From 62f246ac9e3a2f696af4ccdb06dfb0cbb8d9968e Mon Sep 17 00:00:00 2001 From: James Procter Date: Sat, 16 Dec 2023 08:41:16 +0000 Subject: [PATCH] JAL-4366 mat3di score model --- resources/scoreModel/foldseek_mat3di.scm | 26 +++++++++++++++++++++ src/jalview/analysis/scoremodels/ScoreModels.java | 3 +++ 2 files changed, 29 insertions(+) create mode 100644 resources/scoreModel/foldseek_mat3di.scm diff --git a/resources/scoreModel/foldseek_mat3di.scm b/resources/scoreModel/foldseek_mat3di.scm new file mode 100644 index 0000000..428b4bd --- /dev/null +++ b/resources/scoreModel/foldseek_mat3di.scm @@ -0,0 +1,26 @@ +ScoreMatrix Mat3di +# 3Di bit/2 +# Background (precomputed optional): 0.0489372 0.0306991 0.101049 0.0329671 0.0276149 0.0416262 0.0452521 0.030876 0.0297251 0.0607036 0.0150238 0.0215826 0.0783843 0.0512926 0.0264886 0.0610702 0.0201311 0.215998 0.0310265 0.0295417 0.00001 +# Lambda (precomputed optional): 0.351568 + A C D E F G H I K L M N P Q R S T V W Y X +A 6 -3 1 2 3 -2 -2 -7 -3 -3 -10 -5 -1 1 -4 -7 -5 -6 0 -2 0 +C -3 6 -2 -8 -5 -4 -4 -12 -13 1 -14 0 0 1 -1 0 -8 1 -7 -9 0 +D 1 -2 4 -3 0 1 1 -3 -5 -4 -5 -2 1 -1 -1 -4 -2 -3 -2 -2 0 +E 2 -8 -3 9 -2 -7 -4 -12 -10 -7 -17 -8 -6 -3 -8 -10 -10 -13 -6 -3 0 +F 3 -5 0 -2 7 -3 -3 -5 1 -3 -9 -5 -2 2 -5 -8 -3 -7 4 -4 0 +G -2 -4 1 -7 -3 6 3 0 -7 -7 -1 -2 -2 -4 3 -3 4 -6 -4 -2 0 +H -2 -4 1 -4 -3 3 6 -4 -7 -6 -6 0 -1 -3 1 -3 -1 -5 -5 3 0 +I -7 -12 -3 -12 -5 0 -4 8 -5 -11 7 -7 -6 -6 -3 -9 6 -12 -5 -8 0 +K -3 -13 -5 -10 1 -7 -7 -5 9 -11 -8 -12 -6 -5 -9 -14 -5 -15 5 -8 0 +L -3 1 -4 -7 -3 -7 -6 -11 -11 6 -16 -3 -2 2 -4 -4 -9 0 -8 -9 0 +M -10 -14 -5 -17 -9 -1 -6 7 -8 -16 10 -9 -9 -10 -5 -10 3 -16 -6 -9 0 +N -5 0 -2 -8 -5 -2 0 -7 -12 -3 -9 7 0 -2 2 3 -4 0 -8 -5 0 +P -1 0 1 -6 -2 -2 -1 -6 -6 -2 -9 0 4 0 0 -2 -4 0 -4 -5 0 +Q 1 1 -1 -3 2 -4 -3 -6 -5 2 -10 -2 0 5 -2 -4 -5 -1 -2 -5 0 +R -4 -1 -1 -8 -5 3 1 -3 -9 -4 -5 2 0 -2 6 2 0 -1 -6 -3 0 +S -7 0 -4 -10 -8 -3 -3 -9 -14 -4 -10 3 -2 -4 2 6 -6 0 -11 -9 0 +T -5 -8 -2 -10 -3 4 -1 6 -5 -9 3 -4 -4 -5 0 -6 8 -9 -5 -5 0 +V -6 1 -3 -13 -7 -6 -5 -12 -15 0 -16 0 0 -1 -1 0 -9 3 -10 -11 0 +W 0 -7 -2 -6 4 -4 -5 -5 5 -8 -6 -8 -4 -2 -6 -11 -5 -10 8 -6 0 +Y -2 -9 -2 -3 -4 -2 3 -8 -8 -9 -9 -5 -5 -5 -3 -9 -5 -11 -6 9 0 +X 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 diff --git a/src/jalview/analysis/scoremodels/ScoreModels.java b/src/jalview/analysis/scoremodels/ScoreModels.java index d9648ba..3def8c3 100644 --- a/src/jalview/analysis/scoremodels/ScoreModels.java +++ b/src/jalview/analysis/scoremodels/ScoreModels.java @@ -41,6 +41,8 @@ public class ScoreModels private final ScoreMatrix DNA; + private final ScoreMatrix FOLDSEEK3DI; + private static ScoreModels instance; private Map models; @@ -80,6 +82,7 @@ public class ScoreModels BLOSUM62 = loadScoreMatrix("scoreModel/blosum62.scm"); PAM250 = loadScoreMatrix("scoreModel/pam250.scm"); DNA = loadScoreMatrix("scoreModel/dna.scm"); + FOLDSEEK3DI = loadScoreMatrix("scoreModel/foldseek_mat3di.scm"); registerScoreModel(new PIDModel()); registerScoreModel(new FeatureDistanceModel()); } -- 1.7.10.2