From 1df84ab81fcf3e6126cb6352cb9b745f3b3e8f6d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Michal=20Mal=C3=BD?= <malym@ibt.cas.cz>
Date: Wed, 12 Jan 2022 10:24:57 +0100
Subject: [PATCH] Update example in README
---
README.md | 26 ++++++++++++++++++++------
1 file changed, 20 insertions(+), 6 deletions(-)
diff --git a/README.md b/README.md
index dfaf972..b83f08b 100644
--- a/README.md
+++ b/README.md
@@ -30,13 +30,26 @@ try {
'UACGUAAGUA', // Sequence
2639 // Author number of the first residue
);
- // NtC to apply on structural conformation
- $ntcs = [
- new \WebMMB\NtC('A', $rna->authToSeq(2639), $rna->authToSeq(2642), 'AA00', 1.5),
- new \WebMMB\NtC('A', $rna->authToSeq(2642), $rna->authToSeq(2643), 'OP03', 1.5),
- new \WebMMB\NtC('A', $rna->authToSeq(2643), $rna->authToSeq(2644), 'AA08', 1.5),
- new \WebMMB\NtC('A', $rna->authToSeq(2644), $rna->authToSeq(2648), 'AA00', 1.5)
+ // Specify double helix pairing
+ $dh = new \WebMMB\DoubleHelix(
+ 'A',
+ $rna->authToSeq(2639),
+ $rna->authToSeq(2641),
+ 'A',
+ $rna->authToSeq(2648),
+ $rna->authToSeq(2646)
+ );
+ // NtCs to apply on structural conformation
+ $conformations = [
+ new \WebMMB\NtCConformation('A', $rna->authToSeq(2639), $rna->authToSeq(2642), 'AA00', 1.5),
+ new \WebMMB\NtCConformation('A', $rna->authToSeq(2642), $rna->authToSeq(2643), 'OP03', 1.5),
+ new \WebMMB\NtCConformation('A', $rna->authToSeq(2643), $rna->authToSeq(2644), 'AA08', 1.5),
+ new \WebMMB\NtCConformation('A', $rna->authToSeq(2644), $rna->authToSeq(2648), 'AA00', 1.5)
];
+ $ntcs = new \WebMMB\NtCs(
+ $conformations, // List of NtC conformations to apply
+ 3000 // NtC force scale factor - 3000 is the recommended default value
+ );
// Create StandardCommands object
$commands = new \WebMMB\StandardCommands(
1, // First stage
@@ -46,6 +59,7 @@ try {
);
// Set up additional parameters
$commands->compounds = [ $rna ]; // StandardCommands expects an array of compounds
+ $commands->double_helices = [ $dh ];
$commands->ntcs = $ntcs;
// Start the job
--
GitLab