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Sourcecode: pymol version File versions

internal.py

import cmd
import types
import _cmd
import string
import threading
import traceback
import thread
import re
import viewing
import time
import pymol
from operator import add

from chempy import io

from cmd import DEFAULT_ERROR, DEFAULT_SUCCESS, loadable, _load2str, Shortcut, \
   is_string, is_ok

# cache management:

def _cache_validate(_self=cmd):
    r = DEFAULT_SUCCESS
    try:
        _self.lock_data(_self)
        _pymol = _self._pymol
        if not hasattr(_pymol,"_cache"):
            _pymol._cache = []
        if not hasattr(_pymol,"_cache_memory"):
            _pymol._cache_memory = 0
    finally:
        _self.unlock_data(_self)
        
def _cache_clear(_self=cmd):
    r = DEFAULT_SUCCESS
    try:
        _self.lock_data(_self)
        _pymol = _self._pymol
        _pymol._cache = []
        _pymol._cache_memory = 0
    finally:
        _self.unlock_data(_self)
    return r
    
def _cache_mark(_self=cmd):
    r = DEFAULT_SUCCESS
    try:
        _self.lock_data(_self)
        _pymol = _self._pymol
        _cache_validate(_self)
        for entry in _self._pymol._cache: 
            entry[5] = 0.0
    finally:
        _self.unlock_data(_self)
    return r

def _cache_purge(max_size, _self=cmd):
    r = DEFAULT_SUCCESS
    try:
        _self.lock_data(_self)
        _pymol = _self._pymol
        _cache_validate(_self)
        if len(_pymol._cache):
            cur_size = reduce(add,map(lambda x:x[0],_pymol._cache))
            if max_size>=0: # purge to reduce size
                now = time.time()
                # sort by last access time
                new_cache = map(lambda x:[(now-x[5])/x[4],x], _pymol._cache)
                new_cache.sort()
                new_cache = map(lambda x:x[1],new_cache)
                # remove oldest entries one by one until size requirement is met
                while (cur_size>max_size) and (len(new_cache)>1):
                    entry = new_cache.pop() 
                    cur_size = cur_size - entry[0]
                _pymol._cache = new_cache
                _pymol._cache_memory = cur_size
            else: # purge to eliminate unused entries
                new_cache = []
                for entry in _pymol._cache:
                    if entry[5] == 0.0:
                        cur_size = cur_size - entry[0]
                    else:
                        new_cache.append(entry)
                _pymol._cache = new_cache
                _pymol._cache_memory = cur_size
        result = _pymol._cache_memory
    finally:
        _self.unlock_data(_self)
    return result
        
def _cache_get(target, hash_size = None, _self=cmd):
    result = None
    try:
        _self.lock_data(_self)
        try:
            if hash_size == None:
                hash_size = len(target[1])
            key = target[1][0:hash_size]
            # should optimize this with a dictionary lookup, key -> index in _cache
            for entry in _self._pymol._cache:
                if entry[1][0:hash_size] == key:
                    if entry[2] == target[2]:
                        while len(entry)<6:
                            entry.append(0)
                        entry[4] = entry[4] + 1 # access count
                        entry[5] = time.time() # timestamp
                        result = entry[3]
                        break
        except:
            traceback.print_exc()
    finally:
        _self.unlock_data(_self)
    return result

def _cache_set(new_entry, max_size, _self=cmd):
    r = DEFAULT_SUCCESS
    try:
        _self.lock_data(_self)
        _pymol = _self._pymol
        _cache_validate(_self)
        try:
            hash_size = len(new_entry[1])
            key = new_entry[1][0:hash_size]
            count = 0
            found = 0
            new_entry[4] = new_entry[4] + 1 # incr access count
            new_entry[5] = time.time() # timestamp
            for entry in _pymol._cache: 
                if entry[1][0:hash_size] == key:
                    if entry[2] == new_entry[2]: # dupe (shouldn't happen)
                        entry[3] = new_entry[3] 
                        found = 1
                        break
                count = count + 1
            if not found:
                _pymol._cache.append(new_entry)
                _pymol._cache_memory = _pymol._cache_memory + new_entry[0]
                if max_size > 0:
                    if _pymol._cache_memory > max_size:
                        _cache_purge(max_size, _self)
        except:
            traceback.print_exc()
    finally:
        _self.unlock_data(_self)
    return r
        
# ray tracing threads

def _ray_anti_spawn(thread_info,_self=cmd):
    # WARNING: internal routine, subject to change      
    # internal routine to support multithreaded raytracing
    thread_list = []
    for a in thread_info[1:]:
        t = threading.Thread(target=_cmd.ray_anti_thread,
                                    args=(_self._COb,a))
        t.setDaemon(1)
        thread_list.append(t)
    for t in thread_list:
        t.start()
    _cmd.ray_anti_thread(_self._COb,thread_info[0])
    for t in thread_list:
        t.join()

def _ray_hash_spawn(thread_info,_self=cmd):
    # WARNING: internal routine, subject to change      
    # internal routine to support multithreaded raytracing
    thread_list = []
    for a in thread_info[1:]:
        if a != None:
            t = threading.Thread(target=_cmd.ray_hash_thread,
                                 args=(_self._COb,a))
            t.setDaemon(1)
            thread_list.append(t)
    for t in thread_list:
        t.start()
    if thread_info[0] != None:
        _cmd.ray_hash_thread(_self._COb,thread_info[0])
    for t in thread_list:
        t.join()

def _ray_spawn(thread_info,_self=cmd):
    # WARNING: internal routine, subject to change      
    # internal routine to support multithreaded raytracing
    thread_list = []
    for a in thread_info[1:]:
        t = threading.Thread(target=_cmd.ray_trace_thread,
                                    args=(_self._COb,a))
        t.setDaemon(1)
        thread_list.append(t)
    for t in thread_list:
        t.start()
    _cmd.ray_trace_thread(_self._COb,thread_info[0])
    for t in thread_list:
        t.join()

def _coordset_update_thread(list_lock,thread_info,_self=cmd):
    # WARNING: internal routine, subject to change
    while 1:
        list_lock.acquire()
        if not len(thread_info):
            list_lock.release()
            break
        else:
            info = thread_info.pop(0)
            list_lock.release()
        _cmd.coordset_update_thread(_self._COb,info)

def _coordset_update_spawn(thread_info,n_thread,_self=cmd):
    # WARNING: internal routine, subject to change
    if len(thread_info):
        list_lock = threading.Lock() # mutex for list
        thread_list = []
        for a in range(1,n_thread):
            t = threading.Thread(target=_coordset_update_thread,
                                        args=(list_lock,thread_info))
            t.setDaemon(1)
            thread_list.append(t)
        for t in thread_list:
            t.start()
        _coordset_update_thread(list_lock,thread_info)
        for t in thread_list:
            t.join()

def _object_update_thread(list_lock,thread_info,_self=cmd):
    # WARNING: internal routine, subject to change
    while 1:
        list_lock.acquire()
        if not len(thread_info):
            list_lock.release()
            break
        else:
            info = thread_info.pop(0)
            list_lock.release()
        _cmd.object_update_thread(_self._COb,info)

def _object_update_spawn(thread_info,n_thread,_self=cmd):
    # WARNING: internal routine, subject to change
    if len(thread_info):
        list_lock = threading.Lock() # mutex for list
        thread_list = []
        for a in range(1,n_thread):
            t = threading.Thread(target=_object_update_thread,
                                        args=(list_lock,thread_info))
            t.setDaemon(1)
            thread_list.append(t)
        for t in thread_list:
            t.start()
        _object_update_thread(list_lock,thread_info)
        for t in thread_list:
            t.join()

# status reporting

# do command (while API already locked)

def _do(cmmd,log=0,echo=1,_self=cmd):
    return _cmd.do(_self._COb,cmmd,log,echo)

# movie rendering

def _mpng(prefix, first=-1, last=-1, preserve=0, modal=0,
          format=-1, mode=-1, quiet=1, _self=cmd): # INTERNAL
    import sys
    format = int(format)
    # WARNING: internal routine, subject to change
    try:
        _self.lock(_self)   
        fname = prefix
        if re.search("[0-9]*\.png$",fname): # remove numbering, etc.
            fname = re.sub("[0-9]*\.png$","",fname)
        if re.search("[0-9]*\.ppm$",fname):
            if format<0:
                format = 1 # PPM
            fname = re.sub("[0-9]*\.ppm$","",fname)
        if format<0:
            format = 0 # default = PNG
        fname = cmd.exp_path(fname)
        r = _cmd.mpng_(_self._COb,str(fname),int(first),
                       int(last),int(preserve),int(modal),
                       format,int(mode),int(quiet))
    finally:
        _self.unlock(-1,_self)
    return r

# copy image

def _copy_image(_self=cmd,quiet=1):
    r = DEFAULT_ERROR
    try:
        _self.lock(_self)   
        r = _cmd.copy_image(_self._COb,int(quiet))
    finally:
        _self.unlock(r,_self)
    return r


# loading


def _load(oname,finfo,state,ftype,finish,discrete,
          quiet=1,multiplex=0,zoom=-1,mimic=1,
          _self=cmd):
    # WARNING: internal routine, subject to change
    # caller must already hold API lock
    # NOTE: state index assumes 1-based state
    r = DEFAULT_ERROR
    size = 0
    if ftype not in (loadable.model,loadable.brick):
        if ftype == loadable.r3d:
            import cgo
            obj = cgo.from_r3d(finfo)
            if is_ok(obj):
                r = _cmd.load_object(_self._COb,str(oname),obj,int(state)-1,loadable.cgo,
                                      int(finish),int(discrete),int(quiet),
                                      int(zoom))
            else:
                print "Load-Error: Unable to open file '%s'."%finfo
        elif ftype == loadable.cc1: # ChemDraw 3D
            obj = io.cc1.fromFile(finfo)
            if obj:
                r = _cmd.load_object(_self._COb,str(oname),obj,int(state)-1,loadable.model,
                                      int(finish),int(discrete),
                                      int(quiet),int(zoom))
        elif ftype == loadable.moe:
            try:
                # BEGIN PROPRIETARY CODE SEGMENT
                from epymol import moe
                if (string.find(finfo,":")>1):
                    import urllib
                    moe_file = urllib.urlopen(finfo)
                else:
                    moe_file = open(finfo)
                moe_str = moe_file.read()
                moe_file.close()
                r = moe.read_moestr(moe_str,str(oname),int(state),
                                int(finish),int(discrete),int(quiet),int(zoom),_self=_self)

                # END PROPRIETARY CODE SEGMENT
            except ImportError:
                print "Error: .MOE format not supported by this PyMOL build."
                if _self._raising(-1,_self): raise pymol.CmdException

        elif ftype == loadable.mae:
            try:
                # BEGIN PROPRIETARY CODE SEGMENT
                from epymol import mae
                if (string.find(finfo,":")>1):
                    import urllib 
                    mae_file = urllib.urlopen(finfo)
                else:
                    mae_file = open(finfo)
                mae_str = mae_file.read()
                mae_file.close()
                r = mae.read_maestr(mae_str,str(oname),
                                    int(state),
                                    int(finish),int(discrete),
                                    int(quiet),int(zoom),int(multiplex),
                                    int(mimic),
                                    _self=_self)

                # END PROPRIETARY CODE SEGMENT
            except ValueError:
                print "Error: .MAE format not supported by this PyMOL build."
                if _self._raising(-1,_self): raise pymol.CmdException

        else:
            if ftype in _load2str.keys() and (string.find(finfo,":")>1):
                gz = re.search("\.gz$",finfo,re.I)
                try:
                    import urllib
                    tmp_file = urllib.urlopen(finfo)
                except:
                    print "Error: unable to open the URL:\nError:   %s"%finfo
#                    traceback.print_exc()
                    return 0
                finfo = tmp_file.read() 
                if gz:
                    import StringIO
                    fakestream = StringIO.StringIO(finfo)
                    import gzip
                    finfo = gzip.GzipFile(fileobj=fakestream).read()
                ftype = _load2str[ftype]
                tmp_file.close()
            elif ftype in _load2str.keys() and re.search("\.gz$",finfo,re.I):
                import gzip
                finfo = gzip.open(finfo).read()                
                ftype = _load2str[ftype]
            r = _cmd.load(_self._COb,str(oname),finfo,int(state)-1,int(ftype),
                          int(finish),int(discrete),int(quiet),
                          int(multiplex),int(zoom))
    else:
        try:
            x = io.pkl.fromFile(finfo)
            if isinstance(x,types.ListType) or isinstance(x,types.TupleType):
                for a in x:
                    r = _cmd.load_object(_self._COb,str(oname),a,int(state)-1,
                                                int(ftype),0,int(discrete),int(quiet),
                                                int(zoom))
                    if(state>0):
                        state = state + 1
                _cmd.finish_object(_self._COb,str(oname))
            else:
                r = _cmd.load_object(_self._COb,str(oname),x,
                                            int(state)-1,int(ftype),
                                            int(finish),int(discrete),
                                            int(quiet),int(zoom))
        except:
#            traceback.print_exc()
            print "Load-Error: Unable to load file '%s'." % finfo
    return r

# function keys and other specials

def _special(k,x,y,m=0,_self=cmd): # INTERNAL (invoked when special key is pressed)
    pymol=_self._pymol
    # WARNING: internal routine, subject to change
    k=int(k)
    m=int(m)
    my_special = _self.special
    if(m>0) and (m<5):
        my_special = (_self.special,
                      _self.shft_special,
                      _self.ctrl_special,
                      _self.ctsh_special,
                      _self.alt_special)[m]
    if my_special.has_key(k):
        if my_special[k][1]:
            apply(my_special[k][1],my_special[k][2],my_special[k][3])
        else:
            key = my_special[k][0]
            if(m>0) and (m<5):
                key = ('','SHFT-','CTRL-','CTSH-','ALT-')[m] + key
            if pymol._scene_dict.has_key(key): 
                _self.scene(key)
            elif is_string(pymol._scene_dict_sc.interpret(key+"-")):
                _self.scene(pymol._scene_dict_sc[key+"-"])
            elif pymol._view_dict.has_key(key):
                _self.view(key)
            elif is_string(pymol._view_dict_sc.interpret(key+"-")):
                _self.view(pymol._view_dict_sc[key+"-"])
    return None

# control keys

def _ctrl(k,_self=cmd):
    # WARNING: internal routine, subject to change
    if _self.ctrl.has_key(k):
        ck = _self.ctrl[k]
        if ck[0]!=None:
            apply(ck[0],ck[1],ck[2])
    return None

# alt keys

def _alt(k,_self=cmd):
    # WARNING: internal routine, subject to change
    if _self.alt.has_key(k):
        ak = _self.alt[k]
        if ak[0]!=None:
            apply(ak[0],ak[1],ak[2])
    return None

# writing PNG files (thread-unsafe)

def _png(a,width=0,height=0,dpi=-1.0,ray=0,quiet=1,prior=0,format=-1,_self=cmd):
    # INTERNAL - can only be safely called by GLUT thread (unless prior == 1)
    # WARNING: internal routine, subject to change
    try:
        _self.lock(_self)   
        fname = a
        if re.search("\.ppm$",fname):
            if format<0:
                format = 1 # PPM
        elif not re.search("\.png$",fname):
            if a[0:1] != chr(1): # not an encoded file descriptor (integer)
                fname = fname +".png"
        if format<0:
            format = 0 # PNG
        fname = cmd.exp_path(fname)
        r = _cmd.png(_self._COb,str(fname),int(width),int(height),
                     float(dpi),int(ray),int(quiet),int(prior),int(format))
    finally:
        _self.unlock(-1,_self)
    return r

# quitting (thread-specific)

def _quit(_self=cmd):
    pymol=_self._pymol
    # WARNING: internal routine, subject to change
    try:
        _self.lock(_self)
        try: # flush and close log if possible to avoid threading exception
            if pymol._log_file!=None:
                try:
                    pymol._log_file.flush()
                except:
                    pass
                pymol._log_file.close()
                del pymol._log_file
        except:
            pass
        if _self.reaper!=None:
            try:
                _self.reaper.join()
            except:
                pass
        r = _cmd.quit(_self._COb)
    finally:
        _self.unlock(-1,_self)
    return r

# screen redraws (thread-specific)

def _refresh(swap_buffers=1,_self=cmd):  # Only call with GLUT thread!
    # WARNING: internal routine, subject to change
    r = None
    try:
        _self.lock(_self)
        if hasattr(_self._pymol,'glutThread'):
            if thread.get_ident() == _self._pymol.glutThread:
                if swap_buffers:
                    r = _cmd.refresh_now(_self._COb)
                else:
                    r = _cmd.refresh(_self._COb)
            else:
                r = _cmd.refresh_later(_self._COb)                
        else:
            r = _cmd.refresh_later(_self._COb)
    finally:
        _self.unlock(-1,_self)
    return r

# stereo (platform dependent )

def _sgi_stereo(flag): # SGI-SPECIFIC - bad bad bad
    import sys
    # WARNING: internal routine, subject to change
    if sys.platform[0:4]=='irix':
        if os.path.exists("/usr/gfx/setmon"):
            if flag:
                mode = os.environ.get('PYMOL_SGI_STEREO','1024x768_96s')
                os.system("/usr/gfx/setmon -n "+mode)
            else:
                mode = os.environ.get('PYMOL_SGI_MONO','72hz')
                os.system("/usr/gfx/setmon -n "+mode)

# color alias interpretation

def _interpret_color(_self,color):
    # WARNING: internal routine, subject to change
    _validate_color_sc(_self)
    new_color = _self.color_sc.interpret(color)
    if new_color:
        if is_string(new_color):
            return new_color
        else:
            _self.color_sc.auto_err(color,'color')
    else:
        return color

def _validate_color_sc(_self=cmd):
    # WARNING: internal routine, subject to change
    if _self.color_sc == None: # update color shortcuts if needed
        lst = _self.get_color_indices()
        lst.extend([('default',-1),('auto',-2),('current',-3),('atomic',-4)])
        _self.color_sc = Shortcut(map(lambda x:x[0],lst))
        color_dict = {}
        for a in lst: color_dict[a[0]]=a[1]

def _invalidate_color_sc(_self=cmd):
    # WARNING: internal routine, subject to change
    _self.color_sc = None

def _get_color_sc(_self=cmd):
    # WARNING: internal routine, subject to change
    _validate_color_sc(_self=_self)
    return _self.color_sc

def _get_feedback(_self=cmd): # INTERNAL
    # WARNING: internal routine, subject to change
    l = []
    if _self.lock_attempt(_self):
        try:
            r = _cmd.get_feedback(_self._COb)
            while r:
                l.append(r)
                r = _cmd.get_feedback(_self._COb)
        finally:
            _self.unlock(-1,_self)
    else:
        l = None
    return l

get_feedback = _get_feedback # for legacy compatibility

def _fake_drag(_self=cmd): # internal
    _self.lock(_self)
    try:
        _cmd.fake_drag(_self._COb)
    finally:
        _self.unlock(-1,_self)
    return 1

def _sdof(tx,ty,tz,rx,ry,rz,_self=cmd):
    _cmd._sdof(_self._COb,tx,ty,tz,rx,ry,rz)
    
# testing tools

# for comparing floating point numbers calculated using
# different FPUs and which may show some wobble...

def _dump_floats(lst,format="%7.3f",cnt=9):
    # WARNING: internal routine, subject to change
    c = cnt
    for a in lst:
        print format%a,
        c = c -1
        if c<=0:
            print
            c=cnt
    if c!=cnt:
        print

def _dump_ufloats(lst,format="%7.3f",cnt=9):
    # WARNING: internal routine, subject to change
    c = cnt
    for a in lst:
        print format%abs(a),
        c = c -1
        if c<=0:
            print
            c=cnt
    if c!=cnt:
        print

# HUH?
def _adjust_coord(a,i,x):
    a.coord[i]=a.coord[i]+x
    return None



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