adding abcl-cdk examples

abcl-cdk-examples.asd

@@ -0,0 +1,15 @@
+
+(asdf:defsystem :abcl-cdk-examples
+  :name "abcl-cdk-example"
+  :author "Cyrus Harmon"
+  :serial t
+  :default-component-class asdf:cl-source-file
+  :depends-on (abcl-cdk)
+  :components
+  ((:module :examples
+            :components
+            ((:file "examples")))))
+
+(cl:defparameter abcl-cdk-examples-config:*base-directory* 
+  (make-pathname :name "examples/" :type nil :defaults *load-truename*))
+

examples/examples.lisp

@@ -0,0 +1,92 @@
+
+(cl:defpackage :abcl-cdk-examples
+  (:use :common-lisp :abcl-cdk))
+
+(cl:in-package :abcl-cdk-examples)
+
+(jimport |org.openscience.cdk.geometry.cip| |CIPTool|)
+
+#+nil (named-readtables:in-readtable abcl-cdk::abcl-cdk-readtable)
+
+(defparameter *valine* (parse-smiles-string "CC(C)[C](C(=O)O)N"))
+
+(defparameter *l-valine* (parse-smiles-string "CC(C)[C@@H](C(=O)O)N"))
+(abcl-cdk::generate-smiles-string *l-valine*)
+(abcl-cdk::generate-chiral-smiles-string *l-valine*)
+
+(defparameter *d-valine* (parse-smiles-string "CC(C)[C@H](C(=O)O)N"))
+(abcl-cdk::generate-smiles-string *d-valine*)
+(abcl-cdk::generate-chiral-smiles-string *d-valine*)
+
+(mol-to-svg *l-valine* "/tmp/l-valine.svg")
+(mol-to-pdf *l-valine* "/tmp/l-valine.pdf")
+
+(mol-to-pdf (parse-smiles-string "CC(C)[C@@H](C(=O)O)N") "/tmp/l-valine.pdf")
+
+(defparameter *caffeine* (parse-smiles-string "CN1C=NC2=C1C(=O)N(C(=O)N2C)C"))
+(mol-to-svg *caffeine* "/tmp/caffeine.svg")
+(mol-to-pdf *caffeine* "/tmp/caffeine.pdf")
+
+(defparameter *ticagrelor* (parse-smiles-string "CCCSC1=NC2=C(C(=N1)N[C@@H]3C[C@H]3C4=CC(=C(C=C4)F)F)N=NN2[C@@H]5C[C@@H]([C@H]([C@H]5O)O)OCCO"))
+(mol-to-svg *ticagrelor* "/tmp/ticagrelor.svg")
+(mol-to-pdf *ticagrelor* "/tmp/ticagrelor.pdf")
+
+(defparameter *z-tamoxifen* (parse-smiles-string "CC/C(=C(\\C1=CC=CC=C1)/C2=CC=C(C=C2)OCCN(C)C)/C3=CC=CC=C3"))
+(mol-to-svg *z-tamoxifen* "/tmp/z-tamoxifen.svg")
+(mol-to-pdf *z-tamoxifen* "/tmp/z-tamoxifen.pdf")
+
+(defparameter *tamoxifen* (parse-smiles-string "CCC(=C(C1=CC=CC=C1)C2=CC=C(C=C2)OCCN(C)C)C3=CC=CC=C3"))
+(mol-to-svg *tamoxifen* "/tmp/tamoxifen.svg")
+(mol-to-pdf *tamoxifen* "/tmp/tamoxifen.pdf")
+
+(defparameter *alanine* (parse-smiles-string "C[C@@H](C(=O)O)N"))
+(mol-to-pdf *alanine* "/tmp/alanine.pdf")
+
+(defparameter *t2* (parse-smiles-string "CCCSC1=NC2=C(C(=N1)NC3CC3C4=CC(=C(C=C4)F)F)N=NN2C5CC(C(C5O)O)OCCO"))
+(mol-to-pdf *t2* "/tmp/t2.pdf")
+
+(get-inchi *ticagrelor*)
+(get-inchi *caffeine*)
+(get-inchi *t2*)
+(get-inchi *z-tamoxifen*)
+(get-inchi-key *z-tamoxifen*)
+(get-inchi-key *tamoxifen*)
+
+(get-inchi (parse-smiles-string "c1ccccc1"))
+
+(get-inchi (parse-smiles-string "CC(C)C"))
+
+(defparameter *benzene* (parse-smiles-string "c1ccccc1"))
+(defparameter *benzene-2* (parse-smiles-string "C1=CC=CC=C1"))
+(defparameter *pyridine* (parse-smiles-string "n1ccccc1"))
+
+(get-inchi *pyridine*)
+(get-inchi *benzene*)
+(get-inchi *benzene-2*)
+
+(get-inchi (parse-smiles-string "N1=CC=CC=C1"))
+
+(map nil #'describe (items (#"atoms" *benzene-2*)))
+(map nil #'describe (items (#"bonds" *benzene-2*)))
+
+(map nil
+     (lambda (bond)
+       (print (cons (#"getAtom" bond 0)
+                    (#"getAtom" bond 1))))
+     (items (#"bonds" *l-valine*)))
+
+(let* ((mol *l-valine*)
+       (tc (first (items (#"stereoElements" mol)))))
+  (describe
+   (java:jstatic "getCIPChirality" |CIPTool| mol tc)))
+
+(mol-to-pdf *l-valine* "l-valine.pdf")
+(mol-to-pdf *d-valine* "d-valine.pdf")
+
+(defparameter *e-but-2-ene* (parse-smiles-string "[H]\\C(C)=C(\\[H])C"))
+(mol-to-svg *e-but-2-ene* "blog/e-but-2-ene.svg" :width 128 :height 128)
+(mol-to-pdf *e-but-2-ene* "blog/e-but-2-ene.pdf" :width 128 :height 128)
+
+(defparameter *z-but-2-ene* (parse-smiles-string "[H]/C(C)=C(\\[H])C"))
+(mol-to-svg *z-but-2-ene* "blog/z-but-2-ene.svg" :width 128 :height 128)
+(mol-to-pdf *z-but-2-ene* "blog/z-but-2-ene.pdf" :width 128 :height 128)