Exemplo n.º 1
0
    def from_structure(cls, struct, term_decorate=True):
        """
        Instantiates a ResidueTemplateContainer from a Structure instance filled
        with residues

        Parameters
        ----------
        struct : :class:`parmed.structure.Structure`
            The structure from which to generate the ResidueTemplateContainer
            from
        term_decorate : bool, optional
            If True, terminal amino and nucleic acid residues will be adorned as
            follows:

                * N-prepended if it is an N-terminal amino acid
                * C-prepended if it is a C-terminal amino acid
                * 5-appended if it is a 5'-terminal nucleic acid
                * 3-appended if it is a 3'-terminal nucleic acid

            For example, an N-terminal GLY will become NGLY, while a 5'-terminal
            DA will become DA5. Default is True
        """
        inst = cls()
        for res in struct.residues:
            rt = ResidueTemplate.from_residue(res)
            # See if we need to decorate the termini names
            if rt.head is None and rt.tail is not None and term_decorate:
                if AminoAcidResidue.has(rt.name):
                    if len(rt.name) != 4 or rt.name[0] != 'N':
                        rt.name = 'N%s' % rt.name
                elif RNAResidue.has(rt.name) or DNAResidue.has(rt.name):
                    if rt.name[-1] != '5':
                        rt.name = '%s5' % rt.name
            elif rt.tail is None and rt.head is not None and term_decorate:
                if AminoAcidResidue.has(rt.name):
                    if len(rt.name) != 4 or rt.name[0] != 'C':
                        rt.name = 'C%s' % rt.name
                elif RNAResidue.has(rt.name) or DNAResidue.has(rt.name):
                    if rt.name[-1] != '3':
                        rt.name = '%s3' % rt.name
            inst.append(rt)
        inst.box = struct.box
        return inst
Exemplo n.º 2
0
    def from_structure(cls, struct, term_decorate=True):
        """
        Instantiates a ResidueTemplateContainer from a Structure instance filled
        with residues

        Parameters
        ----------
        struct : :class:`parmed.structure.Structure`
            The structure from which to generate the ResidueTemplateContainer
            from
        term_decorate : bool, optional
            If True, terminal amino and nucleic acid residues will be adorned as
            follows:

                * N-prepended if it is an N-terminal amino acid
                * C-prepended if it is a C-terminal amino acid
                * 5-appended if it is a 5'-terminal nucleic acid
                * 3-appended if it is a 3'-terminal nucleic acid

            For example, an N-terminal GLY will become NGLY, while a 5'-terminal
            DA will become DA5. Default is True
        """
        inst = cls()
        for res in struct.residues:
            rt = ResidueTemplate.from_residue(res)
            # See if we need to decorate the termini names
            if rt.head is None and rt.tail is not None and term_decorate:
                if AminoAcidResidue.has(rt.name):
                    if len(rt.name) != 4 or rt.name[0] != 'N':
                        rt.name = 'N%s' % rt.name
                elif RNAResidue.has(rt.name) or DNAResidue.has(rt.name):
                    if rt.name[-1] != '5':
                        rt.name = '%s5' % rt.name
            elif rt.tail is None and rt.head is not None and term_decorate:
                if AminoAcidResidue.has(rt.name):
                    if len(rt.name) != 4 or rt.name[0] != 'C':
                        rt.name = 'C%s' % rt.name
                elif RNAResidue.has(rt.name) or DNAResidue.has(rt.name):
                    if rt.name[-1] != '3':
                        rt.name = '%s3' % rt.name
            inst.append(rt)
        inst.box = struct.box
        return inst
Exemplo n.º 3
0
Arquivo: mol2.py Projeto: drroe/ParmEd
    def write(struct, dest, mol3=False, split=False):
        """ Writes a mol2 file from a structure or residue template

        Parameters
        ----------
        struct : :class:`Structure` or :class:`ResidueTemplate` or
                 :class:`ResidueTemplateContainer`
            The input structure to write the mol2 file from
        dest : str or file-like obj
            Name of the file to write or open file handle to write to
        mol3 : bool, optional
            If True and ``struct`` is a ResidueTemplate or container, write
            HEAD/TAIL sections. Default is False
        split : bool, optional
            If True and ``struct`` is a ResidueTemplateContainer or a Structure
            with multiple residues, each residue is printed in a separate
            @<MOLECULE> section that appear sequentially in the output file
        """
        own_handle = False
        if not hasattr(dest, 'write'):
            own_handle = True
            dest = genopen(dest, 'w')
        if split:
            # Write sequentially if it is a multi-residue container or Structure
            if isinstance(struct, ResidueTemplateContainer):
                for res in struct:
                    Mol2File.write(res, dest, mol3)
                return
            elif isinstance(struct, Structure) and len(struct.residues) > 1:
                for res in ResidueTemplateContainer.from_structure(struct):
                    Mol2File.write(res, dest, mol3)
                return
        try:
            if isinstance(struct, ResidueTemplateContainer):
                natom = sum([len(c) for c in struct])
                # To find the number of bonds, we need to total number of bonds
                # + the number of bonds that would be formed by "stitching"
                # together residues via their head and tail
                bonds = []
                charges = []
                bases = [1 for res in struct]
                for i, res in enumerate(struct):
                    if i < len(struct) - 1:
                        bases[i+1] = bases[i] + len(res)
                for i, res in enumerate(struct):
                    for bond in res.bonds:
                        bonds.append((bond.atom1.idx+bases[i],
                                      bond.atom2.idx+bases[i]))
                    if i < len(struct)-1 and (res.tail is not None and
                            struct[i+1].head is not None):
                        bonds.append((res.tail.idx+bases[i],
                                      struct[i+1].head.idx+bases[i+1]))
                    charges.extend([a.charge for a in res])
                residues = struct
                if not struct.name:
                    name = struct[0].name
                else:
                    name = struct.name
            else:
                natom = len(struct.atoms)
                bonds = [(b.atom1.idx+1, b.atom2.idx+1) for b in struct.bonds]
                if isinstance(struct, ResidueTemplate):
                    residues = [struct]
                    name = struct.name
                else:
                    residues = struct.residues
                    name = struct.residues[0].name
                charges = [a.charge for a in struct.atoms]
            dest.write('@<TRIPOS>MOLECULE\n')
            dest.write('%s' % name)
            dest.write('\n')
            dest.write('%d %d %d 0 1\n' % (natom, len(bonds), len(residues)))
            if len(residues) == 1:
                dest.write('SMALL\n')
            else:
                for residue in residues:
                    if AminoAcidResidue.has(residue.name):
                        dest.write('PROTEIN\n')
                        break
                    if (RNAResidue.has(residue.name) or
                            DNAResidue.has(residue.name)):
                        dest.write('NUCLEIC\n')
                        break
                else:
                    dest.write('BIOPOLYMER\n')
            if not any(charges):
                dest.write('NO_CHARGES\n')
                printchg = False
            else:
                dest.write('USER_CHARGES\n')
                printchg = True
            # Now do ATOM section
            dest.write('@<TRIPOS>ATOM\n')
            j = 1
            for i, res in enumerate(residues):
                for atom in res:
                    try:
                        x = atom.xx
                    except AttributeError:
                        x = 0
                    try:
                        y = atom.xy
                    except AttributeError:
                        y = 0
                    try:
                        z = atom.xz
                    except AttributeError:
                        z = 0
                    dest.write('%8d %-8s %10.4f %10.4f %10.4f %-8s %6d %-8s' % (
                               j, atom.name, x, y, z,
                               atom.type.strip() or atom.name, i+1, res.name))
                    if printchg:
                        dest.write(' %10.6f\n' % atom.charge)
                    else:
                        dest.write('\n')
                    j += 1
            dest.write('@<TRIPOS>BOND\n')
            for i, bond in enumerate(bonds):
                dest.write('%8d %8d %8d 1\n' % (i+1, bond[0], bond[1]))
            dest.write('@<TRIPOS>SUBSTRUCTURE\n')
            first_atom = 0
            for i, res in enumerate(residues):
                if not hasattr(res, 'chain') or not res.chain:
                    chain = '****'
                else:
                    chain = res.chain
                intresbonds = 0
                if isinstance(res, ResidueTemplate):
                    if i != len(residues)-1 and (res.tail is not None and
                            residues[i+1].head is not None):
                        intresbonds += 1
                    if i != 0 and (res.head is not None and residues[i-1].tail
                            is not None):
                        intresbonds += 1
                else:
                    for atom in res:
                        for a2 in atom.bond_partners:
                            if a2.residue is not res:
                                intresbonds += 1
                dest.write('%8d %-8s %8d RESIDUE %4d %-4s ROOT %6d\n' % (i+1,
                           res.name, first_atom+1, 0, chain[:4], intresbonds))
                first_atom += len(res)
            if mol3:
                dest.write('@<TRIPOS>HEADTAIL\n')
                for i, res in enumerate(residues):
                    if isinstance(res, ResidueTemplate):
                        if res.head is not None:
                            dest.write('%s %d\n' % (res.head.name, i+1))
                        else:
                            dest.write('0 0\n')
                        if res.tail is not None:
                            dest.write('%s %d\n' % (res.tail.name, i+1))
                        else:
                            dest.write('0 0\n')
                    else:
                        head = tail = None
                        for atom in res:
                            for a2 in atom.bond_partners:
                                if a2.residue.idx == res.idx - 1:
                                    head = atom
                                if a2.residue.idx == res.idx + 1:
                                    tail = atom
                        if head is not None:
                            dest.write('%s %d\n' % (head.name, i+1))
                        else:
                            dest.write('0 0\n')
                        if tail is not None:
                            dest.write('%s %d\n' % (tail.name, i+1))
                        else:
                            dest.write('0 0\n')
                dest.write('@<TRIPOS>RESIDUECONNECT\n')
                for i, res in enumerate(residues):
                    if isinstance(res, ResidueTemplate):
                        con = [res.head, res.tail, None, None, None, None]
                        for i, a in enumerate(res.connections):
                            con[i+2] = a
                    else:
                        con = [None, None, None, None, None, None]
                        ncon = 2
                        for atom in res:
                            for a2 in atom.bond_partners:
                                if a2.residue.idx == res.idx - 1:
                                    con[0] = atom
                                elif a2.residue.idx == res.idx + 1:
                                    con[1] = atom
                                elif a2.residue.idx != res.idx:
                                    con[ncon] = atom
                                    ncon += 1
                    dest.write('%d' % (i+1))
                    for a in con:
                        if a is not None:
                            dest.write(' %s' % a.name)
                        else:
                            dest.write(' 0')
                    dest.write('\n')
        finally:
            if own_handle: dest.close()
Exemplo n.º 4
0
    def write(struct, dest, mol3=False, split=False):
        """ Writes a mol2 file from a structure or residue template

        Parameters
        ----------
        struct : :class:`Structure` or :class:`ResidueTemplate` or
                 :class:`ResidueTemplateContainer`
            The input structure to write the mol2 file from
        dest : str or file-like obj
            Name of the file to write or open file handle to write to
        mol3 : bool, optional
            If True and ``struct`` is a ResidueTemplate or container, write
            HEAD/TAIL sections. Default is False
        split : bool, optional
            If True and ``struct`` is a ResidueTemplateContainer or a Structure
            with multiple residues, each residue is printed in a separate
            @<MOLECULE> section that appear sequentially in the output file
        """
        own_handle = False
        if not hasattr(dest, 'write'):
            own_handle = True
            dest = genopen(dest, 'w')
        if split:
            # Write sequentially if it is a multi-residue container or Structure
            if isinstance(struct, ResidueTemplateContainer):
                try:
                    for res in struct:
                        Mol2File.write(res, dest, mol3)
                finally:
                    if own_handle: dest.close()
                return
            elif isinstance(struct, Structure) and len(struct.residues) > 1:
                try:
                    for res in ResidueTemplateContainer.from_structure(struct):
                        Mol2File.write(res, dest, mol3)
                finally:
                    if own_handle: dest.close()
                return
        try:
            if isinstance(struct, ResidueTemplateContainer):
                natom = sum([len(c) for c in struct])
                # To find the number of bonds, we need to total number of bonds
                # + the number of bonds that would be formed by "stitching"
                # together residues via their head and tail
                bonds = []
                charges = []
                bases = [1 for res in struct]
                for i, res in enumerate(struct):
                    if i < len(struct) - 1:
                        bases[i+1] = bases[i] + len(res)
                for i, res in enumerate(struct):
                    for bond in res.bonds:
                        bonds.append((bond.atom1.idx+bases[i],
                                      bond.atom2.idx+bases[i]))
                    if i < len(struct)-1 and (res.tail is not None and
                            struct[i+1].head is not None):
                        bonds.append((res.tail.idx+bases[i],
                                      struct[i+1].head.idx+bases[i+1]))
                    charges.extend([a.charge for a in res])
                residues = struct
                name = struct.name or struct[0].name
            else:
                natom = len(struct.atoms)
                bonds = [(b.atom1.idx+1, b.atom2.idx+1) for b in struct.bonds]
                if isinstance(struct, ResidueTemplate):
                    residues = [struct]
                    name = struct.name
                else:
                    residues = struct.residues
                    name = struct.residues[0].name
                charges = [a.charge for a in struct.atoms]
            dest.write('@<TRIPOS>MOLECULE\n')
            dest.write('%s\n' % name)
            dest.write('%d %d %d 0 1\n' % (natom, len(bonds), len(residues)))
            if len(residues) == 1:
                dest.write('SMALL\n')
            else:
                for residue in residues:
                    if AminoAcidResidue.has(residue.name):
                        dest.write('PROTEIN\n')
                        break
                    if (RNAResidue.has(residue.name) or
                            DNAResidue.has(residue.name)):
                        dest.write('NUCLEIC\n')
                        break
                else:
                    dest.write('BIOPOLYMER\n')
            if not any(charges):
                dest.write('NO_CHARGES\n')
                printchg = False
            else:
                dest.write('USER_CHARGES\n')
                printchg = True
            # See if we want to print box info
            if hasattr(struct, 'box') and struct.box is not None:
                box = struct.box
                dest.write('@<TRIPOS>CRYSIN\n')
                dest.write('%10.4f %10.4f %10.4f %10.4f %10.4f %10.4f  1  1\n' %
                           (box[0], box[1], box[2], box[3], box[4], box[5]))
            # Now do ATOM section
            dest.write('@<TRIPOS>ATOM\n')
            j = 1
            for i, res in enumerate(residues):
                for atom in res:
                    try:
                        x = atom.xx
                    except AttributeError:
                        x = 0
                    try:
                        y = atom.xy
                    except AttributeError:
                        y = 0
                    try:
                        z = atom.xz
                    except AttributeError:
                        z = 0
                    dest.write('%8d %-8s %10.4f %10.4f %10.4f %-8s %6d %-8s' % (
                               j, atom.name, x, y, z,
                               atom.type.strip() or atom.name, i+1, res.name))
                    if printchg:
                        dest.write(' %10.6f\n' % atom.charge)
                    else:
                        dest.write('\n')
                    j += 1
            dest.write('@<TRIPOS>BOND\n')
            for i, bond in enumerate(bonds):
                dest.write('%8d %8d %8d 1\n' % (i+1, bond[0], bond[1]))
            dest.write('@<TRIPOS>SUBSTRUCTURE\n')
            first_atom = 0
            for i, res in enumerate(residues):
                if not hasattr(res, 'chain') or not res.chain:
                    chain = '****'
                else:
                    chain = res.chain
                intresbonds = 0
                if isinstance(res, ResidueTemplate):
                    if i != len(residues)-1 and (res.tail is not None and
                            residues[i+1].head is not None):
                        intresbonds += 1
                    if i != 0 and (res.head is not None and residues[i-1].tail
                            is not None):
                        intresbonds += 1
                else:
                    for atom in res:
                        for a2 in atom.bond_partners:
                            if a2.residue is not res:
                                intresbonds += 1
                dest.write('%8d %-8s %8d RESIDUE %4d %-4s ROOT %6d\n' % (i+1,
                           res.name, first_atom+1, 0, chain[:4], intresbonds))
                first_atom += len(res)
            if mol3:
                dest.write('@<TRIPOS>HEADTAIL\n')
                for i, res in enumerate(residues):
                    if isinstance(res, ResidueTemplate):
                        if res.head is not None:
                            dest.write('%s %d\n' % (res.head.name, i+1))
                        else:
                            dest.write('0 0\n')
                        if res.tail is not None:
                            dest.write('%s %d\n' % (res.tail.name, i+1))
                        else:
                            dest.write('0 0\n')
                    else:
                        head = tail = None
                        for atom in res:
                            for a2 in atom.bond_partners:
                                if a2.residue.idx == res.idx - 1:
                                    head = atom
                                if a2.residue.idx == res.idx + 1:
                                    tail = atom
                        if head is not None:
                            dest.write('%s %d\n' % (head.name, i+1))
                        else:
                            dest.write('0 0\n')
                        if tail is not None:
                            dest.write('%s %d\n' % (tail.name, i+1))
                        else:
                            dest.write('0 0\n')
                dest.write('@<TRIPOS>RESIDUECONNECT\n')
                for i, res in enumerate(residues):
                    if isinstance(res, ResidueTemplate):
                        con = [res.head, res.tail, None, None, None, None]
                        for i, a in enumerate(res.connections):
                            con[i+2] = a
                    else:
                        con = [None, None, None, None, None, None]
                        ncon = 2
                        for atom in res:
                            for a2 in atom.bond_partners:
                                if a2.residue.idx == res.idx - 1:
                                    con[0] = atom
                                elif a2.residue.idx == res.idx + 1:
                                    con[1] = atom
                                elif a2.residue.idx != res.idx:
                                    con[ncon] = atom
                                    ncon += 1
                    dest.write('%d' % (i+1))
                    for a in con:
                        if a is not None:
                            dest.write(' %s' % a.name)
                        else:
                            dest.write(' 0')
                    dest.write('\n')
        finally:
            if own_handle: dest.close()
Exemplo n.º 5
0
 def count_nures(parm):
     nnuc = 0
     for res in parm.residues:
         if RNAResidue.has(res.name) or DNAResidue.has(res.name):
             nnuc += 1
     return nnuc
Exemplo n.º 6
0
 def count_nures(parm):
     nnuc = 0
     for res in parm.residues:
         if RNAResidue.has(res.name) or DNAResidue.has(res.name):
             nnuc += 1
     return nnuc