1 files changed, 434 insertions, 0 deletions
diff --git a/plip/basic/supplemental.py b/plip/basic/supplemental.py
new file mode 100644
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+++ b/plip/basic/supplemental.py
@@ -0,0 +1,434 @@
+import gzip
+import itertools
+import os
+import platform
+import re
+import subprocess
+import sys
+import tempfile
+import zipfile
+from collections import namedtuple
+
+import numpy as np
+from openbabel import pybel
+from openbabel.pybel import Atom
+
+from plip.basic import config, logger
+
+logger = logger.get_logger()
+
+# Windows and MacOS
+if os.name != 'nt' and platform.system() != 'Darwin':  # Resource module not available for Windows
+    import resource
+
+# Settings
+np.seterr(all='ignore')  # No runtime warnings
+
+
+def tmpfile(prefix, direc):
+    """Returns the path to a newly created temporary file."""
+    return tempfile.mktemp(prefix=prefix, suffix='.pdb', dir=direc)
+
+
+def is_lig(hetid):
+    """Checks if a PDB compound can be excluded as a small molecule ligand"""
+    h = hetid.upper()
+    return not (h == 'HOH' or h in config.UNSUPPORTED)
+
+
+def extract_pdbid(string):
+    """Use regular expressions to get a PDB ID from a string"""
+    p = re.compile("[0-9][0-9a-z]{3}")
+    m = p.search(string.lower())
+    try:
+        return m.group()
+    except AttributeError:
+        return "UnknownProtein"
+
+
+def whichrestype(atom):
+    """Returns the residue name of an Pybel or OpenBabel atom."""
+    atom = atom if not isinstance(atom, Atom) else atom.OBAtom  # Convert to OpenBabel Atom
+    return atom.GetResidue().GetName() if atom.GetResidue() is not None else None
+
+
+def whichresnumber(atom):
+    """Returns the residue number of an Pybel or OpenBabel atom (numbering as in original PDB file)."""
+    atom = atom if not isinstance(atom, Atom) else atom.OBAtom  # Convert to OpenBabel Atom
+    return atom.GetResidue().GetNum() if atom.GetResidue() is not None else None
+
+
+def whichchain(atom):
+    """Returns the residue number of an PyBel or OpenBabel atom."""
+    atom = atom if not isinstance(atom, Atom) else atom.OBAtom  # Convert to OpenBabel Atom
+    return atom.GetResidue().GetChain() if atom.GetResidue() is not None else None
+
+
+#########################
+# Mathematical operations
+#########################
+
+
+def euclidean3d(v1, v2):
+    """Faster implementation of euclidean distance for the 3D case."""
+    if not len(v1) == 3 and len(v2) == 3:
+        return None
+    return np.sqrt((v1[0] - v2[0]) ** 2 + (v1[1] - v2[1]) ** 2 + (v1[2] - v2[2]) ** 2)
+
+
+def vector(p1, p2):
+    """Vector from p1 to p2.
+    :param p1: coordinates of point p1
+    :param p2: coordinates of point p2
+    :returns : numpy array with vector coordinates
+    """
+    return None if len(p1) != len(p2) else np.array([p2[i] - p1[i] for i in range(len(p1))])
+
+
+def vecangle(v1, v2, deg=True):
+    """Calculate the angle between two vectors
+    :param v1: coordinates of vector v1
+    :param v2: coordinates of vector v2
+    :param deg: whether to return degrees or radians
+    :returns : angle in degree or rad
+    """
+    if np.array_equal(v1, v2):
+        return 0.0
+    dm = np.dot(v1, v2)
+    cm = np.linalg.norm(v1) * np.linalg.norm(v2)
+    angle = np.arccos(dm / cm)  # Round here to prevent floating point errors
+    return np.degrees([angle, ])[0] if deg else angle
+
+
+def normalize_vector(v):
+    """Take a vector and return the normalized vector
+    :param v: a vector v
+    :returns : normalized vector v
+    """
+    norm = np.linalg.norm(v)
+    return v / norm if not norm == 0 else v
+
+
+def centroid(coo):
+    """Calculates the centroid from a 3D point cloud and returns the coordinates
+    :param coo: Array of coordinate arrays
+    :returns : centroid coordinates as list
+    """
+    return list(map(np.mean, (([c[0] for c in coo]), ([c[1] for c in coo]), ([c[2] for c in coo]))))
+
+
+def projection(pnormal1, ppoint, tpoint):
+    """Calculates the centroid from a 3D point cloud and returns the coordinates
+    :param pnormal1: normal of plane
+    :param ppoint: coordinates of point in the plane
+    :param tpoint: coordinates of point to be projected
+    :returns : coordinates of point orthogonally projected on the plane
+    """
+    # Choose the plane normal pointing to the point to be projected
+    pnormal2 = [coo * (-1) for coo in pnormal1]
+    d1 = euclidean3d(tpoint, pnormal1 + ppoint)
+    d2 = euclidean3d(tpoint, pnormal2 + ppoint)
+    pnormal = pnormal1 if d1 < d2 else pnormal2
+    # Calculate the projection of tpoint to the plane
+    sn = -np.dot(pnormal, vector(ppoint, tpoint))
+    sd = np.dot(pnormal, pnormal)
+    sb = sn / sd
+    return [c1 + c2 for c1, c2 in zip(tpoint, [sb * pn for pn in pnormal])]
+
+
+def cluster_doubles(double_list):
+    """Given a list of doubles, they are clustered if they share one element
+    :param double_list: list of doubles
+    :returns : list of clusters (tuples)
+    """
+    location = {}  # hashtable of which cluster each element is in
+    clusters = []
+    # Go through each double
+    for t in double_list:
+        a, b = t[0], t[1]
+        # If they both are already in different clusters, merge the clusters
+        if a in location and b in location:
+            if location[a] != location[b]:
+                if location[a] < location[b]:
+                    clusters[location[a]] = clusters[location[a]].union(clusters[location[b]])  # Merge clusters
+                    clusters = clusters[:location[b]] + clusters[location[b] + 1:]
+                else:
+                    clusters[location[b]] = clusters[location[b]].union(clusters[location[a]])  # Merge clusters
+                    clusters = clusters[:location[a]] + clusters[location[a] + 1:]
+                # Rebuild index of locations for each element as they have changed now
+                location = {}
+                for i, cluster in enumerate(clusters):
+                    for c in cluster:
+                        location[c] = i
+        else:
+            # If a is already in a cluster, add b to that cluster
+            if a in location:
+                clusters[location[a]].add(b)
+                location[b] = location[a]
+            # If b is already in a cluster, add a to that cluster
+            if b in location:
+                clusters[location[b]].add(a)
+                location[a] = location[b]
+            # If neither a nor b is in any cluster, create a new one with a and b
+            if not (b in location and a in location):
+                clusters.append(set(t))
+                location[a] = len(clusters) - 1
+                location[b] = len(clusters) - 1
+    return map(tuple, clusters)
+
+
+#################
+# File operations
+#################
+
+def tilde_expansion(folder_path):
+    """Tilde expansion, i.e. converts '~' in paths into <value of $HOME>."""
+    return os.path.expanduser(folder_path) if '~' in folder_path else folder_path
+
+
+def folder_exists(folder_path):
+    """Checks if a folder exists"""
+    return os.path.exists(folder_path)
+
+
+def create_folder_if_not_exists(folder_path):
+    """Creates a folder if it does not exists."""
+    folder_path = tilde_expansion(folder_path)
+    folder_path = "".join([folder_path, '/']) if not folder_path[-1] == '/' else folder_path
+    direc = os.path.dirname(folder_path)
+    if not folder_exists(direc):
+        os.makedirs(direc)
+
+
+def cmd_exists(c):
+    return subprocess.call("type " + c, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE) == 0
+
+
+################
+# PyMOL-specific
+################
+
+
+def initialize_pymol(options):
+    """Initializes PyMOL"""
+    import pymol
+    # Pass standard arguments of function to prevent PyMOL from printing out PDB headers (workaround)
+    pymol.finish_launching(args=['pymol', options, '-K'])
+    pymol.cmd.reinitialize()
+
+
+def start_pymol(quiet=False, options='-p', run=False):
+    """Starts up PyMOL and sets general options. Quiet mode suppresses all PyMOL output.
+    Command line options can be passed as the second argument."""
+    import pymol
+    pymol.pymol_argv = ['pymol', '%s' % options] + sys.argv[1:]
+    if run:
+        initialize_pymol(options)
+    if quiet:
+        pymol.cmd.feedback('disable', 'all', 'everything')
+
+
+def nucleotide_linkage(residues):
+    """Support for DNA/RNA ligands by finding missing covalent linkages to stitch DNA/RNA together."""
+
+    nuc_covalent = []
+    #######################################
+    # Basic support for RNA/DNA as ligand #
+    #######################################
+    nucleotides = ['A', 'C', 'T', 'G', 'U', 'DA', 'DC', 'DT', 'DG', 'DU']
+    dna_rna = {}  # Dictionary of DNA/RNA residues by chain
+    covlinkage = namedtuple("covlinkage", "id1 chain1 pos1 conf1 id2 chain2 pos2 conf2")
+    # Create missing covlinkage entries for DNA/RNA
+    for ligand in residues:
+        resname, chain, pos = ligand
+        if resname in nucleotides:
+            if chain not in dna_rna:
+                dna_rna[chain] = [(resname, pos), ]
+            else:
+                dna_rna[chain].append((resname, pos))
+    for chain in dna_rna:
+        nuc_list = dna_rna[chain]
+        for i, nucleotide in enumerate(nuc_list):
+            if not i == len(nuc_list) - 1:
+                name, pos = nucleotide
+                nextnucleotide = nuc_list[i + 1]
+                nextname, nextpos = nextnucleotide
+                newlink = covlinkage(id1=name, chain1=chain, pos1=pos, conf1='',
+                                     id2=nextname, chain2=chain, pos2=nextpos, conf2='')
+                nuc_covalent.append(newlink)
+
+    return nuc_covalent
+
+
+def ring_is_planar(ring, r_atoms):
+    """Given a set of ring atoms, check if the ring is sufficiently planar
+    to be considered aromatic"""
+    normals = []
+    for a in r_atoms:
+        adj = pybel.ob.OBAtomAtomIter(a.OBAtom)
+        # Check for neighboring atoms in the ring
+        n_coords = [pybel.Atom(neigh).coords for neigh in adj if ring.IsMember(neigh)]
+        vec1, vec2 = vector(a.coords, n_coords[0]), vector(a.coords, n_coords[1])
+        normals.append(np.cross(vec1, vec2))
+    # Given all normals of ring atoms and their neighbors, the angle between any has to be 5.0 deg or less
+    for n1, n2 in itertools.product(normals, repeat=2):
+        arom_angle = vecangle(n1, n2)
+        if all([arom_angle > config.AROMATIC_PLANARITY, arom_angle < 180.0 - config.AROMATIC_PLANARITY]):
+            return False
+    return True
+
+
+def classify_by_name(names):
+    """Classify a (composite) ligand by the HETID(s)"""
+    if len(names) > 3:  # Polymer
+        if len(set(config.RNA).intersection(set(names))) != 0:
+            ligtype = 'RNA'
+        elif len(set(config.DNA).intersection(set(names))) != 0:
+            ligtype = 'DNA'
+        else:
+            ligtype = "POLYMER"
+    else:
+        ligtype = 'SMALLMOLECULE'
+
+    for name in names:
+        if name in config.METAL_IONS:
+            if len(names) == 1:
+                ligtype = 'ION'
+            else:
+                if "ION" not in ligtype:
+                    ligtype += '+ION'
+    return ligtype
+
+
+def sort_members_by_importance(members):
+    """Sort the members of a composite ligand according to two criteria:
+    1. Split up in main and ion group. Ion groups are located behind the main group.
+    2. Within each group, sort by chain and position."""
+    main = [x for x in members if x[0] not in config.METAL_IONS]
+    ion = [x for x in members if x[0] in config.METAL_IONS]
+    sorted_main = sorted(main, key=lambda x: (x[1], x[2]))
+    sorted_main = sorted(main, key=lambda x: (x[1], x[2]))
+    sorted_ion = sorted(ion, key=lambda x: (x[1], x[2]))
+    return sorted_main + sorted_ion
+
+
+def get_isomorphisms(reference, lig):
+    """Get all isomorphisms of the ligand."""
+    query = pybel.ob.CompileMoleculeQuery(reference.OBMol)
+    mappr = pybel.ob.OBIsomorphismMapper.GetInstance(query)
+    if all:
+        isomorphs = pybel.ob.vvpairUIntUInt()
+        mappr.MapAll(lig.OBMol, isomorphs)
+    else:
+        isomorphs = pybel.ob.vpairUIntUInt()
+        mappr.MapFirst(lig.OBMol, isomorphs)
+        isomorphs = [isomorphs]
+    logger.debug(f'number of isomorphisms: {len(isomorphs)}')
+    # @todo Check which isomorphism to take
+    return isomorphs
+
+
+def canonicalize(lig, preserve_bond_order=False):
+    """Get the canonical atom order for the ligand."""
+    atomorder = None
+    # Get canonical atom order
+
+    lig = pybel.ob.OBMol(lig.OBMol)
+    if not preserve_bond_order:
+        for bond in pybel.ob.OBMolBondIter(lig):
+            if bond.GetBondOrder() != 1:
+                bond.SetBondOrder(1)
+    lig.DeleteData(pybel.ob.StereoData)
+    lig = pybel.Molecule(lig)
+    testcan = lig.write(format='can')
+    try:
+        pybel.readstring('can', testcan)
+        reference = pybel.readstring('can', testcan)
+    except IOError:
+        testcan, reference = '', ''
+    if testcan != '':
+        reference.removeh()
+        isomorphs = get_isomorphisms(reference, lig)  # isomorphs now holds all isomorphisms within the molecule
+        if not len(isomorphs) == 0:
+            smi_dict = {}
+            smi_to_can = isomorphs[0]
+            for x in smi_to_can:
+                smi_dict[int(x[1]) + 1] = int(x[0]) + 1
+            atomorder = [smi_dict[x + 1] for x in range(len(lig.atoms))]
+        else:
+            atomorder = None
+    return atomorder
+
+
+def int32_to_negative(int32):
+    """Checks if a suspicious number (e.g. ligand position) is in fact a negative number represented as a
+    32 bit integer and returns the actual number.
+    """
+    dct = {}
+    if int32 == 4294967295:  # Special case in some structures (note, this is just a workaround)
+        return -1
+    for i in range(-1000, -1):
+        dct[np.uint32(i)] = i
+    if int32 in dct:
+        return dct[int32]
+    else:
+        return int32
+
+
+def read_pdb(pdbfname, as_string=False):
+    """Reads a given PDB file and returns a Pybel Molecule."""
+    pybel.ob.obErrorLog.StopLogging()  # Suppress all OpenBabel warnings
+    if os.name != 'nt':  # Resource module not available for Windows
+        maxsize = resource.getrlimit(resource.RLIMIT_STACK)[-1]
+        resource.setrlimit(resource.RLIMIT_STACK, (min(2 ** 28, maxsize), maxsize))
+    sys.setrecursionlimit(10 ** 5)  # increase Python recursion limit
+    return readmol(pdbfname, as_string=as_string)
+
+
+def read(fil):
+    """Returns a file handler and detects gzipped files."""
+    if os.path.splitext(fil)[-1] == '.gz':
+        return gzip.open(fil, 'rb')
+    elif os.path.splitext(fil)[-1] == '.zip':
+        zf = zipfile.ZipFile(fil, 'r')
+        return zf.open(zf.infolist()[0].filename)
+    else:
+        return open(fil, 'r')
+
+
+def readmol(path, as_string=False):
+    """Reads the given molecule file and returns the corresponding Pybel molecule as well as the input file type.
+    In contrast to the standard Pybel implementation, the file is closed properly."""
+    supported_formats = ['pdb']
+    # Fix for Windows-generated files: Remove carriage return characters
+    if "\r" in path and as_string:
+        path = path.replace('\r', '')
+
+    for sformat in supported_formats:
+        obc = pybel.ob.OBConversion()
+        obc.SetInFormat(sformat)
+        logger.debug(f'detected {sformat} as format, trying to read file with OpenBabel')
+
+        # Read molecules with single bond information
+        if as_string:
+            try:
+                mymol = pybel.readstring(sformat, path)
+            except IOError:
+                logger.error('no valid file format provided')
+                sys.exit(1)
+        else:
+            read_file = pybel.readfile(format=sformat, filename=path, opt={"s": None})
+            try:
+                mymol = next(read_file)
+            except StopIteration:
+                logger.error('file contains no valid molecules')
+                sys.exit(1)
+
+        logger.debug('molecule successfully read')
+
+        # Assign multiple bonds
+        mymol.OBMol.PerceiveBondOrders()
+        return mymol, sformat
+
+    logger.error('no valid file format provided')
+    sys.exit(1)