maeparser

maeparser is a parser for Schrodinger Maestro files.

Structure files (.mae,.maegz,.mae.gz) can contain multiple structures delimited by "f_m_ct". See MaeConstants.hpp for standard block and property names.

To read a structure,

#include "Reader.hpp"

...

FILE* f = fopen("test.mae", "r");
schrodinger::mae::Reader r(f);

std::shared_ptr<schrodinger::mae::Block> b;
while ((b = r.next(schrodinger::mae::CT_BLOCK)) != nullptr) {
  // Parse structure
}
fclose(f);

See also test/UsageDemo.cpp, which reads an example structure and stores it in a dummy Molecule class.

Background

Why do we have a recursive descent parser for mae files instead of using a parser generator like ANTLR or lex/yacc? The main reasons are that the mae format language is 1) pretty simple, 2) unlikely to change significantly, and 3) not a context free grammar. In addition, speed of parsing these files is important.

In what way is the current version of the language not a CFG? Special tokens like block opener { and key/value separator ::: can also be string values because the quotes on string values are not required. This results in complication and pain in attempts to define a grammar.

Why this format?

There are many molecule formats out there, and the significant strength of this one is that it exactly fits the use case of Schrödinger's physics-based modeling. As the primary (and only lossless) Schrödinger output format, any package that wishes to implement lossless data extraction of Maestro output needs to interact directly with this format. This is not an intentional limitation, but is due to the nature of chemical storage formats: it's extremely hard to get a format that's both 1) Flexible enough to hold any type of data and 2) Not so flexible that each user has to implement their own rules. The Maestro format avoids this paradox by having the exact flexibility that Schrödinger's physics based backends require, without additional flexibility that other use cases might demand.

In supporting Schrödinger's backend suite, maeparser is able to handle output from:

Molecular Dynamics applications, such as Desmond and FEP+
Ligand-Protein Docking applications, such as Glide
Homology Modeling and folding applications, such as Prime
Ligand-based search applications, such as Phase and Phase Shape
Quantum Mechanics applications, such as Jaguar
Protein-Protein Docking applications
Many other backends used in both Life and Material Sciences

Installation

Command line installation on a Unix-like operating system follows a typical configure, build, and test procedure. Configuration is via CMake. Here is an example command sequence:

git clone git@github.com:schrodinger/maeparser.git maeparser

# Set up the build configuration
cd maeparser
mkdir build
cd build
export CC=gcc
cmake --verbose ..

# Build it
make

# Run the custom testing
ctest

Defining CC ensures that the specified compiler is used in the build (in the example, it will be the first instance of gcc in one's PATH), and the --verbose argumentenables viewing the gory details of compiling and linking that will be necessary for debugging or reporting issues if the build fails.