gromacs/scaling.py
def scale_impropers(mol, impropers, scale, banned_lines=None):
        """Scale improper dihedrals"""
        if banned_lines is None:
                banned_lines = []
        new_impropers = []
        for im in mol.impropers:
                atypes = (im.atom1.get_atomtype(), im.atom2.get_atomtype(),
                          im.atom3.get_atomtype(), im.atom4.get_atomtype())
                atypes = [a.replace("_", "").replace("=", "") for a in atypes]

                # special-case: this is a [ dihedral ] override in molecule block, continue and don't match
                if im.gromacs['param'] != []:
                    for p in im.gromacs['param']:
                        p['kpsi'] *= scale
                    new_impropers.append(im)
                    continue

                for iswitch in range(32):
                        if  (iswitch%2==0):
                                a1=atypes[0]; a2=atypes[1]; a3=atypes[2]; a4=atypes[3];
                        else:
                                a1=atypes[3]; a2=atypes[2]; a3=atypes[1]; a4=atypes[0];
                        if((iswitch//2)%2==1): a1="X";
                        if((iswitch//4)%2==1): a2="X";
                        if((iswitch//8)%2==1): a3="X";
                        if((iswitch//16)%2==1): a4="X";
                        key = "{0}-{1}-{2}-{3}-{4}".format(a1, a2, a3, a4, im.gromacs['func'])
                        if (key in impropers):
                                for i, imt in enumerate(impropers[key]):
                                        imA = copy.deepcopy(im)
                                        param = copy.deepcopy(imt.gromacs['param'])
                                        # Only check the first dihedral in a list
                                        if not impropers[key][0].line in banned_lines:
                                                for p in param: p['kpsi'] *= scale
                                        imA.gromacs['param'] = param
                                        if i == 0:
                                                imA.comment = "; banned lines {0} found={1}\n ; parameters for types {2}-{3}-{4}-{5}-9 at LINE({6})\n".format(
                                                        " ".join(map(str, banned_lines)),
                                                        1 if imt.line in banned_lines else 0,
                                                        imt.atype1, imt.atype2, imt.atype3, imt.atype4, imt.line)
                                        new_impropers.append(imA)
                                break
        #assert(len(mol.impropers) == new_impropers)
        mol.impropers = new_impropers
        return mol
def scale_impropers(mol, impropers, scale, banned_lines=None):
        """Scale improper dihedrals"""
        if banned_lines is None:
                banned_lines = []
        new_impropers = []
        for im in mol.impropers:
                atypes = (im.atom1.get_atomtype(), im.atom2.get_atomtype(),
                          im.atom3.get_atomtype(), im.atom4.get_atomtype())
                atypes = [a.replace("_", "").replace("=", "") for a in atypes]

                # special-case: this is a [ dihedral ] override in molecule block, continue and don't match
                if im.gromacs['param'] != []:
                    for p in im.gromacs['param']:
                        p['kpsi'] *= scale
                    new_impropers.append(im)
                    continue

                for iswitch in range(32):
                        if  (iswitch%2==0):
                                a1=atypes[0]; a2=atypes[1]; a3=atypes[2]; a4=atypes[3];
                        else:
                                a1=atypes[3]; a2=atypes[2]; a3=atypes[1]; a4=atypes[0];
                        if((iswitch//2)%2==1): a1="X";
                        if((iswitch//4)%2==1): a2="X";
                        if((iswitch//8)%2==1): a3="X";
                        if((iswitch//16)%2==1): a4="X";
                        key = "{0}-{1}-{2}-{3}-{4}".format(a1, a2, a3, a4, im.gromacs['func'])
                        if (key in impropers):
                                for i, imt in enumerate(impropers[key]):
                                        imA = copy.deepcopy(im)
                                        param = copy.deepcopy(imt.gromacs['param'])
                                        # Only check the first dihedral in a list
                                        if not impropers[key][0].line in banned_lines:
                                                for p in param: p['kpsi'] *= scale
                                        imA.gromacs['param'] = param
                                        if i == 0:
                                                imA.comment = "; banned lines {0} found={1}\n ; parameters for types {2}-{3}-{4}-{5}-9 at LINE({6})\n".format(
                                                        " ".join(map(str, banned_lines)),
                                                        1 if imt.line in banned_lines else 0,
                                                        imt.atype1, imt.atype2, imt.atype3, imt.atype4, imt.line)
                                        new_impropers.append(imA)
                                break
        #assert(len(mol.impropers) == new_impropers)
        mol.impropers = new_impropers
        return mol
def scale_impropers ( mol , impropers , scale , banned_lines = None ) : if banned_lines is None : banned_lines = [ ] new_impropers = [ ] for im in mol . impropers : atypes = ( im . atom1 . get_atomtype ( ) , im . atom2 . get_atomtype ( ) , im . atom3 . get_atomtype ( ) , im . atom4 . get_atomtype ( ) ) atypes = [ a . replace ( "_" , "" ) . replace ( "=" , "" ) for a in atypes ] # special-case: this is a [ dihedral ] override in molecule block, continue and don't match if im . gromacs [ 'param' ] != [ ] : for p in im . gromacs [ 'param' ] : p [ 'kpsi' ] *= scale new_impropers . append ( im ) continue for iswitch in range ( 32 ) : if ( iswitch % 2 == 0 ) : a1 = atypes [ 0 ] a2 = atypes [ 1 ] a3 = atypes [ 2 ] a4 = atypes [ 3 ] else : a1 = atypes [ 3 ] a2 = atypes [ 2 ] a3 = atypes [ 1 ] a4 = atypes [ 0 ] if ( ( iswitch // 2 ) % 2 == 1 ) : a1 = "X" if ( ( iswitch // 4 ) % 2 == 1 ) : a2 = "X" if ( ( iswitch // 8 ) % 2 == 1 ) : a3 = "X" if ( ( iswitch // 16 ) % 2 == 1 ) : a4 = "X" key = "{0}-{1}-{2}-{3}-{4}" . format ( a1 , a2 , a3 , a4 , im . gromacs [ 'func' ] ) if ( key in impropers ) : for i , imt in enumerate ( impropers [ key ] ) : imA = copy . deepcopy ( im ) param = copy . deepcopy ( imt . gromacs [ 'param' ] ) # Only check the first dihedral in a list if not impropers [ key ] [ 0 ] . line in banned_lines : for p in param : p [ 'kpsi' ] *= scale imA . gromacs [ 'param' ] = param if i == 0 : imA . comment = "; banned lines {0} found={1}\n ; parameters for types {2}-{3}-{4}-{5}-9 at LINE({6})\n" . format ( " " . join ( map ( str , banned_lines ) ) , 1 if imt . line in banned_lines else 0 , imt . atype1 , imt . atype2 , imt . atype3 , imt . atype4 , imt . line ) new_impropers . append ( imA ) break #assert(len(mol.impropers) == new_impropers) mol . impropers = new_impropers return mol
Scale improper dihedrals
Scale improper dihedrals