How to use naming_scheme method in Lemoncheesecake

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AmberLoader.py

Source:AmberLoader.py

1#!/bin/env python2# -*- coding: utf-8 -*-3import os4import sys5import re6from Sire.IO import *7from Sire.Mol import *8from Sire.CAS import *9from Sire.System import *10from Sire.Move import *11from Sire.MM import *12from Sire.FF import *13from Sire.Units import *14from Sire.Vol import *15from Sire.Maths import *16from Sire.Base import *17from Sire.Qt import *18from Sire.ID import *19from Sire.Config import *20import Sire.Stream21from Sire.Tools import Parameter, resolveParameters22from Sire.Tools.WaterChanger import convertTip3PtoTip4P23###################################24# Parameters used by this module  #25###################################26dobonds = Parameter("move bonds", True, """Whether or not to move the ligands bonds""")27doangles = Parameter("move angles", True, """Whether or not to move the ligands angles""")28dodihedrals = Parameter("move dihedrals", True, """Whether or not to move the ligands dihedrals""")29water_model = Parameter("water model", None,30                        """The water model to use. Note, by default the water model is read from31                           the protein and water crd/top files. If you want to force a change32                           in water model, then set it here, e.g. if you are loading a TIP3P box33                           but want to use TIP4P, then set this parameter to "tip4p".""")34BASE_DIHEDRALH_FLEX = Parameter("h dihedral flex", 30*degrees, "Base dihedral rotation for H")35BASE_DIHEDRAL_FLEX = Parameter("dihedral flex", 20*degrees, "Base dihedral rotation")36BASE_ANGLE_FLEX = Parameter("angle flex", 0.25*degrees, "Base angle rotation")37BASE_BOND_FLEX = Parameter("bond flex", 0.025*angstroms, "Base bond stretch amount")38BASE_TRANSLATION = Parameter("translation", 0.75*angstroms, "Base translation delta amount")39BASE_ROTATION = Parameter("rotation", 30*degrees, "Base rigid body rotation")40BASE_MAXVAR = Parameter("maxvar", 10, "Maximum number of degrees of freedom to move at once")41BASE_MAXVAR_B = Parameter("maxvar bonds", 2, "Maximum number of bonds to move at once")42BASE_MAXVAR_A = Parameter("maxvar angles", 4, "Maximum number of angles to move at once")43BASE_MAXVAR_D = Parameter("maxvar dihedrals", 4, "Maximum number of dihedrals to move at once")44###################################45def getResidueNames(molecule):46    nres = molecule.nResidues()47    resnams = []48    for i in range(0, nres):49        resnams.append( str( molecule.residue(ResIdx(i)).name().value()).upper() )50    return resnams51class NamingScheme:52    def __init__(self):53        self._protein_names = ["GLH", "ILE", "GLN", "GLY", "GLU",54                               "CYS", "HIS", "HID", "SER", "LYS",55                               "LYN", "PRO", "CYX", "HIE", "ASH",56                               "ASN", "HIP", "VAL", "THR", "ASP",57                               "TRP", "PHE", "ALA", "MET", "LEU",58                               "ARG", "TYR", "NME", "ACE"]59        self._water_names = [ "WAT", "T3P", "T4P", "HOH" ]60        self._ion_names = [ "NA+", "Na+", "CA+", "Ca+", "CAL", "CL-", "Cl-" ]61        self._solute_names = [ "LIG" ]62    def proteinsGroupName(self):63        return MGName("protein")64    def solutesGroupName(self):65        return MGName("solute")66    def solventsGroupName(self):67        return MGName("solvent")68    def watersGroupName(self):69        return MGName("water")70    def ionsGroupName(self):71        return MGName("ions")72    def allMoleculesGroupName(self):73        return MGName("all")74    def fixedMoleculesGroupName(self):75        return MGName("fixed_molecules")76    def boundaryMoleculesGroupName(self):77        return MGName("boundary_molecules")78    def mobileProteinSidechainsGroupName(self):79        return MGName("protein_sidechains")80    def mobileProteinBackbonesGroupName(self):81        return MGName("protein_backbones")82    def mobileSolutesGroupName(self):83        return MGName("mobile_solutes")84    def mobileSolventsGroupName(self):85        return MGName("mobile_solvents")86    def addProteinResidueName(self, name):87        self._protein_names.append( name.upper() )88    def addWaterResidueName(self, name):89        self._water_names.append( name.upper() )90    def addSoluteResidueName(self, name):91        self._solute_names.append( name.upper() )92    def addIonResidueName(self, name):93        self._ion_names.append( name.upper() )94    def proteinResidueNames(self):95        return self._protein_names96    def waterResidueNames(self):97        return self._water_names98    def soluteResidueNames(self):99        return self._solute_names100    def ionResidueNames(self):101        return self._ion_names102    def setProteinResidueNames(self, names):103        self._protein_names = []104        for name in names:105            self.addProteinResidueName(name)106    def setWaterResidueNames(self, names):107        self._water_names = []108        for name in names:109            self.addWaterResidueName(name)110    def setSoluteResidueNames(self, name):111        self._solute_names = []112        for name in names:113            self.addSoluteResidueName(name)114    def setIonResidueNames(self, name):115        self._ion_names = []116        for name in names:117            self.addIonResidueName(name)118    def _isType(self, molecule, names, max_residues = None):119        try:120            resnams = getResidueNames(molecule)121        except:122            resnams = molecule123        if max_residues:124            if len(resnams) > max_residues:125                return False126        for resnam in resnams:127            if resnam in names:128                return True129        try:130            if str(molecule.name().value()).upper() in names:131                return True132            else:133                return False134        except:135            return False136    def isProtein(self, molecule):137        return self._isType(molecule, self._protein_names)138    def isWater(self, molecule):139        return self._isType(molecule, self._water_names, 1)140    def isIon(self, molecule):141        return self._isType(molecule, self._ion_names, 1)142    def isSolute(self, molecule):143        return self._isType(molecule, self._solute_names)144def findMolecule(system, molname):145    molecules = system.molecules()146    molname = molname.upper()147    for molnum in molecules.molNums():148        molecule = molecules[molnum][0].molecule()149        if str(molecule.name().value()).upper() == molname:150            return molecule151        resnams = getResidueNames(molecule)152        for resnam in resnams:153            if resnam == molname:154                return molecule155    return None156def addMoleculeToSystem(molecule, system, naming_scheme = NamingScheme()):157    """This function adds the passed molecule to the passed system158       using the passed naming scheme to assign the molecule to the 159       correct molecule group"""160    resnams = getResidueNames(molecule)161    system.add(molecule, MGName(naming_scheme.allMoleculesGroupName().value()))162    if naming_scheme.isSolute(resnams):163        system.add(molecule, MGName(naming_scheme.solutesGroupName().value()))164    elif naming_scheme.isProtein(resnams):165        system.add(molecule, MGName(naming_scheme.proteinsGroupName().value()))166    elif naming_scheme.isWater(resnams):167        system.add(molecule, MGName(naming_scheme.watersGroupName().value()))168        system.add(molecule, MGName(naming_scheme.solventsGroupName().value()))    169    elif naming_scheme.isIon(resnams):170        system.add(molecule, MGName(naming_scheme.ionsGroupName().value()))171        system.add(molecule, MGName(naming_scheme.solventsGroupName().value()))172    elif molecule.nResidues() == 1:173        system.add(molecule, MGName(naming_scheme.solventsGroupName().value()))174    else:175        system.add(molecule, MGName(naming_scheme.solutesGroupName().value()))176def createSystemFrom(molecules, space, system_name, naming_scheme = NamingScheme()):177    """Create a new System from the passed molecules and space,178       sorting the molecules into different molecule groups based on the179       passed naming scheme"""180    system = System(system_name)181    # If requested, change the water model for all water molecules182    if water_model.val == "tip4p":183        molnums = molecules.molNums()184        new_molecules = Molecules()185        print("Forcing all water molecules to use the %s water model..." % water_model.val)186        print("Converting %d molecules..." % len(molnums))187        i = 0188        for molnum in molnums:189            molecule = molecules[molnum].molecule()190            if i % 100 == 0:191                print("%d" % i)                192                sys.stdout.flush()193            elif i % 10 == 0:194                print(".", end=' ')195                sys.stdout.flush()196            i += 1197            if molecule.nAtoms() == 3:198                #Â this could be a TIP3P water199                resname =str(molecule.residue().name().value()).lower()200                if resname == "wat" or resname == "t3p":201                    new_molecule = convertTip3PtoTip4P(molecule)202                    if new_molecule:203                        molecule = new_molecule204            new_molecules.add(molecule)205        print("%d" % i)206        molecules = new_molecules207    nmols = molecules.nMolecules()208    print("Number of molecules == %s" % nmols)209    print("System space == %s" % space)210    if nmols == 0:211        return system212    print("Assigning molecules to molecule groups...")213    solute_group = MoleculeGroup(naming_scheme.solutesGroupName().value())214    protein_group = MoleculeGroup(naming_scheme.proteinsGroupName().value())215    solvent_group = MoleculeGroup(naming_scheme.solventsGroupName().value())216    water_group = MoleculeGroup(naming_scheme.watersGroupName().value())217    ion_group = MoleculeGroup(naming_scheme.ionsGroupName().value())218    all_group = MoleculeGroup(naming_scheme.allMoleculesGroupName().value())219    # The all molecules group has all of the molecules220    all_group.add(molecules)221    system.add(all_group)222    # Run through each molecule and decide what type it is...223    molnums = molecules.molNums()224    molnums.sort()225    central_molecule = None226    solutes = []227    proteins = []228    solvents = []229    waters = []230    ions = []231    for molnum in molnums:232        molecule = molecules[molnum].molecule()233        resnams = getResidueNames(molecule)234        if naming_scheme.isSolute(resnams):235            solutes.append(molecule)236        elif naming_scheme.isProtein(resnams):237            proteins.append(molecule)238        elif naming_scheme.isWater(resnams):239            waters.append(molecule)240        elif naming_scheme.isIon(resnams):241            ions.append(molecule)242        elif molecule.nResidues() == 1:243            solvents.append(molecule)244        else:245            solutes.append(molecule)246    # Ok - we have now divided everything up into groups247    for solute in solutes:248        solute_group.add(solute)249    for protein in proteins:250        protein_group.add(protein)251    for water in waters:252        solvent_group.add(water)253        water_group.add(water)254    for solvent in solvents:255        solvent_group.add(solvent)256    257    for ion in ions:258        solvent_group.add(ion)259        ion_group.add(ion)260    if solute_group.nMolecules() > 0:261        system.add(solute_group)262    if protein_group.nMolecules() > 0:263        system.add(protein_group)264    if solvent_group.nMolecules() > 0:265        system.add(solvent_group)266    if water_group.nMolecules() > 0:267        system.add(water_group)268    if ion_group.nMolecules() > 0:269        system.add(ion_group)    270    print("Number of solute molecules == %s" % solute_group.nMolecules()) 271    print("Number of protein molecules == %s" % protein_group.nMolecules())272    print("Number of ions == %s" % ion_group.nMolecules())273    print("Number of water molecules == %s" % water_group.nMolecules())274    print("Number of solvent molecules == %s" % solvent_group.nMolecules())275    print("(solvent group is waters + ions + unidentified single-residue molecules)")276    system.setProperty("space", space)277    system.add( SpaceWrapper( Vector(0), all_group ) )278    system.applyConstraints()279    print("Returning the constructed system")280    return system281def createSystem(top_file, crd_file, naming_scheme = NamingScheme()):282    """Create a new System from the molecules read in from the passed amber 283       topology and coordinate files. This sorts the molecules into different284       molecule groups based on the passed naming scheme"""285    286    system = MoleculeParser.read(top_file,crd_file)287    # Load all of the molecules and their parameters from288    # the topology and coordinate files289    print("Loading the molecules from the files \"%s\" and \"%s\"..." % \290                  (crd_file, top_file))291    return createSystemFrom(system[MGIdx(0)], system.property("space"), top_file, naming_scheme)292def centerSystem(system, molecule):293    print("Setting the origin of the system to the center of molecule %s (%s)..." % (molecule, molecule.number()))294    center = molecule.evaluate().centerOfMass()295    print("This requires translating everything by %s..." % (-center))    296    297    moved_mols = Molecules()298    for molnum in system.molNums():299        molecule = system[molnum][0].molecule()300        molecule = molecule.move().translate(-center).commit()301        moved_mols.add(molecule)302    system.update(moved_mols)303    return system304def guessTranslation( solute ):305    natoms = solute.nAtoms()306    return (BASE_TRANSLATION.val) / ( natoms / 5 + 1)307def guessRotation( solute ):308    natoms = solute.nAtoms()309    sphere_radius = solute.evaluate().boundingSphere().radius()310    return (BASE_ROTATION.val) / ( sphere_radius ** 2)311def generateFlexibility(solute):312    connectivity = solute.property('connectivity')313    all_bonds = connectivity.getBonds()314    all_angles = connectivity.getAngles()315    all_dihedrals = connectivity.getDihedrals()316    flexibility = Flexibility(solute)317    flexibility.setRotation( guessRotation(solute) )318    flexibility.setTranslation( guessTranslation(solute) )319    try:320        flexibility.setMaximumVar( BASE_MAXVAR.val )321    except:322        flexibility.setMaximumBondVar( BASE_MAXVAR_B.val )323        flexibility.setMaximumAngleVar( BASE_MAXVAR_A.val )324        flexibility.setMaximumDihedralVar( BASE_MAXVAR_D.val )325    # Redundant torsions are discarded according to the following algorithm326    # 1) Do not sample a torsion at0-at1-at2-at3 if a variable torsion has 327    # already been defined around at1-at2 or at2-at1.328    # 2) Do not sample a torsion if it would break a ring329    #330    if dodihedrals.val:331        var_dihedrals = []332        for dihedral in all_dihedrals:333            #print dihedral334            tomove = True335            # print dihedral336            at0 = dihedral.atom0()337            at1 = dihedral.atom1()338            at2 = dihedral.atom2()339            at3 = dihedral.atom3()340            # See if a one of the variable dihedral 341            # already rotates around the same torsion342            for vardih in var_dihedrals:343                if ( ( at1 == vardih.atom1() and at2 == vardih.atom2() ) or 344                     ( at2 == vardih.atom1() and at1 == vardih.atom2() ) ):345                    # Yes so will not move this torsion 346                    tomove = False347                    break348            # If still wondering...See if a rotation around this dihedral would break a ring 349            if tomove:350                try:351                    dihbond = BondID(at1, at2)352                    #print dihbond353                    solute.move().change(dihbond,1*degrees)354                except UserWarning as error:355                    # extract the type of the errror356                    error_type = re.search(r"(Sire\w*::\w*)", str(error)).group(0)357                    if error_type == "SireMol::ring_error":358                        # print "This dof would move a ring and is therefore skipped"359                        tomove = False360                    else:361                        # re-throw the exception362                        raise error 363            if tomove:364                # Find out how many atoms would move 365                #print dihedral366                gr0, gr1 = connectivity.split(at1, at2)367                ngr0 = gr0.nSelected()368                ngr1 = gr1.nSelected()369                if (ngr0 <= ngr1):370                    smallgroup = gr0371                else:372                    smallgroup = gr1373                smallgroup = smallgroup.subtract(at1)374                smallgroup = smallgroup.subtract(at2)375                factor = smallgroup.nSelected()376                flexibility.add(dihedral, BASE_DIHEDRAL_FLEX.val/factor)377                var_dihedrals.append(dihedral)378    # And the angles ....379    if doangles.val:380        moved_atoms = []381        for angle in all_angles:382            # print angle383            at0 = angle.atom0()384            at2 = angle.atom2()385            # Do not sample that dof if an existing dof would already move this atom386            if ( ( at0 in moved_atoms) and (at2 in moved_atoms) ):387                continue388            # Test if the angle breaks a ring, if so do not sample it389            try:390                solute.move().change(angle,1*degrees)391            except UserWarning as error:392                # extract the type of the errror393                error_type = re.search(r"(Sire\w*::\w*)", str(error)).group(0)394                if error_type == "SireMol::ring_error":395                    # print "This dof would move a ring and is therefore skipped"396                    continue397                else:398                    # re-throw the exception399                    raise error 400            gr0, gr1 = connectivity.split(at0, angle.atom1(), at2)401            ngr0 = gr0.nSelected()402            ngr1 = gr1.nSelected()403            if (ngr0 <= ngr1):404                smallgroup = gr0405            else:406                smallgroup = gr1407            factor = smallgroup.nSelected()408            flexibility.add(angle, BASE_ANGLE_FLEX.val/factor)409            if at0 not in moved_atoms:410                moved_atoms.append(at0)411            if at2 not in moved_atoms:412                moved_atoms.append(at2)    413    # And the bonds...414    if dobonds.val:415        for bond in all_bonds:416            try:417                solute.move().change(bond,1*angstrom)418            except UserWarning as error:419                # extract the type of the errror420                error_type = re.search(r"(Sire\w*::\w*)", str(error)).group(0)421                if error_type == "SireMol::ring_error":422                    # print "This dof would move a ring and is therefore skipped"423                    continue424                else:425                    # re-throw the exception426                    raise error 427            gr0, gr1 = connectivity.split(bond.atom0(), bond.atom1() )428            ngr0 = gr0.nSelected()429            ngr1 = gr1.nSelected()430            if (ngr0 <= ngr1):431                smallgroup = gr0432            else:433                smallgroup = gr1434            factor = smallgroup.nSelected()435            flexibility.add(bond, BASE_BOND_FLEX.val/factor)436    return flexibility437def getCoordGroup(atoms, coords_property="coordinates"):438    coords = []439    for i in range(0, atoms.count()):440        atom = atoms[i]441        coords.append(atom.property(coords_property))442    return CoordGroup(coords)443def getAtomNearCOG( molecule ):444        445    mol_centre = molecule.evaluate().center()446    mindist = 99999.0447    448    for x in range(0, molecule.nAtoms()):449        atom = molecule.atoms()[x]   450        at_coords = atom.property('coordinates')451        dist = Vector().distance2(at_coords, mol_centre)452        if dist < mindist:453            mindist = dist454            nearest_atom = atom455    456    return nearest_atom457def addFlexibility(system, reflection_center=None, reflection_radius=None, \458                           naming_scheme=NamingScheme()):459    460    print("Adding flexibility to the system...")461    # create a group for all of the fixed molecules and residues462    fixed_group = MoleculeGroup( naming_scheme.fixedMoleculesGroupName().value() )463    # create a group for the fixed residues that are bonded to the mobile residues464    boundary_group = MoleculeGroup( naming_scheme.boundaryMoleculesGroupName().value() )465    if reflection_center is None or reflection_radius is None:466        print ("No reflection radius or reflection molecule specified, so moving all "467               "molecules and residues in the system.")468        reflection_radius = None469        reflection_center = None470    else:471        print(("Only moving molecules/residues that are within a distance %s A "472               "of the point %s.") % (reflection_radius.value(), reflection_center))473        system.setProperty("reflection center", AtomCoords(CoordGroup(1,reflection_center)))474        system.setProperty("reflection sphere radius", VariantProperty(reflection_radius.to(angstroms)))475    # fit the protein z-matrix templates to all of the protein molecules and add the mobile476    #Â residues to the mobile_sc_group and mobile_bb_group for mobile sidechains and backbones477    if naming_scheme.proteinsGroupName() in system.mgNames():478        protein_group = system[naming_scheme.proteinsGroupName()]479        # create a zmatrix maker that will be used to build the z-matrices for each protein molecule480        zmat_maker = ZmatrixMaker()481        zmat_maker.loadTemplates( os.path.join(parameter_directory, "amber.zmatrices") )482        # now create the molecule groups that hold the flexible side chains and flexible backbone groups483        mobile_sc_group = MoleculeGroup(naming_scheme.mobileProteinSidechainsGroupName().value())484        mobile_bb_group = MoleculeGroup(naming_scheme.mobileProteinBackbonesGroupName().value())485        # the extra atoms moved as part of a backbone move486        hn_atoms = AtomName("N", CaseInsensitive) * AtomName("H", CaseInsensitive) * \487                   AtomName("HN", CaseInsensitive) * AtomName("HN1", CaseInsensitive) * \488                   AtomName("HN2", CaseInsensitive) * AtomName("HN3", CaseInsensitive)489        # loop over each protein molecule490        for molnum in protein_group.molNums():491            protein_mol = protein_group[molnum].molecule()492            print("Applying residue templates for protein %s" % molnum)493            protein_mol = zmat_maker.applyTemplates(protein_mol)494            system.update(protein_mol)495            if reflection_radius:496                space = Cartesian()497                mobile_resnums = []498                # only move side chains within "sc_radius" and backbones within "bb_radius" of the ligand molecule499                print("Looking for which residues are within the reflection sphere...")500                for i in range(0, protein_mol.nResidues()):501                    res = protein_mol.residue( ResIdx(i) )502                    distance = space.minimumDistance(CoordGroup(1,reflection_center), getCoordGroup(res.atoms()))503          504                    if distance < reflection_radius.value():505                        # add the residue to the mobile sidechains group506                        mobile_sc_group.add(res)507                        mobile_resnums.append( res.number() )508                        # now add the atoms needed from the residue to the mobile backbones group509                        atoms = protein_mol.select(ResIdx(i)).selection()510    511                        # for the backbone move to work, the residue must contain512                        #Â  AtomName("CA", CaseInsensitive) and AtomName("N", CaseInsensitive) )513                        has_backbone = False514                        try:515                            if atoms.selected( AtomName("CA", CaseInsensitive) ) and \516                               atoms.selected( AtomName("N", CaseInsensitive) ):517                                has_backbone = True518                        except:519                            pass520                        if has_backbone:521                            if i < (protein_mol.nResidues()-1):522                                try:523                                    atoms.deselect( hn_atoms + ResIdx(i) )524                                except:525                                    pass526                            if i > 0:527                                try:528                                    atoms.select( hn_atoms + ResIdx(i+1) )529                                except:530                                    pass531                            mobile_bb_group.add( PartialMolecule(protein_mol, atoms) )532                        else:533                            print("Not moving backbone of %s as it doesn't contain atoms N or CA" % protein_mol.residue(ResIdx(i)))534                # now loop over all of the residues and work out which ones are fixed, and which ones535                # are bonded to fixed residues536                connectivity = protein_mol.property("connectivity")537                for i in range(0, protein_mol.nResidues()):538                    res = protein_mol.residue( ResIdx(i) )539                    if not res.number() in mobile_resnums:540                        # is this residue bonded to any of the mobile residues? If so, then it is a boundary residue541                        is_boundary = False542                        for bonded_res in connectivity.connectionsTo( res.number() ):543                            bonded_resnum = protein_mol.residue(bonded_res).number()544                            if bonded_resnum in mobile_resnums:545                                is_boundary = True546                                break547                        if is_boundary:548                            boundary_group.add(res)549                        else:550                            fixed_group.add(res)551            else:552                # assume that the backbone and side chains of all residues are flexible553                for i in range(0, protein_mol.nResidues()):554                    res = protein_mol.residue( ResIdx(i) )555                    mobile_sc_group.add(res)556                    atoms = protein_mol.select(ResIdx(i)).selection()557    558                    if i < (protein_mol.nResidues()-1):559                        try:560                            atoms.deselect( hn_atoms + ResIdx(i) )561                        except:562                            pass563                    if i > 0:564                        try:565                            atoms.select( hn_atoms + ResIdx(i+1) )566                        except:567                            pass568                    mobile_bb_group.add( PartialMolecule(protein_mol, atoms) )569        if mobile_sc_group.nMolecules() > 0:570            system.add(mobile_sc_group)571        if mobile_bb_group.nMolecules() > 0:572            system.add(mobile_bb_group)573        print("The number of residues with flexible sidechains equals %s" % mobile_sc_group.nViews())574        print("The number of residues with flexible backbones equals %s" % mobile_bb_group.nViews())575        print("The number of boundary residues equals %s" % boundary_group.nViews())576        print("The number of fixed residues equals %s" % fixed_group.nViews())577    # add all of the mobile solute molecules to the mobile_solute_group and auto-generate578    #Â the z-matricies of all of the mobile solutes579    if naming_scheme.solutesGroupName() in system.mgNames():580        solute_group = system[naming_scheme.solutesGroupName()]581        mobile_solute_group = MoleculeGroup( naming_scheme.mobileSolutesGroupName().value() )582        # store the average solute translation and rotation deltas583        avg_trans_delta = 0584        avg_rot_delta = 0585        for molnum in solute_group.molNums():586            solute_mol = solute_group[molnum].molecule()587            move_solute = True588            # Only move the solute if it is within the sphere cutoff of the ligand (if a ligand and solvent 589            # radius have been specified...)590            if reflection_radius:591                move_solute = (Vector.distance(reflection_center, \592                                  solute_mol.evaluate().centerOfMass()) < reflection_radius.value())593            if move_solute:594                print("\nAuto-detecting the flexible degrees of freedom for solute %s" % molnum)595                # auto-generate the flexibility - bonds, angles and dihedrals596                flexibility = generateFlexibility(solute_mol)597                solute_mol = solute_mol.edit().setProperty("flexibility", flexibility).commit()598                print("\nFlexibility of solute %s equals:" % molnum)599                flex = solute_mol.property("flexibility")600                print(flex)601                avg_trans_delta += flex.translation().to(angstrom)602                avg_rot_delta += flex.rotation().to(degrees)603                system.update(solute_mol)604                mobile_solute_group.add(solute_mol)605            else:606                print("Not moving solute %s as it is outside the spherical solvent cutoff of the ligand." % solute_mol)607                fixed_group.add(solute_mol)608        if mobile_solute_group.nMolecules() > 0:609            system.add(mobile_solute_group)610            system.setProperty("average solute translation delta", \611                                 VariantProperty(avg_trans_delta / mobile_solute_group.nMolecules()))612            system.setProperty("average solute rotation delta", \613                                 VariantProperty(avg_rot_delta / mobile_solute_group.nMolecules()))614        print("\nNumber of mobile solute molecules equals %s" % mobile_solute_group.nMolecules())615    # add all of the mobile solvent molecules to the mobile_solvent_group616    if naming_scheme.solventsGroupName() in system.mgNames():617        solvent_group = system[ naming_scheme.solventsGroupName() ]        618        mobile_solvent_group = MoleculeGroup( naming_scheme.mobileSolventsGroupName().value() )619        print("Adding flexibility to the solvent...")620        if reflection_radius:621            for molnum in solvent_group.molNums():622                solvent_mol = solvent_group[molnum]623                if Vector.distance(reflection_center, solvent_mol.evaluate().centerOfMass()) < reflection_radius.value():624                    mobile_solvent_group.add(solvent_mol)625                else:626                    fixed_group.add(solvent_mol)627        else:628            mobile_solvent_group.add( solvent_group.molecules() )629        if mobile_solvent_group.nMolecules() > 0:630            system.add(mobile_solvent_group)631        print("\nNumber of mobile solvent molecules equals %s" % mobile_solvent_group.nMolecules())632    # All finished - just need to add in the fixed and boundary groups633    if fixed_group.nMolecules() > 0:634        system.add(fixed_group)635    if boundary_group.nMolecules() > 0:636        system.add(boundary_group)    637    print("\nNumber of fixed (or partially fixed) molecules equals %s" % fixed_group.nMolecules())638    return system639def printGroupInfo(system, group_name):640    try:641        group = system[MGName(group_name)]642        print("%s : nMolecules() == %d" % (str(group), group.nMolecules()))643    except:...

renaming.py

Source:renaming.py

1import os, logging, shutil2from .util import zero_prefix_int as padnum3from .util import replace_bad_chars4from .util import normpath5from .util import ensure_utf86from .util import safe_make_dirs7from .util import samefile8from .util import prune_dirs9from .util import make_symlink10from .util import safe_rename11from .dbguy import TVDatabase12from .texceptions import FileExistsError, InvalidDirectoryError13from .texceptions import NoSuchDatabaseError14from . import appconfig15log = logging.getLogger('humblebee')16class NamingScheme(object):17    def ep_filename(self, ep):18        """19        Get bottom level filename for episode.20        """21        raise NotImplementedError22    def season_filename(self, ep):23        """24        Filename of season directory.25        """26        raise NotImplementedError27    def series_filename(self, ep):28        """29        Filename of series directory.30        """31        raise NotImplementedError32    def full_path(self, ep, root=None):33        """34        Get full series/season/ep path.35        Result should be treated as relative to 36        whatver root dir is.37        If `root` is passed, the resulting path will be 38        an absolute path.39        """40        eu = ensure_utf841        fp = os.path.join(42            eu(self.series_filename(ep)),43            eu(self.season_filename(ep)),44            eu(self.ep_filename(ep))45            )46        if root:47            fp = normpath(os.path.join(root, fp))            48        return fp49class Friendly(NamingScheme):50    """51    Series Name (year)/s01/Series Name s01e02 Episode Title.avi52    """53    ep_mask = u'%(series_title)s s%(season_number)se%(ep_number)s%(extra_ep_number)s %(title)s%(ext)s'54    series_mask = u'%(series_title)s (%(series_start_date)s)'55    season_mask = u'season %(season_number)s'56    57    def ep_filename(self, ep):58        epd = dict(ep.items())59        eep = epd['extra_ep_number']60        epd['season_number'] = padnum(epd['season_number'])61        epd['ep_number'] = padnum(epd['ep_number'])62        if eep:63            epd['extra_ep_number'] = 'e'+padnum(eep)64        else:65            epd['extra_ep_number'] = ''             66        p = ep.path()67        if os.path.isdir(p):68            epd['ext'] = ''69        else:70            epd['ext'] = os.path.splitext(p)[1]71        return replace_bad_chars(self.ep_mask % epd)72    def season_filename(self, ep):73        epd = dict(ep.items())74        epd['season_number'] = padnum(ep['season_number'])75        return replace_bad_chars(self.season_mask % epd)76    def series_filename(self, ep):77        """78        Get a series foldername from ep.79        """80        epd = dict(ep.items())81        firstair = ep['series_start_date']82        if firstair:83            epd['series_start_date'] = firstair.year84        else:85            epd['series_start_date'] = 'no-date'86        if ep['series_title'].endswith('(%s)' % epd['series_start_date']):87            epd['series_title'] = ep['series_title'][:-7]88        return replace_bad_chars(self.series_mask % epd)89class Structured(NamingScheme):90    """91    Series Name (year)/s01/Series Name s01e02 Episode Title.avi92    """93    ep_mask = u'%(series_title)s s%(season_number)se%(ep_number)s%(extra_ep_number)s %(title)s%(ext)s'94    series_mask = u'%(series_title)s'95    season_mask = u'season %(season_number)s'96    97    def ep_filename(self, ep):98        epd = dict(ep.items())99        eep = epd['extra_ep_number']100        epd['season_number'] = padnum(epd['season_number'])101        epd['ep_number'] = padnum(epd['ep_number'])102        if eep:103            epd['extra_ep_number'] = 'e'+padnum(eep)104        else:105            epd['extra_ep_number'] = ''             106        p = ep.path()107        if os.path.isdir(p):108            epd['ext'] = ''109        else:110            epd['ext'] = os.path.splitext(p)[1]111        return replace_bad_chars(self.ep_mask % epd)112    def season_filename(self, ep):113        epd = dict(ep.items())114        epd['season_number'] = padnum(ep['season_number'])115        return replace_bad_chars(self.season_mask % epd)116    def series_filename(self, ep):117        """118        Get a series foldername from ep.119        """120        epd = dict(ep.items())121        return replace_bad_chars(self.series_mask % epd)122    123naming_schemes = {124    'friendly' : Friendly,125    'structured' : Structured126    }127class Renamer(object):128    """129    Handles renaming/moving of episodes in both filesystem and database.130    """    131    def __init__(self, rootdir, destdir, naming_scheme='friendly'):132        self.db = TVDatabase(rootdir)133        self.destdir = normpath(destdir)134        self.naming_scheme = naming_schemes[naming_scheme]()135        safe_make_dirs(self.destdir)136        if not samefile(self.destdir, self.db.directory):137            self.destdb = TVDatabase(self.destdir)138            self.destdb.create_database(soft=True)139        else:140            self.destdb = self.db141        self.clutter = appconfig.get('scanner', 'clutter').split(',')142    def update_db_path(self, ep, newpath):143        """144        Update file_path in database for given episode.145        """146        ep['file_path'] = newpath147        return self.destdb.upsert_episode(ep)148    def spare_dest_file(self, fn):149        """150        Move file to _unknown dir.151        """152        pj = os.path.join153        unknown = normpath(154            pj(self.destdir, '_unknown')155            )156        safe_make_dirs(unknown)157        destfile = normpath(158            pj(unknown, os.path.split(fn)[1])159            )160        safe_rename(fn, destfile)161        162    def move_episode(self, ep, force=False):163        """164        Path will be moved to `destdir` in a filename structure 165        decided by `naming_scheme`.166        If `destdir` is the same as `db.directory`, path will also be updated 167        in database.        168        Containing directory of ep is pruned afterwards.169        If the new path currently exists, it will be moved to '_unknown' before 170        ep is put in its place. Unless `force` is True, then it is overwritten.171        """        172        oldfile = ep.path()173        olddir = os.path.dirname(oldfile)174        newfile = self.naming_scheme.full_path(ep, root=self.destdir)175        if samefile(oldfile, newfile):176            return ep177        log.debug('Renaming "%s" -> "%s"', oldfile, newfile)178        pathindb = self.db.path_exists(ep.path('db'))        179        if os.path.exists(newfile) and not force:180            self.spare_dest_file(newfile)181        if os.path.isdir(newfile) and force:182            shutil.rmtree(newfile)183        safe_make_dirs(os.path.dirname(newfile))184        os.rename(oldfile, newfile)185        #if samefile(self.destdir, self.db.directory):186        self.update_db_path(ep, newfile)187        prune_dirs(olddir, root=self.db.directory, clutter=self.clutter)188        return ep189class SymlinkRenamer(Renamer):190    """191    Safer version of Renamer. Creates symlinks in destdir instead of actually moving 192    any files.193    `rootdir` may not be the same as `destdir`194    """    195    def __init__(self, rootdir, destdir, naming_scheme='friendly'):        196        super(SymlinkRenamer, self).__init__(rootdir,destdir,naming_scheme)197        if samefile(self.destdir, self.db.directory):198            raise InvalidDirectoryError(199                'rootdir and destdir can not be the same directory.'200                )201    def move_episode(self, ep, force=True):202        oldfile = ep.path()203        newfile = self.naming_scheme.full_path(ep, root=self.destdir)204        make_symlink(oldfile, newfile, overwrite=True)205def make_unknown_dir(db, destdir):206    """nn207    When symlinks, make a virtual dir based on 208    unparsed_episode table.209    """210    pj = os.path.join211    root = normpath(212        pj(destdir, '_unknown')213        )214    safe_make_dirs(root)        215    q = 'SELECT * FROM unparsed_episode'216    for row in db.execute_query(q):217        path = row['child_path']218        rpath = pj(db.directory, path)219        vpath = pj(root, path)220        if os.path.isdir(rpath):221            safe_make_dirs(vpath)222        else:223            make_symlink(rpath, vpath)224def make_symlinkfs(rootdir, destdir, naming_scheme='friendly'):225    """226    Make a symlinkfs in destdir based on existing database in rootdir.227    """228    db = TVDatabase(rootdir)229    if not db.db_file_exists():230        raise NoSuchDatabaseError(231            'No tv database in "%s", please import first.' % rootdir232            )233    if not os.path.exists(destdir):234        safe_make_dirs(destdir)235    renamer = SymlinkRenamer(rootdir, destdir, naming_scheme=naming_scheme)236    for ep in db.get_episodes():237        renamer.move_episode(ep)    238    make_unknown_dir(db, destdir)239def renamer_all(rootdir, destdir, force=False, naming_scheme='friendly'):240    """241    Rename all episodes in database in `rootdir` to `destdir`.242    """243    db = TVDatabase(rootdir)244    if not db.db_file_exists():245        raise NoSuchDatabaseError(246            'No tv database in "%s", please import first.' % rootdir247            )248    if not os.path.exists(destdir):249        safe_make_dirs(destdir)250    renamer = Renamer(rootdir, destdir, naming_scheme=naming_scheme)251    for ep in db.get_episodes():252        renamer.move_episode(ep, force=force)...

builder.py

Source:builder.py

...145    Inject a fixture into a suite. If no fixture name is specified then the name of the variable holding146    the injected fixture will be used.147    """148    return InjectedFixture(fixture_name)149def _default_naming_scheme(name, description, parameters, nb):150    return name + "_%d" % nb, description + " #%d" % nb151def _format_naming_scheme(name_fmt, description_fmt):152    def naming_scheme(_, __, parameters, ___):153        return name_fmt.format(**parameters), description_fmt.format(**parameters)154    return naming_scheme155class _Parametrized(object):156    def __init__(self, parameters_source, naming_scheme):157        self._parameters_source = parameters_source158        self.naming_scheme = naming_scheme159    @property160    def parameters_source(self):161        source = iter(self._parameters_source)162        try:163            first_item = next(source)164        except StopIteration:165            return166        if type(first_item) is dict:167            yield first_item168            for item in source:169                yield item170        else:171            if type(first_item) in STRING_TYPES:172                names = [s.strip() for s in first_item.split(",")]173            else:174                names = first_item  # assume list or tuple175            for values in source:176                yield dict(zip(names, values))177def parametrized(parameter_source, naming_scheme=_default_naming_scheme):178    # type: (Iterable, Optional[Union[Callable[[str, str, dict, int], Tuple[str, str]], Sequence]]) -> Any179    """180    Decorator, make the test parametrized.181    :param parameter_source: it can be either:182        -  an iterable of dicts, each dict representing the arguments passed to the test183        - a CSV-like mode, where the first element of the list represents the argument names as an str or a sequence184          (example: ``"i,j"`` or ``("i", "j")``) and the remaining elements are sequences of the arguments to be185          passed to the test.186    :param naming_scheme: optional, it can be either:187      - a optional function that takes as parameters the base test name, description, parameters, index188        and must return the expanded test name and description as a two elements list189      - a tuple/list of two (name + description) format strings, example: ``("test_{i}_plus_{j}", "Test {i} plus {j}")``190    """191    def wrapper(obj):192        md = get_metadata(obj)193        md.parametrized = _Parametrized(194            parameter_source,195            naming_scheme if callable(naming_scheme) else _format_naming_scheme(*naming_scheme)196        )197        return obj...

votes.py

Source:votes.py

1import os2import datetime3from zipfile import ZipFile4from billy.scrape.votes import VoteScraper, Vote5class NCVoteScraper(VoteScraper):6    jurisdiction = 'nc'7    def scrape(self, chamber, session):8        # Unfortunately, you now have to request access to FTP.9        # This method of retrieving votes needs to be be changed or10        # fall back to traditional web scraping.11        if session == '2009':12            # 2009 files have a different delimiter and naming scheme.13            vote_data_url = 'ftp://www.ncleg.net/Bill_Status/Vote Data 2009.zip'14            naming_scheme = '{session}{file_label}.txt'15            delimiter = ";"16        else:17            vote_data_url = 'ftp://www.ncleg.net/Bill_Status/Votes%s.zip' % session18            naming_scheme = '{file_label}_{session}.txt'19            delimiter = "\t"20        fname, resp = self.urlretrieve(vote_data_url)21        # fname = "/Users/brian/Downloads/Vote Data 2009.zip"22        zf = ZipFile(fname)23        chamber_code = 'H' if chamber == 'lower' else 'S'24        # Members_YYYY.txt: tab separated25        # 0: id (unique only in chamber)26        # 1: H or S27        # 2: member name28        # 3-5: county, district, party29        # 6: mmUserId30        member_file = zf.open(naming_scheme.format(file_label='Members', session=session))31        members = {}32        for line in member_file.readlines():33            data = line.split(delimiter)34            if data[1] == chamber_code:35                members[data[0]] = data[2]36        # Votes_YYYY.txt37        # 0: sequence number38        # 1: chamber (S/H)39        # 2: date40        # 3: prefix41        # 4: bill_id42        # 5: yes votes43        # 6: no votes44        # 7: excused absences45        # 8: excused votes46        # 9: didn't votes47        # 10: total yes+no48        # 11: sponsor49        # 12: reading info50        # 13: info51        # 20: PASSED/FAILED52        # 21: legislative day53        vote_file = zf.open(naming_scheme.format(file_label='Votes', session=session))54        bill_chambers = {'H':'lower', 'S':'upper'}55        votes = {}56        for line in vote_file.readlines():57            data = line.split(delimiter)58            if len(data) < 24:59                self.warning('line too short %s', data)60                continue61            if data[1] == chamber_code:62                date = datetime.datetime.strptime(data[2][:16],63                                                  '%Y-%m-%d %H:%M')64                if data[3][0] not in bill_chambers:65                    # skip votes that aren't on bills66                    self.log('skipping vote %s' % data[0])67                    continue68                votes[data[0]] = Vote(chamber, date, data[13],69                                      'PASS' in data[20],70                                      int(data[5]),71                                      int(data[6]),72                                      int(data[7])+int(data[8])+int(data[9]),73                                      bill_chamber=bill_chambers[data[3][0]],74                                      bill_id=data[3]+data[4], session=session)75        member_vote_file = zf.open(naming_scheme.format(file_label='MemberVotes', session=session))76        # 0: member id77        # 1: chamber (S/H)78        # 2: vote id79        # 3: vote chamber (always same as 1)80        # 4: vote (Y,N,E,X)81        # 5: pair ID (member)82        # 6: pair order83        # If a vote is paired then it should be counted as an 'other'84        for line in member_vote_file.readlines():85            data = line.split(delimiter)86            if data[1] == chamber_code:87                try:88                    member_voting = members[data[0]]89                except KeyError:90                    self.debug('Member %s not found.' % data[0])91                    continue92                try:93                    vote = votes[data[2]]94                except KeyError:95                    self.debug('Vote %s not found.' % data[2])96                    continue97                # -1 votes are Lt. Gov, not included in count, so we add them98                if data[4] == 'Y' and not data[5]:99                    if data[0] == '-1':100                        vote['yes_count'] += 1101                    vote.yes(member_voting)102                elif data[4] == 'N' and not data[5]:103                    if data[0] == '-1':104                        vote['no_count'] += 1105                    vote.no(member_voting)106                else:107                    # for some reason other_count is high for paired votes108                    if data[5]:109                        vote['other_count'] -= 1110                    # is either E: excused, X: no vote, or paired (doesn't count)111                    vote.other(member_voting)112        for vote in votes.itervalues():113            #vote.validate()114            vote.add_source(vote_data_url)115            self.save_vote(vote)116        # remove file117        zf.close()...

Automation Testing Tutorials

Learn to execute automation testing from scratch with LambdaTest Learning Hub. Right from setting up the prerequisites to run your first automation test, to following best practices and diving deeper into advanced test scenarios. LambdaTest Learning Hubs compile a list of step-by-step guides to help you be proficient with different test automation frameworks i.e. Selenium, Cypress, TestNG etc.