Incorporating DruGUI into ProDy

.gitignore

@@ -17,6 +17,7 @@ sdist
 develop-eggs
 .installed.cfg
 __pycache__
+.DS_Store
 
 # ProDy
 *.nmd

prody/__init__.py

@@ -114,6 +114,11 @@ def turnonDeprecationWarnings(action='always'):
 __all__.extend(dynamics.__all__)
 __all__.append('dynamics')
 
+from . import drugui
+from .drugui import *
+__all__.extend(drugui.__all__)
+__all__.append('drugui')
+
 from . import ensemble
 from .ensemble import *
 __all__.extend(ensemble.__all__)
@@ -134,6 +139,11 @@ def turnonDeprecationWarnings(action='always'):
 __all__.extend(domain_decomposition.__all__)
 __all__.append('domain_decomposition')
 
+from . import drugui
+from .drugui import *
+__all__.extend(drugui.__all__)
+__all__.append('drugui')
+
 #from . import comd
 #from .comd import *
 #__all__.extend(comd.__all__)

prody/drugui/DruGUI-script/0chlcmpall.tcl

@@ -0,0 +1,42 @@
+# 2020-05-12 Ji Young Lee
+
+set struc     ./t0.pdb                       
+set psffi     XXX
+set trajec    RRR                        
+set freq      SSTEP
+set start     FSTEP 
+
+mol load psf $psffi pdb $struc
+animate read dcd $trajec beg $start end -1 skip $freq waitfor all
+
+####wrap
+package require pbctools
+pbc wrap -compound fragment -center com -centersel "protein" -sel " SSS " -all
+
+####alignment
+set ref_molid [molinfo top get id]
+set traj_molid [molinfo top get id]
+
+set calpha "alpha carbon"
+set CAreference [atomselect $ref_molid $calpha frame 0]
+set CAcompare   [atomselect $traj_molid $calpha]
+set System      [atomselect $traj_molid " SSS "]
+
+set num_frames [molinfo $traj_molid get numframes]
+
+for {set f 1} {$f < $num_frames} {incr f} {
+        molinfo $traj_molid set frame $f
+        $CAcompare frame $f
+        $System    frame $f
+        set trans_mat [measure fit $CAcompare $CAreference]
+        $System    move $trans_mat
+}
+####alignment
+
+animate write pdb pp0.pdb beg 0 end 0 sel [atomselect top " SSS "]
+animate write psf pp0.psf beg 0 end 0 sel [atomselect top " SSS "]
+animate write pdb pp1.pdb beg 1 end 1 sel [atomselect top " SSS "]
+animate write psf pp1.psf beg 1 end 1 sel [atomselect top " SSS "]
+animate write dcd pp.dcd  beg 1 end -1 waitfor all sel [atomselect top " SSS "]
+
+exit

prody/drugui/DruGUI-script/1a.sh

@@ -0,0 +1,21 @@
+# 2020-05-12 Ji Young Lee
+
+###Check
+Struc=../md.pdb
+PSFfi=' ..\/md.psf '
+Traje=' ..\/sim.dcd '
+Selec='all     '
+Step=1  
+Start=0
+Head='CRYST1   85.328   96.807   93.491  90     90     90'
+###Check
+
+sed '1,1d' $Struc  >  __test   ## Check!!!
+echo "$Head "      >  t0.pdb
+cat __test         >> t0.pdb
+
+cp 0chlcmpall.tcl ___ligb.tcl
+sed -e "s/XXX/$PSFfi/g" -e "s/RRR/$Traje/g" -e "s/SSS/$Selec/g" -e "s/FSTEP/$Start/g" -e "s/SSTEP/$Step/g" ___ligb.tcl  > __ligb.tcl
+
+vmd -dispdev text -e __ligb.tcl    
+rm __*

prody/drugui/DruGUI-script/druggability/__init__.py

@@ -0,0 +1,31 @@
+# Druggability: Python Package and VMD GUI for Druggability Index Analysis
+# Copyright (C) 2010  Ahmet Bakan <ahb12@pitt.edu>
+# 
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+"""Python Package for druggability index analysis"""
+
+__author__ = 'Ahmet Bakan'
+__copyright__ = 'Copyright (C) 2010  Ahmet Bakan'
+__version__ = '0.5.2'
+
+
+from . import functions
+from . import grid
+from . import probe
+from .functions import pickler
+from .dia import DruggabilityIndexAnalysis as DIA
+
+__all__ = ['DIA', 'pickler']
+

prody/drugui/DruGUI-script/druggability/abase.py

@@ -0,0 +1,250 @@
+# Druggability: Python Package and VMD GUI for Druggability Index Analysis
+# Copyright (C) 2010  Ahmet Bakan <ahb12@pitt.edu>
+# 
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+"""This module defines a base class for other classes. Important features of 
+this base class are its logging and self pickling functionalities.
+
+Classes:
+
+* :class:`ABase`
+
+Functions:
+
+* :func:`get_logger`
+
+"""
+
+__author__ = 'Ahmet Bakan'
+__copyright__ = 'Copyright (C) 2010  Ahmet Bakan'
+__version__ = '0.5.2'
+
+import pickle
+import gzip
+import logging
+import logging.handlers
+import os
+import os.path
+
+LOGGING_LEVELS = {'debug': logging.DEBUG,
+                  'info': logging.INFO,
+                  'warning': logging.WARNING,
+                  'error': logging.ERROR,
+                  'critical': logging.CRITICAL}
+LOGGING_LEVELS.setdefault(logging.INFO)
+
+SIGNATURE = '@>'
+
+__all__ = ['ABase']
+
+def _set_workdir(workdir):
+    """Set a working directory, by creating if it doesn't exist."""
+    if os.path.isabs(workdir):
+        workdir = os.path.relpath(workdir)
+    if not os.path.isdir(workdir):
+        dirs = workdir.split(os.sep)
+        for i in range(len(dirs)):
+            dirname = os.sep.join(dirs[:i+1])
+            try:
+                if not os.path.isdir(dirname): 
+                    os.mkdir(dirname)
+            except OSError:
+                return os.getcwd()
+    return os.path.join(os.getcwd(), workdir)
+
+def get_logger(name, **kwargs):
+    """Return a logger.
+
+    :arg name: name of the logger instance
+    :type name: str
+
+    :keyword verbose: loglevel for console verbosity
+    :type verbose: str, default is "info" 
+
+    :keyword writelog: control logging in a file
+    :type writelog: bool, default is True
+
+    :keyword workdir: location of logfile
+    :type workdir: str, default is "."
+
+    :keyword loglevel: loglevel for logfile verbosity
+    :type loglevel: str, default is "debug"
+
+    :keyword logfilemode: mode in which logfile will be opened 
+    :type logfilemode: str, default is "w"
+
+    :keyword backupcount: number of old *name.log* files to save
+    :type backupcount: int, default is 3
+
+    ======== ==================================================================
+    Loglevel Description
+    ======== ==================================================================
+    debug    Eveything will be printed on the colsole or written into logfile.
+    info     Only brief information will be printed or written.
+    warning  Only critical information will be printed or written.
+    error    This loglevel is equivalent to *warning* in package.
+    critical This loglevel is equivalent to *warning* in package.
+    ======== ==================================================================
+
+
+    """
+    logger = logging.getLogger(name)
+    logger.setLevel(logging.DEBUG)
+
+    if logger.handlers: 
+        return logger
+
+
+    console = logging.StreamHandler()
+    console.setLevel(LOGGING_LEVELS[kwargs.get('verbose', 'info')])
+    console.setFormatter(logging.Formatter(SIGNATURE + ' %(message)s'))
+    logger.addHandler(console)
+
+    if not ('writelog' in kwargs and not kwargs['writelog']):
+        logfilename = os.path.join(kwargs.get('workdir', '.'), name+'.log')
+        rollover = False 
+        # if filemode='a' is provided, rollover is not performed
+        if os.path.isfile(logfilename) and kwargs.get('filemode', None) != 'a':
+            rollover = True
+        logfile = logging.handlers.RotatingFileHandler(logfilename, 
+                    mode=kwargs.get('filemode', 'a'), maxBytes=0,
+                    backupCount=kwargs.get('backupcount', 3))
+        logfile.setLevel(LOGGING_LEVELS[kwargs.get('loglevel', 'debug')])
+        logfile.setFormatter(logging.Formatter('%(message)s'))
+        logger.addHandler(logfile)
+        if rollover:
+            logger.debug('Saving this log file and starting a new one.')
+            logfile.doRollover()
+    return logger
+
+class ABase(object):
+
+    """A base class that provides logging and self pickling functionality.
+
+
+    .. attribute:: name
+
+       Name of the instance, which is frequently used as a prefix to output 
+       names.
+
+    .. attribute:: workdir
+
+       Working directory for the instance, into which outputs are written.
+
+    .. attribute:: logger
+
+       A Python logger for the instance. By default a log file is started for 
+       the instance with the name :file:`workdir/name.log`.
+
+    """
+
+
+    def __init__(self, name, **kwargs):
+        """Instantiate class using an instance name.
+
+        :arg name: name of the class instance
+        :type name: str
+
+        :keyword workdir: location of all outputs and logfile
+        :type workdir: str, default is "."
+
+        :keyword logger: logger instance to log actions and method calls
+        :type logger: logging.Logger, default None
+
+        Unless an existing logger is passed as a keyword argument, a new logger
+        is started for the object. All keyword arguments are passed to the 
+        :meth:`get_logger` method.
+
+        """
+        self.name = name
+
+        if 'wordkdir' in kwargs:
+            workdir = kwargs['workdir']
+        else: 
+            workdir = '.'
+
+        kwargs['workdir'] = _set_workdir(workdir)
+
+        if 'logger' in kwargs:
+            self.logger = kwargs['logger']
+        else:
+            self.logger = get_logger(name, **kwargs)
+        self.logger.info('{0:s} is initialized.'.format(self.name))
+        self.set_workdir(workdir)
+
+    def set_workdir(self, workdir):
+        """Change working directory.
+
+        If *workdir* does not exist, it is created.
+
+        :arg workdir: new working directory
+        :type workdir: str
+
+        """
+        self.workdir = _set_workdir(workdir)
+        self.logger.info('{0:s} working directory is set to "{1:s}".'
+                         .format(self.name, os.path.relpath(workdir)))
+
+    def set_logger(self, **kwargs):
+        """Setup a logger.
+
+        This method can be used to reset current logger or to restart logger
+        after the object is unpickled.
+
+        All keyword arguments are passed to the :func:`get_logger` method.
+
+        """
+        if not kwargs.has_key('filemode'):
+            kwargs['filemode'] = 'a'
+        self.logger = get_logger(self.name, workdir=self.workdir, **kwargs)
+
+    def pickle(self, filename=None, compress=True):
+        """cPickle the object into a file with .dso(.gz) extension.
+
+        Handler objects of logger attribute prevents pickling of this
+        object. Hence, this method is defined. It temporarily removes 
+        handlers from the logger, pickles the object, and restores the 
+        handlers.
+
+        To restore the object, use pickler method in Functions module. 
+
+        :arg filename: name of the file to dump object (without an extension)
+        :type filename: str or None, default is :attr:`ABase.name`
+
+        :arg compress: gzip output
+        :type compress: bool, default is True
+
+        """
+        if filename is None: 
+            filename = os.path.join(self.workdir, self.name)
+        filename += '.dso'
+        if compress: 
+            filename += '.gz'
+            out = gzip.open(filename, 'w')
+        else: 
+            out = open(filename, 'w')
+
+        # spare logger
+        logger = self.logger
+        self.logger = None
+
+        pickle.dump(self, out)
+        out.close()
+
+        # restore logger and kdtree
+        self.logger = logger
+
+        self.logger.info('{0:s} is cPickled into file {1:s}.'
+                         .format(self.name, os.path.relpath(filename)))