from CCP4PluginScript import CInternalPlugin,CPluginScript from PyQt4 import QtCore import os,re,time,sys class coot_rebuild(CPluginScript): #class coot_rebuild(CInternalPlugin): TASKMODULE = 'model_building' # Where this plugin will appear on the gui TASKTITLE = 'Rebuild model with coot' # A short title for gui menu TASKNAME = 'coot_rebuild' # Task name - should be same as class name TASKCOMMAND = 'coot' # The command to run the executable TASKVERSION= 0.0 # Version of this plugin ASYNCHRONOUS = True TIMEOUT_PERIOD = 9999999.9 MAINTAINER = 'martin.noble@newcastle.ac.uk' ERROR_CODES = { 200 : { 'description' : 'Coot exited with error status' }, 201 : { 'description' : 'Failed in harvest operation' },202 : { 'description' : 'Failed in processOutputFiles' }} def makeCommandAndScript(self): import CCP4Utils self.dropDir = os.path.join(self.workDirectory,'COOT_FILE_DROP') if not os.path.exists(self.dropDir): try: os.mkdir(self.dropDir) except: self.dropDir = self.workDirectory print 'Could not make dropDir reset to',self.dropDir ''' # Look for a state file with name like the input coordinate file - # only works if the coord file is from coot if not self.container.inputData.COOTSTATEFILE.isSet() and self.container.inputData.XYZIN.fullPath.count('COOT_FILE_DROP')>0: statePath,fileName = os.path.split(self.container.inputData.XYZIN.fullPath) statePath = os.path.join(statePath,re.sub('output','state',fileName)) print 'coot_rebuild derived state file',statePath, os.path.exists(statePath) if os.path.exists(statePath): self.container.inputData.COOTSTATEFILE.setFullPath(statePath) ''' # Copy a startup state file to the drop directory if self.container.inputData.COOTSTATEFILE.isSet(): self.copyStateFile() ''' import shutil try: shutil.copyfile(self.container.inputData.COOTSTATEFILE.__str__(),os.path.join(self.dropDir,'0-coot-history.py')) except: pass ''' # Make a script file with additional menu options to save to i2 self.cootScriptPath = os.path.normpath(os.path.join(self.workDirectory,'script.py')) if sys.platform == 'win32': self.cootScriptPath = re.sub(r'\\\\',r'\\',self.cootScriptPath) # Declare script text then re.sub in the variables if sys.platform == "win32": i2dir = CCP4Utils.getCCP4I2Dir().replace('\\','/') else: i2dir = CCP4Utils.getCCP4I2Dir() script = """ import os, sys pythonDefsFile = os.path.normpath((os.path.join('"""+i2dir+"""','wrappers','coot_rebuild','script'))) sys.path.append(pythonDefsFile) import ccp4i2CootInterface #Here provide that module with "global function calls it will need for cootFunction in [coot_menubar_menu, add_simple_coot_menu_menuitem, read_pdb, set_molecule_name, make_and_draw_map, read_cif_dictionary, save_coordinates, save_state_file, molecule_chooser_gui, residue_centre, set_rotation_centre]: setattr(ccp4i2CootInterface, cootFunction.__name__, cootFunction) print 'Managed to load ccp4i2CootInterface' ccp4i2Interface = ccp4i2CootInterface.ccp4i2CootInterface(dropDir=r'"""+self.dropDir+"""') print ccp4i2CootInterface, ccp4i2Interface try: ccp4i2Interface.installMenus() except Exception as e: print e """ if self.container.inputData.USEKEYBINDINGS.isSet() and self.container.inputData.USEKEYBINDINGS: script+=""" add_key_binding("Refine Active Residue", "r", lambda: manual_refine_residues(0)) add_key_binding("Refine Active Residue AA", "x", lambda: refine_active_residue()) add_key_binding("Triple Refine", "t", lambda: manual_refine_residues(1)) add_key_binding("Autofit Rotamer", "j", lambda: auto_fit_rotamer_active_residue()) add_key_binding("Pepflip", "q", lambda: pepflip_active_residue()) add_key_binding("Go To Blob", "g", lambda: blob_under_pointer_to_screen_centre()) add_key_binding("Add Water", "w", lambda: place_typed_atom_at_pointer("Water")) add_key_binding("Eigen-flip Ligand", "e", lambda: flip_active_ligand()) def key_binding_func_1(): active_atom = active_residue() if (not active_atom): print "No active atom" else: imol = active_atom[0] chain_id = active_atom[1] res_no = active_atom[2] ins_code = active_atom[3] atom_name = active_atom[4] alt_conf = active_atom[5] add_terminal_residue(imol, chain_id, res_no, "auto", 1) add_key_binding("Add terminal residue", "y", lambda: key_binding_func_1()) def key_binding_func_2(): active_atom = active_residue() if (not active_atom): print "No active atom" else: imol = active_atom[0] chain_id = active_atom[1] res_no = active_atom[2] ins_code = active_atom[3] atom_name = active_atom[4] alt_conf = active_atom[5] fill_partial_residue(imol, chain_id, res_no, ins_code) add_key_binding("Fill Partial", "k", lambda: key_binding_func_2()) add_key_binding("Kill Sidechain", "K", lambda: using_active_atom(delete_residue_sidechain, "aa_imol", "aa_chain_id", "aa_res_no", "aa_ins_code", 0)) refine_residue_sphere_radius = 3.5 # Angstroms add_key_binding("Refine residue in a sphere", "R", lambda: sphere_refine(refine_residue_sphere_radius)) def key_binding_func_21(): if not valid_map_molecule_qm(imol_refinement_map()): info_dialog("Must set the refinement map") else: # not using active atom active_atom = active_residue() if (not active_atom): add_status_bar_text("No active residue") else: imol = active_atom[0] chain_id = active_atom[1] res_no = active_atom[2] ins_code = active_atom[3] atom_name = active_atom[4] alt_conf = active_atom[5] rc_spec = [chain_id, res_no, ins_code] ls = residues_near_residue(imol, rc_spec, 1.9) with_auto_accept([refine_residues, imol, [rc_spec] + ls]) add_key_binding("Neighbours Refine", "h", lambda: key_binding_func_21()) def key_binding_func_3(): if (os.name == 'nt'): home = os.getenv('COOT_HOME') else: home = os.getenv('HOME') dir_1 = os.path.join(home, "data", "rnase") read_pdb(os.path.join(dir_1, "tutorial-modern.pdb")) make_and_draw_map(os.path.join(dir_1, "rnasa-1.8-all_refmac1.mtz"), "/RNASE3GMP/COMPLEX/FWT", "/RNASE3GMP/COMPLEX/PHWT", "", 0, 0) add_key_binding("Load RNAs files", "F9", lambda: key_binding_func_3()) def key_binding_func_4(): keyboard_ghosts_mol = -1 for mol in model_molecule_list(): if (ncs_ghosts(mol)): keyboard_ghosts_mol = mol break if (draw_ncs_ghosts_state(keyboard_ghosts_mol) == 0): make_ncs_ghosts_maybe(keyboard_ghosts_mol) set_draw_ncs_ghosts(keyboard_ghosts_mol, 1) else: set_draw_ncs_ghosts(keyboard_ghosts_mol, 0) add_key_binding("Toggle Ghosts", ":", lambda: key_binding_func_4()) add_key_binding("Hydrogens off", "[", lambda: set_draw_hydrogens(0, 0)) add_key_binding("Hydrogens on", "]", lambda: set_draw_hydrogens(0, 1)) def key_binding_func_5(): active_atom = active_residue() if (not active_atom): add_status_bar_text("No active residue") else: imol = active_atom[0] chain_id = active_atom[1] res_no = active_atom[2] ins_code = active_atom[3] atom_name = active_atom[4] alt_conf = active_atom[5] name = get_rotamer_name(imol, chain_id, res_no, ins_code) if (not name): add_status_bar_text("No Name found") else: if (name == ""): add_status_bar_text("No name for this") else: add_status_bar_text("Rotamer name: " + name) add_key_binding("Rotamer name in Status Bar", "~", lambda: key_binding_func_5()) def key_binding_func_6(): active_atom = active_residue() if (not active_atom): add_status_bar_text("No active residue") else: imol = active_atom[0] chain_id = active_atom[1] res_no = active_atom[2] ins_code = active_atom[3] atom_name = active_atom[4] alt_conf = active_atom[5] regularize_zone(imol, chain_id, res_no - 1, res_no + 1, alt_conf) add_key_binding("Regularize Residues", "B", lambda: key_binding_func_6()) def key_binding_func_7(): using_active_atom([[fit_to_map_by_random_jiggle, ["aa_imol", "aa_chain_id", "aa_res_no", "aa_ins_code"], [100, 1.0]]]) add_key_binding("Jiggle Fit", "J", lambda: key_binding_func_7()) add_key_binding("Delete this water", "D", lambda: delete_atom(*active_residue())) def key_binding_func_8(): using_active_atom(add_terminal_residue, "aa_imol", "aa_chain_id", "aa_res_no", "auto", 1) add_key_binding("Add Terminal Residue", "|", lambda: key_binding_func_8()) add_key_binding("Accept Baton Position", "`", lambda: accept_baton_position()) add_key_binding("Cootilus here", "N", lambda: find_nucleic_acids_local(6.0)) """ if self.container.inputData.XYZIN_LIST.isSet(): try: iFile = 1 for XYZIN in self.container.inputData.XYZIN_LIST: if os.path.isfile(XYZIN.__str__()): script += "try:\n" script += (" MolHandle_"+str(iFile)+"=read_pdb(r'"+XYZIN.__str__()+"')\n") script += (" ccp4i2Interface.patchMoleculeName(MolHandle_"+str(iFile)+",r'"+XYZIN.__str__()+"')\n") script += "except:\n pass\n" else: print 'coot_rebuild.makeCommandAndScript XYZIN does not exist:',XYZIN.__str__() iFile += 1 except: #an issue with the existence of files pass if self.container.inputData.FPHIIN_LIST.isSet(): try: iFile = 1 for FPHIIN in self.container.inputData.FPHIIN_LIST: print ' reading file number ' + str ( iFile ) if os.path.isfile(FPHIIN.__str__()): script += "try:\n" script += (" MapHandle_"+str(iFile)+"=make_and_draw_map(r'"+FPHIIN.__str__()+"', 'F', 'PHI', 'PHI', 0, 0)\n") script += (" ccp4i2Interface.patchMoleculeName(MapHandle_"+str(iFile)+",r'"+FPHIIN.__str__()+"')\n") script += "except:\n pass\n" else: print 'coot_rebuild.makeCommandAndScript FPHIIN does not exist:',FPHIIN.__str__() iFile += 1 except: print ' Exception ' #an issue with the existence of files pass if self.container.inputData.DELFPHIIN_LIST.isSet(): try: iFile = 1 for DELFPHIIN in self.container.inputData.DELFPHIIN_LIST: print ' reading diff file number ' + str ( iFile ) if os.path.isfile(DELFPHIIN.__str__()): script += "try:\n" script += (" DifMapHandle_"+str(iFile)+"=make_and_draw_map(r'"+DELFPHIIN.__str__()+"', 'F', 'PHI', 'PHI', 0, 1)\n") script += (" ccp4i2Interface.patchMoleculeName(DifMapHandle_"+str(iFile)+",r'"+DELFPHIIN.__str__()+"')\n") script += "except:\n pass\n" else: print 'coot_rebuild.makeCommandAndScript FPHIIN does not exist:',DELFPHIIN.__str__() iFile += 1 except: print ' Exception ' #an issue with the existence of files pass if self.container.inputData.COOTSCRIPTFILE.isSet(): scriptLines = open(self.container.inputData.COOTSCRIPTFILE.fullPath.__str__()).readlines() if len(scriptLines)>0: script += 'try:\n' for line in scriptLines: script += (' '+line + '\n') script += 'except:\n pass\n' CCP4Utils.saveFile(self.cootScriptPath,script) clArgs = ['--no-state-script','--python'] #clArgs = ['--python','--pdb',self.container.inputData.XYZIN.fullPath.__str__()] dict_is_meaningful = True if self.container.inputData.DICT.isSet(): try: from Bio.PDB.MMCIF2Dict import MMCIF2Dict mmcif_dict = MMCIF2Dict ( str ( self.container.inputData.DICT.fullPath.__str__() ) ) lib_name = mmcif_dict['_lib_name'] lib_version = mmcif_dict['_lib_version'] lib_update = mmcif_dict['_lib_update'] print lib_name[0] print lib_version[0] print lib_update[0] #MN This test does not work on dicts made by ACEDRG, which show up as ??? for these properties #if lib_name[0] == '?' and lib_version[0] == '?' and lib_update[0] == '?' : # dict_is_meaningful = False except: print 'Bio python probably not available in this build of ccp4' if self.container.inputData.DICT.isSet() and dict_is_meaningful : clArgs += ['--dictionary'] clArgs += [self.container.inputData.DICT.fullPath.__str__()] #MN Please talk to me before changing the below. COOTSTATEFILE has almost no place in how #i2 is used, but is incorporated into script.py above. clArgs += ['--script',self.cootScriptPath ] '''if self.container.inputData.COOTSTATEFILE.exists(): import CCP4Utils contents = CCP4Utils.readFile(self.container.inputData.COOTSTATEFILE.__str__()) if len(contents)>5: clArgs += ['--script',self.container.inputData.COOTSTATEFILE.__str__()] else: clArgs += ['--script',self.cootScriptPath ] else: clArgs += ['--script',self.cootScriptPath ] ''' self.appendCommandLine(clArgs) # Use Qt class to watch the drop directory self.fileSystemWatcher = QtCore.QFileSystemWatcher(parent=self) self.fileSystemWatcher.addPath(self.dropDir) self.connect(self.fileSystemWatcher,QtCore.SIGNAL('directoryChanged(const QString &)'),self.handleFileDrop) return CPluginScript.SUCCEEDED def numberOfOutputFiles(self): import glob outList = glob.glob(os.path.normpath(os.path.join(self.dropDir,'output*.pdb'))) #print 'numberOfOutputFiles outList',os.path.join(self.dropDir,'output*.pdb'),outList #print 'numberOfOutputFiles xmlList',glob.glob(os.path.normpath(os.path.join(self.workDirectory,'*.xml'))) maxIndx = 0 for f in outList: fpath,fname = os.path.split(f) #print 'numberOfOutputFiles fpath,fname', fpath,fname maxIndx = max(maxIndx,int(fname[6:-4])) return maxIndx def handleFileDrop(self,directory): import time,glob print 'coot_rebuild',time.time() print 'coot_rebuild',glob.glob(os.path.join(self.workDirectory,'*.*')) #print 'handleFileDrop',directory #Note that I don't copy the file to the appropriate xyzout filename here, since the file may not yet #be closed and/or flushed def processOutputFiles(self): try: # First up import PDB files that have been output import os, glob, shutil globPath = os.path.normpath(os.path.join(self.dropDir,'output*.pdb')) outList = glob.glob(globPath) xyzoutList = self.container.outputData.XYZOUT for outputPDB in outList: fpath,fname = os.path.split(outputPDB) iFile = int(fname[6:-4]) xyzoutList.append(xyzoutList.makeItem()) outputFilePath = os.path.normpath(os.path.join(self.workDirectory,'XYZOUT_'+str(iFile)+'-coordinates.pdb')) shutil.copyfile(outputPDB, outputFilePath) xyzoutList[-1].setFullPath(outputFilePath) xyzoutList[-1].annotation = "Coot output file number"+str(iFile) xyzoutList[-1].subType = 1 #Ligand builder places output cifs in the coot-cif directory as prorg-out.cif #'prodrgify this residue' places output cifs in the coot-cif directory as prodrg-???.cif #pyrogen create "TLC"_pyrogen.cif cifOutList = glob.glob(os.path.normpath(os.path.join(self.dropDir,'coot-ccp4', 'prodrg-*.cif'))) cifOutList += glob.glob(os.path.normpath(os.path.join(self.workDirectory,'coot-ccp4', 'prodrg-*.cif'))) cifOutList += glob.glob(os.path.normpath(os.path.join(self.workDirectory,'*pyrogen.cif'))) cifOutList += glob.glob(os.path.normpath(os.path.join(self.workDirectory,'acedrg-*.cif'))) dictoutList = self.container.outputData.DICTOUT for iFile, outputCIF in enumerate(cifOutList): fpath,fname = os.path.split(outputCIF) #Currently, there is only one cif generated #iFile = int(fname[10:-4]) dictoutList.append(dictoutList.makeItem()) #outputFilePath = os.path.join(self.workDirectory,'COOT_'+str(iFile)+'-prodrg.cif') outputFilePath = os.path.normpath(os.path.join(self.workDirectory,'COOT-'+str(iFile)+'.cif')) shutil.copyfile(outputCIF, outputFilePath) dictoutList[-1].setFullPath(outputFilePath) if 'acedrg' in fname: annotation='Coot/Acedrg created geometry for ligand' elif 'pyrogen' in fname: annotation='Coot/Pyrogen created geometry for ligand' elif 'prodrg' in fname: annotation='Coot/Prodrg created geometry for ligand' else: annotation='Coot/Prodrg created geometry for ligand' dictoutList[-1].annotation = annotation # Create a trivial xml output file import CCP4Utils from lxml import etree self.xmlroot = etree.Element('coot_rebuild') e = etree.Element('number_output_files') e.text = str(self.numberOfOutputFiles()) e = etree.Element('number_output_dicts') e.text = str(len(dictoutList)) self.xmlroot.append(e) #Separate out here activity to attempt merge into project dictionary....this seems flakey, #but is needed for ongoing work, so I ammaking it give an report a warning in case of failure, rather than #offer the sad face ofdoom try: for dictFile in dictoutList: try: self.mergeDictToProjectLib(fileName=dictFile.__str__()) except: self.addReportWarning('mergeDictToProjectLib raised exception: Does not compromise output Dict') ligNodes = self.xmlroot.xpath('//LIGANDS') if len(ligNodes) == 0: ligNode = etree.SubElement(self.xmlroot,'LIGANDS') else: ligNode = ligNodes[0] try: annotation='Coot/Prodrg created geometry for' for item in dictFile.fileContent.monomerList: lig = etree.SubElement(ligNode,'ligand') lig.text = str(item.three_letter_code) annotation += (' ' + str(item.three_letter_code)) dictFile.annotation = annotation except: self.addReportWarning('fileContent.monomerList raised exception: Does not compromise output Dict') except: self.addReportWarning('failed elsewhere in merging/analysing dicts: Does not compromise output Dict') except: self.appendErrorReport(202,'Data harvesting failed') CCP4Utils.saveEtreeToFile(self.xmlroot,self.makeFileName('PROGRAMXML')) if ( len(outList) + len(cifOutList) ) > 0: return CPluginScript.SUCCEEDED else: return CPluginScript.MARK_TO_DELETE def clearCootWorkingDir(self): # Remove the working directory state and history files import glob zeroFileList = glob.glob(os.path.normpath(os.path.join(self.projectDirectory(),'CCP4_COOT','0-coot*'))) for filn in zeroFileList: os.remove(filn) def copyStateFile(self): import CCP4Utils newText = '' text = CCP4Utils.readFile(self.container.inputData.COOTSTATEFILE.fullPath) for line in text.split('\n'): if line.count('handle-read-draw-molecule'): newText = newText + '(handle-read-draw-molecule "'+self.container.inputData.XYZIN_LIST[0].__str__()+'" 1)\n' else: newText = newText + line +'\n' CCP4Utils.saveFile(os.path.normpath(os.path.join(self.dropDir,'0-coot-history.scm')),text) def addReportWarning(self, text): from lxml import etree warningsNode = None warningsNodes = self.xmlroot.xpath('//Warnings') if len(warningsNodes) == 0: warningsNode = etree.SubElement(self.xmlroot, 'Warnings') else: warningsNode = warningsNodes[0] warningNode = etree.SubElement(warningsNode,'Warning') warningNode.text = text