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Bundles templats and allow coordgen to run without maeparser.
Now templates are always bundled into the coordgen library,
so there is no search on the file system. coordgen can also
be built without maeparser support (USE_MAEPARSER=OFF). This
disables user-local template files, but it allows coordgen
to be built without reliance on the maeparser library
(and therefore without boost).
This is useful for a couple of reasons:
* We definitely see bugs in template discovery
* 3rd party packagers seem to have trouble with
building maeparser.
* Allow use in other novel places that can't use
the boost:: infrastructure required by
maeparser.
maeparser is always required for running the unit tests.
Includes a short Python script for generating the C++ files
describing the templates. This Python script currently requires
use of the Schrodinger Python tools, so it will need to be
manually updated if the templates are updated. There is a test
that will fail if a new template is added but isn't added to
the compiled templates.
run it like:
$SCHRODINGER/run mol_generator.py templates.mae- Loading branch information
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,183 @@ | ||
| """ | ||
| Using the schrodinger Python modules, read a template .mae file to | ||
| generate the coordgen template C++ files. | ||
| """ | ||
|
|
||
| import sys | ||
| import os | ||
| import textwrap | ||
| import argparse | ||
| import subprocess | ||
|
|
||
| from schrodinger import structure | ||
|
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||
| NAME = 'CoordgenTemplates' | ||
|
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||
| # String that creates a molecule and adds it to a container | ||
| # of sketcherMinimizerMolecule* at index i. | ||
| # | ||
| # C++ programmers: `{` and `}` are escaped by duplication, so | ||
| # `{{` means `{`. | ||
| _MOLECULE = """ | ||
| {{ | ||
| auto molecule = new sketcherMinimizerMolecule(); | ||
| std::array<std::tuple<int, float, float>, {atom_total}> atoms = {{{{ | ||
| {atoms} | ||
| }}}}; | ||
| std::array<std::array<int, 3>, {bond_total}> bonds = {{{{ | ||
| {bonds} | ||
| }}}}; | ||
| add_atoms(molecule, atoms); | ||
| add_bonds(molecule, bonds); | ||
| molecules[i] = molecule; | ||
| ++i; | ||
| }} | ||
| """ | ||
|
|
||
| _DOC = """ | ||
| /// | ||
| // Find the templates for coordinate generation | ||
| // | ||
| // Autogenerated, do not edit. | ||
| // | ||
| // $SCHRODINGER/run {script_name} {template_file} | ||
| // | ||
| // generated using {template_file} version {git_hash}. | ||
| // | ||
| """ | ||
|
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||
| _HEADER = """ | ||
| #pragma once | ||
| {doc} | ||
| #include <vector> | ||
| class sketcherMinimizerMolecule; | ||
| namespace schrodinger {{ | ||
| /// | ||
| // Create a new vector of sketcherMinimizerMolecule*. Caller | ||
| // owns the sketcherMinimizerMolecule objects. | ||
| std::vector<sketcherMinimizerMolecule*> coordgen_templates(); | ||
| }} | ||
| """ | ||
|
|
||
| _IMPLEMENTATION = """ | ||
| {doc} | ||
| #include "{name}.h" | ||
| #include <array> | ||
| #include "sketcherMinimizerMolecule.h" | ||
| #include "sketcherMinimizerAtom.h" | ||
| #include "sketcherMinimizerBond.h" | ||
| using std::array; | ||
| using std::tuple; | ||
| template <typename T> | ||
| void add_atoms(sketcherMinimizerMolecule* molecule, const T& atoms) | ||
| {{ | ||
| for (const auto& a: atoms) {{ | ||
| auto atom = molecule->addNewAtom(); | ||
| atom->setAtomicNumber(std::get<0>(a)); | ||
| atom->setCoordinates(sketcherMinimizerPointF(std::get<1>(a), std::get<2>(a))); | ||
| }} | ||
| }} | ||
| template <typename T> | ||
| void add_bonds(sketcherMinimizerMolecule* molecule, const T& bonds) | ||
| {{ | ||
| for (const auto& b: bonds) {{ | ||
| auto* from_atom = molecule->getAtoms().at(b[0]); | ||
| auto* to_atom = molecule->getAtoms().at(b[1]); | ||
| auto bond = molecule->addNewBond(from_atom, to_atom); | ||
| bond->setBondOrder(b[2]); | ||
| }} | ||
| }} | ||
| namespace schrodinger {{ | ||
| std::vector<sketcherMinimizerMolecule*> coordgen_templates() | ||
| {{ | ||
| std::vector<sketcherMinimizerMolecule*> molecules({total}); | ||
| size_t i = 0; | ||
| {body} | ||
| return molecules; | ||
| }} | ||
| }} | ||
| """ | ||
|
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||
|
|
||
| def get_mol_def(st): | ||
| """ | ||
| Use _MOLECULE to define `st` as a sketcherMinimizerMolecule | ||
| """ | ||
| atoms = ( | ||
| f' tuple<int, float, float>({a.atomic_number}, {a.x}f, {a.y}f)' | ||
| for a in st.atom) | ||
| atoms = ',\n'.join(atoms) | ||
|
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||
| bonds = ( | ||
| f' {{ {b.atom1.index - 1}, {b.atom2.index - 1}, {b.order} }}' | ||
| for b in st.bond) | ||
| bonds = ',\n'.join(bonds) | ||
|
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||
| t = _MOLECULE.format( | ||
| bonds=bonds, | ||
| atoms=atoms, | ||
| atom_total=st.atom_total, | ||
| bond_total=len(st.bond)) | ||
| return t | ||
|
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||
|
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| def main(args=None): | ||
| parser = argparse.ArgumentParser(args) | ||
| parser.add_argument('template_file') | ||
|
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| opts = parser.parse_args() | ||
|
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| git_hash = subprocess.check_output( | ||
| ['git', 'log', '-n', '1', '--pretty=format:%H', opts.template_file]) | ||
| git_hash = git_hash.decode().strip()[:20] | ||
| template_dir, template_base_name = os.path.split(opts.template_file) | ||
|
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||
| doc = _DOC.format( | ||
| script_name=os.path.basename(__file__), | ||
| template_file=template_base_name, | ||
| git_hash=git_hash) | ||
|
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| header = _HEADER.format(doc=doc) | ||
|
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| total = structure.count_structures(opts.template_file) | ||
| body = '' | ||
|
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| with structure.StructureReader(opts.template_file) as r: | ||
| for st in r: | ||
| mol_def = get_mol_def(st) | ||
| body += mol_def | ||
| body = textwrap.indent(body, ' ') | ||
|
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| implementation = _IMPLEMENTATION.format( | ||
| doc=doc, name=NAME, body=body, total=total) | ||
|
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| header_path = os.path.join(template_dir, f'{NAME}.h') | ||
| with open(header_path, 'w') as fh: | ||
| fh.write(header) | ||
|
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| implementation_path = os.path.join(template_dir, f'{NAME}.cpp') | ||
| with open(implementation_path, 'w') as fh: | ||
| fh.write(implementation) | ||
|
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||
|
|
||
| if __name__ == '__main__': | ||
| main() |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,60 @@ | ||
| #pragma once | ||
|
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||
| /// | ||
| // Shim for creating sketcherMolecules from .mae files. | ||
|
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| #include "sketcherMinimizerMolecule.h" | ||
| #include "maeparser/MaeConstants.hpp" | ||
| #include "maeparser/Reader.hpp" | ||
|
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| using namespace std; | ||
| using namespace schrodinger; | ||
|
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||
| /// | ||
| // A very simple utility function to parse a mae::Block into a 2D | ||
| // sketcherMinimizerMolecule. Anything beyond atomic number, x and y coordinates | ||
| // and bond orders will be ignored (i.e. no chiralities or stereo bonds will be | ||
| // parsed). | ||
| // | ||
| sketcherMinimizerMolecule* mol_from_mae_block(mae::Block& block) | ||
| { | ||
| auto molecule = new sketcherMinimizerMolecule(); | ||
| // Atom data is in the m_atom indexed block | ||
| { | ||
| const auto atom_data = block.getIndexedBlock(mae::ATOM_BLOCK); | ||
| // All atoms are gauranteed to have these three field names: | ||
| const auto atomic_numbers = | ||
| atom_data->getIntProperty(mae::ATOM_ATOMIC_NUM); | ||
| const auto xs = atom_data->getRealProperty(mae::ATOM_X_COORD); | ||
| const auto ys = atom_data->getRealProperty(mae::ATOM_Y_COORD); | ||
| const auto size = atomic_numbers->size(); | ||
|
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| // atomic numbers, and x, y, and z coordinates | ||
| for (size_t i = 0; i < size; ++i) { | ||
| auto atom = molecule->addNewAtom(); | ||
| atom->setAtomicNumber(atomic_numbers->at(i)); | ||
| atom->setCoordinates(sketcherMinimizerPointF( | ||
| static_cast<float>(xs->at(i)), static_cast<float>(ys->at(i)))); | ||
| } | ||
| } | ||
|
|
||
| // Bond data is in the m_bond indexed block | ||
| { | ||
| const auto bond_data = block.getIndexedBlock(mae::BOND_BLOCK); | ||
| // All bonds are gauranteed to have these three field names: | ||
| auto from_atoms = bond_data->getIntProperty(mae::BOND_ATOM_1); | ||
| auto to_atoms = bond_data->getIntProperty(mae::BOND_ATOM_2); | ||
| auto orders = bond_data->getIntProperty(mae::BOND_ORDER); | ||
| const auto size = from_atoms->size(); | ||
|
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| for (size_t i = 0; i < size; ++i) { | ||
| // Maestro atoms are 1 indexed! | ||
| auto* from_atom = molecule->getAtoms().at(from_atoms->at(i) - 1); | ||
| auto* to_atom = molecule->getAtoms().at(to_atoms->at(i) - 1); | ||
| auto bond = molecule->addNewBond(from_atom, to_atom); | ||
| bond->setBondOrder(orders->at(i)); | ||
| } | ||
| } | ||
|
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||
| return molecule; | ||
| } |
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