From 767a49fc0774a6d9dc2b546a9bb89003d9bd2caf Mon Sep 17 00:00:00 2001 From: djoumbou Date: Wed, 9 Mar 2016 19:55:54 -0700 Subject: [PATCH] updated documentation --- README.md | 2 ++ doc/ClassyFireAPI.html | 2 +- doc/EntityResource.html | 2 +- doc/QueryResource.html | 2 +- doc/SequenceResource.html | 2 +- doc/_index.html | 2 +- doc/file.README.html | 11 +++++++++-- doc/index.html | 11 +++++++++-- doc/top-level-namespace.html | 2 +- 9 files changed, 26 insertions(+), 10 deletions(-) diff --git a/README.md b/README.md index f4a5603..712df06 100644 --- a/README.md +++ b/README.md @@ -57,6 +57,7 @@ > > > > >The sequence's fingerprint is "8bf70c23ac100cd2c3955081d8613325", > > > > The fingerprint is generate by Digest::MD5 from the peptide sequence "APDVQDCPECTLQENPFFSQPGAPILQCMGCCFSRAYPTPLRSKKTMLVQKNVTSESTCCVAKSYNRVTVMGGFKVENHTACHCSTCYYHKS" +> > > > > >The output format is "json" (JSON). @@ -66,6 +67,7 @@ > > >The query label is an identifier > > > > > >The query input contains the compound's identifier (optional) and its structural representation, separated by a tab. The chemical structure is represented either in the [Daylight SMILES](http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html) format, the [InChI](http://www.iupac.org/home/publications/e-resources/inchi.html) format. Moreover, the compound can be represented with its [IUPAC name](http://www.chem.qmul.ac.uk/iupac/). +> > >The input can also be of type [FASTA](https://en.wikipedia.org/wiki/FASTA_format), which contains peptide or nucleotide sequences. > > > >###POST### > >A query can be submitted using the POST method as demonstrated in the following example. diff --git a/doc/ClassyFireAPI.html b/doc/ClassyFireAPI.html index e05c6fe..fb1207f 100644 --- a/doc/ClassyFireAPI.html +++ b/doc/ClassyFireAPI.html @@ -2066,7 +2066,7 @@ text. is fragmented into n part of #slice_length entries each).

diff --git a/doc/EntityResource.html b/doc/EntityResource.html index e6521d8..751e75d 100644 --- a/doc/EntityResource.html +++ b/doc/EntityResource.html @@ -114,7 +114,7 @@ diff --git a/doc/QueryResource.html b/doc/QueryResource.html index 87f20f1..0bad01d 100644 --- a/doc/QueryResource.html +++ b/doc/QueryResource.html @@ -183,7 +183,7 @@ diff --git a/doc/SequenceResource.html b/doc/SequenceResource.html index 4bffc57..25cf179 100644 --- a/doc/SequenceResource.html +++ b/doc/SequenceResource.html @@ -114,7 +114,7 @@ diff --git a/doc/_index.html b/doc/_index.html index 19d7247..75f45b6 100644 --- a/doc/_index.html +++ b/doc/_index.html @@ -140,7 +140,7 @@ diff --git a/doc/file.README.html b/doc/file.README.html index 5b8643f..e3f7fc1 100644 --- a/doc/file.README.html +++ b/doc/file.README.html @@ -154,6 +154,11 @@ this example, the sequence has the fingerprint =

The sequence's fingerprint is “8bf70c23ac100cd2c3955081d8613325”,

+
+

The fingerprint is generate by Digest::MD5 from the peptide sequence +“APDVQDCPECTLQENPFFSQPGAPILQCMGCCFSRAYPTPLRSKKTMLVQKNVTSESTCCVAKSYNRVTVMGGFKVENHTACHCSTCYYHKS”

+
+

The output format is “json” (JSON).

@@ -174,7 +179,9 @@ href="http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html">Daylight SMILES format, the InChI format. Moreover, the compound can be represented with its IUPAC name.

+href="http://www.chem.qmul.ac.uk/iupac/">IUPAC name. The input can also +be of type FASTA, +which contains peptide or nucleotide sequences.

POST

@@ -229,7 +236,7 @@ XML format.

diff --git a/doc/index.html b/doc/index.html index 5b8643f..e3f7fc1 100644 --- a/doc/index.html +++ b/doc/index.html @@ -154,6 +154,11 @@ this example, the sequence has the fingerprint =

The sequence's fingerprint is “8bf70c23ac100cd2c3955081d8613325”,

+
+

The fingerprint is generate by Digest::MD5 from the peptide sequence +“APDVQDCPECTLQENPFFSQPGAPILQCMGCCFSRAYPTPLRSKKTMLVQKNVTSESTCCVAKSYNRVTVMGGFKVENHTACHCSTCYYHKS”

+
+

The output format is “json” (JSON).

@@ -174,7 +179,9 @@ href="http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html">Daylight SMILES format, the InChI format. Moreover, the compound can be represented with its IUPAC name.

+href="http://www.chem.qmul.ac.uk/iupac/">IUPAC name. The input can also +be of type FASTA, +which contains peptide or nucleotide sequences.

POST

@@ -229,7 +236,7 @@ XML format.

diff --git a/doc/top-level-namespace.html b/doc/top-level-namespace.html index e36a234..6cb613a 100644 --- a/doc/top-level-namespace.html +++ b/doc/top-level-namespace.html @@ -105,7 +105,7 @@