""" python/ui/model_fragment.py: CCP4MG Molecular Graphics Program Copyright (C) 2001-2008 University of York, CCLRC This library is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License version 3, modified in accordance with the provisions of the license to address the requirements of UK law. You should have received a copy of the modified GNU Lesser General Public License along with this library. If not, copies may be downloaded from http://www.ccp4.ac.uk/ccp4license.php 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 Lesser General Public License for more details. """ from utils import * import os import string import re from mgapp import * from mmdb2 import * from mmut import * from dataobj import * from model_selection import * from moleculargraphicsmodel import * from resources import * from view import * import build from global_definitions import * import pygl_coord import mmut #----------------------------------------------------------------- #----------------------------------------------------------------- #----------------------------------------------------------------- class model_fragment(ModelAnalysis,DispObj): #----------------------------------------------------------------- #----------------------------------------------------------------- #----------------------------------------------------------------- colour_commands = [ 'onecolour','atomtype','mainside'] colour_code = [ ONECOLOUR, BYATOMTYPE, MAINSIDE] #------------------------------------------------------------------ def __init__(self,parent,name='',visible=1,master_application='', \ duplicate_MMDB=0, **keywords): #------------------------------------------------------------------ global gui DispObj.__init__(self,'model_fragment',name, parent,visible=visible, \ master_application=master_application, \ display_table_visible=0) ModelAnalysis.__init__(self) self.name_label = self.name self.duplicate_MMDB = duplicate_MMDB if self.duplicate_MMDB: self.molHnd = CMMANManager(RESOURCES().SRS,RESOURCES().CMolBondParams) else: self.molHnd = self.parent.molHnd self.selHnd = -1 self.nSelAtoms = 0 self.selAtoms = '' self.update_atomRadii = 0 self.one_colour='red' self.colour='onecolour' self.non_C_mode=-1 self.atomColourVector = None self.style = 'SPHERES' self.update_atomRadii = 0 self.sphere_radii_scale = 0.15 self.Connectivity = Connectivity() self.CMolColour = CMolColour ( self.molHnd, self.selHnd, \ RESOURCES().colourSchemes) # Flag to update display without updating any of the display # attributes - probably set because atom coordinates have # changed self.do_updatedisplay = 0 # Instantiate a a graphics object and assign some parameters import moleculargraphicsmodel import history import model self.graphmod = moleculargraphicsmodel.moleculargraphicsmodel(ui=self) self.graphmod.setparams(molHnd=self.molHnd, \ Connectivity = self.Connectivity, \ diagnostic_timing = history.CHistory.insts.diagnostic['timing']) self.graphmod.setparams(parameters = model.MolDisp.GraphicsParamsManager) self.atomRadii = pygl_coord.DoubleVector(2) self.graphmod.setparams(atomRadii=self.atomRadii) #---------------------------------------------------------------------- def define_selection_range(self,molHnd=None,pResidue=None,link=1,range=0): #---------------------------------------------------------------------- ''' Return a selction command for a range of residues around a focus residue NB Does not handle insertion code and does not check thar residues are connected ''' #seqNum = pResidue.seqNum indx = pResidue.index chn = pResidue.chain #print "define_selection_range",indx,chn resTable = newPPCResidue() nR = intp() pResidue.chain.GetResidueTable(resTable,nR) nRes = nR.value() ifres = max(indx-range,0) ilres = min(indx+range,nRes-2) #print "nRes,ifres,ilres",nRes,ifres,ilres range = '//'+chn.GetChainID()+'/'+str(getPCResidue(resTable,ifres).seqNum)+ \ '-'+str(getPCResidue(resTable,ilres).seqNum) if link: #Add the linked C(i-1) and N(i+1) atoms if ifres>0: Nlink = '//'+chn.GetChainID()+'/'+str(getPCResidue(resTable,ifres-1).seqNum)+'/C' else: Nlink='' if ilres < nRes: Clink = '//'+chn.GetChainID()+'/'+str(getPCResidue(resTable,ilres+1).seqNum)+'/N' else: Clink='' #delPPCResidue(resTable) return [range,Nlink,Clink] #-------------------------------------------------------------------- def set_selection(self,defn=[],command='',extend=0): #-------------------------------------------------------------------- #print "set_selection",defn if self.duplicate_MMDB: if self.duplicate_MMDB == 2: del self.molHnd del self.CMolColour self.molHnd = CMMANManager(RESOURCES().SRS,RESOURCES().CMolBondParams) #print "duplicate_MMDB molHnd",self.molHnd self.CMolColour = CMolColour ( self.molHnd, self.selHnd, \ RESOURCES().colourSchemes) self.graphmod.setparams(molHnd=self.molHnd) rv = self.parent.parse_selection(defn=defn,command=command) if rv[0]: return 1 selHnd = rv[1] self.parent.molHnd.PutSelectedAtoms (selHnd,self.molHnd) #print "Nof atoms in model_fragment",self.molHnd.GetNumberOfAtoms() self.duplicate_MMDB = 2 print "FIXME (model_fragment.py) - A preference here for aromaticize." self.molHnd.GetMolBonds() self.parent.molHnd.DeleteSelection(selHnd) self.do_redraw = 1 if extend: pass else: if self.selHnd: self.molHnd.DeleteSelection(self.selHnd) rv = self.parse_selection(defn=defn,command=command) #print "parse_selection rv",rv if rv[0]: return 1 self.selHnd = rv[1] self.do_redraw = 1 self.update_atomRadii = 1 #-------------------------------------------------------------------- def set_colour(self,one_colour='',colour='',non_C_atomtype=''): #-------------------------------------------------------------------- if one_colour: self.one_colour = one_colour if colour: self.colour = colour if non_C_atomtype: self.non_C_atomtype = non_C_atomtype self.do_recolour = 1 #-------------------------------------------------------------------- def set_style(self,style=''): #-------------------------------------------------------------------- if style: self.style = style #-------------------------------------------------------------------- def delete(self,**keywords): #-------------------------------------------------------------------- DispObj.delete(self) if hasattr(self,'Connectivity') and self.Connectivity: del self.Connectivity if hasattr(self,'CMolColour') and self.CMolColour: del self.CMolColour if (self.duplicate_MMDB): if self.molHnd:del self.molHnd else: if self.selHnd>=0: self.molHnd.DeleteSelection(self.selHnd) self.selHnd = -1 #------------------------------------------------------------------------- def handle_atom_radii(self,ball_radii_scale='',sphere_radii_scale='', **keywords): #------------------------------------------------------------------------- if sphere_radii_scale: sphere_radii_scale = float(sphere_radii_scale) if sphere_radii_scale < 0.001 or sphere_radii_scale > 10.0: return diff = self.sphere_radii_scale - sphere_radii_scale self.sphere_radii_scale = sphere_radii_scale if (diff < -0.001 or diff > 0.001) and self.style == "SPHERES": self.do_redraw = 1 self.update_atomRadii = 1 #------------------------------------------------------------------------ def update_connectivity(self): #------------------------------------------------------------------------ #print "model_fragment update_connectivity" self.Connectivity.Clear() if self.nSelAtoms <= 0: return self.Connectivity.AddBonds(self.molHnd,self.selHnd, self.selAtoms,self.nSelAtoms,0,0) #------------------------------------------------------------------------ def draw (self): #------------------------------------------------------------------------ ''' Called at end of each cycle of a command loop Redraw the graphmod if necessary ''' #print "model_fragment draw",self.do_redraw if self.do_redraw>0: if self.selHnd: """ if self.selAtoms: delPPCAtom(self.selAtoms) """ selindexp = pygl_coord.intp() self.selAtoms = newPPCAtom() #self.nSelAtoms =self.molHnd.GetSelIndex(self.selHnd,self.selAtoms) self.selAtoms = mmut.GetAtomSelIndex(self.molHnd,selHnd,selindexp) self.nSelAtoms = selindexp.value() #print "Number of selected atoms",self.nSelAtoms else: self.selHnd = self.molHnd.NewSelection() """ if self.selAtoms: delPPCAtom(self.selAtoms) """ self.selAtoms = newPPCAtom() self.nSelAtoms = 0 self.update_connectivity() self.do_redraw = 0 self.do_recolour = 1 if self.do_recolour: self.CMolColour.SetSelHandle(self.selHnd) if self.colour_commands.count(self.colour) > 0: ic = self.colour_commands.index(self.colour) RC = self.CMolColour.SetMode (1,self.colour_code[ic],self.non_C_mode) if self.colour == 'onecolour': self.CMolColour.SetOneColour(MGCOLOUR().index(self.one_colour)) self.CMolColour.ReColour() self.atomColourVector = self.CMolColour.GetAtomColourVector() self.do_recolour = 0 if ['SPHERES','BALLSTICK','CIRCLES'].count(self.style): if self.update_atomRadii: #print "updating atomRadii" if self.atomRadii: del self.atomRadii if self.style == "SPHERES": scale = self.sphere_radii_scale elif self.style == "BALLSTICK" or self.style == 'CIRCLES': scale = self.ball_radii_scale self.atomRadii=self.molHnd.GetAtomRadii(self.selHnd,VDWRADIUS,scale) self.graphmod.setparams(atomRadii=self.atomRadii) self.update_atomRadii=0 # Update graphmod parameters #print "calling setparams" self.graphmod.setparams(selHnd=self.selHnd, \ selAtoms = self.selAtoms, \ nSelAtoms = self.nSelAtoms, \ style = self.style, \ visible = self.visible, \ atomColourVector = self.atomColourVector, \ ifColourContinuous = 0 ) if not self.built: build.build.insts.append(self.graphmod) self.built = 1 else: self.graphmod.rebuild() self.do_redraw = 0 #----------------------------------------------------------------------- def set_extent(self): #----------------------------------------------------------------------- self.extent = [0.0,0.0,0.0,0.0,0.0,0.0] if self.nSelAtoms > 0: extptr = self.parent.molHnd.Extent(self.selHnd) tmp = doublea(1) ext=tmp.frompointer(extptr) if ext: self.extent = [] for i in range(0,6): self.extent.append (ext[i]) #print "extent",sel.extent self.origin = [ \ (self.extent[3] + self.extent[0])/2.0, (self.extent[4] + self.extent[1])/2.0, (self.extent[5] + self.extent[2])/2.0 ] #print "sel.origin",sel.origin self.com = [0.0,0.0,0.0]