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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -19,12 +19,16 @@ | |
| __email__ = ['[email protected]', '[email protected]'] | ||
|
|
||
| from prody import LOGGER | ||
| from numbers import Integral, Number | ||
|
|
||
| __all__ = ['addMissingAtoms'] | ||
| __all__ = ['addMissingAtoms', 'fixStructuresMissingAtoms'] | ||
|
|
||
| def addMissingAtoms(infile, method='openbabel', pH=7.0, outfile=None, **kwargs): | ||
| """Function will add hydrogens to the protein and ligand structure using Openbabel [NO11]_ | ||
| or PDBFixer with OpenMM. | ||
| """This function will add hydrogens to the protein and ligand structure using Openbabel [NO11]_ | ||
| or PDBFixer with OpenMM. | ||
| There are also options whether to *model_residues* (default False), *remove_heterogens* | ||
| (default False), *keep_waters* (default True), *overwrite* (default False). | ||
| :arg infile: PDB file name | ||
| :type infile: str | ||
|
|
@@ -53,11 +57,39 @@ def addMissingAtoms(infile, method='openbabel', pH=7.0, outfile=None, **kwargs): | |
| model_residues = kwargs.get("model_residues", False) | ||
| remove_heterogens = kwargs.get("remove_heterogens", False) | ||
| keep_water = kwargs.get("keep_water", True) | ||
| overwrite = kwargs.get("overwrite", False) | ||
|
|
||
| import os | ||
|
|
||
| if not isinstance(model_residues, bool): | ||
| raise TypeError('model_residues should be True or False') | ||
|
|
||
| if not isinstance(remove_heterogens, bool): | ||
| raise TypeError('remove_heterogens should be True or False') | ||
|
|
||
| if not isinstance(keep_water, bool): | ||
| raise TypeError('keep_water should be True or False') | ||
|
|
||
| if not isinstance(overwrite, bool): | ||
| raise TypeError('overwrite should be True or False') | ||
|
|
||
| if not isinstance(infile, str): | ||
| raise TypeError('infile should be a string pointing to a file') | ||
|
|
||
| if not os.path.exists(infile): | ||
| raise ValueError('infile {0} does not exist'.format(infile)) | ||
|
|
||
| if not isinstance(pH, Number): | ||
| raise TypeError('pH should be a number') | ||
|
|
||
| if outfile == None: | ||
| outfile = os.path.join(os.path.split(infile)[0], "addH_" + os.path.split(infile)[1]) | ||
| outfile = os.path.join(os.path.split(infile)[0], | ||
| "addH_" + os.path.split(infile)[1]) | ||
|
|
||
| if os.path.exists(outfile) and not overwrite: | ||
| LOGGER.warn('outfile {0} already exists, so returning it. \ | ||
| Set overwrite=True to overwrite it'.format(outfile)) | ||
| return outfile | ||
|
|
||
| if outfile == infile: | ||
| raise ValueError('outfile cannot be the same as infile') | ||
|
|
@@ -70,17 +102,18 @@ def addMissingAtoms(infile, method='openbabel', pH=7.0, outfile=None, **kwargs): | |
| raise ValueError('Openbabel cannot handle cif files') | ||
|
|
||
| try: | ||
| #import openbabel | ||
| from openbabel import openbabel | ||
| obconversion = openbabel.OBConversion() | ||
| obconversion.SetInFormat("pdb") | ||
| mol = openbabel.OBMol() | ||
| obconversion.ReadFile(mol, infile) | ||
| mol.AddHydrogens() | ||
| obconversion.WriteFile(mol, outfile) | ||
| LOGGER.info("Hydrogens were added to the structure. Structure {0} is saved in the local directry.".format(outfile)) | ||
| except ImportError: | ||
| raise ImportError("Install Openbabel to add hydrogens to the structure or use PDBFixer/OpenMM.") | ||
|
|
||
| obconversion = openbabel.OBConversion() | ||
| obconversion.SetInFormat("pdb") | ||
| mol = openbabel.OBMol() | ||
| obconversion.ReadFile(mol, infile) | ||
| mol.AddHydrogens() | ||
| obconversion.WriteFile(mol, outfile) | ||
| LOGGER.info("Hydrogens were added to the structure. Structure {0} is saved in the local directry.".format(outfile)) | ||
|
|
||
|
|
||
| elif method == 'pdbfixer': | ||
| try: | ||
|
|
@@ -115,3 +148,50 @@ def addMissingAtoms(infile, method='openbabel', pH=7.0, outfile=None, **kwargs): | |
| return outfile | ||
|
|
||
|
|
||
| def fixStructuresMissingAtoms(infiles, method='openbabel', pH=7.0, outfiles=None, **kwargs): | ||
| """This function will add hydrogens to the protein and ligand structure from a set of files | ||
| using Openbabel [NO11]_ or PDBFixer with OpenMM. | ||
| There are also options whether to *model_residues* (default False), *remove_heterogens* | ||
| (default False) and *keep_waters* (default True). | ||
| :arg infiles: a list of PDB file names | ||
| :type infile: list | ||
| :arg method: Name of program which will be use to fix protein structure. | ||
| Two alternative options are available: 'openbabel' and 'pdbfixer'. | ||
| For either option additional software need to be installed: | ||
| 'openbabel': OpenBabel | ||
| 'pdbfixer': PDBFixer and OpenMM | ||
| default is 'openbabel' | ||
| :type method: str | ||
| :arg pH: pH value applyed only for PDBfixer. | ||
| :type pH: int, float | ||
| Instalation of Openbabel: | ||
| conda install -c conda-forge openbabel | ||
| Find more information here: https://anaconda.org/conda-forge/openbabel | ||
| https://github.com/openmm/pdbfixer | ||
| Program will create new file in the same directory with 'addH_' prefix. | ||
| .. [NO11] O'Boyle, N. M., Banck M., James C. A., Morley C., Vandermeersch T., Hutchison G. R. | ||
| Open Babel: An open chemical toolbox *Journal of cheminformatics* **2011** 3:1-14. """ | ||
|
|
||
| if not isinstance(infiles, list): | ||
| raise TypeError('infiles should be a list') | ||
|
|
||
| if outfiles is None: | ||
| outfiles = [None for infile in infiles] | ||
|
|
||
| if not isinstance(outfiles, list): | ||
| raise TypeError('outfiles should be None or a list') | ||
| if len(outfiles) != len(infiles): | ||
| raise ValueError('outfiles should have the same length as infiles') | ||
|
|
||
| results = [] | ||
| for i, infile in enumerate(infiles): | ||
| results.append(addMissingAtoms(infile, method, pH, | ||
| outfiles[i], **kwargs)) | ||
| return results | ||
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