Part of PR pkg/55755.
This is Schroedinger, Inc's 2D coordinate generation. It was formerly
proprietary code, but is now released under the BSD license.
The emphasis of these algorithms are on quality of 2D coordinates rather than
speed of generation. The algorithm distinguishes itself from many others by
doing well with both macrocycles and metal complexes. It also does extremely
well on typical drug-like small molecules, and has been validated on millions
of compounds.
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.
Construct and analyze projection matrix models from a demography study
of marked individuals classified by age or stage. The package covers
methods described in Matrix Population Models by Caswell (2001) and
Quantitative Conservation Biology by Morris and Doak (2002).
The Biopython package contains high-quality, reusable modules and
scripts written in Python to make it as easy as possible to use Python
for bioinformatics. The Biopython includes the follwing: the ability
to parse bioinformatics files into python utilizable data structures,
including support for the formats such as Blast output, Clustalw,
FASTA, GenBank, PubMed and Medicine, various Expasy files, SCOP,
Rebase, UniGene, and SwissProt.
BCFtools is a program for variant calling and manipulating files in the Variant
Call Format (VCF) and its binary counterpart BCF. All commands work
transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.
In order to avoid tedious repetion, throughout this document we will use "VCF"
and "BCF" interchangeably, unless specifically noted.
Most commands accept VCF, bgzipped VCF and BCF with filetype detected
automatically even when streaming from a pipe. Indexed VCF and BCF work in all
situations. Unindexed VCF and BCF and streams work in most, but not all
situations. In general, whenever multiple VCFs are read simultaneously, they
must be indexed and therefore also compressed.
Primer3 is a widely used program for designing PCR primers (PCR =
"Polymerase Chain Reaction"). PCR is an essential and ubiquitous tool
in genetics and molecular biology. Primer3 can also design
hybridization probes and sequencing primers.
