_plus_one_conc" : 0.0,# ###
++ "apbs_mode" : 'Linearized Poisson-Boltzmann Equation',# ###
++ "ion_plus_one_conc" : 0.15,# ###
+ "ion_plus_one_rad" : 2.0,# ###
+ "ion_plus_two_conc" : 0.0,# ###
+ "ion_plus_two_rad" : 2.0,# ###
+- "ion_minus_one_conc" : 0.0,# ###
+- "ion_minus_one_rad" : 2.0,# ###
++ "ion_minus_one_conc" : 0.15,# ###
++ "ion_minus_one_rad" : 1.8,# ###
+ "ion_minus_two_conc" : 0.0,# ###
+ "ion_minus_two_rad" : 2.0,# ###
+- "max_grid_points" : 1200000,
++ #"max_mem_allowed" : 400,
++ "max_mem_allowed" : 1500,
+ "potential_at_sas" : 0,
+- "surface_solvent" : 0,
++ "surface_solvent" : 1,
+ #"grid_buffer" : 0,
+ #"grid_buffer" : 20,
+ "bcfl" : 'Single DH sphere', # Boundary condition flag for APBS ###
+ "sdens": 10.0, # Specify the number of grid points per square-angstrom to use in Vacc object. Ignored when srad is 0.0 (see srad) or srfm is spl2 (see srfm). There is a direct correlation between the value used for the Vacc sphere density, the accuracy of the Vacc object, and the APBS calculation time. APBS default value is 10.0.
+- "chgm" : 'Cubic b-splines', # Charge disc method for APBS ###
++ "chgm" : 'Cubic B-splines', # Charge disc method for APBS ###
+ }
+
++def run(prog,args):
++ '''
++ wrapper to handle spaces on windows.
++ prog is the full path to the program.
++ args is a string that we will split up for you.
++ or a tuple. or a list. your call.
++
++ return value is (retval,prog_out)
++
++ e.g.
++
++ (retval,prog_out) = run("/bin/ls","-al /tmp/myusername")
++ '''
++ verbose=True
++ try:
++ import subprocess,tempfile
++
++ if type(args) == type(''):
++ args = tuple(args.split())
++ elif type(args) in (type([]),type(())):
++ args = tuple(args)
++ if os.name in 'nt dos'.split():
++ # turns out not to be necessary with subprocess
++ #prog = r'"%s"'%prog
++ pass
++ args = (prog,) + args
++ output_file = tempfile.TemporaryFile(mode="w+")
++ if verbose:
++ print "Running",args
++ retcode = subprocess.call(args,stdout=output_file.fileno(),stderr=subprocess.STDOUT)
++ output_file.seek(0)
++ prog_out = output_file.read()
++ output_file.close() #windows doesn't do this automatically
++ if verbose:
++ print "Results were:"
++ print "Return value:",retcode
++ print "Output:"
++ print prog_out
++ return (retcode,prog_out)
++ except ImportError:
++ # probably python <= 2.4
++ if type(args) != type(''):
++ args = ' '.join(args)
++ cmd = prog + ' ' + args
++ if verbose:
++ print "Running",cmd
++ retcode = os.system(cmd)
++ # cannot return prog_out via os.system
++ if verbose:
++ print "Results were:"
++ print "Return value:",retcode
++ print "Output:"
++ print "\tcould not find subprocess module, so no output reported"
++ return (retcode,'')
++
+ class FileDialogButtonClassFactory:
+ def get(fn,filter='*'):
+ """This returns a FileDialogButton class that will
+@@ -484,8 +408,16 @@
+ return FileDialogButton
+ get = staticmethod(get)
+
++
+ class VisualizationGroup(Pmw.Group):
+ def __init__(self,*args,**kwargs):
++ my_options = 'visgroup_num'.split()
++ for option in my_options:
++ # use these options as attributes of this class
++ # and remove them from the kwargs dict before
++ # passing on to Pmw.Group.__init__().
++ setattr(self,option,kwargs.pop(option))
++ kwargs['tag_text'] = kwargs['tag_text'] + ' (%s)'%self.visgroup_num
+ Pmw.Group.__init__(self,*args,**kwargs)
+ self.refresh()
+ self.show_ms = False
+@@ -536,7 +468,7 @@
+ self.surface_solvent = IntVar()
+ self.surface_solvent.set(defaults['surface_solvent'])
+ self.sol_checkbutton = Checkbutton(self.ms_group.interior(),
+- text = "Solvent accesssible surface",
++ text = "Solvent accessible surface",
+ variable = self.surface_solvent)
+ self.sol_checkbutton.pack()
+ self.potential_at_sas = IntVar()
+@@ -586,7 +518,7 @@
+ self.pi_buttonbox.alignbuttons()
+ self.pos_surf_val = Pmw.Counter(self.pi_group.interior(),
+ labelpos = 'w',
+- label_text = 'Contour (kT)',
++ label_text = 'Contour (kT/e)',
+ orient = 'vertical',
+ entry_width = 4,
+ entryfield_value = 1,
+@@ -605,7 +537,7 @@
+ self.ni_buttonbox.alignbuttons()
+ self.neg_surf_val = Pmw.Counter(self.ni_group.interior(),
+ labelpos = 'w',
+- label_text = 'Contour (kT)',
++ label_text = 'Contour (kT/e)',
+ orient = 'vertical',
+ entry_width = 4,
+ entryfield_value = -1,
+@@ -633,10 +565,23 @@
+ def hideMolSurface(self):
+ pymol.cmd.hide('surface',self.molecule.getvalue())
+
++ def getRampName(self):
++ #return 'e_lvl'
++ idx = [i for i in pymol.cmd.get_names() if pymol.cmd.get_type(i)=='object:molecule'].index(self.molecule.getvalue())
++ return '_'.join(('e_lvl',str(idx),str(self.visgroup_num)))
++
++ def getIsoPosName(self):
++ idx = [i for i in pymol.cmd.get_names() if pymol.cmd.get_type(i)=='object:map'].index(self.map.getvalue())
++ return '_'.join(('iso_pos',str(idx),str(self.visgroup_num)))
++
++ def getIsoNegName(self):
++ idx = [i for i in pymol.cmd.get_names() if pymol.cmd.get_type(i)=='object:map'].index(self.map.getvalue())
++ return '_'.join(('iso_neg',str(idx),str(self.visgroup_num)))
++
+ def updateMolSurface(self):
+- ramp_name = 'e_lvl'
+- map_name = self.map.getvalue()
+ molecule_name = self.molecule.getvalue()
++ ramp_name = self.getRampName()
++ map_name = self.map.getvalue()
+ low = float(self.mol_surf_low.getvalue())
+ mid = float(self.mol_surf_middle.getvalue())
+ high = float(self.mol_surf_high.getvalue())
+@@ -653,43 +598,53 @@
+ pymol.cmd.set('surface_ramp_above_mode',self.potential_at_sas.get(),molecule_name)
+ pymol.cmd.show('surface',molecule_name)
+ pymol.cmd.refresh()
+- pymol.cmd.recolor()
++ pymol.cmd.recolor(molecule_name)
+
+ def showPosSurface(self):
+ self.updatePosSurface()
+ def hidePosSurface(self):
+- pymol.cmd.hide('everything','iso_pos')
++ pymol.cmd.hide('everything',self.getIsoPosName())
+ def updatePosSurface(self):
+- pymol.cmd.delete('iso_pos')
+- pymol.cmd.isosurface('iso_pos',self.map.getvalue(),float(self.pos_surf_val.getvalue()))
+- pymol.cmd.color('blue','iso_pos')
+- pymol.cmd.show('everything','iso_pos')
++ pymol.cmd.delete(self.getIsoPosName())
++ pymol.cmd.isosurface(self.getIsoPosName(),self.map.getvalue(),float(self.pos_surf_val.getvalue()))
++ pymol.cmd.color('blue',self.getIsoPosName())
++ pymol.cmd.show('everything',self.getIsoPosName())
+ def showNegSurface(self):
+ self.updateNegSurface()
+ def hideNegSurface(self):
+- pymol.cmd.hide('everything','iso_neg')
++ pymol.cmd.hide('everything',self.getIsoNegName())
+ def updateNegSurface(self):
+- pymol.cmd.delete('iso_neg')
+- pymol.cmd.isosurface('iso_neg',self.map.getvalue(),float(self.neg_surf_val.getvalue()))
+- pymol.cmd.color('red','iso_neg')
+- pymol.cmd.show('everything','iso_neg')
++ pymol.cmd.delete(self.getIsoNegName())
++ pymol.cmd.isosurface(self.getIsoNegName(),self.map.getvalue(),float(self.neg_surf_val.getvalue()))
++ pymol.cmd.color('red',self.getIsoNegName())
++ pymol.cmd.show('everything',self.getIsoNegName())
+
+ class APBSTools:
+
+ def setPqrFile(self,name):
+ print " APBS Tools: set pqr file to",name
+ self.pqr_to_use.setvalue(name)
++ self.radiobuttons.setvalue('Use another PQR')
+ def getPqrFilename(self):
+ if self.radiobuttons.getvalue() != 'Use another PQR':
+-# print 'radiobutton said to generate it',self.radiobuttons.getvalue(),'so i am returning',self.pymol_generated_pqr_filename.getvalue()
+ return self.pymol_generated_pqr_filename.getvalue()
+ else:
+-# print 'radiobutton told me to use another',self.radiobuttons.getvalue(),'so i am returning',self.pqr_to_use.getvalue()
+ return self.pqr_to_use.getvalue()
+ def setPsizeLocation(self,value):
+ self.psize.setvalue(value)
+ def setBinaryLocation(self,value):
+ self.binary.setvalue(value)
++ def setPdb2pqrLocation(self,value):
++ self.pdb2pqr.setvalue(value)
++
++ def setPymolGeneratedPqrFilename(self,value):
++ self.pymol_generated_pqr_filename.setvalue(value)
++ def setPymolGeneratedPdbFilename(self,value):
++ self.pymol_generated_pdb_filename.setvalue(value)
++ def setPymolGeneratedDxFilename(self,value):
++ self.pymol_generated_dx_filename.setvalue(value)
++ def setPymolGeneratedInFilename(self,value):
++ self.pymol_generated_in_filename.setvalue(value)
+
+ def __init__(self,app):
+ parent = app.root
+@@ -705,7 +660,7 @@
+ Pmw.setbusycursorattributes(self.dialog.component('hull'))
+
+ w = Tkinter.Label(self.dialog.interior(),
+- text = 'PyMOL APBS Tools\nMichael Lerner, 2004 - www.umich.edu/~mlerner/Pymol\n(incorporates modifications by WLD)',
++ text = 'PyMOL APBS Tools\nMichael Lerner, 2007 - www.umich.edu/~mlerner/Pymol\n(incorporates modifications by WLD)',
+ background = 'black',
+ foreground = 'white',
+ #pady = 20,
+@@ -736,18 +691,26 @@
+ )
+ for text in ('Use PyMOL generated PQR and existing Hydrogens and termini',
+ 'Use PyMOL generated PQR and PyMOL generated Hydrogens and termini',
+- 'Use another PQR'):
++ 'Use another PQR',
++ 'Use PDB2PQR',):
+ self.radiobuttons.add(text)
+ self.radiobuttons.setvalue('Use PyMOL generated PQR and PyMOL generated Hydrogens and termini')
+
++ self.pdb2pqr_options = Pmw.EntryField(group.interior(),
++ labelpos='w',
++ label_text='pdb2pqr command line options: ',
++ value='--ff=AMBER',
++ )
++
+ self.pqr_to_use = Pmw.EntryField(group.interior(),
+ labelpos='w',
+ label_pyclass = FileDialogButtonClassFactory.get(self.setPqrFile,'*.pqr'),
+ label_text='\tChoose Externally Generated PQR:',
+ )
++
+
+
+- for entry in (self.selection,self.map,self.radiobuttons,self.pqr_to_use):
++ for entry in (self.selection,self.map,self.radiobuttons,self.pdb2pqr_options,self.pqr_to_use):
+ #for entry in (self.selection,self.map,self.radiobuttons,):
+ entry.pack(fill='x',padx=4,pady=1) # vertical
+
+@@ -779,16 +742,16 @@
+ group = Pmw.Group(page,tag_text='Other')
+ group.pack(fill='both',expand=1, padx=4, pady=5)
+ group.grid(column=1, row=1,columnspan=4)
+- self.max_grid_points = Pmw.EntryField(group.interior(),labelpos='w',
+- label_text = 'Maximum Grid Points:',
+- value = str(defaults['max_grid_points']),
++ self.max_mem_allowed = Pmw.EntryField(group.interior(),labelpos='w',
++ label_text = 'Maximum Memory Allowed (MB):',
++ value = str(defaults['max_mem_allowed']),
+ validate = {'validator' : 'real',
+ 'min':1,}
+ )
+ self.apbs_mode = Pmw.OptionMenu(group.interior(),
+ labelpos = 'w',
+ label_text = 'APBS Mode',
+- items = ('Nonlinear Poisson-Boltzmann Equation','Linear Poisson-Boltzmann Equation',),
++ items = ('Nonlinear Poisson-Boltzmann Equation','Linearized Poisson-Boltzmann Equation',),
+ initialitem = defaults['apbs_mode'],
+ )
+ self.apbs_mode.pack(fill='x',expand=1,padx=4)
+@@ -814,23 +777,23 @@
+ self.bcfl = Pmw.OptionMenu(group.interior(),
+ labelpos = 'w',
+ label_text = 'Boundary Condition',
+- items = ('Zero','Single DH sphere','Multiple DH spheres','Focusing',),
++ items = ('Zero','Single DH sphere','Multiple DH spheres',), #'Focusing',),
+ initialitem = defaults['bcfl'],
+ )
+ self.chgm = Pmw.OptionMenu(group.interior(),
+ labelpos = 'w',
+ label_text = 'Charge disc method',
+- items = ('Linear','Cubic b-splines',),
++ items = ('Linear','Cubic B-splines','Quintic B-splines',),
+ initialitem = defaults['chgm'],
+ )
+ self.srfm = Pmw.OptionMenu(group.interior(),
+ labelpos = 'w',
+ label_text = 'Surface Calculation Method',
+- items = ('Mol surf for epsilon; inflated VdW for kappa, no smoothing','Same, but with harmonic average smoothing','Cubic spline',),
++ items = ('Mol surf for epsilon; inflated VdW for kappa, no smoothing','Same, but with harmonic average smoothing','Cubic spline','Similar to cubic spline, but with 7th order polynomial'),
+ initialitem = 'Same, but with harmonic average smoothing',
+ )
+ #for entry in (self.apbs_mode,self.system_temp,self.solvent_radius,):
+- for entry in (self.max_grid_points,self.solvent_radius,self.system_temp,self.sdens,self.apbs_mode,self.bcfl,self.chgm,self.srfm):
++ for entry in (self.max_mem_allowed,self.solvent_radius,self.system_temp,self.sdens,self.apbs_mode,self.bcfl,self.chgm,self.srfm):
+ entry.pack(fill='x',expand=1,padx=4,pady=1) # vertical
+
+
+@@ -839,7 +802,7 @@
+ group.grid(column=0, row=1, )
+ self.ion_plus_one_conc = Pmw.EntryField(group.interior(),
+ labelpos='w',
+- label_text='Ion Concentration (+1):',
++ label_text='Ion Concentration (M) (+1):',
+ validate={'validator':'real','min':0},
+ value = str(defaults['ion_plus_one_conc']),
+ )
+@@ -851,7 +814,7 @@
+ )
+ self.ion_minus_one_conc = Pmw.EntryField(group.interior(),
+ labelpos='w',
+- label_text='Ion Concentration (-1):',
++ label_text='Ion Concentration (M) (-1):',
+ validate={'validator':'real','min':0},
+ value = str(defaults['ion_minus_one_conc']),
+ )
+@@ -863,7 +826,7 @@
+ )
+ self.ion_plus_two_conc = Pmw.EntryField(group.interior(),
+ labelpos='w',
+- label_text='Ion Concentration (+2):',
++ label_text='Ion Concentration (M) (+2):',
+ validate={'validator':'real','min':0},
+ value = str(defaults['ion_plus_two_conc']),
+ )
+@@ -875,7 +838,7 @@
+ )
+ self.ion_minus_two_conc = Pmw.EntryField(group.interior(),
+ labelpos='w',
+- label_text='Ion Concentration (-2):',
++ label_text='Ion Concentration (M) (-2):',
+ validate={'validator':'real','min':0},
+ value = str(defaults['ion_minus_two_conc']),
+ )
+@@ -954,7 +917,7 @@
+
+ page.grid_rowconfigure(2,weight=1)
+ page.grid_columnconfigure(5,weight=1)
+- page = self.notebook.add('APBS Location')
++ page = self.notebook.add('Program Locations')
+ group = Pmw.Group(page,tag_text='Locations')
+ group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
+ def quickFileValidation(s):
+@@ -962,108 +925,141 @@
+ elif os.path.isfile(s): return Pmw.OK
+ elif os.path.exists(s): return Pmw.PARTIAL
+ else: return Pmw.PARTIAL
+-
+- global APBS_BINARY_LOCATION, APBS_PSIZE_LOCATION
+- if APBS_BINARY_LOCATION is None:
+- if 'APBS_BINARY' in os.environ:
+- APBS_BINARY_LOCATION = os.environ['APBS_BINARY']
+- else:
+- APBS_BINARY_LOCATION = distutils.spawn.find_executable('apbs')
+- if APBS_BINARY_LOCATION is None:
+- APBS_BINARY_LOCATION = ''
+-
+- if APBS_PSIZE_LOCATION is None:
+- if 'APBS_PSIZE' in os.environ:
+- APBS_PSIZE_LOCATION = os.environ['APBS_PSIZE']
+- else:
+- APBS_PSIZE_LOCATION = ''
++ def quickFileDirValidation(s):
++ '''
++ assumes s ends in filename
++ '''
++ if os.path.exists(s) and not os.path.isfile(s):
++ return Pmw.PARTIAL
++ if os.path.isdir(os.path.split(s)[0]):
++ return Pmw.OK
++ return Pmw.PARTIAL
+
+ self.binary = Pmw.EntryField(group.interior(),
+ labelpos='w',
+ label_pyclass = FileDialogButtonClassFactory.get(self.setBinaryLocation),
+ validate = {'validator':quickFileValidation,},
+- value = APBS_BINARY_LOCATION,
+- label_text = 'APBS binary location:')
++ value = get_default_location('apbs_binary'),
++ label_text = 'APBS binary location:',
++ )
+ self.binary.pack(fill = 'x', padx = 20, pady = 10)
+ self.psize = Pmw.EntryField(group.interior(),
+ labelpos='w',
+ label_pyclass = FileDialogButtonClassFactory.get(self.setPsizeLocation),
+ validate = {'validator':quickFileValidation,},
+ #value = '/usr/local/apbs-0.3.1/tools/manip/psize.py',
+- value = APBS_PSIZE_LOCATION,
++ value = get_default_location('apbs_psize'),
+ label_text = 'APBS psize.py location:',
+ )
+ self.psize.pack(fill = 'x', padx = 20, pady = 10)
++ self.pdb2pqr = Pmw.EntryField(group.interior(),
++ labelpos='w',
++ label_pyclass = FileDialogButtonClassFactory.get(self.setPdb2pqrLocation),
++ validate = {'validator':quickFileValidation,},
++ value = get_default_location('pdb2pqr'),
++ label_text = 'pdb2pqr location:',
++ )
++ self.pdb2pqr.pack(fill = 'x', padx = 20, pady = 10)
++
++
+ label = Tkinter.Label(group.interior(),
+ pady = 10,
+ justify=LEFT,
+- text = """You must have APBS installed on your system.
++ text = """You must have APBS version >= 0.5.0 installed on your system.
+
+-The PyMOL APBS tools can calculate proper grid dimensions and spacing (we ensure the the
+-fine mesh spacing is 0.5A or finer). If you wish to use APBS's psize.py to set up the
+-grid, make sure that the path is set correctly above.
++The PyMOL APBS tools can calculate proper grid dimensions and spacing (we attempt to make
++the fine mesh spacing 0.5A or finer, but we will make it coarser if forced to by the
++Maximum Grid Points setting in the configuration pane). If you wish to use APBS's psize.py
++to set up the grid, make sure that the path is set correctly above.
++
++PyMOL can generate PQR files using standard protein residues and AMBER charges. If you
++wish to use PDB2PQR instead, make sure that it is installed and that the path is set
++correctly above.
+
+-If PyMOL does not automatically find apbs or psize.py, you may set the environment variables
+-APBS_BINARY and APBS_PSIZE to point to them respectively.
++If PyMOL does not automatically find apbs, psize.py, or pdb2pqr, you may set the environment
++variables APBS_BINARY, APBS_PSIZE and APBS_PDB2PQR to point to them respectively.
+ """,
+ )
+ label.pack()
++
+
+ page = self.notebook.add('Temporary File Locations')
+ group = Pmw.Group(page,tag_text='Locations')
+ group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
++## self.pymol_generated_file_directory = Pmw.EntryField(group.interior(),
++## labelpos = 'w',
++## label_text = 'Directory containing temporary files: ',
++## value = TEMPORARY_FILE_DIR,
+ self.pymol_generated_pqr_filename = Pmw.EntryField(group.interior(),
+ labelpos = 'w',
++ label_pyclass = FileDialogButtonClassFactory.get(self.setPymolGeneratedPqrFilename),
++ validate = {'validator':quickFileDirValidation,},
+ label_text = 'Temporary PQR file: ',
+- value = 'pymol-generated.pqr',
++ value = os.path.join(get_default_location('temp','dir'),'pymol-generated.pqr'),
+ )
+ self.pymol_generated_pqr_filename.pack(fill = 'x', padx = 20, pady = 10)
+
+ self.pymol_generated_pdb_filename = Pmw.EntryField(group.interior(),
+ labelpos = 'w',
++ label_pyclass = FileDialogButtonClassFactory.get(self.setPymolGeneratedPdbFilename),
++ validate = {'validator':quickFileDirValidation,},
+ label_text = 'Temporary PDB file: ',
+- value = 'pymol-generated.pdb',
++ value = os.path.join(get_default_location('temp','dir'),'pymol-generated.pdb'),
+ )
+ self.pymol_generated_pdb_filename.pack(fill = 'x', padx = 20, pady = 10)
+
+ self.pymol_generated_dx_filename = Pmw.EntryField(group.interior(),
+ labelpos = 'w',
++ label_pyclass = FileDialogButtonClassFactory.get(self.setPymolGeneratedDxFilename),
++ validate = {'validator':quickFileDirValidation,},
+ label_text = 'Temporary DX file: ',
+- value = 'pymol-generated.dx',
++ value = os.path.join(get_default_location('temp','dir'),'pymol-generated.dx'),
+ )
+ self.pymol_generated_dx_filename.pack(fill = 'x', padx = 20, pady = 10)
+
+- self.pymol_generated_in_filename = Pmw.EntryField(group.interior(),
+- labelpos = 'w',
+- label_text = 'APBS input file: ',
+- value = 'pymol-generated.in',
+- )
++
++ self.pymol_generated_in_filename = Pmw.EntryField(group.interior(),
++ labelpos='w',
++ label_pyclass = FileDialogButtonClassFactory.get(self.setPymolGeneratedInFilename),
++ validate = {'validator':quickFileDirValidation,},
++ value = os.path.join(get_default_location('temp','dir'),'pymol-generated.in'),
++ label_text = 'APBS input file:')
+ self.pymol_generated_in_filename.pack(fill = 'x', padx = 20, pady = 10)
+
+- # Create a visualization page
+- page = self.notebook.add('Visualization')
+- #group = Pmw.Group(page,tag_text='Visualization')
+- #group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
+- group = VisualizationGroup(page,tag_text='Visualization')
++ label = Tkinter.Label(group.interior(),
++ pady = 10,
++ justify=LEFT,
++ text = """You can automatically set the default location of temporary files
++by setting the environment variable TEMP.
++""",
++ )
++ label.pack()
++ # Create the visualization pages
++ page = self.notebook.add('Visualization (1)')
++ group = VisualizationGroup(page,tag_text='Visualization',visgroup_num=1)
++ self.visualization_group_1 = group
+ group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
+-
++
++ page = self.notebook.add('Visualization (2)')
++ group = VisualizationGroup(page,tag_text='Visualization',visgroup_num=2)
++ self.visualization_group_2 = group
++ group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
++
+
+
+ # Create a couple of other empty pages
+ page = self.notebook.add('About')
+ group = Pmw.Group(page, tag_text='About PyMOL APBS Tools')
+ group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
+- label = Tkinter.Label(group.interior(),
+- pady = 10,
+- justify=LEFT,
+- text = """
+-This plugin integrates PyMOL (http://pymol.org/) with APBS (http://agave.wustl.edu/apbs/).
++ text = """This plugin integrates PyMOL (http://PyMOL.org/) with APBS (http://apbs.sourceforge.net/).
++
++It requires APBS version >= 0.5.0.
+
+-It should be fairly self-explanatory. In the simplest case,
++In the simplest case,
+
+ 1) Load a structure into PyMOL.
+ 2) Start this plugin.
+-3) Make sure that the path to the APBS binary is correct on the "APBS Location" tab.
++3) Make sure that the path to the APBS binary is correct on the "Program Locations" tab.
+ 4) Click the "Set grid" button to set up the grid.
+ 5) Click the "Run APBS" button.
+
+@@ -1071,10 +1067,50 @@
+ - Warren DeLano for everything involving PyMOL
+ - Nathan Baker and Todd Dolinsky for everything involving APBS
+
+-Created by Michael Lerner <http://www.umich.edu/~mlerner/Pymol/> mglerner@gmail.com
+-Carlson Group, University of Michigan <http://www.umich.edu/~carlsonh/>
+-""")
+- label.pack()
++Created by Michael Lerner (http://www.umich.edu/~mlerner/PyMOL/) mglerner@gmail.com
++Carlson Group, University of Michigan (http://www.umich.edu/~carlsonh/)
++
++Please contact the author and cite this plugin if you use it in a publication.
++
++Citation for this plugin:
++ MG Lerner and HA Carlson. APBS plugin for PyMOL, 2006,
++ University of Michigan, Ann Arbor.
++
++Citation for PyMOL may be found here:
++ http://pymol.sourceforge.net/faq.html#CITE
++
++Citation for APBS:
++ Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
++ nanosystems: application to microtubules and the ribosome. Proc.
++ Natl. Acad. Sci. USA 98, 10037-10041 2001.
++
++Citation for PDB2PQR:
++ Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA.
++ PDB2PQR: an automated pipeline for the setup, execution,
++ and analysis of Poisson-Boltzmann electrostatics calculations.
++ Nucleic Acids Research 32 W665-W667 (2004).
++"""
++ if 0:
++ label = Tkinter.Label(group.interior(),
++ pady = 10,
++ justify=LEFT,
++ text = text)
++
++ label.pack()
++ else:
++ #
++ # Add this as text in a scrollable pane.
++ # Code based on Caver plugin
++ # http://loschmidt.chemi.muni.cz/caver/index.php
++ #
++ interior_frame=Frame(group.interior())
++ bar=Scrollbar(interior_frame,)
++ text_holder=Text(interior_frame,yscrollcommand=bar.set,background="#ddddff",font="Times 14")
++ bar.config(command=text_holder.yview)
++ text_holder.insert(END,text)
++ text_holder.pack(side=LEFT,expand="yes",fill="both")
++ bar.pack(side=LEFT,expand="yes",fill="y")
++ interior_frame.pack(expand="yes",fill="both")
+
+ self.notebook.setnaturalsize()
+
+@@ -1094,8 +1130,14 @@
+ good = self.generateApbsInputFile()
+ if not good:
+ return False
+- if self.radiobuttons.getvalue() != 'Use another PQR':
+- good = self.generatePqrFile()
++ if self.radiobuttons.getvalue() == 'Use another PQR':
++ pass
++ elif self.radiobuttons.getvalue() == 'Use PDB2PQR':
++ good = self.generatePdb2pqrPqrFile()
++ if not good:
++ return False
++ else: # it's one of the pymol-generated options
++ good = self.generatePymolPqrFile()
+ if not good:
+ return False
+ if os.path.exists(self.pymol_generated_dx_filename.getvalue()):
+@@ -1104,9 +1146,20 @@
+ except:
+ traceback.print_exc()
+ pass
+- command = "%s %s" % (self.binary.getvalue(),self.pymol_generated_in_filename.getvalue())
+- os.system(command)
++ #command = "%s %s" % (self.binary.getvalue(),self.pymol_generated_in_filename.getvalue())
++ #os.system(command)
++
++ #
++ # NOTE: if there are spaces in the directory name that contains pymol_generated_in_filename,
++ # our run command will want to split it up into several arguments if we pass it as a
++ # string. So, we pass it as a tuple.
++ #
++ (retval,progout) = run(self.binary.getvalue(),(self.pymol_generated_in_filename.getvalue(),))
+ pymol.cmd.load(self.pymol_generated_dx_filename.getvalue(),self.map.getvalue())
++ self.visualization_group_1.refresh()
++ self.visualization_group_2.refresh()
++ self.notebook.tab('Visualization (1)').focus_set()
++ self.notebook.selectpage('Visualization (1)')
+ elif result == 'Set grid':
+ self.runPsize()
+ else:
+@@ -1126,6 +1179,101 @@
+ APBS_PSIZE_LOCATION = self.psize.getvalue()
+ self.dialog.withdraw()
+
++
++ def fixColumns(self,sel):
++ """
++ Make sure that everything fits into the correct columns.
++ This means doing some rounding. It also means getting rid of
++ chain, occupancy and b-factor information.
++ """
++ #pymol.cmd.alter_state(1,'all','(x,y,z)=(int(x*1000)/1000.0, int(y*1000)/1000.0, int(z*1000)/1000.0)')
++ #pymol.cmd.alter_state(1,'all','(x,y,z)=float("%.2f"%x),float("%.2f"%y),float("%.2f"%z)')
++ pymol.cmd.alter_state(1,'all','(x,y,z)=float("%.3f"%x),float("%.3f"%y),float("%.3f"%z)')
++ pymol.cmd.alter(sel,'chain=""')
++ pymol.cmd.alter(sel,'b=0')
++ pymol.cmd.alter(sel,'q=0')
++
++ def cleanupGeneratedPdbOrPqrFile(self,filename):
++ """
++ More cleanup on PQR files.
++
++ pdb2pqr will happily write out a file where the coordinate
++ columns overlap if you have -100.something as one of the
++ coordinates, like
++
++ 90.350 97.230-100.010
++
++ and so will PyMOL. We can't just assume that it's 0-1
++ because pdb2pqr will debump things and write them out with
++ 3 digits post-decimal. Bleh.
++ """
++ f = file(filename,'r')
++ txt = f.read()
++ f.close()
++ f = file(filename,'w')
++ #
++ # So, I guess it's time to become a little more proficient with
++ # regex matches. I want to find ".NNN-" where NNN is a number
++ #
++ # In the meantime, we'll just truncate.
++ #
++ for c in '0123456789':
++ txt = txt.replace(c+'-1',' -1')
++ f.write(txt)
++ f.close()
++
++ def getUnassignedAtomsFromPqr(self,fname):
++ """
++ Here is a comment from Todd Dolinsky via email:
++
++ There's a couple of different errors which can be printed out via REMARK 5 lines; a good sample is:
++
++ REMARK 1 PQR file generated by PDB2PQR (Version 1.2.0)
++ REMARK 1
++ REMARK 1 Forcefield Used: charmm
++ REMARK 1
++ REMARK 1 pKas calculated by propka and assigned using pH 7.00
++ REMARK 1
++ REMARK 5 WARNING: Propka determined the following residues to be
++ REMARK 5 in a protonation state not supported by the
++ REMARK 5 charmm forcefield!
++ REMARK 5 All were reset to their standard pH 7.0 state.
++ REMARK 5
++ REMARK 5 CYS 61 2 (negative)
++ REMARK 5 CYS 79 2 (negative)
++ REMARK 5
++ REMARK 5 WARNING: Unable to debump ALA 1 19
++ REMARK 5 WARNING: Unable to debump MET 1 151
++ REMARK 5 WARNING: Unable to debump PRO 1 258
++ REMARK 5 WARNING: Unable to debump GLY 2 8
++ REMARK 5 WARNING: Unable to debump THR 3 118
++ REMARK 5
++ REMARK 5 WARNING: PDB2PQR was unable to assign charges
++ REMARK 5 to the following atoms (omitted below):
++ REMARK 5 6657 O1 in TRS 900
++ REMARK 5 6658 C2 in TRS 900
++ REMARK 5 6659 C3 in TRS 900
++ REMARK 5 6660 C4 in TRS 900
++ REMARK 5 6661 O5 in TRS 900
++ REMARK 5 6662 C6 in TRS 900
++ REMARK 5 6663 O7 in TRS 900
++ REMARK 5 6664 N8 in TRS 900
++ REMARK 5
++ REMARK 6 Total charge on this protein: -1.0000 e
++ REMARK 6
++
++ If all you care about is the atom number, you can probably regexp match on the 'in' field, something like
++
++ >>> re.compile('REMARK 5 *(\d)* \w* in').findall(text) # Text contains PQR output string
++ ['6657', '6658', '6659', '6660', '6661', '6662', '6663', '6664']
++
++ Or you can grab any other useful information - I'd say that using a regular expression like this would be the best option to ensure you don't get false positives.
++ """
++ f = file(fname)
++ unassigned = re.compile('REMARK 5 *(\d+) \w* in').findall(f.read()) # Text contains PQR output string
++ f.close()
++ return '+'.join(unassigned)
++
+ def runPsize(self):
+ class NoPsize(Exception):
+ pass
+@@ -1149,7 +1297,9 @@
+ # WLD
+ sel = "((%s) or (neighbor (%s) and hydro))"%(
+ self.selection.getvalue(), self.selection.getvalue())
++ self.fixColumns(sel)
+ pymol.cmd.save(pdb_filename,sel)
++ self.cleanupGeneratedPdbOrPqrFile(pdb_filename)
+ f.close()
+ size = psize.Psize()
+ size.runPsize(pdb_filename)
+@@ -1158,6 +1308,8 @@
+ # could use procgrid for multiprocessors
+ finegridpoints = size.getFineGridPoints() # dime
+ center = size.getCenter() # cgcent and fgcent
++
++ print "Getting dimensions from APBS psize.py"
+
+ except (NoPsize,ImportError):
+ #
+@@ -1184,6 +1336,7 @@
+ return False
+
+ box_length = [maxs[i] - mins[i] for i in range(3)]
++ #box_length = [maxs[i] - mins[i] +2.0 for i in range(3)]
+ center = [(maxs[i] + mins[i])/2.0 for i in range(3)]
+ #
+ # psize expands the molecular dimensions by CFAC (which defaults
+@@ -1243,9 +1396,14 @@
+ return False
+
+ if (finegridpoints[0]>0) and (finegridpoints[1]>0) and (finegridpoints[2]>0):
+- max_grid_points = float(self.max_grid_points.getvalue())
++ max_mem_allowed = float(self.max_mem_allowed.getvalue())
++ max_grid_points = max_mem_allowed*1024*1024/200.
+ product = float(finegridpoints[0] * finegridpoints[1] * finegridpoints[2])
+- if product>max_grid_points:
++ mem_used = 200.0 * product / 1024 / 1024
++ if mem_used>max_mem_allowed:
++ error_message = "The ideal grid spacing for this calculation is %s.\n"%finegridpoints
++ error_message += "That would require %.1fMB of memory.\n"%mem_used
++ error_message += "You have the maximum allowed set to %.1fMB.\n"%max_mem_allowed
+ print "Maximum number of grid points exceeded. Old grid dimensions were",finegridpoints
+ factor = pow(max_grid_points/product,0.333333333)
+ finegridpoints[0] = (int(factor*finegridpoints[0]/2))*2+1
+@@ -1283,6 +1441,14 @@
+ #print finegridpoints[i],divmod(finegridpoints[i] - 1,32),
+ finegridpoints[i] = divmod(finegridpoints[i] - 1,32)[0]*32 + 1
+ print "New grid dimensions are",finegridpoints
++ error_message += "We have therefore rounded down to %s,\n"%finegridpoints
++ #product = float(finegridpoints[0] * finegridpoints[1] * finegridpoints[2])
++ error_message += "which will use %.1fMB.\n"%(finegridpoints[0]*finegridpoints[1]*finegridpoints[2]*200./1024/1024)
++ error_message += "You should be aware of this rounding."
++ error_dialog = Pmw.MessageDialog(self.parent,
++ title="Warning",
++ message_text = error_message)
++ error_dialog.activate()
+ print " APBS Tools: coarse grid: (%5.3f,%5.3f,%5.3f)"%tuple(coarsedim)
+ self.grid_coarse_x.setvalue(coarsedim[0])
+ self.grid_coarse_y.setvalue(coarsedim[1])
+@@ -1301,7 +1467,7 @@
+ self.grid_points_z.setvalue(finegridpoints[2])
+
+ def generateApbsInputFile(self):
+- if self.checkInput(silent=True):
++ if self.checkInput(silent=False):
+ #
+ # set up our variables
+ #
+@@ -1321,15 +1487,23 @@
+ bcflmap = {'Zero': 'zero',
+ 'Single DH sphere': 'sdh',
+ 'Multiple DH spheres': 'mdh',
+- 'Focusing': 'focus',
++ #'Focusing': 'focus',
+ }
+ bcfl = bcflmap[self.bcfl.getvalue()]
+
+ chgmmap = {'Linear':'spl0',
+- 'Cubic b-splines':'spl2',
++ 'Cubic B-splines':'spl2',
++ 'Quintic B-splines':'spl4',
+ }
+ chgm = chgmmap[self.chgm.getvalue()]
+
++ srfmmap = {'Mol surf for epsilon; inflated VdW for kappa, no smoothing':'mol',
++ 'Same, but with harmonic average smoothing':'smol',
++ 'Cubic spline':'spl2',
++ 'Similar to cubic spline, but with 7th order polynomial':'spl4',}
++
++ srfm = srfmmap[self.srfm.getvalue()]
++
+ dx_filename = self.pymol_generated_dx_filename.getvalue()
+ if dx_filename.endswith('.dx'):
+ dx_filename = dx_filename[:-3]
+@@ -1352,6 +1526,7 @@
+ float(self.interior_dielectric.getvalue()),
+ float(self.solvent_dielectric.getvalue()),
+ chgm,
++ srfm,
+ float(self.solvent_radius.getvalue()),
+ float(self.system_temp.getvalue()),
+ float(self.sdens.getvalue()),
+@@ -1456,10 +1631,77 @@
+ return False
+
+ return True
++
++
++ def generatePdb2pqrPqrFile(self,silent=False):
++ """use pdb2pqr to generate a pqr file
++ """
++ if not silent:
++ def show_error(message):
++ error_dialog = Pmw.MessageDialog(self.parent,
++ title = 'Error',
++ message_text = message,
++ )
++ junk = error_dialog.activate()
++ else:
++ def show_error(message):
++ pass
++
++ #
++ # First, generate a PDB file
++ #
++ pdb_filename = self.pymol_generated_pdb_filename.getvalue()
++ try:
++ f = file(pdb_filename,'w')
++ f.close()
++ except:
++ show_error('Please set a temporary PDB file location that you have permission to edit')
++ return False
++ # copied from WLD code
++ sel = "((%s) or (neighbor (%s) and hydro))"%(
++ self.selection.getvalue(), self.selection.getvalue())
++ self.fixColumns(sel)
++ pymol.cmd.save(pdb_filename,sel)
++ self.cleanupGeneratedPdbOrPqrFile(pdb_filename)
++
++ #
++ # Now, generate a PQR file
++ #
++## command_line = '%s %s %s %s'%(self.pdb2pqr.getvalue(),
++## self.pdb2pqr_options.getvalue(),
++## pdb_filename,
++## self.pymol_generated_pqr_filename.getvalue(),
++## )
++## print "RAN",command_line
++## result = os.system(command_line)
++ #
++ # We have to be a little cute about args, because pdb2pqr_options could have several options in it.
++ args = '%s %s %s' %(self.pdb2pqr_options.getvalue(),
++ pdb_filename,
++ self.pymol_generated_pqr_filename.getvalue(),
++ )
++ (retval,progout) = run(self.pdb2pqr.getvalue(),args)
++
++
++ if retval != 0:
++ show_error('Could not run pdb2pqr: %s %s\n\n%s'%(self.pdb2pqr.getvalue(),
++ args,
++ progout)
++ )
++ return False
++ self.cleanupGeneratedPdbOrPqrFile(self.pymol_generated_pqr_filename.getvalue())
++ unassigned_atoms = self.getUnassignedAtomsFromPqr(self.pymol_generated_pqr_filename.getvalue())
++ if unassigned_atoms:
++ pymol.cmd.select('unassigned','ID %s'%unassigned_atoms)
++ message_text = "Unable to assign parameters for the %s atoms in selection 'unassigned'.\nPlease either remove these unassigned atoms and re-start the calculation\nor fix their parameters in the generated PQR file and run the calculation\nusing the modified PQR file (select 'Use another PQR' in 'Main')."%len(unassigned_atoms.split('+'))
++ print "Unassigned atom IDs",unassigned_atoms
++ show_error(message_text)
++ return False
++ return True
+
+
+- def generatePqrFile(self):
+- """generate a pqr file
++ def generatePymolPqrFile(self):
++ """generate a pqr file from pymol
+
+ This will also call through to champ to set the Hydrogens and charges
+ if it needs to. If it does that, it may change the value self.selection
+@@ -1484,28 +1726,29 @@
+ junk = error_dialog.activate()
+ return False
+
+- if REAL_PYMOL:
+- # PyMOL + champ == pqr
+- from chempy.champ import assign
+- if self.radiobuttons.getvalue() == 'Use PyMOL generated PQR and PyMOL generated Hydrogens and termini':
+- pymol.cmd.remove('hydro and %s'%sel)
+- assign.missing_c_termini(sel)
+- assign.formal_charges(sel)
+- pymol.cmd.h_add(sel)
+-# WLD (code now unnecessary)
+-# new_hydros = '(hydro and neighbor %s)'%sel
+-# sel = '%s or %s' % (sel,new_hydros)
+- assign.amber99(sel)
+-# WLD (code now unnecessary)
+-# if not self.selection.getvalue() in '(all) all'.split():
+-# self.selection.setvalue(sel)
++ # PyMOL + champ == pqr
++ from chempy.champ import assign
++ if self.radiobuttons.getvalue() == 'Use PyMOL generated PQR and PyMOL generated Hydrogens and termini':
++ pymol.cmd.remove('hydro and %s'%sel)
++ assign.missing_c_termini(sel)
++ assign.formal_charges(sel)
++ pymol.cmd.h_add(sel)
++ # WLD (code now unnecessary)
++ # new_hydros = '(hydro and neighbor %s)'%sel
++ # sel = '%s or %s' % (sel,new_hydros)
++ assign.amber99(sel)
++ # WLD (code now unnecessary)
++ # if not self.selection.getvalue() in '(all) all'.split():
++ # self.selection.setvalue(sel)
+
+ #
+ # Get rid of chain information
+ #
+-# WLD -- PyMOL now does this automatically with PQR files
+-# pymol.cmd.alter(sel,'chain = ""')
++ # WLD -- PyMOL now does this automatically with PQR files
++ # pymol.cmd.alter(sel,'chain = ""')
++ self.fixColumns(sel)
+ pymol.cmd.save(pqr_filename,sel)
++ self.cleanupGeneratedPdbOrPqrFile(pqr_filename)
+ missed_count = pymol.cmd.count_atoms("("+sel+") and flag 23")
+ if missed_count > 0:
+ pymol.cmd.select("unassigned","("+sel+") and flag 23")
+@@ -1896,6 +2139,7 @@
+ ion_minus_two_conc,ion_minus_two_rad,
+ interior_dielectric, solvent_dielectric,
+ chgm,
++ srfm,
+ solvent_radius,
+ system_temp,
+ sdens,
+@@ -1906,7 +2150,7 @@
+ #
+ # How shall we set up the grid? We'll use cglen, fglen, cgcent, fgcent
+ # and dime.
+- # This allows people to automate things (e.g. "Alanine scanning")
++ # This allows people to automate things.
+ #
+
+ #
+@@ -1935,10 +2179,10 @@
+ %s # solve the full nonlinear PBE with npbe
+ #lpbe # solve the linear PBE with lpbe
+ bcfl %s # Boundary condition flag
+- # 0 => Zero
+- # 1 => Single DH sphere
+- # 2 => Multiple DH spheres
+- # 4 => Focusing
++ # 0 or zero => Zero
++ # 1 or sdh => Single DH sphere
++ # 2 or mdh => Multiple DH spheres
++ # 4 or focus => Focusing
+ #
+ #ion 1 0.000 2.0 # Counterion declaration:
+ ion 1 %f %f # Counterion declaration:
+@@ -1948,23 +2192,25 @@
+ pdie %f # Solute dielectric
+ sdie %f # Solvent dielectric
+ chgm %s # Charge disc method
+- # 0 is linear splines
+- # 1 is cubic b-splines
++ # spl0 is linear splines
++ # spl2 is cubic B-splines
++ # spl4 is quintic B-splines
+ mol 1 # which molecule to use
+- srfm smol # Surface calculation method
+- # 0 => Mol surface for epsilon;
+- # inflated VdW for kappa; no
+- # smoothing
+- # 1 => As 0 with harmoic average
+- # smoothing
+- # 2 => Cubic spline
++ srfm %s # Surface calculation method
++ # mol => Mol surface for epsilon;
++ # inflated VdW for kappa; no
++ # smoothing
++ # smol => As 0 with harmoic average
++ # smoothing
++ # spl2 => Cubic spline
++ # spl4 => Like spl2, but 7th-order polynomial
+ srad %f # Solvent radius (1.4 for water)
+ swin 0.3 # Surface cubic spline window .. default 0.3
+ temp %f # System temperature (298.15 default)
+ sdens %f # Specify the number of grid points per square-angstrom to use in Vacc object. Ignored when srad is 0.0 (see srad) or srfm is spl2 (see srfm). There is a direct correlation between the value used for the Vacc sphere density, the accuracy of the Vacc object, and the APBS calculation time. APBS default value is 10.0.
+- gamma 0.105 # Surface tension parameter for apolar forces (in kJ/mol/A^2)
+- # only used for force calculations, so we don't care, but
+- # it's always required, and 0.105 is the default
++ #gamma 0.105 # Surface tension parameter for apolar forces (in kJ/mol/A^2)
++ # # only used for force calculations, so we don't care, but
++ # # it's always required, and 0.105 is the default
+ calcenergy no # Energy I/O to stdout
+ # 0 => don't write out energy
+ # 1 => write out total energy
+@@ -1994,6 +2240,7 @@
+ ion_minus_two_conc,ion_minus_two_rad,
+ interior_dielectric, solvent_dielectric,
+ chgm,
++ srfm,
+ solvent_radius,
+ system_temp,
+ sdens,
diff --git a/sci-chemistry/pymol/files/nosplash-gentoo.patch b/sci-chemistry/pymol/files/nosplash-gentoo.patch
new file mode 100644
index 000000000..0ef65b1d8
--- /dev/null
+++ b/sci-chemistry/pymol/files/nosplash-gentoo.patch
@@ -0,0 +1,9 @@
+--- modules/pymol/invocation.py.orig 2008-06-26 20:55:25.000000000 +0200
++++ modules/pymol/invocation.py 2008-06-26 20:56:06.000000000 +0200
+@@ -373,6 +373,4 @@
+ if loaded_something and (options.after_load_script!=""):
+ options.deferred.append(options.after_load_script)
+ options.deferred.extend(final_actions)
+- if options.show_splash and not options.no_gui:
+- options.deferred.insert(0,"_do__ cmd.splash(1)")
+
diff --git a/sci-chemistry/pymol/files/pymol-1.1-r1-data-path.patch b/sci-chemistry/pymol/files/pymol-1.1-r1-data-path.patch
new file mode 100644
index 000000000..329b68292
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol-1.1-r1-data-path.patch
@@ -0,0 +1,51 @@
+diff -urN pymol-9999.orig/modules/pymol/commanding.py pymol-9999/modules/pymol/commanding.py
+--- pymol-9999.orig/modules/pymol/commanding.py 2008-01-11 13:23:32.000000000 +0100
++++ pymol-9999/modules/pymol/commanding.py 2008-01-11 13:22:57.000000000 +0100
+@@ -198,11 +198,11 @@
+ _self.unlock(0,_self)
+ r = DEFAULT_SUCCESS
+ if show_splash==1: # generic / open-source
+- png_path = _self.exp_path("$PYMOL_PATH/data/pymol/splash.png")
++ png_path = _self.exp_path("$PYMOL_DATA/pymol/splash.png")
+ elif show_splash==2: # evaluation builds
+- png_path = _self.exp_path("$PYMOL_PATH/data/pymol/epymol.png")
++ png_path = _self.exp_path("$PYMOL_DATA/pymol/epymol.png")
+ else: # incentive builds
+- png_path = _self.exp_path("$PYMOL_PATH/data/pymol/ipymol.png")
++ png_path = _self.exp_path("$PYMOL_DATA/pymol/ipymol.png")
+ if os.path.exists(png_path):
+ _self.do("_ cmd.load_png('%s',0,quiet=1)"%png_path)
+ else:
+#diff -urN pymol-9999.orig/modules/pymol/fitting.py pymol-9999/modules/pymol/fitting.py
+#--- pymol-9999.orig/modules/pymol/fitting.py 2008-01-11 13:23:32.000000000 +0100
+#+++ pymol-9999/modules/pymol/fitting.py 2008-01-11 13:23:00.000000000 +0100
+#@@ -68,7 +68,7 @@
+# if string.lower(matrix)=='none':
+# matrix=''
+# if len(matrix):
+#- mfile = cmd.exp_path("$PYMOL_PATH/data/pymol/matrices/"+matrix)
+#+ mfile = cmd.exp_path("$PYMOL_DATA/pymol/matrices/"+matrix)
+# else:
+# mfile = ''
+# # delete existing alignment object (if asked to reset it)
+#@@ -135,7 +135,7 @@
+# if string.lower(matrix)=='none':
+# matrix=''
+# if len(matrix):
+#- mfile = cmd.exp_path("$PYMOL_PATH/data/pymol/matrices/"+matrix)
+#+ mfile = cmd.exp_path("$PYMOL_DATA/pymol/matrices/"+matrix)
+# else:
+# mfile = ''
+# if object==None: object=''
+diff -urN pymol-9999.orig/modules/pymol/importing.py pymol-9999/modules/pymol/importing.py
+--- pymol-9999.orig/modules/pymol/importing.py 2008-01-11 13:23:32.000000000 +0100
++++ pymol-9999/modules/pymol/importing.py 2008-01-11 13:23:02.000000000 +0100
+@@ -171,7 +171,7 @@
+ r = DEFAULT_ERROR
+
+
+- tables = { 'cmyk' : "$PYMOL_PATH/data/pymol/cmyk.png",
++ tables = { 'cmyk' : "$PYMOL_DATA/pymol/cmyk.png",
+ 'pymol' : 'pymol',
+ 'rgb' : 'rgb' }
+
diff --git a/sci-chemistry/pymol/files/pymol-1.1-r1-shaders.patch b/sci-chemistry/pymol/files/pymol-1.1-r1-shaders.patch
new file mode 100644
index 000000000..7f4a24f48
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol-1.1-r1-shaders.patch
@@ -0,0 +1,11 @@
+diff -uarN pymol-9999.orig/setup.py pymol-9999/setup.py
+--- pymol-9999.orig/setup.py 2008-06-18 11:47:58.000000000 +0200
++++ pymol-9999/setup.py 2008-06-18 11:48:52.000000000 +0200
+@@ -143,6 +143,7 @@
+ def_macros=[("_PYMOL_MODULE",None),
+ ("_PYMOL_INLINE",None),
+ ("_PYMOL_FREETYPE",None),
++ ("_PYMOL_OPENGL_SHADERS",None),
+ # Numeric Python support
+ # ("_PYMOL_NUMPY",None),
+ # VMD plugin support