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Bug/bindings fulfill requirements #10

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Bug/bindings fulfill requirements #10

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c7b25a3
Updated CMakeLists.txt for macOS to compile with llvm clang and openmp.
danny305 May 3, 2021
6d47a28
Merge branch 'cmake-bug' into mac-dev
danny305 May 3, 2021
31a19f4
Added capability to write real cif file to stdout.
danny305 May 4, 2021
22a85ed
refactored cif.cpp
danny305 May 4, 2021
71767d1
gemmi writes to output file instead of stdout.
danny305 May 4, 2021
454f92d
added check to ensure input file is a .cif file.
danny305 May 4, 2021
2298eb9
corrected the created date
danny305 May 20, 2021
0c86941
Updating with dockerfile from master
danny305 Jun 25, 2021
ae658c6
made cmake the same as master;cloning this branch instead in Dockerfile
danny305 Jun 25, 2021
0a1cf42
fixed chain reference error in MCRA
danny305 Jun 26, 2021
8a48e87
refactored cif writing and unneccesary openmp linking.
danny305 Jun 26, 2021
ef8726c
Merge branch 'feature/docker'; adding README commit
danny305 Jun 26, 2021
dfeab72
Merge remote-tracking branch 'upstream/master'; upstream added featur…
danny305 Jun 29, 2021
c68fd06
Merge remote-tracking branch 'upstream/master'
danny305 Jul 7, 2021
00006fd
patched fulfill_requirements bug
danny305 Jul 7, 2021
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7 changes: 3 additions & 4 deletions src/python.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -49,8 +49,6 @@ Molecules::Molecules(const std::string &filename, bool read_hetatm = true, bool
if (ms.molecules().empty()) {
throw std::runtime_error("No molecules were loaded from the input file");
}

ms.fulfill_requirements({RequiredFeatures::DISTANCE_TREE, RequiredFeatures::BOND_DISTANCES});
}


Expand Down Expand Up @@ -130,7 +128,7 @@ calculate_charges(struct Molecules &molecules, const std::string &method_name, s
}

std::string parameter_file = (std::string(INSTALL_DIR) + "/share/parameters/" + parameters_name.value() + ".json");
if (not parameter_file.empty()) {
if (!parameter_file.empty()) {
parameters = std::make_unique<Parameters>(parameter_file);
auto unclassified = molecules.ms.classify_set_from_parameters(*parameters, false, true);
if (unclassified) {
Expand All @@ -141,14 +139,15 @@ calculate_charges(struct Molecules &molecules, const std::string &method_name, s

method->set_parameters(parameters.get());

molecules.ms.fulfill_requirements(method->get_requirements());

/* Use only default values */
for (const auto &[opt, info]: method->get_options()) {
method->set_option_value(opt, info.default_value);
}

std::map<std::string, std::vector<double>> charges;
for (auto &mol: molecules.ms.molecules()) {

auto results = method->calculate_charges(mol);
if (std::any_of(results.begin(), results.end(), [](double chg) { return not isfinite(chg); })) {
fmt::print("Incorrect values encoutened for: {}. Skipping molecule.\n", mol.name());
Expand Down